[gmx-users] Signal: Floating point exception (8) Signal code: Floating point divide-by-zero (3)

[Dave M]

Hi Mark,

Thanks just opened new issue. My all simulations are performed using
gromacs2019.4 and to be consistent to report the results I would like to
keep same version. But this specific case is creating trouble. What is best
I can do? if I use a different gromacs version for this specific case then
it would look bit unusual from reviewer's point of view.

Dave

On Thu, Dec 12, 2019 at 1:20 AM Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> That sounds very much like a bug, but it's hard to say where it comes from.
> Can you please open an issue at https://redmine.gromacs.org/ and attach
> your .tpr files plus a log file from a failing run and the above stack
> trace?
>
> Mark
>
> On Thu, 12 Dec 2019 at 08:37, Dave M <dave.gromax at gmail.com> wrote:
>
> > Hi All,
> >
> > I am getting errors which I don't understand. I ran a simulation (gromacs
> > 2019.4) which completed fine. Then, with exactly the same system and mdp
> > files, I ran three repeats with different velocity seeds (so initial
> > configuration is same) but each simulation ended incomplete at different
> > time steps. My system does not blow or anything like that. Every time am
> > getting this error for the repeats with different velocity seeds. Also,
> if
> > I use cpt file to restart the job it ends at the same time step where it
> > got killed earlier.
> > My command line is:
> > gmx_mpi mdrun -deffnm 04-run -rdd 2.0
> >
> > *** Process received signal ***
> >
> >  Signal: Floating point exception (8)
> >
> >  Signal code: Floating point divide-by-zero (3)
> >
> >  Failing at address: 0x7ff112f22075
> >
> >  [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x3ef20)[0x7ff11c40cf20]
> >
> >  [ 1] /lib/x86_64-linux-gnu/libm.so.6(+0x86075)[0x7ff112f22075]
> >
> >  [ 2]
> >
> >
> /usr/local/gromacs/gromacs2019_4/lib/libgromacs_mpi.so.4(_ZSt3logf+0x1d)[0x7ff11d576c10]
> >
> >  [ 3]
> >
> >
> /usr/local/gromacs/gromacs2019_4/lib/libgromacs_mpi.so.4(_ZN3gmx17GammaDistributionIfEclINS_12ThreeFry2x64ILj64EEEEEfRT_RKNS1_10param_typeE+0x21f)[0x7ff11e1302bf]
> >
> >  [ 4]
> >
> >
> /usr/local/gromacs/gromacs2019_4/lib/libgromacs_mpi.so.4(_ZN3gmx17GammaDistributionIfEclINS_12ThreeFry2x64ILj64EEEEEfRT_+0x27)[0x7ff11e12fdd7]
> >
> >  [ 5]
> >
> >
> /usr/local/gromacs/gromacs2019_4/lib/libgromacs_mpi.so.4(+0x13cecd1)[0x7ff11e12ecd1]
> >
> >  [ 6]
> >
> >
> /usr/local/gromacs/gromacs2019_4/lib/libgromacs_mpi.so.4(+0x13cee10)[0x7ff11e12ee10]
> >
> >  [ 7]
> >
> >
> /usr/local/gromacs/gromacs2019_4/lib/libgromacs_mpi.so.4(_Z15vrescale_tcouplPK10t_inputreclP14gmx_ekindata_tfPd+0x1de)[0x7ff11e12f0a6]
> >
> >  [ 8]
> >
> >
> /usr/local/gromacs/gromacs2019_4/lib/libgromacs_mpi.so.4(_Z14update_tcouplelPK10t_inputrecP7t_stateP14gmx_ekindata_tPK9t_extmassPK9t_mdatoms+0x1b3)[0x7ff11e1d6339]
> >
> >  [ 9]
> >
> >
> /usr/local/gromacs/gromacs2019_4/lib/libgromacs_mpi.so.4(_ZN3gmx10Integrator5do_mdEv+0x43eb)[0x7ff11e286d45]
> >
> >  [10]
> >
> >
> /usr/local/gromacs/gromacs2019_4/lib/libgromacs_mpi.so.4(_ZN3gmx10Integrator3runEjb+0x1a7)[0x7ff11e280a1b]
> >
> >  [11]
> >
> >
> /usr/local/gromacs/gromacs2019_4/lib/libgromacs_mpi.so.4(_ZN3gmx8Mdrunner8mdrunnerEv+0x3a69)[0x7ff11e2a79e5]
> >
> >  [12] gmx_mpi(+0xe37c)[0x55a41da7937c]
> >
> >  [13]
> >
> >
> /usr/local/gromacs/gromacs2019_4/lib/libgromacs_mpi.so.4(+0x64e29f)[0x7ff11d3ae29f]
> >
> >  [14]
> >
> >
> /usr/local/gromacs/gromacs2019_4/lib/libgromacs_mpi.so.4(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x3d6)[0x7ff11d3aff16]
> >
> >  [15] gmx_mpi(+0xbaa1)[0x55a41da76aa1]
> >
> >  [16]
> > /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7)[0x7ff11c3efb97]
> >
> >  [17] gmx_mpi(+0xb91a)[0x55a41da7691a]
> >
> > Any idea what could be wrong? Suggestions much appreciated.
> >
> > Thanks.
> >
> > Dave
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>