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

David Lister me at davidlister.ca
Fri Feb 1 16:43:49 CET 2019


Hi Roland,

This is using gcc version 7.3.0.

The output of gmx_d --version is:

$ ./bin/gmx_d --version
               :-) GROMACS - gmx_d, 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_d, 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
Command line:
  gmx_d --version

GROMACS version:    2018.5
Precision:          double
Memory model:       64 bit
MPI library:        thread_mpi
OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 64)
GPU support:        disabled
SIMD instructions:  AVX_512
FFT library:        fftw-3.3.8-sse2-avx-avx2-avx2_128-avx512
RDTSCP usage:       enabled
TNG support:        enabled
Hwloc support:      hwloc-1.11.6
Tracing support:    disabled
Built on:           2019-02-01 03:19:10
Built by:           david at computer [CMAKE]
Build OS/arch:      Linux 4.15.0-45-generic x86_64
Build CPU vendor:   Intel
Build CPU brand:    Intel(R) Core(TM) i9-7900X CPU @ 3.30GHz
Build CPU family:   6   Model: 85   Stepping: 4
Build CPU features: aes apic avx avx2 avx512f avx512cd avx512bw
avx512vl clfsh cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr
nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp rtm
sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
C compiler:         /usr/bin/cc GNU 7.3.0
C compiler flags:    -mavx512f -mfma     -O3 -DNDEBUG
-funroll-all-loops -fexcess-precision=fast
C++ compiler:       /usr/bin/c++ GNU 7.3.0
C++ compiler flags:  -mavx512f -mfma    -std=c++11   -O3 -DNDEBUG
-funroll-all-loops -fexcess-precision=fast

Cheers,

David


On Thu, Jan 31, 2019 at 11:28 PM Schulz, Roland <roland.schulz at intel.com>
wrote:

> Hi,
>
> What compiler are you using? Please also paste the output of "gmx
> -version".
>
> Roland
>
> > -----Original Message-----
> > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> > [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of
> > David Lister
> > Sent: Thursday, January 31, 2019 8:00 PM
> > To: gromacs.org_gmx-users at maillist.sys.kth.se
> > Subject: [gmx-users] Make check not passing tests on 2018.5
> >
> > 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
> >
> > 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.
> >
> > 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
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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