Gromacs Job Scripts

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Revision as of 17:30, 13 September 2012 by Taylor (talk | contribs) (Created page with "==Serial== <source lang=bash> #!/bin/bash # #PBS -r n #PBS -N Gromacs #PBS -o stdout #PBS -e stderr #PBS -j oe #PBS -m abe #PBS -M YOUR_MAIL_ADDRESS_HERE #PBS -l nodes=1:ppn=1...")
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Serial

#!/bin/bash
#
#PBS -r n
#PBS -N Gromacs
#PBS -o stdout
#PBS -e stderr
#PBS -j oe
#PBS -m abe
#PBS -M YOUR_MAIL_ADDRESS_HERE
#PBS -l nodes=1:ppn=1
#PBS -l pmem=200mb
#PBS -l walltime=01:00:00

module load intel
module load gromacs

cd $PBS_O_WORKDIR

mdrun_d < gromacs.in > gromacs.out 2>&1

Parallel (MPI)

#!/bin/bash
#
#PBS -r n
#PBS -N Gromacs
#PBS -o stdout
#PBS -e stderr
#PBS -j oe
#PBS -m abe
#PBS -M YOUR_MAIL_ADDRESS_HERE
#PBS -l nodes=2:ppn=4
#PBS -l pmem=200mb
#PBS -l walltime=01:00:00

module load intel
module load openmpi
module load gromacs

cd $PBS_O_WORKDIR

mpiexec mdrun_mpi_d < gromacs.in > gromacs.out 2>&1