the small flag on the environment line denotes the number of jobs that have completed successfully (return code == 0 or ignored)
On 21/07/16 15:09, Delay Etienne wrote:
> I have forgotten to say ... nothing comes back from the cluster ...
> (the small flag signification ? )
>
> E.
>
> Le 21/07/2016 à 12:21, Mathieu Leclaire a écrit :
>> 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
>>>>
>>>
>>
>>
>
>
>
> _______________________________________________
> 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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