From: Bennion, Brian (bennion1_at_llnl.gov)
Date: Wed Dec 02 2020 - 17:05:50 CST
You will be needing to use at least 10 more nodes to approach the throughput you are accustomed to seeing. That is where MPI or Ifiniban will be playing the key role in the calculations.
Your sysadmin will be able to tell you if/what mpi exists on the cluster.
From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of McGuire, Kelly <mcg05004_at_byui.edu>
Sent: Wednesday, December 2, 2020 2:51 PM
To: namd-l_at_ks.uiuc.edu <namd-l_at_ks.uiuc.edu>
Subject: namd-l: CPU vs GPU Question
In all of my simulations so far, I have used one node with 4xP100 GPUs and 24 CPU cores. I usually get ~40 ns/day with a system between 75,000 and 150,000 atoms. I am now trying to do a simulation that is 1.4 million atoms. Currently getting ~4 ns/day.
What is a better approach to speed up this simulation as atom number scales? More GPUs on one node or more CPUs and use multiple nodes? Where does MPI come into play here?
Dr. Kelly L. McGuire
Department of Physiology and Developmental Biology
Brigham Young University
Provo, UT 84602
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