Re: namd on AWS

From: Sanjay Hari (shari_at_universalsequencing.com)
Date: Tue Oct 01 2019 - 05:42:15 CDT

I really like the AMI. Some details would help here, such as your run command, number of processors invoked, and benchmark statistics. The gpu tutorial gives a good primer on benchmarking cuda-accelerated runs.
________________________________
From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of Miro Astore <miro.astore_at_gmail.com>
Sent: Tuesday, October 1, 2019 1:02:14 AM
To: Namd Mailing List <namd-l_at_ks.uiuc.edu>
Subject: namd-l: namd on AWS

Hello everyone.

I am trying to run the namd AMI package and I'm not getting very good performance. I've tried a few types of p2 and p3 node types and I can't get comparable performance to my university's HPC clusters when running 2 workloads on the same node. ~200000 atom system. The performance doesn't appear to be very different from copying over the precompiled binary from the website. Just wondering if anyone else has encountered this issue.

https://aws.amazon.com/marketplace/pp/B06VSMMHRY

Completely possible I'm just not running things in the correct way, so I would be very interested to see how you guys run things.

Best, Miro

This archive was generated by hypermail 2.1.6 : Sat Dec 07 2019 - 23:20:51 CST