Bug#838591: gcc-6: GROMACS compiled with gcc 6.2.0-4 fails the tests
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
>
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