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

[CHEN Pan]

Hi Mark,

What's the difference between the frames read and the frames analyzed?
Since g_sans read a frame, it's going to analyze it. Right or no?

By using -prframe and -sqframe flags, g_sans is going to analyze on each
frame in the trajectory, I would say the error depends on both (the frames
read and the frames analyzed).

2015-03-24 12:07 GMT+01:00 Mark Abraham <mark.j.abraham at gmail.com>:

> Hi,
>
> Does the erroneous behaviour depend on the number of frames read, or the
> number of frames analyzed?
>
> Mark
>
> On Tue, Mar 24, 2015 at 11:21 AM, CHEN Pan <evan.pan.chen at gmail.com>
> wrote:
>
> > 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
> > --
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-- 
Pan Chen
Postdoctoral Associate
Tailor-Made Fuels from Biomass
AICES Graduate School
RWTH Aachen University
+49(0)241 8099205