Job submission to Lonestar on TACC

From: Ali Emileh (ali.emileh_at_gmail.com)
Date: Wed Mar 04 2009 - 17:19:03 CST

Hi everyone,

I have been trying to run a job on Lonestar with no success yet. None of
the module swap command
that the NAMDWiki article asks to use or the touch .nosoft command works. I
tried to use the runbatch
command which I think is in another user's directory (the one pointed to, in
NAMDWiki, tg455591).
It does work but terminates without any warning or error, pretty early in
the run , saying it was 'killed
by a signal external to LSF'. Contacting the support staff @ Teragrid I was
told that using BSUB cmmand is not the right
way to submit jobs and you should use the modules. But loading the NAMD
module only sets up
env variables. I don't know what is the command that actually runs namd.

Reading the Lonestar documents, it seems that "ibrun" is the command that
uses the different #BSUB
options to run jobs but I can't figure out how to connect these bits
together. Has anyone tried to use
Lonestar using the runbatch script there? Any guidance will be highly
appreciated.

Thank you,
Ali

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