[gmx-users] Gromacs on SGI Altix

[Erik Lindahl]

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

-----------------------------------------------------------
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