reassign 838591 gromacs thanks there is no evidence provided if gromacs has invalid code which is now triggered by GCC 6, or of this is a real GCC issue.
Please provide a self-contained test case if possible. On 22.09.2016 19:09, Vedran Miletić wrote: > Package: gcc-6 > Version: 6.2.0-4 > Severity: important > > Dear Maintainer, > > Building GROMACS branch release-2016 from source with gcc 6.2.0-4 and running > tests results in: > > Test project /home/vedranm/workspace/CompChem/gromacs/build-gcc > Start 1: TestUtilsUnitTests > 1/20 Test #1: TestUtilsUnitTests ............... Passed 0.29 sec > Start 2: GmxlibTests > 2/20 Test #2: GmxlibTests ...................... Passed 0.06 sec > Start 3: MdlibUnitTest > 3/20 Test #3: MdlibUnitTest .................... Passed 0.04 sec > Start 4: CommandLineUnitTests > 4/20 Test #4: CommandLineUnitTests .............***Exception: SegFault > 0.07 sec > [==========] Running 46 tests from 6 test cases. > [----------] Global test environment set-up. > [----------] 3 tests from CommandLineHelpModuleTest > [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp > [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (25 ms) > [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic > > Start 5: FFTUnitTests > 5/20 Test #5: FFTUnitTests ..................... Passed 0.94 sec > Start 6: MathUnitTests > 6/20 Test #6: MathUnitTests .................... Passed 0.05 sec > Start 7: RandomUnitTests > 7/20 Test #7: RandomUnitTests .................. Passed 0.06 sec > Start 8: OnlineHelpUnitTests > 8/20 Test #8: OnlineHelpUnitTests ..............***Exception: SegFault > 0.07 sec > [==========] Running 22 tests from 4 test cases. > [----------] Global test environment set-up. > [----------] 6 tests from TextTableFormatterTest > [ RUN ] TextTableFormatterTest.HandlesBasicCase > [ OK ] TextTableFormatterTest.HandlesBasicCase (6 ms) > [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles > [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms) > [ RUN ] TextTableFormatterTest.HandlesIndentation > [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms) > [ RUN ] TextTableFormatterTest.HandlesOverflowingLines > [ OK ] TextTableFormatterTest.HandlesOverflowingLines (4 ms) > [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding > [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (1 ms) > [ RUN ] TextTableFormatterTest.HandlesEmptyColumns > [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms) > [----------] 6 tests from TextTableFormatterTest (12 ms total) > > [----------] 3 tests from HelpManagerTest > [ RUN ] HelpManagerTest.HandlesRootTopic > > Start 9: OptionsUnitTests > 9/20 Test #9: OptionsUnitTests .................***Exception: SegFault > 0.03 sec > [==========] Running 74 tests from 10 test cases. > [----------] Global test environment set-up. > [----------] 5 tests from AbstractOptionStorageTest > [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish > > Start 10: UtilityUnitTests > 10/20 Test #10: UtilityUnitTests ................. Passed 0.14 sec > Start 11: FileIOTests > 11/20 Test #11: FileIOTests ...................... Passed 0.07 sec > Start 12: SimdUnitTests > 12/20 Test #12: SimdUnitTests .................... Passed 0.18 sec > Start 13: LegacyToolsTests > 13/20 Test #13: LegacyToolsTests ................. Passed 0.47 sec > Start 14: GmxPreprocessTests > 14/20 Test #14: GmxPreprocessTests ............... Passed 0.29 sec > Start 15: CorrelationsTest > 15/20 Test #15: CorrelationsTest ................. Passed 0.79 sec > Start 16: AnalysisDataUnitTests > 16/20 Test #16: AnalysisDataUnitTests ............