Difference between revisions of "Gromacs Job Scripts"

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<!--
 
==Serial==
 
==Serial==
 
<source lang=bash>
 
<source lang=bash>
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mdrun_d < gromacs.in > gromacs.out 2>&1
 
mdrun_d < gromacs.in > gromacs.out 2>&1
 
</source>
 
</source>
 +
-->
  
 
==Parallel (MPI)==
 
==Parallel (MPI)==
 
<source lang=bash>
 
<source lang=bash>
 
#!/bin/bash
 
#!/bin/bash
#
+
#SBATCH --account=ufhpc
#PBS -r n
+
#SBATCH --qos=ufhpc
#PBS -N Gromacs
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#SBATCH --mail-user=YOUR_MAIL_ADDRESS_HERE
#PBS -o stdout
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#SBATCH --mail-type=FAIL,BEGIN,END
#PBS -e stderr
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#SBATCH --output=stdout
#PBS -j oe
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#SBATCH --ntasks=8
#PBS -m abe
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#SBATCH --nodes=2
#PBS -M YOUR_MAIL_ADDRESS_HERE
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#SBATCH --mem-per-cpu=200mb
#PBS -l nodes=2:ppn=4
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#SBATCH --time=01:00:00
#PBS -l pmem=200mb
 
#PBS -l walltime=01:00:00
 
  
 
module load intel
 
module load intel
 
module load openmpi
 
module load openmpi
 
module load gromacs
 
module load gromacs
 
cd $PBS_O_WORKDIR
 
  
 
mpiexec mdrun_mpi_d < gromacs.in > gromacs.out 2>&1
 
mpiexec mdrun_mpi_d < gromacs.in > gromacs.out 2>&1
 
</source>
 
</source>
 +
<!--
 
==GPU Acceleration (Single GPU, Gromacs 4.6.5)==
 
==GPU Acceleration (Single GPU, Gromacs 4.6.5)==
 
<source lang=bash>
 
<source lang=bash>
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exit 0
 
exit 0
 
</source>
 
</source>
 
+
-->
 +
<!--
 
==GPU Acceleration (Multiple GPUs, Gromacs 4.6.5)==
 
==GPU Acceleration (Multiple GPUs, Gromacs 4.6.5)==
 
<source lang=bash>
 
<source lang=bash>
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exit 0
 
exit 0
 
</source>
 
</source>
 +
-->

Revision as of 18:46, 1 August 2016


Parallel (MPI)

#!/bin/bash
#SBATCH --account=ufhpc
#SBATCH --qos=ufhpc
#SBATCH --mail-user=YOUR_MAIL_ADDRESS_HERE
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --output=stdout
#SBATCH --ntasks=8
#SBATCH --nodes=2
#SBATCH --mem-per-cpu=200mb
#SBATCH --time=01:00:00

module load intel
module load openmpi
module load gromacs

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