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 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
>>
>>
>>
>> _______________________________________________
>> 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
