Re: [AMBER] AMBER/sander parallel performance problem

From: Niel Henriksen <niel.henriksen.utah.edu>
Date: Thu, 28 Jul 2011 18:18:43 -0600

oops, i didn't read closely enough.
You have a lot of cores per node.
pmemd.MPI still might be the answer.

--Niel
________________________________________
From: Niel Henriksen [niel.henriksen.utah.edu]
Sent: Thursday, July 28, 2011 6:16 PM
To: AMBER Mailing List
Subject: Re: [AMBER] AMBER/sander parallel performance problem

In my experience, sander.MPI does not scale well past 3 or 4 nodes.
Try pmemd.MPI for better scaling.

--Niel
________________________________________
From: Jyh-Shyong [jyhshyong0.gmail.com]
Sent: Thursday, July 28, 2011 6:00 PM
To: amber.ambermd.org
Subject: [AMBER] AMBER/sander parallel performance problem

Dear Amber users,

I just installed Amber11 on our new cluster computer, and ran some test
cases on it.
Each node has 48 cores, and all nodes are connected with QDR infiniband.

I built parallel version of sander with both mvapich2-1.5 and
openmpi-1.4.3. The
performance of the program is quite strange:

Here is a case using 1 core, it took about 1 hr and 24 min:
| Job began at 10:00:53.602 on 07/27/2011
| Setup done at 10:00:54.844 on 07/27/2011
| Run done at 11:23:48.604 on 07/27/2011

And the case using 48 core (one computing node), it took about 9 min 40s

| Job began at 20:32:36.572 on 07/28/2011
| Setup done at 20:32:38.436 on 07/28/2011
| Run done at 20:41:17.902 on 07/28/2011

It is nice.

However, the case using 192 cores (4 computing nodes), it took about 12
min. !
| Job began at 20:20:14.506 on 07/28/2011
| Setup done at 20:20:17.208 on 07/28/2011
| Run done at 20:31:26.587 on 07/28/2011

Something is wrong when using more than one computing node, I
followed the installation
guide and compile the program using both intel and gcc compiler with MKL
lilbrary. I always
got the similar result.

Any hint on how this could happen and who to fix the problem?

Thanks.

Jyh-Shyong Ho, Ph.D.
Research Scientist
National Center for High Performance Computing
Hsinchu, Taiwan, ROC

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Received on Thu Jul 28 2011 - 17:30:06 PDT
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