==811881== Memcheck, a memory error detector ==811881== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==811881== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==811881== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/heart/test/TestExtendedVsBidomainProblem -malloc_debug -malloc_dump -memory_info ==811881== Parent PID: 790921 ==811881== ==811881== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==811881== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==811881== ==811881== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==811881== at 0xA98879E: getsockopt_syscall (getsockopt.c:29) ==811881== by 0xA98879E: getsockopt (getsockopt.c:94) ==811881== by 0x14AA1157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==811881== by 0x14AA8A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==811881== by 0x14AAFDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==811881== by 0x149AF3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==811881== by 0x14928E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==811881== by 0x140E7E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==811881== by 0xF8EF4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==811881== by 0xC089418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==811881== by 0xC022D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==811881== by 0xAD19D38: PetscInitialize (pinit.c:924) ==811881== by 0xA25F58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==811881== by 0xA25F5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==811881== by 0x1374BE: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==811881== by 0x13200F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==811881== by 0x13546E: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==811881== by 0x13530E: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==811881== by 0x1359A5: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==811881== by 0x130340: main (TestExtendedVsBidomainProblem.cpp:19) ==811881== Address 0x1ffeffdf9c is on thread 1's stack ==811881== in frame #2, created by pmix_ptl_base_make_connection (???:) ==811881== { 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 } ==811881== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==811881== at 0xA98879E: getsockopt_syscall (getsockopt.c:29) ==811881== by 0xA98879E: getsockopt (getsockopt.c:94) ==811881== by 0x14AA1157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==811881== by 0x14AA8A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==811881== by 0x14AAFDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==811881== by 0x149AF3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==811881== by 0x14928E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==811881== by 0x140E7E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==811881== by 0xF8EF4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==811881== by 0xC089418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==811881== by 0xC022D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==811881== by 0xAD19D38: PetscInitialize (pinit.c:924) ==811881== by 0xA25F58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==811881== by 0xA25F5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==811881== by 0x1374BE: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==811881== by 0x13200F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==811881== by 0x13546E: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==811881== by 0x13530E: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==811881== by 0x1359A5: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==811881== by 0x130340: main (TestExtendedVsBidomainProblem.cpp:19) ==811881== Address 0x1ffeffdf9c is on thread 1's stack ==811881== in frame #2, created by pmix_ptl_base_make_connection (???:) ==811881== { 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 } ==811881== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==811881== at 0xA988C7E: setsockopt_syscall (setsockopt.c:29) ==811881== by 0xA988C7E: setsockopt (setsockopt.c:95) ==811881== by 0x14AA8BA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==811881== by 0x14AAFDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==811881== by 0x149AF3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==811881== by 0x14928E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==811881== by 0x140E7E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==811881== by 0xF8EF4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==811881== by 0xC089418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==811881== by 0xC022D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==811881== by 0xAD19D38: PetscInitialize (pinit.c:924) ==811881== by 0xA25F58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==811881== by 0xA25F5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==811881== by 0x1374BE: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==811881== by 0x13200F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==811881== by 0x13546E: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==811881== by 0x13530E: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==811881== by 0x1359A5: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==811881== by 0x130340: main (TestExtendedVsBidomainProblem.cpp:19) ==811881== { 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 } ==811881== Syscall param pwrite64(buf) points to uninitialised byte(s) ==811881== at 0xA9739EF: __libc_pwrite64 (pwrite64.c:25) ==811881== by 0xA9739EF: pwrite (pwrite64.c:23) ==811881== by 0x1831E9D2: mca_fbtl_posix_pwritev (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_fbtl_posix.so) ==811881== by 0x1832E419: mca_common_ompio_file_write (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==811881== by 0x1832E79A: mca_common_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==811881== by 0x1821989A: mca_io_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_io_ompio.so) ==811881== by 0xC0166A7: PMPI_File_write_at (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==811881== by 0xC871FEB: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811881== by 0xC6B14ED: H5FD_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811881== by 0xC694313: H5F__accum_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811881== by 0xC78F442: H5PB_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811881== by 0xC69BDEA: H5F_block_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811881== by 0xC625E98: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811881== by 0xC8653F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811881== by 0xC8669CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811881== by 0xC86747E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811881== by 0xC60254C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811881== by 0xC69A936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811881== by 0xC69B3FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811881== by 0xC69EBB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811881== by 0xC69EEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811881== by 0xC70E51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811881== by 0xC70E5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811881== by 0xC69B831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811881== by 0xC690881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811881== by 0xA18E967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==811881== by 0xA189647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==811881== by 0xA1896ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==811881== by 0x6874A03: AbstractCardiacProblem<1u, 