Re: NAMD CUDA performance degradation

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Jul 23 2009 - 15:19:16 CDT

On Thu, 2009-07-23 at 14:31 -0500, Thomas C. Bishop wrote:
> Ok so I downloaded NAMD/FFT/TCl/CHARM and did the compile thing for our GPU
> system (2x Tesla C1060 that do show up on namd output as binding)

> The upshot: compiling as per instructions is a no brainer (if I can do it...)
>
> The downside: CUDA runs slower than w/out (hmm.. maybe I shouldn't be one
> doing this )
>
> Below are benchmarks lines from the two systems.
> the hardware is 16core/NODE w/ 2GPUs. I'm running on 1 NODE to avoid network
> issues.

tom,

using 16 cores (what CPU is this?) with two GPUs is overdoing it.
how fast does it run with 2 or 4 cores? with and without?

cheers,
   axel.

> THE NAMD LOGS HAVE THESE MESSAGES:
>
> Bad result from CmiGetPesOnPhysicalNode!
> pe 10 physnode rank 0 of 1 is 0
>
> AND
>
> Charm warning> Randomization of stack pointer is turned on in Kernel,
> run 'echo 0 > /proc/sys/kernel/randomize_va_space' as root to disable it.
> Thread migration may not work!
>
>
> Suggestions?
>
> Tom
>
>
>
> SYTEM 1: 134335 ATOMS protein-DNA complex
> ***************************
>
> cuda.16.out:Info: Benchmark time: 16 CPUs 0.23318 s/step 1.34942 days/ns
> 76.3906 MB memory
> cuda.16.out:Info: Benchmark time: 16 CPUs 0.233269 s/step 1.34994 days/ns
> 76.4316 MB memory
>
> nocuda.16.out:Info: Benchmark time: 16 CPUs 0.213155 s/step 1.23353 days/ns
> 82.3376 MB memory
> nocuda.16.out:Info: Benchmark time: 16 CPUs 0.213293 s/step 1.23433 days/ns
> 82.5941 MB memory
>
>
> SYSTEM 2: the APO system ~100,000 atoms
> *******************
> apo.cuda.16.out:Info: Benchmark time: 16 CPUs 0.178929 s/step 2.07094 days/ns
> 55.6983 MB memory
> apo.cuda.16.out:Info: Benchmark time: 16 CPUs 0.178775 s/step 2.06915 days/ns
> 55.7847 MB memory
>
> apo.nocuda.16.out:Info: Benchmark time: 16 CPUs 0.171169 s/step 1.98112
> days/ns 61.6952 MB memory
> apo.nocuda.16.out:Info: Benchmark time: 16 CPUs 0.17114 s/step 1.98078 days/ns
> 61.3251 MB memory
>
>
>

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.

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