[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

    [ The following text is in the "ISO-8859-1" character set. ]
    [ Your display is set for the "ISO-8859-10" character set.  ]
    [ Some special characters may be displayed incorrectly. ]

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:

    3.2 - The $PATH seen inside the /bin/bash script which runs in the 
same host is just:

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


To unsubscribe, e-mail: users-unsubscribe at gridengine.sunsource.net
For additional commands, e-mail: users-help at gridengine.sunsource.net

More information about the gridengine-users mailing list