1.
2. Workflow Editor
Workflow Editor allows to analyse the workflow's (e.g. ETS) Code Parameters.
Each actor with Code Parameters can store them inside workflow file (XML).
You can easily get these parameters by calling workflow-editor with proper arguments.
To use the tool, you need to load module workflow-editor
> module load workflow-editor
2.1. Getting help
To get basic overview of available options call workflow-editor with help argument
> usage: workflow-editor -help print this message -actors list all actors with Code Parameters -version print the version information and exit -workflow <file> analyze this workflow file -output <file> name of the output workflow -actor <actorname> name of the actor we will retrieve -xml list Code Parameters for actor -dxml list default Code Parameters for actor -xsd list XSD definition of Code Parameters for actor -validate <dest> validate with [workflow|kepler] -actorxml show XML Code Parameters inside actor -actorxsd show XSD Code Parameters inside actor -actordxml show Default XML Code Parameters inside actor -updatexml update XML inside workflow using actor's version -updatexsd update XSD inside workflow using actor's version -updatedxml update default XML inside workflow using actor's version
2.2. Listing actors inside workflow
You can get the list of all actors that have Code Parameters by calling workflow-editor with "-actors" argument (remember to pass workflow as well)
> workflow-editor -actors -workflow workflow_ets.xml 12:29:25.267 [main] INFO pl.psnc.kepler.commands.CommandGetActors - WEILAND - eu.itm.TCIWEILAND.TCIWEILAND 12:29:25.269 [main] INFO pl.psnc.kepler.commands.CommandGetActors - emeq_inside_simple_init - eu.itm.emeq.emeq 12:29:25.269 [main] INFO pl.psnc.kepler.commands.CommandGetActors - addICant - eu.itm.addICant.addICant 12:29:25.269 [main] INFO pl.psnc.kepler.commands.CommandGetActors - spider_inside_consistent_init - eu.itm.spider.spider 12:29:25.270 [main] INFO pl.psnc.kepler.commands.CommandGetActors - TGLF - eu.itm.TCITGLF.TCITGLF 12:29:25.270 [main] INFO pl.psnc.kepler.commands.CommandGetActors - chease - eu.itm.chease.chease 12:29:25.270 [main] INFO pl.psnc.kepler.commands.CommandGetActors - TORAYFOM - eu.itm.TORAYFOM.TORAYFOM 12:29:25.270 [main] INFO pl.psnc.kepler.commands.CommandGetActors - synchrotron_cytran - eu.itm.synchrotron_cytran.synchrotron_cytran 12:29:25.270 [main] INFO pl.psnc.kepler.commands.CommandGetActors - GLF23 - eu.itm.TCIGLF23.TCIGLF23 12:29:25.270 [main] INFO pl.psnc.kepler.commands.CommandGetActors - QLK - eu.itm.TCIQLK.TCIQLK 12:29:25.270 [main] INFO pl.psnc.kepler.commands.CommandGetActors - icdept - eu.itm.icdept.icdept 12:29:25.270 [main] INFO pl.psnc.kepler.commands.CommandGetActors - EDWM - eu.itm.TCIEDWM.TCIEDWM 12:29:25.270 [main] INFO pl.psnc.kepler.commands.CommandGetActors - afsi - eu.itm.afsi.afsi 12:29:25.270 [main] INFO pl.psnc.kepler.commands.CommandGetActors - ntmets - eu.itm.ntmets.ntmets 12:29:25.270 [main] INFO pl.psnc.kepler.commands.CommandGetActors - SOURCE_COMBINER - eu.itm.sourcecombiner.sourcecombiner 12:29:25.270 [main] INFO pl.psnc.kepler.commands.CommandGetActors - impuritymanipulator - eu.itm.impuritymanipulator.impuritymanipulator 12:29:25.270 [main] INFO pl.psnc.kepler.commands.CommandGetActors - ascot4parallel - eu.itm.ascot4parallel.ascot4parallel 12:29:25.270 [main] INFO pl.psnc.kepler.commands.CommandGetActors - emeq_inside_consistent_init - eu.itm.emeq.emeq 12:29:25.270 [main] INFO pl.psnc.kepler.commands.CommandGetActors - NCLASS - eu.itm.TCINCLASSZ.TCINCLASSZ 12:29:25.270 [main] INFO pl.psnc.kepler.commands.CommandGetActors - toric - eu.itm.toric.toric 12:29:25.271 [main] INFO pl.psnc.kepler.commands.CommandGetActors - EDWMZ - eu.itm.TCIEDWMZ.TCIEDWMZ 12:29:25.271 [main] INFO pl.psnc.kepler.commands.CommandGetActors - nemo - eu.itm.nemo.nemo 12:29:25.271 [main] INFO pl.psnc.kepler.commands.CommandGetActors - MMM - eu.itm.TCIMMM.TCIMMM 12:29:25.271 [main] INFO pl.psnc.kepler.commands.CommandGetActors - lion - eu.itm.LIONslice.LIONslice 12:29:25.271 [main] INFO pl.psnc.kepler.commands.CommandGetActors - pellettrigger - eu.itm.pellettrigger.pellettrigger 12:29:25.271 [main] INFO pl.psnc.kepler.commands.CommandGetActors - cyrano-in-loop - eu.itm.Cyrano.Cyrano 12:29:25.271 [main] INFO pl.psnc.kepler.commands.CommandGetActors - spot - eu.itm.spot.spot 12:29:25.271 [main] INFO pl.psnc.kepler.commands.CommandGetActors - teffcvg - eu.itm.teffcvg.teffcvg 12:29:25.271 [main] INFO pl.psnc.kepler.commands.CommandGetActors - deltacombiner - eu.itm.deltacombiner.deltacombiner 12:29:25.271 [main] INFO pl.psnc.kepler.commands.CommandGetActors - StixReDist - eu.itm.StixReDist.StixReDist 12:29:25.271 [main] INFO pl.psnc.kepler.commands.CommandGetActors - ascot4serial - eu.itm.ascot4serial.ascot4serial 12:29:25.271 [main] INFO pl.psnc.kepler.commands.CommandGetActors - nuclearsim - eu.itm.nuclearsim.nuclearsim 12:29:25.271 [main] INFO pl.psnc.kepler.commands.CommandGetActors - sawcrash - eu.itm.sawcrash.sawcrash 12:29:25.271 [main] INFO pl.psnc.kepler.commands.CommandGetActors - spider_inside_simple_init - eu.itm.spider.spider 12:29:25.271 [main] INFO pl.psnc.kepler.commands.CommandGetActors - IMP4imp - eu.itm.IMP4imp.IMP4imp 12:29:25.271 [main] INFO pl.psnc.kepler.commands.CommandGetActors - nbisim - eu.itm.nbisim.nbisim 12:29:25.271 [main] INFO pl.psnc.kepler.commands.CommandGetActors - hcd2coresource - eu.itm.hcd2coresource.hcd2coresource 12:29:25.271 [main] INFO pl.psnc.kepler.commands.CommandGetActors - gray - eu.itm.gray.gray 12:29:25.272 [main] INFO pl.psnc.kepler.commands.CommandGetActors - RELAX - eu.itm.RELAX.RELAX 12:29:25.272 [main] INFO pl.psnc.kepler.commands.CommandGetActors - gaussiansources - eu.itm.gausiansources.gausiansources 12:29:25.272 [main] INFO pl.psnc.kepler.commands.CommandGetActors - nbisim2 - eu.itm.nbisim2.nbisim2 12:29:25.272 [main] INFO pl.psnc.kepler.commands.CommandGetActors - RITM - eu.itm.TCIRITM.TCIRITM 12:29:25.272 [main] INFO pl.psnc.kepler.commands.CommandGetActors - addECant - eu.itm.addECant.addECant 12:29:25.272 [main] INFO pl.psnc.kepler.commands.CommandGetActors - checktearing - eu.itm.checktearing.checktearing 12:29:25.272 [main] INFO pl.psnc.kepler.commands.CommandGetActors - hcd2corefast - eu.itm.hcd2corefast.hcd2corefast 12:29:25.272 [main] INFO pl.psnc.kepler.commands.CommandGetActors - pelletactor - eu.itm.pelletactor.pelletactor 12:29:25.272 [main] INFO pl.psnc.kepler.commands.CommandGetActors - sawupdate - eu.itm.sawupdate.sawupdate 12:29:25.272 [main] INFO pl.psnc.kepler.commands.CommandGetActors - cyrano - eu.itm.Cyrano.Cyrano 12:29:25.272 [main] INFO pl.psnc.kepler.commands.CommandGetActors - ntmDeffTLets - eu.itm.ntmDeffTLets.ntmDeffTLets 12:29:25.272 [main] INFO pl.psnc.kepler.commands.CommandGetActors - cece - eu.itm.cece.cece 12:29:25.272 [main] INFO pl.psnc.kepler.commands.CommandGetActors - sawcrit - eu.itm.sawcrit.sawcrit 12:29:25.272 [main] INFO pl.psnc.kepler.commands.CommandGetActors - chease_inside_consistent_init - eu.itm.chease.chease 12:29:25.272 [main] INFO pl.psnc.kepler.commands.CommandGetActors - nbifiller - eu.itm.nbifiller.nbifiller 12:29:25.272 [main] INFO pl.psnc.kepler.commands.CommandGetActors - NEO - eu.itm.TCINEO.TCINEO 12:29:25.272 [main] INFO pl.psnc.kepler.commands.CommandGetActors - risk - eu.itm.risk.risk 12:29:25.273 [main] INFO pl.psnc.kepler.commands.CommandGetActors - emeq - eu.itm.emeq.emeq 12:29:25.273 [main] INFO pl.psnc.kepler.commands.CommandGetActors - travis - eu.itm.travis.travis 12:29:25.273 [main] INFO pl.psnc.kepler.commands.CommandGetActors - spider - eu.itm.spider.spider 12:29:25.273 [main] INFO pl.psnc.kepler.commands.CommandGetActors - chease_inside_simple_init - eu.itm.chease.chease 12:29:25.273 [main] INFO pl.psnc.kepler.commands.CommandGetActors - BgB_JETTO_Particles - eu.itm.BgB_JETTO_Particles.BgB_JETTO_Particles 12:29:25.273 [main] INFO pl.psnc.kepler.commands.CommandGetActors - lion-in-loop - eu.itm.LIONslice.LIONslice
