[gmx-users] Make check not passing tests on 2018.5
Szilárd Páll
pall.szilard at gmail.com
Tue Feb 12 00:15:10 CET 2019
What about the other checks I suggested? IS the failing test 100%
reproducible with AVX_512?
--
Szilárd
On Mon, Feb 11, 2019 at 9:15 PM David Lister <me at davidlister.ca> wrote:
>
> 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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