[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
spoel at xray.bmc.uu.se
Thu Mar 10 20:39:58 CET 2005
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
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
--
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
More information about the gromacs.org_gmx-users
mailing list