[gmx-users] Make check not passing tests on 2018.5
Schulz, Roland
roland.schulz at intel.com
Fri Feb 1 05:32:10 CET 2019
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
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