[gmx-users] Bus error

[Erik Marklund]

Hi users,

A simulation of mine ran fine for 3955000 steps and then failed with a Bus error shown below. I compiled gromacs 4.5.5 with gcc 4.5.3, fftw 3.2.2, and linked to openmpi 1.4.5. Anyone recognize this?

[q6:22593] *** Process received signal ***
[q6:22593] Signal: Bus error (7)
[q6:22593] Signal code:  (2)
[q6:22593] Failing at address: 0x2b8d50c71b20
[q6:22597] *** Process received signal ***
[q6:22597] Signal: Bus error (7)
[q6:22597] Signal code:  (2)
[q6:22597] Failing at address: 0x2aedade56b20
[q6:22595] *** Process received signal ***
[q6:22595] Signal: Bus error (7)
[q6:22595] Signal code:  (2)
[q6:22595] Failing at address: 0x2abd765a5b20
[q6:22594] *** Process received signal ***
[q6:22594] Signal: Bus error (7)
[q6:22594] Signal code:  (2)
[q6:22594] Failing at address: 0x2adc173a2b20
[q6:22596] *** Process received signal ***
[q6:22596] Signal: Bus error (7)
[q6:22596] Signal code:  (2)
[q6:22596] Failing at address: 0x2b839de73b20
runcommands: line 1: 22573 Bus error               (core dumped) mpirun mdrun_mpi -deffnm run -c run.pdb -cpi -cpo -maxh 24 -npme 32

-----------------------------------------------
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 6688        fax: +46 18 511 755
erikm at xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html