==811870== Memcheck, a memory error detector ==811870== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==811870== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==811870== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/heart/test/TestArchivingExtendedBidomain -malloc_debug -malloc_dump -memory_info ==811870== Parent PID: 790921 ==811870== ==811870== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==811870== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==811870== ==811870== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==811870== at 0xBAD179E: getsockopt_syscall (getsockopt.c:29) ==811870== by 0xBAD179E: getsockopt (getsockopt.c:94) ==811870== by 0x14AA3157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==811870== by 0x14AAAA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==811870== by 0x14AB1DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==811870== by 0x149B13C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==811870== by 0x1492AE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==811870== by 0x140E9E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==811870== by 0xF89E4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==811870== by 0xB3AF418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==811870== by 0xB348D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==811870== by 0xA03FD38: PetscInitialize (pinit.c:924) ==811870== by 0x9EAF58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==811870== by 0x9EAF5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==811870== by 0x137FD0: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==811870== by 0x132C1D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==811870== by 0x135C1A: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==811870== by 0x135B15: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==811870== by 0x136129: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==811870== by 0x1313D0: main (TestArchivingExtendedBidomain.cpp:18) ==811870== Address 0x1ffeffdfac is on thread 1's stack ==811870== in frame #2, created by pmix_ptl_base_make_connection (???:) ==811870== { Memcheck:Param socketcall.getsockopt(optlen) fun:getsockopt_syscall fun:getsockopt fun:pmix_ptl_base_set_timeout fun:pmix_ptl_base_make_connection obj:/usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2 fun:PMIx_Init fun:ext3x_client_init obj:/usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so fun:orte_init fun:ompi_mpi_init fun:PMPI_Init_thread fun:PetscInitialize fun:_ZN15PetscSetupUtils15InitialisePetscEv fun:_ZN15PetscSetupUtils11CommonSetupEv fun:_ZN10PetscSetup10setUpWorldEv fun:_ZN7CxxTest20RealWorldDescription5setUpEv fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==811870== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==811870== at 0xBAD179E: getsockopt_syscall (getsockopt.c:29) ==811870== by 0xBAD179E: getsockopt (getsockopt.c:94) ==811870== by 0x14AA3157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==811870== by 0x14AAAA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==811870== by 0x14AB1DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==811870== by 0x149B13C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==811870== by 0x1492AE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==811870== by 0x140E9E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==811870== by 0xF89E4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==811870== by 0xB3AF418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==811870== by 0xB348D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==811870== by 0xA03FD38: PetscInitialize (pinit.c:924) ==811870== by 0x9EAF58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==811870== by 0x9EAF5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==811870== by 0x137FD0: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==811870== by 0x132C1D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==811870== by 0x135C1A: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==811870== by 0x135B15: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==811870== by 0x136129: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==811870== by 0x1313D0: main (TestArchivingExtendedBidomain.cpp:18) ==811870== Address 0x1ffeffdfac is on thread 1's stack ==811870== in frame #2, created by pmix_ptl_base_make_connection (???:) ==811870== { Memcheck:Param socketcall.getsockopt(optlen_out) fun:getsockopt_syscall fun:getsockopt fun:pmix_ptl_base_set_timeout fun:pmix_ptl_base_make_connection obj:/usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2 fun:PMIx_Init fun:ext3x_client_init obj:/usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so fun:orte_init fun:ompi_mpi_init fun:PMPI_Init_thread fun:PetscInitialize fun:_ZN15PetscSetupUtils15InitialisePetscEv fun:_ZN15PetscSetupUtils11CommonSetupEv fun:_ZN10PetscSetup10setUpWorldEv fun:_ZN7CxxTest20RealWorldDescription5setUpEv fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==811870== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==811870== at 0xBAD1C7E: setsockopt_syscall (setsockopt.c:29) ==811870== by 0xBAD1C7E: setsockopt (setsockopt.c:95) ==811870== by 0x14AAABA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==811870== by 0x14AB1DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==811870== by 0x149B13C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==811870== by 