[gridengine users] command runs in grid engine but does not complete.

Alex Chekholko chekh at stanford.edu
Mon Jun 8 19:10:14 UTC 2015


What was the "grid reconfiguration"?

On 06/08/2015 11:42 AM, Dan Hyatt wrote:
>
> We are running a binary program called metaanalysis, which the user says
> was working prior to a grid reconfiguration.
>
>
> qsub -cwd -b y /dsg_cent/bin/metal < c22srcfile.txt > c22SBP.log
>
> This starts, runs, creates the logs, and then fails to create the data
> files
> qsub -cwd -b y  /dsg_cent/bin/metal < c22srcfile.txt > c22SBP.log
>
> -rw-rw-r-- 1 aldi   genetics 8523209 Jun  8 09:53 c22GENOA.SBP.EA.M1.csv
> -rw-rw-r-- 1 aldi   genetics 8660667 Jun  8 09:53 c22FamHS.SBP.ea.M1.csv
> -rw-rw-r-- 1 aldi   genetics 6025412 Jun  8 09:53 c22HYPERGEN.SBP.EA.M1.csv
> -rw-rw-r-- 1 aldi   genetics    2061 Jun  8 09:53 c22srcfile.txt
> -rw-rw-r-- 1 dhyatt genetics      43 Jun  8 13:40 c22SBP.log
> -rw-r--r-- 1 dhyatt genetics       0 Jun  8 13:40 metal.e1043
> -rw-r--r-- 1 dhyatt genetics    2743 Jun  8 13:40 metal.o1043
> [dhyatt at blade5-2-1 c22
>
>   the control/output file indicates everything runs there are .o and .e
> files, but no data
>
>
> The command line works fine, and creates the data files. But I need to
> run large jobs on the queue
>
> -rw-rw-r-- 1 aldi   genetics  8523209 Jun  8 09:53 c22GENOA.SBP.EA.M1.csv
> -rw-rw-r-- 1 aldi   genetics  8660667 Jun  8 09:53 c22FamHS.SBP.ea.M1.csv
> -rw-rw-r-- 1 aldi   genetics  6025412 Jun  8 09:53
> c22HYPERGEN.SBP.EA.M1.csv
> -rw-rw-r-- 1 aldi   genetics     2061 Jun  8 09:53 c22srcfile.txt
> -rw-rw-r-- 1 dhyatt genetics  8177082 Jun  8 13:39 METAANALYSIS1.TBL
> -rw-rw-r-- 1 dhyatt genetics     1054 Jun  8 13:39 METAANALYSIS1.TBL.info
> -rw-rw-r-- 1 dhyatt genetics 10487038 Jun  8 13:39 METAANALYSIS2.TBL
> -rw-rw-r-- 1 dhyatt genetics     1316 Jun  8 13:39 METAANALYSIS2.TBL.info
> -rw-rw-r-- 1 dhyatt genetics     5030 Jun  8 13:39 c22SBP.log
>
> any thoughts?
>
> Dan
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-- 
Alex Chekholko chekh at stanford.edu




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