[gmx-users] known bug? compiling gromacs 3.2.1 with gcc 3.3.5 using -march=athlon-whatever gives strange mdrun results on AMD athlon systems

[David]

On Thu, 2005-03-10 at 13:25 -0600, Sabuj Pattanayek wrote:
> Hi,
> 
> Has anyone had problems with strange mdrun results after running a 
> simulation with gromacs 3.2.1 compiled using -march=athlon-xp or 
> -march=athlon-mp on athlon-xp and athlon-mp systems? For example here 
> are some sections from some log files (naming is like this: 
> energyMinimization_systemType_gccMarchCompileFlag):
> 
> this output is "correct" (from em-celeronM_pentium4.log):
> 
> Steepest Descents converged to Fmax < 1000 in 37 steps
> Potential Energy  = -3.9011406e+04
> Maximum force     =  9.3552039e+02 on atom 88
> Norm of force     =  6.2108813e+03
>  NODE (s)   Real (s)      (%)
> Time:     23.000     23.000    100.0
> 
> "incorrect" output (from em-xp2800_athlon-xp.log)
> 
> Steepest Descents converged to machine precision in 15 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy  =            nan
> Maximum force     =  2.2911844e+04 on atom 836
> Norm of force     =  9.9849359e+04
> NODE (s)   Real (s)      (%)
> Time:      6.000      6.000    100.0
> 
> ...compiling gromacs 3.2.1 on athlon systems with -march=i686 fixes this 
> problem (from em-xp2800_i686.log):
> 
> Steepest Descents converged to Fmax < 1000 in 37 steps
> Potential Energy  = -3.9011410e+04
> Maximum force     =  9.3552039e+02 on atom 88
> Norm of force     =  6.2109053e+03
> NODE (s)   Real (s)      (%)
> Time:     14.000     14.000    100.0
> 
> I found a similar post here 
> http://www.gromacs.org/pipermail/gmx-users/2003-May/005614.html and 
> under "Which machine do you recommend?" at 
> http://www.gromacs.org/benchmarks/single.php it says athlon bugs were 
> fixed in gromacs 3.2.1? Is this related to the same problem or is this a 
> gcc bug? Is there even any loss of performance when compiling with i686 
> rather than athlon-xp or -mp? I tried to compare with a pentium4 3.2 GHz 
> machine with gromacs compiled using -march=pentium4 but the same 
> simulation takes 50-60 seconds (slower than the celeron M 1.3GHz)! The 
> compilations were done using gcc version 3.3.5, lam-mpi 7.0.6, fftw 
> 3.0.1, and using single precision.
If you omit the -march options it will probably do the right thing. If
your new pentium is slower it may be because it is running a 64 bit OS. 
Compile gromacs on a 32 bit OS and run the code on your 64 bit OS and it
will be fine.


> 
> Thanks,
> Sabuj Pattanayek
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-- 
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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