[torqueusers] /usr/local/bin in the pbs environment

Dimitrakakis Georgios giwrgis at chemistry.uoc.gr
Mon Apr 12 15:18:21 MDT 2010


My problem is that I am "sourcing" the .bashrc

In the pbs file I have the following line

source ~/.bashr_modified

where ".bashr_modified" is a modified version of the original .bashrc

Needless to say that if I do it manually it works just fine.

G.

> On Mon, Apr 12, 2010 at 2:48 PM, Greenseid, Joseph M (IS)
> <Joseph.Greenseid at ngc.com> wrote:
>> Does it look like the environment corresponds to what's in the
>> pbs_environment file in your pbs spool directory?
>
> It looks like it "doubles" the path after /home/user/bin without some
> of the items at the beginning of the $PATH. Not at all sure how that's
> happening.
>
> Here's the .pbs file :
>
> ###
> #!/bin/tcsh
> #PBS -M devnull
> #PBS -m bae
> #PBS -l nodes=1:ppn=1
> #PBS -l mem=100mb
> #PBS -l walltime=00:1:00
> #PBS -j oe
>
> cd ~/pbstest
> which qsub
> echo $PATH
> cat /dev/urandom > /dev/null
> ###
>
> Here's "echo $PATH" from the shell on the same machine where the job ran:
>
> /usr/lib64/qt-3.3/bin:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/usr/X11R6/bin:/sb/apps/Linux/x86_64/bin:/sb/apps/Linux/bin:.:/sb/apps/Linux/opt/bin:/home/user/bin
>
> and here's the output from the .pbs run :
>
> Warning: no access to tty (Bad file descriptor).
> Thus no job control in this shell.
> qsub: Command not found.
> /usr/lib64/qt-3.3/bin:/usr/kerberos/bin:/bin:/usr/bin:/usr/X11R6/bin:/sb/apps/Linux/x86_64/bin:/sb/apps/Linux/bin:.:/sb/apps/Linux/opt/bin:/home/user/bin:/sb/apps/Linux/x86_64/bin:/sb/apps/Linux/bin:.:/sb/apps/Linux/opt/bin:/home/user/bin
> =>> PBS: job killed: walltime 101 exceeded limit 60
> Terminated
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