NAMD on Stampede 2

From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Thu Oct 05 2017 - 18:23:05 CDT

• Next message: Giacomo Fiorin: "Re: NAMD on Stampede 2"
• Previous message: Brian Radak: "Re: convergence criterion of free energy perturbation (FEP) simulations for pKa calculation"
• Next in thread: Giacomo Fiorin: "Re: NAMD on Stampede 2"
• Reply: Giacomo Fiorin: "Re: NAMD on Stampede 2"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hello,

I am trying to run NAMD on Stampede 2 but it is not scaling the way it
should. Here is what I have in my submission script

*module load intel/16.0.3module load impimodule load namd/2.12mpiexec -np 2
namd2 +ppn 64 filename.conf > logfile.log*

I have also tried "ibrun" instead of mpiexec but the problem persists.

Best,
Chitrak.

• Next message: Giacomo Fiorin: "Re: NAMD on Stampede 2"
• Previous message: Brian Radak: "Re: convergence criterion of free energy perturbation (FEP) simulations for pKa calculation"
• Next in thread: Giacomo Fiorin: "Re: NAMD on Stampede 2"
• Reply: Giacomo Fiorin: "Re: NAMD on Stampede 2"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:21:42 CST