I have found the culprit. It was because shell in queue was set to /bin/csh. I changed it to /bin/sh and it's working now. Though I don't know why.
Now how do I set the default shell for new queues? I didn't see it in the cluster config. -----Original Message----- From: Reuti [mailto:re...@staff.uni-marburg.de] Sent: Tuesday, April 18, 2017 8:57 To: John_Tai Cc: users@gridengine.org Subject: Re: [gridengine users] qsub EDA tool Hi, > Am 18.04.2017 um 10:42 schrieb John_Tai <john_...@smics.com>: > > Picking up an old thread. > > I ran command qsub -V -b y -cwd -now n -j y env and in the output log it > doesn't contain the path in the current shell, which should be: > --------------------------------------------- > # echo $path $path ≠ $PATH, is this a typo. The ":" are replaced by a " "? > /home/sge/sge6.2u6/bin/lx24-amd64 > /tools/cadence/virtuoso/IC617.500.0900_20170202/tools/dracula/bin > /tools/cadence/virtuoso/IC617.500.0900_20170202/tools/dfII/bin > /tools/cadence/virtuoso/IC617.500.0900_20170202/tools/bin > /tools/cadence/virtuoso/IC617.500.0900_20170202/bin > /home/sge/sge6.1/bin/lx24-amd64 /home/sge/sge6.2u6/bin/lx24-amd64 /bin > /usr/bin /usr/local/bin /usr/X11R6/bin /home/johnt/bin . /home/sge/bin > /home/DI/TOOLS/bin . /home/IPproj/IOproject/quan/Flatten > ----------------------------------------------- > > > > Instead this is the output: > ------------------------------------------------ > johnt@ibm044: /home/johnt/temp # more env.o5032117 |grep -i path > MANPATH=/home/sge/sge6.2u6/man:/usr/share/man:/usr/X11R6/man:/usr/kerb > eros/man > PATH=/home/sge/sge6.2u6/bin/lx24-amd64:/bin:/usr/bin:/usr/local/bin:/usr/X11R6/bin:/home/johnt/bin:. What is strange is, that the scratch directory is completely missing here. This should usually be included (to look for any wrappers therein). > OPERA_PLUGIN_PATH=/usr/java/jre1.5.0_01/plugin/i386/ns7 > NPX_PLUGIN_PATH=/usr/java/jre1.5.0_01/plugin/i386/ns7 > LD_LIBRARY_PATH=/usr/lib:/usr/local/lib:/usr/lib64:/usr/local/lib64 > SGE_BINARY_PATH=/home/sge/sge6.2u6/bin/lx24-amd64 > SGE_O_PATH=/home/sge/sge6.2u6/bin/lx24-amd64:/tools/cadence/virtuoso/I > C617.500.0900_20170202/tools/dracula/bin:/tools/cadence/virtuoso/IC617 > .500.0900_20170202/tools/dfII/bin:/tools/cadence/virtuoso/IC617.500.09 > 00_20170202/tools/bin:/tools/cadence/virtuoso/IC617.500.0900_20170202/ > bin:/home/sge/sge6.1/bin/lx24-amd64:/home/sge/sge6.2u6/bin/lx24-amd64: > /bin:/usr/bin:/usr/local/bin:/usr/X11R6/bin:/home/johnt/bin:.:/home/sg > e/bin:/home/DI/TOOLS/bin:.:/home/IPproj/IOproject/quan/Flatten > SGE_STDIN_PATH=/dev/null > SGE_STDOUT_PATH=/home/johnt/temp/env.o5032117 > SGE_STDERR_PATH=/home/johnt/temp/env.o5032117 > SGE_CWD_PATH=/home/johnt/temp > johnt@ibm044: /home/johnt/temp # > -------------------------------------------------------------- What is sourced and set in a batch job depends on the shell_start_mode in the queue configuration. It might also be the case, that something is set by /etc/profile or /etc/profile.local which is not available on the exechosts. I remember this: http://gridengine.org/pipermail/users/2012-April/003322.html -- Reuti ________________________________ This email (including its attachments, if any) may be confidential and proprietary information of SMIC, and intended only for the use of the named recipient(s) above. Any unauthorized use or disclosure of this email is strictly prohibited. If you are not the intended recipient(s), please notify the sender immediately and delete this email from your computer. _______________________________________________ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users
