Re: Running NAMD at TACC (Ranger)

From: JC Gumbart (
Date: Sun Mar 30 2008 - 13:20:45 CDT

I remember this being a frequent problem in the past. Sometimes we
would have to submit ten times before getting it to run. I haven't
run there much recently though, so I'm not sure what has happened
since. We'll ask around to see if anyone else is experiencing this.

On Mar 30, 2008, at 9:28 AM, Peter Freddolino wrote:

> Hi Jim,
> that's... odd. Quite a few of those in the ks.uiuc domain have been
> running happily on ranger. Just to separate out multiple causes of
> problems, can you run a benchmark system (apo AI or ubiquitin)
> successfully? How large is the system you're trying to run?
> Best,
> Peter
> Jim Pfaendtner wrote:
>> Hi,
>> I am trying to run namd on the new Ranger cluster at TACC. I am
>> using the script from the namd wiki that is listed here (~tg455591/
>> NAMD_scripts/runbatch) to submit my jobs.
>> I frequently am getting the following message in my log file:
>> TACC: Starting up job 57208
>> TACC: Setting up parallel environment for MVAPICH-1 mpirun.
>> TACC: Setup complete. Running job script.
>> TACC: starting parallel tasks...
>> and then the system just hangs and the job doesn't run. There
>> doesn't appear to be any rhyme or reason for why this happens as
>> far as I can tell. I have tried to run with up to 30 nodes but as
>> few as 10 or 15.
>> Have other people had good luck with namd on Ranger? Any help
>> would be appreciated.
>> thanks,
>> Jim

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