[gmx-users] GMX 4.0.5 on Altix 3700 BX2: Assembly Optimizations fixed?
David van der Spoel
spoel at xray.bmc.uu.se
Thu Sep 17 19:23:40 CEST 2009
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
Don't know, it must be something trivial I assume, but it is quite
> Thanks a lot.
>> 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,
>>>> gmx-users mailing list gmx-users at gromacs.org
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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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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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