[gmx-users] Possible problem in trxio.c

[David van der Spoel]

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.
________________________________________________________________________
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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