This hands on tutorial is aimed to introduce the user in the mpi and gpu job management through the Molecular Dynamics solver called NAMD. This software scales very well and is not memory intensive. You can download and upload the hands-on files here.
For our Hands On we will equilibrate a water drop through different architectures(STD nodes and GPU node).
H2O Molecule
Modify the water_std.slm file to work on $SCRATCH directory (it requieres to move inputs to $SCRATCH).
Modify the water_std.slm file to move the output to a folder called outputs inside the original namd_tutorial folder.
More specific
GPU Version
Edit your “Executable” and final sections to adapt it to a threaded GPU run (not MPI).
Compare the results between architectures. Which one is faster?
#SBATCH -n 24 #SBATCH --mem-per-cpu=3900Mb #SBATCH –p std #SBATCH -t 10 |
cd $SCRATCH cp -r /scratch/$USER/namd/water* . |
module load namd/2.13 srun `which namd2` water.namd > water_std.out |
mkdir -p ~/namd/water/output cp water_std.out ~/namd/water/output/ |
sbatch water_std.slm |
#SBATCH -N 1 #SBATCH -n 48 |
#SBATCH -n 24 #SBATCH –N 1 #SBATCH -p gpu #SBATCH --gres=gpu:1 |
`which namd2` > water_gpu.out mkdir -p ~/namd/water/output cp water_std.out ~/namd/water/output/ |