[gmx-users] segfault on Gromacs 4.6.3 (cuda)

Szilárd Páll szilard.pall at cbr.su.se
Mon Sep 9 22:35:44 CEST 2013


First of all, icc 11 is not well tested and there have been reports
about it compiling broken code. This could explain the crash, but
you'd need to do a bit more testing to confirm. Regading the GPU
detection error, if you use a driver which is incompatible with the
CUDA runtime (at least as high API version, see the mdrun log header's
last two lines) and at the moment, some of such cases are not detected
particularly gracefully.

A few things to try:
- use gcc, 4.7 is as fast or faster than any icc;
- run with the "-nb cpu" option; does it still crash?
- run with GPU detection completely disabled*
- run the regressiontests; try using CPUs only*

*You can set the GMX_DISABLE_GPU_DETECTION environment variable to
completely disable the GPU detection.


On Mon, Sep 9, 2013 at 9:52 PM, Guanglei Cui
<amber.mail.archive at gmail.com> wrote:
> Dear GMX users,
> I recently compiled Gromacs 4.6.3 with CUDA (Intel compiler 11.x, SSE2, and
> CUDA SDK 5.0.35). I was doing a test run with simply 'mdrun -deffnm
> eq2_npt_verlet' (letting mdrun figure out what to use). I received the
> error telling me my graphics driver was older than the CUDA SDK, and
> regular CPU code would be used instead. Then, it crashed with Segmentation
> Fault. The code runs properly on another node where the graphics driver is
> more up to date. I wonder if the crashing is somewhat expected, and
> therefore I should prepare different binaries based on  the capabilities of
> different nodes. Thanks.
> Best regards,
> --
> Guanglei Cui
> --
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