[kepler-dev] r8319 - in kepler.build/branches/1.0: . preparation preparation/module-info preparation/workflows
Chad Berkley
berkley at nceas.ucsb.edu
Mon Nov 17 09:28:23 PST 2008
Hi,
Did you mean to put this in the kepler.build directory? kepler.build is
reserved for the build system. I think it probably belongs in the
kepler/trunk/workflows directory. If you didn't mean to put it there,
could you please move it?
thanks,
chad
koehler at ecoinformatics.org wrote:
> Author: koehler
> Date: 2008-11-17 09:21:58 -0800 (Mon, 17 Nov 2008)
> New Revision: 8319
>
> Added:
> kepler.build/branches/1.0/preparation/
> kepler.build/branches/1.0/preparation/module-info/
> kepler.build/branches/1.0/preparation/module-info/module-locations.txt
> kepler.build/branches/1.0/preparation/module-info/modules.txt
> kepler.build/branches/1.0/preparation/preparation.iml
> kepler.build/branches/1.0/preparation/workflows/
> kepler.build/branches/1.0/preparation/workflows/preparation-comadv1.moml
> kepler.build/branches/1.0/preparation/workflows/preparation-pre1v4.moml
> Log:
> preparation workflow with parameters in COMAD and SDF
>
> Added: kepler.build/branches/1.0/preparation/module-info/module-locations.txt
> ===================================================================
>
> Added: kepler.build/branches/1.0/preparation/module-info/modules.txt
> ===================================================================
> --- kepler.build/branches/1.0/preparation/module-info/modules.txt (rev 0)
> +++ kepler.build/branches/1.0/preparation/module-info/modules.txt 2008-11-17 17:21:58 UTC (rev 8319)
> @@ -0,0 +1,6 @@
> +preparation
> +comad-mods
> +comad
> +loader
> +kepler
> +ptolemy
> \ No newline at end of file
>
> Added: kepler.build/branches/1.0/preparation/preparation.iml
> ===================================================================
> --- kepler.build/branches/1.0/preparation/preparation.iml (rev 0)
> +++ kepler.build/branches/1.0/preparation/preparation.iml 2008-11-17 17:21:58 UTC (rev 8319)
> @@ -0,0 +1,13 @@
> +<?xml version="1.0" encoding="UTF-8"?>
> +<module relativePaths="true" type="JAVA_MODULE" version="4">
> + <component name="NewModuleRootManager" inherit-compiler-output="true">
> + <exclude-output />
> + <content url="file://$MODULE_DIR$">
> + <sourceFolder url="file://$MODULE_DIR$/src/main/java" isTestSource="false" />
> + </content>
> + <orderEntry type="inheritedJdk" />
> + <orderEntry type="sourceFolder" forTests="false" />
> + <orderEntryProperties />
> + </component>
> +</module>
> +
>
> Added: kepler.build/branches/1.0/preparation/workflows/preparation-comadv1.moml
> ===================================================================
> --- kepler.build/branches/1.0/preparation/workflows/preparation-comadv1.moml (rev 0)
> +++ kepler.build/branches/1.0/preparation/workflows/preparation-comadv1.moml 2008-11-17 17:21:58 UTC (rev 8319)
> @@ -0,0 +1,6471 @@
> +<?xml version="1.0" standalone="no"?>
> +<!DOCTYPE entity PUBLIC "-//UC Berkeley//DTD MoML 1//EN"
> + "http://ptolemy.eecs.berkeley.edu/xml/dtd/MoML_1.dtd">
> +<entity name="preparation-comadv1" class="ptolemy.actor.TypedCompositeActor">
> + <property name="_createdBy" class="ptolemy.kernel.attributes.VersionAttribute" value="7.0.2">
> + </property>
> + <property name="ComadDirector" class="org.kepler.domains.ComadDirector">
> + <property name="timeResolution" class="ptolemy.moml.SharedParameter" value="1E-10">
> + </property>
> + <property name="initialQueueCapacity" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + <property name="maximumQueueCapacity" class="ptolemy.data.expr.Parameter" value="65536">
> + </property>
> + <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:ppod.daks.org:director:2:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.kepler.domains.ComadDirector">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:ppod.daks.org:class:2:1">
> + </property>
> + </property>
> + <property name="semanticType" class="org.kepler.sms.SemanticType" value="urn:lsid:ppod.daks.org:onto:1#Directors">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-355.0, -155.0]">
> + </property>
> + </property>
> + <property name="_windowProperties" class="ptolemy.actor.gui.WindowPropertiesAttribute" value="{bounds={176, 105, 830, 853}, maximized=false}">
> + </property>
> + <property name="_vergilSize" class="ptolemy.actor.gui.SizeAttribute" value="[547, 732]">
> + </property>
> + <property name="_vergilZoomFactor" class="ptolemy.data.expr.ExpertParameter" value="1.0">
> + </property>
> + <property name="_vergilCenter" class="ptolemy.data.expr.ExpertParameter" value="{-341.7789277772645, 162.0}">
> + </property>
> + <entity name="CollectionComposer" class="org.kepler.coactors.CollectionComposer">
> + <property name="Signature" class="org.kepler.util.CoactorParameter" value="">
> + </property>
> + <property name="Read scope" class="org.kepler.util.CoactorParameter" value="">
> + </property>
> + <property name="collectionXml" class="ptolemy.kernel.util.StringAttribute" value=" <Metadata key="repository" type="StringToken" class="ptolemy.data.StringToken">https://outrage.ca.sandia.gov/svn/s3d/simulators/S3D-IO</Metadata> <Metadata key="repository2" type="StringToken" class="ptolemy.data.StringToken">https://outrage.ca.sandia.gov/svn/s3d/test_suite</Metadata> <Metadata key="target" type="StringToken" class="ptolemy.data.StringToken">cobalt at localhost</Metadata> <Metadata key="dir" type="StringToken" class="ptolemy.data.StringToken">test_suite</Metadata> <Metadata key="tempdir" type="StringToken" class="ptolemy.data.StringToken">temp_build_directory</Metadata> <Metadata key="emptydir" type="StringToken&quo
t;
> class="ptolemy.data.StringToken">empty_temp_build_directory</Metadata> <Metadata key="mask" type="StringToken" class="ptolemy.data.StringToken">{"[0-9]-*"}</Metadata> <Metadata key="dirprefix" type="StringToken" class="ptolemy.data.StringToken">s3d_run_</Metadata> <Metadata key="targetdir" type="StringToken" class="ptolemy.data.StringToken">~</Metadata> <Metadata key="jobscriptlocation" type="StringToken" class="ptolemy.data.StringToken">~/Documents/davis-1/project/S3D-IO/run/job_XT4.sh</Metadata> <Metadata key="jobcommand" type="StringToken" class="ptolemy.data.StringToken">~/bin/qsub job_XT4.sh;</Metadata> <Metadata key="localtempdir" type="StringToken" class="ptolemy.data
.S
> tringToken">~</Metadata> <Collection label="Job"> </Collection> ">
> + <property name="CollectionXmlStyle" class="ptolemy.actor.gui.style.TextStyle">
> + <property name="height" class="ptolemy.data.expr.Parameter" value="10">
> + </property>
> + <property name="width" class="ptolemy.data.expr.Parameter" value="30">
> + </property>
> + </property>
> + </property>
> + <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:ppod.daks.org:actor:6:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.kepler.coactors.CollectionComposer">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:ppod.daks.org:class:6:1">
> + </property>
> + </property>
> + <property name="semanticType" class="org.kepler.sms.SemanticType" value="urn:lsid:ppod.daks.org:onto:1#ComadGeneralActors">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-540.0, -75.0]">
> + </property>
> + </entity>
> + <entity name="Checkout_1" class="org.kepler.coactors.CompositeCoactor">
> + <property name="Read scope" class="org.kepler.util.CoactorParameter" value="Job">
> + </property>
> + <property name="_createdBy" class="ptolemy.kernel.attributes.VersionAttribute" value="7.0.2">
> + </property>
> + <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:ppod.daks.org:composite:100:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.kepler.coactors.CompositeCoactor">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:ppod.daks.org:class:100:1">
> + </property>
> + </property>
> + <property name="semanticType" class="org.kepler.sms.SemanticType" value="urn:lsid:ppod.daks.org:onto:1#ComadGeneralActors">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-425.0, -30.0]">
> + </property>
> + <property name="_windowProperties" class="ptolemy.actor.gui.WindowPropertiesAttribute" value="{bounds={408, 217, 883, 853}, maximized=false}">
> + </property>
> + <property name="_vergilSize" class="ptolemy.actor.gui.SizeAttribute" value="[600, 732]">
> + </property>
> + <property name="_vergilZoomFactor" class="ptolemy.data.expr.ExpertParameter" value="1.0">
> + </property>
> + <property name="_vergilCenter" class="ptolemy.data.expr.ExpertParameter" value="{-78.0, 178.0}">
> + </property>
> + <property name="SDF Director" class="ptolemy.domains.sdf.kernel.SDFDirector">
> + <property name="iterations" class="ptolemy.data.expr.Parameter" value="0">
> + </property>
> + <property name="vectorizationFactor" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + <property name="allowDisconnectedGraphs" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="allowRateChanges" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="constrainBufferSizes" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + <property name="period" class="ptolemy.data.expr.Parameter" value="0.0">
> + </property>
> + <property name="synchronizeToRealTime" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="timeResolution" class="ptolemy.moml.SharedParameter" value="1E-10">
> + </property>
> + <property name="Scheduler" class="ptolemy.domains.sdf.kernel.SDFScheduler">
> + <property name="constrainBufferSizes" class="ptolemy.data.expr.Parameter" value="constrainBufferSizes">
> + </property>
> + </property>
> +<property name="KeplerDocumentation" class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> +<property name="description" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="author" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Steve Neuendorffer</configure></property>
> +<property name="version" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="userLevelDocumentation" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>
> +<p>The SDF Director is often used to oversee fairly simple, sequential workflows in which the director can determine the order of actor invocation from the workflow. Types of workflows that would run well under an SDF Director include processing and reformatting tabular data, converting one data type to another, and reading and plotting a series of data points. A workflow in which an image is read, processed (rotated, scaled, clipped, filtered, etc.), and then displayed, is also an example of a sequential workflow that requires a director simply to ensure that each actor fires in the proper order (i.e., that each actor executes only after it receives its required inputs).</p>
> +
> +<p>The SDF Director is very efficient and will not tax system resources with overhead. However, this efficiency requires that certain conditions be met, namely that the data consumption and production rate of each actor in an SDF workflow be constant and declared. If an actor reads one piece of data and calculates and outputs a single result, it must always read and output a single token of data. This data rate cannot change during workflow execution and, in general, workflows that require dynamic scheduling and/or flow control cannot use this director. Additionally, the SDF Director has no understanding of passing time (at least by default), and actors that depend on a notion of time may not work as expected. For example, a TimedPlotter actor will plot all values at time zero when used in SDF. </p>
> +
> +<p>By default, the SDF Director requires that all actors in its workflow be connected. Otherwise, the director cannot account for concurrency between disconnected workflow parts. Usually, a PN Director should be used for workflows that contain disconnected actors; however, the SDF Director's allowDisconnectedGraphs parameter may also be set to true. The SDF Director will then schedule each disconnected "island" independently. The director cannot infer the sequential relationship between disconnected actors (i.e., nothing forces the director to finish executing all actors on one island before firing actors on another). However, the order of execution within each island should be correct. Usually, disconnected graphs in an SDF model indicate an error.</p>
> +
> +<p>Because SDF Directors schedule actors to fire only after they receive their inputs, workflows that require loops (feeding an actor's output back into its input port for further processing) can cause "deadlock" errors. The deadlock errors occur because the actor depends on its own output value as an initial input. To fix this problem, use a SampleDelay actor to generate and inject an initial input value into the workflow.</p>
> +
> +<p>The SDF Director determines the order in which actors execute and how many times each actor needs to be fired to complete a single iteration of the workflow. This schedule is calculated BEFORE the director begins to iterate the workflow. Because the SDF Director calculates a schedule in advance, it is quite efficient. However, SDF workflows must be static. In other words, the same number of tokens must be consumed/produced at every iteration of the workflow. Workflows that require dynamic control structures, such as a BooleanSwitch actor that sends output on one of two ports depending on the value of a 'control', cannot be used with an SDF Director because the number of tokens on each output can change for each execution.</p>
> +
> +<p>Unless otherwise specified, the SDF Director assumes that each actor consumes and produces exactly one token per channel on each firing. Actors that do not follow the one-token-per-channel firing convention (e.g., Repeat or Ramp) must declare the number of tokens they produce or consume via the appropriate parameters. </p>
> +
> +<p>The number of times a workflow is iterated is controlled by the director's iterations parameter. By default, this parameter is set to "0". Note that "0" does not mean "no iterations." Rather, "0" means that the workflow will iterate forever. Values greater than zero specify the actual number of times the director should execute the entire workflow. A value of 1, meaning that the director will run the workflow once, is often the best setting when building an SDF workflow. </p>
> +
> +<p>The amount of data processed by an SDF workflow is a function of both the number of times the workflow iterates and the value of the director's vectorizationFactor parameter. The vectorizationFactor is used to increase the efficiency of a workflow by increasing the number of times actors fire each time the workflow iterates. If the parameter is set to a positive integer (other than 1), the director will fire each actor the specified number of times more than normal. The default is 1, indicating that no vectorization should be performed. Keep in mind that changing the vectorizationFactor parameter changes the meaning of a nested SDF workflow and may cause deadlock in a workflow that uses it. </p>
> +
> +<p>The SDF Director has several advanced parameters that are generally only relevant when an SDF workflow contains composite components. In most cases the period, timeResolution, synchronizeToRealTime, allowRateChanges, timeResolution, and constrainBufferSizes parameters can be left at their default values.</p>
> +
> +<p>For more information about the SDF Director, see the Ptolemy documentation (http://ptolemy.eecs.berkeley.edu/papers/05/ptIIdesign3-domains/ptIIdesign3-domains.pdf).</p>
> +
> +</configure></property>
> +<property name="prop:allowDisconnectedGraphs" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether to allow disconnected actors in the workflow (by default, all actors are required to be connected). If disconnected actors are permitted, the SDF Director will schedule each disconnected 'island' independently. Nothing "forces" the director to finish executing all actors on one island before firing actors on another. However, the order of execution within each island should be correct. Usually, disconnected graphs in an SDF workflow indicate an error.</configure></property>
> +<property name="prop:allowRateChanges" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether dynamic rate changes are permitted or not. By default, rate changes are not permitted, and the director will perform a check to disallow such workflows. If the parameter is selected, then workflows that require rate parameters to be modified during execution are valid, and the SDF Director will dynamically compute a new schedule at runtime. This is an advanced parameter that can usually be left at its default value.</configure></property>
> +<property name="prop:timeResolution" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The time precision used by this director. All time values are rounded to the nearest multiple of this number. The value is a double that defaults to "1E-10" (which is 10-10). This is an advanced parameter that can usually be left at its default value.</configure></property>
> +<property name="prop:constrainBufferSizes" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether buffer sizes are fixed. By default, buffers are fixed, and attempts to write to the buffer that cause the buffer to exceed its scheduled size result in an error. This is an advanced parameter that can usually be left at its default value.</configure></property>
> +<property name="prop:iterations" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify the number of times a workflow is iterated. By default, this parameter is set to "0". Note that "0" does not mean "no iterations." Rather, "0" means that the workflow will iterate forever. Values greater than zero specify the actual number of times the director should execute the entire workflow. A value of 1, meaning that the director will run the workflow once, is often the best setting when building an SDF workflow. </configure></property>
> +<property name="prop:vectorizationFactor" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The vectorizationFactor is used to increase the efficiency of a workflow by increasing the number of times actors fire each time the workflow iterates. If the parameter is set to a positive integer (other than 1), the director will fire each actor the specified number of times more than normal. The default is 1, indicating that no vectorization should be performed. Keep in mind that changing the vectorizationFactor parameter changes the meaning of a nested SDF workflow and may cause deadlock in a workflow that uses it. </configure></property>
> +<property name="prop:synchronizeToRealTime" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether the execution should synchronize to real time or not. By default, the director does not synchronize to real time. If synchronize is selected, the director will only process the workflow when elapsed real time matches the product of the period parameter and the iteration count. Note: if the period parameter has a value of 0.0 (the default), then selecting this parameter has no effect. This is an advanced parameter that can usually be left at its default value.</configure></property>
> +<property name="prop:period" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The time period of each iteration. The value is a double that defaults to 0.0, which means that the director does not increment workflow time. If the value greater than 0.0, the actor will increment workflow time each time it fires. This is an advanced parameter that can usually be left at its default value. </configure></property>
> +</property> <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:director:1:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.domains.sdf.kernel.SDFDirector">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:directorclass:1:1">
> + </property>
> + </property>
> + <property name="semanticType00" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#Director">
> + </property>
> + <property name="semanticType11" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#Director">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-165.0, -80.0]">
> + </property>
> + </property>
> + <port name="input" class="org.kepler.util.CollectionIOPort">
> + <property name="input"/>
> + <property name="dataType" class="ptolemy.kernel.util.StringAttribute" value="general">
> + </property>
> + <property name="isMultiport" class="ptolemy.kernel.util.StringAttribute" value="false">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-455.0, 25.0]">
> + </property>
> + </port>
> + <port name="output" class="org.kepler.util.CollectionIOPort">
> + <property name="output"/>
> + <property name="multiport"/>
> + <property name="dataType" class="ptolemy.kernel.util.StringAttribute" value="unknown">
> + </property>
> + <property name="isMultiport" class="ptolemy.kernel.util.StringAttribute" value="true">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="{75.0, 40.0}">
> + </property>
> + </port>
> + <port name="StringToken [key=target, peer]" class="org.kepler.util.CollectionIOPort">
> + <property name="input"/>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-400.0, 0.0]">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="NORTH">
> + </property>
> + </port>
> + <port name="StringToken [key=repository, peer]" class="org.kepler.util.CollectionIOPort">
> + <property name="input"/>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-425.0, 75.0]">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="SOUTH">
> + </property>
> + </port>
> + <entity name="SSH Execute cmd" class="org.kepler.actor.ssh.ExecuteCmd">
> + <property name="target" class="ptolemy.actor.parameters.PortParameter" value=""yildiz at home.ccs.ornl.gov"">
> + </property>
> + <property name="timeoutSeconds" class="ptolemy.data.expr.Parameter" value="0">
> + </property>
> + <property name="cleanupAfterError" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="thirdParty" class="ptolemy.actor.parameters.PortParameter" value="""">
> + </property>
> +<property name="KeplerDocumentation" class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> +<property name="description" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="author" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Norbert Podhorszki</configure></property>
> +<property name="version" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>1.1 March 2008</configure></property>
> +<property name="userLevelDocumentation" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>
> +
> + <p>The SSHExecuteCmd actor connects to a remote host using SSH protocol and executes a command. If the host is an empty string or "local", the Java
> + Runtime will be used for execution instead of SSH. After the command terminates, the actor returns the stdout, stderr, and exit code of the operation.</p>
> +
> +<p>Set the <i>timeoutSeconds</i> parameter to terminate the command after a specified amount of time. Specify 0 to wait indefinitely for command termination. If connecting to a Unix host, use the <i>cleanupAfterError</i>
> +Parameter to kill the remote process (and all of its children) after an error or timeout. Set this parameter only if connecting to a Unix server (other platforms do not support it).
> +</p>
> +
> +<p>Note: Streaming of output during the command execution is not currently
> + implemented.</p>
> +
> + <p><b>Third party operation.</b>
> + If the remote command is expected to ask for a password
> + (or passphrase when connecting to a remote host with public-key authentication)
> + set the port/parameter <i>thirdParty</i> for the user at host:port of that third party
> + (it can be the same as <i>target</i> if a sudo command is executed).</p>
> +
> + <p>The authentication to the third party should be the same from the target
> + host and from Kepler's local host. Kepler authenticates (by opening a channel)
> + to the third party and then it provides the password/passphrase used for the
> + authentication to the command on the target host. Therefore, this actor cannot be
> + used to reach a remote host through a proxy machine and execute a command there.</p>
> +
> + <p>The third party execution can be used e.g. to execute and ssh/scp command
> + that connects to another host, also reachable from Kepler's host, to execute external
> + data transfer commands (bbcp, GridFTP, SRM-Lite etc) or sudo commands.</p>
> +
> + <p>The actor will first authenticate Kepler to the third party host
> + (if not yet done by other actors, e.g. SshSession). During the execution of the command,
> + it looks for the appearance of the string 'password' or 'passphrase' in the stdout/stderr
> + streams (case-insensitively). If such string is found, it writes the authentication code
> + stored within Kepler used for the authentication. Therefore, the command must read the
> + password on the standard input, not directly from the terminal device.
> + This process is performed only once!</p>
> +
> + <p>The underlying java code does not have pseudo-terminal emulation, so if you cannot
> + force the command to read passwords from the stdin (e.g. scp command), you have to use an
> + external tool to execute the command through a pseudo-terminal. <b>ptyexec</b> is provided
> + in the <i>org.kepler.ssh</i> package, a C program, that should be compiled and put into the path
> + on the target machine. Then you can execute <i>"ptyexec scp ..."</i>. It works on Linux only.</p>
> +
> +</configure></property>
> +<property name="port:stdout" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Output of the command as it would output to the standard shell. If there is an SSH connection related error (or timeout) the value will be an empty string. </configure></property>
> +<property name="port:stderr" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Any errors that were reported by the remote execution or while connecting. If there is an SSH connection related error (or timeout) the value will be an empty string. </configure></property>
> +<property name="port:target" class="ptolemy.kernel.util.ConfigurableAttribute"><configure> The machine to be used at job submission. It should be null, "" or "local" for the local machine or [user@]host to denote a remote machine accessible with SSH. If user is not provided, the local username will be used. If port is not provided, the default port 22 will be applied. This parameter is read once at initialize. </configure></property>
> +<property name="port:command" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The command to be executed on the remote host, specified as a string (e.g., "uname -a; date") </configure></property>
> +<property name="port:exitcode" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The exit code of the command. If there is an SSH connection related error (or timeout) the exitcode will be -32767 </configure></property>
> +<property name="port:errors" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The string representation of actor execution errors, if any.
> + </configure></property>
> +<property name="prop:timeoutSeconds" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Timeout in seconds. The command will be timed out after the specified amount of time. Specify 0 to wait indefinitely for command termination. </configure></property>
> +<property name="prop:streaming mode" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether the output should be sent in a streaming mode.
> + Note: Streaming is not currently implemented.
