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 <m...@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.szil...@gmail.com> wrote: > > > On Fri, Feb 1, 2019 at 5:01 AM David Lister <m...@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 > > > -- > > > 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? 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