[gmx-users] Gromacs 4.6 segmentation fault with mdrun

Szilárd Páll szilard.pall at cbr.su.se
Thu Nov 29 02:49:58 CET 2012

Dear Makoto Yoneya,

Thank you for the feedback, it is of great help!

I will try to reproduce the issue because mdrun should not segfault with
any gcc version 4.3 and above. Could you please provide two more things:
- a log file of the failed run using the latest code from git;
- run mdrun with the "-debug 1" option, 0 steps is enough and provide the
mdrun.debug output?

These would be very useful to know the exact software setup you are using
(detailed information in the new header of the mdrun's log files) and the
location of the crash (based on the debug output).

(Large?) Attachments might still be turned off for the list so please
upload the files somewhere and send us a link (pastebin or a similar
service is fine).

Thank you in advance,


On Tue, Nov 27, 2012 at 11:43 PM, Makoto Yoneya <makoto-yoneya at aist.go.jp>wrote:

> Dear GROMACS users:
> On "Gromacs 4.6 segmentation fault with mdrun",
> I'd also met the same segmentation fault problem with gromacs-4.6.
> on my linux box with GTX-580.
> For my case, change the compilor solved this problem.
> Raf Ponsaerts wrote he used
> > gcc 4.4.5 (Debian 4.4.5-8), Linux kernel 3.1.1
> > CMake 2.8.7 .
> These were same in the version when I first met the problem.
> After that, I'd tried Intel compilor instead of gcc-4.4.x,
> then the GPU jobs runs without the segmentation fault.
> I also tried gcc-4.6.x and it also runs without
> any faults (I'm using CentOS and its gcc version is currentry
> gcc-4.4.x. Then, I had to compile gcc-4.6.x from the source.
> gcc-4.7.x can't use with CUDA-4.2 since it only suppoorts
> up to gcc-4.6.x.).
> I suggest to try either intel compilor or gcc-4.6.x instead of
> gcc-4.4.x.
> Makoto Yoneya, Dr.
> AIST, Japan
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