> + </configure></property>
> +<property name="prop:thirdParty" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The third party machine where the command wants to connect and needs to authenticate. Kepler can be used to do the authentication and then provide the password or private-key passphrase to the command. It should be defined as [user@]host[:port]. </configure></property>
> +<property name="prop:target" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The machine to be used at job submission. It should be null, "" or "local" for the local machine or [user@]host to denote a remote machine accessible with SSH. If user is not provided, the local username will be used. If port is not provided, the default port 22 will be applied. This parameter is read once at initialize. </configure></property>
> +<property name="prop:cleanupAfterError" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Kill remote process(es) after an error or timeout. Set this parameter only if connecting to a Unix server (other platforms do not support it). All processes belonging to the same group as the remote command (i.e., its children) will be killed. </configure></property>
> +</property> <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:506:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.kepler.actor.ssh.ExecuteCmd">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1213:1">
> + </property>
> + </property>
> + <property name="semanticType00" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ExternalExecutionEnvironmentActor">
> + </property>
> + <property name="semanticType21" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#SSH">
> + </property>
> + <property name="semanticType41" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:4:1#CPES">
> + </property>
> + <property name="semanticType22" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#Tutorial">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-135.0, 20.0]">
> + </property>
> + <port name="target" class="ptolemy.actor.parameters.ParameterPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="command" class="ptolemy.actor.TypedIOPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="stdout" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="stderr" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="exitcode" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="errors" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="thirdParty" class="ptolemy.actor.parameters.ParameterPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + </entity>
> + <entity name="Expression" class="ptolemy.actor.lib.Expression">
> + <property name="expression" class="ptolemy.kernel.util.StringAttribute" value=""echo co "+repository">
> + <property name="_hide" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </property>
> +<property name="KeplerDocumentation" class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> +<property name="description" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="author" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Xiaojun Liu, Edward A. Lee, Steve Neuendorffer</configure></property>
> +<property name="version" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="userLevelDocumentation" class="ptolemy.kernel.util.ConfigurableAttribute"><configure><p>The Expression actor evaluates a specified expression (e.g., an addition or multiplication operation), which may reference the values of user-specified input ports, the current time, or the actor's iteration count. The actor outputs the value of the evaluated expression. </p>
> +
> +<p>Expressions are specified in the Ptolemy expression language via the expression parameter. For more information about the expression language, see http://ptolemy.eecs.berkeley.edu/papers/05/ptIIdesign1-intro/ptIIdesign1-intro.pdf. </p>
> +
> +<p>By default, the expression parameter is empty, and attempting to execute the actor without first specifying an expression generates an error. Expressions can refer to the values of inputs by the port name; to the current time by the identifier "time"; and to the current iteration count by the identifier "iteration." </p>
> +
> +<p>Input ports are created by the user and correspond to variables used in the specified expression. Currently, the Expression actor does not support input multiports. The actor requires all of its inputs to be present. If inputs are not all present, then the actor will generate an error. </p>
> +
> +<p>Note: the Expression actor can be used instead of many of the arithmetic actors, such as AddSubtract, MultiplyDivide, and TrigFunction. However, those actors will be usually be more efficient, and sometimes more convenient to use.</p></configure></property>
> +<property name="port:output" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>An output port that broadcasts the value of the evaluated expression. The actor automatically determines the type based on the type of the input.</configure></property>
> +<property name="prop:expression" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>An expression to evaluate. Expressions are specified in the Ptolemy expression language. For more information about the expression language, see http://ptolemy.eecs.berkeley.edu/papers/05/ptIIdesign1-intro/ptIIdesign1-intro.pdf. By default, the parameter is empty, and attempting to execute the actor without first specifying an expression generates an error. Expressions can refer to the values of inputs by the port name; to the current time by the identifier "time"; and to the current iteration count by the identifier "iteration."</configure></property>
> +</property> <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:75:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.Expression">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:950:1">
> + </property>
> + </property>
> + <property name="semanticType00" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#MathOperationActor">
> + </property>
> + <property name="semanticType11" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#GeneralPurpose">
> + </property>
> + <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
> + <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
> + </property>
> + <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
> + </property>
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-285.0, 85.0]">
> + </property>
> + <port name="output" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + </port>
> + <port name="repository" class="ptolemy.actor.TypedIOPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="false">
> + </property>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + </port>
> + </entity>
> + <relation name="relation" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <relation name="relation2" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <relation name="relation4" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <link port="StringToken [key=target, peer]" relation="relation"/>
> + <link port="StringToken [key=repository, peer]" relation="relation4"/>
> + <link port="SSH Execute cmd.target" relation="relation"/>
> + <link port="SSH Execute cmd.command" relation="relation2"/>
> + <link port="Expression.output" relation="relation2"/>
> + <link port="Expression.repository" relation="relation4"/>
> + </entity>
> + <entity name="Checkout_2" class="org.kepler.coactors.CompositeCoactor">
> + <property name="Read scope" class="org.kepler.util.CoactorParameter" value="Job">
> + </property>
> + <property name="_createdBy" class="ptolemy.kernel.attributes.VersionAttribute" value="7.0.2">
> + </property>
> + <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:ppod.daks.org:composite:100:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.kepler.coactors.CompositeCoactor">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:ppod.daks.org:class:100:1">
> + </property>
> + </property>
> + <property name="semanticType" class="org.kepler.sms.SemanticType" value="urn:lsid:ppod.daks.org:onto:1#ComadGeneralActors">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-310.0, -30.0]">
> + </property>
> + <property name="_windowProperties" class="ptolemy.actor.gui.WindowPropertiesAttribute" value="{bounds={408, 217, 883, 853}, maximized=false}">
> + </property>
> + <property name="_vergilSize" class="ptolemy.actor.gui.SizeAttribute" value="[600, 732]">
> + </property>
> + <property name="_vergilZoomFactor" class="ptolemy.data.expr.ExpertParameter" value="1.0">
> + </property>
> + <property name="_vergilCenter" class="ptolemy.data.expr.ExpertParameter" value="{-168.0, 178.0}">
> + </property>
> + <property name="SDF Director" class="ptolemy.domains.sdf.kernel.SDFDirector">
> + <property name="iterations" class="ptolemy.data.expr.Parameter" value="0">
> + </property>
> + <property name="vectorizationFactor" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + <property name="allowDisconnectedGraphs" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="allowRateChanges" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="constrainBufferSizes" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + <property name="period" class="ptolemy.data.expr.Parameter" value="0.0">
> + </property>
> + <property name="synchronizeToRealTime" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="timeResolution" class="ptolemy.moml.SharedParameter" value="1E-10">
> + </property>
> + <property name="Scheduler" class="ptolemy.domains.sdf.kernel.SDFScheduler">
> + <property name="constrainBufferSizes" class="ptolemy.data.expr.Parameter" value="constrainBufferSizes">
> + </property>
> + </property>
> +<property name="KeplerDocumentation" class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> +<property name="description" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="author" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Steve Neuendorffer</configure></property>
> +<property name="version" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="userLevelDocumentation" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>
> +<p>The SDF Director is often used to oversee fairly simple, sequential workflows in which the director can determine the order of actor invocation from the workflow. Types of workflows that would run well under an SDF Director include processing and reformatting tabular data, converting one data type to another, and reading and plotting a series of data points. A workflow in which an image is read, processed (rotated, scaled, clipped, filtered, etc.), and then displayed, is also an example of a sequential workflow that requires a director simply to ensure that each actor fires in the proper order (i.e., that each actor executes only after it receives its required inputs).</p>
> +
> +<p>The SDF Director is very efficient and will not tax system resources with overhead. However, this efficiency requires that certain conditions be met, namely that the data consumption and production rate of each actor in an SDF workflow be constant and declared. If an actor reads one piece of data and calculates and outputs a single result, it must always read and output a single token of data. This data rate cannot change during workflow execution and, in general, workflows that require dynamic scheduling and/or flow control cannot use this director. Additionally, the SDF Director has no understanding of passing time (at least by default), and actors that depend on a notion of time may not work as expected. For example, a TimedPlotter actor will plot all values at time zero when used in SDF. </p>
> +
> +<p>By default, the SDF Director requires that all actors in its workflow be connected. Otherwise, the director cannot account for concurrency between disconnected workflow parts. Usually, a PN Director should be used for workflows that contain disconnected actors; however, the SDF Director's allowDisconnectedGraphs parameter may also be set to true. The SDF Director will then schedule each disconnected "island" independently. The director cannot infer the sequential relationship between disconnected actors (i.e., nothing forces the director to finish executing all actors on one island before firing actors on another). However, the order of execution within each island should be correct. Usually, disconnected graphs in an SDF model indicate an error.</p>
> +
> +<p>Because SDF Directors schedule actors to fire only after they receive their inputs, workflows that require loops (feeding an actor's output back into its input port for further processing) can cause "deadlock" errors. The deadlock errors occur because the actor depends on its own output value as an initial input. To fix this problem, use a SampleDelay actor to generate and inject an initial input value into the workflow.</p>
> +
> +<p>The SDF Director determines the order in which actors execute and how many times each actor needs to be fired to complete a single iteration of the workflow. This schedule is calculated BEFORE the director begins to iterate the workflow. Because the SDF Director calculates a schedule in advance, it is quite efficient. However, SDF workflows must be static. In other words, the same number of tokens must be consumed/produced at every iteration of the workflow. Workflows that require dynamic control structures, such as a BooleanSwitch actor that sends output on one of two ports depending on the value of a 'control', cannot be used with an SDF Director because the number of tokens on each output can change for each execution.</p>
> +
> +<p>Unless otherwise specified, the SDF Director assumes that each actor consumes and produces exactly one token per channel on each firing. Actors that do not follow the one-token-per-channel firing convention (e.g., Repeat or Ramp) must declare the number of tokens they produce or consume via the appropriate parameters. </p>
> +
> +<p>The number of times a workflow is iterated is controlled by the director's iterations parameter. By default, this parameter is set to "0". Note that "0" does not mean "no iterations." Rather, "0" means that the workflow will iterate forever. Values greater than zero specify the actual number of times the director should execute the entire workflow. A value of 1, meaning that the director will run the workflow once, is often the best setting when building an SDF workflow. </p>
> +
> +<p>The amount of data processed by an SDF workflow is a function of both the number of times the workflow iterates and the value of the director's vectorizationFactor parameter. The vectorizationFactor is used to increase the efficiency of a workflow by increasing the number of times actors fire each time the workflow iterates. If the parameter is set to a positive integer (other than 1), the director will fire each actor the specified number of times more than normal. The default is 1, indicating that no vectorization should be performed. Keep in mind that changing the vectorizationFactor parameter changes the meaning of a nested SDF workflow and may cause deadlock in a workflow that uses it. </p>
> +
> +<p>The SDF Director has several advanced parameters that are generally only relevant when an SDF workflow contains composite components. In most cases the period, timeResolution, synchronizeToRealTime, allowRateChanges, timeResolution, and constrainBufferSizes parameters can be left at their default values.</p>
> +
> +<p>For more information about the SDF Director, see the Ptolemy documentation (http://ptolemy.eecs.berkeley.edu/papers/05/ptIIdesign3-domains/ptIIdesign3-domains.pdf).</p>
> +
> +</configure></property>
> +<property name="prop:allowDisconnectedGraphs" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether to allow disconnected actors in the workflow (by default, all actors are required to be connected). If disconnected actors are permitted, the SDF Director will schedule each disconnected 'island' independently. Nothing "forces" the director to finish executing all actors on one island before firing actors on another. However, the order of execution within each island should be correct. Usually, disconnected graphs in an SDF workflow indicate an error.</configure></property>
> +<property name="prop:allowRateChanges" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether dynamic rate changes are permitted or not. By default, rate changes are not permitted, and the director will perform a check to disallow such workflows. If the parameter is selected, then workflows that require rate parameters to be modified during execution are valid, and the SDF Director will dynamically compute a new schedule at runtime. This is an advanced parameter that can usually be left at its default value.</configure></property>
> +<property name="prop:constrainBufferSizes" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether buffer sizes are fixed. By default, buffers are fixed, and attempts to write to the buffer that cause the buffer to exceed its scheduled size result in an error. This is an advanced parameter that can usually be left at its default value.</configure></property>
> +<property name="prop:timeResolution" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The time precision used by this director. All time values are rounded to the nearest multiple of this number. The value is a double that defaults to "1E-10" (which is 10-10). This is an advanced parameter that can usually be left at its default value.</configure></property>
> +<property name="prop:iterations" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify the number of times a workflow is iterated. By default, this parameter is set to "0". Note that "0" does not mean "no iterations." Rather, "0" means that the workflow will iterate forever. Values greater than zero specify the actual number of times the director should execute the entire workflow. A value of 1, meaning that the director will run the workflow once, is often the best setting when building an SDF workflow. </configure></property>
> +<property name="prop:vectorizationFactor" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The vectorizationFactor is used to increase the efficiency of a workflow by increasing the number of times actors fire each time the workflow iterates. If the parameter is set to a positive integer (other than 1), the director will fire each actor the specified number of times more than normal. The default is 1, indicating that no vectorization should be performed. Keep in mind that changing the vectorizationFactor parameter changes the meaning of a nested SDF workflow and may cause deadlock in a workflow that uses it. </configure></property>
> +<property name="prop:synchronizeToRealTime" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether the execution should synchronize to real time or not. By default, the director does not synchronize to real time. If synchronize is selected, the director will only process the workflow when elapsed real time matches the product of the period parameter and the iteration count. Note: if the period parameter has a value of 0.0 (the default), then selecting this parameter has no effect. This is an advanced parameter that can usually be left at its default value.</configure></property>
> +<property name="prop:period" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The time period of each iteration. The value is a double that defaults to 0.0, which means that the director does not increment workflow time. If the value greater than 0.0, the actor will increment workflow time each time it fires. This is an advanced parameter that can usually be left at its default value. </configure></property>
> +</property> <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:director:1:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.domains.sdf.kernel.SDFDirector">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:directorclass:1:1">
> + </property>
> + </property>
> + <property name="semanticType00" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#Director">
> + </property>
> + <property name="semanticType11" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#Director">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="{-155.0, -70.0}">
> + </property>
> + </property>
> + <port name="input" class="org.kepler.util.CollectionIOPort">
> + <property name="input"/>
> + <property name="dataType" class="ptolemy.kernel.util.StringAttribute" value="general">
> + </property>
> + <property name="isMultiport" class="ptolemy.kernel.util.StringAttribute" value="false">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="{-445.0, 35.0}">
> + </property>
> + </port>
> + <port name="output" class="org.kepler.util.CollectionIOPort">
> + <property name="output"/>
> + <property name="multiport"/>
> + <property name="dataType" class="ptolemy.kernel.util.StringAttribute" value="unknown">
> + </property>
> + <property name="isMultiport" class="ptolemy.kernel.util.StringAttribute" value="true">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="{85.0, 50.0}">
> + </property>
> + </port>
> + <port name="StringToken [key=target, peer]" class="org.kepler.util.CollectionIOPort">
> + <property name="input"/>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="{-310.0, -10.0}">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="NORTH">
> + </property>
> + </port>
> + <port name="StringToken [key=repository2, peer]" class="org.kepler.util.CollectionIOPort">
> + <property name="input"/>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="{-370.0, 50.0}">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="SOUTH">
> + </property>
> + </port>
> + <entity name="SSH Execute cmd" class="org.kepler.actor.ssh.ExecuteCmd">
> + <property name="target" class="ptolemy.actor.parameters.PortParameter" value=""yildiz at home.ccs.ornl.gov"">
> + </property>
> + <property name="timeoutSeconds" class="ptolemy.data.expr.Parameter" value="0">
> + </property>
> + <property name="cleanupAfterError" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="thirdParty" class="ptolemy.actor.parameters.PortParameter" value="""">
> + </property>
> +<property name="KeplerDocumentation" class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> +<property name="description" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="author" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Norbert Podhorszki</configure></property>
> +<property name="version" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>1.1 March 2008</configure></property>
> +<property name="userLevelDocumentation" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>
> +
> + <p>The SSHExecuteCmd actor connects to a remote host using SSH protocol and executes a command. If the host is an empty string or "local", the Java
> + Runtime will be used for execution instead of SSH. After the command terminates, the actor returns the stdout, stderr, and exit code of the operation.</p>
> +
> +<p>Set the <i>timeoutSeconds</i> parameter to terminate the command after a specified amount of time. Specify 0 to wait indefinitely for command termination. If connecting to a Unix host, use the <i>cleanupAfterError</i>
> +Parameter to kill the remote process (and all of its children) after an error or timeout. Set this parameter only if connecting to a Unix server (other platforms do not support it).
> +</p>
> +
> +<p>Note: Streaming of output during the command execution is not currently
> + implemented.</p>
> +
> + <p><b>Third party operation.</b>
> + If the remote command is expected to ask for a password
> + (or passphrase when connecting to a remote host with public-key authentication)
> + set the port/parameter <i>thirdParty</i> for the user at host:port of that third party
> + (it can be the same as <i>target</i> if a sudo command is executed).</p>
> +
> + <p>The authentication to the third party should be the same from the target
> + host and from Kepler's local host. Kepler authenticates (by opening a channel)
> + to the third party and then it provides the password/passphrase used for the
> + authentication to the command on the target host. Therefore, this actor cannot be
> + used to reach a remote host through a proxy machine and execute a command there.</p>
> +
> + <p>The third party execution can be used e.g. to execute and ssh/scp command
> + that connects to another host, also reachable from Kepler's host, to execute external
> + data transfer commands (bbcp, GridFTP, SRM-Lite etc) or sudo commands.</p>
> +
> + <p>The actor will first authenticate Kepler to the third party host
> + (if not yet done by other actors, e.g. SshSession). During the execution of the command,
> + it looks for the appearance of the string 'password' or 'passphrase' in the stdout/stderr
> + streams (case-insensitively). If such string is found, it writes the authentication code
> + stored within Kepler used for the authentication. Therefore, the command must read the
> + password on the standard input, not directly from the terminal device.
> + This process is performed only once!</p>
> +
> + <p>The underlying java code does not have pseudo-terminal emulation, so if you cannot
> + force the command to read passwords from the stdin (e.g. scp command), you have to use an
> + external tool to execute the command through a pseudo-terminal. <b>ptyexec</b> is provided
> + in the <i>org.kepler.ssh</i> package, a C program, that should be compiled and put into the path
> + on the target machine. Then you can execute <i>"ptyexec scp ..."</i>. It works on Linux only.</p>
> +
> +</configure></property>
> +<property name="port:stdout" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Output of the command as it would output to the standard shell. If there is an SSH connection related error (or timeout) the value will be an empty string. </configure></property>
> +<property name="port:stderr" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Any errors that were reported by the remote execution or while connecting. If there is an SSH connection related error (or timeout) the value will be an empty string. </configure></property>
> +<property name="port:target" class="ptolemy.kernel.util.ConfigurableAttribute"><configure> The machine to be used at job submission. It should be null, "" or "local" for the local machine or [user@]host to denote a remote machine accessible with SSH. If user is not provided, the local username will be used. If port is not provided, the default port 22 will be applied. This parameter is read once at initialize. </configure></property>
> +<property name="port:command" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The command to be executed on the remote host, specified as a string (e.g., "uname -a; date") </configure></property>
> +<property name="port:errors" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The string representation of actor execution errors, if any.
> + </configure></property>
> +<property name="port:exitcode" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The exit code of the command. If there is an SSH connection related error (or timeout) the exitcode will be -32767 </configure></property>
> +<property name="prop:timeoutSeconds" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Timeout in seconds. The command will be timed out after the specified amount of time. Specify 0 to wait indefinitely for command termination. </configure></property>
> +<property name="prop:streaming mode" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether the output should be sent in a streaming mode.
> + Note: Streaming is not currently implemented.
> + </configure></property>
> +<property name="prop:thirdParty" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The third party machine where the command wants to connect and needs to authenticate. Kepler can be used to do the authentication and then provide the password or private-key passphrase to the command. It should be defined as [user@]host[:port]. </configure></property>
> +<property name="prop:cleanupAfterError" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Kill remote process(es) after an error or timeout. Set this parameter only if connecting to a Unix server (other platforms do not support it). All processes belonging to the same group as the remote command (i.e., its children) will be killed. </configure></property>
> +<property name="prop:target" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The machine to be used at job submission. It should be null, "" or "local" for the local machine or [user@]host to denote a remote machine accessible with SSH. If user is not provided, the local username will be used. If port is not provided, the default port 22 will be applied. This parameter is read once at initialize. </configure></property>
> +</property> <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:506:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.kepler.actor.ssh.ExecuteCmd">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1213:1">
> + </property>
> + </property>
> + <property name="semanticType00" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ExternalExecutionEnvironmentActor">
> + </property>
> + <property name="semanticType21" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#SSH">
> + </property>
> + <property name="semanticType41" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:4:1#CPES">
> + </property>
> + <property name="semanticType22" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#Tutorial">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="{-125.0, 30.0}">
> + </property>
> + <port name="target" class="ptolemy.actor.parameters.ParameterPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="command" class="ptolemy.actor.TypedIOPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="stdout" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="stderr" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="exitcode" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="errors" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="thirdParty" class="ptolemy.actor.parameters.ParameterPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + </entity>
> + <entity name="Expression" class="ptolemy.actor.lib.Expression">
> + <property name="expression" class="ptolemy.kernel.util.StringAttribute" value=""echo co "+repository">
> + <property name="_hide" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </property>
> +<property name="KeplerDocumentation" class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> +<property name="description" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="author" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Xiaojun Liu, Edward A. Lee, Steve Neuendorffer</configure></property>
> +<property name="version" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="userLevelDocumentation" class="ptolemy.kernel.util.ConfigurableAttribute"><configure><p>The Expression actor evaluates a specified expression (e.g., an addition or multiplication operation), which may reference the values of user-specified input ports, the current time, or the actor's iteration count. The actor outputs the value of the evaluated expression. </p>
> +
> +<p>Expressions are specified in the Ptolemy expression language via the expression parameter. For more information about the expression language, see http://ptolemy.eecs.berkeley.edu/papers/05/ptIIdesign1-intro/ptIIdesign1-intro.pdf. </p>
> +
> +<p>By default, the expression parameter is empty, and attempting to execute the actor without first specifying an expression generates an error. Expressions can refer to the values of inputs by the port name; to the current time by the identifier "time"; and to the current iteration count by the identifier "iteration." </p>
> +
> +<p>Input ports are created by the user and correspond to variables used in the specified expression. Currently, the Expression actor does not support input multiports. The actor requires all of its inputs to be present. If inputs are not all present, then the actor will generate an error. </p>
> +
> +<p>Note: the Expression actor can be used instead of many of the arithmetic actors, such as AddSubtract, MultiplyDivide, and TrigFunction. However, those actors will be usually be more efficient, and sometimes more convenient to use.</p></configure></property>
> +<property name="port:output" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>An output port that broadcasts the value of the evaluated expression. The actor automatically determines the type based on the type of the input.</configure></property>
> +<property name="prop:expression" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>An expression to evaluate. Expressions are specified in the Ptolemy expression language. For more information about the expression language, see http://ptolemy.eecs.berkeley.edu/papers/05/ptIIdesign1-intro/ptIIdesign1-intro.pdf. By default, the parameter is empty, and attempting to execute the actor without first specifying an expression generates an error. Expressions can refer to the values of inputs by the port name; to the current time by the identifier "time"; and to the current iteration count by the identifier "iteration."</configure></property>
> +</property> <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:75:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.Expression">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:950:1">
> + </property>
> + </property>
> + <property name="semanticType00" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#MathOperationActor">
> + </property>
> + <property name="semanticType11" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#GeneralPurpose">
> + </property>
> + <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
> + <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
> + </property>
> + <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
> + </property>
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="{-275.0, 95.0}">
> + </property>
> + <port name="output" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + </port>
> + <port name="repository" class="ptolemy.actor.TypedIOPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="false">
> + </property>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + </port>
> + </entity>
> + <relation name="relation" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <relation name="relation2" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <relation name="relation4" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <link port="StringToken [key=target, peer]" relation="relation"/>
> + <link port="StringToken [key=repository2, peer]" relation="relation4"/>
> + <link port="SSH Execute cmd.target" relation="relation"/>
> + <link port="SSH Execute cmd.command" relation="relation2"/>
> + <link port="Expression.output" relation="relation2"/>
> + <link port="Expression.repository" relation="relation4"/>
> + </entity>
> + <entity name="SSH_Dir" class="org.kepler.coactors.CompositeCoactor">
> + <property name="Read scope" class="org.kepler.util.CoactorParameter" value="Job">
> + </property>
> + <property name="_createdBy" class="ptolemy.kernel.attributes.VersionAttribute" value="7.0.2">
> + </property>
> + <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:ppod.daks.org:composite:100:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.kepler.coactors.CompositeCoactor">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:ppod.daks.org:class:100:1">
> + </property>
> + </property>
> + <property name="semanticType" class="org.kepler.sms.SemanticType" value="urn:lsid:ppod.daks.org:onto:1#ComadGeneralActors">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-205.0, -30.0]">
> + </property>
> + <property name="_windowProperties" class="ptolemy.actor.gui.WindowPropertiesAttribute" value="{bounds={500, 189, 883, 853}, maximized=false}">
> + </property>
> + <property name="_vergilSize" class="ptolemy.actor.gui.SizeAttribute" value="[600, 732]">
> + </property>
> + <property name="_vergilZoomFactor" class="ptolemy.data.expr.ExpertParameter" value="1.0">
> + </property>
> + <property name="_vergilCenter" class="ptolemy.data.expr.ExpertParameter" value="{-9.0, 84.0}">
> + </property>
> + <property name="SDF Director" class="ptolemy.domains.sdf.kernel.SDFDirector">
> + <property name="iterations" class="ptolemy.data.expr.Parameter" value="0">
> + </property>
> + <property name="vectorizationFactor" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + <property name="allowDisconnectedGraphs" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="allowRateChanges" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="constrainBufferSizes" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + <property name="period" class="ptolemy.data.expr.Parameter" value="0.0">
> + </property>
> + <property name="synchronizeToRealTime" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="timeResolution" class="ptolemy.moml.SharedParameter" value="1E-10">
> + </property>
> + <property name="Scheduler" class="ptolemy.domains.sdf.kernel.SDFScheduler">
> + <property name="constrainBufferSizes" class="ptolemy.data.expr.Parameter" value="constrainBufferSizes">
> + </property>
> + </property>
> +<property name="KeplerDocumentation" class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> +<property name="description" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="author" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Steve Neuendorffer</configure></property>
> +<property name="version" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="userLevelDocumentation" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>
> +<p>The SDF Director is often used to oversee fairly simple, sequential workflows in which the director can determine the order of actor invocation from the workflow. Types of workflows that would run well under an SDF Director include processing and reformatting tabular data, converting one data type to another, and reading and plotting a series of data points. A workflow in which an image is read, processed (rotated, scaled, clipped, filtered, etc.), and then displayed, is also an example of a sequential workflow that requires a director simply to ensure that each actor fires in the proper order (i.e., that each actor executes only after it receives its required inputs).</p>
> +
> +<p>The SDF Director is very efficient and will not tax system resources with overhead. However, this efficiency requires that certain conditions be met, namely that the data consumption and production rate of each actor in an SDF workflow be constant and declared. If an actor reads one piece of data and calculates and outputs a single result, it must always read and output a single token of data. This data rate cannot change during workflow execution and, in general, workflows that require dynamic scheduling and/or flow control cannot use this director. Additionally, the SDF Director has no understanding of passing time (at least by default), and actors that depend on a notion of time may not work as expected. For example, a TimedPlotter actor will plot all values at time zero when used in SDF. </p>
> +
> +<p>By default, the SDF Director requires that all actors in its workflow be connected. Otherwise, the director cannot account for concurrency between disconnected workflow parts. Usually, a PN Director should be used for workflows that contain disconnected actors; however, the SDF Director's allowDisconnectedGraphs parameter may also be set to true. The SDF Director will then schedule each disconnected "island" independently. The director cannot infer the sequential relationship between disconnected actors (i.e., nothing forces the director to finish executing all actors on one island before firing actors on another). However, the order of execution within each island should be correct. Usually, disconnected graphs in an SDF model indicate an error.</p>
> +
> +<p>Because SDF Directors schedule actors to fire only after they receive their inputs, workflows that require loops (feeding an actor's output back into its input port for further processing) can cause "deadlock" errors. The deadlock errors occur because the actor depends on its own output value as an initial input. To fix this problem, use a SampleDelay actor to generate and inject an initial input value into the workflow.</p>
> +
> +<p>The SDF Director determines the order in which actors execute and how many times each actor needs to be fired to complete a single iteration of the workflow. This schedule is calculated BEFORE the director begins to iterate the workflow. Because the SDF Director calculates a schedule in advance, it is quite efficient. However, SDF workflows must be static. In other words, the same number of tokens must be consumed/produced at every iteration of the workflow. Workflows that require dynamic control structures, such as a BooleanSwitch actor that sends output on one of two ports depending on the value of a 'control', cannot be used with an SDF Director because the number of tokens on each output can change for each execution.</p>
> +
> +<p>Unless otherwise specified, the SDF Director assumes that each actor consumes and produces exactly one token per channel on each firing. Actors that do not follow the one-token-per-channel firing convention (e.g., Repeat or Ramp) must declare the number of tokens they produce or consume via the appropriate parameters. </p>
> +
> +<p>The number of times a workflow is iterated is controlled by the director's iterations parameter. By default, this parameter is set to "0". Note that "0" does not mean "no iterations." Rather, "0" means that the workflow will iterate forever. Values greater than zero specify the actual number of times the director should execute the entire workflow. A value of 1, meaning that the director will run the workflow once, is often the best setting when building an SDF workflow. </p>
> +
