Re: NAMD 2.7b1 on NCSA Abe

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Thu Apr 30 2009 - 12:15:37 CDT

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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