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--- comet [2017/12/21 14:58] – created admin
+++ comet [2019/01/31 10:35] (current) – edit
@@ Line 1: / Line 1: @@
-test
+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