[gmx-users] Help with a failing test - gromacs 2019.4 - Test 42

[Raymond Arter]

Hi Szilard,

I just found time to rerun the tests and your suggestion worked.

Many thanks for this.

Regards,

T.

On Wed, 16 Oct 2019 at 13:43, Szilárd Páll <pall.szilard at gmail.com> wrote:

> Hi,
>
> The issue is an internal error triggered by the domain decomposition not
> liking 14 cores in your CPU which lead to a prime rank count.
> To ensure the tests pass I suggest trying to force only one device to be
> used in make check, e.g. CUDA_VISIBLE_DEVICES=0 make check; alternatively
> you can run the regressiontests manually.
>
> Cheers,
> --
> Szilárd
>
>
> On Thu, Oct 10, 2019 at 6:01 PM Raymond Arter <raymondarter at gmail.com>
> wrote:
>
> > Hi,
> >
> > When performing a "make check" on Gromacs 2019.4, I'm getting test 42
> > failing.
> > It gives the error:
> >
> >         Mdrun cannot use the requested (or automatic) number of ranks,
> > retrying with 8
> >
> > And the mdrun.out and md.log of swap_x reports:
> >
> >         The number of ranks you selected (14) contains a large prime
> factor
> > 7.
> >
> > I've included the necessary parts of the logs below. Any help would be
> > appreciated
> > since I haven't come across this error before.
> >
> > Regards,
> >
> > T.
> >
> >
> > CentOS Linux release 7.6.1810 (Core)
> > CPU: Intel Xeon Gold 6132
> > Tesla V100
> > Cuda: 10.1
> > Driver: 418.40.04
> >
> > Output of "make check"
> >
> > 42/46 Test #42: regressiontests/complex .............***Failed  145.88
> sec
> >
> > GROMACS:      gmx mdrun, version 2019.4
> > Executable:   /gromacs/2019.4/gromacs-2019.4/build/bin/gmx
> > Data prefix:  /gromacs/2019.4/gromacs-2019.4 (source tree)
> > Working dir:
> >  /gromacs/2019.4/gromacs-2019.4/build/tests/regressiontests-2019.4
> > Command line:
> >   gmx mdrun -h
> >
> > Thanx for Using GROMACS - Have a Nice Day
> >
> > Mdrun cannot use the requested (or automatic) number of ranks, retrying
> > with 8.
> >
> > Abnormal return value for ' gmx mdrun    -nb cpu   -notunepme >mdrun.out
> > 2>&1' was 1
> > Retrying mdrun with better settings...
> > Re-running orientation-restraints using CPU-based PME
> > Re-running pull_geometry_angle using CPU-based PME
> > Re-running pull_geometry_angle-axis using CPU-based PME
> > Re-running pull_geometry_dihedral using CPU-based PME
> >
> > Abnormal return value for ' gmx mdrun       -notunepme >mdrun.out 2>&1'
> was
> > -1
> > FAILED. Check mdrun.out, md.log file(s) in swap_x for swap_x
> >
> > Abnormal return value for ' gmx mdrun       -notunepme >mdrun.out 2>&1'
> was
> > -1
> > FAILED. Check mdrun.out, md.log file(s) in swap_y for swap_y
> >
> > Abnormal return value for ' gmx mdrun       -notunepme >mdrun.out 2>&1'
> was
> > -1
> > FAILED. Check mdrun.out, md.log file(s) in swap_z for swap_z
> > 3 out of 55 complex tests FAILED
> >
> > From the following directory:
> >
> >
> /gromacs/2019.4/gromacs-2019.4/build/tests/regressiontests-2019.4/complex/swap_x
> > and I get the same errors for swap_y and swap_z
> >
> > == mdrun.out ==
> >
> > GROMACS:      gmx mdrun, version 2019.4
> > Executable:   /gromacs/2019.4/gromacs-2019.4/build/bin/gmx
> > Data prefix:  /gromacs/2019.4/gromacs-2019.4 (source tree)
> > Working dir:
> >
> >
> /gromacs/2019.4/gromacs-2019.4/build/tests/regressiontests-2019.4/complex/swap_x
> > Command line:
> >   gmx mdrun -notunepme
> >
> > Reading file topol.tpr, VERSION 2019.4 (single precision)
> > Changing nstlist from 10 to 50, rlist from 1.011 to 1.137
> >
> > -------------------------------------------------------
> > Program:     gmx mdrun, version 2019.4
> > Source file: src/gromacs/domdec/domdec_setup.cpp (line 764)
> > MPI rank:    0 (out of 14)
> >
> > Fatal error:
> > The number of ranks you selected (14) contains a large prime factor 7. In
> > most
> > cases this will lead to bad performance. Choose a number with smaller
> prime
> > factors or set the decomposition (option -dd) manually.
> >
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > -------------------------------------------------------
> >
> > == md.out ==
> >
> > Changing nstlist from 10 to 50, rlist from 1.011 to 1.137
> >
> > Initializing Domain Decomposition on 14 ranks
> > Dynamic load balancing: locked
> > Minimum cell size due to atom displacement: 0.692 nm
> > Initial maximum distances in bonded interactions:
> >     two-body bonded interactions: 0.403 nm, Exclusion, atoms 184 187
> >   multi-body bonded interactions: 0.403 nm, Ryckaert-Bell., atoms 184 187
> > Minimum cell size due to bonded interactions: 0.443 nm
> > Maximum distance for 3 constraints, at 120 deg. angles, all-trans: 0.459
> nm
> > Estimated maximum distance required for P-LINCS: 0.459 nm
> >
> > -------------------------------------------------------
> > Program:     gmx mdrun, version 2019.4
> > Source file: src/gromacs/domdec/domdec_setup.cpp (line 764)
> > MPI rank:    0 (out of 14)
> >
> > Fatal error:
> > The number of ranks you selected (14) contains a large prime factor 7. In
> > most
> > cases this will lead to bad performance. Choose a number with smaller
> prime
> > factors or set the decomposition (option -dd) manually.
> >
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > -------------------------------------------------------
> > --
> > 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.