Hi Brad,

Absolutely nothing about these jobs in the handler logs?

--nate

On Wed, Nov 30, 2016 at 8:20 PM, Langhorst, Brad <Langhorst@neb.com> wrote:

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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