***Exception: SegFault > 0.06 sec > [==========] Running 69 tests from 14 test cases. > [----------] Global test environment set-up. > [----------] 3 tests from AnalysisDataInitializationTest > [ RUN ] AnalysisDataInitializationTest.BasicInitialization > [ OK ] AnalysisDataInitializationTest.BasicInitialization (1 ms) > [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules > [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (17 ms) > [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules > [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms) > [----------] 3 tests from AnalysisDataInitializationTest (18 ms total) > > [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = > (anonymous namespace)::SimpleInputData > [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly > > Start 17: SelectionUnitTests > 17/20 Test #17: SelectionUnitTests ............... Passed 0.72 sec > Start 18: TrajectoryAnalysisUnitTests > 18/20 Test #18: TrajectoryAnalysisUnitTests ......***Exception: SegFault > 0.06 sec > [==========] Running 48 tests from 8 test cases. > [----------] Global test environment set-up. > [----------] 11 tests from AngleModuleTest > [ RUN ] AngleModuleTest.ComputesSimpleAngles > > WARNING: If there are molecules in the input trajectory file > that are broken across periodic boundaries, they > cannot be made whole (or treated as whole) without > you providing a run input file. > > > Start 19: MdrunTests > 19/20 Test #19: MdrunTests ....................... Passed 11.17 sec > Start 20: MdrunMpiTests > 20/20 Test #20: MdrunMpiTests .................... Passed 0.63 sec > > 75% tests passed, 5 tests failed out of 20 > > Label Time Summary: > GTest = 3.91 sec (17 tests) > IntegrationTest = 11.64 sec (2 tests) > MpiIntegrationTest = 0.63 sec (1 test) > UnitTest = 3.91 sec (17 tests) > > Total Test time (real) = 16.61 sec > > The following tests FAILED: > 4 - CommandLineUnitTests (SEGFAULT) > 8 - OnlineHelpUnitTests (SEGFAULT) > 9 - OptionsUnitTests (SEGFAULT) > 16 - AnalysisDataUnitTests (SEGFAULT) > 18 - TrajectoryAnalysisUnitTests (SEGFAULT) > Errors while running CTest > CMakeFiles/run-ctest.dir/build.make:57: recipe for target > 'CMakeFiles/run-ctest' failed > make[3]: *** [CMakeFiles/run-ctest] Error 8 > CMakeFiles/Makefile2:99: recipe for target 'CMakeFiles/run-ctest.dir/all' > failed > make[2]: *** [CMakeFiles/run-ctest.dir/all] Error 2 > CMakeFiles/Makefile2:171: recipe for target 'CMakeFiles/check.dir/rule' failed > make[1]: *** [CMakeFiles/check.dir/rule] Error 2 > Makefile:234: recipe for target 'check' failed > make: *** [check] Error 2 > > gcc 5.4.1-2 and Fedora's gcc 6.2.1-2 work fine. > > -- System Information: > Debian Release: stretch/sid > APT prefers unstable > APT policy: (500, 'unstable'), (1, 'experimental') > Architecture: amd64 (x86_64) > Foreign Architectures: i386, armhf > > Kernel: Linux 4.7.0-1-amd64 (SMP w/2 CPU cores) > Locale: LANG=en_GB.UTF-8, LC_CTYPE=en_GB.UTF-8 (charmap=UTF-8) > Shell: /bin/sh linked to /bin/dash > Init: systemd (via /run/systemd/system) > > Versions of packages gcc-6 depends on: > ii binutils 2.27-8 > ii cpp-6 6.2.0-4 > ii gcc-6-base 6.2.0-4 > ii libc6 2.24-3 > ii libcc1-0 6.2.0-4 > ii libgcc-6-dev 6.2.0-4 > ii libgcc1 1:6.2.0-4 > ii libgmp10 2:6.1.1+dfsg-1 > ii libisl15 0.17.1-1 > ii libmpc3 1.0.3-1 > ii libmpfr4 3.1.4-2 > ii libstdc++6 6.2.0-4 > ii zlib1g 1:1.2.8.dfsg-2+b1 > > Versions of packages gcc-6 recommends: > ii libc6-dev 2.24-3 > > Versions of packages gcc-6 suggests: > pn gcc-6-doc <none> > pn gcc-6-locales <none> > ii gcc-6-multilib 6.2.0-4 > pn libasan3-dbg <none> > pn libatomic1-dbg <none> > pn libcilkrts5-dbg <none> > pn libgcc1-dbg <none> > pn libgomp1-dbg <none> > pn libitm1-dbg <none> > pn liblsan0-dbg <none> > pn libmpx2-dbg <none> > pn libquadmath0-dbg <none> > pn libtsan0-dbg <none> > pn libubsan0-dbg <none> > > -- no debconf information >