[gmx-users] Gromacs on SGI Altix

Mingfeng Yang mfyang at gmail.com
Tue Jan 3 17:52:09 CET 2006

Erik Lindahl wrote:
> Hi,
>> 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.
> Cheers,
> Erik
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 
> Stockholm
> Phone: +46 8 5537 8564     Fax: +46 8 5537 8214
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