Re: Job submission to Lonestar on TACC

From: Peter Freddolino (
Date: Thu Mar 05 2009 - 02:15:57 CST

Hi Ali,

could you be a bit more specific about what they said about using bsub?
The lonestar user guide is fairly clear about bsub being the correct way
to submit jobs. I have used the runbatch script on lonestar successfully
as recently as about 6 months ago, but haven't had time on lonestar lately.

You may wish to try starting an interactive run
( under "Running
Code") and then executing the ibrun command that is found in the
runbatch script and seeing if you get the same result (and any
additional output).


Ali Emileh wrote:
> 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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