Difference between revisions of "Gromacs Job Scripts"

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(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==
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[[Category:Software]]
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<source lang=bash>
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;Note: Use 'module spider gromacs' to find available gromacs versions. The module loads below may be outdated.
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[[Gromacs|back to the Gromacs page]]
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==Parallel (MPI)==
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<pre>
 
#!/bin/bash
 
#!/bin/bash
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#
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#SBATCH --job-name=gromacs
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#PBS -r n
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#SBATCH --mail-user=YOUR_MAIL_ADDRESS_HERE
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#PBS -N Gromacs
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#SBATCH --mail-type=FAIL,BEGIN,END
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#PBS -o stdout
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#SBATCH --output=gmx-%j.out
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#PBS -e stderr
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#SBATCH --ntasks=2
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#PBS -j oe
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#SBATCH --cpus-per-task=4
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#PBS -m abe
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#SBATCH --ntasks-per-socket=1
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#PBS -M YOUR_MAIL_ADDRESS_HERE
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#SBATCH --distribution=cyclic:block
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#PBS -l nodes=1:ppn=1
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#SBATCH --time=24:00:00
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#PBS -l pmem=200mb
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#SBATCH --mem-per-cpu=1gb
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#PBS -l walltime=01:00:00
 
  
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module load intel
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module purge
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module load gromacs
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ml gcc/8.2.0 openmpi/4.0.1 gromacs/2019.2
  
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cd $PBS_O_WORKDIR
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export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
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srun --mpi=pmix_v3 gmx mdrun -ntomp ${SLURM_CPUS_PER_TASK} -s topol.tpr
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</pre>
  
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mdrun_d < gromacs.in > gromacs.out 2>&1
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==GPU Acceleration (MPI + multiple GPUs)==
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</source>
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<pre>
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==Parallel (MPI)==
 
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<source lang=bash>
 
 
#!/bin/bash
 
#!/bin/bash
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#
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#SBATCH --job-name=multi-gpu
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#PBS -r n
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#SBATCH --mail-user=YOUR_MAIL_ADDRESS_HERE
−
#PBS -N Gromacs
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#SBATCH --mail-type=FAIL,BEGIN,END
−
#PBS -o stdout
+
#SBATCH --output=gromacs_%j.log
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#PBS -e stderr
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#SBATCH --nodes=1
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#PBS -j oe
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#SBATCH --ntasks=2
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#PBS -m abe
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#SBATCH --tasks-per-node=2
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#PBS -M YOUR_MAIL_ADDRESS_HERE
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#SBATCH --cpus-per-task=7
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#PBS -l nodes=2:ppn=4
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#SBATCH --ntasks-per-socket=1
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#PBS -l pmem=200mb
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#SBATCH --distribution=cyclic:block
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#PBS -l walltime=01:00:00
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#SBATCH --time=2:00:00
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#SBATCH --mem-per-cpu=1gb
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#SBATCH --partition=hpg2-gpu
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#SBATCH --gres=gpu:a100:2
  
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module load intel
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module load gcc/5.2.0  openmpi/1.10.2 gromacs/2016.3-CUDA
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module load openmpi
 
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module load gromacs
 
  
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cd $PBS_O_WORKDIR
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export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
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srun --mpi=pmi2 --accel-bind=g --ntasks=$SLURM_NTASKS gmx mdrun -v
  
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mpiexec mdrun_mpi_d < gromacs.in > gromacs.out 2>&1
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</pre>
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</source>
 

Latest revision as of 14:40, 20 July 2022

Note
Use 'module spider gromacs' to find available gromacs versions. The module loads below may be outdated.

back to the Gromacs page

Parallel (MPI)

#!/bin/bash
#SBATCH --job-name=gromacs
#SBATCH --mail-user=YOUR_MAIL_ADDRESS_HERE
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --output=gmx-%j.out
#SBATCH --ntasks=2
#SBATCH --cpus-per-task=4
#SBATCH --ntasks-per-socket=1
#SBATCH --distribution=cyclic:block
#SBATCH --time=24:00:00
#SBATCH --mem-per-cpu=1gb

module purge
ml gcc/8.2.0 openmpi/4.0.1 gromacs/2019.2

export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
srun --mpi=pmix_v3 gmx mdrun -ntomp ${SLURM_CPUS_PER_TASK} -s topol.tpr

GPU Acceleration (MPI + multiple GPUs)

#!/bin/bash
#SBATCH --job-name=multi-gpu
#SBATCH --mail-user=YOUR_MAIL_ADDRESS_HERE
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --output=gromacs_%j.log
#SBATCH --nodes=1
#SBATCH --ntasks=2
#SBATCH --tasks-per-node=2
#SBATCH --cpus-per-task=7
#SBATCH --ntasks-per-socket=1
#SBATCH --distribution=cyclic:block
#SBATCH --time=2:00:00
#SBATCH --mem-per-cpu=1gb
#SBATCH --partition=hpg2-gpu
#SBATCH --gres=gpu:a100:2

module load gcc/5.2.0  openmpi/1.10.2 gromacs/2016.3-CUDA

export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
srun --mpi=pmi2 --accel-bind=g --ntasks=$SLURM_NTASKS gmx mdrun -v
Retrieved from "https://help.rc.ufl.edu/mediawiki/index.php?title=Gromacs_Job_Scripts&oldid=24584"