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[Anton Gladky <question252053@xxxxxxxxxxxxxxxxxxxxx>]

Question #252053 on Yade changed:
https://answers.launchpad.net/yade/+question/252053

    Status: Open => Answered

Anton Gladky proposed the following answer:
Hi,

It looks like the problem is not with Yade, but with your
script. Please, test it on your local machine first.

There is my PBS-script for yade
===================================================
#!/bin/bash
#PBS -N YADERhmLiqConf
#PBS -l select=1:ncpus=12:mem=10gb
#PBS -l walltime=167:59:00
#PBS -m abe
#PBS -o YADERheomLiqMHom.Out
#PBS -e YADERheomLiqMHom.err

. /etc/profile.d/modules.sh
module load vtk/5.10.1
module load openmpi/gcc/64/1.4.5

PBS_O_WORKDIR=$HOME/yade/simulation/2014_07_17_RheomLiqMHom
cd $PBS_O_WORKDIR

$HOME/yade/inst/bin/yade-trunk-batch -j12 multy-test
rheometer_yade_batch.py

===================================================

Can you run yade --test and yade --check in that environment?

Cheers

Anton


2014-07-23 12:22 GMT+02:00 Carl B. Kissell
<question252053@xxxxxxxxxxxxxxxxxxxxx>:
> New question #252053 on Yade:
> https://answers.launchpad.net/yade/+question/252053
>
> Yade of version 1.0 is installed successfully on our cluster by compiling it from the source.
> It could able to run interactively when it is submitted,
> Yade is getting the exit signal strangely when we were trying to assign the Yade job through PBS, The following log shows that the Yade is executing the part of our code but not fully.
>
>>>From error file KM-MKR.e47892
> [user99@login1 test]$ cat KM-MKR.e47892
> Welcome to Yade Unknown
> TCP python prompt on localhost:9000, auth cookie `eksyau'
> Running script tBed30.py
>
>>>From out file
> Warning: no access to tty (Bad file descriptor).
> Thus no job control in this shell.
> XMLRPC info provider on http://localhost:21000
> 5.18508611496e-08
> [[ ^L clears screen, ^U kills line. F8 plot. ]]
>   Yade [  1  ]:
> Do you really want to exit ([y]/n)?
>
> I could see that my output files are created and left empty.
> The same program could able to run the job interactively on the particular node.
> We have tried all the other methods to hold the yade  not to be killing itself but somehow yade is processing the kill signal.
> PBS SCRIPTS
>
> [user99@login1 test]$ cat yade_pbsrun.sh
> #! /bin/tcsh
> #PBS -l walltime=48:00:00
> #PBS -N KM-MKR
> #PBS -q workq
> #PBS -l select=1:ncpus=16
> ##PBS -l place=scatter:excl
> #PBS -V
>
> # Go to the directory from which you submitted the job
> #cd $PBS_O_WORKDIR
> cd /scratch/user99/test
> /home/user99/build_7/YADE/bin/yade-Unknown tBed30.py
>
> #./run_sin.sh && echo 1 > logfile &
> #while [ ! -s $logfile ]; do sleep 1; done
> #PID=$! #catch the last PID
> #wait $PID
> #/home/user99/build_7/YADE/bin/yade-Unknown tBed30.py
>
> Looking forward your suggestions.
> Thanks.
>
>
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