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

[Dave M]

Hi Paul,
Thanks. My replies below:

On Thu, Dec 12, 2019 at 2:32 AM Paul bauer <paul.bauer.q at gmail.com> wrote:

> Hello,
>
> I'll have a look later today.
> Can you also give as information about your build configuration?
>

If I am not wrong you mean this:
-DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=on -DGMX_MPI=on
-DGMX_GPU=on -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs/gromacs2019_4
-DGMX_FFT_LIBRARY=fftw3 -DCMAKE_BUILD_TYPE=Debug



> If you could upload a log file from mdrun to Redmine it should be enough.
>

The error is not reported in the log file. But I have uploaded now.


>
> Thanks
>
> Paul
>
> On 12/12/2019 11:28, Dave M wrote:
> > 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
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> >> --
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>
> --
> Paul Bauer, PhD
> GROMACS Release Manager
> KTH Stockholm, SciLifeLab
> 0046737308594
>
> --
> Gromacs Users mailing list
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