[Swift-user] job waiting

[Yue, Chen - BMD]

Hi,
 
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>
<pool handle="NCSAMERCURY">
    <gridftp url="gsiftp://gridftp-hg.ncsa.teragrid.org"/>
    <execution provider="coaster" url="grid-hg.ncsa.teragrid.org" jobManager="gt2:PBS"/>
    <workdirectory>/gpfs_scratch1/yuechen/swiftwork</workdirectory>
 </pool>


Thank you very much!

Best regards,

Chen, Yue




This email is intended only for the use of the individual or entity to which it is addressed and may contain information that is privileged and confidential. If the reader of this email message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication is prohibited. If you have received this email in error, please notify the sender and destroy/delete all copies of the transmittal. Thank you.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/swift-user/attachments/20090418/5539d765/attachment.html>