[StarCluster] SGE Execution errors - Ubuntu 12.04 Official

[Stephen Smith]

The shell environment has not been modified, though I did seem to leave 
off the first two lines of the error on my last email:

-bash: module: line 1: syntax error: unexpected end of file
-bash: error importing function definition for `BASH_FUNC_module'

After some digging around, it appears it might be related to the 
ShellShock updates:  here and here. 

If it were, what would be the best way to address?






From:   Rayson Ho <raysonlogin at gmail.com>
To:     Stephen Smith <stephen.smith at electrolux.com>
Cc:     "starcluster at mit.edu" <starcluster at mit.edu>
Date:   11/17/2014 03:38 PM
Subject:        Re: [StarCluster] SGE Execution errors - Ubuntu 12.04 
Official



Are starenv & remove_doubleqoutes the bash functions defined in your shell 
environment?

Rayson

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Open Grid Scheduler - The Official Open Source Grid Engine
http://gridscheduler.sourceforge.net/
http://gridscheduler.sourceforge.net/GridEngine/GridEngineCloud.html

On Mon, Nov 17, 2014 at 2:06 PM, Stephen Smith <
stephen.smith at electrolux.com> wrote:
Hello, 

I'm getting the following errors when submitting a job to SGE via qsub.  
I'm running the 12.04 Ubuntu starcluster AMI, modified only with the 
installation of the software I would like to run.  I received these same 
errors with a CentOS7 AMI I built from scratch as well - I'm not sure what

I'm missing.  Any thoughts as to the cause? 

/opt/sge6/default/spool/exec_spool_local/node001/job_scripts/1: line 11: 
/opt/sge6/default/spool/exec_spool_local/node001/job_scripts/starenv: No 
such file or directory 
/opt/sge6/default/spool/exec_spool_local/node001/job_scripts/1: line 24: 
reset_env: command not found 
/opt/sge6/default/spool/exec_spool_local/node001/job_scripts/1: line 28: 
init_timers: command not found 
/opt/sge6/default/spool/exec_spool_local/node001/job_scripts/1: line 29: 
start_finetimer: command not found 
/opt/sge6/default/spool/exec_spool_local/node001/job_scripts/1: line 33: 
stop_timer: command not found 
/opt/sge6/default/spool/exec_spool_local/node001/job_scripts/1: line 39: 
remove_doublequotes: command not found 
/opt/sge6/default/spool/exec_spool_local/node001/job_scripts/1: line 39: 
remove_doublequotes: command not found 
/opt/sge6/default/spool/exec_spool_local/node001/job_scripts/1: line 39: 
remove_doublequotes: command not found 
/opt/sge6/default/spool/exec_spool_local/node001/job_scripts/1: line 39: 
remove_doublequotes: command not found 
/opt/sge6/default/spool/exec_spool_local/node001/job_scripts/1: line 39: 
remove_doublequotes: command not found 
/opt/sge6/default/spool/exec_spool_local/node001/job_scripts/1: line 39: 
remove_doublequotes: command not found 
/opt/sge6/default/spool/exec_spool_local/node001/job_scripts/1: line 39: 
remove_doublequotes: command not found 
/opt/sge6/default/spool/exec_spool_local/node001/job_scripts/1: line 39: 
remove_doublequotes: command not found 
/opt/sge6/default/spool/exec_spool_local/node001/job_scripts/1: line 39: 
remove_doublequotes: command not found 
/opt/sge6/default/spool/exec_spool_local/node001/job_scripts/1: line 39: 
remove_doublequotes: command not found 
/opt/sge6/default/spool/exec_spool_local/node001/job_scripts/1: line 39: 
remove_doublequotes: command not found 
/opt/sge6/default/spool/exec_spool_local/node001/job_scripts/1: line 39: 
remove_doublequotes: command not found 
/opt/sge6/default/spool/exec_spool_local/node001/job_scripts/1: line 39: 
remove_doublequotes: command not found 
/opt/sge6/default/spool/exec_spool_local/node001/job_scripts/1: line 39: 
remove_doublequotes: command not found 
/opt/sge6/default/spool/exec_spool_local/node001/job_scripts/1: line 81: 
start_timer: command not found 
/opt/sge6/default/spool/exec_spool_local/node001/job_scripts/1: line 93: 
substitute_spaceescape: command not found 
/opt/sge6/default/spool/exec_spool_local/node001/job_scripts/1: line 93: 
substitute_spaceescape: command not found 
/opt/sge6/default/spool/exec_spool_local/node001/job_scripts/1: line 93: 
substitute_spaceescape: command not found 
/opt/sge6/default/spool/exec_spool_local/node001/job_scripts/1: line 93: 
substitute_spaceescape: command not found 
/opt/sge6/default/spool/exec_spool_local/node001/job_scripts/1: line 93: 
substitute_spaceescape: command not found 
/opt/sge6/default/spool/exec_spool_local/node001/job_scripts/1: line 93: 
substitute_spaceescape: command not found 
/opt/sge6/default/spool/exec_spool_local/node001/job_scripts/1: line 93: 
substitute_spaceescape: command not found 
/opt/sge6/default/spool/exec_spool_local/node001/job_scripts/1: line 93: 
substitute_spaceescape: command not found 
/opt/sge6/default/spool/exec_spool_local/node001/job_scripts/1: line 93: 
substitute_spaceescape: command not found 
/opt/sge6/default/spool/exec_spool_local/node001/job_scripts/1: line 93: 
substitute_spaceescape: command not found 


Thanks in advance, 
Stephen
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