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:

tou! ch: cannot touch `/home/galaxy/.drmaa/9167860.pbs-master2.embl.de.started': Permission denied /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 grateful!

Hi L-A, This path appears to be part of pbs-drmaa: http://apps.man.poznan.pl/trac/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. --nate

Thanks, L-A ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:

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