> +<p>The amount of data processed by an SDF workflow is a function of both the number of times the workflow iterates and the value of the director's vectorizationFactor parameter. The vectorizationFactor is used to increase the efficiency of a workflow by increasing the number of times actors fire each time the workflow iterates. If the parameter is set to a positive integer (other than 1), the director will fire each actor the specified number of times more than normal. The default is 1, indicating that no vectorization should be performed. Keep in mind that changing the vectorizationFactor parameter changes the meaning of a nested SDF workflow and may cause deadlock in a workflow that uses it. </p>
> +
> +<p>The SDF Director has several advanced parameters that are generally only relevant when an SDF workflow contains composite components. In most cases the period, timeResolution, synchronizeToRealTime, allowRateChanges, timeResolution, and constrainBufferSizes parameters can be left at their default values.</p>
> +
> +<p>For more information about the SDF Director, see the Ptolemy documentation (http://ptolemy.eecs.berkeley.edu/papers/05/ptIIdesign3-domains/ptIIdesign3-domains.pdf).</p>
> +
> +</configure></property>
> +<property name="prop:allowDisconnectedGraphs" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether to allow disconnected actors in the workflow (by default, all actors are required to be connected). If disconnected actors are permitted, the SDF Director will schedule each disconnected 'island' independently. Nothing "forces" the director to finish executing all actors on one island before firing actors on another. However, the order of execution within each island should be correct. Usually, disconnected graphs in an SDF workflow indicate an error.</configure></property>
> +<property name="prop:allowRateChanges" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether dynamic rate changes are permitted or not. By default, rate changes are not permitted, and the director will perform a check to disallow such workflows. If the parameter is selected, then workflows that require rate parameters to be modified during execution are valid, and the SDF Director will dynamically compute a new schedule at runtime. This is an advanced parameter that can usually be left at its default value.</configure></property>
> +<property name="prop:timeResolution" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The time precision used by this director. All time values are rounded to the nearest multiple of this number. The value is a double that defaults to "1E-10" (which is 10-10). This is an advanced parameter that can usually be left at its default value.</configure></property>
> +<property name="prop:constrainBufferSizes" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether buffer sizes are fixed. By default, buffers are fixed, and attempts to write to the buffer that cause the buffer to exceed its scheduled size result in an error. This is an advanced parameter that can usually be left at its default value.</configure></property>
> +<property name="prop:iterations" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify the number of times a workflow is iterated. By default, this parameter is set to "0". Note that "0" does not mean "no iterations." Rather, "0" means that the workflow will iterate forever. Values greater than zero specify the actual number of times the director should execute the entire workflow. A value of 1, meaning that the director will run the workflow once, is often the best setting when building an SDF workflow. </configure></property>
> +<property name="prop:vectorizationFactor" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The vectorizationFactor is used to increase the efficiency of a workflow by increasing the number of times actors fire each time the workflow iterates. If the parameter is set to a positive integer (other than 1), the director will fire each actor the specified number of times more than normal. The default is 1, indicating that no vectorization should be performed. Keep in mind that changing the vectorizationFactor parameter changes the meaning of a nested SDF workflow and may cause deadlock in a workflow that uses it. </configure></property>
> +<property name="prop:synchronizeToRealTime" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether the execution should synchronize to real time or not. By default, the director does not synchronize to real time. If synchronize is selected, the director will only process the workflow when elapsed real time matches the product of the period parameter and the iteration count. Note: if the period parameter has a value of 0.0 (the default), then selecting this parameter has no effect. This is an advanced parameter that can usually be left at its default value.</configure></property>
> +<property name="prop:period" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The time period of each iteration. The value is a double that defaults to 0.0, which means that the director does not increment workflow time. If the value greater than 0.0, the actor will increment workflow time each time it fires. This is an advanced parameter that can usually be left at its default value. </configure></property>
> +</property> <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:director:1:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.domains.sdf.kernel.SDFDirector">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:directorclass:1:1">
> + </property>
> + </property>
> + <property name="semanticType00" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#Director">
> + </property>
> + <property name="semanticType11" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#Director">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[20.0, -85.0]">
> + </property>
> + </property>
> + <port name="input" class="org.kepler.util.CollectionIOPort">
> + <property name="input"/>
> + <property name="dataType" class="ptolemy.kernel.util.StringAttribute" value="general">
> + </property>
> + <property name="isMultiport" class="ptolemy.kernel.util.StringAttribute" value="false">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="{-305.0, 0.0}">
> + </property>
> + </port>
> + <port name="output" class="org.kepler.util.CollectionIOPort">
> + <property name="output"/>
> + <property name="multiport"/>
> + <property name="dataType" class="ptolemy.kernel.util.StringAttribute" value="unknown">
> + </property>
> + <property name="isMultiport" class="ptolemy.kernel.util.StringAttribute" value="true">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="{390.0, 60.0}">
> + </property>
> + </port>
> + <port name="StringToken [key=target]" class="org.kepler.util.CollectionIOPort">
> + <property name="input"/>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-240.0, -55.0]">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="NORTH">
> + </property>
> + </port>
> + <port name="StringToken [key=dir]" class="org.kepler.util.CollectionIOPort">
> + <property name="input"/>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-255.0, -10.0]">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="NORTH">
> + </property>
> + </port>
> + <port name="StringToken [key=mask]" class="org.kepler.util.CollectionIOPort">
> + <property name="input"/>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-245.0, 50.0]">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="NORTH">
> + </property>
> + </port>
> + <port name="StringToken [key=repository]" class="org.kepler.util.CollectionIOPort">
> + <property name="input"/>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-200.0, 80.0]">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="SOUTH">
> + </property>
> + </port>
> + <port name="DirNames/StringToken+" class="org.kepler.util.CollectionIOPort">
> + <property name="output"/>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[130.0, 25.0]">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="SOUTH">
> + </property>
> + </port>
> + <port name="StringToken [key=tempdir]" class="org.kepler.util.CollectionIOPort">
> + <property name="input"/>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-235.0, 175.0]">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="SOUTH">
> + </property>
> + </port>
> + <port name="DirNames/StringToken [key=tempdir]" class="org.kepler.util.CollectionIOPort">
> + <property name="output"/>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-100.0, 175.0]">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="NORTH">
> + </property>
> + </port>
> + <port name="DirNames/StringToken [key=target]" class="org.kepler.util.CollectionIOPort">
> + <property name="output"/>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-10.0, -120.0]">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="SOUTH">
> + </property>
> + </port>
> + <entity name="SshDirectoryList_v1_" class="org.kepler.actors.io.SshDirectoryList_v1_2">
> + <property name="target" class="ptolemy.actor.parameters.PortParameter" value="">
> + </property>
> + <property name="dir" class="ptolemy.actor.parameters.PortParameter" value="">
> + </property>
> + <property name="newFilesOnly" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-25.0, -10.0]">
> + </property>
> + </entity>
> + <relation name="relation" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <relation name="relation2" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <relation name="relation5" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <relation name="relation4" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <relation name="relation6" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + <vertex name="vertex" value="[-105.0, -45.0]">
> + </vertex>
> + </relation>
> + <link port="StringToken [key=target]" relation="relation6"/>
> + <link port="StringToken [key=dir]" relation="relation5"/>
> + <link port="StringToken [key=repository]" relation="relation"/>
> + <link port="DirNames/StringToken+" relation="relation2"/>
> + <link port="StringToken [key=tempdir]" relation="relation4"/>
> + <link port="DirNames/StringToken [key=tempdir]" relation="relation4"/>
> + <link port="DirNames/StringToken [key=target]" relation="relation6"/>
> + <link port="SshDirectoryList_v1_.target" relation="relation6"/>
> + <link port="SshDirectoryList_v1_.dir" relation="relation5"/>
> + <link port="SshDirectoryList_v1_.trigger" relation="relation"/>
> + <link port="SshDirectoryList_v1_.newFiles" relation="relation2"/>
> + </entity>
> + <entity name="CollectionDisplay" class="org.kepler.coactors.CollectionDisplay">
> + <property name="Signature" class="org.kepler.util.CoactorParameter" value="">
> + </property>
> + <property name="Read scope" class="org.kepler.util.CoactorParameter" value="/">
> + </property>
> + <property name="showDetails" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + <property name="showProvenance" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + <property name="stringsOnSingleLines" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + <property name="columnsDisplayed" class="ptolemy.data.expr.Parameter" value="60">
> + </property>
> + <property name="rowsDisplayed" class="ptolemy.data.expr.Parameter" value="20">
> + </property>
> + <property name="clearDisplayOn" class="ptolemy.data.expr.StringParameter" value="">
> + </property>
> + <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:ppod.daks.org:actor:7:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.kepler.coactors.CollectionDisplay">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:ppod.daks.org:class:7:1">
> + </property>
> + </property>
> + <property name="semanticType" class="org.kepler.sms.SemanticType" value="urn:lsid:ppod.daks.org:onto:1#ComadGeneralActors">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-210.0, 395.0]">
> + </property>
> + </entity>
> + <entity name="SSH_Merge2" class="org.kepler.coactors.CompositeCoactor">
> + <property name="Read scope" class="org.kepler.util.CoactorParameter" value="Job/DirNames">
> + </property>
> + <property name="_createdBy" class="ptolemy.kernel.attributes.VersionAttribute" value="7.0.2">
> + </property>
> + <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:ppod.daks.org:composite:100:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.kepler.coactors.CompositeCoactor">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:ppod.daks.org:class:100:1">
> + </property>
> + </property>
> + <property name="semanticType" class="org.kepler.sms.SemanticType" value="urn:lsid:ppod.daks.org:onto:1#ComadGeneralActors">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-325.0, 85.0]">
> + </property>
> + <property name="_windowProperties" class="ptolemy.actor.gui.WindowPropertiesAttribute" value="{bounds={408, 217, 883, 853}, maximized=false}">
> + </property>
> + <property name="_vergilSize" class="ptolemy.actor.gui.SizeAttribute" value="[600, 732]">
> + </property>
> + <property name="_vergilZoomFactor" class="ptolemy.data.expr.ExpertParameter" value="1.0">
> + </property>
> + <property name="_vergilCenter" class="ptolemy.data.expr.ExpertParameter" value="{-320.0, 138.0}">
> + </property>
> + <property name="SDF Director" class="ptolemy.domains.sdf.kernel.SDFDirector">
> + <property name="iterations" class="ptolemy.data.expr.Parameter" value="0">
> + </property>
> + <property name="vectorizationFactor" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + <property name="allowDisconnectedGraphs" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="allowRateChanges" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="constrainBufferSizes" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + <property name="period" class="ptolemy.data.expr.Parameter" value="0.0">
> + </property>
> + <property name="synchronizeToRealTime" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="timeResolution" class="ptolemy.moml.SharedParameter" value="1E-10">
> + </property>
> + <property name="Scheduler" class="ptolemy.domains.sdf.kernel.SDFScheduler">
> + <property name="constrainBufferSizes" class="ptolemy.data.expr.Parameter" value="constrainBufferSizes">
> + </property>
> + </property>
> +<property name="KeplerDocumentation" class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> +<property name="description" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="author" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Steve Neuendorffer</configure></property>
> +<property name="version" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="userLevelDocumentation" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>
> +<p>The SDF Director is often used to oversee fairly simple, sequential workflows in which the director can determine the order of actor invocation from the workflow. Types of workflows that would run well under an SDF Director include processing and reformatting tabular data, converting one data type to another, and reading and plotting a series of data points. A workflow in which an image is read, processed (rotated, scaled, clipped, filtered, etc.), and then displayed, is also an example of a sequential workflow that requires a director simply to ensure that each actor fires in the proper order (i.e., that each actor executes only after it receives its required inputs).</p>
> +
> +<p>The SDF Director is very efficient and will not tax system resources with overhead. However, this efficiency requires that certain conditions be met, namely that the data consumption and production rate of each actor in an SDF workflow be constant and declared. If an actor reads one piece of data and calculates and outputs a single result, it must always read and output a single token of data. This data rate cannot change during workflow execution and, in general, workflows that require dynamic scheduling and/or flow control cannot use this director. Additionally, the SDF Director has no understanding of passing time (at least by default), and actors that depend on a notion of time may not work as expected. For example, a TimedPlotter actor will plot all values at time zero when used in SDF. </p>
> +
> +<p>By default, the SDF Director requires that all actors in its workflow be connected. Otherwise, the director cannot account for concurrency between disconnected workflow parts. Usually, a PN Director should be used for workflows that contain disconnected actors; however, the SDF Director's allowDisconnectedGraphs parameter may also be set to true. The SDF Director will then schedule each disconnected "island" independently. The director cannot infer the sequential relationship between disconnected actors (i.e., nothing forces the director to finish executing all actors on one island before firing actors on another). However, the order of execution within each island should be correct. Usually, disconnected graphs in an SDF model indicate an error.</p>
> +
> +<p>Because SDF Directors schedule actors to fire only after they receive their inputs, workflows that require loops (feeding an actor's output back into its input port for further processing) can cause "deadlock" errors. The deadlock errors occur because the actor depends on its own output value as an initial input. To fix this problem, use a SampleDelay actor to generate and inject an initial input value into the workflow.</p>
> +
> +<p>The SDF Director determines the order in which actors execute and how many times each actor needs to be fired to complete a single iteration of the workflow. This schedule is calculated BEFORE the director begins to iterate the workflow. Because the SDF Director calculates a schedule in advance, it is quite efficient. However, SDF workflows must be static. In other words, the same number of tokens must be consumed/produced at every iteration of the workflow. Workflows that require dynamic control structures, such as a BooleanSwitch actor that sends output on one of two ports depending on the value of a 'control', cannot be used with an SDF Director because the number of tokens on each output can change for each execution.</p>
> +
> +<p>Unless otherwise specified, the SDF Director assumes that each actor consumes and produces exactly one token per channel on each firing. Actors that do not follow the one-token-per-channel firing convention (e.g., Repeat or Ramp) must declare the number of tokens they produce or consume via the appropriate parameters. </p>
> +
> +<p>The number of times a workflow is iterated is controlled by the director's iterations parameter. By default, this parameter is set to "0". Note that "0" does not mean "no iterations." Rather, "0" means that the workflow will iterate forever. Values greater than zero specify the actual number of times the director should execute the entire workflow. A value of 1, meaning that the director will run the workflow once, is often the best setting when building an SDF workflow. </p>
> +
> +<p>The amount of data processed by an SDF workflow is a function of both the number of times the workflow iterates and the value of the director's vectorizationFactor parameter. The vectorizationFactor is used to increase the efficiency of a workflow by increasing the number of times actors fire each time the workflow iterates. If the parameter is set to a positive integer (other than 1), the director will fire each actor the specified number of times more than normal. The default is 1, indicating that no vectorization should be performed. Keep in mind that changing the vectorizationFactor parameter changes the meaning of a nested SDF workflow and may cause deadlock in a workflow that uses it. </p>
> +
> +<p>The SDF Director has several advanced parameters that are generally only relevant when an SDF workflow contains composite components. In most cases the period, timeResolution, synchronizeToRealTime, allowRateChanges, timeResolution, and constrainBufferSizes parameters can be left at their default values.</p>
> +
> +<p>For more information about the SDF Director, see the Ptolemy documentation (http://ptolemy.eecs.berkeley.edu/papers/05/ptIIdesign3-domains/ptIIdesign3-domains.pdf).</p>
> +
> +</configure></property>
> +<property name="prop:allowDisconnectedGraphs" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether to allow disconnected actors in the workflow (by default, all actors are required to be connected). If disconnected actors are permitted, the SDF Director will schedule each disconnected 'island' independently. Nothing "forces" the director to finish executing all actors on one island before firing actors on another. However, the order of execution within each island should be correct. Usually, disconnected graphs in an SDF workflow indicate an error.</configure></property>
> +<property name="prop:allowRateChanges" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether dynamic rate changes are permitted or not. By default, rate changes are not permitted, and the director will perform a check to disallow such workflows. If the parameter is selected, then workflows that require rate parameters to be modified during execution are valid, and the SDF Director will dynamically compute a new schedule at runtime. This is an advanced parameter that can usually be left at its default value.</configure></property>
> +<property name="prop:timeResolution" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The time precision used by this director. All time values are rounded to the nearest multiple of this number. The value is a double that defaults to "1E-10" (which is 10-10). This is an advanced parameter that can usually be left at its default value.</configure></property>
> +<property name="prop:constrainBufferSizes" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether buffer sizes are fixed. By default, buffers are fixed, and attempts to write to the buffer that cause the buffer to exceed its scheduled size result in an error. This is an advanced parameter that can usually be left at its default value.</configure></property>
> +<property name="prop:iterations" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify the number of times a workflow is iterated. By default, this parameter is set to "0". Note that "0" does not mean "no iterations." Rather, "0" means that the workflow will iterate forever. Values greater than zero specify the actual number of times the director should execute the entire workflow. A value of 1, meaning that the director will run the workflow once, is often the best setting when building an SDF workflow. </configure></property>
> +<property name="prop:vectorizationFactor" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The vectorizationFactor is used to increase the efficiency of a workflow by increasing the number of times actors fire each time the workflow iterates. If the parameter is set to a positive integer (other than 1), the director will fire each actor the specified number of times more than normal. The default is 1, indicating that no vectorization should be performed. Keep in mind that changing the vectorizationFactor parameter changes the meaning of a nested SDF workflow and may cause deadlock in a workflow that uses it. </configure></property>
> +<property name="prop:synchronizeToRealTime" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether the execution should synchronize to real time or not. By default, the director does not synchronize to real time. If synchronize is selected, the director will only process the workflow when elapsed real time matches the product of the period parameter and the iteration count. Note: if the period parameter has a value of 0.0 (the default), then selecting this parameter has no effect. This is an advanced parameter that can usually be left at its default value.</configure></property>
> +<property name="prop:period" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The time period of each iteration. The value is a double that defaults to 0.0, which means that the director does not increment workflow time. If the value greater than 0.0, the actor will increment workflow time each time it fires. This is an advanced parameter that can usually be left at its default value. </configure></property>
> +</property> <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:director:1:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.domains.sdf.kernel.SDFDirector">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:directorclass:1:1">
> + </property>
> + </property>
> + <property name="semanticType00" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#Director">
> + </property>
> + <property name="semanticType11" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#Director">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="{-145.0, -60.0}">
> + </property>
> + </property>
> + <port name="input" class="org.kepler.util.CollectionIOPort">
> + <property name="input"/>
> + <property name="dataType" class="ptolemy.kernel.util.StringAttribute" value="general">
> + </property>
> + <property name="isMultiport" class="ptolemy.kernel.util.StringAttribute" value="false">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-465.0, -105.0]">
> + </property>
> + </port>
> + <port name="output" class="org.kepler.util.CollectionIOPort">
> + <property name="output"/>
> + <property name="multiport"/>
> + <property name="dataType" class="ptolemy.kernel.util.StringAttribute" value="unknown">
> + </property>
> + <property name="isMultiport" class="ptolemy.kernel.util.StringAttribute" value="true">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="{95.0, 60.0}">
> + </property>
> + </port>
> + <port name="StringToken" class="org.kepler.util.CollectionIOPort">
> + <property name="input"/>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="{-375.0, 60.0}">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="NORTH">
> + </property>
> + </port>
> + <port name="StringToken [key=tempdir]" class="org.kepler.util.CollectionIOPort">
> + <property name="input"/>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-540.0, 125.0]">
> + </property>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="NORTH">
> + </property>
> + </port>
> + <port name="StringToken [key=target]" class="org.kepler.util.CollectionIOPort">
> + <property name="input"/>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-390.0, -10.0]">
> + </property>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="SOUTH">
> + </property>
> + </port>
> + <port name="StringToken [key=S3D]" class="org.kepler.util.CollectionIOPort">
> + <property name="input"/>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-545.0, 185.0]">
> + </property>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="SOUTH">
> + </property>
> + </port>
> + <entity name="SSH Execute cmd" class="org.kepler.actor.ssh.ExecuteCmd">
> + <property name="target" class="ptolemy.actor.parameters.PortParameter" value=""yildiz at home.ccs.ornl.gov"">
> + </property>
> + <property name="timeoutSeconds" class="ptolemy.data.expr.Parameter" value="0">
> + </property>
> + <property name="cleanupAfterError" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="thirdParty" class="ptolemy.actor.parameters.PortParameter" value="""">
> + </property>
> +<property name="KeplerDocumentation" class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> +<property name="description" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="author" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Norbert Podhorszki</configure></property>
> +<property name="version" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>1.1 March 2008</configure></property>
> +<property name="userLevelDocumentation" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>
> +
> + <p>The SSHExecuteCmd actor connects to a remote host using SSH protocol and executes a command. If the host is an empty string or "local", the Java
> + Runtime will be used for execution instead of SSH. After the command terminates, the actor returns the stdout, stderr, and exit code of the operation.</p>
> +
> +<p>Set the <i>timeoutSeconds</i> parameter to terminate the command after a specified amount of time. Specify 0 to wait indefinitely for command termination. If connecting to a Unix host, use the <i>cleanupAfterError</i>
> +Parameter to kill the remote process (and all of its children) after an error or timeout. Set this parameter only if connecting to a Unix server (other platforms do not support it).
> +</p>
> +
> +<p>Note: Streaming of output during the command execution is not currently
> + implemented.</p>
> +
> + <p><b>Third party operation.</b>
> + If the remote command is expected to ask for a password
> + (or passphrase when connecting to a remote host with public-key authentication)
> + set the port/parameter <i>thirdParty</i> for the user at host:port of that third party
> + (it can be the same as <i>target</i> if a sudo command is executed).</p>
> +
> + <p>The authentication to the third party should be the same from the target
> + host and from Kepler's local host. Kepler authenticates (by opening a channel)
> + to the third party and then it provides the password/passphrase used for the
> + authentication to the command on the target host. Therefore, this actor cannot be
> + used to reach a remote host through a proxy machine and execute a command there.</p>
> +
> + <p>The third party execution can be used e.g. to execute and ssh/scp command
> + that connects to another host, also reachable from Kepler's host, to execute external
> + data transfer commands (bbcp, GridFTP, SRM-Lite etc) or sudo commands.</p>
> +
> + <p>The actor will first authenticate Kepler to the third party host
> + (if not yet done by other actors, e.g. SshSession). During the execution of the command,
> + it looks for the appearance of the string 'password' or 'passphrase' in the stdout/stderr
> + streams (case-insensitively). If such string is found, it writes the authentication code
> + stored within Kepler used for the authentication. Therefore, the command must read the
> + password on the standard input, not directly from the terminal device.
> + This process is performed only once!</p>
> +
> + <p>The underlying java code does not have pseudo-terminal emulation, so if you cannot
> + force the command to read passwords from the stdin (e.g. scp command), you have to use an
> + external tool to execute the command through a pseudo-terminal. <b>ptyexec</b> is provided
> + in the <i>org.kepler.ssh</i> package, a C program, that should be compiled and put into the path
> + on the target machine. Then you can execute <i>"ptyexec scp ..."</i>. It works on Linux only.</p>
> +
> +</configure></property>
> +<property name="port:stdout" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Output of the command as it would output to the standard shell. If there is an SSH connection related error (or timeout) the value will be an empty string. </configure></property>
> +<property name="port:stderr" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Any errors that were reported by the remote execution or while connecting. If there is an SSH connection related error (or timeout) the value will be an empty string. </configure></property>
> +<property name="port:target" class="ptolemy.kernel.util.ConfigurableAttribute"><configure> The machine to be used at job submission. It should be null, "" or "local" for the local machine or [user@]host to denote a remote machine accessible with SSH. If user is not provided, the local username will be used. If port is not provided, the default port 22 will be applied. This parameter is read once at initialize. </configure></property>
> +<property name="port:command" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The command to be executed on the remote host, specified as a string (e.g., "uname -a; date") </configure></property>
> +<property name="port:exitcode" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The exit code of the command. If there is an SSH connection related error (or timeout) the exitcode will be -32767 </configure></property>
> +<property name="port:errors" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The string representation of actor execution errors, if any.
> + </configure></property>
> +<property name="prop:timeoutSeconds" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Timeout in seconds. The command will be timed out after the specified amount of time. Specify 0 to wait indefinitely for command termination. </configure></property>
> +<property name="prop:streaming mode" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether the output should be sent in a streaming mode.
> + Note: Streaming is not currently implemented.
> + </configure></property>
> +<property name="prop:thirdParty" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The third party machine where the command wants to connect and needs to authenticate. Kepler can be used to do the authentication and then provide the password or private-key passphrase to the command. It should be defined as [user@]host[:port]. </configure></property>
> +<property name="prop:target" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The machine to be used at job submission. It should be null, "" or "local" for the local machine or [user@]host to denote a remote machine accessible with SSH. If user is not provided, the local username will be used. If port is not provided, the default port 22 will be applied. This parameter is read once at initialize. </configure></property>
> +<property name="prop:cleanupAfterError" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Kill remote process(es) after an error or timeout. Set this parameter only if connecting to a Unix server (other platforms do not support it). All processes belonging to the same group as the remote command (i.e., its children) will be killed. </configure></property>
> +</property> <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:506:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.kepler.actor.ssh.ExecuteCmd">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1213:1">
> + </property>
> + </property>
> + <property name="semanticType00" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ExternalExecutionEnvironmentActor">
> + </property>
> + <property name="semanticType21" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#SSH">
> + </property>
> + <property name="semanticType41" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:4:1#CPES">
> + </property>
> + <property name="semanticType22" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#Tutorial">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="{-70.0, 35.0}">
> + </property>
> + <port name="target" class="ptolemy.actor.parameters.ParameterPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="command" class="ptolemy.actor.TypedIOPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="stdout" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="stderr" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="exitcode" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="errors" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="thirdParty" class="ptolemy.actor.parameters.ParameterPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + </entity>
> + <entity name="Expression" class="ptolemy.actor.lib.Expression">
> + <property name="expression" class="ptolemy.kernel.util.StringAttribute" value=""cp -r "+dir+"/"+name+"/* "+tempdir+"/"+name">
> + <property name="_hide" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </property>
> +<property name="KeplerDocumentation" class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> +<property name="description" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="author" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Xiaojun Liu, Edward A. Lee, Steve Neuendorffer</configure></property>
> +<property name="version" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="userLevelDocumentation" class="ptolemy.kernel.util.ConfigurableAttribute"><configure><p>The Expression actor evaluates a specified expression (e.g., an addition or multiplication operation), which may reference the values of user-specified input ports, the current time, or the actor's iteration count. The actor outputs the value of the evaluated expression. </p>
> +
> +<p>Expressions are specified in the Ptolemy expression language via the expression parameter. For more information about the expression language, see http://ptolemy.eecs.berkeley.edu/papers/05/ptIIdesign1-intro/ptIIdesign1-intro.pdf. </p>
> +
> +<p>By default, the expression parameter is empty, and attempting to execute the actor without first specifying an expression generates an error. Expressions can refer to the values of inputs by the port name; to the current time by the identifier "time"; and to the current iteration count by the identifier "iteration." </p>
> +
> +<p>Input ports are created by the user and correspond to variables used in the specified expression. Currently, the Expression actor does not support input multiports. The actor requires all of its inputs to be present. If inputs are not all present, then the actor will generate an error. </p>
> +
> +<p>Note: the Expression actor can be used instead of many of the arithmetic actors, such as AddSubtract, MultiplyDivide, and TrigFunction. However, those actors will be usually be more efficient, and sometimes more convenient to use.</p></configure></property>
> +<property name="port:output" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>An output port that broadcasts the value of the evaluated expression. The actor automatically determines the type based on the type of the input.</configure></property>
> +<property name="prop:expression" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>An expression to evaluate. Expressions are specified in the Ptolemy expression language. For more information about the expression language, see http://ptolemy.eecs.berkeley.edu/papers/05/ptIIdesign1-intro/ptIIdesign1-intro.pdf. By default, the parameter is empty, and attempting to execute the actor without first specifying an expression generates an error. Expressions can refer to the values of inputs by the port name; to the current time by the identifier "time"; and to the current iteration count by the identifier "iteration."</configure></property>
> +</property> <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:75:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.Expression">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:950:1">
> + </property>
> + </property>
> + <property name="semanticType00" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#MathOperationActor">
> + </property>
> + <property name="semanticType11" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#GeneralPurpose">
> + </property>
> + <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
> + <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
> + </property>
> + <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
> + </property>
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-110.0, 140.0]">
> + </property>
> + <port name="output" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + </port>
> + <port name="name" class="ptolemy.actor.TypedIOPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="false">
> + </property>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + </port>
> + <port name="tempdir" class="ptolemy.actor.TypedIOPort">
> + <property name="input"/>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + </port>
> + <port name="dir" class="ptolemy.actor.TypedIOPort">
> + <property name="input"/>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + </port>
> + </entity>
> + <relation name="relation2" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <relation name="relation3" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <relation name="relation4" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <relation name="relation" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <relation name="relation5" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <link port="StringToken" relation="relation"/>
> + <link port="StringToken [key=tempdir]" relation="relation4"/>
> + <link port="StringToken [key=target]" relation="relation3"/>
> + <link port="StringToken [key=S3D]" relation="relation5"/>
> + <link port="SSH Execute cmd.target" relation="relation3"/>
> + <link port="SSH Execute cmd.command" relation="relation2"/>
> + <link port="Expression.output" relation="relation2"/>
> + <link port="Expression.name" relation="relation"/>
> + <link port="Expression.tempdir" relation="relation4"/>
> + <link port="Expression.dir" relation="relation5"/>
> + </entity>
> + <entity name="SSH_Dir2 neccessary ????" class="org.kepler.coactors.CompositeCoactor">
> + <property name="Read scope" class="org.kepler.util.CoactorParameter" value="Job">
> + </property>
> + <property name="_createdBy" class="ptolemy.kernel.attributes.VersionAttribute" value="7.0.2">
> + </property>
> + <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:ppod.daks.org:composite:100:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.kepler.coactors.CompositeCoactor">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:ppod.daks.org:class:100:1">
> + </property>
> + </property>
> + <property name="semanticType" class="org.kepler.sms.SemanticType" value="urn:lsid:ppod.daks.org:onto:1#ComadGeneralActors">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-225.0, 85.0]">
> + </property>
> + <property name="_windowProperties" class="ptolemy.actor.gui.WindowPropertiesAttribute" value="{bounds={374, 183, 883, 853}, maximized=false}">
> + </property>
> + <property name="_vergilSize" class="ptolemy.actor.gui.SizeAttribute" value="[600, 732]">
> + </property>
> + <property name="_vergilZoomFactor" class="ptolemy.data.expr.ExpertParameter" value="1.0">
> + </property>
> + <property name="_vergilCenter" class="ptolemy.data.expr.ExpertParameter" value="{43.0, 84.0}">
> + </property>
> + <property name="SDF Director" class="ptolemy.domains.sdf.kernel.SDFDirector">
