Hi John,
Thanks for your reply, the qstat printout is below. It just shows the
last job on this machine occurred last Wed 9 Sep.
Checked the PBS logs - there is no activity at all.
Note - this is a VM, single node, everything is installed on this
one-node-VM pretending to be a cluster.
I'm using PBSPro 12, with Centos 6.4, DRMAA plugin (libdrmaa.so).
I'm quite experienced with HPC and PBSpro, but almost zero experience in
setting up drmaa to connect with Galaxy.
I can't help but feeling there is some step in setting up the DRMAA <->
Galaxy connection that I have missed.
Seems like Galaxy can talk to DRMAA, but PBSpro has not receieved any
info at all.
Do you have any other suggestions? Is there a recipe to setup Galaxy for
DRMAA with PBSPro?
I've gone through these sites many times and cannot see what I missed.
https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer
https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster
https://wiki.galaxyproject.org/Admin/Config/Jobs - describes job_conf.xml
http://dev.list.galaxyproject.org/ - galaxy-dev@lists.galaxyproject.org
[galaxy_user@bio galaxy-dist]$ qstat -x
Job idName User Time Use S Queue
- -
0.bio STDINroot 00:00:00 F workq
1.bio STDINchee 00:00:00 F workq
2.bio STDINroot 00:00:00 F workq
4.bio dummychee 00:00:00 F normal
5.bio dummychee 00:00:00 F normal
6.bio dummychee 00:00:00 F normal
7.bio STDINroot 00:00:00 F workq
9.bio STDINroot 00:00:00 F workq
10.bioSTDINgalaxy_user 00:00:00 F workq
11.bioSTDINroot 00:00:00 F workq
[galaxy_user@bio galaxy-dist]$ qstat -xansw 11
bio.centos64:
Req'd Req'd Elap
Job ID UsernameQueue Jobname
SessID NDS TSK Memory Time S Time
-- --- ---
--- - -- - - -
11.bio.centos64rootworkq STDIN
14321 ---- ---- F 00:00:
05
bio/0
Job run at Wed Sep 09 at 19:27 on (bio:ncpus=1) and finished
On 14/09/2015 10:55 PM, John Chilton wrote:
This means the job has probably been queued in PBS, do you want to run
qstat as the Galaxy user on the command line and see if you can see
the Galaxy job - it may just be sitting there waiting for resources to
run. The PBS logs might have more information at this point.
-John
On Mon, Sep 14, 2015 at 7:35 AM, Clinton Chee <c...@altair.com> wrote:
Hi Nate,
Also, the only configuration I did on my Galaxy installation is the
job_conf.xml file. I have not edited any of the other xml files or used
other config sample files.
Should I also have edited some other XML configuration files.
Also, do I need to have run any of the executbales in the main directory,
besides ./run.sh?
The list of files in config/ is:
[galaxy_user@bio config]$ ls -latrF
total 312
-rw-rw-r-- 1 galaxy_user galaxy_user 416 Sep 3 10:42
disposable_email_blacklist.conf.sample
-rw-rw-r-- 1 galaxy_user galaxy_user 44878 Sep 3 10:42
datatypes_conf.xml.sample
-rw-rw-r-- 1 galaxy_user galaxy_user55 Sep 3 10:42
data_manager_conf.xml.sample
-rw-rw-r-- 1 galaxy_user galaxy_user Sep 3 10:42
auth_conf.xml.sample
-rw-rw-r-- 1 galaxy_user galaxy_user 234 Sep 3 10:42
external_service_types_conf.xml.sample
-rw-rw-r-- 1 galaxy_user galaxy_user 48599 Sep 3 10:42 galaxy.ini.sample
-rw-rw-r-- 1 galaxy_user galaxy_user 463 Sep 3 10:42
job_conf.xml.sample_basic
-rw-rw-r-- 1 galaxy_user galaxy_user 30390 Sep 3 10:42
job_conf.xml.sample_advanced
-rw-rw-r-- 1 galaxy_user galaxy_user68 Sep 3 10:42
migrated_tools_conf.xml.sample
-rw-rw-r-- 1 galaxy_user galaxy_user 725 Sep 3 10:42
job_resource_params_conf.xml.sample
-rw-rw-r-- 1 galaxy_user galaxy_user 6728 Sep 3 10:42
job_metrics_conf.xml.sample
-rw-rw-r-- 1 galaxy_user galaxy_user 220 Sep 3 10:42
openid_conf.xml.sample
-rw-rw-r-- 1 galaxy_user galaxy_user 2165 Sep 3 10:42
object_store_conf.xml.sample
drwxrwxr-x 4 galaxy_user galaxy_user 4096 Sep 3 10:42 plugins/
-rw-rw-r-- 1 galaxy_user galaxy_user69 Sep 3 10:42
shed_tool_conf.xml.sample
-rw-rw-r-- 1 galaxy_user galaxy_user55 Sep 3 10:42
shed_data_manager_conf.xml.sample
-rw-rw-r-- 1 galaxy_user galaxy_user 3139 Sep 3 10:42
reports_wsgi.ini.sample
-rw-rw-r-- 1 galaxy_user galaxy_user 288 Sep 3 10:42
tool_sheds_conf.xml.sample
-rw-rw-r-- 1 galaxy_user galaxy_user 5552 Sep 3 10:42
tool_shed.ini.sample
-rw-rw-r-- 1 galaxy_user galaxy_user 3273
