In the listing window you can also get the standard error output. (You should also update openmole since a bug concernig the preferences as been fixed yesterday, it will avoid filling the space on your cluster....)
Le 21/07/2016 à 11:27, Delay Etienne a écrit :
> :-) haha verbose mode !
>
> org.openmole.core.exception.InternalProcessingError: Error for context
> values in CARETask@-2074200986 {i3=15, i4=2, i5=9,
> oMSeed=1496850577635224077}
> 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.workflow.execution.local.LocalExecutor.withRedirectedOutput(LocalExecutor.scala:131)
> 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_grid.R --args 15 2 9] 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)
> ... 12 more
>
>
> Le 21/07/2016 à 10:46, Romain Reuillon a écrit :
>> 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
>>
>>
>>
>>
>> _______________________________________________
>> 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
