===== Amber =====
==== Amber 20 ====
=== sander ===
Script ''slurm-amber-20-cpu.sh'' to run ''sander.MPI'' on 2 nodes (16 tasks per node):
#!/bin/bash --login
#SBATCH --job-name=amber20cpu
#SBATCH --output=%x.o%j
#SBATCH --error=%x.e%j
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=16
#SBATCH --time=0-01:00:00
#SBATCH --mem=16G
#SBATCH --partition=cpu
#SBATCH --constraint='broadwell|skylake'
#SBATCH --account=
shopt -q login_shell || exit 1
module load gnu8 openmpi4
module load apptainer/1.0
container='/hpc/share/applications/amber/20/amber-20-cpu'
bind="${GROUP:+$GROUP,}${ARCHIVE:+$ARCHIVE,}${SCRATCH:+$SCRATCH,}$(test -d /node && echo /node)"
mpirun \
apptainer exec ${bind:+--bind $bind} "$container.sif" \
sander.MPI -p complex_azd.prmtop -c complex_azd.inpcrd -ref complex_azd.inpcrd -i min1.in -o min1.out -r min1.crd -O
=== pmemd.cuda ===
Script ''slurm-amber-20-gpu.sh'' to run ''pmemd.cuda'' on 1 node with 1 GPU (4 tasks per node):
#!/bin/bash --login
#SBATCH --job-name=amber20gpu
#SBATCH --output=%x.o%j
#SBATCH --error=%x.e%j
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=4
#SBATCH --gres=gpu:1
#SBATCH --time=0-01:00:00
#SBATCH --mem=16G
#SBATCH --partition=gpu
#SBATCH --account=
shopt -q login_shell || exit 1
module load apptainer/1.0
container='/hpc/share/applications/amber/20/amber-20-gpu'
bind="${GROUP:+$GROUP,}${ARCHIVE:+$ARCHIVE,}${SCRATCH:+$SCRATCH,}$(test -d /node && echo /node)"
bind="${bind:+$bind,}/opt/hpc/system/nvidia/driver:/usr/local/nvidia/lib,/opt/hpc/system/nvidia/driver:/usr/local/nvidia/bin"
apptainer exec ${bind:+--bind $bind} "$container.sif" \
pmemd.cuda -i min.in -o test-min.out -p test.prmtop -c test.inpcrd -r test-min.rst -ref test.inpcrd -e test-min.en -inf test-min.mdinfo -O
apptainer exec ${bind:+--bind $bind} "$container.sif" \
pmemd.cuda -i test_amber_MD.in -o test-MD.out -p test.prmtop -c test-min.rst -r test-MD.rst -x test-MD.nc -e test-MD.en -inf test-MD.mdinfo -O
=== pdb4amber ===
Run the following commands on the login node to open a shell on the compute node:
srun \
--nodes=1 \
--ntasks-per-node=4 \
--time=0-01:00:00 \
--mem=16G \
--partition=cpu \
--qos=cpu \
--constraint='broadwell|skylake' \
--account= \
--pty \
bash
As usual the argument to the
--account=
option must be the account you intend to use.
On the compute node run a shell within the ''amber/20/cpu'' container:
module load apptainer/1.0
module load amber/20/cpu
apptainer shell "$CONTAINER"
Inside the container run ''pdb4amber'':
pdb4amber
To exit the container run ''exit''.
To exit the shell on the compute node run the ''exit''.