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

[Paul bauer]

Hello,

I'll have a look later today.
Can you also give as information about your build configuration?
If you could upload a log file from mdrun to Redmine it should be enough.

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
>>> --
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-- 
Paul Bauer, PhD
GROMACS Release Manager
KTH Stockholm, SciLifeLab
0046737308594