Hi all,<div>first of all, thanks to the Galaxy Team for this really useful software. Actually I don&#39;t really know if my problem is related with Galaxy or with Torque/Maui but I didn&#39;t find any solution looking in both Torque and Maui user lists, so I hope that some of you with more experience could give me some good advices. I&#39;m trying to set up Galaxy in a small local virtual environment in order to test it. I started with 2 virtual ubuntu servers called galaxy1 and galaxy2. On galaxy1 I succesfully installed Galaxy, Apache, Torque and Maui. I&#39;m using Postgres ad DBMS. It is installed on another &quot;real&quot; DB server. The virtual server galaxy2 is used as node. Galaxy is working like a charm locally but when I try to use Torque problems arise. Torque alone works correctly. That means that I can submit a job with qsub and everything works. The 2 virtual server (galaxy1 and galaxy2) share a directory (through NFS) in which I installed Galaxy following the &quot;unified method&quot; from the documentation.</div>

<div>Now, as I said, Galaxy alone works, Torque/Maui alone works. When I put the two together nothing works.</div><div>As a test I upload (using local runner) a gff file. Then I try to make a filter to the gff using &quot;Filter and sort -&gt; Extract features&quot;. When I run this tool the corresponding job on the Torque queue runs forever in Hold state. I report some output from diagnose programs:</div>
<div>The diagnose -j reports the following:</div><div><br></div><div><div>Name                  State Par Proc QOS     WCLimit R  Min     User    Group  Account  QueuedTime  Network  Opsys   Arch    Mem   Disk  Procs       Class Features</div>
<div><br></div><div>29                     Hold DEF    1 DEF     1:00:00 0    1   galaxy   galaxy        -    00:02:36   [NONE] [NONE] [NONE]    &gt;=0    &gt;=0    NC0   [batch:1] [NONE]</div></div><div><br></div><div>While the showq command reports</div>
<div><br></div><div><div>ACTIVE JOBS--------------------</div><div>JOBNAME            USERNAME      STATE  PROC   REMAINING            STARTTIME</div><div><br></div><div><br></div><div>     0 Active Jobs       0 of    1 Processors Active (0.00%)</div>
<div><br></div><div>IDLE JOBS----------------------</div><div>JOBNAME            USERNAME      STATE  PROC     WCLIMIT            QUEUETIME</div><div><br></div><div><br></div><div>0 Idle Jobs</div><div><br></div><div>BLOCKED JOBS----------------</div>
<div>JOBNAME            USERNAME      STATE  PROC     WCLIMIT            QUEUETIME</div><div><br></div><div>29                   galaxy       Hold     1     1:00:00  Wed May  4 03:56:40</div></div><div><br></div><div><br>
</div><div>The checkjob reports:</div><div><div>checking job 29</div><div><br></div><div>State: Hold</div><div>Creds:  user:galaxy  group:galaxy  class:batch  qos:DEFAULT</div><div>WallTime: 00:00:00 of 1:00:00</div><div>
SubmitTime: Wed May  4 03:56:40</div><div>  (Time Queued  Total: 00:03:07  Eligible: 00:00:01)</div><div><br></div><div>The qstat -f reports</div><div><br></div><div><div>Job Id: <a href="http://33.galaxy1.research.intra.ismaa.it">33.galaxy1.research.intra.ismaa.it</a></div>
<div>    Job_Name = <a href="mailto:27_Extract_features1_marco.moretto@iasma.it">27_Extract_features1_marco.moretto@iasma.it</a></div><div>    Job_Owner = <a href="mailto:galaxy@galaxy1.research.intra.ismaa.it">galaxy@galaxy1.research.intra.ismaa.it</a></div>
<div>    job_state = W</div><div>    queue = batch</div><div>    server = <a href="http://galaxy1.research.intra.ismaa.it">galaxy1.research.intra.ismaa.it</a></div><div>    ctime = Wed May  4 04:56:36 2011</div><div>    Error_Path = galaxy1:/mnt/equallogic1/galaxy/galaxy-dist/database/pbs/27.e</div>
<div><br></div><div>    exec_host = galaxy2/0</div><div>    exec_port = 15003</div><div>    Execution_Time = Wed May  4 05:26:41 2011</div><div>    mtime = Wed May  4 04:56:37 2011</div><div>    Output_Path = galaxy1:/mnt/equallogic1/galaxy/galaxy-dist/database/pbs/27.</div>
