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 ?
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--
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
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_______________________________________________
OpenMOLE-users mailing list
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http://fedex.iscpif.fr/mailman/listinfo/openmole-users
