[GE users] "shell_start_mode=unix_behavior" and environment variables problems

Gon?alo Borges goncalo at lip.pt
Tue Jul 31 19:14:19 BST 2007


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Dear All,

1 - A user is trying to submit a /bin/bash script to SGE. Both in the 
submission host and exec host where the job is supposed to run, the 
default shell definition for this user is /bin/csh. The default 
definition for the cluster queue is also /bin/csh.

2 - In the cluster queue definition, I've configure 
"shell_starting_mode=unix_behavior" in order for the system to ignore 
the cluster queue shell definition (bin/csh) and take into account the 
first line of the user script, which is #! /bin/bash.

[root at sge01 Conf]# qconf -sq compasslip | grep shell
shell                 /bin/csh
shell_start_mode      unix_behavior


3 - What happens is that the environment is changed when the user 
submits the script. Check for example $PATH env variable:
    3.1 - In the exec host, the $PATH variable seen from this user 
account is:
PATH=/home/comp/helena/bin:/home/comp/helena/scripts:/usr/sue/bin:/bin:/usr/local/bin:/usr/local/bin/X11:/usr/bin:/usr/bin/X11:
            
/cern/pro/bin:/usr/java/j2sdk1.4.2_08/bin:/usr/local/sge/pro/bin/lx26-x86:/usr/local/sge/utils_scripts:/opt/lcg/bin:/usr/kerberos/bin:
            
/opt/edg/openmpi/bin:/opt/edg/bin:/opt/globus/bin:/opt/globus/sbin:/opt/mpi/bin:/usr/local/root/pro/bin:/opt/d-cache/dcap/bin:.:
            
/opt/d-cache//srm/bin:/opt/d-cache//dcap/bin:/opt/glite/bin:/opt/glite/externals/bin:/opt/gpt/sbin:/opt/d-cache/srm/bin:/usr/X11R6/bin

    3.2 - The $PATH seen inside the /bin/bash script which runs in the 
same host is just:
PATH=/tmp/62806.1.compasslip:/usr/local/bin:/bin:/usr/bin

There are other env variable which disappear or are simply defined 
differently. The most immediate consequence is that since $PATH is not 
defined as the user would expect, some command simply do not work for 
the user.

I'm doing something wrong? Is there a workaround to this?

Thanks in advance
Cheers
Goncalo

 

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