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

Mark Abraham mark.j.abraham at gmail.com
Wed Feb 27 22:26:06 CET 2013

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)

If the compiler version is the standard 4.5.3 provided for Cygwin (
http://cygwin.com/packages/gcc4/), then that is close to the 4.5.2 that we
know has AVX problems. There are certainly versions of gcc in its 4.4-4.6
series that are known to have broken support for intrinsics, e.g.

- Gromacs 4.6 runs fine if compiled w/GMX_CPU_ACCELERATION=SSE2,
>    even if PME involved (see below)

That's consistent with a broken compiler.

> - 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

Is there any other version of GROMACS installed? We didn't bump the shared
object version for a very long time, so conflicts there could occur. We've
bumped them for upcoming releases.

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).

I'd add that the GROMACS installation instructions do recommend the latest
version of whatever compiler. Just using the compiler that came with your
distro is somewhat likely to be broken according to the age of that
compiler and your hardware. But it's good to know that the Cygwin gcc is
suspicious, because we can warn people in future.


> "works on my machine"-instructions: =>
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