From: Kenneth Huang (kennethneltharion_at_gmail.com)
Date: Tue Jan 19 2016 - 17:15:39 CST
Jeff,
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.
#!/bin/bash
#PBS -q workq
#PBS -A
#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
#PBS -M khuang8_at_student.gsu.edu
export TASKS_PER_HOST=20
export THREADS_HOST=1
module add namd/2.10b1/CUDA-65-INTEL-140-MVAPICH2-2.0
module load python
cd $PBS_O_WORKDIR
mpirun -n 100 -f $PBS_NODEFILE `which namd2` dimer.namd
Best,
Kenneth
On Tue, Jan 19, 2016 at 5:21 PM, Jeff Comer <jeffcomer_at_gmail.com> 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
>
-- Ask yourselves, all of you, what power would hell have if those imprisoned here could not dream of heaven?
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