Hi Etienne,
On 19/07/16 14:15, Delay Etienne wrote: > Hoho > Nice Romain ! True ... It doesn't embed files in: > > r_run_netlogo/rootfs/home/delaye/github/projet42/nlogo/data/maps_space/ > > Any ideas how to do that ? I have found the manual > https://github.com/proot-me/PRoot/blob/master/doc/care/manual.txt you can also check the OpenMOLE specific documentation here: http://next.openmole.org/Documentation_Language_Tasks_Native.html > > so my care command look like that : > > ./care-x86_64 -r /home/delaye/github/projet42/nlogo/data/maps_agents/* > -r /home/delaye/github/projet42/nlogo/data/maps_space/ -r > /home/delaye/github/projet42/nlogo/data/ -r > /home/delaye/github/projet42/netlogo-5.3.1-64/app/ -o > r_run_netlogo.tar.gz.bin R --slave -f netlogo_run.R --args 4 > > But it doesn't take care of files in > /home/delaye/github/projet42/nlogo/data/maps_space/ .... > - from which directory are you running this command (pwd)? - stupid question, but are you sure that this R + netlogo code accesses /home/delaye/github/projet42/nlogo/data/maps_space? one thing that can happen is if your code checks the presence of generated results before running, then it could be that nothing is actually executed when CARE packages your code, so maps_space ends up never being accessed Cheers J. > E. > > > Le 19/07/2016 à 15:06, Romain Reuillon a écrit : >> Hi Etienne, >> >> do you manage to reexecute you CARE archive outside of openmole ? You >> may try it by running ./carearchivename.tgz.bin >> >> Romain >> >> Le 19/07/2016 à 15:00, Delay Etienne a écrit : >>> After some investigation ... It seems to be care my problem ... >>> >>> OpenMole said : Java-Object{org.nlogo.nvm.EngineException: The file >>> /home/delaye/github/projet42/nlogo/data/maps_agents/input_agents_100_10_.txt >>> >>> cannot be found}" >>> >>> So how to specify in Care to embed recursively directory and files ? >>> >>> E. >>> >>> Le 19/07/2016 à 14:12, Delay Etienne a écrit : >>>> Hi all, >>>> Today I'm trying to run an R script that embeds and command >>>> NetLogo. It >>>> seems tricky to configure with Care and I need a hand ... >>>> >>>> first of all OpenMole send me that : >>>> >>>> org.openmole.core.exception.InternalProcessingError: Error for context >>>> values in CARETask@-208567776 {i=10, oMSeed=-1969014527224670348} >>>> at >>>> org.openmole.core.workflow.tools.InputOutputCheck$class.perform(InputOutputCheck.scala:94) >>>> >>>> >>>> >>>> at >>>> org.openmole.plugin.task.care.CARETask.perform(CARETask.scala:71) >>>> at >>>> org.openmole.core.workflow.task.Task$class.perform(Task.scala:59) >>>> at >>>> org.openmole.plugin.task.care.CARETask.perform(CARETask.scala:71) >>>> at >>>> org.openmole.core.workflow.job.MoleJob.perform(MoleJob.scala:102) >>>> at >>>> org.openmole.core.workflow.execution.local.LocalExecutor$$anonfun$1$$anonfun$apply$1.apply(LocalExecutor.scala:82) >>>> >>>> >>>> >>>> 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(OutputManager.scala:99) >>>> >>>> >>>> >>>> at >>>> org.openmole.core.workflow.execution.local.LocalExecutor.withRedirectedOutput(LocalExecutor.scala:128) >>>> >>>> >>>> >>>> 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.InternalProcessingError: Error >>>> executing command": >>>> [./re-execute.sh R --slave -f netlogo_run.R --args 10] return code was >>>> not 0 but 1 >>>> at >>>> org.openmole.plugin.task.care.CARETask$$anonfun$process$1.apply(CARETask.scala:159) >>>> >>>> >>>> >>>> at >>>> org.openmole.plugin.task.care.CARETask$$anonfun$process$1.apply(CARETask.scala:93) >>>> >>>> >>>> >>>> at >>>> org.openmole.plugin.task.external.External.withWorkDir(External.scala:176) >>>> >>>> >>>> at >>>> org.openmole.plugin.task.care.CARETask.process(CARETask.scala:93) >>>> at >>>> org.openmole.core.workflow.task.Task$$anonfun$perform$1.apply(Task.scala:59) >>>> >>>> >>>> >>>> at >>>> org.openmole.core.workflow.task.Task$$anonfun$perform$1.apply(Task.scala:59) >>>> >>>> >>>> >>>> at >>>> org.openmole.core.workflow.tools.InputOutputCheck$class.perform(InputOutputCheck.scala:91) >>>> >>>> >>>> >>>> ... 13 more >>>> >>>> In attachment you can find my oms file and my script R . >>>> >>>> Someone has ever played in this situation ? >>>> >>>> >>>> _______________________________________________ >>>> OpenMOLE-users mailing list >>>> [email protected] >>>> http://fedex.iscpif.fr/mailman/listinfo/openmole-users >>>> >>> >> >> >> >> >> _______________________________________________ >> 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
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