[Swift-user] job waiting

Yue, Chen - BMD yuechen at bsd.uchicago.edu
Sat Apr 18 14:03:24 CDT 2009

I'm using Swift and PTMap to analyze E coli genome data. Right now, I'm only mapped on SDSC DTF and NCSA mercury, so I'm trying to use only these two computer clusters. Total number of jobs should be around 4127. After it started, the application runs normally. However, after 3769 jobs returned successfully, it could not receive any more data and the system kept waiting. On these computers, if I use qstat, I cannot find any active job. In my email, I received 45 emails like the following:
PBS Job Id: 1932326.tg-master.ncsa.teragrid.org
Job Name:   null
job deleted
Job deleted at request of root at tg-master.ncsa.teragrid.org
MOAB_INFO:  job exceeded wallclock limit
I'm wondering if I did something wrong and how I can avoid this situation. The log of the search should be /home/yuechen/PTMap2/PTMap2-unmod-20090418-1254-d8loarc1.log.

/************* The swift script I used is /home/yuechen/PTMap2/PTMap2-unmod.swift

/************* tc.data is /home/yuechen/PTMap2/tc.data

/************* sites.xml is /home/yuechen/PTMap2/sites.xml and the following are the two sites I used.

 <pool handle="SDSC_dtf_prews_pbs">
   <gridftp  url="gsiftp://tg-gridftp.sdsc.teragrid.org:2811/" />
   <jobmanager universe="vanilla" url="tg-login1.sdsc.teragrid.org:2119/jobmanager-pbs" major="2" />
   <workdirectory >/gpfs-wan/scratch/yuechen</workdirectory>
   <profile namespace="globus" key="queue">fast</profile>
<pool handle="NCSAMERCURY">
    <gridftp url="gsiftp://gridftp-hg.ncsa.teragrid.org"/>
    <execution provider="coaster" url="grid-hg.ncsa.teragrid.org" jobManager="gt2:PBS"/>

Thank you very much!

Best regards,

Chen, Yue

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