[gmx-users] Re: latest benchmarks (Itanium/Xeon/Opteron)

Erik Lindahl lindahl at csb.stanford.edu
Mon Jan 19 15:13:00 CET 2004


> On Mon, 2004-01-19 at 14:46, Michel Cuendet wrote:
>>   The --disable-software-sqrt option doesn't help. I noted also that
>> gromacs single precision computes wrong results (box exploding
>> systematically), whereas double precision doesn't take more time and
>> gives more reasonable output.
> This shouldn't be... What system is that? Is it reproducible, i.e. the
> same tpr gives different results in single and double?

I think I've disabled software sqrt by default on ia64, so that  
explains the lack of effect.

To help isolate the problem, check if it occurs:

(A) when you use gcc
(B) when you use a lower level of optimization (e.g. -O1)

Using the Intel Fortran compiler might give you slightly better  
performance, otherwise you'll have to wait a *little* while longer for  
the assembly loops.



>> IPO: performing multi-file optimizations
>> ../mdlib/.libs/libmd.a: could not read symbols: Archive has no index;
>> run ranlib to add one
>>    Is there any simple way to work this out ?
> Hm, past experience with IPO on SGI machines taught me that there is
> nothing much to gain there. In particular since we don't really call  
> any
> functions from one module that would gain from inlining into another
> module.
>> P.S. :  If needed, I could run benchmarks for developpers on either
>> opteron+myrinet or itanium2.
> Thanks, that will come in useful at some stage.
> --  
> David.
> _______________________________________________________________________ 
> _
> David van der Spoel, PhD, Assist. 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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