Apparently i need more coffee this morning ... Collaborative editing with pair programming on openmole workflow probably solve this human problem in the future :)
Now, it works, thanks @john ! 2016-11-14 11:54 GMT+01:00 Jonathan Passerat-Palmbach < [email protected]>: > Hey Seb, > > If you go for the first syntax where you copy the whole folder as a > resource to the SystemExecTask, then you need to update the command line to > reflect the actual path to the script: > > bash emergence2/script.sh > > The whole emergence2 folder is copied in the task's working directory so > script.sh is not in the current directory but under emergence2 > > Cheers > J. > > On 14 November 2016 10:35:57 GMT+00:00, sebastien rey coyrehourcq < > [email protected]> wrote: > >> Hi, >> >> I try to run a simple workflow which first replace ${value} into some >> xml template file (parameters.xml), >> and then copy this file into one location in my workdirectory (for >> example */emergence2/models/parameters/*) >> >> The templatefileTask work well, but i have some problem to understand how >> the SystemExecTask works. >> >> I need to embark all the files into */emergence2/ folder *which contain >> scripts.sh and model to run (the second command for my execSystemTask after >> script.sh which copy the file at the good place) , but the task only >> works with *resources += workDirectory / "emergence2/scripts.sh"* and >> not with *resources += workDirectory / "emergence2" * >> >> The *bash script.sh* only display the content of the current directory >> at this moment, so it works. >> >> *The workflow : * >> >> val fileoutput = Val[File] >> val neighboor = Val[String] >> val output = Val[String] >> val error = Val[String] >> >> val templateTask = >> TemplateFileTask(workDirectory / "parameters.xml",fileoutput) set ( >> inputs += neighboor, >> neighboor:= "RandomPairwise" >> ) >> >> val scriptTask = >> SystemExecTask("bash script.sh ${fileoutput}") set ( >> inputs += fileoutput, >> resources += workDirectory / "emergence2/", *//DONT WORKS* >> resources += workDirectory / "emergence2/script.sh", *//WORKS* >> stdOut := output, >> stdErr := error >> ) >> >> templateTask -- scriptTask hook ToStringHook() >> >> *The error : * >> >> org.openmole.core.exception.InternalProcessingError: Error for context >> values in SystemExecTask@497205009 {fileoutput=/home/reyman/.open >> mole/Dunwich/.tmp/c8f5a347-1de3-43ec-aa74-ee2e2fa53afa/ex >> ecutionf38eb62e-844f-403f-a971-934961a362ba/parameters.xml55 >> 7c4e5c-cac4-458b-a5bb-7a9cc2901b6a.tmp, oMSeed=695454068716827435} >> at org.openmole.core.workflow.tools.InputOutputCheck$class.perf >> orm(InputOutputCheck.scala:95) >> at org.openmole.plugin.task.systemexec.SystemExecTask.perform( >> SystemExecTask.scala:71) >> at org.openmole.core.workflow.task.Task$class.perform(Task.scala:39) >> at org.openmole.plugin.task.systemexec.SystemExecTask.perform( >> SystemExecTask.scala:71) >> at org.openmole.core.workflow.job.MoleJob.perform(MoleJob.scala:101) >> at org.openmole.core.workflow.execution.local.LocalExecutor$$ >> anonfun$1$$anonfun$apply$1.apply(LocalExecutor.scala:85) >> at org.openmole.core.workflow.execution.local.LocalExecutor$$ >> anonfun$1$$anonfun$apply$1.apply(LocalExecutor.scala:64) >> at scala.collection.immutable.List.foreach(List.scala:381) >> at org.openmole.core.workflow.execution.local.LocalExecutor$$ >> anonfun$1.apply(LocalExecutor.scala:64) >> at org.openmole.core.workflow.execution.local.LocalExecutor$$ >> anonfun$1.apply(LocalExecutor.scala:61) >> at org.openmole.core.output.OutputManager$.withStreamOutputs(Ou >> tputManager.scala:99) >> at org.openmole.core.workflow.execution.local.LocalExecutor.wit >> hRedirectedOutput(LocalExecutor.scala:136) >> at org.openmole.core.workflow.execution.local.LocalExecutor.run >> (LocalExecutor.scala:61) >> at java.lang.Thread.run(Thread.java:745) >> >> *Caused by: org.openmole.core.exception.In >> <http://org.openmole.core.exception.In>ternalProcessingError: Error >> executing command"}:[bash script.sh >> /home/reyman/.openmole/Dunwich/.tmp/c8f5a347-1de3-43ec-aa74-ee2e2fa53afa/executionf38eb62e-844f-403f-a971-934961a362ba/parameters.xml557c4e5c-cac4-458b-a5bb-7a9cc2901b6a.tmp] >> return code was not 0 but 127* >> >> *Any idea ?* >> >> --- >> Sébastien Rey Coyrehourcq >> Research Engineer, BAP E, UMR IDEES >> Sent from Nylas N1 <https://nylas.com/n1?ref=n1>, the extensible, open >> source mail client. >> >> ------------------------------ >> >> OpenMOLE-users mailing list >> [email protected] >> http://fedex.iscpif.fr/mailman/listinfo/openmole-users >> >> > -- > Jonathan Passerat-Palmbach, PhD > Research Associate > Department of Computing > Imperial College London > > South Kensington Campus > Huxley Building - room 344 > 180 Queen's Gate > London SW7 2AZ > -- <http://stackoverflow.com/users/385881/reyman64>
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