> + <property name="iterations" class="ptolemy.data.expr.Parameter" value="0">
> + </property>
> + <property name="vectorizationFactor" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + <property name="allowDisconnectedGraphs" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="allowRateChanges" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="constrainBufferSizes" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + <property name="period" class="ptolemy.data.expr.Parameter" value="0.0">
> + </property>
> + <property name="synchronizeToRealTime" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="timeResolution" class="ptolemy.moml.SharedParameter" value="1E-10">
> + </property>
> + <property name="Scheduler" class="ptolemy.domains.sdf.kernel.SDFScheduler">
> + <property name="constrainBufferSizes" class="ptolemy.data.expr.Parameter" value="constrainBufferSizes">
> + </property>
> + </property>
> +<property name="KeplerDocumentation" class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> +<property name="description" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="author" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Steve Neuendorffer</configure></property>
> +<property name="version" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="userLevelDocumentation" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>
> +<p>The SDF Director is often used to oversee fairly simple, sequential workflows in which the director can determine the order of actor invocation from the workflow. Types of workflows that would run well under an SDF Director include processing and reformatting tabular data, converting one data type to another, and reading and plotting a series of data points. A workflow in which an image is read, processed (rotated, scaled, clipped, filtered, etc.), and then displayed, is also an example of a sequential workflow that requires a director simply to ensure that each actor fires in the proper order (i.e., that each actor executes only after it receives its required inputs).</p>
> +
> +<p>The SDF Director is very efficient and will not tax system resources with overhead. However, this efficiency requires that certain conditions be met, namely that the data consumption and production rate of each actor in an SDF workflow be constant and declared. If an actor reads one piece of data and calculates and outputs a single result, it must always read and output a single token of data. This data rate cannot change during workflow execution and, in general, workflows that require dynamic scheduling and/or flow control cannot use this director. Additionally, the SDF Director has no understanding of passing time (at least by default), and actors that depend on a notion of time may not work as expected. For example, a TimedPlotter actor will plot all values at time zero when used in SDF. </p>
> +
> +<p>By default, the SDF Director requires that all actors in its workflow be connected. Otherwise, the director cannot account for concurrency between disconnected workflow parts. Usually, a PN Director should be used for workflows that contain disconnected actors; however, the SDF Director's allowDisconnectedGraphs parameter may also be set to true. The SDF Director will then schedule each disconnected "island" independently. The director cannot infer the sequential relationship between disconnected actors (i.e., nothing forces the director to finish executing all actors on one island before firing actors on another). However, the order of execution within each island should be correct. Usually, disconnected graphs in an SDF model indicate an error.</p>
> +
> +<p>Because SDF Directors schedule actors to fire only after they receive their inputs, workflows that require loops (feeding an actor's output back into its input port for further processing) can cause "deadlock" errors. The deadlock errors occur because the actor depends on its own output value as an initial input. To fix this problem, use a SampleDelay actor to generate and inject an initial input value into the workflow.</p>
> +
> +<p>The SDF Director determines the order in which actors execute and how many times each actor needs to be fired to complete a single iteration of the workflow. This schedule is calculated BEFORE the director begins to iterate the workflow. Because the SDF Director calculates a schedule in advance, it is quite efficient. However, SDF workflows must be static. In other words, the same number of tokens must be consumed/produced at every iteration of the workflow. Workflows that require dynamic control structures, such as a BooleanSwitch actor that sends output on one of two ports depending on the value of a 'control', cannot be used with an SDF Director because the number of tokens on each output can change for each execution.</p>
> +
> +<p>Unless otherwise specified, the SDF Director assumes that each actor consumes and produces exactly one token per channel on each firing. Actors that do not follow the one-token-per-channel firing convention (e.g., Repeat or Ramp) must declare the number of tokens they produce or consume via the appropriate parameters. </p>
> +
> +<p>The number of times a workflow is iterated is controlled by the director's iterations parameter. By default, this parameter is set to "0". Note that "0" does not mean "no iterations." Rather, "0" means that the workflow will iterate forever. Values greater than zero specify the actual number of times the director should execute the entire workflow. A value of 1, meaning that the director will run the workflow once, is often the best setting when building an SDF workflow. </p>
> +
> +<p>The amount of data processed by an SDF workflow is a function of both the number of times the workflow iterates and the value of the director's vectorizationFactor parameter. The vectorizationFactor is used to increase the efficiency of a workflow by increasing the number of times actors fire each time the workflow iterates. If the parameter is set to a positive integer (other than 1), the director will fire each actor the specified number of times more than normal. The default is 1, indicating that no vectorization should be performed. Keep in mind that changing the vectorizationFactor parameter changes the meaning of a nested SDF workflow and may cause deadlock in a workflow that uses it. </p>
> +
> +<p>The SDF Director has several advanced parameters that are generally only relevant when an SDF workflow contains composite components. In most cases the period, timeResolution, synchronizeToRealTime, allowRateChanges, timeResolution, and constrainBufferSizes parameters can be left at their default values.</p>
> +
> +<p>For more information about the SDF Director, see the Ptolemy documentation (http://ptolemy.eecs.berkeley.edu/papers/05/ptIIdesign3-domains/ptIIdesign3-domains.pdf).</p>
> +
> +</configure></property>
> +<property name="prop:allowDisconnectedGraphs" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether to allow disconnected actors in the workflow (by default, all actors are required to be connected). If disconnected actors are permitted, the SDF Director will schedule each disconnected 'island' independently. Nothing "forces" the director to finish executing all actors on one island before firing actors on another. However, the order of execution within each island should be correct. Usually, disconnected graphs in an SDF workflow indicate an error.</configure></property>
> +<property name="prop:allowRateChanges" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether dynamic rate changes are permitted or not. By default, rate changes are not permitted, and the director will perform a check to disallow such workflows. If the parameter is selected, then workflows that require rate parameters to be modified during execution are valid, and the SDF Director will dynamically compute a new schedule at runtime. This is an advanced parameter that can usually be left at its default value.</configure></property>
> +<property name="prop:constrainBufferSizes" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether buffer sizes are fixed. By default, buffers are fixed, and attempts to write to the buffer that cause the buffer to exceed its scheduled size result in an error. This is an advanced parameter that can usually be left at its default value.</configure></property>
> +<property name="prop:timeResolution" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The time precision used by this director. All time values are rounded to the nearest multiple of this number. The value is a double that defaults to "1E-10" (which is 10-10). This is an advanced parameter that can usually be left at its default value.</configure></property>
> +<property name="prop:iterations" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify the number of times a workflow is iterated. By default, this parameter is set to "0". Note that "0" does not mean "no iterations." Rather, "0" means that the workflow will iterate forever. Values greater than zero specify the actual number of times the director should execute the entire workflow. A value of 1, meaning that the director will run the workflow once, is often the best setting when building an SDF workflow. </configure></property>
> +<property name="prop:vectorizationFactor" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The vectorizationFactor is used to increase the efficiency of a workflow by increasing the number of times actors fire each time the workflow iterates. If the parameter is set to a positive integer (other than 1), the director will fire each actor the specified number of times more than normal. The default is 1, indicating that no vectorization should be performed. Keep in mind that changing the vectorizationFactor parameter changes the meaning of a nested SDF workflow and may cause deadlock in a workflow that uses it. </configure></property>
> +<property name="prop:synchronizeToRealTime" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether the execution should synchronize to real time or not. By default, the director does not synchronize to real time. If synchronize is selected, the director will only process the workflow when elapsed real time matches the product of the period parameter and the iteration count. Note: if the period parameter has a value of 0.0 (the default), then selecting this parameter has no effect. This is an advanced parameter that can usually be left at its default value.</configure></property>
> +<property name="prop:period" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The time period of each iteration. The value is a double that defaults to 0.0, which means that the director does not increment workflow time. If the value greater than 0.0, the actor will increment workflow time each time it fires. This is an advanced parameter that can usually be left at its default value. </configure></property>
> +</property> <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:director:1:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.domains.sdf.kernel.SDFDirector">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:directorclass:1:1">
> + </property>
> + </property>
> + <property name="semanticType00" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#Director">
> + </property>
> + <property name="semanticType11" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#Director">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="{30.0, -75.0}">
> + </property>
> + </property>
> + <port name="input" class="org.kepler.util.CollectionIOPort">
> + <property name="input"/>
> + <property name="dataType" class="ptolemy.kernel.util.StringAttribute" value="general">
> + </property>
> + <property name="isMultiport" class="ptolemy.kernel.util.StringAttribute" value="false">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="{-295.0, 10.0}">
> + </property>
> + </port>
> + <port name="output" class="org.kepler.util.CollectionIOPort">
> + <property name="output"/>
> + <property name="multiport"/>
> + <property name="dataType" class="ptolemy.kernel.util.StringAttribute" value="unknown">
> + </property>
> + <property name="isMultiport" class="ptolemy.kernel.util.StringAttribute" value="true">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="{400.0, 70.0}">
> + </property>
> + </port>
> + <port name="StringToken [key=target]" class="org.kepler.util.CollectionIOPort">
> + <property name="input"/>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="{-230.0, -45.0}">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="NORTH">
> + </property>
> + </port>
> + <port name="StringToken [key=tempdir]" class="org.kepler.util.CollectionIOPort">
> + <property name="input"/>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="{-245.0, 0.0}">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="NORTH">
> + </property>
> + </port>
> + <port name="StringToken [key=mask]" class="org.kepler.util.CollectionIOPort">
> + <property name="input"/>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-240.0, 50.0]">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="NORTH">
> + </property>
> + </port>
> + <port name="StringToken [key=repository]" class="org.kepler.util.CollectionIOPort">
> + <property name="input"/>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="{-190.0, 90.0}">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="NORTH">
> + </property>
> + </port>
> + <port name="TempDirNames/StringToken+" class="org.kepler.util.CollectionIOPort">
> + <property name="output"/>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="{140.0, 35.0}">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="SOUTH">
> + </property>
> + </port>
> + <port name="TempDirNames/StringToken [key=tempdir]" class="org.kepler.util.CollectionIOPort">
> + <property name="output"/>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-20.0, 185.0]">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="SOUTH">
> + </property>
> + </port>
> + <port name="TempDirNames/StringToken [key=target]" class="org.kepler.util.CollectionIOPort">
> + <property name="output"/>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="{0.0, -110.0}">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="SOUTH">
> + </property>
> + </port>
> + <entity name="SshDirectoryList_v1_" class="org.kepler.actors.io.SshDirectoryList_v1_2">
> + <property name="target" class="ptolemy.actor.parameters.PortParameter" value="">
> + </property>
> + <property name="dir" class="ptolemy.actor.parameters.PortParameter" value="">
> + </property>
> + <property name="newFilesOnly" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="{-15.0, 0.0}">
> + </property>
> + </entity>
> + <relation name="relation" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <relation name="relation2" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <relation name="relation4" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + <vertex name="vertex" value="[-75.0, 125.0]">
> + </vertex>
> + </relation>
> + <relation name="relation6" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + <vertex name="vertex" value="[-105.0, -45.0]">
> + </vertex>
> + </relation>
> + <link port="StringToken [key=target]" relation="relation6"/>
> + <link port="StringToken [key=tempdir]" relation="relation4"/>
> + <link port="StringToken [key=repository]" relation="relation"/>
> + <link port="TempDirNames/StringToken+" relation="relation2"/>
> + <link port="TempDirNames/StringToken [key=tempdir]" relation="relation4"/>
> + <link port="TempDirNames/StringToken [key=target]" relation="relation6"/>
> + <link port="SshDirectoryList_v1_.target" relation="relation6"/>
> + <link port="SshDirectoryList_v1_.dir" relation="relation4"/>
> + <link port="SshDirectoryList_v1_.trigger" relation="relation"/>
> + <link port="SshDirectoryList_v1_.newFiles" relation="relation2"/>
> + </entity>
> + <entity name="SSH_Dir_Create2" class="org.kepler.coactors.CompositeCoactor">
> + <property name="Read scope" class="org.kepler.util.CoactorParameter" value="Job/TempDirNames">
> + </property>
> + <property name="_createdBy" class="ptolemy.kernel.attributes.VersionAttribute" value="7.0.2">
> + </property>
> + <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:localhost:entity:1:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.kepler.coactors.CompositeCoactor">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:ppod.daks.org:class:100:1">
> + </property>
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-545.0, 225.0]">
> + </property>
> + <property name="_windowProperties" class="ptolemy.actor.gui.WindowPropertiesAttribute" value="{bounds={433, 247, 883, 853}, maximized=false}">
> + </property>
> + <property name="_vergilSize" class="ptolemy.actor.gui.SizeAttribute" value="[600, 732]">
> + </property>
> + <property name="_vergilZoomFactor" class="ptolemy.data.expr.ExpertParameter" value="1.0">
> + </property>
> + <property name="_vergilCenter" class="ptolemy.data.expr.ExpertParameter" value="{-150.0, 138.0}">
> + </property>
> + <property name="semanticType0" class="org.kepler.sms.SemanticType" value="urn:lsid:ppod.daks.org:onto:1#ComadGeneralActors">
> + </property>
> + <property name="SDF Director" class="ptolemy.domains.sdf.kernel.SDFDirector">
> + <property name="iterations" class="ptolemy.data.expr.Parameter" value="0">
> + </property>
> + <property name="vectorizationFactor" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + <property name="allowDisconnectedGraphs" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="allowRateChanges" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="constrainBufferSizes" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + <property name="period" class="ptolemy.data.expr.Parameter" value="0.0">
> + </property>
> + <property name="synchronizeToRealTime" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="timeResolution" class="ptolemy.moml.SharedParameter" value="1E-10">
> + </property>
> + <property name="Scheduler" class="ptolemy.domains.sdf.kernel.SDFScheduler">
> + <property name="constrainBufferSizes" class="ptolemy.data.expr.Parameter" value="constrainBufferSizes">
> + </property>
> + </property>
> +<property name="KeplerDocumentation" class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> +<property name="description" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="author" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Steve Neuendorffer</configure></property>
> +<property name="version" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="userLevelDocumentation" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>
> +<p>The SDF Director is often used to oversee fairly simple, sequential workflows in which the director can determine the order of actor invocation from the workflow. Types of workflows that would run well under an SDF Director include processing and reformatting tabular data, converting one data type to another, and reading and plotting a series of data points. A workflow in which an image is read, processed (rotated, scaled, clipped, filtered, etc.), and then displayed, is also an example of a sequential workflow that requires a director simply to ensure that each actor fires in the proper order (i.e., that each actor executes only after it receives its required inputs).</p>
> +
> +<p>The SDF Director is very efficient and will not tax system resources with overhead. However, this efficiency requires that certain conditions be met, namely that the data consumption and production rate of each actor in an SDF workflow be constant and declared. If an actor reads one piece of data and calculates and outputs a single result, it must always read and output a single token of data. This data rate cannot change during workflow execution and, in general, workflows that require dynamic scheduling and/or flow control cannot use this director. Additionally, the SDF Director has no understanding of passing time (at least by default), and actors that depend on a notion of time may not work as expected. For example, a TimedPlotter actor will plot all values at time zero when used in SDF. </p>
> +
> +<p>By default, the SDF Director requires that all actors in its workflow be connected. Otherwise, the director cannot account for concurrency between disconnected workflow parts. Usually, a PN Director should be used for workflows that contain disconnected actors; however, the SDF Director's allowDisconnectedGraphs parameter may also be set to true. The SDF Director will then schedule each disconnected "island" independently. The director cannot infer the sequential relationship between disconnected actors (i.e., nothing forces the director to finish executing all actors on one island before firing actors on another). However, the order of execution within each island should be correct. Usually, disconnected graphs in an SDF model indicate an error.</p>
> +
> +<p>Because SDF Directors schedule actors to fire only after they receive their inputs, workflows that require loops (feeding an actor's output back into its input port for further processing) can cause "deadlock" errors. The deadlock errors occur because the actor depends on its own output value as an initial input. To fix this problem, use a SampleDelay actor to generate and inject an initial input value into the workflow.</p>
> +
> +<p>The SDF Director determines the order in which actors execute and how many times each actor needs to be fired to complete a single iteration of the workflow. This schedule is calculated BEFORE the director begins to iterate the workflow. Because the SDF Director calculates a schedule in advance, it is quite efficient. However, SDF workflows must be static. In other words, the same number of tokens must be consumed/produced at every iteration of the workflow. Workflows that require dynamic control structures, such as a BooleanSwitch actor that sends output on one of two ports depending on the value of a 'control', cannot be used with an SDF Director because the number of tokens on each output can change for each execution.</p>
> +
> +<p>Unless otherwise specified, the SDF Director assumes that each actor consumes and produces exactly one token per channel on each firing. Actors that do not follow the one-token-per-channel firing convention (e.g., Repeat or Ramp) must declare the number of tokens they produce or consume via the appropriate parameters. </p>
> +
> +<p>The number of times a workflow is iterated is controlled by the director's iterations parameter. By default, this parameter is set to "0". Note that "0" does not mean "no iterations." Rather, "0" means that the workflow will iterate forever. Values greater than zero specify the actual number of times the director should execute the entire workflow. A value of 1, meaning that the director will run the workflow once, is often the best setting when building an SDF workflow. </p>
> +
> +<p>The amount of data processed by an SDF workflow is a function of both the number of times the workflow iterates and the value of the director's vectorizationFactor parameter. The vectorizationFactor is used to increase the efficiency of a workflow by increasing the number of times actors fire each time the workflow iterates. If the parameter is set to a positive integer (other than 1), the director will fire each actor the specified number of times more than normal. The default is 1, indicating that no vectorization should be performed. Keep in mind that changing the vectorizationFactor parameter changes the meaning of a nested SDF workflow and may cause deadlock in a workflow that uses it. </p>
> +
> +<p>The SDF Director has several advanced parameters that are generally only relevant when an SDF workflow contains composite components. In most cases the period, timeResolution, synchronizeToRealTime, allowRateChanges, timeResolution, and constrainBufferSizes parameters can be left at their default values.</p>
> +
> +<p>For more information about the SDF Director, see the Ptolemy documentation (http://ptolemy.eecs.berkeley.edu/papers/05/ptIIdesign3-domains/ptIIdesign3-domains.pdf).</p>
> +
> +</configure></property>
> +<property name="prop:allowDisconnectedGraphs" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether to allow disconnected actors in the workflow (by default, all actors are required to be connected). If disconnected actors are permitted, the SDF Director will schedule each disconnected 'island' independently. Nothing "forces" the director to finish executing all actors on one island before firing actors on another. However, the order of execution within each island should be correct. Usually, disconnected graphs in an SDF workflow indicate an error.</configure></property>
> +<property name="prop:allowRateChanges" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether dynamic rate changes are permitted or not. By default, rate changes are not permitted, and the director will perform a check to disallow such workflows. If the parameter is selected, then workflows that require rate parameters to be modified during execution are valid, and the SDF Director will dynamically compute a new schedule at runtime. This is an advanced parameter that can usually be left at its default value.</configure></property>
> +<property name="prop:timeResolution" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The time precision used by this director. All time values are rounded to the nearest multiple of this number. The value is a double that defaults to "1E-10" (which is 10-10). This is an advanced parameter that can usually be left at its default value.</configure></property>
> +<property name="prop:constrainBufferSizes" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether buffer sizes are fixed. By default, buffers are fixed, and attempts to write to the buffer that cause the buffer to exceed its scheduled size result in an error. This is an advanced parameter that can usually be left at its default value.</configure></property>
> +<property name="prop:iterations" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify the number of times a workflow is iterated. By default, this parameter is set to "0". Note that "0" does not mean "no iterations." Rather, "0" means that the workflow will iterate forever. Values greater than zero specify the actual number of times the director should execute the entire workflow. A value of 1, meaning that the director will run the workflow once, is often the best setting when building an SDF workflow. </configure></property>
> +<property name="prop:vectorizationFactor" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The vectorizationFactor is used to increase the efficiency of a workflow by increasing the number of times actors fire each time the workflow iterates. If the parameter is set to a positive integer (other than 1), the director will fire each actor the specified number of times more than normal. The default is 1, indicating that no vectorization should be performed. Keep in mind that changing the vectorizationFactor parameter changes the meaning of a nested SDF workflow and may cause deadlock in a workflow that uses it. </configure></property>
> +<property name="prop:synchronizeToRealTime" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether the execution should synchronize to real time or not. By default, the director does not synchronize to real time. If synchronize is selected, the director will only process the workflow when elapsed real time matches the product of the period parameter and the iteration count. Note: if the period parameter has a value of 0.0 (the default), then selecting this parameter has no effect. This is an advanced parameter that can usually be left at its default value.</configure></property>
> +<property name="prop:period" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The time period of each iteration. The value is a double that defaults to 0.0, which means that the director does not increment workflow time. If the value greater than 0.0, the actor will increment workflow time each time it fires. This is an advanced parameter that can usually be left at its default value. </configure></property>
> +</property> <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:director:1:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.domains.sdf.kernel.SDFDirector">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:directorclass:1:1">
> + </property>
> + </property>
> + <property name="semanticType00" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#Director">
> + </property>
> + <property name="semanticType11" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#Director">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="{40.0, -65.0}">
> + </property>
> + </property>
> + <port name="input" class="org.kepler.util.CollectionIOPort">
> + <property name="input"/>
> + <property name="dataType" class="ptolemy.kernel.util.StringAttribute" value="general">
> + </property>
> + <property name="isMultiport" class="ptolemy.kernel.util.StringAttribute" value="false">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="{-280.0, 60.0}">
> + </property>
> + </port>
> + <port name="output" class="org.kepler.util.CollectionIOPort">
> + <property name="output"/>
> + <property name="multiport"/>
> + <property name="dataType" class="ptolemy.kernel.util.StringAttribute" value="unknown">
> + </property>
> + <property name="isMultiport" class="ptolemy.kernel.util.StringAttribute" value="true">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="{275.0, 95.0}">
> + </property>
> + </port>
> + <port name="StringToken" class="org.kepler.util.CollectionIOPort">
> + <property name="input"/>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-220.0, 35.0]">
> + </property>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="NORTH">
> + </property>
> + </port>
> + <port name="StringToken [key=emptydir]" class="org.kepler.util.CollectionIOPort">
> + <property name="input"/>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-360.0, 170.0]">
> + </property>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="NORTH">
> + </property>
> + </port>
> + <port name="StringToken [key=target]" class="org.kepler.util.CollectionIOPort">
> + <property name="input"/>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="{-380.0, 0.0}">
> + </property>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="SOUTH">
> + </property>
> + </port>
> + <entity name="SSH Directory Creator" class="org.kepler.actor.ssh.DirectoryCreator">
> + <property name="target" class="ptolemy.actor.parameters.PortParameter" value=""yildiz at home.ccs.ornl.gov"">
> + </property>
> + <property name="dir" class="ptolemy.actor.parameters.PortParameter" value=""temp_build_directory"">
> + </property>
> + <property name="parent" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> +<property name="KeplerDocumentation" class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> +<property name="description" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="author" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Norbert Podhorszki</configure></property>
> +<property name="version" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="userLevelDocumentation" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>
> +
> +<p>The SSHDirectoryCreator actor creates a local or remote directory. The actor reads the path to a target machine as well as the name of the directory to create. The actor outputs the operation results: true if the directory is created successfully, and false if not. In addition, the actor outputs the text of generated error messages, if any.</p>
> +
> +<p>For remote operations, a relative path is relative to the home directory. For local operations, a relative path is relative to the current directory. If the 'parent' flag is set, intermediate directories in the provided path will be created if necessary. </p>
> +
> +</configure></property>
> +<property name="port:succ" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>A Boolean token: true if the operation is successful, false if not. </configure></property>
> +<property name="port:error" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The actor's execution errors, if any; otherwise an empty string. </configure></property>
> +<property name="port:dir" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The path to the target directory. This parameter is read once at initialize. </configure></property>
> +<property name="port:target" class="ptolemy.kernel.util.ConfigurableAttribute"><configure> The machine to be used at job submission. It should be null, "" or "local" for the local machine or [user@]host to denote a remote machine accessible with SSH. This parameter is read once at initialize. </configure></property>
> +<property name="prop:dir" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The path to the directory to be read on the target machines. This parameter is read once at initialize. </configure></property>
> +<property name="prop:parent" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether parent directories should be created recursively if necessary. If the 'parent' flag is set the operation is considered successful even if the directory already exists. </configure></property>
> +<property name="prop:target" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The machine to be used at job submission. It should be null, "" or "local" for the local machine or [user@]host to denote a remote machine accessible with ssh. This parameter is read once at initialize. </configure></property>
> +</property> <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:514:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.kepler.actor.ssh.DirectoryCreator">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1209:1">
> + </property>
> + </property>
> + <property name="semanticType11" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ExternalExecutionEnvironmentActor">
> + </property>
> + <property name="semanticType21" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#SSH">
> + </property>
> + <property name="semanticType41" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:4:1#CPES">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="{110.0, 45.0}">
> + </property>
> + <property name="" class="ptolemy.vergil.basic.DocAttribute">
> + <property name="description" class="ptolemy.data.expr.StringParameter" value=" <p>The SSHDirectoryCreator actor creates a local or remote directory. The actor reads the path to a target machine as well as the name of the directory to create. The actor outputs the operation results: true if the directory is created successfully, and false if not. In addition, the actor outputs the text of generated error messages, if any.</p> <p>For remote operations, a relative path is relative to the home directory. For local operations, a relative path is relative to the current directory. If the 'parent' flag is set, intermediate directories in the provided path will be created if necessary. </p> ">
> + </property>
> + <property name="author" class="ptolemy.kernel.util.StringAttribute" value="Norbert Podhorszki">
> + </property>
> + <property name="version" class="ptolemy.kernel.util.StringAttribute" value="null">
> + </property>
> + <property name="parent (parameter)" class="ptolemy.data.expr.StringParameter" value="Specify whether parent directories should be created recursively if necessary. If the 'parent' flag is set the operation is considered successful even if the directory already exists. ">
> + </property>
> + <property name="succ (port)" class="ptolemy.kernel.util.StringAttribute" value="A Boolean token: true if the operation is successful, false if not. ">
> + </property>
> + <property name="error (port)" class="ptolemy.kernel.util.StringAttribute" value="The actor's execution errors, if any; otherwise an empty string. ">
> + </property>
> + <property name="dir (port)" class="ptolemy.kernel.util.StringAttribute" value="The path to the target directory. This parameter is read once at initialize. ">
> + </property>
> + <property name="target (port)" class="ptolemy.kernel.util.StringAttribute" value=" The machine to be used at job submission. It should be null, "" or "local" for the local machine or [user@]host to denote a remote machine accessible with SSH. This parameter is read once at initialize. ">
> + </property>
> + <property name="dir (parameter)" class="ptolemy.data.expr.StringParameter" value="The path to the directory to be read on the target machines. This parameter is read once at initialize. ">
> + </property>
> + <property name="target (parameter)" class="ptolemy.data.expr.StringParameter" value="The machine to be used at job submission. It should be null, "" or "local" for the local machine or [user@]host to denote a remote machine accessible with ssh. This parameter is read once at initialize. ">
> + </property>
> + </property>
> + <port name="target" class="ptolemy.actor.parameters.ParameterPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="dir" class="ptolemy.actor.parameters.ParameterPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="succ" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="error" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + </entity>
> + <entity name="Expression" class="ptolemy.actor.lib.Expression">
> + <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="emptydir+"/"+dir">
> + <property name="_hide" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </property>
> +<property name="KeplerDocumentation" class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> +<property name="description" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="author" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Xiaojun Liu, Edward A. Lee, Steve Neuendorffer</configure></property>
> +<property name="version" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="userLevelDocumentation" class="ptolemy.kernel.util.ConfigurableAttribute"><configure><p>The Expression actor evaluates a specified expression (e.g., an addition or multiplication operation), which may reference the values of user-specified input ports, the current time, or the actor's iteration count. The actor outputs the value of the evaluated expression. </p>
> +
> +<p>Expressions are specified in the Ptolemy expression language via the expression parameter. For more information about the expression language, see http://ptolemy.eecs.berkeley.edu/papers/05/ptIIdesign1-intro/ptIIdesign1-intro.pdf. </p>
> +
> +<p>By default, the expression parameter is empty, and attempting to execute the actor without first specifying an expression generates an error. Expressions can refer to the values of inputs by the port name; to the current time by the identifier "time"; and to the current iteration count by the identifier "iteration." </p>
> +
> +<p>Input ports are created by the user and correspond to variables used in the specified expression. Currently, the Expression actor does not support input multiports. The actor requires all of its inputs to be present. If inputs are not all present, then the actor will generate an error. </p>
> +
> +<p>Note: the Expression actor can be used instead of many of the arithmetic actors, such as AddSubtract, MultiplyDivide, and TrigFunction. However, those actors will be usually be more efficient, and sometimes more convenient to use.</p></configure></property>
> +<property name="port:output" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>An output port that broadcasts the value of the evaluated expression. The actor automatically determines the type based on the type of the input.</configure></property>
> +<property name="prop:expression" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>An expression to evaluate. Expressions are specified in the Ptolemy expression language. For more information about the expression language, see http://ptolemy.eecs.berkeley.edu/papers/05/ptIIdesign1-intro/ptIIdesign1-intro.pdf. By default, the parameter is empty, and attempting to execute the actor without first specifying an expression generates an error. Expressions can refer to the values of inputs by the port name; to the current time by the identifier "time"; and to the current iteration count by the identifier "iteration."</configure></property>
> +</property> <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:75:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.Expression">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:950:1">
> + </property>
> + </property>
> + <property name="semanticType00" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#MathOperationActor">
> + </property>
> + <property name="semanticType11" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#GeneralPurpose">
> + </property>
> + <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
> + <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
> + </property>
> + <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
> + </property>
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="{-50.0, 140.0}">
> + </property>
> + <port name="output" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + </port>
> + <port name="dir" class="ptolemy.actor.TypedIOPort">
> + <property name="input"/>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="false">
> + </property>
> + </port>
> + <port name="emptydir" class="ptolemy.actor.TypedIOPort">
> + <property name="input"/>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + </port>
> + </entity>
> + <relation name="relation" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <relation name="relation4" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <relation name="relation2" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <relation name="relation3" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <link port="StringToken" relation="relation2"/>
> + <link port="StringToken [key=emptydir]" relation="relation3"/>
