"This job is waiting to run"

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"This job is waiting to run"

ryang
I tried setting up Galaxy to use Sun Grid Engine, but failed miserably.  I removed my config/job_conf.xml hoping Galaxy would revert to its default state, but jobs are no longer being dispatched.  I don't see any errors in the log. 

How can I get Galaxy to 1) use SGE, or 2) revert to its default state for running jobs.  The page, https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster isn't 100% clear on how to set up a simply configuration for SGE.  I'd be happy to contribute mine as an example, if I can get it running.


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Re: "This job is waiting to run"

John Chilton-4
Assuming grid engine is working outside of Galaxy and the Galaxy user
can say qsub files just fine - then you need to install the sun grid
engine libdrmaa package - or build from scratch. Assuming you have
done that and the resulting .so file is
/usr/lib/gridengine-drmaa/lib/libdrmaa.so. Then all you should have to
do is create a config/job_conf.xml file in your Galaxy root that looks
something like this:

<?xml version="1.0"?>
<job_conf>
    <plugins workers="2">
        <plugin id="gridengine" type="runner"
load="galaxy.jobs.runners.drmaa:DRMAAJobRunner">
            <param
id="drmaa_library_path">/usr/lib/gridengine-drmaa/lib/libdrmaa.so</param>
        </plugin>
    </plugins>
    <handlers default="main">
        <handler id="main" />
    </handlers>
    <destinations default="cluster">
        <destination id="cluster" runner="gridengine"/>
    </destinations>
    <tools>
    </tools>
    <limits>
        <!--
        <limit type="registered_user_concurrent_jobs">2</limit>
        <limit type="unregistered_user_concurrent_jobs">1</limit>
        <limit type="job_walltime">24:00:00</limit>
        -->
    </limits>
</job_conf>

A slightly more complicated setup with supervisor, uwsgi, multiple
handlers, etc... all on grid engine is covered in this tutorial that
Nate put together last year
(https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay/AdminWalkthrough#Configure_Galaxy).
This job_conf.xml is a stripped down version of the one from that
tutorial.

In terms of rolling back and just getting jobs to start running again
- you need to remove $GALAXY_ROOT/config/job_conf.xml and
$GALAXY_ROOT/job_conf.xml and things should start working using the
local runner again. If this isn't working - there maybe a problem in
your galaxy.ini file - I would need to know what properties were being
set in there to know more though.

-John


On Mon, Feb 2, 2015 at 12:53 PM, Ryan G <[hidden email]> wrote:

> I tried setting up Galaxy to use Sun Grid Engine, but failed miserably.  I
> removed my config/job_conf.xml hoping Galaxy would revert to its default
> state, but jobs are no longer being dispatched.  I don't see any errors in
> the log.
>
> How can I get Galaxy to 1) use SGE, or 2) revert to its default state for
> running jobs.  The page,
> https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster isn't 100%
> clear on how to set up a simply configuration for SGE.  I'd be happy to
> contribute mine as an example, if I can get it running.
>
>
> ___________________________________________________________
> 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/
___________________________________________________________
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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To search Galaxy mailing lists use the unified search at:
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Re: "This job is waiting to run"

ryang
Thank you.  its was the job_conf.xml that wasn't set up properly.  I have a simply job_conf.xml that works well.  sharing for the group:

<?xml version="1.0"?>
<job_conf>
    <plugins workers="4">
        <!-- "workers" is the number of threads for the runner's work queue.
             The default from <plugins> is used if not defined for a <plugin>.
          -->
        <!-- <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/> -->
        <plugin id="sge" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner">
            <!-- Override the $DRMAA_LIBRARY_PATH environment variable -->
            <param id="drmaa_library_path">/opt/sge/ge2011.11/lib/linux-x64/libdrmaa.so</param>
        </plugin>
    </plugins>

    <handlers default="sge_handler">
        <handler id="sge_handler">
            <plugin id="sge"/>
        </handler>
    </handlers>

    <destinations default="sge_cluster">
        <destination id="sge_cluster" runner="sge" />
    </destinations>

</job_conf>



On Thu, Feb 5, 2015 at 10:03 PM, John Chilton <[hidden email]> wrote:
Assuming grid engine is working outside of Galaxy and the Galaxy user
can say qsub files just fine - then you need to install the sun grid
engine libdrmaa package - or build from scratch. Assuming you have
done that and the resulting .so file is
/usr/lib/gridengine-drmaa/lib/libdrmaa.so. Then all you should have to
do is create a config/job_conf.xml file in your Galaxy root that looks
something like this:

<?xml version="1.0"?>
<job_conf>
    <plugins workers="2">
        <plugin id="gridengine" type="runner"
load="galaxy.jobs.runners.drmaa:DRMAAJobRunner">
            <param
id="drmaa_library_path">/usr/lib/gridengine-drmaa/lib/libdrmaa.so</param>
        </plugin>
    </plugins>
    <handlers default="main">
        <handler id="main" />
    </handlers>
    <destinations default="cluster">
        <destination id="cluster" runner="gridengine"/>
    </destinations>
    <tools>
    </tools>
    <limits>
        <!--
        <limit type="registered_user_concurrent_jobs">2</limit>
        <limit type="unregistered_user_concurrent_jobs">1</limit>
        <limit type="job_walltime">24:00:00</limit>
        -->
    </limits>
</job_conf>

A slightly more complicated setup with supervisor, uwsgi, multiple
handlers, etc... all on grid engine is covered in this tutorial that
Nate put together last year
(https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay/AdminWalkthrough#Configure_Galaxy).
This job_conf.xml is a stripped down version of the one from that
tutorial.

In terms of rolling back and just getting jobs to start running again
- you need to remove $GALAXY_ROOT/config/job_conf.xml and
$GALAXY_ROOT/job_conf.xml and things should start working using the
local runner again. If this isn't working - there maybe a problem in
your galaxy.ini file - I would need to know what properties were being
set in there to know more though.

-John


On Mon, Feb 2, 2015 at 12:53 PM, Ryan G <[hidden email]> wrote:
> I tried setting up Galaxy to use Sun Grid Engine, but failed miserably.  I
> removed my config/job_conf.xml hoping Galaxy would revert to its default
> state, but jobs are no longer being dispatched.  I don't see any errors in
> the log.
>
> How can I get Galaxy to 1) use SGE, or 2) revert to its default state for
> running jobs.  The page,
> https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster isn't 100%
> clear on how to set up a simply configuration for SGE.  I'd be happy to
> contribute mine as an example, if I can get it running.
>
>
> ___________________________________________________________
> 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/


___________________________________________________________
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/