[gmx-users] Possible problem in trxio.c

David van der Spoel spoel at xray.bmc.uu.se
Thu Jul 1 16:52:56 CEST 2004

On Thu, 2004-07-01 at 16:25, Pierfrancesco Zuccato wrote:
> [Sorry, I've sent it in HTML, now reversing to text mode]
> Dear David,
> here are the VERY preliminary results. I've run d.dppc as I have 
> downloaded it from the gromacs site.
> Please do not consider these numbers as significant for any comparisions 
> between processors/architecture. This is NOT optimized.
> I think that it should be possible to improve performance by changing 
> compilation options (expecially in fftw and gromacs).
> For the time being I just wanted to check if the code compiled and run 
> successfully.
> Are there any news on the new assembly loops for the Opteron?
> I read a message mentioning that gromacs 4 will know of the k8 architecture.
This will not make a big change, at least not for single precision.
According to Erik L. the performance is identical.

> What do you think of creating a page on the gromacs site with the best 
> optimization flags for the major processors? I guess that most users 
> have tried this, but it is quite complex and time-consuming. I'm 
> thinking of something like a Wiki.
Could be useful, we could do it at gromacs.org, but the disadvantage of
a Wiki (as compared to a mailing list) is that you have to go there and
check out stuff.

> It would also be great to have a place where people could share 
> protocols for the most common simulations.this would make it easier to 
> learn (for novices) and to compare (for experts)
We could add a section on the web site where people could upload input
files, like you can already do with topologies, or, alternatively a few
examples of "recommended" parameters.

> System: Opteron quad processor
> vendor_id : AuthenticAMD

Your numbers are a bit disappointing indeed, I wonder whether it could
be due to the compiler. Portland is even slower than gcc! For your
fastest run you got 612 ps/day on 4 processors, compared to my 414
ps/day on a dual Opteron. However, I used the Intel compiler and MPICH
(comes with the Rocks cluster).

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone:  +46 18 471 4205  fax: +46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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