> + <link port="StringToken [key=target]" relation="relation4"/>
> + <link port="SSH Directory Creator.target" relation="relation4"/>
> + <link port="SSH Directory Creator.dir" relation="relation"/>
> + <link port="Expression.output" relation="relation"/>
> + <link port="Expression.dir" relation="relation2"/>
> + <link port="Expression.emptydir" relation="relation3"/>
> + </entity>
> + <entity name="CMAKE" class="org.kepler.coactors.CompositeCoactor">
> + <property name="Read scope" class="org.kepler.util.CoactorParameter" value="Job/TempDirNames">
> + </property>
> + <property name="_createdBy" class="ptolemy.kernel.attributes.VersionAttribute" value="7.0.2">
> + </property>
> + <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:ppod.daks.org:composite:100:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.kepler.coactors.CompositeCoactor">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:ppod.daks.org:class:100:1">
> + </property>
> + </property>
> + <property name="semanticType" class="org.kepler.sms.SemanticType" value="urn:lsid:ppod.daks.org:onto:1#ComadGeneralActors">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-440.0, 225.0]">
> + </property>
> + <property name="Annotation" class="ptolemy.vergil.kernel.attributes.TextAttribute">
> + <property name="_hideName" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + <property name="_hideAllParameters" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + <property name="textSize" class="ptolemy.data.expr.Parameter" value="11">
> + </property>
> + <property name="textColor" class="ptolemy.actor.gui.ColorAttribute" value="{0.0, 0.0, 1.0, 1.0}">
> + </property>
> + <property name="fontFamily" class="ptolemy.data.expr.StringParameter" value="SansSerif">
> + </property>
> + <property name="bold" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="italic" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="text" class="ptolemy.kernel.util.StringAttribute" value="The make install is lunched for the test case">
> + <property name="_style" class="ptolemy.actor.gui.style.TextStyle">
> + <property name="height" class="ptolemy.data.expr.Parameter" value="20">
> + </property>
> + <property name="width" class="ptolemy.data.expr.Parameter" value="80">
> + </property>
> + </property>
> + </property>
> +<property name="KeplerDocumentation" class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> +<property name="description" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="author" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Edward A. Lee</configure></property>
> +<property name="version" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="userLevelDocumentation" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Use the Annotation attribute to annotate a workflow. Double-click the attribute to customize the content, font size, color, and basic formatting (bold and italics).</configure></property>
> +<property name="prop:fontFamily" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The font face. Select a font from the drop-down menu. The default is "SansSerif".</configure></property>
> +<property name="prop:italic" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Select to indicate that the type should be italics. By default, type will not be italicized.</configure></property>
> +<property name="prop:bold" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Select to indicate that the type should be bold. By default, type will not be bold.</configure></property>
> +<property name="prop:textColor" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The font color. Specify a string representing an array of four elements: red, green, blue, and alpha, where alpha is transparency. The default is an opaque black, {0.0, 0.0, 0.0, 1.0}</configure></property>
> +<property name="prop:textSize" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The font size. Select an integer from the drop-down menu or specify a new size by typing it directly into the value field. The default is 14.</configure></property>
> +<property name="prop:text" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The text of the annotation.</configure></property>
> +</property> <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:436:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.vergil.kernel.attributes.TextAttribute">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1199:1">
> + </property>
> + </property>
> + <property name="semanticType00" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#DocumentationActor">
> + </property>
> + <property name="semanticType11" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#WorkflowDocumentation">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-700.0, -230.0]">
> + </property>
> + </property>
> + <property name="SDF Director" class="ptolemy.domains.sdf.kernel.SDFDirector">
> + <property name="iterations" class="ptolemy.data.expr.Parameter" value="0">
> + </property>
> + <property name="vectorizationFactor" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + <property name="allowDisconnectedGraphs" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="allowRateChanges" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="constrainBufferSizes" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + <property name="period" class="ptolemy.data.expr.Parameter" value="0.0">
> + </property>
> + <property name="synchronizeToRealTime" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="timeResolution" class="ptolemy.moml.SharedParameter" value="1E-10">
> + </property>
> + <property name="Scheduler" class="ptolemy.domains.sdf.kernel.SDFScheduler">
> + <property name="constrainBufferSizes" class="ptolemy.data.expr.Parameter" value="constrainBufferSizes">
> + </property>
> + </property>
> +<property name="KeplerDocumentation" class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> +<property name="description" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="author" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Steve Neuendorffer</configure></property>
> +<property name="version" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="userLevelDocumentation" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>
> +<p>The SDF Director is often used to oversee fairly simple, sequential workflows in which the director can determine the order of actor invocation from the workflow. Types of workflows that would run well under an SDF Director include processing and reformatting tabular data, converting one data type to another, and reading and plotting a series of data points. A workflow in which an image is read, processed (rotated, scaled, clipped, filtered, etc.), and then displayed, is also an example of a sequential workflow that requires a director simply to ensure that each actor fires in the proper order (i.e., that each actor executes only after it receives its required inputs).</p>
> +
> +<p>The SDF Director is very efficient and will not tax system resources with overhead. However, this efficiency requires that certain conditions be met, namely that the data consumption and production rate of each actor in an SDF workflow be constant and declared. If an actor reads one piece of data and calculates and outputs a single result, it must always read and output a single token of data. This data rate cannot change during workflow execution and, in general, workflows that require dynamic scheduling and/or flow control cannot use this director. Additionally, the SDF Director has no understanding of passing time (at least by default), and actors that depend on a notion of time may not work as expected. For example, a TimedPlotter actor will plot all values at time zero when used in SDF. </p>
> +
> +<p>By default, the SDF Director requires that all actors in its workflow be connected. Otherwise, the director cannot account for concurrency between disconnected workflow parts. Usually, a PN Director should be used for workflows that contain disconnected actors; however, the SDF Director's allowDisconnectedGraphs parameter may also be set to true. The SDF Director will then schedule each disconnected "island" independently. The director cannot infer the sequential relationship between disconnected actors (i.e., nothing forces the director to finish executing all actors on one island before firing actors on another). However, the order of execution within each island should be correct. Usually, disconnected graphs in an SDF model indicate an error.</p>
> +
> +<p>Because SDF Directors schedule actors to fire only after they receive their inputs, workflows that require loops (feeding an actor's output back into its input port for further processing) can cause "deadlock" errors. The deadlock errors occur because the actor depends on its own output value as an initial input. To fix this problem, use a SampleDelay actor to generate and inject an initial input value into the workflow.</p>
> +
> +<p>The SDF Director determines the order in which actors execute and how many times each actor needs to be fired to complete a single iteration of the workflow. This schedule is calculated BEFORE the director begins to iterate the workflow. Because the SDF Director calculates a schedule in advance, it is quite efficient. However, SDF workflows must be static. In other words, the same number of tokens must be consumed/produced at every iteration of the workflow. Workflows that require dynamic control structures, such as a BooleanSwitch actor that sends output on one of two ports depending on the value of a 'control', cannot be used with an SDF Director because the number of tokens on each output can change for each execution.</p>
> +
> +<p>Unless otherwise specified, the SDF Director assumes that each actor consumes and produces exactly one token per channel on each firing. Actors that do not follow the one-token-per-channel firing convention (e.g., Repeat or Ramp) must declare the number of tokens they produce or consume via the appropriate parameters. </p>
> +
> +<p>The number of times a workflow is iterated is controlled by the director's iterations parameter. By default, this parameter is set to "0". Note that "0" does not mean "no iterations." Rather, "0" means that the workflow will iterate forever. Values greater than zero specify the actual number of times the director should execute the entire workflow. A value of 1, meaning that the director will run the workflow once, is often the best setting when building an SDF workflow. </p>
> +
> +<p>The amount of data processed by an SDF workflow is a function of both the number of times the workflow iterates and the value of the director's vectorizationFactor parameter. The vectorizationFactor is used to increase the efficiency of a workflow by increasing the number of times actors fire each time the workflow iterates. If the parameter is set to a positive integer (other than 1), the director will fire each actor the specified number of times more than normal. The default is 1, indicating that no vectorization should be performed. Keep in mind that changing the vectorizationFactor parameter changes the meaning of a nested SDF workflow and may cause deadlock in a workflow that uses it. </p>
> +
> +<p>The SDF Director has several advanced parameters that are generally only relevant when an SDF workflow contains composite components. In most cases the period, timeResolution, synchronizeToRealTime, allowRateChanges, timeResolution, and constrainBufferSizes parameters can be left at their default values.</p>
> +
> +<p>For more information about the SDF Director, see the Ptolemy documentation (http://ptolemy.eecs.berkeley.edu/papers/05/ptIIdesign3-domains/ptIIdesign3-domains.pdf).</p>
> +
> +</configure></property>
> +<property name="prop:allowDisconnectedGraphs" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether to allow disconnected actors in the workflow (by default, all actors are required to be connected). If disconnected actors are permitted, the SDF Director will schedule each disconnected 'island' independently. Nothing "forces" the director to finish executing all actors on one island before firing actors on another. However, the order of execution within each island should be correct. Usually, disconnected graphs in an SDF workflow indicate an error.</configure></property>
> +<property name="prop:allowRateChanges" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether dynamic rate changes are permitted or not. By default, rate changes are not permitted, and the director will perform a check to disallow such workflows. If the parameter is selected, then workflows that require rate parameters to be modified during execution are valid, and the SDF Director will dynamically compute a new schedule at runtime. This is an advanced parameter that can usually be left at its default value.</configure></property>
> +<property name="prop:timeResolution" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The time precision used by this director. All time values are rounded to the nearest multiple of this number. The value is a double that defaults to "1E-10" (which is 10-10). This is an advanced parameter that can usually be left at its default value.</configure></property>
> +<property name="prop:constrainBufferSizes" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether buffer sizes are fixed. By default, buffers are fixed, and attempts to write to the buffer that cause the buffer to exceed its scheduled size result in an error. This is an advanced parameter that can usually be left at its default value.</configure></property>
> +<property name="prop:iterations" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify the number of times a workflow is iterated. By default, this parameter is set to "0". Note that "0" does not mean "no iterations." Rather, "0" means that the workflow will iterate forever. Values greater than zero specify the actual number of times the director should execute the entire workflow. A value of 1, meaning that the director will run the workflow once, is often the best setting when building an SDF workflow. </configure></property>
> +<property name="prop:vectorizationFactor" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The vectorizationFactor is used to increase the efficiency of a workflow by increasing the number of times actors fire each time the workflow iterates. If the parameter is set to a positive integer (other than 1), the director will fire each actor the specified number of times more than normal. The default is 1, indicating that no vectorization should be performed. Keep in mind that changing the vectorizationFactor parameter changes the meaning of a nested SDF workflow and may cause deadlock in a workflow that uses it. </configure></property>
> +<property name="prop:synchronizeToRealTime" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether the execution should synchronize to real time or not. By default, the director does not synchronize to real time. If synchronize is selected, the director will only process the workflow when elapsed real time matches the product of the period parameter and the iteration count. Note: if the period parameter has a value of 0.0 (the default), then selecting this parameter has no effect. This is an advanced parameter that can usually be left at its default value.</configure></property>
> +<property name="prop:period" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The time period of each iteration. The value is a double that defaults to 0.0, which means that the director does not increment workflow time. If the value greater than 0.0, the actor will increment workflow time each time it fires. This is an advanced parameter that can usually be left at its default value. </configure></property>
> +</property> <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:director:1:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.domains.sdf.kernel.SDFDirector">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:directorclass:1:1">
> + </property>
> + </property>
> + <property name="semanticType00" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#Director">
> + </property>
> + <property name="semanticType11" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#Director">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-875.0, -630.0]">
> + </property>
> + </property>
> + <property name="_windowProperties" class="ptolemy.actor.gui.WindowPropertiesAttribute" value="{bounds={527, 22, 1382, 1058}, maximized=false}">
> + </property>
> + <property name="_vergilSize" class="ptolemy.actor.gui.SizeAttribute" value="[1099, 937]">
> + </property>
> + <property name="_vergilZoomFactor" class="ptolemy.data.expr.ExpertParameter" value="1.0">
> + </property>
> + <property name="_vergilCenter" class="ptolemy.data.expr.ExpertParameter" value="{-462.5, -84.5}">
> + </property>
> + <port name="input" class="org.kepler.util.CollectionIOPort">
> + <property name="input"/>
> + <property name="dataType" class="ptolemy.kernel.util.StringAttribute" value="general">
> + </property>
> + <property name="isMultiport" class="ptolemy.kernel.util.StringAttribute" value="false">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-145.0, -360.0]">
> + </property>
> + </port>
> + <port name="output" class="org.kepler.util.CollectionIOPort">
> + <property name="output"/>
> + <property name="multiport"/>
> + <property name="dataType" class="ptolemy.kernel.util.StringAttribute" value="unknown">
> + </property>
> + <property name="isMultiport" class="ptolemy.kernel.util.StringAttribute" value="true">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-95.0, -360.0]">
> + </property>
> + </port>
> + <port name="StringToken" class="ptolemy.actor.TypedIOPort">
> + <property name="input"/>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-1070.0, -325.0]">
> + </property>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="NORTH">
> + </property>
> + </port>
> + <port name="StringToken [key=tempdir]" class="org.kepler.util.CollectionIOPort">
> + <property name="input"/>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-995.0, -480.0]">
> + </property>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="NORTH">
> + </property>
> + </port>
> + <port name="StringToken [key=target]" class="org.kepler.util.CollectionIOPort">
> + <property name="input"/>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-605.0, -655.0]">
> + </property>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="NORTH">
> + </property>
> + </port>
> + <port name="StringToken [key=emptydir]" class="org.kepler.util.CollectionIOPort">
> + <property name="input"/>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-990.0, -620.0]">
> + </property>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="SOUTH">
> + </property>
> + </port>
> + <port name="StringToken [key=dirprefix]" class="org.kepler.util.CollectionIOPort">
> + <property name="input"/>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-1010.0, -170.0]">
> + </property>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="SOUTH">
> + </property>
> + </port>
> + <entity name="SSH Execute cmd" class="org.kepler.actor.ssh.ExecuteCmd">
> + <property name="target" class="ptolemy.actor.parameters.PortParameter" value="">
> + </property>
> + <property name="timeoutSeconds" class="ptolemy.data.expr.Parameter" value="0">
> + </property>
> + <property name="cleanupAfterError" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="thirdParty" class="ptolemy.actor.parameters.PortParameter" value="""">
> + </property>
> +<property name="KeplerDocumentation" class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> +<property name="description" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="author" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Norbert Podhorszki</configure></property>
> +<property name="version" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>1.1 March 2008</configure></property>
> +<property name="userLevelDocumentation" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>
> +
> + <p>The SSHExecuteCmd actor connects to a remote host using SSH protocol and executes a command. If the host is an empty string or "local", the Java
> + Runtime will be used for execution instead of SSH. After the command terminates, the actor returns the stdout, stderr, and exit code of the operation.</p>
> +
> +<p>Set the <i>timeoutSeconds</i> parameter to terminate the command after a specified amount of time. Specify 0 to wait indefinitely for command termination. If connecting to a Unix host, use the <i>cleanupAfterError</i>
> +Parameter to kill the remote process (and all of its children) after an error or timeout. Set this parameter only if connecting to a Unix server (other platforms do not support it).
> +</p>
> +
> +<p>Note: Streaming of output during the command execution is not currently
> + implemented.</p>
> +
> + <p><b>Third party operation.</b>
> + If the remote command is expected to ask for a password
> + (or passphrase when connecting to a remote host with public-key authentication)
> + set the port/parameter <i>thirdParty</i> for the user at host:port of that third party
> + (it can be the same as <i>target</i> if a sudo command is executed).</p>
> +
> + <p>The authentication to the third party should be the same from the target
> + host and from Kepler's local host. Kepler authenticates (by opening a channel)
> + to the third party and then it provides the password/passphrase used for the
> + authentication to the command on the target host. Therefore, this actor cannot be
> + used to reach a remote host through a proxy machine and execute a command there.</p>
> +
> + <p>The third party execution can be used e.g. to execute and ssh/scp command
> + that connects to another host, also reachable from Kepler's host, to execute external
> + data transfer commands (bbcp, GridFTP, SRM-Lite etc) or sudo commands.</p>
> +
> + <p>The actor will first authenticate Kepler to the third party host
> + (if not yet done by other actors, e.g. SshSession). During the execution of the command,
> + it looks for the appearance of the string 'password' or 'passphrase' in the stdout/stderr
> + streams (case-insensitively). If such string is found, it writes the authentication code
> + stored within Kepler used for the authentication. Therefore, the command must read the
> + password on the standard input, not directly from the terminal device.
> + This process is performed only once!</p>
> +
> + <p>The underlying java code does not have pseudo-terminal emulation, so if you cannot
> + force the command to read passwords from the stdin (e.g. scp command), you have to use an
> + external tool to execute the command through a pseudo-terminal. <b>ptyexec</b> is provided
> + in the <i>org.kepler.ssh</i> package, a C program, that should be compiled and put into the path
> + on the target machine. Then you can execute <i>"ptyexec scp ..."</i>. It works on Linux only.</p>
> +
> +</configure></property>
> +<property name="port:stdout" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Output of the command as it would output to the standard shell. If there is an SSH connection related error (or timeout) the value will be an empty string. </configure></property>
> +<property name="port:stderr" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Any errors that were reported by the remote execution or while connecting. If there is an SSH connection related error (or timeout) the value will be an empty string. </configure></property>
> +<property name="port:target" class="ptolemy.kernel.util.ConfigurableAttribute"><configure> The machine to be used at job submission. It should be null, "" or "local" for the local machine or [user@]host to denote a remote machine accessible with SSH. If user is not provided, the local username will be used. If port is not provided, the default port 22 will be applied. This parameter is read once at initialize. </configure></property>
> +<property name="port:command" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The command to be executed on the remote host, specified as a string (e.g., "uname -a; date") </configure></property>
> +<property name="port:errors" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The string representation of actor execution errors, if any.
> + </configure></property>
> +<property name="port:exitcode" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The exit code of the command. If there is an SSH connection related error (or timeout) the exitcode will be -32767 </configure></property>
> +<property name="prop:timeoutSeconds" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Timeout in seconds. The command will be timed out after the specified amount of time. Specify 0 to wait indefinitely for command termination. </configure></property>
> +<property name="prop:streaming mode" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether the output should be sent in a streaming mode.
> + Note: Streaming is not currently implemented.
> + </configure></property>
> +<property name="prop:thirdParty" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The third party machine where the command wants to connect and needs to authenticate. Kepler can be used to do the authentication and then provide the password or private-key passphrase to the command. It should be defined as [user@]host[:port]. </configure></property>
> +<property name="prop:cleanupAfterError" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Kill remote process(es) after an error or timeout. Set this parameter only if connecting to a Unix server (other platforms do not support it). All processes belonging to the same group as the remote command (i.e., its children) will be killed. </configure></property>
> +<property name="prop:target" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The machine to be used at job submission. It should be null, "" or "local" for the local machine or [user@]host to denote a remote machine accessible with SSH. If user is not provided, the local username will be used. If port is not provided, the default port 22 will be applied. This parameter is read once at initialize. </configure></property>
> +</property> <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:506:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.kepler.actor.ssh.ExecuteCmd">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1213:1">
> + </property>
> + </property>
> + <property name="semanticType00" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ExternalExecutionEnvironmentActor">
> + </property>
> + <property name="semanticType21" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#SSH">
> + </property>
> + <property name="semanticType41" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:4:1#CPES">
> + </property>
> + <property name="semanticType22" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#Tutorial">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-345.0, -265.0]">
> + </property>
> + <port name="target" class="ptolemy.actor.parameters.ParameterPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="command" class="ptolemy.actor.TypedIOPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="stdout" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="stderr" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="exitcode" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="errors" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="thirdParty" class="ptolemy.actor.parameters.ParameterPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + </entity>
> + <entity name="SSH Execute cmd2" class="org.kepler.actor.ssh.ExecuteCmd">
> + <property name="target" class="ptolemy.actor.parameters.PortParameter" value="">
> + </property>
> + <property name="timeoutSeconds" class="ptolemy.data.expr.Parameter" value="0">
> + </property>
> + <property name="cleanupAfterError" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="thirdParty" class="ptolemy.actor.parameters.PortParameter" value="""">
> + </property>
> +<property name="KeplerDocumentation" class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> +<property name="description" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="author" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Norbert Podhorszki</configure></property>
> +<property name="version" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>1.1 March 2008</configure></property>
> +<property name="userLevelDocumentation" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>
> +
> + <p>The SSHExecuteCmd actor connects to a remote host using SSH protocol and executes a command. If the host is an empty string or "local", the Java
> + Runtime will be used for execution instead of SSH. After the command terminates, the actor returns the stdout, stderr, and exit code of the operation.</p>
> +
> +<p>Set the <i>timeoutSeconds</i> parameter to terminate the command after a specified amount of time. Specify 0 to wait indefinitely for command termination. If connecting to a Unix host, use the <i>cleanupAfterError</i>
> +Parameter to kill the remote process (and all of its children) after an error or timeout. Set this parameter only if connecting to a Unix server (other platforms do not support it).
> +</p>
> +
> +<p>Note: Streaming of output during the command execution is not currently
> + implemented.</p>
> +
> + <p><b>Third party operation.</b>
> + If the remote command is expected to ask for a password
> + (or passphrase when connecting to a remote host with public-key authentication)
> + set the port/parameter <i>thirdParty</i> for the user at host:port of that third party
> + (it can be the same as <i>target</i> if a sudo command is executed).</p>
> +
> + <p>The authentication to the third party should be the same from the target
> + host and from Kepler's local host. Kepler authenticates (by opening a channel)
> + to the third party and then it provides the password/passphrase used for the
> + authentication to the command on the target host. Therefore, this actor cannot be
> + used to reach a remote host through a proxy machine and execute a command there.</p>
> +
> + <p>The third party execution can be used e.g. to execute and ssh/scp command
> + that connects to another host, also reachable from Kepler's host, to execute external
> + data transfer commands (bbcp, GridFTP, SRM-Lite etc) or sudo commands.</p>
> +
> + <p>The actor will first authenticate Kepler to the third party host
> + (if not yet done by other actors, e.g. SshSession). During the execution of the command,
> + it looks for the appearance of the string 'password' or 'passphrase' in the stdout/stderr
> + streams (case-insensitively). If such string is found, it writes the authentication code
> + stored within Kepler used for the authentication. Therefore, the command must read the
> + password on the standard input, not directly from the terminal device.
> + This process is performed only once!</p>
> +
> + <p>The underlying java code does not have pseudo-terminal emulation, so if you cannot
> + force the command to read passwords from the stdin (e.g. scp command), you have to use an
> + external tool to execute the command through a pseudo-terminal. <b>ptyexec</b> is provided
> + in the <i>org.kepler.ssh</i> package, a C program, that should be compiled and put into the path
> + on the target machine. Then you can execute <i>"ptyexec scp ..."</i>. It works on Linux only.</p>
> +
> +</configure></property>
> +<property name="port:stdout" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Output of the command as it would output to the standard shell. If there is an SSH connection related error (or timeout) the value will be an empty string. </configure></property>
> +<property name="port:stderr" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Any errors that were reported by the remote execution or while connecting. If there is an SSH connection related error (or timeout) the value will be an empty string. </configure></property>
> +<property name="port:target" class="ptolemy.kernel.util.ConfigurableAttribute"><configure> The machine to be used at job submission. It should be null, "" or "local" for the local machine or [user@]host to denote a remote machine accessible with SSH. If user is not provided, the local username will be used. If port is not provided, the default port 22 will be applied. This parameter is read once at initialize. </configure></property>
> +<property name="port:command" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The command to be executed on the remote host, specified as a string (e.g., "uname -a; date") </configure></property>
> +<property name="port:exitcode" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The exit code of the command. If there is an SSH connection related error (or timeout) the exitcode will be -32767 </configure></property>
> +<property name="port:errors" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The string representation of actor execution errors, if any.
> + </configure></property>
> +<property name="prop:timeoutSeconds" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Timeout in seconds. The command will be timed out after the specified amount of time. Specify 0 to wait indefinitely for command termination. </configure></property>
> +<property name="prop:streaming mode" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether the output should be sent in a streaming mode.
> + Note: Streaming is not currently implemented.
> + </configure></property>
> +<property name="prop:thirdParty" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The third party machine where the command wants to connect and needs to authenticate. Kepler can be used to do the authentication and then provide the password or private-key passphrase to the command. It should be defined as [user@]host[:port]. </configure></property>
> +<property name="prop:target" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The machine to be used at job submission. It should be null, "" or "local" for the local machine or [user@]host to denote a remote machine accessible with SSH. If user is not provided, the local username will be used. If port is not provided, the default port 22 will be applied. This parameter is read once at initialize. </configure></property>
> +<property name="prop:cleanupAfterError" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Kill remote process(es) after an error or timeout. Set this parameter only if connecting to a Unix server (other platforms do not support it). All processes belonging to the same group as the remote command (i.e., its children) will be killed. </configure></property>
> +</property> <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:506:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.kepler.actor.ssh.ExecuteCmd">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1213:1">
> + </property>
> + </property>
> + <property name="semanticType00" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ExternalExecutionEnvironmentActor">
> + </property>
> + <property name="semanticType21" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#SSH">
> + </property>
> + <property name="semanticType41" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:4:1#CPES">
> + </property>
> + <property name="semanticType22" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#Tutorial">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-320.0, -555.0]">
> + </property>
> + <port name="target" class="ptolemy.actor.parameters.ParameterPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="command" class="ptolemy.actor.TypedIOPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="stdout" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="stderr" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="exitcode" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="errors" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="thirdParty" class="ptolemy.actor.parameters.ParameterPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + </entity>
> + <entity name="SSH Execute cmd3" class="org.kepler.actor.ssh.ExecuteCmd">
> + <property name="target" class="ptolemy.actor.parameters.PortParameter" value="">
> + </property>
> + <property name="timeoutSeconds" class="ptolemy.data.expr.Parameter" value="0">
> + </property>
> + <property name="cleanupAfterError" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="thirdParty" class="ptolemy.actor.parameters.PortParameter" value="""">
> + </property>
> +<property name="KeplerDocumentation" class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> +<property name="description" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="author" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Norbert Podhorszki</configure></property>
> +<property name="version" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>1.1 March 2008</configure></property>
> +<property name="userLevelDocumentation" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>
> +
> + <p>The SSHExecuteCmd actor connects to a remote host using SSH protocol and executes a command. If the host is an empty string or "local", the Java
> + Runtime will be used for execution instead of SSH. After the command terminates, the actor returns the stdout, stderr, and exit code of the operation.</p>
> +
> +<p>Set the <i>timeoutSeconds</i> parameter to terminate the command after a specified amount of time. Specify 0 to wait indefinitely for command termination. If connecting to a Unix host, use the <i>cleanupAfterError</i>
> +Parameter to kill the remote process (and all of its children) after an error or timeout. Set this parameter only if connecting to a Unix server (other platforms do not support it).
> +</p>
> +
> +<p>Note: Streaming of output during the command execution is not currently
> + implemented.</p>
> +
> + <p><b>Third party operation.</b>
> + If the remote command is expected to ask for a password
> + (or passphrase when connecting to a remote host with public-key authentication)
> + set the port/parameter <i>thirdParty</i> for the user at host:port of that third party
> + (it can be the same as <i>target</i> if a sudo command is executed).</p>
> +
> + <p>The authentication to the third party should be the same from the target
> + host and from Kepler's local host. Kepler authenticates (by opening a channel)
> + to the third party and then it provides the password/passphrase used for the
> + authentication to the command on the target host. Therefore, this actor cannot be
> + used to reach a remote host through a proxy machine and execute a command there.</p>
> +
> + <p>The third party execution can be used e.g. to execute and ssh/scp command
> + that connects to another host, also reachable from Kepler's host, to execute external
> + data transfer commands (bbcp, GridFTP, SRM-Lite etc) or sudo commands.</p>
> +
> + <p>The actor will first authenticate Kepler to the third party host
> + (if not yet done by other actors, e.g. SshSession). During the execution of the command,
> + it looks for the appearance of the string 'password' or 'passphrase' in the stdout/stderr
> + streams (case-insensitively). If such string is found, it writes the authentication code
> + stored within Kepler used for the authentication. Therefore, the command must read the
> + password on the standard input, not directly from the terminal device.
> + This process is performed only once!</p>
> +
> + <p>The underlying java code does not have pseudo-terminal emulation, so if you cannot
> + force the command to read passwords from the stdin (e.g. scp command), you have to use an
> + external tool to execute the command through a pseudo-terminal. <b>ptyexec</b> is provided
> + in the <i>org.kepler.ssh</i> package, a C program, that should be compiled and put into the path
> + on the target machine. Then you can execute <i>"ptyexec scp ..."</i>. It works on Linux only.</p>
> +
> +</configure></property>
> +<property name="port:stdout" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Output of the command as it would output to the standard shell. If there is an SSH connection related error (or timeout) the value will be an empty string. </configure></property>
> +<property name="port:stderr" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Any errors that were reported by the remote execution or while connecting. If there is an SSH connection related error (or timeout) the value will be an empty string. </configure></property>
> +<property name="port:target" class="ptolemy.kernel.util.ConfigurableAttribute"><configure> The machine to be used at job submission. It should be null, "" or "local" for the local machine or [user@]host to denote a remote machine accessible with SSH. If user is not provided, the local username will be used. If port is not provided, the default port 22 will be applied. This parameter is read once at initialize. </configure></property>
> +<property name="port:command" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The command to be executed on the remote host, specified as a string (e.g., "uname -a; date") </configure></property>
> +<property name="port:errors" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The string representation of actor execution errors, if any.
> + </configure></property>
> +<property name="port:exitcode" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The exit code of the command. If there is an SSH connection related error (or timeout) the exitcode will be -32767 </configure></property>
> +<property name="prop:timeoutSeconds" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Timeout in seconds. The command will be timed out after the specified amount of time. Specify 0 to wait indefinitely for command termination. </configure></property>
> +<property name="prop:streaming mode" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether the output should be sent in a streaming mode.
> + Note: Streaming is not currently implemented.
