[gmx-developers] Gromacs test regression failed
Александр Лашков
alashkov83 at gmail.com
Mon Oct 28 09:32:15 CET 2019
Dear developers team. I tried compile gromacs 2019.4 on IBM POWER 8 machine
with cida support. Version 2018 oon this configuration compile is ok.
Configuration:
OS: Ubuntu 16.04
Comiller: default for thos OS version (GCC)
CUDA: 9.2
Configuration:
-DGMX_OPENMP=ON \
-DGMX_GPU=ON \
-DGMX_MPI=OFF \
-DGMX_BUILD_OWN_FFTW=ON \
-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda \
-DCMAKE_INSTALL_PREFIX=/gromacs \
-DREGRESSIONTEST_DOWNLOAD=ON \
-DGMX_SIMD=IBM_VSX
Output:
42/46 Test #42: regressiontests/complex .............***Failed 24.58 sec
:-) GROMACS - gmx mdrun, 2019.4 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Paul Bauer Herman J.C.
Berendsen
Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios
Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
Alfons Sijbers Peter Tieleman Jon Vincent 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) 2001-2018, 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 2019.4
Executable: /gromacs-build/bin/gmx
Data prefix: /gromacs-src (source tree)
Working dir: /gromacs-build/tests/regressiontests-2019.4
Command line:
gmx 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 mdrun -nb cpu -notunepme >mdrun.out
2>&1' was 1
Retrying mdrun with better settings...
Abnormal return value for ' gmx mdrun -ntmpi 12 -notunepme >mdrun.out
2>&1' was 1
Retrying mdrun with better settings...
Abnormal return value for ' gmx mdrun -ntmpi 12 -ntomp 1 -notunepme
>mdrun.out 2>&1' was -1
FAILED. Check mdrun.out, md.log file(s) in dd121 for dd121
Mdrun cannot use the requested (or automatic) number of OpenMP threads,
retrying with 8.
Abnormal return value for ' gmx mdrun -ntmpi 1 -notunepme >mdrun.out
2>&1' was 1
Retrying mdrun with better settings...
Abnormal return value for ' gmx mdrun -notunepme >mdrun.out 2>&1' was
-1
FAILED. Check mdrun.out, md.log file(s) in nbnxn-ljpme-geometric for
nbnxn-ljpme-geometric
Abnormal return value for ' gmx mdrun -notunepme >mdrun.out 2>&1' was
-1
FAILED. Check mdrun.out, md.log file(s) in nbnxn-ljpme-LB-geometric for
nbnxn-ljpme-LB-geometric
Abnormal return value for ' gmx mdrun -ntmpi 6 -notunepme >mdrun.out
2>&1' was 1
Retrying mdrun with better settings...
Abnormal return value for ' gmx mdrun -ntmpi 6 -ntomp 1 -notunepme
>mdrun.out 2>&1' was -1
FAILED. Check mdrun.out, md.log file(s) in nbnxn_vsite for nbnxn_vsite
Mdrun cannot use the requested (or automatic) number of OpenMP threads,
retrying with 8.
Abnormal return value for ' gmx mdrun -ntmpi 1 -notunepme >mdrun.out
2>&1' was 1
Retrying mdrun with better settings...
Abnormal return value for ' gmx mdrun -ntmpi 1 -ntomp 8 -notunepme
>mdrun.out 2>&1' was -1
FAILED. Check mdrun.out, md.log file(s) in orientation-restraints for
orientation-restraints
Abnormal return value for ' gmx mdrun -notunepme >mdrun.out 2>&1' was
-1
FAILED. Check mdrun.out, md.log file(s) in pull_geometry_angle for
pull_geometry_angle
Abnormal return value for ' gmx mdrun -notunepme >mdrun.out 2>&1' was
-1
FAILED. Check mdrun.out, md.log file(s) in pull_geometry_angle-axis for
pull_geometry_angle-axis
Abnormal return value for ' gmx mdrun -notunepme >mdrun.out 2>&1' was
-1
FAILED. Check mdrun.out, md.log file(s) in pull_geometry_dihedral for
pull_geometry_dihedral
8 out of 51 complex tests FAILED
Start 43: regressiontests/kernel
43/46 Test #43: regressiontests/kernel .............. Passed 38.07 sec
Start 44: regressiontests/freeenergy
44/46 Test #44: regressiontests/freeenergy ..........***Failed 11.42 sec
:-) GROMACS - gmx mdrun, 2019.4 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Paul Bauer Herman J.C.
Berendsen
Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios
Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
Alfons Sijbers Peter Tieleman Jon Vincent 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) 2001-2018, 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 2019.4
Executable: /gromacs-build/bin/gmx
Data prefix: /gromacs-src (source tree)
Working dir: /gromacs-build/tests/regressiontests-2019.4
Command line:
gmx 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 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 mdrun -nb cpu -notunepme >mdrun.out
2>&1' was 1
Retrying mdrun with better settings...
FAILED. Check checkpot.out (36 errors), checkforce.out (20 errors) file(s)
in vdwalone for vdwalone
1 out of 10 freeenergy tests FAILED
Start 45: regressiontests/rotation
45/46 Test #45: regressiontests/rotation ............ Passed 2.92 sec
Start 46: regressiontests/essentialdynamics
46/46 Test #46: regressiontests/essentialdynamics ...***Failed 2.63 sec
:-) GROMACS - gmx mdrun, 2019.4 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Paul Bauer Herman J.C.
