[gmx-users] GMX 4.0.5 on Altix 3700 BX2: Assembly Optimizations fixed?

Carsten Kutzner ckutzne at gwdg.de
Thu Sep 17 17:40:38 CEST 2009

Hi Steve,

I made some tests on an Altix 4700 some time ago because I ran into
the same problem. If you use the fortran loops (--enable-fortran, which
is the default on sgi) you do not loose much performance. Here are
my benchmark results with a 80000 atom protein+bilayer+water
simulation on a single core:

inner loops  ns/day
C                 0.12
fortran         0.29
assembly    0.32

This was with gromacs 3.3, where the assembly kernels still worked on
that machine.


On Sep 17, 2009, at 5:19 PM, Steve Cousins wrote:

> I have installed Gromacs 4.0.5 on a 64 CPU Altix 3700 BX2 and when  
> running mdrun it just seems to spin there. It uses 100% of one CPU  
> but doesn't finish. I scanned through the list and found that I  
> should try setting the NOASSEMBLYLOOPS environment variable. By  
> doing this it runs now and the gmxtest.pl script comes out with most  
> tests passing.
> Is there some way to compile gromacs to be able to use the assembly  
> optimizations for the Itanium2 processor? I'm using the Intel 11.1  
> compilers (icc and ifort). Am I missing much performance by not  
> being able to take advantage of the optimizations?
> Thanks a lot,
> Steve
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Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302

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