Bug#838591: gcc-6: GROMACS compiled with gcc 6.2.0-4 fails the tests
On 09/27/2016 09:20 PM, Matthias Klose wrote: > 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. > Indeed, after installing updates from unstable for the last few days this is now working correctly, even though neither GROMACS nor GCC changed. Apologies for misjudgment, please mark as invalid. Thanks, Vedran -- Vedran Miletić vedran.miletic.net
Bug#838591: [Debichem-devel] Processed: Re: Bug#838591: gcc-6: GROMACS compiled with gcc 6.2.0-4 fails the tests
tags 838591 + moreinfo unreproducible thanks On Tue, Sep 27, 2016 at 07:24:06PM +, Debian Bug Tracking System wrote: > Bug reassigned from package 'gcc-6' to 'gromacs'. Hi Vedran, I am not able to reproduce this failure with gromacs 2016-3 + gcc-6 6.2.0-4 in a clean sid chroot. If this is built against the Debian version of gromacs (it was unclear to me from reading the bug report), additional information is necessary - exact version, any nonstandard build options, the full configure/build log, and the output of the failing tests. If it's not from a Debian source package and build environment, it's probably best to take it to GROMACS upstream first. However, if it's specific to a build with OpenMPI, please check that you're either using the latest packages or have downgraded all the way to a 1.x version - it's been undergoing a lot of churn lately, and a number of packages depending on it have encountered various test failures, often architecture-specific. -- Nicholas Breen nbr...@debian.org
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 ... Passed0.29 sec > Start 2: GmxlibTests > 2/20 Test #2: GmxlibTests .. Passed0.06 sec > Start 3: MdlibUnitTest > 3/20 Test #3: MdlibUnitTest Passed0.04 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 . Passed0.94 sec > Start 6: MathUnitTests > 6/20 Test #6: MathUnitTests Passed0.05 sec > Start 7: RandomUnitTests > 7/20 Test #7: RandomUnitTests .. Passed0.06 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 . Passed0.14 sec > Start 11: FileIOTests > 11/20 Test #11: FileIOTests .. Passed0.07 sec > Start 12: SimdUnitTests > 12/20 Test #12: SimdUnitTests Passed0.18 sec > Start 13: LegacyToolsTests > 13/20 Test #13: LegacyToolsTests . Passed0.47 sec > Start 14: GmxPreprocessTests > 14/20 Test #14: GmxPreprocessTests ... Passed0.29 sec > Start 15: CorrelationsTest > 15/20 Test #15: CorrelationsTest . Passed0.79 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 ... Passed0.72 sec > Start 18: TrajectoryAnalysisUnitTests > 18/20 Test #18: TrajectoryAnalysisUnitTests ..***Exception: Seg
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 ... Passed0.29 sec Start 2: GmxlibTests 2/20 Test #2: GmxlibTests .. Passed0.06 sec Start 3: MdlibUnitTest 3/20 Test #3: MdlibUnitTest Passed0.04 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 . Passed0.94 sec Start 6: MathUnitTests 6/20 Test #6: MathUnitTests Passed0.05 sec Start 7: RandomUnitTests 7/20 Test #7: RandomUnitTests .. Passed0.06 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 . Passed0.14 sec Start 11: FileIOTests 11/20 Test #11: FileIOTests .. Passed0.07 sec Start 12: SimdUnitTests 12/20 Test #12: SimdUnitTests Passed0.18 sec Start 13: LegacyToolsTests 13/20 Test #13: LegacyToolsTests . Passed0.47 sec Start 14: GmxPreprocessTests 14/20 Test #14: GmxPreprocessTests ... Passed0.29 sec Start 15: CorrelationsTest 15/20 Test #15: CorrelationsTest . Passed0.79 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 ... Passed0.72 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: MdrunT
