Steve Cousins wrote:
On Thu, 17 Sep 2009, Carsten Kutzner wrote:
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.
Hi Carsten,
Thanks for the message. Since you say --enable-fortran is the default on
the SGI, I take it that it is already doing this even though I didn't
specify it. Correct? I guess it makes sense to just specify it to be sure.
Since there is a 10% speedup by going back to version 3.3, is there any
reason *not* to use 3.3 instead on the Altix? I'm sure there are other
bug fixes and features since then but I don't know much about MD so I
don't know how important they are. I'm just getting it to run on our
machine so the chemists can run the code.
Scaling is much better in 4.0.x. If you use more than 8 cores that
should compensate for the loss in single precision performance.
In addition there are other new features and bug fixes of course.
Since the optimizations worked in 3.3, it *seems* like it might not be
too bad to get them to work with the new version. Probably 4.0 was a
major re-write though. Are there any plans for fixing the IA64
optimizations?
Don't know, it must be something trivial I assume, but it is quite
specialist work.
Thanks a lot.
Steve
Carsten
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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