gromacs failed to build from source in Fedora rawhide/f32 https://koji.fedoraproject.org/koji/taskinfo?taskID=41318028 For details on the mass rebuild see: https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild Please fix gromacs at your earliest convenience and set the bug's status to ASSIGNED when you start fixing it. If the bug remains in NEW state for 8 weeks, gromacs will be orphaned. Before branching of Fedora 33, gromacs will be retired, if it still fails to build. For more details on the FTBFS policy, please visit: https://fedoraproject.org/wiki/Fails_to_build_from_source
Created attachment 1659221 [details] build.log file build.log too big, will only attach last 32768 bytes
Created attachment 1659222 [details] root.log file root.log too big, will only attach last 32768 bytes
Created attachment 1659223 [details] state.log
The ppc64 error: -- Could not find any flag to build test source (this could be due to either the compiler or binutils) CMake Error at cmake/gmxManageSimd.cmake:51 (message): Cannot find IBM VSX compiler flag. Use a newer compiler, or disable SIMD support (slower). Call Stack (most recent call first): cmake/gmxManageSimd.cmake:265 (gmx_give_fatal_error_when_simd_support_not_found) CMakeLists.txt:719 (gmx_manage_simd) -- Configuring incomplete, errors occurred! Something is wrong with SIMD flag. On aarch64 the error is: Mdrun cannot use the requested (or automatic) number of ranks, retrying with 8. Abnormal return value for ' gmx mdrun -nb cpu -notunepme >mdrun.out 2>&1' was 1 Retrying mdrun with better settings... ..... 98% tests passed, 1 tests failed out of 46 Label Time Summary: GTest = 33.68 sec*proc (40 tests) IntegrationTest = 6.53 sec*proc (5 tests) MpiTest = 2.22 sec*proc (3 tests) SlowTest = 20.76 sec*proc (1 test) UnitTest = 6.39 sec*proc (34 tests) Total Test time (real) = 2697.26 sec The following tests FAILED: 43 - regressiontests/kernel (Timeout) Errors while running CTest
Using "mock -r fedora-rawhide-ppc64le --no-clean gromacs-2019.5-2.fc32.1.src.rpm" I get a: +++ /usr/bin/ps -p 160 -ocomm= Signal 4 (ILL) caught by ps (3.3.15). /usr/bin/ps:ps/display.c:66: please report this bug ++ my_shell=
This bug appears to have been reported against 'rawhide' during the Fedora 32 development cycle. Changing version to 32.
Details on the aarch64 error: 22/27 Test #22: UtilityMpiUnitTests ..............***Failed 0.52 sec Invalid error code (-2) (error ring index 127 invalid) INTERNAL ERROR: invalid error code fffffffe (Ring Index out of range) in MPID_nem_tcp_init:373 Invalid error code (-2) (error ring index 127 invalid) INTERNAL ERROR: invalid error code fffffffe (Ring Index out of range) in MPID_nem_tcp_init:373 Fatal error in PMPI_Init_thread: Other MPI error, error stack: MPIR_Init_thread(586)..............: MPID_Init(224).....................: channel initialization failed MPIDI_CH3_Init(105)................: MPID_nem_init(324).................: MPID_nem_tcp_init(175).............: MPID_nem_tcp_get_business_card(401): MPID_nem_tcp_init(373).............: gethostbyname failed, 9642102373514ac7b8330d80c6ee96d2 (errno 0) Invalid error code (-2) (error ring index 127 invalid) Fatal error in PMPI_Init_thread: Other MPI error, error stack: MPIR_Init_thread(586)..............: MPID_Init(224).....................: channel initialization failed MPIDI_CH3_Init(105)................: MPID_nem_init(324).................: MPID_nem_tcp_init(175).............: MPID_nem_tcp_get_business_card(401): MPID_nem_tcp_init(373).............: gethostbyname failed, 9642102373514ac7b8330d80c6ee96d2 (errno 0) So this seems to be a bug in mpich.
ppc64le issue reported upstream: https://redmine.gromacs.org/issues/3380
(In reply to Christoph Junghans from comment #7) > Details on the aarch64 error: > 22/27 Test #22: UtilityMpiUnitTests ..............***Failed 0.52 sec > Invalid error code (-2) (error ring index 127 invalid) > INTERNAL ERROR: invalid error code fffffffe (Ring Index out of range) in > MPID_nem_tcp_init:373 > Invalid error code (-2) (error ring index 127 invalid) > INTERNAL ERROR: invalid error code fffffffe (Ring Index out of range) in > MPID_nem_tcp_init:373 > Fatal error in PMPI_Init_thread: Other MPI error, error stack: > MPIR_Init_thread(586)..............: > MPID_Init(224).....................: channel initialization failed > MPIDI_CH3_Init(105)................: > MPID_nem_init(324).................: > MPID_nem_tcp_init(175).............: > MPID_nem_tcp_get_business_card(401): > MPID_nem_tcp_init(373).............: gethostbyname failed, > 9642102373514ac7b8330d80c6ee96d2 (errno 0) > Invalid error code (-2) (error ring index 127 invalid) > Fatal error in PMPI_Init_thread: Other MPI error, error stack: > MPIR_Init_thread(586)..............: > MPID_Init(224).....................: channel initialization failed > MPIDI_CH3_Init(105)................: > MPID_nem_init(324).................: > MPID_nem_tcp_init(175).............: > MPID_nem_tcp_get_business_card(401): > MPID_nem_tcp_init(373).............: gethostbyname failed, > 9642102373514ac7b8330d80c6ee96d2 (errno 0) > > So this seems to be a bug in mpich. MPICH issuue patched here: https://src.fedoraproject.org/rpms/mpich/pull-request/2
Dear Maintainer, your package has not been built successfully in 32. Action is required from you. If you can fix your package to build, perform a build in koji, and either create an update in bodhi, or close this bug without creating an update, if updating is not appropriate [1]. If you are working on a fix, set the status to ASSIGNED to acknowledge this. Following the latest policy for such packages [2], your package will be orphaned if this bug remains in NEW state more than 8 weeks. A week before the mass branching of Fedora 33 according to the schedule [3], any packages not successfully rebuilt at least on Fedora 31 will be retired regardless of the status of this bug. [1] https://fedoraproject.org/wiki/Updates_Policy [2] https://docs.fedoraproject.org/en-US/fesco/Fails_to_build_from_source_Fails_to_install/ [3] https://fedoraproject.org/wiki/Releases/33/Schedule