[gmx-users] g_sans_mpi problem: bus error (core dumped)

[CHEN Pan]

Dear all,

I am using g_sans_mpi (4.6.4 version) to calculate a SANS curve of a system
containing about 15000 atoms in total (water, urea, NaOH and oligomers).
The command used are listed below.

*echo 0 | g_sans_mpi -f ../md.xtc -s ../md.tpr -pr -sq -pbc -mode direct
-xvg none -b 50000 -e 100000*

The thing is that with calculation for 5 ns of MD trajectory, no error
occurred, whereas for calculation of 50 ns trajectory. An error message
shows " zsh: bus error (core dumped)", or shows "segmentation fault 11"
sometime. With increasing memory or increasing number of threads (-nt)
didn't help.

I have googled for both "g_sans" and "bus error". It seems nobody has ever
meet such problem with using g_sans. I understand the manual says that
computational cost is going to increase when using -pr and -sq, as well as
the increase of number of system particles. Then I tried to calculate SANS
curves for each frame with the following command. Still, the same error
occurred after reading over 10 ns of frames.

*echo 0 | g_sans_mpi -f ../md.xtc -s ../md.tpr -prframe -sqframe -pbc -mode
direct -xvg none -b 50000 -e 100000*

Welcome for any comments and potential explanations.

Best,
Pan