Re: LSU SuperMIC

From: Kenneth Huang (
Date: Tue Jan 19 2016 - 17:15:39 CST


Try the below- I'll forewarn that it's been a while since I ran NAMD on the
cluster, and that the below is for running on with CPUs only- I think that
there's now Xeon Phis also available, and GPUs tentatively available on a
somewhat limited basis.

#PBS -q workq
#PBS -l walltime=72:00:00
#PBS -l nodes=5:ppn=20
#PBS -N dimer
#PBS -o dimer.out
#PBS -e dimer.err
#PBS -m abe

export TASKS_PER_HOST=20
module add namd/2.10b1/CUDA-65-INTEL-140-MVAPICH2-2.0
module load python


mpirun -n 100 -f $PBS_NODEFILE `which namd2` dimer.namd



On Tue, Jan 19, 2016 at 5:21 PM, Jeff Comer <> wrote:

> Hi,
> Does anyone have experience running NAMD on Louisiana State University's
> SuperMIC computer? Any scripts to share?
> Thanks!
> Jeff
> –––––––––––––––––––––––––––––––––––———————
> Jeffrey Comer, PhD
> Assistant Professor
> Institute of Computational Comparative Medicine
> Nanotechnology Innovation Center of Kansas State
> Kansas State University
> Office: P-213 Mosier Hall
> Phone: 785-532-6311

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