2.3. Retrieving XML/Default XML/XSD for actor
Once you have the name of the actor, you can list it's Code Parameters
# User's Code Parameters
> workflow-editor -xml -actor risk -workflow workflow_ets.xml
<?xml version="1.0" encoding="UTF-8"?>
<?jaxfront version=2.66;time=2014-10-28 17:14:54.425?>
<parameters xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<n_out_profiles>20</n_out_profiles>
<dx_resolution>0.02</dx_resolution>
<fac_implicit>0.7</fac_implicit>
<debug_mode>0</debug_mode>
</parameters>
# Default Code Parameters
> workflow-editor -dxml -actor risk -workflow workflow_ets.xml
<?xml version="1.0" encoding="UTF-8"?>
<parameters>
<!-- Resolution of the output 1D-profiles -->
<n_out_profiles> 30 </n_out_profiles>
<!-- Normalized velocity resolution (v/vth) -->
<dx_resolution> 0.01 </dx_resolution>
<!-- Implicit/explicit contribution for integration scheme (Crank-Nicholson or so) -->
<fac_implicit> 0.7 </fac_implicit>
</parameters>
# XSD based definition of Code Parameters
> workflow-editor -xsd -actor risk -workflow workflow_ets.xml
<?xml version="1.0" encoding="UTF-8"?>
<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"
elementFormDefault="qualified">
<xs:annotation>
<xs:documentation>Code parameters for Risk (Fokker-Planck code)</xs:documentation>
</xs:annotation>
<xs:simpleType name="integer_minInclusive_2">
<xs:restriction base="xs:integer">
<xs:minInclusive value="2"/>
</xs:restriction>
</xs:simpleType>
<xs:simpleType name="float_minInclusive_dot0001">
<xs:restriction base="xs:float">
<xs:minInclusive value="0.0001"/>
</xs:restriction>
</xs:simpleType>
<xs:simpleType name="float_minInclusive_dot1">
<xs:restriction base="xs:float">
<xs:minInclusive value="0.1"/>
</xs:restriction>
</xs:simpleType>
<!-- document element -->
<xs:element name="parameters">
<xs:complexType>
<xs:all>
<xs:element ref="n_out_profiles" minOccurs="0"/>
<xs:element ref="dx_resolution" minOccurs="0"/>
<xs:element ref="fac_implicit" minOccurs="0"/>
</xs:all>
</xs:complexType>
</xs:element>
<!-- Resolution of the output 1D profiles -->
<xs:element name="n_out_profiles" type="integer_minInclusive_2">
<xs:annotation>
<xs:documentation>Resolution of the output 1D profiles</xs:documentation>
</xs:annotation>
</xs:element>
<!-- Normalized velocity resolution (v/vth) -->
<xs:element name="dx_resolution" type="float_minInclusive_dot0001">
<xs:annotation>
<xs:documentation>Normalized velocity resolution (v/vth)</xs:documentation>
</xs:annotation>
</xs:element>
<!-- Implicit/explicit contribution for integration scheme (Crank-Nicholson or so) -->
<xs:element name="fac_implicit" type="float_minInclusive_dot1">
<xs:annotation>
<xs:documentation>Implicit/explicit contribution for integration scheme (Crank-Nicholson or so)</xs:documentation>
</xs:annotation>
</xs:element>
</xs:schema>
You can combine command (e.g. get everything at once)
workflow-editor -xsd -xml -dxml -actor risk -workflow workflow_ets.xml
2.4. Getting Code Parameters from actor (installed inside Kepler)
It may happen that Code Parameters inside actor's code (inside Kepler) differ from data stored inside workflow. This can happen whenever you try to open workflow with more recent version of Kepler.
