On Wed, Sep 19, 2012 at 11:43 PM, marawan hussain
<marawanhussain.yahoo.com>wrote:
> Dear AMBER usesrs,
> I tried to monitor the performance with different libraries and number of
> processors, the results are in the follwoing table:
> Number of processor Performance(ns/day) MPI Library
> 2 0.15
> mvapich2
> 4 0.21
> mvapich2
> 8 0.28
> mvapich2
> 16 0.20
> mvapich2
> 32 0.03
> mvapich2
>
>
>
> Could someone comment on this
>
/*
http://ambermd.org/amber10.bench1.html (similar performance for pmemd
12) */
Joking aside, many things affect performance -- interconnect, compilers,
your computer system, your simulated system, sander vs. pmemd (pmemd is
much better), PME vs. GB (GB scales much better), NTP vs. NVT vs. NVE (NVE
is fastest), ig=-1 for Langevin dynamics vs. ig>0 (ig=-1 scales better for
langevin dynamics), and so on (there are a lot more).
If you can't get your calculations to scale similar to what is found on the
benchmark site, I would probably blame poor interconnect first (note it's
not just the speed of the interconnect, but also the interconnect topology
that plays a role in modulating parallel scaling). Unfortunately, if your
cluster has a bottleneck that isn't present in the benchmark test systems,
there's no getting around that unless you're willing to replace that
hardware (and there are way to many possibilities for us to benchmark even
a representative fraction of different cluster configurations).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Sep 19 2012 - 21:00:03 PDT
