Re: namd on AWS

From: Milad Lagzian (milad.lagzian_at_gmail.com)
Date: Thu Oct 03 2019 - 00:39:20 CDT

A distant related question that I never got an answer for that in this
forum.

Why gpu acceleration does not work properly (Very low performance) on the
windows platform??

I appreciate any help you can provide.

Regards,

On Thu, Oct 3, 2019 at 00:19 Miro Astore <miro.astore_at_gmail.com> wrote:

> So you're getting a performance penalty too?
>
> I spoke to some people from AWS and they seemed surprised and skeptical
> that things were slower on their platform. Perhaps there is a system I
> could benchmark to show them.
>
> Best, Miro
>
> On Thu., 3 Oct. 2019, 02:02 Sanjay Hari, <shari_at_universalsequencing.com>
> wrote:
>
>> 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>
>> Date: Wed, 2 Oct 2019 at 11:04
>> Subject: Re: namd-l: namd on AWS
>> To: Sanjay Hari <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>
>> 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 <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
>>
>>

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