[gmx-users] mdrun segmentation fault for new build of gromacs 4.6.1
roland at utk.edu
Fri Jun 7 05:10:13 CEST 2013
I recommend to run the regressiontests. The simplest way is to build
GROMACS with cmake -DREGRESSIONTEST_DOWNLOAD, and run make check.
for more details.
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:
> 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
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