Most common scenario when "it works from the command line" but "it does
not work in grid engine" is usually:
- Different shell environment between command-line and batch execution
(especially if SGE is running in POSIX_COMPLIANT mode)
- Different ENV variables between CLI and batch environment
- Different PATH definition between CLI and batch environment
Usually when faced with this problem I submit a shell script that dumps
PATH, ENV and other interesting info and then I compare that to the
environment where my command line example is working.
You also have two different user IDs shown in the output. Is the userID
that is running the job trying to create a data file that may already
exist and perhaps be owned by a different user?
Dan Hyatt <mailto:dhy...@dsgmail.wustl.edu>
June 8, 2015 at 2:42 PM
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@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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