Re: [gmx-users] Make check not passing tests on 2018.5
That's quite interesting, I wonder what it is about my system that is causing the issue. If it means anything, this is on a fresh install of Ubuntu 18.04. I've had a chance to experiment with compilers on my system. GCC 8.2.0 passes with avx-512. Using a freshly compiled version of GCC 7.3.0 and tried it, but it showed the same behavior as before: failing make check with avx-512 and passing with avx2-256. Cheers, David On Fri, Feb 15, 2019 at 7:53 AM Szilárd Páll wrote: > Forgot to get back, but same here, I checked on a Core i9 with gcc 7.3 > (compiled from source though) and could not reproduce it. > -- > Szilárd > > > On Thu, Feb 14, 2019 at 6:36 PM Schulz, Roland > wrote: > > > 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 > > 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 > > 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 > > 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 exe
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 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 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 > wrote: > > > > > On Fri, Feb 1, 2019 at 5:01 AM David Lister 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 ... Passed3.01 > 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 BjelkmarAldert van Buuren Rudi van Drunen Anton > > > Feenstra > > > > Gerrit GroenhofAleksei Iupinov Christoph Junghans Anca > Hamuraru > > > > Vincent Hindriksen Dimitrios KarkoulisPeter KassonJiri > Kraus > > > > Carsten Kutzner Per Larsson Justin A. LemkulViveca > > > Lindahl > > > > Magnus Lundborg Pieter MeulenhoffErik Marklund Teemu > Murtola > > > > Szilard Pall Sander Pronk Roland Schulz Alexey > > > Shvetsov > > > >Michael Shirts Alfons Sijbers Peter TielemanTeemu > > > Virolainen > > > > Christian WennbergMaarten 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 Ni
Re: [gmx-users] Make check not passing tests on 2018.5
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 wrote: > On Fri, Feb 1, 2019 at 5:01 AM David Lister 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 ... Passed3.01 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 BjelkmarAldert van Buuren Rudi van Drunen Anton > Feenstra > > Gerrit GroenhofAleksei Iupinov Christoph Junghans Anca Hamuraru > > Vincent Hindriksen Dimitrios KarkoulisPeter KassonJiri Kraus > > Carsten Kutzner Per Larsson Justin A. LemkulViveca > Lindahl > > Magnus Lundborg Pieter MeulenhoffErik Marklund Teemu Murtola > > Szilard Pall Sander Pronk Roland Schulz Alexey > Shvetsov > >Michael Shirts Alfons Sijbers Peter TielemanTeemu > Virolainen > > Christian WennbergMaarten 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. > > >
Re: [gmx-users] Make check not passing tests on 2018.5
Hi Roland, This is using gcc version 7.3.0. The output of gmx_d --version is: $ ./bin/gmx_d --version :-) GROMACS - gmx_d, 2018.5 (double precision) (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par BjelkmarAldert van Buuren Rudi van Drunen Anton Feenstra Gerrit GroenhofAleksei Iupinov Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios KarkoulisPeter KassonJiri Kraus Carsten Kutzner Per Larsson Justin A. LemkulViveca Lindahl Magnus Lundborg Pieter MeulenhoffErik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter TielemanTeemu Virolainen Christian WennbergMaarten 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_d, 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 Command line: gmx_d --version GROMACS version:2018.5 Precision: double Memory model: 64 bit MPI library:thread_mpi OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) GPU support:disabled SIMD instructions: AVX_512 FFT library:fftw-3.3.8-sse2-avx-avx2-avx2_128-avx512 RDTSCP usage: enabled TNG support:enabled Hwloc support: hwloc-1.11.6 Tracing support:disabled Built on: 2019-02-01 03:19:10 Built by: david@computer [CMAKE] Build OS/arch: Linux 4.15.0-45-generic x86_64 Build CPU vendor: Intel Build CPU brand:Intel(R) Core(TM) i9-7900X CPU @ 3.30GHz Build CPU family: 6 Model: 85 Stepping: 4 Build CPU features: aes apic avx avx2 avx512f avx512cd avx512bw avx512vl clfsh cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic C compiler: /usr/bin/cc GNU 7.3.0 C compiler flags:-mavx512f -mfma -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast C++ compiler: /usr/bin/c++ GNU 7.3.0 C++ compiler flags: -mavx512f -mfma-std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast Cheers, David On Thu, Jan 31, 2019 at 11:28 PM Schulz, Roland wrote: > Hi, > > What compiler are you using? Please also paste the output of "gmx > -version". > > 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: Thursday, January 31, 2019 8:00 PM > > To: gromacs.org_gmx-users@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 ... Passed3.01 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 BjelkmarAldert van Buuren Rudi van Drunen Anton > Feenstra > > Gerrit GroenhofAleksei Iupinov Christoph Junghans Anca Hamuraru > > Vincent Hindriksen Dimitrios KarkoulisPeter KassonJiri Kraus > > Carsten Kutzner Per Larsson Justin A. LemkulViveca > Lindahl > > Magnus Lundborg
[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 ... Passed3.01 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 BjelkmarAldert van Buuren Rudi van Drunen Anton Feenstra Gerrit GroenhofAleksei Iupinov Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios KarkoulisPeter KassonJiri Kraus Carsten Kutzner Per Larsson Justin A. LemkulViveca Lindahl Magnus Lundborg Pieter MeulenhoffErik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter TielemanTeemu Virolainen Christian WennbergMaarten 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 ... Passed9.27 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 . Passed3.60 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
