[torqueusers] checkpointable jobs lose environment variables?

Grigory Shamov gas5x at yahoo.com
Fri Jun 1 11:21:47 MDT 2012


Dear Sredar,

Thank you! It does fix the problem for bash. Although the environments are not identical completely for 'qsub' and 'qsub -c' yet, sufficiently more is passed through now. 

But still it is somewhat confusing why it happens so.

--
Grigory Shamov


--- On Fri, 6/1/12, Sreedhar M <sm4082 at nyu.edu> wrote:

> From: Sreedhar M <sm4082 at nyu.edu>
> Subject: Re: [torqueusers] checkpointable jobs lose environment variables?
> To: "Torque Users Mailing List" <torqueusers at supercluster.org>
> Date: Friday, June 1, 2012, 7:54 AM
> 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
> >> 
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> > torqueusers at supercluster.org
> > http://www.supercluster.org/mailman/listinfo/torqueusers
> 
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