[gmx-users] Gromacs on SGI Altix
mfyang at gmail.com
Tue Jan 3 17:52:09 CET 2006
Erik Lindahl wrote:
>> Thank you, Florian! I will try d.dppc. I have another question. Is
>> Gromacs specifically optimized for x86 machines, and the power of
>> Itanium2 is not fully used. Because for Amber8, my Itanium2 is
>> almost two times faster than my opteron, but for Gromacs, opteron is
>> slightly (~1.2 times) faster than Itanium2. Other factors are almost
>> same. Just due to the reason that there is no assembly loops
>> optimization for IA64?
> There are certainly assembly loops for IA64 (trust me, I handcoded
> them :-), it is just that the SIMD units of x86 machines enable much
> higher single precision throughput due to 4-fold parallelization,
> which we're happy to take advantage of in our assembly loops.
> If you compare double precision performance the difference between x86
> and ia64 will be much smaller.
Thank you, Erik! Anyway, I am impressed by the efficiency of Gromacs,
especially its performance on our opteron cluster. The scaling for the
SGI altix has come out; this time, with 2CPUs, it's 1.8 times faster
than single CPU. I don't care too much about altix, coz most of my job
will be run on opteron.
> Erik Lindahl <lindahl at sbc.su.se> Backup address:
> <erik.lindahl at gmail.com>
> Assistant Professor, Computational Structural Biology
> Stockholm Bioinformatics Center, Stockholm University, SE 106 91
> Phone: +46 8 5537 8564 Fax: +46 8 5537 8214
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