Berendsen
Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios
Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
Alfons Sijbers Peter Tieleman Jon Vincent 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) 2001-2018, 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 2019.4
Executable: /gromacs-build/bin/gmx
Data prefix: /gromacs-src (source tree)
Working dir: /gromacs-build/tests/regressiontests-2019.4
Command line:
gmx 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 mdrun -ei sam.edi -eo flooding1.xvg
>mdrun.out 2>&1' was 1
Retrying mdrun with better settings...
Abnormal return value for ' gmx mdrun -ntmpi 8 -ei sam.edi -eo
flooding1.xvg >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 mdrun -ei sam.edi -eo flooding2.xvg
>mdrun.out 2>&1' was 1
Retrying mdrun with better settings...
Abnormal return value for ' gmx mdrun -ntmpi 8 -ei sam.edi -eo
flooding2.xvg >mdrun.out 2>&1' was 1
Retrying mdrun with better settings...
Here follows a list of the lines in edsam_reference.xvg and flooding2.xvg
which did not
pass the comparison test within a tolerance of 0.025
Lines ref cmp Reference This test Error
61 63 0.414582 0.442268 2.768600e-02
62 64 0.425532 0.454254 2.872200e-02
63 65 0.436537 0.467285 3.074800e-02
Here follows a list of the lines in edsam_reference.xvg and flooding2.xvg
which did not
pass the comparison test within a tolerance of 250
Lines ref cmp Reference This test Error
47 49 6725.78 6457.51 2.682700e+02
48 50 5601.98 5276.28 3.257000e+02
49 51 4620.28 4253.37 3.669100e+02
50 52 3799.76 3392.82 4.069400e+02
51 53 3144.11 2713.27 4.308400e+02
52 54 2625.88 2195 4.308800e+02
53 55 2188.89 1777.02 4.118700e+02
54 56 1789.84 1408.52 3.813200e+02
55 57 1411.59 1078.64 3.329500e+02
56 58 1064.07 796.564 2.675060e+02
Here follows a list of the lines in edsam_reference.xvg and flooding2.xvg
which did not
pass the comparison test within a tolerance of 1000
Lines ref cmp Reference This test Error
60 62 4919.61 3845.16 1.074450e+03
61 63 4270.9 2886.58 1.384320e+03
62 64 3723.39 2287.31 1.436080e+03
63 65 3173.13 1635.76 1.537370e+03
64 66 2504 1338.07 1.165930e+03
Here follows a list of the lines in edsam_reference.xvg and flooding2.xvg
which did not
pass the comparison test within a tolerance of 0.025
Lines ref cmp Reference This test Error
54 56 0.0639331 0.0369573 2.697580e-02
55 57 0.0436037 0.0123194 3.128430e-02
56 58 0.0195254 -0.0102041 2.972950e-02
57 59 -0.00319758 -0.0283589 2.516132e-02
64 66 -0.0909715 -0.117208 2.623650e-02
Here follows a list of the lines in edsam_reference.xvg and flooding2.xvg
which did not
pass the comparison test within a tolerance of 250
Lines ref cmp Reference This test Error
47 49 6725.78 6457.51 2.682700e+02
48 50 5601.98 5276.28 3.257000e+02
49 51 4620.28 4253.37 3.669100e+02
50 52 3799.76 3392.82 4.069400e+02
51 53 3144.11 2713.27 4.308400e+02
52 54 2625.88 2195 4.308800e+02
53 55 2188.89 1777.02 4.118700e+02
54 56 1789.84 1408.52 3.813200e+02
55 57 1411.59 1078.64 3.329500e+02
56 58 1064.07 796.564 2.675060e+02
Here follows a list of the lines in edsam_reference.xvg and flooding2.xvg
which did not
pass the comparison test within a tolerance of 1000
Lines ref cmp Reference This test Error
52 54 -9914.28 -8897.92 1.016360e+03
53 55 -9058.36 -7857.58 1.200780e+03
54 56 -8196.65 -6847.87 1.348780e+03
55 57 -7180.18 -5615.97 1.564210e+03
56 58 -5976.27 -4489.79 1.486480e+03
57 59 -4840.12 -3582.05 1.258070e+03
63 65 -1026.31 220.73 1.247040e+03
64 66 -451.423 860.42 1.311843e+03
65 67 225.316 1397.03 1.171714e+03
66 68 864.206 1909.95 1.045744e+03
Essential dynamics tests FAILED with 43 errors!
91% tests passed, 4 tests failed out of 46
Label Time Summary:
GTest = 47.80 sec (40 tests)
IntegrationTest = 18.73 sec (5 tests)
MpiTest = 0.03 sec (3 tests)
SlowTest = 24.93 sec (1 test)
UnitTest = 4.15 sec (34 tests)
Total Test time (real) = 130.73 sec
The following tests FAILED:
3 - MdlibUnitTest (Failed)
42 - regressiontests/complex (Failed)
44 - regressiontests/freeenergy (Failed)
46 - regressiontests/essentialdynamics (Failed)
Errors while running CTest
make[3]: *** [CMakeFiles/run-ctest-nophys] Error 8
CMakeFiles/run-ctest-nophys.dir/build.make:57: recipe for target
'CMakeFiles/run-ctest-nophys' failed
CMakeFiles/Makefile2:1167: recipe for target
'CMakeFiles/run-ctest-nophys.dir/all' failed
make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Error 2
CMakeFiles/Makefile2:978: recipe for target 'CMakeFiles/check.dir/rule'
failed
make[1]: *** [CMakeFiles/check.dir/rule] Error 2
Makefile:546: recipe for target 'check' failed
make: *** [check] Error 2
Sincerely,
Alexander Lashkov
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