From: Roberts, Jason (Jason.Roberts_at_mh.org.au)
Date: Sun Sep 16 2012 - 17:08:55 CDT
We are running a 2U rack (2x Xeon E5645, 4xM2090) and although I don't have the same setup I ran the Apoa1 benchmark allocating 6 cores and 1 M2090 (./namd2 +idlepoll +p6 +devices 0 apoa1.namd > apoa1_6.out). The default benchmark gave 0.049 s/step. I changed the outputEnergies and outputTiming values to 1000 and extended the run to 10000 steps and got 0.038 s/step.
If I run the last simulation with 1 core and 1 GPU (./namd2 +idlepoll +p1 +devices 0 apoa1.namd > apoa1_1.out) I get 0.122 s/step.
Hope this helps.
PS, if anyone is interested, I ran multiple simultaneous runs with different combinations of CPU and GPU allocations and obtained the following results:
Apoa1 (10,000 steps, timestep = 1, outputs at 1000steps)
1 run (12xThreads 4xM2090) = 0.015 s/step
1 run (24xThreads 4xM2090) = 0.016 s/step
2 runs (6xThreads, 2xM2090) each = 0.027 s/step
2 runs (12xThreads, 4xM2090 shared) = 0.026 s/step
4 runs (3xThreads, 1xM2090) each = 0.051 s/step
4 runs (6xThreads, 4xM2090 shared) = 0.046 s/step
8 runs (3xThreads, 4xM2090 shared) = 0.088 s/step
(Hyperthreading is ON)
Jason A. Roberts
Senior Medical Scientist
National Enterovirus Reference Laboratory
WHO Poliomyelitis Regional Reference Laboratory
VIDRL, 10 Wreckyn Street,
North Melbourne, Australia, 3051
Phone: +613 9342 2607
Fax: +613 9342 2665
email: polio_at_mh.org.au (lab enquiries)
web site: www.vidrl.org.au
Date: Fri, 14 Sep 2012 09:50:41 -0400
From: Guanglei Cui <amber.mail.archive_at_gmail.com>
Subject: Re: namd-l: GTX-660 Ti benchmark
I'm curious what kind of performance I should expect from a M2090 card (Intel Xeon X5670, CentOS 5.8). With 1 CPU and 1GPU, I get 0.11 s/step on Apoa1 (2000 steps, timestep 1) using the namd2.9 multicore CUDA binary from the NAMD website. I suspect this is a reasonable speed. I wonder if someone would kindly point out what a reasonable expectation is for this type of setup, and how to achieve that. Thanks very much.
On Thu, Sep 13, 2012 at 11:10 PM, Wenyu Zhong <wenyuzhong_at_gmail.com> wrote:
> Sorry, a correction.
> The power consumption with i5_at_3.7G+660ti running apoa1 is about 200w,
> and with i5_at_3.7G+2*460 is about 260w.
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