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