VMD-L Mailing List
From: Roman Petrenko (rpetrenko_at_gmail.com)
Date: Mon Feb 16 2009 - 22:07:30 CST
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sorry, the subject line meant to be "vmd with cuda1.1"
runtime cpu 101489 sec
runtime gpu 234 seconds
still similar speedup 433.7
could it be due to some threads interference?
Using 4 CPUs
thread 0 started...
thread 3 started...
thread 2 started...
thread 1 started...
why is it using 4 threads? i submitted a job with -lnodes=1:ppn=1 option.
i'll update later on what compiler was used.
On Mon, Feb 16, 2009 at 10:56 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> The GFLOPS numbers indicate the number of floating point
> calculations, but not the runtime. The speedup is based on the
> different in runtime not on GFLOPS. There are various differences
> in the algorithm used on the GPU vs. the algorithm used on the CPU,
> making the CPU more efficient in GFLOPS/runtime than the GPU is.
> I think if you divide the runtimes out, you'll get a speedup closer
> to the range we see, assuming you run a build done with the Intel
> compiler and not just GCC. GCC doesn't generate very good code for
> this particular kernel, and just using the Intel compilers will
> improve the CPU performance by a large factor vs. GCC.
> Let me know if you have further questions.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Feb 16, 2009 at 10:47:16PM -0500, Roman Petrenko wrote:
>> Hi all,
>> i ran time-averaged coulomb potential evaluations (downloaded from vmd
>> cuda website) and got more than 500 speedup on nvidia 9800 gpu vs cpu.
>> gpu speed 265.45 GFLOPS
>> cpu(4 threads) speed 0.497122 GFLOPS
>>
>> how is it possible? According to John Stone presentations the speedup
>> is expected to be at around 30 or 100.
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>
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