[gmx-users] GPU warnings

Szilárd Páll szilard.pall at cbr.su.se
Tue Dec 11 19:02:08 CET 2012

On Tue, Dec 11, 2012 at 6:49 PM, Mirco Wahab <
mirco.wahab at chemie.tu-freiberg.de> wrote:

> Am 11.12.2012 16:04, schrieb Szilárd Páll:
>  It looks like some gcc 4.7-s don't work with CUDA, although I've been
>> using
>> various Ubuntu/Linaro versions, most recently 4.7.2 and had no
>> issues whatsoever. Some people seem to have bumped into the same problem
>> (see http://goo.gl/1onBz or http://goo.gl/JEnuk) and the suggested fix is
>> to put
>> #undef _GLIBCXX_USE_INT128
>> in a header and pre-include it for nvcc by calling it like this:
>> nvcc --pre-include undef_atomics_int128.h
> The same problem occurs in SuSE 12.2/x64 with it's default 4.7.2
> (20120920).
> Another possible fix on SuSE 12.2: install the (older) gcc repository
> from 12.1/x64 (with lower priority), install the gcc/g++ 4.6 from there
> as an alternative compiler and select the "active gcc" through the
> "update-alternatives --config gcc" mechanism. This works very well.

Thanks for the info. The Ubuntu/Linaro version must have a fix for
this. Unfortunately, we can't do much about it and gcc 4.7 is anyway
blocked by the CUDA 5.0 headers.

FYI: Verlet scheme nonbonded kernels (and probably the group scheme as
well), especially with AVX, can be quite a bit slower with older gcc

I find it really annoying (and stupid) that NVIDIA did not fix their
compiler to work with gcc 4.7 which had already been out for almost a half
a year at the time of the CUDA 5.0 release.


> Regards
> M.
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