AMBER molecular dynamics package.
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:
#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 $workdir
executable=$PBS_O_WORKDIR/mpi_test.x cp $executable $workdir
cp data.d $PBS_O_WORKDIR cd /tmp rm -rf $workdir