running NAMD with Slurm on cluster

From: Seibold, Steve Allan (stevesei_at_ku.edu)
Date: Wed Jan 09 2019 - 09:08:57 CST

I using a Slurm script for running NAMD across several machines (or attempting to that is). When I run 2 nodes with each having 15 cores, the Slurm output says, I am running "2 nodes" each with "15 cores". A total of 30 cores; however, my namd output (log file) says that I am running on 15 cores...

Below is my command line information...I know I don't use "+p ", but I have tried "mpirun" , "charmrun", and "mpiexe" placement in the below command line and I get "no such file or directory"...

I am using the NAMD_2.13 binary obtained from NAMD site...Do I need to build/compile it instead with mpi..?

~/NAMD2/NAMD_2.13_Linux-x86_64/namd2 md6_3BP.namd

Thanks, Steve

This archive was generated by hypermail 2.1.6 : Mon Sep 16 2019 - 23:20:14 CDT