@Jonathan and Romain Thank you for this explanation. So if I have 1123
in the flag and 445 in the flame -> some result are turning back ? At
this point nothing in openMole in my results directory ... in fact, I
haven't any result directory yet !
@Romain ./re-execute.sh R --slave -f netlogo_run_grid.R --args 16 1 12
work for me outside openMole!
Etienne
Le 21/07/2016 à 16:26, Romain Reuillon a écrit :
Actually it reflect the job ended on the cluster before result checking.
If the result is bad they will turn into flame...
Le 21/07/2016 à 16:20, Jonathan Passerat-Palmbach a écrit :
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 ?
------------------------------------------------------------------------
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------------------------------------------------------------------------
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
_______________________________________________
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
--
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
_______________________________________________
OpenMOLE-users mailing list
[email protected]
http://fedex.iscpif.fr/mailman/listinfo/openmole-users