> + </configure></property>
> +<property name="prop:thirdParty" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The third party machine where the command wants to connect and needs to authenticate. Kepler can be used to do the authentication and then provide the password or private-key passphrase to the command. It should be defined as [user@]host[:port]. </configure></property>
> +<property name="prop:cleanupAfterError" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Kill remote process(es) after an error or timeout. Set this parameter only if connecting to a Unix server (other platforms do not support it). All processes belonging to the same group as the remote command (i.e., its children) will be killed. </configure></property>
> +<property name="prop:target" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The machine to be used at job submission. It should be null, "" or "local" for the local machine or [user@]host to denote a remote machine accessible with SSH. If user is not provided, the local username will be used. If port is not provided, the default port 22 will be applied. This parameter is read once at initialize. </configure></property>
> +</property> <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:506:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.kepler.actor.ssh.ExecuteCmd">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1213:1">
> + </property>
> + </property>
> + <property name="semanticType00" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ExternalExecutionEnvironmentActor">
> + </property>
> + <property name="semanticType21" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#SSH">
> + </property>
> + <property name="semanticType41" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:4:1#CPES">
> + </property>
> + <property name="semanticType22" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#Tutorial">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-345.0, -100.0]">
> + </property>
> + <port name="target" class="ptolemy.actor.parameters.ParameterPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="command" class="ptolemy.actor.TypedIOPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="stdout" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="stderr" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="exitcode" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="errors" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="thirdParty" class="ptolemy.actor.parameters.ParameterPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + </entity>
> + <entity name="SSH Execute cmd4" class="org.kepler.actor.ssh.ExecuteCmd">
> + <property name="target" class="ptolemy.actor.parameters.PortParameter" value="">
> + </property>
> + <property name="timeoutSeconds" class="ptolemy.data.expr.Parameter" value="0">
> + </property>
> + <property name="cleanupAfterError" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="thirdParty" class="ptolemy.actor.parameters.PortParameter" value="""">
> + </property>
> +<property name="KeplerDocumentation" class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> +<property name="description" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="author" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Norbert Podhorszki</configure></property>
> +<property name="version" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>1.1 March 2008</configure></property>
> +<property name="userLevelDocumentation" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>
> +
> + <p>The SSHExecuteCmd actor connects to a remote host using SSH protocol and executes a command. If the host is an empty string or "local", the Java
> + Runtime will be used for execution instead of SSH. After the command terminates, the actor returns the stdout, stderr, and exit code of the operation.</p>
> +
> +<p>Set the <i>timeoutSeconds</i> parameter to terminate the command after a specified amount of time. Specify 0 to wait indefinitely for command termination. If connecting to a Unix host, use the <i>cleanupAfterError</i>
> +Parameter to kill the remote process (and all of its children) after an error or timeout. Set this parameter only if connecting to a Unix server (other platforms do not support it).
> +</p>
> +
> +<p>Note: Streaming of output during the command execution is not currently
> + implemented.</p>
> +
> + <p><b>Third party operation.</b>
> + If the remote command is expected to ask for a password
> + (or passphrase when connecting to a remote host with public-key authentication)
> + set the port/parameter <i>thirdParty</i> for the user at host:port of that third party
> + (it can be the same as <i>target</i> if a sudo command is executed).</p>
> +
> + <p>The authentication to the third party should be the same from the target
> + host and from Kepler's local host. Kepler authenticates (by opening a channel)
> + to the third party and then it provides the password/passphrase used for the
> + authentication to the command on the target host. Therefore, this actor cannot be
> + used to reach a remote host through a proxy machine and execute a command there.</p>
> +
> + <p>The third party execution can be used e.g. to execute and ssh/scp command
> + that connects to another host, also reachable from Kepler's host, to execute external
> + data transfer commands (bbcp, GridFTP, SRM-Lite etc) or sudo commands.</p>
> +
> + <p>The actor will first authenticate Kepler to the third party host
> + (if not yet done by other actors, e.g. SshSession). During the execution of the command,
> + it looks for the appearance of the string 'password' or 'passphrase' in the stdout/stderr
> + streams (case-insensitively). If such string is found, it writes the authentication code
> + stored within Kepler used for the authentication. Therefore, the command must read the
> + password on the standard input, not directly from the terminal device.
> + This process is performed only once!</p>
> +
> + <p>The underlying java code does not have pseudo-terminal emulation, so if you cannot
> + force the command to read passwords from the stdin (e.g. scp command), you have to use an
> + external tool to execute the command through a pseudo-terminal. <b>ptyexec</b> is provided
> + in the <i>org.kepler.ssh</i> package, a C program, that should be compiled and put into the path
> + on the target machine. Then you can execute <i>"ptyexec scp ..."</i>. It works on Linux only.</p>
> +
> +</configure></property>
> +<property name="port:stdout" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Output of the command as it would output to the standard shell. If there is an SSH connection related error (or timeout) the value will be an empty string. </configure></property>
> +<property name="port:stderr" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Any errors that were reported by the remote execution or while connecting. If there is an SSH connection related error (or timeout) the value will be an empty string. </configure></property>
> +<property name="port:target" class="ptolemy.kernel.util.ConfigurableAttribute"><configure> The machine to be used at job submission. It should be null, "" or "local" for the local machine or [user@]host to denote a remote machine accessible with SSH. If user is not provided, the local username will be used. If port is not provided, the default port 22 will be applied. This parameter is read once at initialize. </configure></property>
> +<property name="port:command" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The command to be executed on the remote host, specified as a string (e.g., "uname -a; date") </configure></property>
> +<property name="port:exitcode" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The exit code of the command. If there is an SSH connection related error (or timeout) the exitcode will be -32767 </configure></property>
> +<property name="port:errors" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The string representation of actor execution errors, if any.
> + </configure></property>
> +<property name="prop:timeoutSeconds" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Timeout in seconds. The command will be timed out after the specified amount of time. Specify 0 to wait indefinitely for command termination. </configure></property>
> +<property name="prop:streaming mode" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether the output should be sent in a streaming mode.
> + Note: Streaming is not currently implemented.
> + </configure></property>
> +<property name="prop:thirdParty" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The third party machine where the command wants to connect and needs to authenticate. Kepler can be used to do the authentication and then provide the password or private-key passphrase to the command. It should be defined as [user@]host[:port]. </configure></property>
> +<property name="prop:target" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The machine to be used at job submission. It should be null, "" or "local" for the local machine or [user@]host to denote a remote machine accessible with SSH. If user is not provided, the local username will be used. If port is not provided, the default port 22 will be applied. This parameter is read once at initialize. </configure></property>
> +<property name="prop:cleanupAfterError" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Kill remote process(es) after an error or timeout. Set this parameter only if connecting to a Unix server (other platforms do not support it). All processes belonging to the same group as the remote command (i.e., its children) will be killed. </configure></property>
> +</property> <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:506:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.kepler.actor.ssh.ExecuteCmd">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1213:1">
> + </property>
> + </property>
> + <property name="semanticType00" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ExternalExecutionEnvironmentActor">
> + </property>
> + <property name="semanticType21" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#SSH">
> + </property>
> + <property name="semanticType41" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:4:1#CPES">
> + </property>
> + <property name="semanticType22" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#Tutorial">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-335.0, 20.0]">
> + </property>
> + <port name="target" class="ptolemy.actor.parameters.ParameterPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="command" class="ptolemy.actor.TypedIOPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="stdout" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="stderr" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="exitcode" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="errors" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="thirdParty" class="ptolemy.actor.parameters.ParameterPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + </entity>
> + <entity name="Expression" class="ptolemy.actor.lib.Expression">
> + <property name="expression" class="ptolemy.kernel.util.StringAttribute" value=""cd "+emptydir+"/"+name">
> + <property name="_hide" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </property>
> +<property name="KeplerDocumentation" class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> +<property name="description" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="author" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Xiaojun Liu, Edward A. Lee, Steve Neuendorffer</configure></property>
> +<property name="version" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="userLevelDocumentation" class="ptolemy.kernel.util.ConfigurableAttribute"><configure><p>The Expression actor evaluates a specified expression (e.g., an addition or multiplication operation), which may reference the values of user-specified input ports, the current time, or the actor's iteration count. The actor outputs the value of the evaluated expression. </p>
> +
> +<p>Expressions are specified in the Ptolemy expression language via the expression parameter. For more information about the expression language, see http://ptolemy.eecs.berkeley.edu/papers/05/ptIIdesign1-intro/ptIIdesign1-intro.pdf. </p>
> +
> +<p>By default, the expression parameter is empty, and attempting to execute the actor without first specifying an expression generates an error. Expressions can refer to the values of inputs by the port name; to the current time by the identifier "time"; and to the current iteration count by the identifier "iteration." </p>
> +
> +<p>Input ports are created by the user and correspond to variables used in the specified expression. Currently, the Expression actor does not support input multiports. The actor requires all of its inputs to be present. If inputs are not all present, then the actor will generate an error. </p>
> +
> +<p>Note: the Expression actor can be used instead of many of the arithmetic actors, such as AddSubtract, MultiplyDivide, and TrigFunction. However, those actors will be usually be more efficient, and sometimes more convenient to use.</p></configure></property>
> +<property name="port:output" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>An output port that broadcasts the value of the evaluated expression. The actor automatically determines the type based on the type of the input.</configure></property>
> +<property name="prop:expression" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>An expression to evaluate. Expressions are specified in the Ptolemy expression language. For more information about the expression language, see http://ptolemy.eecs.berkeley.edu/papers/05/ptIIdesign1-intro/ptIIdesign1-intro.pdf. By default, the parameter is empty, and attempting to execute the actor without first specifying an expression generates an error. Expressions can refer to the values of inputs by the port name; to the current time by the identifier "time"; and to the current iteration count by the identifier "iteration."</configure></property>
> +</property> <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:75:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.Expression">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:950:1">
> + </property>
> + </property>
> + <property name="semanticType00" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#MathOperationActor">
> + </property>
> + <property name="semanticType11" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#GeneralPurpose">
> + </property>
> + <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
> + <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
> + </property>
> + <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
> + </property>
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-605.0, -350.0]">
> + </property>
> + <port name="name" class="ptolemy.actor.TypedIOPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + </port>
> + <port name="sycn" class="ptolemy.actor.TypedIOPort">
> + <property name="input"/>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="SOUTH">
> + </property>
> + <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + </port>
> + <port name="emptydir" class="ptolemy.actor.TypedIOPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + </port>
> + </entity>
> + <entity name="Expression2" class="ptolemy.actor.lib.Expression">
> + <property name="expression" class="ptolemy.kernel.util.StringAttribute" value=""cd "+emptydir+"/"+name">
> + <property name="_hide" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </property>
> +<property name="KeplerDocumentation" class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> +<property name="description" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="author" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Xiaojun Liu, Edward A. Lee, Steve Neuendorffer</configure></property>
> +<property name="version" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="userLevelDocumentation" class="ptolemy.kernel.util.ConfigurableAttribute"><configure><p>The Expression actor evaluates a specified expression (e.g., an addition or multiplication operation), which may reference the values of user-specified input ports, the current time, or the actor's iteration count. The actor outputs the value of the evaluated expression. </p>
> +
> +<p>Expressions are specified in the Ptolemy expression language via the expression parameter. For more information about the expression language, see http://ptolemy.eecs.berkeley.edu/papers/05/ptIIdesign1-intro/ptIIdesign1-intro.pdf. </p>
> +
> +<p>By default, the expression parameter is empty, and attempting to execute the actor without first specifying an expression generates an error. Expressions can refer to the values of inputs by the port name; to the current time by the identifier "time"; and to the current iteration count by the identifier "iteration." </p>
> +
> +<p>Input ports are created by the user and correspond to variables used in the specified expression. Currently, the Expression actor does not support input multiports. The actor requires all of its inputs to be present. If inputs are not all present, then the actor will generate an error. </p>
> +
> +<p>Note: the Expression actor can be used instead of many of the arithmetic actors, such as AddSubtract, MultiplyDivide, and TrigFunction. However, those actors will be usually be more efficient, and sometimes more convenient to use.</p></configure></property>
> +<property name="port:output" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>An output port that broadcasts the value of the evaluated expression. The actor automatically determines the type based on the type of the input.</configure></property>
> +<property name="prop:expression" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>An expression to evaluate. Expressions are specified in the Ptolemy expression language. For more information about the expression language, see http://ptolemy.eecs.berkeley.edu/papers/05/ptIIdesign1-intro/ptIIdesign1-intro.pdf. By default, the parameter is empty, and attempting to execute the actor without first specifying an expression generates an error. Expressions can refer to the values of inputs by the port name; to the current time by the identifier "time"; and to the current iteration count by the identifier "iteration."</configure></property>
> +</property> <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:75:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.Expression">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:950:1">
> + </property>
> + </property>
> + <property name="semanticType00" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#MathOperationActor">
> + </property>
> + <property name="semanticType11" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#GeneralPurpose">
> + </property>
> + <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
> + <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
> + </property>
> + <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
> + </property>
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-620.0, -425.0]">
> + </property>
> + <port name="name" class="ptolemy.actor.TypedIOPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + </port>
> + <port name="sycn" class="ptolemy.actor.TypedIOPort">
> + <property name="input"/>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="NORTH">
> + </property>
> + <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + </port>
> + <port name="emptydir" class="ptolemy.actor.TypedIOPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + </port>
> + </entity>
> + <entity name="Expression3" class="ptolemy.actor.lib.Expression">
> + <property name="expression" class="ptolemy.kernel.util.StringAttribute" value="dirprefix+name">
> + <property name="_hide" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </property>
> +<property name="KeplerDocumentation" class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> +<property name="description" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="author" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Xiaojun Liu, Edward A. Lee, Steve Neuendorffer</configure></property>
> +<property name="version" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="userLevelDocumentation" class="ptolemy.kernel.util.ConfigurableAttribute"><configure><p>The Expression actor evaluates a specified expression (e.g., an addition or multiplication operation), which may reference the values of user-specified input ports, the current time, or the actor's iteration count. The actor outputs the value of the evaluated expression. </p>
> +
> +<p>Expressions are specified in the Ptolemy expression language via the expression parameter. For more information about the expression language, see http://ptolemy.eecs.berkeley.edu/papers/05/ptIIdesign1-intro/ptIIdesign1-intro.pdf. </p>
> +
> +<p>By default, the expression parameter is empty, and attempting to execute the actor without first specifying an expression generates an error. Expressions can refer to the values of inputs by the port name; to the current time by the identifier "time"; and to the current iteration count by the identifier "iteration." </p>
> +
> +<p>Input ports are created by the user and correspond to variables used in the specified expression. Currently, the Expression actor does not support input multiports. The actor requires all of its inputs to be present. If inputs are not all present, then the actor will generate an error. </p>
> +
> +<p>Note: the Expression actor can be used instead of many of the arithmetic actors, such as AddSubtract, MultiplyDivide, and TrigFunction. However, those actors will be usually be more efficient, and sometimes more convenient to use.</p></configure></property>
> +<property name="port:output" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>An output port that broadcasts the value of the evaluated expression. The actor automatically determines the type based on the type of the input.</configure></property>
> +<property name="prop:expression" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>An expression to evaluate. Expressions are specified in the Ptolemy expression language. For more information about the expression language, see http://ptolemy.eecs.berkeley.edu/papers/05/ptIIdesign1-intro/ptIIdesign1-intro.pdf. By default, the parameter is empty, and attempting to execute the actor without first specifying an expression generates an error. Expressions can refer to the values of inputs by the port name; to the current time by the identifier "time"; and to the current iteration count by the identifier "iteration."</configure></property>
> +</property> <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:75:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.Expression">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:950:1">
> + </property>
> + </property>
> + <property name="semanticType00" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#MathOperationActor">
> + </property>
> + <property name="semanticType11" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#GeneralPurpose">
> + </property>
> + <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
> + <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
> + </property>
> + <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
> + </property>
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-725.0, -185.0]">
> + </property>
> + <port name="name" class="ptolemy.actor.TypedIOPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + </port>
> + <port name="sycn" class="ptolemy.actor.TypedIOPort">
> + <property name="input"/>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="NORTH">
> + </property>
> + <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + </port>
> + <port name="dirprefix" class="ptolemy.actor.TypedIOPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + </port>
> + </entity>
> + <entity name="Expression4" class="ptolemy.actor.lib.Expression">
> + <property name="expression" class="ptolemy.kernel.util.StringAttribute" value=""cd "+emptydir+"/"+name+"; ~/bin/cmake ~/"+tempdir+"/"+name">
> + <property name="_hide" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </property>
> +<property name="KeplerDocumentation" class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> +<property name="description" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="author" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Xiaojun Liu, Edward A. Lee, Steve Neuendorffer</configure></property>
> +<property name="version" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="userLevelDocumentation" class="ptolemy.kernel.util.ConfigurableAttribute"><configure><p>The Expression actor evaluates a specified expression (e.g., an addition or multiplication operation), which may reference the values of user-specified input ports, the current time, or the actor's iteration count. The actor outputs the value of the evaluated expression. </p>
> +
> +<p>Expressions are specified in the Ptolemy expression language via the expression parameter. For more information about the expression language, see http://ptolemy.eecs.berkeley.edu/papers/05/ptIIdesign1-intro/ptIIdesign1-intro.pdf. </p>
> +
> +<p>By default, the expression parameter is empty, and attempting to execute the actor without first specifying an expression generates an error. Expressions can refer to the values of inputs by the port name; to the current time by the identifier "time"; and to the current iteration count by the identifier "iteration." </p>
> +
> +<p>Input ports are created by the user and correspond to variables used in the specified expression. Currently, the Expression actor does not support input multiports. The actor requires all of its inputs to be present. If inputs are not all present, then the actor will generate an error. </p>
> +
> +<p>Note: the Expression actor can be used instead of many of the arithmetic actors, such as AddSubtract, MultiplyDivide, and TrigFunction. However, those actors will be usually be more efficient, and sometimes more convenient to use.</p></configure></property>
> +<property name="port:output" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>An output port that broadcasts the value of the evaluated expression. The actor automatically determines the type based on the type of the input.</configure></property>
> +<property name="prop:expression" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>An expression to evaluate. Expressions are specified in the Ptolemy expression language. For more information about the expression language, see http://ptolemy.eecs.berkeley.edu/papers/05/ptIIdesign1-intro/ptIIdesign1-intro.pdf. By default, the parameter is empty, and attempting to execute the actor without first specifying an expression generates an error. Expressions can refer to the values of inputs by the port name; to the current time by the identifier "time"; and to the current iteration count by the identifier "iteration."</configure></property>
> +</property> <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:75:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.Expression">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:950:1">
> + </property>
> + </property>
> + <property name="semanticType00" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#MathOperationActor">
> + </property>
> + <property name="semanticType11" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#GeneralPurpose">
> + </property>
> + <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
> + <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
> + </property>
> + <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
> + </property>
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="{-700.0, -535.0}">
> + </property>
> + <port name="name" class="ptolemy.actor.TypedIOPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + </port>
> + <port name="emptydir" class="ptolemy.actor.TypedIOPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + </port>
> + <port name="tempdir" class="ptolemy.actor.TypedIOPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + </port>
> + </entity>
> + <entity name="SSH Directory Creator" class="org.kepler.actor.ssh.DirectoryCreator">
> + <property name="target" class="ptolemy.actor.parameters.PortParameter" value="">
> + </property>
> + <property name="dir" class="ptolemy.actor.parameters.PortParameter" value=""/"">
> + </property>
> + <property name="parent" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> +<property name="KeplerDocumentation" class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> +<property name="description" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="author" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Norbert Podhorszki</configure></property>
> +<property name="version" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="userLevelDocumentation" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>
> +
> +<p>The SSHDirectoryCreator actor creates a local or remote directory. The actor reads the path to a target machine as well as the name of the directory to create. The actor outputs the operation results: true if the directory is created successfully, and false if not. In addition, the actor outputs the text of generated error messages, if any.</p>
> +
> +<p>For remote operations, a relative path is relative to the home directory. For local operations, a relative path is relative to the current directory. If the 'parent' flag is set, intermediate directories in the provided path will be created if necessary. </p>
> +
> +</configure></property>
> +<property name="port:succ" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>A Boolean token: true if the operation is successful, false if not. </configure></property>
> +<property name="port:dir" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The path to the target directory. This parameter is read once at initialize. </configure></property>
> +<property name="port:error" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The actor's execution errors, if any; otherwise an empty string. </configure></property>
> +<property name="port:target" class="ptolemy.kernel.util.ConfigurableAttribute"><configure> The machine to be used at job submission. It should be null, "" or "local" for the local machine or [user@]host to denote a remote machine accessible with SSH. This parameter is read once at initialize. </configure></property>
> +<property name="prop:dir" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The path to the directory to be read on the target machines. This parameter is read once at initialize. </configure></property>
> +<property name="prop:parent" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether parent directories should be created recursively if necessary. If the 'parent' flag is set the operation is considered successful even if the directory already exists. </configure></property>
> +<property name="prop:target" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The machine to be used at job submission. It should be null, "" or "local" for the local machine or [user@]host to denote a remote machine accessible with ssh. This parameter is read once at initialize. </configure></property>
> +</property> <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:514:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.kepler.actor.ssh.DirectoryCreator">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1209:1">
> + </property>
> + </property>
> + <property name="semanticType11" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ExternalExecutionEnvironmentActor">
> + </property>
> + <property name="semanticType21" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#SSH">
> + </property>
> + <property name="semanticType41" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:4:1#CPES">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-350.0, -195.0]">
> + </property>
> + <port name="target" class="ptolemy.actor.parameters.ParameterPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="dir" class="ptolemy.actor.parameters.ParameterPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="succ" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="error" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + </entity>
> + <entity name="Expression5" class="ptolemy.actor.lib.Expression">
> + <property name="expression" class="ptolemy.kernel.util.StringAttribute" value=""cp -r "+emptydir+"/s3d_run/* "+dirprefix+name">
> + <property name="_hide" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </property>
> +<property name="KeplerDocumentation" class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> +<property name="description" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="author" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Xiaojun Liu, Edward A. Lee, Steve Neuendorffer</configure></property>
> +<property name="version" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="userLevelDocumentation" class="ptolemy.kernel.util.ConfigurableAttribute"><configure><p>The Expression actor evaluates a specified expression (e.g., an addition or multiplication operation), which may reference the values of user-specified input ports, the current time, or the actor's iteration count. The actor outputs the value of the evaluated expression. </p>
> +
> +<p>Expressions are specified in the Ptolemy expression language via the expression parameter. For more information about the expression language, see http://ptolemy.eecs.berkeley.edu/papers/05/ptIIdesign1-intro/ptIIdesign1-intro.pdf. </p>
> +
> +<p>By default, the expression parameter is empty, and attempting to execute the actor without first specifying an expression generates an error. Expressions can refer to the values of inputs by the port name; to the current time by the identifier "time"; and to the current iteration count by the identifier "iteration." </p>
> +
> +<p>Input ports are created by the user and correspond to variables used in the specified expression. Currently, the Expression actor does not support input multiports. The actor requires all of its inputs to be present. If inputs are not all present, then the actor will generate an error. </p>
> +
> +<p>Note: the Expression actor can be used instead of many of the arithmetic actors, such as AddSubtract, MultiplyDivide, and TrigFunction. However, those actors will be usually be more efficient, and sometimes more convenient to use.</p></configure></property>
> +<property name="port:output" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>An output port that broadcasts the value of the evaluated expression. The actor automatically determines the type based on the type of the input.</configure></property>
> +<property name="prop:expression" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>An expression to evaluate. Expressions are specified in the Ptolemy expression language. For more information about the expression language, see http://ptolemy.eecs.berkeley.edu/papers/05/ptIIdesign1-intro/ptIIdesign1-intro.pdf. By default, the parameter is empty, and attempting to execute the actor without first specifying an expression generates an error. Expressions can refer to the values of inputs by the port name; to the current time by the identifier "time"; and to the current iteration count by the identifier "iteration."</configure></property>
> +</property> <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:75:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.Expression">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:950:1">
> + </property>
> + </property>
> + <property name="semanticType00" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#MathOperationActor">
> + </property>
> + <property name="semanticType11" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#GeneralPurpose">
> + </property>
> + <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
> + <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
> + </property>
> + <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
> + </property>
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-605.0, -80.0]">
> + </property>
> + <port name="name" class="ptolemy.actor.TypedIOPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + </port>
> + <port name="sycn" class="ptolemy.actor.TypedIOPort">
> + <property name="input"/>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="NORTH">
> + </property>
> + <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + </port>
> + <port name="emptydir" class="ptolemy.actor.TypedIOPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + </port>
> + <port name="dirprefix" class="ptolemy.actor.TypedIOPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + </port>
> + </entity>
> + <entity name="SSH Execute cmd5" class="org.kepler.actor.ssh.ExecuteCmd">
> + <property name="target" class="ptolemy.actor.parameters.PortParameter" value="">
> + </property>
> + <property name="timeoutSeconds" class="ptolemy.data.expr.Parameter" value="0">
> + </property>
> + <property name="cleanupAfterError" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="thirdParty" class="ptolemy.actor.parameters.PortParameter" value="""">
> + </property>
> +<property name="KeplerDocumentation" class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> +<property name="description" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="author" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Norbert Podhorszki</configure></property>
> +<property name="version" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>1.1 March 2008</configure></property>
> +<property name="userLevelDocumentation" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>
> +
> + <p>The SSHExecuteCmd actor connects to a remote host using SSH protocol and executes a command. If the host is an empty string or "local", the Java
> + Runtime will be used for execution instead of SSH. After the command terminates, the actor returns the stdout, stderr, and exit code of the operation.</p>
> +
> +<p>Set the <i>timeoutSeconds</i> parameter to terminate the command after a specified amount of time. Specify 0 to wait indefinitely for command termination. If connecting to a Unix host, use the <i>cleanupAfterError</i>
> +Parameter to kill the remote process (and all of its children) after an error or timeout. Set this parameter only if connecting to a Unix server (other platforms do not support it).
> +</p>
> +
> +<p>Note: Streaming of output during the command execution is not currently
> + implemented.</p>
> +
> + <p><b>Third party operation.</b>
> + If the remote command is expected to ask for a password
> + (or passphrase when connecting to a remote host with public-key authentication)
> + set the port/parameter <i>thirdParty</i> for the user at host:port of that third party
> + (it can be the same as <i>target</i> if a sudo command is executed).</p>
> +
> + <p>The authentication to the third party should be the same from the target
> + host and from Kepler's local host. Kepler authenticates (by opening a channel)
> + to the third party and then it provides the password/passphrase used for the
> + authentication to the command on the target host. Therefore, this actor cannot be
> + used to reach a remote host through a proxy machine and execute a command there.</p>
> +
> + <p>The third party execution can be used e.g. to execute and ssh/scp command
> + that connects to another host, also reachable from Kepler's host, to execute external
> + data transfer commands (bbcp, GridFTP, SRM-Lite etc) or sudo commands.</p>
> +
> + <p>The actor will first authenticate Kepler to the third party host
> + (if not yet done by other actors, e.g. SshSession). During the execution of the command,
> + it looks for the appearance of the string 'password' or 'passphrase' in the stdout/stderr
> + streams (case-insensitively). If such string is found, it writes the authentication code
> + stored within Kepler used for the authentication. Therefore, the command must read the
> + password on the standard input, not directly from the terminal device.
> + This process is performed only once!</p>
> +
> + <p>The underlying java code does not have pseudo-terminal emulation, so if you cannot
> + force the command to read passwords from the stdin (e.g. scp command), you have to use an
> + external tool to execute the command through a pseudo-terminal. <b>ptyexec</b> is provided
> + in the <i>org.kepler.ssh</i> package, a C program, that should be compiled and put into the path
> + on the target machine. Then you can execute <i>"ptyexec scp ..."</i>. It works on Linux only.</p>
> +
> +</configure></property>
> +<property name="port:stdout" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Output of the command as it would output to the standard shell. If there is an SSH connection related error (or timeout) the value will be an empty string. </configure></property>
> +<property name="port:stderr" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Any errors that were reported by the remote execution or while connecting. If there is an SSH connection related error (or timeout) the value will be an empty string. </configure></property>
> +<property name="port:target" class="ptolemy.kernel.util.ConfigurableAttribute"><configure> The machine to be used at job submission. It should be null, "" or "local" for the local machine or [user@]host to denote a remote machine accessible with SSH. If user is not provided, the local username will be used. If port is not provided, the default port 22 will be applied. This parameter is read once at initialize. </configure></property>
> +<property name="port:command" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The command to be executed on the remote host, specified as a string (e.g., "uname -a; date") </configure></property>
> +<property name="port:exitcode" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The exit code of the command. If there is an SSH connection related error (or timeout) the exitcode will be -32767 </configure></property>
> +<property name="port:errors" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The string representation of actor execution errors, if any.
> + </configure></property>
> +<property name="prop:timeoutSeconds" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Timeout in seconds. The command will be timed out after the specified amount of time. Specify 0 to wait indefinitely for command termination. </configure></property>
> +<property name="prop:streaming mode" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether the output should be sent in a streaming mode.
> + Note: Streaming is not currently implemented.
