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Update examples to StdEnv/2023, amber/22, ambertools/23.5
(→Single GPU job: Clarify tasks/CPUs) |
(Update examples to StdEnv/2023, amber/22, ambertools/23.5) |
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| Line 88: | Line 88: | ||
#SBATCH --gpus-per-node=1 | #SBATCH --gpus-per-node=1 | ||
#SBATCH --mem-per-cpu=2000 | #SBATCH --mem-per-cpu=2000 | ||
#SBATCH --time=10: | #SBATCH --time=10:00:00 | ||
module purge | module purge | ||
module load StdEnv/ | module load StdEnv/2023 gcc/12.3 openmpi/4.1.5 cuda/12.2 amber/22 | ||
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 | ||
}} | }} | ||
| Line 105: | Line 107: | ||
#SBATCH --ntasks-per-node=64 | #SBATCH --ntasks-per-node=64 | ||
#SBATCH --mem-per-cpu=2000 | #SBATCH --mem-per-cpu=2000 | ||
#SBATCH --time=1: | #SBATCH --time=1:00:00 | ||
module purge | module purge | ||
module load StdEnv/ | module load StdEnv/2023 gcc/12.3 openmpi/4.1.5 amber/22 | ||
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 | ||
}} | }} | ||
| Line 125: | Line 129: | ||
<!--T:52--> | <!--T:52--> | ||
module purge | module purge | ||
module load StdEnv/ | module load StdEnv/2023 gcc/12.3 openmpi/4.1.5 cuda/12.2 ambertools/23.5 | ||
<!--T:53--> | <!--T:53--> | ||
| Line 141: | Line 145: | ||
#SBATCH --mem-per-cpu=4000 | #SBATCH --mem-per-cpu=4000 | ||
#SBATCH --time=1:00:00 | #SBATCH --time=1:00:00 | ||
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 | ||
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 | ||
}} | }} | ||