[gmx-users] Make check not passing tests on 2018.5

David Lister me at davidlister.ca
Mon Feb 11 21:13:03 CET 2019 

Hello,

My bad, I copied my single precision build by mistake, this is what was
used originally for double precision:

cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_BUILD_OWN_FFTW=ON
-DCMAKE_BUILD_TYPE=Release -DGMX_BUILD_UNITTESTS=ON
-DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-2018.5 -DGMX_DOUBLE=on

Adding -DGMX_SIMD=AVX2_256 did resolve the problem, thank-you for the help!
I did not test different compilers as I don't have any others on my system
at the moment.

Cheers,
David

On Tue, Feb 5, 2019 at 7:15 AM Szilárd Páll <pall.szilard at gmail.com> wrote:

> On Fri, Feb 1, 2019 at 5:01 AM David Lister <me at davidlister.ca> wrote:
> >
> > Hello,
> >
> > I've compiled gromacs 2018.5 in double precision a couple times now and
> it
> > keeps on failing the same tests every time. This is on Ubuntu 18.04 with
> an
> > i9 7900X.
> >
> > The cmake I used was:
> > cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=on
> -DGMX_BUILD_OWN_FFTW=ON
> > -DCMAKE_BUILD_TYPE=Release -DGMX_BUILD_UNITTESTS=ON
> > -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-2018.5
>
> That couldn't have been the cmake invocation as it's not double
> precision build (and -DGMX_GPU=on is not valid in a double precision
> build).
>
> >
> > The problem with make check is:
> >
> > 34/39 Test #34: regressiontests/simple ...........   Passed    3.01 sec
> >       Start 35: regressiontests/complex
> > 35/39 Test #35: regressiontests/complex ..........***Failed   34.69 sec
> > Will test using executable suffix _d
> >              :-) GROMACS - gmx mdrun, 2018.5 (double precision) (-:
> >
> >                             GROMACS is written by:
> >      Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C.
> Berendsen
> >     Par Bjelkmar    Aldert van Buuren   Rudi van Drunen     Anton
> Feenstra
> >   Gerrit Groenhof    Aleksei Iupinov   Christoph Junghans   Anca Hamuraru
> >  Vincent Hindriksen Dimitrios Karkoulis    Peter Kasson        Jiri Kraus
> >   Carsten Kutzner      Per Larsson      Justin A. Lemkul    Viveca
> Lindahl
> >   Magnus Lundborg   Pieter Meulenhoff    Erik Marklund      Teemu Murtola
> >     Szilard Pall       Sander Pronk      Roland Schulz     Alexey
> Shvetsov
> >    Michael Shirts     Alfons Sijbers     Peter Tieleman    Teemu
> Virolainen
> >  Christian Wennberg    Maarten Wolf
> >                            and the project leaders:
> >         Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
> >
> > Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> > Copyright (c) 2001-2017, The GROMACS development team at
> > Uppsala University, Stockholm University and
> > the Royal Institute of Technology, Sweden.
> > check out http://www.gromacs.org for more information.
> >
> > GROMACS is free software; you can redistribute it and/or modify it
> > under the terms of the GNU Lesser General Public License
> > as published by the Free Software Foundation; either version 2.1
> > of the License, or (at your option) any later version.
> >
> > GROMACS:      gmx mdrun, version 2018.5 (double precision)
> > Executable:   /home/david/gromacs-2018.5/build/bin/gmx_d
> > Data prefix:  /home/david/gromacs-2018.5 (source tree)
> > Working dir:
> /home/david/gromacs-2018.5/build/tests/regressiontests-2018.5
> > Command line:
> >   gmx_d 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_d mdrun    -nb cpu   -notunepme
> > >mdrun.out 2>&1' was 1
> > Retrying mdrun with better settings...
> > Mdrun cannot use the requested (or automatic) number of ranks, retrying
> with 8.
> >
> > Abnormal return value for ' gmx_d mdrun    -nb cpu   -notunepme
> > >mdrun.out 2>&1' was 1
> > Retrying mdrun with better settings...
> > FAILED. Check checkpot.out (69 errors), checkforce.out (224 errors)
> > file(s) in distance_restraints for distance_restraints
> > Mdrun cannot use the requested (or automatic) number of ranks, retrying
> with 8.
> >
> > Abnormal return value for ' gmx_d mdrun    -nb cpu   -notunepme
> > >mdrun.out 2>&1' was 1
> > Retrying mdrun with better settings...
> > Mdrun cannot use the requested (or automatic) number of ranks, retrying
> with 8.
> >
> > Abnormal return value for ' gmx_d mdrun       -notunepme >mdrun.out
