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
$HOME/yade/inst/bin/yade-trunk-batch -j12 multy-test
rheometer_yade_batch.py
===================================================
Can you run yade --test and yade --check in that environment?
Cheers
Anton
2014-07-23 12:22 GMT+02:00 Carl B. Kissell
<[email protected]>:
> New question #252053 on Yade:
> https://answers.launchpad.net/yade/+question/252053
>
> Yade of version 1.0 is installed successfully on our cluster by compiling it
> from the source.
> It could able to run interactively when it is submitted,
> Yade is getting the exit signal strangely when we were trying to assign the
> Yade job through PBS, The following log shows that the Yade is executing the
> part of our code but not fully.
>
>>>From error file KM-MKR.e47892
> [user99@login1 test]$ 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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