Difference between revisions of "Amber Job Sample Scripts"

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(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...")
 
 
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[[Category:Software]]
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[[Amber|Back to the Amber app page]]
 
= Serial Submission Script =
 
= Serial Submission Script =
  
Line 5: Line 7:
 
<source lang=bash>
 
<source lang=bash>
 
#!/bin/bash
 
#!/bin/bash
#SBATCH --job-name=<job_name>
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#SBATCH --job-name=<JOBNAME>
#SBATCH --mail-user=<user@ufl.edu>
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#SBATCH --mail-user=<EMAIL>
 
#SBATCH --mail-type=FAIL,END
 
#SBATCH --mail-type=FAIL,END
#SBATCH --output <out.out>
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#SBATCH --output <my_job-%j.out>
#SBATCH --error <out.err>
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#SBATCH --error <my_job-%j.err>
 
#SBATCH --nodes=1
 
#SBATCH --nodes=1
 
#SBATCH --ntasks=1
 
#SBATCH --ntasks=1
#SBATCH --mem-per-cpu=1G
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#SBATCH --mem-per-cpu=2G
 
#SBATCH --time=01:00:00
 
#SBATCH --time=01:00:00
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#SBATCH --account=<GROUP>
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#SBATCH --array=<BEGIN-END>
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 +
module load intel/2016.0.109 amber/14
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 +
sander -O -i amber.in -o amber.log -p amber.prmtop  -c amber.inpcrd
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</source>
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 +
= MPI Submission Script =
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 +
The following job script runs sander.MPI on two nodes with four processors each.
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 +
<source lang=bash>
 +
#!/bin/bash
 +
#SBATCH --job-name=<JOBNAME>
 +
#SBATCH --mail-user=<EMAIL>
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#SBATCH --mail-type=FAIL,END
 +
#SBATCH --output <my_job-%j.out>
 +
#SBATCH --error <my_job-%j.err>
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#SBATCH --nodes=1
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#SBATCH --ntasks=<number of tasks>
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#SBATCH --mem-per-cpu=2G
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#SBATCH --time=01:00:00
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#SBATCH --account=<GROUP>
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#SBATCH --array=<BEGIN-END>
  
 
module load intel/2016.0.109 openmpi/1.10.2 amber/14
 
module load intel/2016.0.109 openmpi/1.10.2 amber/14
  
echo $PBS_O_WORKDIR
 
cd $PBS_O_WORKDIR
 
  
sander -O -i amber.in -o amber.log -p amber.prmtop  -c amber.inpcrd
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mpiexec sander.MPI -O -i amber.in -o amber.log -p amber.prmtop  -c amber.inpcrd
 
</source>
 
</source>

Latest revision as of 17:38, 26 June 2017

Back to the Amber app page

Serial Submission Script

The following job script runs sander on a single processor.

#!/bin/bash
#SBATCH --job-name=<JOBNAME>
#SBATCH --mail-user=<EMAIL>
#SBATCH --mail-type=FAIL,END
#SBATCH --output <my_job-%j.out>
#SBATCH --error <my_job-%j.err>
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --mem-per-cpu=2G
#SBATCH --time=01:00:00
#SBATCH --account=<GROUP>
#SBATCH --array=<BEGIN-END>

module load intel/2016.0.109 amber/14

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=<JOBNAME>
#SBATCH --mail-user=<EMAIL>
#SBATCH --mail-type=FAIL,END
#SBATCH --output <my_job-%j.out>
#SBATCH --error <my_job-%j.err>
#SBATCH --nodes=1
#SBATCH --ntasks=<number of tasks>
#SBATCH --mem-per-cpu=2G
#SBATCH --time=01:00:00
#SBATCH --account=<GROUP>
#SBATCH --array=<BEGIN-END>

module load intel/2016.0.109 openmpi/1.10.2 amber/14


mpiexec sander.MPI -O -i amber.in -o amber.log -p amber.prmtop  -c amber.inpcrd