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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Received on Mon Nov 17 2014 - 16:52:13 EST