[torqueusers] checkpointable jobs lose environment variables?

Sreedhar M sm4082 at nyu.edu
Fri Jun 1 08:54:06 MDT 2012


Hi Griogory,

Can you try adding

#PBS -V

to your script. Not sure whether it'd fix it. But worth giving it a try.

Sreedhar Manchu
HPC Support Specialist
ITS-Esystems/Research Services
New York University, NY - 100012

On Jun 1, 2012, at 10:37 AM, Grigory Shamov wrote:

> Actually, if I switch to tcsh, for both job script itself and #PBS -S, the environment gets passed somehow. But it case of bash it doesnt!
> 
> 
> --
> Grigory Shamov
> 
> 
> --- On Thu, 5/31/12, Grigory Shamov <gas5x at yahoo.com> wrote:
> 
>> From: Grigory Shamov <gas5x at yahoo.com>
>> Subject: [torqueusers] checkpointable jobs lose environment variables?
>> To: torqueusers at supercluster.org
>> Date: Thursday, May 31, 2012, 1:28 PM
>> Hi All,
>> 
>> I have tried to install the BLCR checkpoint/restart (0.8.4)
>> -enabled Torque (2.5.11), on a few old CentOS 5 machines we
>> have (kernels 2.6.18.308, 2.6.18.194). I have built Torque
>> with --enable-blcr switch, and the BLCR was installed as a
>> system RPM (to /usr/bin etc.). 
>> 
>> The simple seconds-counting test seem to work. However, an
>> user application test failed, the reason being unaccessible
>> environment modules. I've checked with 'env' command and
>> found, that while normal 'qsub' passes all the environment,
>> 'qsub -c' does not. 
>> 
>> The job script was really minimal. 
>> 
>> #!/bin/bash
>> #PBS -N test
>> #PBS -l procs=2,walltime=21:10,mem=2mb
>> #PBS -r y
>> #PBS -S /bin/bash
>> #
>> 
>> env
>> 
>> cd $PBS_O_WORKDIR
>> ./test.x
>> # done
>> 
>> Results of 'env' differ, that for 'qsub -c' almost only
>> $PBS_* things are passed, while for 'qsub' there would be
>> everything. 
>> 
>> Could you please tell whether it is a desired behaviour or a
>> bug, or is there a way to pass environment explicitly for
>> 'qsub -c'?
>> 
>> Thank you very much!
>> 
>> --
>> Grigory Shamov
>> HPC Analyst,
>> University of Manitoba
>> 
>> _______________________________________________
>> torqueusers mailing list
>> torqueusers at supercluster.org
>> http://www.supercluster.org/mailman/listinfo/torqueusers
>> 
> _______________________________________________
> torqueusers mailing list
> torqueusers at supercluster.org
> http://www.supercluster.org/mailman/listinfo/torqueusers



More information about the torqueusers mailing list