Re: NAMD 2.7b1 on NCSA Abe

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Apr 30 2009 - 06:41:50 CDT

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

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