> + </configure></property>
> +<property name="prop:thirdParty" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The third party machine where the command wants to connect and needs to authenticate. Kepler can be used to do the authentication and then provide the password or private-key passphrase to the command. It should be defined as [user@]host[:port]. </configure></property>
> +<property name="prop:target" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The machine to be used at job submission. It should be null, "" or "local" for the local machine or [user@]host to denote a remote machine accessible with SSH. If user is not provided, the local username will be used. If port is not provided, the default port 22 will be applied. This parameter is read once at initialize. </configure></property>
> +<property name="prop:cleanupAfterError" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Kill remote process(es) after an error or timeout. Set this parameter only if connecting to a Unix server (other platforms do not support it). All processes belonging to the same group as the remote command (i.e., its children) will be killed. </configure></property>
> +</property> <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:506:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.kepler.actor.ssh.ExecuteCmd">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1213:1">
> + </property>
> + </property>
> + <property name="semanticType00" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ExternalExecutionEnvironmentActor">
> + </property>
> + <property name="semanticType21" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#SSH">
> + </property>
> + <property name="semanticType41" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:4:1#CPES">
> + </property>
> + <property name="semanticType22" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#Tutorial">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-355.0, -375.0]">
> + </property>
> + <port name="target" class="ptolemy.actor.parameters.ParameterPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="command" class="ptolemy.actor.TypedIOPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="stdout" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="stderr" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="exitcode" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="errors" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="thirdParty" class="ptolemy.actor.parameters.ParameterPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + </entity>
> + <entity name="Expression7" class="ptolemy.actor.lib.Expression">
> + <property name="expression" class="ptolemy.kernel.util.StringAttribute" value=""rm -rf "+emptydir+"/s3d_run/"">
> + <property name="_hide" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </property>
> +<property name="KeplerDocumentation" class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> +<property name="description" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="author" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Xiaojun Liu, Edward A. Lee, Steve Neuendorffer</configure></property>
> +<property name="version" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="userLevelDocumentation" class="ptolemy.kernel.util.ConfigurableAttribute"><configure><p>The Expression actor evaluates a specified expression (e.g., an addition or multiplication operation), which may reference the values of user-specified input ports, the current time, or the actor's iteration count. The actor outputs the value of the evaluated expression. </p>
> +
> +<p>Expressions are specified in the Ptolemy expression language via the expression parameter. For more information about the expression language, see http://ptolemy.eecs.berkeley.edu/papers/05/ptIIdesign1-intro/ptIIdesign1-intro.pdf. </p>
> +
> +<p>By default, the expression parameter is empty, and attempting to execute the actor without first specifying an expression generates an error. Expressions can refer to the values of inputs by the port name; to the current time by the identifier "time"; and to the current iteration count by the identifier "iteration." </p>
> +
> +<p>Input ports are created by the user and correspond to variables used in the specified expression. Currently, the Expression actor does not support input multiports. The actor requires all of its inputs to be present. If inputs are not all present, then the actor will generate an error. </p>
> +
> +<p>Note: the Expression actor can be used instead of many of the arithmetic actors, such as AddSubtract, MultiplyDivide, and TrigFunction. However, those actors will be usually be more efficient, and sometimes more convenient to use.</p></configure></property>
> +<property name="port:output" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>An output port that broadcasts the value of the evaluated expression. The actor automatically determines the type based on the type of the input.</configure></property>
> +<property name="prop:expression" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>An expression to evaluate. Expressions are specified in the Ptolemy expression language. For more information about the expression language, see http://ptolemy.eecs.berkeley.edu/papers/05/ptIIdesign1-intro/ptIIdesign1-intro.pdf. By default, the parameter is empty, and attempting to execute the actor without first specifying an expression generates an error. Expressions can refer to the values of inputs by the port name; to the current time by the identifier "time"; and to the current iteration count by the identifier "iteration."</configure></property>
> +</property> <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:75:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.Expression">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:950:1">
> + </property>
> + </property>
> + <property name="semanticType00" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#MathOperationActor">
> + </property>
> + <property name="semanticType11" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#GeneralPurpose">
> + </property>
> + <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
> + <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
> + </property>
> + <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
> + </property>
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-680.0, 40.0]">
> + </property>
> + <port name="input" class="ptolemy.actor.TypedIOPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + </port>
> + <port name="emptydir" class="ptolemy.actor.TypedIOPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + </port>
> + </entity>
> + <relation name="relation3" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <relation name="relation4" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <relation name="relation5" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <relation name="relation8" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <relation name="relation10" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <relation name="relation11" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <relation name="relation12" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <relation name="relation15" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <relation name="relation19" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <relation name="relation14" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + <vertex name="vertex1" value="[-930.0, -325.0]">
> + </vertex>
> + </relation>
> + <relation name="relation" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <relation name="relation2" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <relation name="relation7" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + <vertex name="vertex1" value="[-450.0, -660.0]">
> + </vertex>
> + </relation>
> + <relation name="relation6" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <relation name="relation13" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + <vertex name="vertex1" value="[-970.0, -385.0]">
> + </vertex>
> + </relation>
> + <relation name="relation16" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + <vertex name="vertex1" value="[-885.0, -135.0]">
> + </vertex>
> + </relation>
> + <link port="StringToken" relation="relation14"/>
> + <link port="StringToken [key=tempdir]" relation="relation6"/>
> + <link port="StringToken [key=target]" relation="relation7"/>
> + <link port="StringToken [key=emptydir]" relation="relation13"/>
> + <link port="StringToken [key=dirprefix]" relation="relation16"/>
> + <link port="SSH Execute cmd.target" relation="relation7"/>
> + <link port="SSH Execute cmd.command" relation="relation15"/>
> + <link port="SSH Execute cmd.stdout" relation="relation11"/>
> + <link port="SSH Execute cmd2.target" relation="relation7"/>
> + <link port="SSH Execute cmd2.command" relation="relation"/>
> + <link port="SSH Execute cmd2.stdout" relation="relation2"/>
> + <link port="SSH Execute cmd3.target" relation="relation7"/>
> + <link port="SSH Execute cmd3.command" relation="relation3"/>
> + <link port="SSH Execute cmd3.stdout" relation="relation12"/>
> + <link port="SSH Execute cmd4.target" relation="relation7"/>
> + <link port="SSH Execute cmd4.command" relation="relation5"/>
> + <link port="Expression.output" relation="relation4"/>
> + <link port="Expression.name" relation="relation14"/>
> + <link port="Expression.sycn" relation="relation11"/>
> + <link port="Expression.emptydir" relation="relation13"/>
> + <link port="Expression2.output" relation="relation15"/>
> + <link port="Expression2.name" relation="relation14"/>
> + <link port="Expression2.sycn" relation="relation2"/>
> + <link port="Expression2.emptydir" relation="relation13"/>
> + <link port="Expression3.output" relation="relation10"/>
> + <link port="Expression3.name" relation="relation14"/>
> + <link port="Expression3.sycn" relation="relation19"/>
> + <link port="Expression3.dirprefix" relation="relation16"/>
> + <link port="Expression4.output" relation="relation"/>
> + <link port="Expression4.name" relation="relation14"/>
> + <link port="Expression4.emptydir" relation="relation13"/>
> + <link port="Expression4.tempdir" relation="relation6"/>
> + <link port="SSH Directory Creator.target" relation="relation7"/>
> + <link port="SSH Directory Creator.dir" relation="relation10"/>
> + <link port="SSH Directory Creator.succ" relation="relation8"/>
> + <link port="Expression5.output" relation="relation3"/>
> + <link port="Expression5.name" relation="relation14"/>
> + <link port="Expression5.sycn" relation="relation8"/>
> + <link port="Expression5.emptydir" relation="relation13"/>
> + <link port="Expression5.dirprefix" relation="relation16"/>
> + <link port="SSH Execute cmd5.target" relation="relation7"/>
> + <link port="SSH Execute cmd5.command" relation="relation4"/>
> + <link port="SSH Execute cmd5.stdout" relation="relation19"/>
> + <link port="Expression7.output" relation="relation5"/>
> + <link port="Expression7.input" relation="relation12"/>
> + <link port="Expression7.emptydir" relation="relation13"/>
> + </entity>
> + <entity name="SSH_Submit2Cluster" class="org.kepler.coactors.CompositeCoactor">
> + <property name="Read scope" class="org.kepler.util.CoactorParameter" value="Job/DirNames">
> + </property>
> + <property name="_createdBy" class="ptolemy.kernel.attributes.VersionAttribute" value="7.0.2">
> + </property>
> + <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:ppod.daks.org:composite:100:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.kepler.coactors.CompositeCoactor">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:ppod.daks.org:class:100:1">
> + </property>
> + </property>
> + <property name="semanticType" class="org.kepler.sms.SemanticType" value="urn:lsid:ppod.daks.org:onto:1#ComadGeneralActors">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-340.0, 225.0]">
> + </property>
> + <property name="_windowProperties" class="ptolemy.actor.gui.WindowPropertiesAttribute" value="{bounds={408, 217, 883, 853}, maximized=false}">
> + </property>
> + <property name="_vergilSize" class="ptolemy.actor.gui.SizeAttribute" value="[600, 732]">
> + </property>
> + <property name="_vergilZoomFactor" class="ptolemy.data.expr.ExpertParameter" value="1.0">
> + </property>
> + <property name="_vergilCenter" class="ptolemy.data.expr.ExpertParameter" value="{-287.0, 90.0}">
> + </property>
> + <property name="SDF Director" class="ptolemy.domains.sdf.kernel.SDFDirector">
> + <property name="iterations" class="ptolemy.data.expr.Parameter" value="0">
> + </property>
> + <property name="vectorizationFactor" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + <property name="allowDisconnectedGraphs" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="allowRateChanges" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="constrainBufferSizes" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + <property name="period" class="ptolemy.data.expr.Parameter" value="0.0">
> + </property>
> + <property name="synchronizeToRealTime" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="timeResolution" class="ptolemy.moml.SharedParameter" value="1E-10">
> + </property>
> + <property name="Scheduler" class="ptolemy.domains.sdf.kernel.SDFScheduler">
> + <property name="constrainBufferSizes" class="ptolemy.data.expr.Parameter" value="constrainBufferSizes">
> + </property>
> + </property>
> +<property name="KeplerDocumentation" class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> +<property name="description" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="author" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Steve Neuendorffer</configure></property>
> +<property name="version" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="userLevelDocumentation" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>
> +<p>The SDF Director is often used to oversee fairly simple, sequential workflows in which the director can determine the order of actor invocation from the workflow. Types of workflows that would run well under an SDF Director include processing and reformatting tabular data, converting one data type to another, and reading and plotting a series of data points. A workflow in which an image is read, processed (rotated, scaled, clipped, filtered, etc.), and then displayed, is also an example of a sequential workflow that requires a director simply to ensure that each actor fires in the proper order (i.e., that each actor executes only after it receives its required inputs).</p>
> +
> +<p>The SDF Director is very efficient and will not tax system resources with overhead. However, this efficiency requires that certain conditions be met, namely that the data consumption and production rate of each actor in an SDF workflow be constant and declared. If an actor reads one piece of data and calculates and outputs a single result, it must always read and output a single token of data. This data rate cannot change during workflow execution and, in general, workflows that require dynamic scheduling and/or flow control cannot use this director. Additionally, the SDF Director has no understanding of passing time (at least by default), and actors that depend on a notion of time may not work as expected. For example, a TimedPlotter actor will plot all values at time zero when used in SDF. </p>
> +
> +<p>By default, the SDF Director requires that all actors in its workflow be connected. Otherwise, the director cannot account for concurrency between disconnected workflow parts. Usually, a PN Director should be used for workflows that contain disconnected actors; however, the SDF Director's allowDisconnectedGraphs parameter may also be set to true. The SDF Director will then schedule each disconnected "island" independently. The director cannot infer the sequential relationship between disconnected actors (i.e., nothing forces the director to finish executing all actors on one island before firing actors on another). However, the order of execution within each island should be correct. Usually, disconnected graphs in an SDF model indicate an error.</p>
> +
> +<p>Because SDF Directors schedule actors to fire only after they receive their inputs, workflows that require loops (feeding an actor's output back into its input port for further processing) can cause "deadlock" errors. The deadlock errors occur because the actor depends on its own output value as an initial input. To fix this problem, use a SampleDelay actor to generate and inject an initial input value into the workflow.</p>
> +
> +<p>The SDF Director determines the order in which actors execute and how many times each actor needs to be fired to complete a single iteration of the workflow. This schedule is calculated BEFORE the director begins to iterate the workflow. Because the SDF Director calculates a schedule in advance, it is quite efficient. However, SDF workflows must be static. In other words, the same number of tokens must be consumed/produced at every iteration of the workflow. Workflows that require dynamic control structures, such as a BooleanSwitch actor that sends output on one of two ports depending on the value of a 'control', cannot be used with an SDF Director because the number of tokens on each output can change for each execution.</p>
> +
> +<p>Unless otherwise specified, the SDF Director assumes that each actor consumes and produces exactly one token per channel on each firing. Actors that do not follow the one-token-per-channel firing convention (e.g., Repeat or Ramp) must declare the number of tokens they produce or consume via the appropriate parameters. </p>
> +
> +<p>The number of times a workflow is iterated is controlled by the director's iterations parameter. By default, this parameter is set to "0". Note that "0" does not mean "no iterations." Rather, "0" means that the workflow will iterate forever. Values greater than zero specify the actual number of times the director should execute the entire workflow. A value of 1, meaning that the director will run the workflow once, is often the best setting when building an SDF workflow. </p>
> +
> +<p>The amount of data processed by an SDF workflow is a function of both the number of times the workflow iterates and the value of the director's vectorizationFactor parameter. The vectorizationFactor is used to increase the efficiency of a workflow by increasing the number of times actors fire each time the workflow iterates. If the parameter is set to a positive integer (other than 1), the director will fire each actor the specified number of times more than normal. The default is 1, indicating that no vectorization should be performed. Keep in mind that changing the vectorizationFactor parameter changes the meaning of a nested SDF workflow and may cause deadlock in a workflow that uses it. </p>
> +
> +<p>The SDF Director has several advanced parameters that are generally only relevant when an SDF workflow contains composite components. In most cases the period, timeResolution, synchronizeToRealTime, allowRateChanges, timeResolution, and constrainBufferSizes parameters can be left at their default values.</p>
> +
> +<p>For more information about the SDF Director, see the Ptolemy documentation (http://ptolemy.eecs.berkeley.edu/papers/05/ptIIdesign3-domains/ptIIdesign3-domains.pdf).</p>
> +
> +</configure></property>
> +<property name="prop:allowDisconnectedGraphs" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether to allow disconnected actors in the workflow (by default, all actors are required to be connected). If disconnected actors are permitted, the SDF Director will schedule each disconnected 'island' independently. Nothing "forces" the director to finish executing all actors on one island before firing actors on another. However, the order of execution within each island should be correct. Usually, disconnected graphs in an SDF workflow indicate an error.</configure></property>
> +<property name="prop:allowRateChanges" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether dynamic rate changes are permitted or not. By default, rate changes are not permitted, and the director will perform a check to disallow such workflows. If the parameter is selected, then workflows that require rate parameters to be modified during execution are valid, and the SDF Director will dynamically compute a new schedule at runtime. This is an advanced parameter that can usually be left at its default value.</configure></property>
> +<property name="prop:timeResolution" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The time precision used by this director. All time values are rounded to the nearest multiple of this number. The value is a double that defaults to "1E-10" (which is 10-10). This is an advanced parameter that can usually be left at its default value.</configure></property>
> +<property name="prop:constrainBufferSizes" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether buffer sizes are fixed. By default, buffers are fixed, and attempts to write to the buffer that cause the buffer to exceed its scheduled size result in an error. This is an advanced parameter that can usually be left at its default value.</configure></property>
> +<property name="prop:iterations" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify the number of times a workflow is iterated. By default, this parameter is set to "0". Note that "0" does not mean "no iterations." Rather, "0" means that the workflow will iterate forever. Values greater than zero specify the actual number of times the director should execute the entire workflow. A value of 1, meaning that the director will run the workflow once, is often the best setting when building an SDF workflow. </configure></property>
> +<property name="prop:vectorizationFactor" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The vectorizationFactor is used to increase the efficiency of a workflow by increasing the number of times actors fire each time the workflow iterates. If the parameter is set to a positive integer (other than 1), the director will fire each actor the specified number of times more than normal. The default is 1, indicating that no vectorization should be performed. Keep in mind that changing the vectorizationFactor parameter changes the meaning of a nested SDF workflow and may cause deadlock in a workflow that uses it. </configure></property>
> +<property name="prop:synchronizeToRealTime" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether the execution should synchronize to real time or not. By default, the director does not synchronize to real time. If synchronize is selected, the director will only process the workflow when elapsed real time matches the product of the period parameter and the iteration count. Note: if the period parameter has a value of 0.0 (the default), then selecting this parameter has no effect. This is an advanced parameter that can usually be left at its default value.</configure></property>
> +<property name="prop:period" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The time period of each iteration. The value is a double that defaults to 0.0, which means that the director does not increment workflow time. If the value greater than 0.0, the actor will increment workflow time each time it fires. This is an advanced parameter that can usually be left at its default value. </configure></property>
> +</property> <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:director:1:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.domains.sdf.kernel.SDFDirector">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:directorclass:1:1">
> + </property>
> + </property>
> + <property name="semanticType00" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#Director">
> + </property>
> + <property name="semanticType11" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#Director">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="{-145.0, -60.0}">
> + </property>
> + </property>
> + <port name="input" class="org.kepler.util.CollectionIOPort">
> + <property name="input"/>
> + <property name="dataType" class="ptolemy.kernel.util.StringAttribute" value="general">
> + </property>
> + <property name="isMultiport" class="ptolemy.kernel.util.StringAttribute" value="false">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="{-435.0, 45.0}">
> + </property>
> + </port>
> + <port name="output" class="org.kepler.util.CollectionIOPort">
> + <property name="output"/>
> + <property name="multiport"/>
> + <property name="dataType" class="ptolemy.kernel.util.StringAttribute" value="unknown">
> + </property>
> + <property name="isMultiport" class="ptolemy.kernel.util.StringAttribute" value="true">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="{95.0, 60.0}">
> + </property>
> + </port>
> + <port name="StringToken" class="org.kepler.util.CollectionIOPort">
> + <property name="input"/>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-390.0, 50.0]">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="NORTH">
> + </property>
> + </port>
> + <port name="StringToken [key=target]" class="org.kepler.util.CollectionIOPort">
> + <property name="input"/>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-485.0, -75.0]">
> + </property>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="NORTH">
> + </property>
> + </port>
> + <port name="StringToken [key=dirprefix]" class="org.kepler.util.CollectionIOPort">
> + <property name="input"/>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-520.0, 165.0]">
> + </property>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="SOUTH">
> + </property>
> + </port>
> + <entity name="SSH Execute cmd" class="org.kepler.actor.ssh.ExecuteCmd">
> + <property name="target" class="ptolemy.actor.parameters.PortParameter" value="">
> + </property>
> + <property name="timeoutSeconds" class="ptolemy.data.expr.Parameter" value="0">
> + </property>
> + <property name="cleanupAfterError" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="thirdParty" class="ptolemy.actor.parameters.PortParameter" value="""">
> + </property>
> +<property name="KeplerDocumentation" class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> +<property name="description" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="author" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Norbert Podhorszki</configure></property>
> +<property name="version" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>1.1 March 2008</configure></property>
> +<property name="userLevelDocumentation" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>
> +
> + <p>The SSHExecuteCmd actor connects to a remote host using SSH protocol and executes a command. If the host is an empty string or "local", the Java
> + Runtime will be used for execution instead of SSH. After the command terminates, the actor returns the stdout, stderr, and exit code of the operation.</p>
> +
> +<p>Set the <i>timeoutSeconds</i> parameter to terminate the command after a specified amount of time. Specify 0 to wait indefinitely for command termination. If connecting to a Unix host, use the <i>cleanupAfterError</i>
> +Parameter to kill the remote process (and all of its children) after an error or timeout. Set this parameter only if connecting to a Unix server (other platforms do not support it).
> +</p>
> +
> +<p>Note: Streaming of output during the command execution is not currently
> + implemented.</p>
> +
> + <p><b>Third party operation.</b>
> + If the remote command is expected to ask for a password
> + (or passphrase when connecting to a remote host with public-key authentication)
> + set the port/parameter <i>thirdParty</i> for the user at host:port of that third party
> + (it can be the same as <i>target</i> if a sudo command is executed).</p>
> +
> + <p>The authentication to the third party should be the same from the target
> + host and from Kepler's local host. Kepler authenticates (by opening a channel)
> + to the third party and then it provides the password/passphrase used for the
> + authentication to the command on the target host. Therefore, this actor cannot be
> + used to reach a remote host through a proxy machine and execute a command there.</p>
> +
> + <p>The third party execution can be used e.g. to execute and ssh/scp command
> + that connects to another host, also reachable from Kepler's host, to execute external
> + data transfer commands (bbcp, GridFTP, SRM-Lite etc) or sudo commands.</p>
> +
> + <p>The actor will first authenticate Kepler to the third party host
> + (if not yet done by other actors, e.g. SshSession). During the execution of the command,
> + it looks for the appearance of the string 'password' or 'passphrase' in the stdout/stderr
> + streams (case-insensitively). If such string is found, it writes the authentication code
> + stored within Kepler used for the authentication. Therefore, the command must read the
> + password on the standard input, not directly from the terminal device.
> + This process is performed only once!</p>
> +
> + <p>The underlying java code does not have pseudo-terminal emulation, so if you cannot
> + force the command to read passwords from the stdin (e.g. scp command), you have to use an
> + external tool to execute the command through a pseudo-terminal. <b>ptyexec</b> is provided
> + in the <i>org.kepler.ssh</i> package, a C program, that should be compiled and put into the path
> + on the target machine. Then you can execute <i>"ptyexec scp ..."</i>. It works on Linux only.</p>
> +
> +</configure></property>
> +<property name="port:stdout" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Output of the command as it would output to the standard shell. If there is an SSH connection related error (or timeout) the value will be an empty string. </configure></property>
> +<property name="port:stderr" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Any errors that were reported by the remote execution or while connecting. If there is an SSH connection related error (or timeout) the value will be an empty string. </configure></property>
> +<property name="port:target" class="ptolemy.kernel.util.ConfigurableAttribute"><configure> The machine to be used at job submission. It should be null, "" or "local" for the local machine or [user@]host to denote a remote machine accessible with SSH. If user is not provided, the local username will be used. If port is not provided, the default port 22 will be applied. This parameter is read once at initialize. </configure></property>
> +<property name="port:command" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The command to be executed on the remote host, specified as a string (e.g., "uname -a; date") </configure></property>
> +<property name="port:exitcode" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The exit code of the command. If there is an SSH connection related error (or timeout) the exitcode will be -32767 </configure></property>
> +<property name="port:errors" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The string representation of actor execution errors, if any.
> + </configure></property>
> +<property name="prop:timeoutSeconds" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Timeout in seconds. The command will be timed out after the specified amount of time. Specify 0 to wait indefinitely for command termination. </configure></property>
> +<property name="prop:streaming mode" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether the output should be sent in a streaming mode.
> + Note: Streaming is not currently implemented.
