On Nov 30, 2016, at 4:27 PM, Nate Coraor <nate@bx.psu.edu> wrote:

Seems on the up 'n up. Can you check the `handler` column of the job table in the database for the jobs in question?

   id   |        create_time         |  state  | handler  |       

 537202 | 2016-11-30 05:49:35.363694 | new     | handler0 |

 537201 | 2016-11-30 05:40:08.343855 | new     | handler0 |

 537200 | 2016-11-30 05:39:20.394128 | new     | handler1 |

 537199 | 2016-11-30 05:38:03.913992 | new     | handler0 |

So hander0 and handler1

Brad

On Wed, Nov 30, 2016 at 4:14 PM, Langhorst, Brad <Langhorst@neb.com> wrote:

nope - 

I limit local jobs to 8, but no jobs go to that destination

2 handlers, a few jobs that reserve more cores.

here’s my job.conf

<?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" workers="4"/>

        <plugin id="gridengine" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner">

            <!-- Override the $DRMAA_LIBRARY_PATH environment variable -->

            <param id="drmaa_library_path">/opt/gridengine/lib/linux-x64/libdrmaa.so</param>

        </plugin>

    </plugins>

    <handlers default="handlers">

        <handler id="handler0" tags='handlers'>

            <plugin id="gridengine"/>

        </handler>

        <handler id="handler1" tags='handlers'>

            <plugin id="gridengine"/>

        </handler>

    </handlers>

    <destinations default="gridengine">

        <destination id="local" runner="local"/>

        <destination id="gridengine" runner="gridengine" tags="rockscluster">

<param id="embed_metadata_in_job">True</param>

<env exec="source /mnt/galaxy/data/galaxy/cluster_env/bin/activate"/>

</destination>

        <destination id="gridengine_8" runner="gridengine" tags="rockscluster,8cores">

<param id="embed_metadata_in_job">True</param>

        <param id="nativeSpecification">-pe smp 8</param>

<env exec="source /mnt/galaxy/data/galaxy/cluster_env/bin/activate"/>

        </destination>

        <destination id="gridengine_16" runner="gridengine" tags="rockscluster,16cores">

<param id="embed_metadata_in_job">True</param>

                <param id="nativeSpecification">-pe smp 16</param>

<env exec="source /mnt/galaxy/data/galaxy/cluster_env/bin/activate"/>

        </destination>

        <destination id="gridengine_16_long" runner="gridengine" tags="rockscluster,16cores,longrun">

<param id="embed_metadata_in_job">True</param>

                <param id="nativeSpecification">-pe smp 16 -P longrun</param>

<env exec="source /mnt/galaxy/data/galaxy/cluster_env/bin/activate"/>

        </destination>

<destination id="gridengine_32_long" runner="gridengine" tags="rockscluster,32cores,longrun">

                <param id="embed_metadata_in_job">True</param>

                <param id="nativeSpecification">-pe smp 32 -P longrun</param>

                <env exec="source /mnt/galaxy/data/galaxy/cluster_env/bin/activate"/>

</destination>

    </destinations>

    <tools>

    <tool id="bowtie2" destination="8cores"/>

    <tool id="bismark_bowtie2" destination="8cores"/>

    <tool id="freebayes" destination="8cores"/>

    <tool id="tophat2" destination="8cores"/>

    <tool id="hisat"  destination="8cores"/>

    <tool id="hisat2"  destination="8cores"/>

    <tool id="trinityrnaseq" destination="longrun"/>

    <tool id="cufflinks" destination="8cores"/>

<tool id="stringtie" destination="16cores"/>

<tool id="mira_4_0_de_novo" destination="8cores"/>

    </tools>

    <limits>

        <limit type="destination_total_concurrent_jobs" id="local">8</limit>

    </limits>

</job_conf>

Brad

—
Brad Langhorst, Ph.D.
Development Scientist
New England Biolabs

On Nov 30, 2016, at 4:05 PM, Nate Coraor <nate@bx.psu.edu> wrote:

Hi Brad,

Do you have any kind of strange job mapping going on, or job limits configured?

--nate

On Wed, Nov 30, 2016 at 1:01 AM, Langhorst, Brad <Langhorst@neb.com> wrote:

Hi:

I have one user who’s jobs won’t execute on my local instance.

The user was mysteriously listed as inactive.

I reactivated and restored the handlers, still jobs are not executing.

The user has plenty of quota (82%  used)

Anybody have an idea about what might be wrong with this user?

I have impersonated the user, jobs can be added 

galaxy.util.object_wrapper WARNING 2016-11-30 00:40:08,118 Unable to create dynamic subclass for <type 'instance'>, None: metaclass conflict: the metaclass of a derived class must be a (non-strict) subclass of the metaclasses of all its bases

galaxy.tools.actions INFO 2016-11-30 00:40:08,271 Handled output (153.865 ms)

galaxy.tools.actions INFO 2016-11-30 00:40:08,330 Verified access to datasets (5.648 ms)

galaxy.tools.execute DEBUG 2016-11-30 00:40:08,490 Tool [toolshed.g2.bx.psu.edu/repos/jjohnson/fastqc/FastQC/1.0.0] created job [537201] (384.040 ms)

galaxy.tools.execute DEBUG 2016-11-30 00:40:08,498 Executed all jobs for tool request: (413.473 ms)

10.254.254.95 - - [30/Nov/2016:00:40:07 -0400] "POST /api/tools HTTP/1.0" 200 - "http://galaxy.neb.com/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_12_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/54.0.2840.99 Safari/537.36 OPR/41.0.2353.69”

but they never get scheduled or run.

Nothing else in the logs after submitting the job.

They just remain in this state:

This is a new dataset and not all of its data are available yet

Any ideas?

Brad

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