RE: namd on AWS

From: Sanjay Hari (shari_at_universalsequencing.com)
Date: Wed Oct 02 2019 - 11:00:55 CDT

That sounds about right. I get 0.06 days/ns on a system with a fourth as many atoms, on a p2.xlarge with 4 cpus. I think the main advantages are cost (overnight run on a spot instance was $3) and not having any overhead or maintenance for maintaining a cluster.

From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> On Behalf Of Miro Astore
Sent: Tuesday, October 1, 2019 11:47 PM
To: Namd Mailing List <namd-l_at_ks.uiuc.edu>
Subject: Fwd: namd-l: namd on AWS


---------- Forwarded message ---------
From: Miro Astore <miro.astore_at_gmail.com<mailto:miro.astore_at_gmail.com>>
Date: Wed, 2 Oct 2019 at 11:04
Subject: Re: namd-l: namd on AWS
To: Sanjay Hari <shari_at_universalsequencing.com<mailto:shari_at_universalsequencing.com>>

Thanks Sanjay,

I have tried a few things and experimented with numactl. At the moment I'm using, on a p3.8xlarge
charmrun namd +p8 +devices 3 smd.conf | tee smd.conf.log &

and my benchmark is 0.141994 days/ns

Best, Miro

On Tue, 1 Oct 2019 at 20:44, Sanjay Hari <shari_at_universalsequencing.com<mailto:shari_at_universalsequencing.com>> wrote:
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<mailto:owner-namd-l_at_ks.uiuc.edu> <owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu>> on behalf of Miro Astore <miro.astore_at_gmail.com<mailto:miro.astore_at_gmail.com>>
Sent: Tuesday, October 1, 2019 1:02:14 AM
To: Namd Mailing List <namd-l_at_ks.uiuc.edu<mailto: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

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