[gmx-users] Gromacs 4.6 crashes w/AVX acceleration on cygwin

Szilárd Páll szilard.pall at cbr.su.se
Wed Feb 27 21:21:24 CET 2013


Thanks for the detailed information!

The only reason why cygwin is cumbersome is that we are not testing it
actively, have we had a developer or contributor working with cygwin there
would be no issues.

In any case, especially because there is performance involved, we should
try to get the AVX issue solved. First and foremost, would you mind filing
a redmine issue on the issue (or if you consider the dll problem annoying,
feel free to file a second one).

However, before filing the AVX bug report, please try the following:
- A newer gcc, preferably 4.7; although in *nix 4.5 seems to work with AVX,
it's best if we have things tested with the latest gcc.
- SSE4.1 acceleration; beside that this should be faster than SSE2, but if
that doesn't work either something is seriously broken.

If you manage to get performance numbers with the above, please provide
them, here for the sake of completeness. I would be surprised if VS2010
would outperform gcc 4.7, though.



On Wed, Feb 27, 2013 at 8:31 PM, Mirco Wahab <
mirco.wahab at chemie.tu-freiberg.de> wrote:

> Out of curiosity, I installed cygwin  1.7.17-1 on my AMD/FX-8350
> workplace box (W8Pro/x64). This is what I found out:
> - Gromacs 4.6 compiles smooth but crashes w/native(AVX_128) on
>    simulation start with loads of fp errors (non-reproducible,
>    sometimes stops w/no error at all, just stops)
> - Gromacs 4.6 runs fine if compiled w/GMX_CPU_ACCELERATION=SSE2,
>    even if PME involved (see below)
> - Gromacs shared executables (runtime-dlls) didn't start due to
>    some erratic dlopen problems with I didn't understand. By
>    using GMX_PREFER_STATIC_LIBS=ON, this was solved
> I testet a "Martini"-system of ~1 Mio particles (a 50^3nm water
> box with a vesicle). Performance comparison:
>   VS2010(x64)      - md/cut-off/Reaction-Field : 37.460 ns/day
>   cygwin/gcc 4.5.3 - md/cut-off/Reaction-Field : 30.304 ns/day
>   VS2010(x64)      - md/cut-off/PME : 10.874 ns/day
>   cygwin/gcc 4.5.3 - md/cut-off/PME :  9.283 ns/day
> The fftw3f used was installed before from source. I'll attach
> a recipe for both builds and some more hints below.
> Resumé: cygwin installation of Gromacs 4.6 is (still) cumbersome
> and may throw up suprising errors. For windows users, looks much
> more promising (imho!) to build Gromacs with the Visual Studio
> compiler (which is, through combination of VS2010 express +
> SDK 7.1, free of cost).
> "works on my machine"-instructions: =>
> --
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