Hi Etienne, did you click on update in the env detail to get a listing of the errors ?
Romain Le 21/07/2016 à 10:41, Delay Etienne a écrit : > Hi all, hi Jonathan, > Ok after taking a look yesterday on your fork ... I have taken another > way ... I'm using the Rdata format ... and with a "traditional" Care > use ... It works on my localhost > > This morning I'm on the SLURMenvironnement ... and it seems to work > but not totally . In the execution GUI ... the small flame and the > number associated is not a good sign (c.f. attachment)? > > How can I have information about what is going wrong ? > > E. > > Le 20/07/2016 à 11:57, Jonathan Passerat-Palmbach a écrit : >> Actually the rearchiver script might not be the best option for you. >> It's more intended to modify a script in the archive, for example add a >> line to your R script. >> >> It looks that your maps_space could be provided as a resource to the >> CARETask, similarly to how you can do it to ship a common piece of code >> or data to the other tasks. You can specify the path where it should >> appear at re-execution, OpenMOLE will do the path translation for you. >> >> If it varies with the parallel instances of the task, maybe it's more an >> inputFiles though. >> >> On 20 July 2016 10:28:09 BST, Etienne DELAY >> <[email protected]> wrote: >> >> Hi Jonathan, >> It's exactly what append ! I have got a csv table with 1440 path >> needed >> for my exploration ... >> >> When I run >> >> ./care-x86_64 -r /opt/netlogo-5.3.1-64/app/ -r >> /home/delaye/github/projet42/nlogo/data/ -r >> /home/delaye/github/projet42/nlogo/data/maps_space/ -r >> /home/delaye/github/projet42/nlogo/data/maps_agents/ -o >> myscript.tar.gz.bin R --slave -f netlogo_run.R --args 4 >> >> It only embeds line 4 of my table (--args 4) to all my CSV files in >> "/home/delaye/github/projet42/nlogo/data/maps_space/" aren't red >> by care ... >> >> Is there an elegant way to force care to embed all files in a >> directory ? >> >> E. >> >> Cordialement >> >> Etienne DELAY >> Chaire: Capital environnemental et gestion durable des cours d'eau >> laboratoire GEOLAB UMR 6042 CNRS >> Université de Limoges, FLSH >> 39E rue Camille Guérin 87036 Limoges >> blog : http://elcep.legtux.org >> >> Le 19/07/2016 à 18:36, Jonathan Passerat-Palmbach a écrit : >> >> 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 tha t 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 <http://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 >> >> >> >> >> ------------------------------------------------------------------------ >> >> 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 > > > > _______________________________________________ > OpenMOLE-users mailing list > [email protected] > http://fedex.iscpif.fr/mailman/listinfo/openmole-users
signature.asc
Description: OpenPGP digital signature
_______________________________________________ OpenMOLE-users mailing list [email protected] http://fedex.iscpif.fr/mailman/listinfo/openmole-users
