[gmx-users] Slow opterons : low Mega Flops

Erik Lindahl lindahl at sbc.su.se
Mon Sep 12 22:32:30 CEST 2005


We need details, details, details :-)

1. Skip MPI when it comes to basic performance testing.
2. Compile FFTW 2.1.5 and Gromacs (preferrably the new release  
candidate at ftp://ftp.gromacs.org/pub/beta/ ) with default options.
3. Download the standard benchmarks from www.gromacs.org
4. If you get results that seem to differ significantly from the ones  
quoted on the benchmark page, report with your CPU type and frequency  
here, and the exact results you get.

Remember to say whether you are running the operating system in 32 or  
64 bit mode, and check the logfile whether it is using assembly loops.

Check that you are not running other heavy jobs in the node when  
testing - Gromacs defaults to nice 19 (only use idle cycles), which  
means it's going to yield to almost everything else. At the end of  
the run you'll get a report both of the actual time, and the time  
used by Gromacs.



On Sep 12, 2005, at 9:53 PM, Gia Maisuradze wrote:

> Hi,
> I'm getting really slow performance on my opteron system,  
> performance that is roughly half that of my old athlon mp system.   
> I've tried recompiling the program with various options, mpi, no  
> mpi, threading, no threading, cpu optimized, not optimized, etc.   
> Does anyone work with opterons under suse 9.3 and have an idea  
> about what the best options for compiling lam, fftw, and gromacs  
> should be?
> Thanks,
> Gia Maisuradze
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