Re: Fwd: Job submission to Lonestar on TACC

From: Peter Freddolino (
Date: Thu Mar 05 2009 - 20:04:29 CST

Hi Ali,
could you let me know exactly what command you are using to run namd?

There is no need to make use of the TACC namd module if you use the run
scripts in Jim's home directory.


Ali Emileh wrote:
> Peter,
> Thanks for the tips.
> You are right about the user portal explicitly stating BSUB as the job
> running program.
> In the email they said "... you have 'bsub' command line with all the
> parameter setup for
> your run. But it is not the way you submit batch jobs on Lonestar ..."
> "... Please comment
> out the 'bsub' line and put options with #BSUB syntax." It may suggest
> that there is only
> a syntax prefereance (passing options through #BSUB and not the command
> line?) and
> nothing more. As just a random guess, I thought it terminates the job
> because I'm running
> namd off someone else's directory. So now I'm submitting the one in the
> path the module
> command points to. It's on the queue now.
> What I still can't understand is how I'm supposed to make use of the
> MODULE command.
> Even when I do put it in the script, it returns "Command not found"!!!
> while I still can run it
> in normal environment. I don't know how I'm supposed to use the module
> system.
> Ali
> ---------- Forwarded message ----------
> From: *Peter Freddolino* <
> <>>
> Date: Thu, Mar 5, 2009 at 3:15 AM
> Subject: Re: namd-l: Job submission to Lonestar on TACC
> To: Ali Emileh < <>>
> Cc: <>
> 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).
> Best,
> Peter
> 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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