From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu May 05 2011 - 08:57:18 CDT
one more comment. the apoa1 test is not a very realistic test,
as it uses rather short cutoffs and thus has less work in the
non-bonded kernel, which is the GPU accelerated part in NAMD.
i would do another comparison with longer cutoffs and pit
CPU vs. GPU and that should - in theory - make the GPUs
look a bit better.
2011/5/5 Nicholas M Glykos <glykos_at_mbg.duth.gr>:
> Hi Dave,
>> 12 CPU core + 4 GPU : 0,34 days/ns
> For the same test (apoa1), we get 0.29 days/ns from an i7 (four cores)
> plus a single GTX295 card˛, so I would suspect that there is space for
> improvement with your hardware. FYI, we perform the cuda run with
> something like /usr/local/namd_cuda/charmrun ++local \
> /usr/local/namd_cuda/namd2 +p4 +idlepoll +noAnytimeMigration \
> +setcpuaffinity +LBSameCpus something.conf
> ˛ http://norma.mbg.duth.gr/index.php?id=about:benchmarks:namdv27cuda
> Dr Nicholas M. Glykos, Department of Molecular Biology
> and Genetics, Democritus University of Thrace, University Campus,
> Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
> Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 Institute for Computational Molecular Science Temple University, Philadelphia PA, USA.
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