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Here is the instructions to run NAMD on Expanse.
Your work directory is as /expanse/lustre/scratch/$USER/temp_project/
Example files for equilibrium run (first-dyn.csh and first-dyn.scr) and production run (dyn.csh, dyn.scr, dyn-1.inp, and dyn-2.inp) could be found as follows:
For CPU nodes @ /expanse/lustre/scratch/mkhsieh/temp_project/namd_run/cpu/
Note:
Each standard compute node has ~256 GB of memory and 128 cores
Each standard node core will be allocated 1 GB of memory, users should explicitly include the –mem directive to request additional memory; Max. memory per compute node –mem = 248G
Example of SBATCH lines
#SBATCH --job-name=your_job_name #SBATCH --account=**ask Dr. Klauda** #SBATCH --partition=shared #SBATCH --nodes=1 #SBATCH --ntasks-per-node=32 #SBATCH --cpus-per-task=1 #SBATCH --mem=64G #SBATCH --time=48:00:00
For GPU nodes @ /expanse/lustre/scratch/mkhsieh/temp_project/namd_run/gpu
Note:
Each GPU node has 4 GPUs, ~384GB of memory and 40 cores
Default resource allocation for 1 GPU = 1 GPU, 1 CPU, and 1G of memory, users will need to explicitly ask for additional resources in their job script.
For max memory on a GPU node, users should request –mem = 374G; A GPU SU is equivalent to 1GPU, <10CPUs, and <96G of memory.
Example of SBATCH lines
#SBATCH --job-name=your_job_name #SBATCH --account=**ask Dr. Klauda** #SBATCH --partition=gpu-shared #SBATCH --nodes=1 #SBATCH --ntasks-per-node=1 #SBATCH --cpus-per-task=10 #SBATCH --mem=95G #SBATCH --gpus=1 #SBATCH --time=48:00:00