next.openmole.org
Le 21/07/2016 à 12:18, Delay Etienne a écrit :
> Is there some binary for the last version of Openmole ?
>
> E.
>
> Le 21/07/2016 à 11:31, Romain Reuillon a écrit :
>> 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
>>>>
>>>
>>
>>
>>
>>
>> _______________________________________________
>> OpenMOLE-users mailing list
>> [email protected]
>> http://fedex.iscpif.fr/mailman/listinfo/openmole-users
>>
>
--
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