[gmx-users] mdrun segmentation fault for new build of gromacs 4.6.1

[Roland Schulz]

Hi,

I recommend to run the regressiontests. The simplest way is to build
GROMACS with cmake -DREGRESSIONTEST_DOWNLOAD, and run make check.
See http://www.gromacs.org/Documentation/Installation_Instructions#.c2.a7_4.12._Testing_GROMACS_for_correctness
for more details.

Roland

On Thu, Jun 6, 2013 at 4:56 PM, Amil G. Anderson
<aanderson at wittenberg.edu> wrote:
> Gromacs users:
>
> I have just built and installed gromacs-4.6.1 on my Xeon 5500 compute cluster running Centos 5.  The installation was done with gcc 4.7.0
>
> I have run a simple test (the old tutor/gmxdemo) which fails at the first mdrun step with a segmentation fault.  The command line for this step is:
>
> mdrun -nt 1 -s cpeptide_em -o cpeptide_em -c cpeptide_b4pr -v -debug 1
>
> where I have included the debug flag and have restricted the run to one core.  The files associated with this run are located at:
>
> https://www.dropbox.com/sh/h6867f7ivl5pcl9/j9gt9CsVdP
>
>
> I have done a test build of gromacs-4.5.4 (version I have been running the last year) with the same build environment as the 4.6.1 build, including using cmake.  The rebuild of gromacs-4.5.4 runs the demo completely.
>
> Given the limited information for the run (segmentation fault seems to occur just after reading in the parameters), I'm not sure how to further pursue the source of this error.  I have also tried building gromacs-4.6.2 but have the same error for mdrun.
>
> Thanks for any insight that you may be able to provide.
>
> Dr. Amil Anderson
> Associate Professor of Chemistry
> Wittenberg University
>
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>



-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309