0x1492AE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==811870== by 0x140E9E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==811870== by 0xF89E4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==811870== by 0xB3AF418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==811870== by 0xB348D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==811870== by 0xA03FD38: PetscInitialize (pinit.c:924) ==811870== by 0x9EAF58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==811870== by 0x9EAF5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==811870== by 0x137FD0: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==811870== by 0x132C1D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==811870== by 0x135C1A: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==811870== by 0x135B15: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==811870== by 0x136129: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==811870== by 0x1313D0: main (TestArchivingExtendedBidomain.cpp:18) ==811870== { Memcheck:Param setsockopt(optlen) fun:setsockopt_syscall fun:setsockopt fun:pmix_ptl_base_make_connection obj:/usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2 fun:PMIx_Init fun:ext3x_client_init obj:/usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so fun:orte_init fun:ompi_mpi_init fun:PMPI_Init_thread fun:PetscInitialize fun:_ZN15PetscSetupUtils15InitialisePetscEv fun:_ZN15PetscSetupUtils11CommonSetupEv fun:_ZN10PetscSetup10setUpWorldEv fun:_ZN7CxxTest20RealWorldDescription5setUpEv fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==811870== Syscall param pwrite64(buf) points to uninitialised byte(s) ==811870== at 0xBABC9EF: __libc_pwrite64 (pwrite64.c:25) ==811870== by 0xBABC9EF: pwrite (pwrite64.c:23) ==811870== by 0x17B209D2: mca_fbtl_posix_pwritev (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_fbtl_posix.so) ==811870== by 0x17B30419: mca_common_ompio_file_write (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==811870== by 0x17B3079A: mca_common_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==811870== by 0x17A1B89A: mca_io_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_io_ompio.so) ==811870== by 0xB33C6A7: PMPI_File_write_at (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==811870== by 0xD552FEB: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811870== by 0xD3924ED: H5FD_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811870== by 0xD375313: H5F__accum_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811870== by 0xD470442: H5PB_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811870== by 0xD37CDEA: H5F_block_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811870== by 0xD306E98: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811870== by 0xD5463F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811870== by 0xD5479CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811870== by 0xD54847E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811870== by 0xD2E354C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811870== by 0xD37B936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811870== by 0xD37C3FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811870== by 0xD37FBB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811870== by 0xD37FEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811870== by 0xD3EF51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811870== by 0xD3EF5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811870== by 0xD37C831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811870== by 0xD371881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811870== by 0x9DDE967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==811870== by 0x9DD9647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==811870== by 0x9DD96ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==811870== by 0x688B5FB: AbstractCardiacProblem<2u, 2u, 3u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==811870== by 0x688B19B: AbstractCardiacProblem<2u, 2u, 3u>::Solve() (AbstractCardiacProblem.cpp:582) ==811870== by 0x13BEF2: TestArchivingExtendedBidomain::Run2DSimulationSaveAfterThreemilliSecondsIntraStim(FileFinder, std::__cxx11::basic_string, std::allocator >) (TestArchivingExtendedBidomain.hpp:291) ==811870== by 0x13A853: TestArchivingExtendedBidomain::TestArchivingProblemIntraStim() (TestArchivingExtendedBidomain.hpp:160) ==811870== by 0x13DED0: TestDescription_TestArchivingExtendedBidomain_TestArchivingProblemIntraStim::runTest() (TestArchivingExtendedBidomain.cpp:30) ==811870== by 0x132454: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==811870== by 0x135EC8: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==811870== by 0x135DAD: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==811870== by 0x135C53: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==811870== by 0x135B15: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==811870== by 0x136129: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==811870== by 0x1313D0: main (TestArchivingExtendedBidomain.cpp:18) ==811870== Address 0x164de5ee is 62 bytes inside a block of size 320 alloc'd ==811870== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==811870== by 0xD306E26: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811870== by 0xD5463F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811870== by 