On Apr 25, 2012, at 9:22 AM, Louise-Amélie Schmitt wrote:
> Hi everyone,
> I'm (still) having issues with running jobs as the real user on our PBS Pro
> cluster. When I try running a job, it ends up in error state and displays
> the following error message:
> ch: cannot
> touch `/home/galaxy/.drmaa/9167860.pbs-master2.embl.de.started': Permission
> /g/funcgen/galaxy-dev/database/pbs/galaxy_1516.sh: line 15: syntax error:
> unexpected end of file
> /var/spool/PBS/mom_priv/jobs/9167860.pbs-master2.embl.de.SC: line 1:
> /home/galaxy/.drmaa/9167860.pbs-master2.embl.de.exitcode: Permission denied
> I suspect this is due to some code executed as the real user (since the
> permission is denied) but then why looking at /home/galaxy instead of
> /home/realuser ?
> If you have any idea about what's going on, please share, I'll be forever
This path appears to be part of pbs-drmaa:
Namely, the user_state_dir option. You may need to write out a pbs_drmaa.conf
for each job or user and then set $PBS_DRMAA_CONF to point to that user's
config file before initializing the session in scripts/drmaa_external_runner.py
You may also be able to get away with making the user_state_dir world writable,
although this comes with security implications.
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