Re: NAMD 2.7b1 on NCSA Abe

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Apr 30 2009 - 20:11:27 CDT

Hi Gianluca,
where is $NPROCS defined? I don't see it defined in your script before
it is used. Any reason you're not just using the official 2.7b1 script
(~jphillip/NAMD_scripts/runbatch_2.7b1)?
Peter

Gianluca Interlandi wrote:
> Hi Peter,
>
> Sorry, I made a mistake when I copy-pasted the command line into the
> e-mail. I am actually using the namd binary:
>
> mpirun -machinefile $PBS_NODEFILE -np $NPROCS \
> ~jphillip/NAMD_2.7b1_Linux-x86_64/namd2 config.namd
>
> Gianluca
>
> On Thu, 30 Apr 2009, Peter Freddolino wrote:
>
>> Hi Gianluca,
>> ~jphillip/NAMD_2.7b1_Linux-x86_64 is not the namd binary;
>> ~jphillip/NAMD_2.7b1_Linux-x86_64/namd2 is the namd binary. You might
>> want to start by making that the command that is being run by mpirun.
>> Best,
>> Peter
>>
>> Gianluca Interlandi wrote:
>>> I have been trying to run NAMD2.7b1 on Abe but I have run into some
>>> problems. I am using:
>>>
>>> #!/bin/csh
>>> #PBS -l nodes=4:ppn=8
>>> #PBS -l walltime=02:00:00
>>>
>>> mpirun -machinefile $PBS_NODEFILE -np $NPROCS \
>>> ~jphillip/NAMD_2.7b1_Linux-x86_64 config.namd
>>>
>>> I found the executable thanks to the NAMD WIKI:
>>> http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdAtNCSA
>>>
>>> It seems that NAMD instead of running in parallel it starts 32
>>> independent single CPU simulations:
>>>
>>> Charm++> cpu topology info is being gathered!
>>> Charm++> 1 unique compute nodes detected!
>>>
>>> It repeats the above 32 times. Am I using it incorrectly?
>>>
>>> Thanks,
>>>
>>> Gianluca
>>
>>
>
> -----------------------------------------------------
> Gianluca Interlandi, PhD gianluca_at_u.washington.edu
> +1 (206) 685 4435
> +1 (206) 714 4303
> http://artemide.bioeng.washington.edu/
>
> Postdoc at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
> -----------------------------------------------------

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