You can retrieve information about Code Parameters inside actor by calling workflow-editor with -actorxml/-actordxml/-actorxsd.
Note that getting information from actors requires recompilation of the actor. Getting information regarding Code Parameters is a new feature in FC2K and will not work for old actors (e.g. imported into Kepler using import_actor).
> workflow-editor -actorxsd -actor nocpoparam -workflow workflow.xml
<?xml version="1.0" encoding="utf-8"?>
<!-- RFOF code parameters XML schema -->
<xs:schema
xmlns:xs="http://www.w3.org/2001/XMLSchema"
elementFormDefault="qualified">
<xs:simpleType name="FloatList">
<xs:list itemType="xs:float"/>
</xs:simpleType>
<xs:simpleType name="IntegerList">
<xs:list itemType="xs:integer"/>
</xs:simpleType>
<xs:simpleType name="BooleanList">
<xs:list itemType="xs:boolean"/>
</xs:simpleType>
<xs:element name="parameters">
<xs:complexType>
<xs:all>
<xs:element ref="r"/>
<xs:element ref="i"/>
<xs:element ref="boolean"/>
<xs:element ref="realVec"/>
<xs:element ref="intVec"/>
<xs:element ref="booleanVec"/>
</xs:all>
</xs:complexType>
</xs:element>
<xs:element name="r" type="xs:float">
<xs:annotation>
<xs:documentation>A real value</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="i" type="xs:integer">
<xs:annotation>
<xs:documentation>An integer number</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="boolean" type="xs:boolean">
<xs:annotation>
<xs:documentation>An integer number</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="realVec" type="FloatList">
<xs:annotation>
<xs:documentation>A real valued vector</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="intVec" type="IntList">
<xs:annotation>
<xs:documentation>An integer valued vector</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="booleanVec" type="BooleanList">
<xs:annotation>
<xs:documentation>An boolean valued vector</xs:documentation>
</xs:annotation>
</xs:element>
</xs:schema>
Note that you need to pass workflow as well. This is related to the fact that you can have multiple actors (inside workflow) that are actually pointing to the very same actor's code inside Kepler.
2.5. Replacing Batch Submission Scripts inside workfow
Whenever actor is put on canvas it takes all the parameters from the actor that is currently installed inside Kepler. This may lead to divergence between workflow and Kepler installation. Typical use-case where you may experience issues:
- create actor for Gateway
- put MPI (batch) based actor on canvas
- transfer workflow to JET
- there is an issue - Gateway's based submission system differs from JET's, so does the content of workflow (embedded batch submission script).
With new release of workflow-editor it's possible to update workflow such way it reflects the batch script from Kepler installation you want to use.
> module load workflow-editor/rc > ./bin/workflow-editor \ -updatebatch \ -actor nocpompibatch \ -workflow `pwd`/workflow.xml \ -output workflow_out.xml 11:41:16.558 [main] INFO pl.psnc.kepler.CLIParse - Parsing XML file 11:41:16.591 [main] INFO pl.psnc.kepler.CLIParse - Creating Kepler based workflow 11:41:16.943 [main] INFO pl.psnc.kepler.commands.CommandUpdateActorBatchScript - I have found batch script for actor: nocpompibatch
there is also a possibility to pass batch script from the file. In this case, you can set the value inside workflow to whatever you like. This is useful in case you have some custom settings inside batch script.