> + </configure></property>
> +<property name="prop:thirdParty" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The third party machine where the command wants to connect and needs to authenticate. Kepler can be used to do the authentication and then provide the password or private-key passphrase to the command. It should be defined as [user@]host[:port]. </configure></property>
> +<property name="prop:target" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The machine to be used at job submission. It should be null, "" or "local" for the local machine or [user@]host to denote a remote machine accessible with SSH. If user is not provided, the local username will be used. If port is not provided, the default port 22 will be applied. This parameter is read once at initialize. </configure></property>
> +<property name="prop:cleanupAfterError" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Kill remote process(es) after an error or timeout. Set this parameter only if connecting to a Unix server (other platforms do not support it). All processes belonging to the same group as the remote command (i.e., its children) will be killed. </configure></property>
> +</property> <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:506:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.kepler.actor.ssh.ExecuteCmd">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1213:1">
> + </property>
> + </property>
> + <property name="semanticType00" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ExternalExecutionEnvironmentActor">
> + </property>
> + <property name="semanticType21" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#SSH">
> + </property>
> + <property name="semanticType41" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:4:1#CPES">
> + </property>
> + <property name="semanticType22" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#Tutorial">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-45.0, 35.0]">
> + </property>
> + <port name="target" class="ptolemy.actor.parameters.ParameterPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="command" class="ptolemy.actor.TypedIOPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="stdout" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="stderr" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="exitcode" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="errors" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="thirdParty" class="ptolemy.actor.parameters.ParameterPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + </entity>
> + <entity name="Expression" class="ptolemy.actor.lib.Expression">
> + <property name="expression" class="ptolemy.kernel.util.StringAttribute" value=""cp -r s3d_run* "+targetdir">
> + <property name="_hide" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </property>
> +<property name="KeplerDocumentation" class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> +<property name="description" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="author" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Xiaojun Liu, Edward A. Lee, Steve Neuendorffer</configure></property>
> +<property name="version" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="userLevelDocumentation" class="ptolemy.kernel.util.ConfigurableAttribute"><configure><p>The Expression actor evaluates a specified expression (e.g., an addition or multiplication operation), which may reference the values of user-specified input ports, the current time, or the actor's iteration count. The actor outputs the value of the evaluated expression. </p>
> +
> +<p>Expressions are specified in the Ptolemy expression language via the expression parameter. For more information about the expression language, see http://ptolemy.eecs.berkeley.edu/papers/05/ptIIdesign1-intro/ptIIdesign1-intro.pdf. </p>
> +
> +<p>By default, the expression parameter is empty, and attempting to execute the actor without first specifying an expression generates an error. Expressions can refer to the values of inputs by the port name; to the current time by the identifier "time"; and to the current iteration count by the identifier "iteration." </p>
> +
> +<p>Input ports are created by the user and correspond to variables used in the specified expression. Currently, the Expression actor does not support input multiports. The actor requires all of its inputs to be present. If inputs are not all present, then the actor will generate an error. </p>
> +
> +<p>Note: the Expression actor can be used instead of many of the arithmetic actors, such as AddSubtract, MultiplyDivide, and TrigFunction. However, those actors will be usually be more efficient, and sometimes more convenient to use.</p></configure></property>
> +<property name="port:output" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>An output port that broadcasts the value of the evaluated expression. The actor automatically determines the type based on the type of the input.</configure></property>
> +<property name="prop:expression" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>An expression to evaluate. Expressions are specified in the Ptolemy expression language. For more information about the expression language, see http://ptolemy.eecs.berkeley.edu/papers/05/ptIIdesign1-intro/ptIIdesign1-intro.pdf. By default, the parameter is empty, and attempting to execute the actor without first specifying an expression generates an error. Expressions can refer to the values of inputs by the port name; to the current time by the identifier "time"; and to the current iteration count by the identifier "iteration."</configure></property>
> +</property> <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:75:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.Expression">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:950:1">
> + </property>
> + </property>
> + <property name="semanticType00" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#MathOperationActor">
> + </property>
> + <property name="semanticType11" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#GeneralPurpose">
> + </property>
> + <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
> + <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
> + </property>
> + <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
> + </property>
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-270.0, 75.0]">
> + </property>
> + <port name="output" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + </port>
> + <port name="name" class="ptolemy.actor.TypedIOPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="false">
> + </property>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + </port>
> + <port name="targetdir" class="ptolemy.actor.TypedIOPort">
> + <property name="input"/>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + </port>
> + </entity>
> + <relation name="relation2" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <relation name="relation4" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <relation name="relation" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <relation name="relation3" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <link port="StringToken" relation="relation"/>
> + <link port="StringToken [key=target]" relation="relation4"/>
> + <link port="StringToken [key=dirprefix]" relation="relation3"/>
> + <link port="SSH Execute cmd.target" relation="relation4"/>
> + <link port="SSH Execute cmd.command" relation="relation2"/>
> + <link port="Expression.output" relation="relation2"/>
> + <link port="Expression.name" relation="relation"/>
> + <link port="Expression.targetdir" relation="relation3"/>
> + </entity>
> + <entity name="SSH_Submit2Cluster2" class="org.kepler.coactors.CompositeCoactor">
> + <property name="Read scope" class="org.kepler.util.CoactorParameter" value="Job/TempDirNames">
> + </property>
> + <property name="_createdBy" class="ptolemy.kernel.attributes.VersionAttribute" value="7.0.2">
> + </property>
> + <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:ppod.daks.org:composite:100:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.kepler.coactors.CompositeCoactor">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:ppod.daks.org:class:100:1">
> + </property>
> + </property>
> + <property name="semanticType" class="org.kepler.sms.SemanticType" value="urn:lsid:ppod.daks.org:onto:1#ComadGeneralActors">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-235.0, 225.0]">
> + </property>
> + <property name="_windowProperties" class="ptolemy.actor.gui.WindowPropertiesAttribute" value="{bounds={408, 217, 883, 853}, maximized=false}">
> + </property>
> + <property name="_vergilSize" class="ptolemy.actor.gui.SizeAttribute" value="[600, 732]">
> + </property>
> + <property name="_vergilZoomFactor" class="ptolemy.data.expr.ExpertParameter" value="1.0">
> + </property>
> + <property name="_vergilCenter" class="ptolemy.data.expr.ExpertParameter" value="{-316.0, 178.0}">
> + </property>
> + <property name="SDF Director" class="ptolemy.domains.sdf.kernel.SDFDirector">
> + <property name="iterations" class="ptolemy.data.expr.Parameter" value="0">
> + </property>
> + <property name="vectorizationFactor" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + <property name="allowDisconnectedGraphs" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="allowRateChanges" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="constrainBufferSizes" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + <property name="period" class="ptolemy.data.expr.Parameter" value="0.0">
> + </property>
> + <property name="synchronizeToRealTime" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="timeResolution" class="ptolemy.moml.SharedParameter" value="1E-10">
> + </property>
> + <property name="Scheduler" class="ptolemy.domains.sdf.kernel.SDFScheduler">
> + <property name="constrainBufferSizes" class="ptolemy.data.expr.Parameter" value="constrainBufferSizes">
> + </property>
> + </property>
> +<property name="KeplerDocumentation" class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> +<property name="description" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="author" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Steve Neuendorffer</configure></property>
> +<property name="version" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="userLevelDocumentation" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>
> +<p>The SDF Director is often used to oversee fairly simple, sequential workflows in which the director can determine the order of actor invocation from the workflow. Types of workflows that would run well under an SDF Director include processing and reformatting tabular data, converting one data type to another, and reading and plotting a series of data points. A workflow in which an image is read, processed (rotated, scaled, clipped, filtered, etc.), and then displayed, is also an example of a sequential workflow that requires a director simply to ensure that each actor fires in the proper order (i.e., that each actor executes only after it receives its required inputs).</p>
> +
> +<p>The SDF Director is very efficient and will not tax system resources with overhead. However, this efficiency requires that certain conditions be met, namely that the data consumption and production rate of each actor in an SDF workflow be constant and declared. If an actor reads one piece of data and calculates and outputs a single result, it must always read and output a single token of data. This data rate cannot change during workflow execution and, in general, workflows that require dynamic scheduling and/or flow control cannot use this director. Additionally, the SDF Director has no understanding of passing time (at least by default), and actors that depend on a notion of time may not work as expected. For example, a TimedPlotter actor will plot all values at time zero when used in SDF. </p>
> +
> +<p>By default, the SDF Director requires that all actors in its workflow be connected. Otherwise, the director cannot account for concurrency between disconnected workflow parts. Usually, a PN Director should be used for workflows that contain disconnected actors; however, the SDF Director's allowDisconnectedGraphs parameter may also be set to true. The SDF Director will then schedule each disconnected "island" independently. The director cannot infer the sequential relationship between disconnected actors (i.e., nothing forces the director to finish executing all actors on one island before firing actors on another). However, the order of execution within each island should be correct. Usually, disconnected graphs in an SDF model indicate an error.</p>
> +
> +<p>Because SDF Directors schedule actors to fire only after they receive their inputs, workflows that require loops (feeding an actor's output back into its input port for further processing) can cause "deadlock" errors. The deadlock errors occur because the actor depends on its own output value as an initial input. To fix this problem, use a SampleDelay actor to generate and inject an initial input value into the workflow.</p>
> +
> +<p>The SDF Director determines the order in which actors execute and how many times each actor needs to be fired to complete a single iteration of the workflow. This schedule is calculated BEFORE the director begins to iterate the workflow. Because the SDF Director calculates a schedule in advance, it is quite efficient. However, SDF workflows must be static. In other words, the same number of tokens must be consumed/produced at every iteration of the workflow. Workflows that require dynamic control structures, such as a BooleanSwitch actor that sends output on one of two ports depending on the value of a 'control', cannot be used with an SDF Director because the number of tokens on each output can change for each execution.</p>
> +
> +<p>Unless otherwise specified, the SDF Director assumes that each actor consumes and produces exactly one token per channel on each firing. Actors that do not follow the one-token-per-channel firing convention (e.g., Repeat or Ramp) must declare the number of tokens they produce or consume via the appropriate parameters. </p>
> +
> +<p>The number of times a workflow is iterated is controlled by the director's iterations parameter. By default, this parameter is set to "0". Note that "0" does not mean "no iterations." Rather, "0" means that the workflow will iterate forever. Values greater than zero specify the actual number of times the director should execute the entire workflow. A value of 1, meaning that the director will run the workflow once, is often the best setting when building an SDF workflow. </p>
> +
> +<p>The amount of data processed by an SDF workflow is a function of both the number of times the workflow iterates and the value of the director's vectorizationFactor parameter. The vectorizationFactor is used to increase the efficiency of a workflow by increasing the number of times actors fire each time the workflow iterates. If the parameter is set to a positive integer (other than 1), the director will fire each actor the specified number of times more than normal. The default is 1, indicating that no vectorization should be performed. Keep in mind that changing the vectorizationFactor parameter changes the meaning of a nested SDF workflow and may cause deadlock in a workflow that uses it. </p>
> +
> +<p>The SDF Director has several advanced parameters that are generally only relevant when an SDF workflow contains composite components. In most cases the period, timeResolution, synchronizeToRealTime, allowRateChanges, timeResolution, and constrainBufferSizes parameters can be left at their default values.</p>
> +
> +<p>For more information about the SDF Director, see the Ptolemy documentation (http://ptolemy.eecs.berkeley.edu/papers/05/ptIIdesign3-domains/ptIIdesign3-domains.pdf).</p>
> +
> +</configure></property>
> +<property name="prop:allowDisconnectedGraphs" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether to allow disconnected actors in the workflow (by default, all actors are required to be connected). If disconnected actors are permitted, the SDF Director will schedule each disconnected 'island' independently. Nothing "forces" the director to finish executing all actors on one island before firing actors on another. However, the order of execution within each island should be correct. Usually, disconnected graphs in an SDF workflow indicate an error.</configure></property>
> +<property name="prop:allowRateChanges" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether dynamic rate changes are permitted or not. By default, rate changes are not permitted, and the director will perform a check to disallow such workflows. If the parameter is selected, then workflows that require rate parameters to be modified during execution are valid, and the SDF Director will dynamically compute a new schedule at runtime. This is an advanced parameter that can usually be left at its default value.</configure></property>
> +<property name="prop:constrainBufferSizes" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether buffer sizes are fixed. By default, buffers are fixed, and attempts to write to the buffer that cause the buffer to exceed its scheduled size result in an error. This is an advanced parameter that can usually be left at its default value.</configure></property>
> +<property name="prop:timeResolution" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The time precision used by this director. All time values are rounded to the nearest multiple of this number. The value is a double that defaults to "1E-10" (which is 10-10). This is an advanced parameter that can usually be left at its default value.</configure></property>
> +<property name="prop:iterations" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify the number of times a workflow is iterated. By default, this parameter is set to "0". Note that "0" does not mean "no iterations." Rather, "0" means that the workflow will iterate forever. Values greater than zero specify the actual number of times the director should execute the entire workflow. A value of 1, meaning that the director will run the workflow once, is often the best setting when building an SDF workflow. </configure></property>
> +<property name="prop:vectorizationFactor" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The vectorizationFactor is used to increase the efficiency of a workflow by increasing the number of times actors fire each time the workflow iterates. If the parameter is set to a positive integer (other than 1), the director will fire each actor the specified number of times more than normal. The default is 1, indicating that no vectorization should be performed. Keep in mind that changing the vectorizationFactor parameter changes the meaning of a nested SDF workflow and may cause deadlock in a workflow that uses it. </configure></property>
> +<property name="prop:synchronizeToRealTime" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether the execution should synchronize to real time or not. By default, the director does not synchronize to real time. If synchronize is selected, the director will only process the workflow when elapsed real time matches the product of the period parameter and the iteration count. Note: if the period parameter has a value of 0.0 (the default), then selecting this parameter has no effect. This is an advanced parameter that can usually be left at its default value.</configure></property>
> +<property name="prop:period" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The time period of each iteration. The value is a double that defaults to 0.0, which means that the director does not increment workflow time. If the value greater than 0.0, the actor will increment workflow time each time it fires. This is an advanced parameter that can usually be left at its default value. </configure></property>
> +</property> <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:director:1:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.domains.sdf.kernel.SDFDirector">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:directorclass:1:1">
> + </property>
> + </property>
> + <property name="semanticType00" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#Director">
> + </property>
> + <property name="semanticType11" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#Director">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="{-135.0, -50.0}">
> + </property>
> + </property>
> + <port name="input" class="org.kepler.util.CollectionIOPort">
> + <property name="input"/>
> + <property name="dataType" class="ptolemy.kernel.util.StringAttribute" value="general">
> + </property>
> + <property name="isMultiport" class="ptolemy.kernel.util.StringAttribute" value="false">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-410.0, -25.0]">
> + </property>
> + </port>
> + <port name="output" class="org.kepler.util.CollectionIOPort">
> + <property name="output"/>
> + <property name="multiport"/>
> + <property name="dataType" class="ptolemy.kernel.util.StringAttribute" value="unknown">
> + </property>
> + <property name="isMultiport" class="ptolemy.kernel.util.StringAttribute" value="true">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="{105.0, 70.0}">
> + </property>
> + </port>
> + <port name="StringToken" class="org.kepler.util.CollectionIOPort">
> + <property name="input"/>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-450.0, 55.0]">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="NORTH">
> + </property>
> + </port>
> + <port name="StringToken [key=dirprefix]" class="org.kepler.util.CollectionIOPort">
> + <property name="input"/>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="{-555.0, 235.0}">
> + </property>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="NORTH">
> + </property>
> + </port>
> + <port name="StringToken [key=target]" class="org.kepler.util.CollectionIOPort">
> + <property name="input"/>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-310.0, -30.0]">
> + </property>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="NORTH">
> + </property>
> + </port>
> + <port name="StringToken [key=jobscriptlocation]" class="org.kepler.util.CollectionIOPort">
> + <property name="input"/>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-585.0, 105.0]">
> + </property>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="SOUTH">
> + </property>
> + </port>
> + <port name="StringToken [key=targetdir]" class="org.kepler.util.CollectionIOPort">
> + <property name="input"/>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-590.0, 145.0]">
> + </property>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.SingletonParameter" value="true">
> + </property>
> + <property name="_cardinal" class="ptolemy.kernel.util.StringAttribute" value="SOUTH">
> + </property>
> + </port>
> + <entity name="SSH Execute cmd" class="org.kepler.actor.ssh.ExecuteCmd">
> + <property name="target" class="ptolemy.actor.parameters.PortParameter" value="">
> + </property>
> + <property name="timeoutSeconds" class="ptolemy.data.expr.Parameter" value="0">
> + </property>
> + <property name="cleanupAfterError" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="thirdParty" class="ptolemy.actor.parameters.PortParameter" value="""">
> + </property>
> +<property name="KeplerDocumentation" class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> +<property name="description" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="author" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Norbert Podhorszki</configure></property>
> +<property name="version" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>1.1 March 2008</configure></property>
> +<property name="userLevelDocumentation" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>
> +
> + <p>The SSHExecuteCmd actor connects to a remote host using SSH protocol and executes a command. If the host is an empty string or "local", the Java
> + Runtime will be used for execution instead of SSH. After the command terminates, the actor returns the stdout, stderr, and exit code of the operation.</p>
> +
> +<p>Set the <i>timeoutSeconds</i> parameter to terminate the command after a specified amount of time. Specify 0 to wait indefinitely for command termination. If connecting to a Unix host, use the <i>cleanupAfterError</i>
> +Parameter to kill the remote process (and all of its children) after an error or timeout. Set this parameter only if connecting to a Unix server (other platforms do not support it).
> +</p>
> +
> +<p>Note: Streaming of output during the command execution is not currently
> + implemented.</p>
> +
> + <p><b>Third party operation.</b>
> + If the remote command is expected to ask for a password
> + (or passphrase when connecting to a remote host with public-key authentication)
> + set the port/parameter <i>thirdParty</i> for the user at host:port of that third party
> + (it can be the same as <i>target</i> if a sudo command is executed).</p>
> +
> + <p>The authentication to the third party should be the same from the target
> + host and from Kepler's local host. Kepler authenticates (by opening a channel)
> + to the third party and then it provides the password/passphrase used for the
> + authentication to the command on the target host. Therefore, this actor cannot be
> + used to reach a remote host through a proxy machine and execute a command there.</p>
> +
> + <p>The third party execution can be used e.g. to execute and ssh/scp command
> + that connects to another host, also reachable from Kepler's host, to execute external
> + data transfer commands (bbcp, GridFTP, SRM-Lite etc) or sudo commands.</p>
> +
> + <p>The actor will first authenticate Kepler to the third party host
> + (if not yet done by other actors, e.g. SshSession). During the execution of the command,
> + it looks for the appearance of the string 'password' or 'passphrase' in the stdout/stderr
> + streams (case-insensitively). If such string is found, it writes the authentication code
> + stored within Kepler used for the authentication. Therefore, the command must read the
> + password on the standard input, not directly from the terminal device.
> + This process is performed only once!</p>
> +
> + <p>The underlying java code does not have pseudo-terminal emulation, so if you cannot
> + force the command to read passwords from the stdin (e.g. scp command), you have to use an
> + external tool to execute the command through a pseudo-terminal. <b>ptyexec</b> is provided
> + in the <i>org.kepler.ssh</i> package, a C program, that should be compiled and put into the path
> + on the target machine. Then you can execute <i>"ptyexec scp ..."</i>. It works on Linux only.</p>
> +
> +</configure></property>
> +<property name="port:stdout" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Output of the command as it would output to the standard shell. If there is an SSH connection related error (or timeout) the value will be an empty string. </configure></property>
> +<property name="port:stderr" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Any errors that were reported by the remote execution or while connecting. If there is an SSH connection related error (or timeout) the value will be an empty string. </configure></property>
> +<property name="port:target" class="ptolemy.kernel.util.ConfigurableAttribute"><configure> The machine to be used at job submission. It should be null, "" or "local" for the local machine or [user@]host to denote a remote machine accessible with SSH. If user is not provided, the local username will be used. If port is not provided, the default port 22 will be applied. This parameter is read once at initialize. </configure></property>
> +<property name="port:command" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The command to be executed on the remote host, specified as a string (e.g., "uname -a; date") </configure></property>
> +<property name="port:errors" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The string representation of actor execution errors, if any.
> + </configure></property>
> +<property name="port:exitcode" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The exit code of the command. If there is an SSH connection related error (or timeout) the exitcode will be -32767 </configure></property>
> +<property name="prop:timeoutSeconds" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Timeout in seconds. The command will be timed out after the specified amount of time. Specify 0 to wait indefinitely for command termination. </configure></property>
> +<property name="prop:streaming mode" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether the output should be sent in a streaming mode.
> + Note: Streaming is not currently implemented.
> + </configure></property>
> +<property name="prop:thirdParty" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The third party machine where the command wants to connect and needs to authenticate. Kepler can be used to do the authentication and then provide the password or private-key passphrase to the command. It should be defined as [user@]host[:port]. </configure></property>
> +<property name="prop:cleanupAfterError" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Kill remote process(es) after an error or timeout. Set this parameter only if connecting to a Unix server (other platforms do not support it). All processes belonging to the same group as the remote command (i.e., its children) will be killed. </configure></property>
> +<property name="prop:target" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>The machine to be used at job submission. It should be null, "" or "local" for the local machine or [user@]host to denote a remote machine accessible with SSH. If user is not provided, the local username will be used. If port is not provided, the default port 22 will be applied. This parameter is read once at initialize. </configure></property>
> +</property> <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:506:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.kepler.actor.ssh.ExecuteCmd">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:1213:1">
> + </property>
> + </property>
> + <property name="semanticType00" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#ExternalExecutionEnvironmentActor">
> + </property>
> + <property name="semanticType21" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#SSH">
> + </property>
> + <property name="semanticType41" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:4:1#CPES">
> + </property>
> + <property name="semanticType22" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#Tutorial">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="{-35.0, 45.0}">
> + </property>
> + <port name="target" class="ptolemy.actor.parameters.ParameterPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="command" class="ptolemy.actor.TypedIOPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="stdout" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="stderr" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="exitcode" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="errors" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + <port name="thirdParty" class="ptolemy.actor.parameters.ParameterPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="_hide" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </port>
> + </entity>
> + <entity name="Expression" class="ptolemy.actor.lib.Expression">
> + <property name="expression" class="ptolemy.kernel.util.StringAttribute" value=""cp "+jobscriptlocation+" "+targetdir+"/"+dirprefix+name+"/run;"">
> + <property name="_hide" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + </property>
> +<property name="KeplerDocumentation" class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> +<property name="description" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="author" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Xiaojun Liu, Edward A. Lee, Steve Neuendorffer</configure></property>
> +<property name="version" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="userLevelDocumentation" class="ptolemy.kernel.util.ConfigurableAttribute"><configure><p>The Expression actor evaluates a specified expression (e.g., an addition or multiplication operation), which may reference the values of user-specified input ports, the current time, or the actor's iteration count. The actor outputs the value of the evaluated expression. </p>
> +
> +<p>Expressions are specified in the Ptolemy expression language via the expression parameter. For more information about the expression language, see http://ptolemy.eecs.berkeley.edu/papers/05/ptIIdesign1-intro/ptIIdesign1-intro.pdf. </p>
> +
> +<p>By default, the expression parameter is empty, and attempting to execute the actor without first specifying an expression generates an error. Expressions can refer to the values of inputs by the port name; to the current time by the identifier "time"; and to the current iteration count by the identifier "iteration." </p>
> +
> +<p>Input ports are created by the user and correspond to variables used in the specified expression. Currently, the Expression actor does not support input multiports. The actor requires all of its inputs to be present. If inputs are not all present, then the actor will generate an error. </p>
> +
> +<p>Note: the Expression actor can be used instead of many of the arithmetic actors, such as AddSubtract, MultiplyDivide, and TrigFunction. However, those actors will be usually be more efficient, and sometimes more convenient to use.</p></configure></property>
> +<property name="port:output" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>An output port that broadcasts the value of the evaluated expression. The actor automatically determines the type based on the type of the input.</configure></property>
> +<property name="prop:expression" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>An expression to evaluate. Expressions are specified in the Ptolemy expression language. For more information about the expression language, see http://ptolemy.eecs.berkeley.edu/papers/05/ptIIdesign1-intro/ptIIdesign1-intro.pdf. By default, the parameter is empty, and attempting to execute the actor without first specifying an expression generates an error. Expressions can refer to the values of inputs by the port name; to the current time by the identifier "time"; and to the current iteration count by the identifier "iteration."</configure></property>
> +</property> <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:kepler-project.org:actor:75:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="ptolemy.actor.lib.Expression">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:kepler-project.org:class:950:1">
> + </property>
> + </property>
> + <property name="semanticType00" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:1:1#MathOperationActor">
> + </property>
> + <property name="semanticType11" class="org.kepler.sms.SemanticType" value="urn:lsid:localhost:onto:2:1#GeneralPurpose">
> + </property>
> + <property name="_icon" class="ptolemy.vergil.icon.BoxedValueIcon">
> + <property name="attributeName" class="ptolemy.kernel.util.StringAttribute" value="expression">
> + </property>
> + <property name="displayWidth" class="ptolemy.data.expr.Parameter" value="60">
> + </property>
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="[-190.0, 125.0]">
> + </property>
> + <port name="output" class="ptolemy.actor.TypedIOPort">
> + <property name="output"/>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + </port>
> + <port name="name" class="ptolemy.actor.TypedIOPort">
> + <property name="input"/>
> + <property name="_showName" class="ptolemy.data.expr.SingletonParameter" value="false">
> + </property>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + </port>
> + <port name="jobscriptlocation" class="ptolemy.actor.TypedIOPort">
> + <property name="input"/>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + </port>
> + <port name="targetdir" class="ptolemy.actor.TypedIOPort">
> + <property name="input"/>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + </port>
> + <port name="dirprefix" class="ptolemy.actor.TypedIOPort">
> + <property name="input"/>
> + <property name="_type" class="ptolemy.actor.TypeAttribute" value="string">
> + </property>
> + </port>
> + </entity>
> + <relation name="relation2" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <relation name="relation3" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <relation name="relation" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <relation name="relation4" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <relation name="relation5" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <relation name="relation6" class="ptolemy.actor.TypedIORelation">
> + <property name="width" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + </relation>
> + <link port="StringToken" relation="relation"/>
> + <link port="StringToken [key=dirprefix]" relation="relation4"/>
> + <link port="StringToken [key=target]" relation="relation3"/>
> + <link port="StringToken [key=jobscriptlocation]" relation="relation5"/>
> + <link port="StringToken [key=targetdir]" relation="relation6"/>
> + <link port="SSH Execute cmd.target" relation="relation3"/>
> + <link port="SSH Execute cmd.command" relation="relation2"/>
> + <link port="Expression.output" relation="relation2"/>
> + <link port="Expression.name" relation="relation"/>
> + <link port="Expression.jobscriptlocation" relation="relation5"/>
> + <link port="Expression.targetdir" relation="relation6"/>
> + <link port="Expression.dirprefix" relation="relation4"/>
> + </entity>
> + <entity name="SSH_Submit2Cluster3" class="org.kepler.coactors.CompositeCoactor">
> + <property name="Read scope" class="org.kepler.util.CoactorParameter" value="Job/TempDirNames">
> + </property>
> + <property name="_createdBy" class="ptolemy.kernel.attributes.VersionAttribute" value="7.0.2">
> + </property>
> + <property name="entityId" class="org.kepler.moml.NamedObjId" value="urn:lsid:ppod.daks.org:composite:100:1">
> + </property>
> + <property name="class" class="ptolemy.kernel.util.StringAttribute" value="org.kepler.coactors.CompositeCoactor">
> + <property name="id" class="ptolemy.kernel.util.StringAttribute" value="urn:lsid:ppod.daks.org:class:100:1">
> + </property>
> + </property>
> + <property name="semanticType" class="org.kepler.sms.SemanticType" value="urn:lsid:ppod.daks.org:onto:1#ComadGeneralActors">
> + </property>
> + <property name="_location" class="ptolemy.kernel.util.Location" value="{-570.0, 345.0}">
> + </property>
> + <property name="_windowProperties" class="ptolemy.actor.gui.WindowPropertiesAttribute" value="{bounds={260, 153, 883, 853}, maximized=false}">
> + </property>
> + <property name="_vergilSize" class="ptolemy.actor.gui.SizeAttribute" value="[600, 732]">
> + </property>
> + <property name="_vergilZoomFactor" class="ptolemy.data.expr.ExpertParameter" value="1.0">
> + </property>
> + <property name="_vergilCenter" class="ptolemy.data.expr.ExpertParameter" value="{-307.0, 178.0}">
> + </property>
> + <property name="SDF Director" class="ptolemy.domains.sdf.kernel.SDFDirector">
> + <property name="iterations" class="ptolemy.data.expr.Parameter" value="0">
> + </property>
> + <property name="vectorizationFactor" class="ptolemy.data.expr.Parameter" value="1">
> + </property>
> + <property name="allowDisconnectedGraphs" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="allowRateChanges" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="constrainBufferSizes" class="ptolemy.data.expr.Parameter" value="true">
> + </property>
> + <property name="period" class="ptolemy.data.expr.Parameter" value="0.0">
> + </property>
> + <property name="synchronizeToRealTime" class="ptolemy.data.expr.Parameter" value="false">
> + </property>
> + <property name="timeResolution" class="ptolemy.moml.SharedParameter" value="1E-10">
> + </property>
> + <property name="Scheduler" class="ptolemy.domains.sdf.kernel.SDFScheduler">
> + <property name="constrainBufferSizes" class="ptolemy.data.expr.Parameter" value="constrainBufferSizes">
> + </property>
> + </property>
> +<property name="KeplerDocumentation" class="ptolemy.vergil.basic.KeplerDocumentationAttribute">
> +<property name="description" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="author" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Steve Neuendorffer</configure></property>
> +<property name="version" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>null</configure></property>
> +<property name="userLevelDocumentation" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>
> +<p>The SDF Director is often used to oversee fairly simple, sequential workflows in which the director can determine the order of actor invocation from the workflow. Types of workflows that would run well under an SDF Director include processing and reformatting tabular data, converting one data type to another, and reading and plotting a series of data points. A workflow in which an image is read, processed (rotated, scaled, clipped, filtered, etc.), and then displayed, is also an example of a sequential workflow that requires a director simply to ensure that each actor fires in the proper order (i.e., that each actor executes only after it receives its required inputs).</p>
> +
> +<p>The SDF Director is very efficient and will not tax system resources with overhead. However, this efficiency requires that certain conditions be met, namely that the data consumption and production rate of each actor in an SDF workflow be constant and declared. If an actor reads one piece of data and calculates and outputs a single result, it must always read and output a single token of data. This data rate cannot change during workflow execution and, in general, workflows that require dynamic scheduling and/or flow control cannot use this director. Additionally, the SDF Director has no understanding of passing time (at least by default), and actors that depend on a notion of time may not work as expected. For example, a TimedPlotter actor will plot all values at time zero when used in SDF. </p>
> +
> +<p>By default, the SDF Director requires that all actors in its workflow be connected. Otherwise, the director cannot account for concurrency between disconnected workflow parts. Usually, a PN Director should be used for workflows that contain disconnected actors; however, the SDF Director's allowDisconnectedGraphs parameter may also be set to true. The SDF Director will then schedule each disconnected "island" independently. The director cannot infer the sequential relationship between disconnected actors (i.e., nothing forces the director to finish executing all actors on one island before firing actors on another). However, the order of execution within each island should be correct. Usually, disconnected graphs in an SDF model indicate an error.</p>
> +
> +<p>Because SDF Directors schedule actors to fire only after they receive their inputs, workflows that require loops (feeding an actor's output back into its input port for further processing) can cause "deadlock" errors. The deadlock errors occur because the actor depends on its own output value as an initial input. To fix this problem, use a SampleDelay actor to generate and inject an initial input value into the workflow.</p>
> +
> +<p>The SDF Director determines the order in which actors execute and how many times each actor needs to be fired to complete a single iteration of the workflow. This schedule is calculated BEFORE the director begins to iterate the workflow. Because the SDF Director calculates a schedule in advance, it is quite efficient. However, SDF workflows must be static. In other words, the same number of tokens must be consumed/produced at every iteration of the workflow. Workflows that require dynamic control structures, such as a BooleanSwitch actor that sends output on one of two ports depending on the value of a 'control', cannot be used with an SDF Director because the number of tokens on each output can change for each execution.</p>
> +
> +<p>Unless otherwise specified, the SDF Director assumes that each actor consumes and produces exactly one token per channel on each firing. Actors that do not follow the one-token-per-channel firing convention (e.g., Repeat or Ramp) must declare the number of tokens they produce or consume via the appropriate parameters. </p>
> +
> +<p>The number of times a workflow is iterated is controlled by the director's iterations parameter. By default, this parameter is set to "0". Note that "0" does not mean "no iterations." Rather, "0" means that the workflow will iterate forever. Values greater than zero specify the actual number of times the director should execute the entire workflow. A value of 1, meaning that the director will run the workflow once, is often the best setting when building an SDF workflow. </p>
> +
> +<p>The amount of data processed by an SDF workflow is a function of both the number of times the workflow iterates and the value of the director's vectorizationFactor parameter. The vectorizationFactor is used to increase the efficiency of a workflow by increasing the number of times actors fire each time the workflow iterates. If the parameter is set to a positive integer (other than 1), the director will fire each actor the specified number of times more than normal. The default is 1, indicating that no vectorization should be performed. Keep in mind that changing the vectorizationFactor parameter changes the meaning of a nested SDF workflow and may cause deadlock in a workflow that uses it. </p>
> +
> +<p>The SDF Director has several advanced parameters that are generally only relevant when an SDF workflow contains composite components. In most cases the period, timeResolution, synchronizeToRealTime, allowRateChanges, timeResolution, and constrainBufferSizes parameters can be left at their default values.</p>
> +
> +<p>For more information about the SDF Director, see the Ptolemy documentation (http://ptolemy.eecs.berkeley.edu/papers/05/ptIIdesign3-domains/ptIIdesign3-domains.pdf).</p>
> +
> +</configure></property>
> +<property name="prop:allowDisconnectedGraphs" class="ptolemy.kernel.util.ConfigurableAttribute"><configure>Specify whether to allow disconnected actors in the wo