Problem with DRMAA and Pbs Pro
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
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
Thanks for the report and the workaround. I have opened a Pull Request to make this truncation the default behavior in Galaxy 16.04. https://github.com/galaxyproject/galaxy/pull/2265 -John On Thu, Apr 28, 2016 at 5:43 AM, Tiziano Flati <tiziano.flati@gmail.com> wrote:
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:
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
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participants (2)
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John Chilton -
Tiziano Flati