[gridengine users] qsub EDA tool

Reuti reuti at staff.uni-marburg.de
Wed Apr 19 11:29:47 UTC 2017


Hi,

> Am 19.04.2017 um 04:27 schrieb John_Tai <John_Tai at smics.com>:
> 
> 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.

What is the setting of shell_startup_mode – POSIX_COMPLIANT? Different shells read different profile files. Maybe the -V settings was simply overridden by something it found in the profile. With the wrong shell selected, the script will most likely crash when feed to the wrong interpreter.



> Now how do I set the default shell for new queues? I didn't see it in the cluster config.

There is none. The default for a new queue is /bin/csh, but how often do you create new cluster queues? Most of the time I set "shell_startuup_mode unix_behavior" anyway by hand when creating a new queue.

-- Reuti


> -----Original Message-----
> From: Reuti [mailto:reuti at staff.uni-marburg.de]
> Sent: Tuesday, April 18, 2017 8:57
> To: John_Tai
> Cc: users at gridengine.org
> Subject: Re: [gridengine users] qsub EDA tool
> 
> Hi,
> 
>> Am 18.04.2017 um 10:42 schrieb John_Tai <John_Tai at 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 at 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 at 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
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