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

Paul bauer Thu, 12 Dec 2019 02:33:22 -0800

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.abra...@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.gro...@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-requ...@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-requ...@gromacs.org.


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

--
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-requ...@gromacs.org.

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

Reply via email to