> module load workflow-editor/rc > ./bin/workflow-editor \ -updatebatch \ -actor nocpompibatch \ -batchfile `pwd`/new_script.txt \ -workflow `pwd`/workflow.xml \ -output workflow_out.xml 11:41:16.558 [main] INFO pl.psnc.kepler.CLIParse - Parsing XML file 11:41:16.591 [main] INFO pl.psnc.kepler.CLIParse - Creating Kepler based workflow 11:41:16.943 [main] INFO pl.psnc.kepler.commands.CommandUpdateActorBatchScript - I have found batch script for actor: nocpompibatch
2.6. Helper script for listing all "broken" actors inside workflow file
It may happen that workflow contains inconsistent Code Parameters for an actor. For example, XML doesn't conform to XSD stored inside workflow. You can make bulk check of workflow by creating wrapper script.
make sure to save this script in $HOME/bulk_check.sh
#!/bin/bash
while read p; do
echo "----- Validating actor: ${p} -----"
./bin/workflow-editor -validate -workflow $1 -actor ${p}
echo "----------------------"
done <$2
To make it work, you will also need list of all actors that belong to workflow and have Code Parameters.
# I assume that you have file "workflow_ets.xml" inside your $HOME > workflow-editor -actors -workflow ~/workflow_ets.xml | cut -f2 -d "-" > ~/actors_to_check > chmod +x $HOME/bulk_check.sh > $HOME/bulk_check.sh $HOME/workflow_ets.xml $HOME/actors_to_check
After running this script you will get the list of all actors that have some sort of issues related to XSD vs. XML inside Code Parameters.
2.7. Further development
There are few more features that have to be developed to make the tool more useful
- diff functionality for XML files (comparison of XML inside workflow and XML inside actor)
- storing new XML inside workflow
- at the moment, XML stored inside workflow is always treated as most recent one
- in case changes inside XSD/XML, in the actor, we may end up with situation where XML stored inside workflow is incompatible with required format
- we can't easily update this information (note that there were different solutions suggested but no final decision was taken)
- it's possible to use Kepler's parsing engine to update information inside workflow "as it would be modified by Kepler
DONE: there will be new feature that will allow to "inject" new code parameters into workflow
workflow-editor -updatexml file.xml -workflow ~/workflow_ets.xml -actor name_of_the_actor
- DONE: replacing XML inside workflow with one taken from actor (similar to step above, but source of the xml file will be different)
- DONE: validation of workflow's XML against actor's XSD
- this feature will allow us to determine whether code parameters inside workflow make any sense when it comes to actor's requirements
- it will allow to verify workflow's compatibility against different releases of Kepler + actors
- error handling
- at the moment, errors are not handled in nice, user friendly way - i need to fix that
- proper handling of missing actor inside workflow
- proper handling of missing actor inside Kepler
- proper handling of actor that was not generated with new FC2K features (extracted code parameters)
- helper scripts
- DONE: listing all the actors that are "broken"
- DONE: extracting XSD/XML/Default XML from workflow in human readable format (all at once)
- adding feature that will allow to analyze Kepler installaion
- list all ITM/IMAS based actors
- validate all the actors inside Kepler
- removing XSD/Default XML from workflow
- at the moment, situation is very unclear when it comes to code parameters - we are mixing sources of information
- Code Parameters (modified by user) are taken from Workflow
- XSD is always taken from actor
- Code Parameters for new actor (dropped on canvas) are taken from actor's code
- this may lead to situation where two instances of the same actor have completely different sets of parameters
- The only reasonable thing we should keep in workflow are modified code parameters (we have now ability to validate them)
- It makes no sense to keep XSD
- It makes no sense to keep Default XML
- We can introduce XML validation into workflow execution
- Once workflow is started, each and every actor that has code parameters can validate whether parameters make sense
- In case parameters are not valid we can inform user that something fishy is going on
- we need further modifications of FC2K so we can mix up actors
- at the moment, workflow-editor is not able to determine whether actor supports new functionalities or not - it blindly assumes that actors were generated using new FC2K
- i need to extend actors such way workflow-editor is capable of checking whether actor supports CodeParameters in new fashion or not