0xD5479CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811870== by 0xD54847E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811870== by 0xD2E354C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811870== by 0xD37B936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811870== by 0xD37C3FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811870== by 0xD37FBB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811870== by 0xD37FEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811870== by 0xD3EF51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811870== by 0xD3EF5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811870== by 0xD37C831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811870== by 0xD371881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811870== by 0x9DDE967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==811870== by 0x9DD9647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==811870== by 0x9DD96ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==811870== by 0x688B5FB: AbstractCardiacProblem<2u, 2u, 3u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==811870== by 0x688B19B: AbstractCardiacProblem<2u, 2u, 3u>::Solve() (AbstractCardiacProblem.cpp:582) ==811870== by 0x13BEF2: TestArchivingExtendedBidomain::Run2DSimulationSaveAfterThreemilliSecondsIntraStim(FileFinder, std::__cxx11::basic_string, std::allocator >) (TestArchivingExtendedBidomain.hpp:291) ==811870== by 0x13A853: TestArchivingExtendedBidomain::TestArchivingProblemIntraStim() (TestArchivingExtendedBidomain.hpp:160) ==811870== by 0x13DED0: TestDescription_TestArchivingExtendedBidomain_TestArchivingProblemIntraStim::runTest() (TestArchivingExtendedBidomain.cpp:30) ==811870== by 0x132454: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==811870== by 0x135EC8: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==811870== by 0x135DAD: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==811870== by 0x135C53: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==811870== by 0x135B15: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==811870== by 0x136129: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==811870== by 0x1313D0: main (TestArchivingExtendedBidomain.cpp:18) ==811870== { Memcheck:Param pwrite64(buf) fun:__libc_pwrite64 fun:pwrite fun:mca_fbtl_posix_pwritev fun:mca_common_ompio_file_write fun:mca_common_ompio_file_write_at fun:mca_io_ompio_file_write_at fun:PMPI_File_write_at obj:/usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0 fun:H5FD_write fun:H5F__accum_write fun:H5PB_write fun:H5F_block_write fun:H5C__flush_single_entry fun:H5C_apply_candidate_list fun:H5AC__run_sync_point fun:H5AC__flush_entries fun:H5AC_flush obj:/usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0 fun:H5F__dest fun:H5F_try_close fun:H5F__close_cb fun:H5I_dec_ref fun:H5I_dec_app_ref fun:H5F__close fun:H5Fclose fun:_ZN14Hdf5DataWriter5CloseEv fun:_ZN14Hdf5DataWriterD1Ev fun:_ZN14Hdf5DataWriterD0Ev fun:_ZN22AbstractCardiacProblemILj2ELj2ELj3EE24CloseFilesAndPostProcessEv fun:_ZN22AbstractCardiacProblemILj2ELj2ELj3EE5SolveEv fun:_ZN29TestArchivingExtendedBidomain50Run2DSimulationSaveAfterThreemilliSecondsIntraStimE10FileFinderNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE fun:_ZN29TestArchivingExtendedBidomain29TestArchivingProblemIntraStimEv fun:_ZN75TestDescription_TestArchivingExtendedBidomain_TestArchivingProblemIntraStim7runTestEv fun:_ZN7CxxTest19RealTestDescription3runEv fun:_ZN7CxxTest10TestRunner7runTestERNS_15TestDescriptionE fun:_ZN7CxxTest10TestRunner8runSuiteERNS_16SuiteDescriptionE fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==811870== ==811870== FILE DESCRIPTORS: 9 open (3 std) at exit. ==811870== Open file descriptor 12: ==811870== at 0xBABF22D: pipe (pipe.c:29) ==811870== by 0x140EA07D: ??? ==811870== by 0xF89E4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==811870== by 0xB3AF418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==811870== by 0xB348D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==811870== by 0xA03FD38: PetscInitialize (pinit.c:924) ==811870== by 0x9EAF58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==811870== by 0x9EAF5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==811870== by 0x137FD0: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==811870== by 0x132C1D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==811870== by 0x135C1A: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==811870== by 0x135B15: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==811870== by 0x136129: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==811870== by 0x1313D0: main (TestArchivingExtendedBidomain.cpp:18) ==811870== ==811870== Open file descriptor 8: /dev/shm/open_mpi.0000 ==811870== at 0xBAC3BCC: __open_nocancel (open64_nocancel.c:39) ==811870== by 0xBA47C4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==811870== by 0x9EE7822: ??? ==811870== by 0x9EE796F: ??? ==811870== by 0xF9436DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==811870== by 0xF943938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==811870== by 0xF8F9922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==811870== by 0xF89E2DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==811870== by 0xB3AF418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==811870== by 0xB348D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==811870== by 