Difference between revisions of "Amber Job Sample Scripts"
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Sharath1231 (talk | contribs) (Created page with "= Serial Submission Script = The following job script runs sander on a single processor. <source lang=bash> #!/bin/bash #SBATCH --job-name=<job_name> #SBATCH --mail-user=<us...") |
Sharath1231 (talk | contribs) |
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The following job script runs sander on a single processor. | The following job script runs sander on a single processor. | ||
| + | |||
| + | <source lang=bash> | ||
| + | #!/bin/bash | ||
| + | #SBATCH --job-name=<job_name> | ||
| + | #SBATCH --mail-user=<user@ufl.edu> | ||
| + | #SBATCH --mail-type=FAIL,END | ||
| + | #SBATCH --output <out.out> | ||
| + | #SBATCH --error <out.err> | ||
| + | #SBATCH --nodes=1 | ||
| + | #SBATCH --ntasks=1 | ||
| + | #SBATCH --mem-per-cpu=1G | ||
| + | #SBATCH --time=01:00:00 | ||
| + | |||
| + | module load intel/2016.0.109 amber/14 | ||
| + | |||
| + | echo $PBS_O_WORKDIR | ||
| + | cd $PBS_O_WORKDIR | ||
| + | |||
| + | sander -O -i amber.in -o amber.log -p amber.prmtop -c amber.inpcrd | ||
| + | </source> | ||
| + | |||
| + | = MPI Submission Script = | ||
| + | |||
| + | The following job script runs sander.MPI on two nodes with four processors each. | ||
<source lang=bash> | <source lang=bash> | ||
| Line 20: | Line 44: | ||
cd $PBS_O_WORKDIR | cd $PBS_O_WORKDIR | ||
| − | sander -O -i amber.in -o amber.log -p amber.prmtop -c amber.inpcrd | + | mpiexec sander.MPI -O -i amber.in -o amber.log -p amber.prmtop -c amber.inpcrd |
</source> | </source> | ||
Revision as of 20:49, 18 July 2016
Serial Submission Script
The following job script runs sander on a single processor.
#!/bin/bash
#SBATCH --job-name=<job_name>
#SBATCH --mail-user=<user@ufl.edu>
#SBATCH --mail-type=FAIL,END
#SBATCH --output <out.out>
#SBATCH --error <out.err>
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --mem-per-cpu=1G
#SBATCH --time=01:00:00
module load intel/2016.0.109 amber/14
echo $PBS_O_WORKDIR
cd $PBS_O_WORKDIR
sander -O -i amber.in -o amber.log -p amber.prmtop -c amber.inpcrd
MPI Submission Script
The following job script runs sander.MPI on two nodes with four processors each.
#!/bin/bash
#SBATCH --job-name=<job_name>
#SBATCH --mail-user=<user@ufl.edu>
#SBATCH --mail-type=FAIL,END
#SBATCH --output <out.out>
#SBATCH --error <out.err>
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --mem-per-cpu=1G
#SBATCH --time=01:00:00
module load intel/2016.0.109 openmpi/1.10.2 amber/14
echo $PBS_O_WORKDIR
cd $PBS_O_WORKDIR
mpiexec sander.MPI -O -i amber.in -o amber.log -p amber.prmtop -c amber.inpcrd