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 id            Name             User              Time Use S Queue
----------------  ---------------- ----------------  -------- - -----
0.bio             STDIN            root              00:00:00 F workq
1.bio             STDIN            chee              00:00:00 F workq
2.bio             STDIN            root              00:00:00 F workq
4.bio             dummy            chee              00:00:00 F normal
5.bio             dummy            chee              00:00:00 F normal
6.bio             dummy            chee              00:00:00 F normal
7.bio             STDIN            root              00:00:00 F workq
9.bio             STDIN            root              00:00:00 F workq
10.bio            STDIN            galaxy_user       00:00:00 F workq
11.bio            STDIN            root              00:00:00 F workq

[galaxy_user@bio galaxy-dist]$ qstat -xansw 11
bio.centos64:
Req'd  Req'd   Elap
Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time ------------------------------ --------------- --------------- --------------- -------- ---- ----- ------ ----- - ----- 11.bio.centos64 root workq 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_user    55 Sep  3 10:42
data_manager_conf.xml.sample
-rw-rw-r--  1 galaxy_user galaxy_user  4444 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_user    68 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_user    69 Sep  3 10:42
shed_tool_conf.xml.sample
-rw-rw-r--  1 galaxy_user galaxy_user    55 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 Sep  3 10:42
tool_data_table_conf.xml.sample
-rw-rw-r--  1 galaxy_user galaxy_user  4925 Sep  3 10:42
tool_conf.xml.sample
-rw-rw-r--  1 galaxy_user galaxy_user  5840 Sep  3 10:42 tool_conf.xml.main
-rw-rw-r--  1 galaxy_user galaxy_user    41 Sep  3 10:42
shed_tool_data_table_conf.xml.sample
-rw-rw-r--  1 galaxy_user galaxy_user   548 Sep  3 10:42
workflow_schedulers_conf.xml.sample
-rw-rw-r--  1 galaxy_user galaxy_user    68 Sep  3 10:52
migrated_tools_conf.xml
-rw-rw-r--  1 galaxy_user galaxy_user    69 Sep  3 10:52 shed_tool_conf.xml
-rw-rw-r--  1 galaxy_user galaxy_user    41 Sep  3 10:52
shed_tool_data_table_conf.xml
-rw-rw-r--  1 galaxy_user galaxy_user    55 Sep  3 10:52
shed_data_manager_conf.xml
-rw-------  1 root        root            0 Sep  4 17:12 STDIN.o2
-rw-------  1 root        root            0 Sep  4 17:12 STDIN.e2
-rw-rw-r--  1 galaxy_user galaxy_user   512 Sep  4 22:11 job_conf.xml.sample
-rw-rw-r--  1 galaxy_user galaxy_user 48599 Sep  4 22:42 galaxy.ini
-rw-rw-r--  1 galaxy_user galaxy_user   631 Sep  7 14:48 job_conf.xmlDRA
-rw-r--r--  1 galaxy_user galaxy_user   909 Sep 14 16:20 job_conf.xml
drwxrwxr-x  3 galaxy_user galaxy_user  4096 Sep 14 16:23 ./
drwxrwxr-x 24 galaxy_user galaxy_user  4096 Sep 14 16:27 ../


On 14/09/2015 4:22 PM, Clinton Chee wrote:

Hi Nate,

I was trying the Galaxy configuration using the tips you suggested - I think
I got one step ahead, but stuck again.
Now  the job status says "waiting to run"

I got a screenshot attached - focussing on job 42 - which is a Sort job
using a dataset I downloaded. Please note, I am setting up Galaxy, but I am
not a bioinfomatics person.
I'm a PBS person and need to use DRMAA - and I'm not sure how else to debug
this.

Below is the job_conf.xml  - I've also tried the hostname apart from
localhost.