<div>        o</div><div>    qtime = Wed May  4 04:56:36 2011</div><div>    Resource_List.neednodes = 1</div><div>    Resource_List.nodect = 1</div><div>    Resource_List.nodes = 1</div><div>    Resource_List.walltime = 01:00:00</div>
<div>    stagein = /mnt/equallogic1/galaxy/tmp/dataset_18.dat@galaxy1:/mnt/equallog</div><div>        ic1/galaxy/galaxy-dist/database/files/000/dataset_18.dat,</div><div>        /mnt/equallogic1/galaxy/tmp/dataset_30.dat@galaxy1:/mnt/equallogic1/g</div>
<div>        alaxy/galaxy-dist/database/files/000/dataset_30.dat</div><div>    stageout = /mnt/equallogic1/galaxy/galaxy-dist/database/files/000/dataset_</div><div>        30.dat@galaxy1:/mnt/equallogic1/galaxy/galaxy-dist/database/files/000/</div>
<div>        dataset_30.dat</div><div>    substate = 37</div><div>    Variable_List = PBS_O_QUEUE=batch,</div><div>        PBS_O_HOST=<a href="http://galaxy1.research.intra.ismaa.it">galaxy1.research.intra.ismaa.it</a></div>
<div>    euser = galaxy</div><div>    egroup = galaxy</div><div>    hashname = <a href="http://33.galaxy1.research.intra.ismaa.it">33.galaxy1.research.intra.ismaa.it</a></div><div>    queue_rank = 33</div><div>    queue_type = E</div>
</div><div><br></div><div>StartDate: -00:03:06  Wed May  4 03:56:41</div><div>Total Tasks: 1</div><div><br></div><div>Req[0]  TaskCount: 1  Partition: DEFAULT</div><div>Network: [NONE]  Memory &gt;= 0  Disk &gt;= 0  Swap &gt;= 0</div>
<div>Opsys: [NONE]  Arch: [NONE]  Features: [NONE]</div><div><br></div><div><br></div><div>IWD: [NONE]  Executable:  [NONE]</div><div>Bypass: 0  StartCount: 1</div><div>PartitionMask: [ALL]</div><div>PE:  1.00  StartPriority:  1</div>
<div>cannot select job 29 for partition DEFAULT (non-idle state &#39;Hold&#39;)</div><div><br></div><div>and finally the tracejob reports</div><div><br></div><div><div>/var/spool/torque/server_priv/accounting/20110504: Permission denied</div>
<div>/var/spool/torque/mom_logs/20110504: No such file or directory</div><div>/var/spool/torque/sched_logs/20110504: No such file or directory</div><div><br></div><div>Job: <a href="http://33.galaxy1.research.intra.ismaa.it">33.galaxy1.research.intra.ismaa.it</a></div>
<div><br></div><div>05/04/2011 04:56:36  S    enqueuing into batch, state 1 hop 1</div><div>05/04/2011 04:56:36  S    Job Queued at request of <a href="mailto:galaxy@galaxy1.research.intra.ismaa.it">galaxy@galaxy1.research.intra.ismaa.it</a>, owner = <a href="mailto:galaxy@galaxy1.research.intra.ismaa.it">galaxy@galaxy1.research.intra.ismaa.it</a>, job name =</div>
<div>                          <a href="mailto:27_Extract_features1_marco.moretto@iasma.it">27_Extract_features1_marco.moretto@iasma.it</a>, queue = batch</div><div>05/04/2011 04:56:37  S    Job Run at request of <a href="mailto:galaxy@galaxy1.research.intra.ismaa.it">galaxy@galaxy1.research.intra.ismaa.it</a></div>
<div>05/04/2011 04:56:41  S    Email &#39;s&#39; to <a href="mailto:galaxy@galaxy1.research.intra.ismaa.it">galaxy@galaxy1.research.intra.ismaa.it</a> failed: Child process &#39;sendmail -f adm <a href="mailto:galaxy@galaxy1.research.intra.ismaa.it">galaxy@galaxy1.research.intra.ismaa.it</a>&#39;</div>
<div>                          returned 127 (errno 10:No child processes)</div></div><div><br></div><div>The only clear thing to me is that after the submission the scheduler puts it in a Hold state. But I cannot understand why. I also try to run the Galaxy-generated sh script with qsub. Following the Galaxy log:</div>
<div>galaxy.jobs.runners.pbs DEBUG 2011-05-04 04:56:36,748 (27) submitting file /mnt/equallogic1/galaxy/galaxy-dist/database/pbs/27.sh</div><div><br></div><div>I copied and run the 27.sh script with the command:</div><div>
qsub 27.sh</div><div>And the job runs correctly. So what it is not clear to me is if the problem is related to Torque/Maui or is related to the way in which the job is submitted from Galaxy.</div><div><br></div><div>Sorry for the very long e-mail and thank you very much for any help.</div>
<div><br></div>
---<br>Marco<br>
</div>