Question: Job waiting problem on my galaxy
1
gravatar for jp.of.mars
2.3 years ago by
jp.of.mars10
jp.of.mars10 wrote:

Hello,

I'm just installed a galaxy server with a postgresql database and with proftpd for ftp upload. When I want to upload a file (with ftp or directly), I get a succesful message in the upload windows but the job is waiting to run.

This is a configuration problem ? or right acces problem ?

thanks for your help !!

waiting job galaxy • 859 views
ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by jp.of.mars10

what happens when you click on the 'Refresh history' buton (circular arrows) in the top right hand corner?

ADD REPLYlink written 2.3 years ago by Hotz, Hans-Rudolf1.8k

Nothing. I always have "job is waiting to run"

I try to get data from UCSC and I have the same problem.

ADD REPLYlink written 2.3 years ago by jp.of.mars10

do you have any running processes as well?

ADD REPLYlink written 2.3 years ago by Hotz, Hans-Rudolf1.8k

do you test from the same server you have galaxy installed on? or are you connecting from your PC/laptop? If the latter, it could be a proxy problem?

ADD REPLYlink written 2.3 years ago by Hotz, Hans-Rudolf1.8k

The galaxy server is on a Supercomputers and I test it from my MAC with google chrome. The both are on the same network.

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by jp.of.mars10

Do you have admin access to the Galaxy instance? If so, have a look in the log files immediately after submitting a job. I have this sort of issue when the connection between Galaxy and the scheduler we use on our cluster breaks (the logs then mention something related to that).

ADD REPLYlink written 2.3 years ago by Devon Ryan1.9k

I check the server log (/var/log), I don't see anything. And when I launch an upload I get only this in the terminal :

galaxy.tools DEBUG 2016-08-25 10:10:43,873 Validated and populated state for tool request (61.527 ms) galaxy.tools.actions.upload DEBUG 2016-08-25 10:10:43,976 Persisted uploads (60.435 ms) galaxy.tools.actions.upload DEBUG 2016-08-25 10:10:44,174 Checked and cleaned uploads (195.613 ms) galaxy.tools.actions.upload_common INFO 2016-08-25 10:10:44,232 tool upload1 created job id 31 galaxy.tools.actions.upload DEBUG 2016-08-25 10:10:44,516 Created upload job (341.523 ms) galaxy.tools.execute DEBUG 2016-08-25 10:10:44,526 Tool [upload1] created job [31] (610.742 ms) galaxy.tools.execute DEBUG 2016-08-25 10:10:44,548 Executed 1 job(s) for tool upload1 request: (673.487 ms)

ADD REPLYlink written 2.3 years ago by jp.of.mars10
0
gravatar for jp.of.mars
2.3 years ago by
jp.of.mars10
jp.of.mars10 wrote:

I create a new job_conf.xml file and job starts :

the job_conf.xml file :

 <?xml version="1.0"?>
 <job_conf>
 <plugins workers="32">  
      <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> 
      <plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner">

    </plugin>

</plugins>

<handlers>
    <handler id="main"/>
</handlers>

<destinations default="local">

    <destination id="local" runner="local"/>
    <destination id="drmaa" runner="drmaa">
      <param id="nativeSpecification">-l walltime=10:00:00,ncpus=32,mem=48GB</param>    
      <param id="-q">workq_p</param>
      <env id="JAVA_OPTIONS">-XX:ParallelGCThreads=1</env>
      <env id="JAVA_OPTIONS_NT">-XX:ParallelGCThreads=3</env>
      <env id="JAVA_OPTIONS_FOR">-XX:ParallelGCThreads=4</env>
    </destination>
</destinations>
</job_conf>
ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by jp.of.mars10
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