> 2>&1' was 1
> > Retrying mdrun with better settings...
> > Mdrun cannot use the requested (or automatic) number of ranks, retrying
> with 8.
> >
> > Abnormal return value for ' gmx_d mdrun       -notunepme >mdrun.out
> 2>&1' was 1
> > Retrying mdrun with better settings...
> > FAILED. Check checkpot.out (16 errors), checkforce.out (1362 errors)
> > file(s) in orientation-restraints for orientation-restraints
> > 2 out of 51 complex tests FAILED
> >
> >       Start 36: regressiontests/kernel
> > 36/39 Test #36: regressiontests/kernel ...........   Passed   55.12 sec
> >       Start 37: regressiontests/freeenergy
> > 37/39 Test #37: regressiontests/freeenergy .......   Passed    9.27 sec
> >       Start 38: regressiontests/pdb2gmx
> > 38/39 Test #38: regressiontests/pdb2gmx ..........   Passed   16.95 sec
> >       Start 39: regressiontests/rotation
> > 39/39 Test #39: regressiontests/rotation .........   Passed    3.60 sec
> >
> > 97% tests passed, 1 tests failed out of 39
> >
> > Label Time Summary:
> > GTest              =   4.54 sec*proc (33 tests)
> > IntegrationTest    =   2.03 sec*proc (3 tests)
> > MpiTest            =   0.20 sec*proc (3 tests)
> > UnitTest           =   2.51 sec*proc (30 tests)
> >
> > Total Test time (real) = 127.19 sec
> >
> > The following tests FAILED:
> >          35 - regressiontests/complex (Failed)
> > Errors while running CTest
> > CMakeFiles/run-ctest-nophys.dir/build.make:57: recipe for target
> > 'CMakeFiles/run-ctest-nophys' failed
> > make[3]: *** [CMakeFiles/run-ctest-nophys] Error 8
> > CMakeFiles/Makefile2:1385: recipe for target
> > 'CMakeFiles/run-ctest-nophys.dir/all' failed
> > make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Error 2
> > CMakeFiles/Makefile2:1165: recipe for target 'CMakeFiles/check.dir/rule'
> failed
> > make[1]: *** [CMakeFiles/check.dir/rule] Error 2
> > Makefile:626: recipe for target 'check' failed
> > make: *** [check] Error 2
> >
> > Looking at the log file for the orientation-restraints test shows
> > different energies calculated for some terms. The different terms are
> > bolded, but if that doesn't carry the LJ, Coulomb, Potential, Kinetic,
> > Total, Conserved, Temperature, Pressure and Constr rmsd are all
> > different. In most cases significantly.
>
> Looks like the short-range forces are quite a bit off. I can not
> reproduce the issue on similar hardware (although with vanilla gcc
> 7.3).
>
> Can you please do a few tests which might give a hint where the issue is:
> - see if the error is reproducible across multiple runs
> - try with -DGMX_SIMD=AVX2_256
> - try a different compiler (e.g. gcc 8 or clang)
>
> Cheers,
> --
> Szilárd
>
> >
> > From reference_d.log:
> >    Energies (kJ/mol)
> >            Bond            U-B    Proper Dih.  Improper Dih.      CMAP
> Dih.
> >     8.49937e+02    2.39137e+03    1.86371e+03    1.57563e+02
>  -3.65191e+02
> >           LJ-14     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul.
> recip.
> >     9.32112e+02    1.40820e+04   -*1.21790e+03*   *-2.01406e+04*
> 4.96236e+01
> >   Orient. Rest.   Ori. R. RMSD      Potential    Kinetic En.   Total
> Energy
> >     2.68612e+00    1.95988e+00   *-1.39474e+03*    *3.19608e+03*
> > *1.80134e+03*
> >   Conserved En.    Temperature Pressure (bar)   Constr. rmsd
> >     *1.80134e+03*    *3.03394e+02*   *-4.01423e+01*    *6.77807e-09*
> >
> > And from my system:
> >    Energies (kJ/mol)
> >            Bond            U-B    Proper Dih.  Improper Dih.      CMAP
> Dih.
> >     8.49937e+02    2.39137e+03    1.86371e+03    1.57563e+02
>  -3.65191e+02
> >           LJ-14     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul.
> recip.
> >     9.32112e+02    1.40820e+04   *-3.34280e+02   -3.70272e+03*
> 4.96236e+01
> >   Orient. Rest.   Ori. R. RMSD      Potential    Kinetic En.   Total
> Energy
> >     2.68612e+00    1.95988e+00    *1.59268e+04    3.21311e+03*
> *1.91399e+04*
> >   Conserved En.    Temperature Pressure (bar)   Constr. rmsd
> >     *1.91399e+04    3.05010e+02    1.11267e+02    7.18413e-09*
> >
> > Any help on how resolve this would be greatly appreciated.
> >
> > Cheers,
> >
> > David
> > --
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> >
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