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

On Wed, Nov 30, 2016 at 4:14 PM, Langhorst, Brad <langho...@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 <n...@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 <langho...@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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>
>
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