Here is the instructions to run NAMD on comet supercomputer:
your work directory is as follows: /oasis/scratch/comet/username all the files that you need to start a simulation are: equil.scr (for equilibrating a system with membrane) dyn.csh dyn.scr last.seqno dyn-1.inp dyn-2.inp
These files can be accessed in the following directory: /oasis/scratch/comet/jklauda/temp_project/pla18/popc/r1/namd
The following is an example of using GPU nodes on comet: In this example we are using 4 gpu nodes of type k80. Users should always set –ntasks-per-node equal to 6 x [number of GPUs] requested on all k80 “gpu-shared” jobs, and 7 x [number of GPUs] requested on all p100 “gpu-shared” jobs, to ensure proper resource distribution by the scheduler.
#!/bin/csh
#SBATCH -A mda123
#SBATCH –job-name=popcr1
#SBATCH –partition=gpu
#SBATCH –nodes=1
#SBATCH –ntasks-per-node=24
#SBATCH –export=ALL
#SBATCH –no-requeue
#SBATCH –gres=gpu:k80:4
#SBATCH -t 24:00:00
#
More information about comet supercomputer can be accessed from the following link: https://www.sdsc.edu/support/user_guides/comet.html