I can't reproduce this. For me the regressiontests pass with gcc 7.3, AVX_512, double.
Roland > -----Original Message----- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of > David Lister > Sent: Tuesday, February 12, 2019 4:59 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Make check not passing tests on 2018.5 > > I have yet to have a chance to test a different compiler. The AVX_512 is > reproducible and showed the same error in 3 tests. > > I hope to check gcc 8 later this week. > > Cheers, > David > > On Mon, Feb 11, 2019 at 6:15 PM Szilárd Páll <pall.szil...@gmail.com> wrote: > > > 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? 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