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AMBER: Difference between revisions
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(Add MPI job examples for all clusters) |
(Marked this version for translation) |
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#SBATCH --time=10:00:00 | #SBATCH --time=10:00:00 | ||
<!--T:54--> | |||
module purge | module purge | ||
module load StdEnv/2023 gcc/12.3 openmpi/4.1.5 cuda/12.2 amber/22 | module load StdEnv/2023 gcc/12.3 openmpi/4.1.5 cuda/12.2 amber/22 | ||
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pmemd.cuda -O -i input.in -p topol.parm7 -c coord.rst7 -o output.mdout -r restart.rst7 | pmemd.cuda -O -i input.in -p topol.parm7 -c coord.rst7 -o output.mdout -r restart.rst7 | ||
}} | }} | ||
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=== CPU-only parallel MPI job === <!--T:47--> | === CPU-only parallel MPI job === <!--T:47--> | ||
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<tabs> | <tabs> | ||
<tab name="Graham"> | <tab name="Graham"> | ||
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#SBATCH --time=1:00:00 | #SBATCH --time=1:00:00 | ||
<!--T:57--> | |||
module purge | module purge | ||
module load StdEnv/2023 gcc/12.3 openmpi/4.1.5 amber/22 | module load StdEnv/2023 gcc/12.3 openmpi/4.1.5 amber/22 | ||
<!--T:58--> | |||
srun pmemd.MPI -O -i input.in -p topol.parm7 -c coord.rst7 -o output.mdout -r restart.rst7 | srun pmemd.MPI -O -i input.in -p topol.parm7 -c coord.rst7 -o output.mdout -r restart.rst7 | ||
}}</tab> | }}</tab> | ||
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#SBATCH --time=1:00:00 | #SBATCH --time=1:00:00 | ||
<!--T:59--> | |||
module purge | module purge | ||
module load StdEnv/2023 gcc/12.3 openmpi/4.1.5 amber/22 | module load StdEnv/2023 gcc/12.3 openmpi/4.1.5 amber/22 | ||
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srun pmemd.MPI -O -i input.in -p topol.parm7 -c coord.rst7 -o output.mdout -r restart.rst7 | srun pmemd.MPI -O -i input.in -p topol.parm7 -c coord.rst7 -o output.mdout -r restart.rst7 | ||
}}</tab> | }}</tab> | ||
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#SBATCH --time=1:00:00 | #SBATCH --time=1:00:00 | ||
<!--T:61--> | |||
module purge | module purge | ||
module load StdEnv/2023 gcc/12.3 openmpi/4.1.5 amber/22 | module load StdEnv/2023 gcc/12.3 openmpi/4.1.5 amber/22 | ||
<!--T:62--> | |||
srun pmemd.MPI -O -i input.in -p topol.parm7 -c coord.rst7 -o output.mdout -r restart.rst7 | srun pmemd.MPI -O -i input.in -p topol.parm7 -c coord.rst7 -o output.mdout -r restart.rst7 | ||
}}</tab> | }}</tab> | ||
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#SBATCH --time=1:00:00 | #SBATCH --time=1:00:00 | ||
<!--T:63--> | |||
module purge | module purge | ||
module load StdEnv/2023 gcc/12.3 openmpi/4.1.5 amber/22 | module load StdEnv/2023 gcc/12.3 openmpi/4.1.5 amber/22 | ||
<!--T:64--> | |||
srun pmemd.MPI -O -i input.in -p topol.parm7 -c coord.rst7 -o output.mdout -r restart.rst7 | srun pmemd.MPI -O -i input.in -p topol.parm7 -c coord.rst7 -o output.mdout -r restart.rst7 | ||
}}</tab> | }}</tab> | ||
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#SBATCH --time=1:00:00 | #SBATCH --time=1:00:00 | ||
<!--T:65--> | |||
module purge | module purge | ||
module load StdEnv/2023 gcc/12.3 openmpi/4.1.5 amber/22 | module load StdEnv/2023 gcc/12.3 openmpi/4.1.5 amber/22 | ||
<!--T:66--> | |||
srun pmemd.MPI -O -i input.in -p topol.parm7 -c coord.rst7 -o output.mdout -r restart.rst7 | srun pmemd.MPI -O -i input.in -p topol.parm7 -c coord.rst7 -o output.mdout -r restart.rst7 | ||
}}</tab> | }}</tab> | ||
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#SBATCH --time=1:00:00 | #SBATCH --time=1:00:00 | ||
<!--T:67--> | |||
module purge | module purge | ||
module load module load StdEnv/2023 gcc/12.3 openmpi/4.1.5 amber/22 | module load module load StdEnv/2023 gcc/12.3 openmpi/4.1.5 amber/22 | ||
<!--T:68--> | |||
srun MMPBSA.py.MPI -O -i mmpbsa.in -o mmpbsa.dat -sp solvated_complex.parm7 -cp complex.parm7 -rp receptor.parm7 -lp ligand.parm7 -y trajectory.nc | srun MMPBSA.py.MPI -O -i mmpbsa.in -o mmpbsa.dat -sp solvated_complex.parm7 -cp complex.parm7 -rp receptor.parm7 -lp ligand.parm7 -y trajectory.nc | ||
}} | }} | ||