[gmx-developers] Profiling

Erik Lindahl lindahl at cbr.su.se
Fri Oct 31 21:29:23 CET 2008


I've periodically checked with Shark on Macs (including Core2 CPUs),  
and the pattern hasn't changed that much, apart from tables getting  
relatively more expensive (memory access).

I forgot exactly what % of theoretical peak we achieve, but suffice to  
say it's embarrassing (which it didn't use to be :-)

However, I also checked a lot of the nonbonded kernel options when  
testing 4.0, and most of the things like inlining 1/sqrt, force  
prefetching, etc. don't make sense anymore - compilers do a pretty  
good job there nowadays.



On Oct 31, 2008, at 8:55 PM, David van der Spoel wrote:

> On Fri, 31 Oct 2008, Roland Schulz wrote:
>> Hi,
>> as a follow up to the other tools thread (finding functions):
>> Two profiling tools, which may be not so well known, and I think a  
>> very
>> useful are:
>> mpiP (mpip.sourceforge.net): It measures MPI time per code line
>> (traceback possible). One only needs to compile with -g and link  
>> the mpip
>> library. It gives a very quick overview why runtime is different on
>> different clusters.
>> hpctookit (hpctoolkit.org/): It uses sampling to pinpoint the  
>> number of
>> spent cycles, caches misses, FLOPs to the code line (also for  
>> assembler).
>> By keeping the sampling interval long enough the overhead is  
>> neglictable.
>> In case someone is interested I'm happy to give some more  
>> information or
>> examples.
>> Can you recommend any other tools besides those and MPE/jumpshot?
>> Roland
> Did ayone profile the serial code recently on a modern processor?  
> Back in the day we used to make very good use of available hardware  
> (Pentium 3). Butit would be interesting to first how efficient the  
> code is now, (% of theoretical flops) and where the bottlenecks  
> currently are.
>> --
>> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Professor of Biology
> 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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