Hi TACC Team,
I am a new user of TACC and was setting up NAMD3 to run in GPU resident mode. When I tried the method in the docs, it gave errors. It might be worth adding a new section on GPU resident setup, and I wanted to report what worked for me.
I didn't try non-resident methods, which I think are what is used in the docs. All this was on LS6. I used the A100, but I'm testing it on H100 as well. Should work on A100-small, but I haven't tested it there yet.
To set up GPUresident mode, you need "GPUresident on" inserted in the input file.
Then, I set it up using this SLURM file:
#SBATCH -N 1 # Total number of nodes
#SBATCH -n 1 # Total number of mpi tasks
#SBATCH -p gpu-a100 # Queue name
#SBATCH -t 24:00:00 # Run time (hh:mm:ss) - 24 hours
module load gcc/11.2
module load mkl
module load cuda/12.2
module load namd_gpu_resident/3.0.2
cd $SLURM_SUBMIT_DIR
ibrun namd3 +setcpuaffinity step7.1_production.inp > step7.1.log
The performance was really good here, at 100 ns/day for my system. I didn't do extensive benchmarking, but I did explore a few different optimization options, and this seemed to be best. Thought I would pass this on in case it is helpful. Thanks,
Michael Marty
Hi TACC Team,
I am a new user of TACC and was setting up NAMD3 to run in GPU resident mode. When I tried the method in the docs, it gave errors. It might be worth adding a new section on GPU resident setup, and I wanted to report what worked for me.
I didn't try non-resident methods, which I think are what is used in the docs. All this was on LS6. I used the A100, but I'm testing it on H100 as well. Should work on A100-small, but I haven't tested it there yet.
To set up GPUresident mode, you need "GPUresident on" inserted in the input file.
Then, I set it up using this SLURM file:
The performance was really good here, at 100 ns/day for my system. I didn't do extensive benchmarking, but I did explore a few different optimization options, and this seemed to be best. Thought I would pass this on in case it is helpful. Thanks,
Michael Marty