<?xml version="1.0"?>
<!-- A sample job config that explicitly configures job running the way it
is configured by default (if there is no expl
icit config). -->
<job_conf>
     <plugins>
         <plugin id="local" type="runner"
load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
         <plugin id="drmaa" type="runner"
load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" workers="4"/>
     </plugins>
     <handlers default="localhost">
         <handler id="localhost"/>
     </handlers>
     <destinations default="drmaa">
         <destination id="local" runner="local"/>
         <destination id="drmaa" runner="drmaa">
                 <param id="nativeSpecification">-q workq@localhost</param>
         </destination>
     </destinations>
</job_conf>


Thanks
Clinton

On 9/09/2015 4:44 AM, Nate Coraor wrote:

Hi Clinton,

On Mon, Sep 7, 2015 at 2:23 AM, Clinton Chee <c...@altair.com> wrote:
Dear Galaxy devs / support,

I am trying to understand the following snippet from job_conf.xml (I want
to use drmaa v1)
------------
<destination id="pbs_drmaa_orion" runner="drmaa" tags="merc">
             <param id="destination">galaxy@merc</param>
  </destination>
------------


Based on someone's configuration above, I am trying to customize to my
system.

I'm trying to understand where/how the parameters are associated?
- tags?

Tags are identifiers used to map tools to destinations. You probably do not
need to use them, but if you wanted to have a tool (or the default
destination) send jobs to more than one destination (selected at random),
tags are used for that. They can also be used for setting job concurrency
limits.

- destination in param id? is this the queue?  I also checked the DRMAA
specification but cannot find any "destination" as a keyword.

I am not sure where this example came from but I don't believe it would work
- the "destination" param works with the "pbs" runner, but the pbs runner
only works with Torque, as far as I know. The drmaa runner expects params
that conform to the DRMAA specification, the most common of which is
`nativeSpecification`. If you wanted to set the destination for PBS Pro
using the drmaa runner, the param would be:

     <param id="nativeSpecification">-q queue@server_name</param>

- galaxy@merc?   is merc pointing to the hostname, and galaxy the queue
name? (I know the instution's cluster is called "merc", but I don't know if
the "merc" in the tag is for convenience or is being read as the hostname?

That format is a PBS destination identifier, so `galaxy` is the queue on the
PBS server `merc`.

Hope this helps, please let us know if this doesn't clear things up.

--nate


I've looked through:
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

but cannot make sense, eg. for "tags" is says "Tags to which this
destination belongs."
Eg. "tags="longwalltime,bigcluster""


Do you have more detailed documention on configuration?

Thanks
Clinton


--
________________________________
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workload management suite, please visit pbsworks.com
________________________________
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___________________________________________________________
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--
________________________________
PBS WorksTM named #1 software product!
HPCwire Reader’s Choice Awards 2014

For more information on Altair’s award-winning HPC
workload management suite, please visit pbsworks.com
________________________________
Clinton Chee (PhD)
PBS Application Engineer
Altair - Innovation Intelligence
Mob: 61 (0)402 058 983
Email: c...@altair.com
Skype: live:clinton.chee
Twitter: @xtechnotes
PBSWorks: Facebook | Google+ | Linkedin | Twitter | YouTube
Australia Toll Free: 1800 174 396
Urgent / Emergency: pbs-supp...@india.altair.com



--
________________________________
PBS WorksTM named #1 software product!
HPCwire Reader’s Choice Awards 2014

For more information on Altair’s award-winning HPC
workload management suite, please visit pbsworks.com
________________________________
Clinton Chee (PhD)
PBS Application Engineer
Altair - Innovation Intelligence
Mob: 61 (0)402 058 983
Email: c...@altair.com
Skype: live:clinton.chee
Twitter: @xtechnotes
PBSWorks: Facebook | Google+ | Linkedin | Twitter | YouTube
Australia Toll Free: 1800 174 396
Urgent / Emergency: pbs-supp...@india.altair.com

___________________________________________________________
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:
   https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/


--
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HPCwire Reader’s Choice Awards 2014
*
For more information on Altair’s award-winning HPC
workload management suite, please visit pbsworks.com <http://pbsworks.com> *
------------------------------------------------------------------------
Clinton Chee (PhD)
PBS Application Engineer
Altair - Innovation Intelligence
Mob: 61 (0)402 058 983
Email: c...@altair.com
Skype: live:clinton.chee
Twitter: @xtechnotes <https://twitter.com/xtechnotes>
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