AMBER

As all application SW on stallo you should use module to load it into your environment, using the command:

$ module load amber

Only pmemd and sander is compiled in parallel versions.

The installation should support the netCDF format.

amber is compiled to use MKL, if you really know what you are doing you can change the default setting of OMP_NUM_THREADS to something else than one.

here is a short sample job script:

#!/bin/bash

#PBS -lnodes=2:ppn=8:ib
#PBS -lwalltime=12:00:00
#PBS -lpvmem=2000MB
#PBS -m abe
#PBS -A NAME_OF_MY_CPU_ACCOUNT

workdir=/global/work/$USER/$PBS_JOBID
mkdir -p $workdir

cd $PBS_O_WORKDIR

executable=$PBS_O_WORKDIR/mpi_test.x
cp $executable $workdir

cd $workdir

mpirun ./mpi_test.x

cp data.d $PBS_O_WORKDIR
cd /tmp
rm -rf $workdir

http://ambermd.org/