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

[David van der Spoel]

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
>> http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne
>>
>>
>>
>>
>>
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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