[torqueusers] checkpointable jobs lose environment variables?

Grigory Shamov gas5x at yahoo.com
Fri Jun 1 08:37:04 MDT 2012


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
> 
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