Re: [galaxy-dev] Problem with DRMAA and Pbs Pro

28 Apr 2016

      Solved.

For your information: the problem was in the job name length: in fact,
PBSPro puts a limitation on the job name length of 15-characters. Galaxy
was automatically assigning a job name (of the form
g18_COMMANDNAME_USERNAME) which was in fact too long.

2016-04-27 12:44 GMT+02:00 Tiziano Flati <tiziano.flati@gmail.com>:
...
Hi all,
I am trying to use the pbs-drmaa library to let Galaxy "see" our cluster.
We have PBS Pro, so I followed the instructions found here:
http://apps.man.poznan.pl/trac/pbs-drmaa
- I installed the library through:
./configure --with-pbs=$PBS_HOME --prefix=$HOME
make
make install
where PBS_HOME points to the local pbs installation folder (the one with
bin, etc, lib folders and so on) and $HOME points to my user's home dir.
- I have set the DRMAA_LIBRARY_PATH env variable:
env | grep DRMAA_LIBRARY_PATH
DRMAA_LIBRARY_PATH=$HOME/lib/libdrmaa.so
Here is my job_conf.xml:
<?xml version="1.0"?>
<job_conf>
    <plugins>
        <plugin id="local" type="runner"
load="galaxy.jobs.runners.local:LocalJobRunner"/>
        <plugin id="drmaa" type="runner"
load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/>
    </plugins>
    <handlers>
        <handler id="main"/>
    </handlers>
    <destinations default="queue">
        <destination id="local" runner="local"/>
        <destination id="queue" runner="drmaa">
                <param id="nativeSpecification">-A cin_galaxy</param>
        </destination>
    </destinations>
</job_conf>
But when I use the nativeSpecification parameter (with -A account
parameter), I receive the following error, with no further specification of
what the error can be (it says "Illegal attribute or resource value"
without saying which one triggered the error):
galaxy.jobs.runners.drmaa DEBUG 2016-04-27 12:18:26,782 (15) native
specification is: -A cin_galaxy
galaxy.jobs.runners.drmaa ERROR 2016-04-27 12:18:26,784 (15)
drmaa.Session.runJob() failed unconditionally
Traceback (most recent call last):
  File "$GALAXY_DIR/lib/galaxy/jobs/runners/drmaa.py", line 179, in
queue_job
    external_job_id = self.ds.runJob(jt)
  File "$GALAXY_DIR/.venv/lib/python2.6/site-packages/drmaa/session.py",
line 314, in runJob
    c(drmaa_run_job, jid, sizeof(jid), jobTemplate)
  File "$GALAXY_DIR/.venv/lib/python2.6/site-packages/drmaa/helpers.py",
line 299, in c
    return f(*(args + (error_buffer, sizeof(error_buffer))))
  File "$GALAXY_DIR/.venv/lib/python2.6/site-packages/drmaa/errors.py",
line 151, in error_check
    raise _ERRORS[code - 1](error_string)
*InvalidAttributeValueException: code 14: Illegal attribute or resource
value: Illegal attribute or resource value*
Can you please help me understanding the cause of the problem? Any help
would be most appreciated!
Thank you very much!
Tiziano Flati