0xA03FD38: PetscInitialize (pinit.c:924) ==811870== by 0x9EAF58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==811870== by 0x9EAF5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==811870== by 0x137FD0: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==811870== by 0x132C1D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==811870== by 0x135C1A: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==811870== by 0x135B15: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==811870== by 0x136129: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==811870== by 0x1313D0: main (TestArchivingExtendedBidomain.cpp:18) ==811870== ==811870== Open file descriptor 116: ==811870== ==811870== ==811870== Open file descriptor 111: ==811870== ==811870== ==811870== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestArchivingExtendedBidomain_valgrind.txt ==811870== ==811870== ==811870== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==811870== ==811870== ==811870== ==811870== HEAP SUMMARY: ==811870== in use at exit: 701,234 bytes in 9,387 blocks ==811870== total heap usage: 353,890 allocs, 344,503 frees, 1,455,044,518 bytes allocated ==811870== ==811870== 552 bytes in 1 blocks are definitely lost in loss record 44 of 67 ==811870== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==811870== by 0x149B8C13: ??? ==811870== by 0x149B922C: ??? ==811870== by 0x1492C4B7: ??? ==811870== by 0xB31515A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==811870== by 0xB3AFA97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==811870== by 0xB348D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==811870== by 0xA03FD38: PetscInitialize (pinit.c:924) ==811870== by 0x9EAF58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==811870== by 0x9EAF5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==811870== by 0x137FD0: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==811870== by 0x132C1D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==811870== by 0x135C1A: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==811870== by 0x135B15: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==811870== by 0x136129: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==811870== by 0x1313D0: main (TestArchivingExtendedBidomain.cpp:18) ==811870== { Memcheck:Leak match-leak-kinds: definite fun:calloc obj:* obj:* obj:* fun:ompi_proc_complete_init fun:ompi_mpi_init fun:PMPI_Init_thread fun:PetscInitialize fun:_ZN15PetscSetupUtils15InitialisePetscEv fun:_ZN15PetscSetupUtils11CommonSetupEv fun:_ZN10PetscSetup10setUpWorldEv fun:_ZN7CxxTest20RealWorldDescription5setUpEv fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==811870== 685,191 (136 direct, 685,055 indirect) bytes in 1 blocks are definitely lost in loss record 67 of 67 ==811870== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==811870== by 0x15B2B74E: ??? ==811870== by 0x15B2BE0B: ??? ==811870== by 0x15B2EF56: ??? ==811870== by 0x15B2465D: ??? ==811870== by 0x15B24FA3: ??? ==811870== by 0xF9AFF05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==811870== by 0xF98BAE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==811870== by 0xF93CCB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==811870== by 0xF869EF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==811870== by 0x140EAF03: ??? ==811870== by 0xF89E4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==811870== by 0xB3AF418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==811870== by 0xB348D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==811870== by 0xA03FD38: PetscInitialize (pinit.c:924) ==811870== by 0x9EAF58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==811870== by 0x9EAF5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==811870== by 0x137FD0: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==811870== by 0x132C1D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==811870== by 0x135C1A: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==811870== by 0x135B15: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==811870== by 0x136129: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==811870== by 0x1313D0: main (TestArchivingExtendedBidomain.cpp:18) ==811870== { Memcheck:Leak match-leak-kinds: definite fun:calloc obj:* obj:* obj:* obj:* obj:* obj:/usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2 fun:hwloc_topology_load fun:opal_hwloc_base_get_topology fun:orte_ess_base_proc_binding obj:* fun:orte_init fun:ompi_mpi_init fun:PMPI_Init_thread fun:PetscInitialize fun:_ZN15PetscSetupUtils15InitialisePetscEv fun:_ZN15PetscSetupUtils11CommonSetupEv fun:_ZN10PetscSetup10setUpWorldEv fun:_ZN7CxxTest20RealWorldDescription5setUpEv fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==811870== LEAK SUMMARY: ==811870== definitely lost: 688 bytes in 2 blocks ==811870== indirectly lost: 1,760 bytes in 16 blocks ==811870== possibly lost: 0 bytes in 0 blocks ==811870== still reachable: 1,531 bytes in 6 blocks ==811870== suppressed: 697,255 bytes in 9,363 blocks ==811870== Reachable blocks (those to which a pointer was found) are not shown. ==811870== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==811870== ==811870== Use --track-origins=yes to see where uninitialised values come from ==811870== For lists of detected and suppressed errors, rerun with: -s ==811870== ERROR SUMMARY: 23 errors from 6 contexts (suppressed: 30 from 30)