1u, 2u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==811881== by 0x68745A3: AbstractCardiacProblem<1u, 1u, 2u>::Solve() (AbstractCardiacProblem.cpp:582) ==811881== by 0x13A877: TestExtendedVsBidomainProblem::RunBidomain() (TestExtendedVsBidomainProblem.hpp:226) ==811881== by 0x13A9DE: TestExtendedVsBidomainProblem::TestCompareStimulationOfFirstCell() (TestExtendedVsBidomainProblem.hpp:233) ==811881== by 0x147B3C: TestDescription_TestExtendedVsBidomainProblem_TestCompareStimulationOfFirstCell::runTest() (TestExtendedVsBidomainProblem.cpp:31) ==811881== by 0x13160A: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==811881== by 0x13571C: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==811881== by 0x135601: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==811881== by 0x1354A7: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==811881== by 0x13530E: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==811881== by 0x1359A5: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==811881== by 0x130340: main (TestExtendedVsBidomainProblem.cpp:19) ==811881== Address 0x16544e4e is 62 bytes inside a block of size 320 alloc'd ==811881== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==811881== by 0xC625E26: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811881== by 0xC8653F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811881== by 0xC8669CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811881== by 0xC86747E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811881== by 0xC60254C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811881== by 0xC69A936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811881== by 0xC69B3FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811881== by 0xC69EBB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811881== by 0xC69EEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811881== by 0xC70E51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811881== by 0xC70E5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811881== by 0xC69B831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811881== by 0xC690881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==811881== by 0xA18E967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==811881== by 0xA189647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==811881== by 0xA1896ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==811881== by 0x6874A03: AbstractCardiacProblem<1u, 1u, 2u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==811881== by 0x68745A3: AbstractCardiacProblem<1u, 1u, 2u>::Solve() (AbstractCardiacProblem.cpp:582) ==811881== by 0x13A877: TestExtendedVsBidomainProblem::RunBidomain() (TestExtendedVsBidomainProblem.hpp:226) ==811881== by 0x13A9DE: TestExtendedVsBidomainProblem::TestCompareStimulationOfFirstCell() (TestExtendedVsBidomainProblem.hpp:233) ==811881== by 0x147B3C: TestDescription_TestExtendedVsBidomainProblem_TestCompareStimulationOfFirstCell::runTest() (TestExtendedVsBidomainProblem.cpp:31) ==811881== by 0x13160A: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==811881== by 0x13571C: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==811881== by 0x135601: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==811881== by 0x1354A7: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==811881== by 0x13530E: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==811881== by 0x1359A5: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==811881== by 0x130340: main (TestExtendedVsBidomainProblem.cpp:19) ==811881== { 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:_ZN22AbstractCardiacProblemILj1ELj1ELj2EE24CloseFilesAndPostProcessEv fun:_ZN22AbstractCardiacProblemILj1ELj1ELj2EE5SolveEv fun:_ZN29TestExtendedVsBidomainProblem11RunBidomainEv fun:_ZN29TestExtendedVsBidomainProblem33TestCompareStimulationOfFirstCellEv fun:_ZN79TestDescription_TestExtendedVsBidomainProblem_TestCompareStimulationOfFirstCell7runTestEv fun:_ZN7CxxTest19RealTestDescription3runEv fun:_ZN7CxxTest10TestRunner7runTestERNS_15TestDescriptionE fun:_ZN7CxxTest10TestRunner8runSuiteERNS_16SuiteDescriptionE fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==811881== ==811881== FILE DESCRIPTORS: 9 open (3 std) at exit. ==811881== Open file descriptor 12: ==811881== at 0xA97622D: pipe (pipe.c:29) ==811881== by 0x140E807D: ??? ==811881== by 0xF8EF4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==811881== by 0xC089418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==811881== by 0xC022D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==811881== by 0xAD19D38: PetscInitialize (pinit.c:924) ==811881== by 0xA25F58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==811881== by 0xA25F5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==811881== by 0x1374BE: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==811881== by 0x13200F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==811881== by 0x13546E: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==811881== by 0x13530E: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==811881== by 0x1359A5: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==811881== by 0x130340: main (TestExtendedVsBidomainProblem.cpp:19) ==811881== ==811881== Open file descriptor 8: /dev/shm/open_mpi.0000 ==811881== at 0xA97ABCC: __open_nocancel (open64_nocancel.c:39) ==811881== by 0xA8FEC4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==811881== by 0xA297822: ??? ==811881== by 0xA29796F: ??? ==811881== by 0xF9946DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==811881== by 0xF994938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==811881== by 0xF94A922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==811881== by 0xF8EF2DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==811881== by 0xC089418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==811881== by 0xC022D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==811881== by 0xAD19D38: PetscInitialize (pinit.c:924) ==811881== by 0xA25F58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==811881== by 0xA25F5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==811881== by 0x1374BE: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==811881== by 0x13200F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==811881== by 0x13546E: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==811881== by 0x13530E: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==811881== by 0x1359A5: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==811881== by 0x130340: main (TestExtendedVsBidomainProblem.cpp:19) ==811881== ==811881== Open file descriptor 116: ==811881== ==811881== ==811881== Open file descriptor 111: ==811881== ==811881== ==811881== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestExtendedVsBidomainProblem_valgrind.txt ==811881== ==811881== ==811881== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==811881== ==811881== ==811881== ==811881== HEAP SUMMARY: ==811881== in use at exit: 701,234 bytes in 9,387 blocks ==811881== total heap usage: 467,807 allocs, 458,420 frees, 1,461,029,267 bytes allocated ==811881== ==811881== 552 bytes in 1 blocks are definitely lost in loss record 43 of 69 ==811881== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==811881== by 0x149B6C13: ??? ==811881== by 0x149B722C: ??? ==811881== by 0x1492A4B7: ??? ==811881== by 0xBFEF15A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==811881== by 0xC089A97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==811881== by 0xC022D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==811881== by 0xAD19D38: PetscInitialize (pinit.c:924) ==811881== by 0xA25F58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==811881== by 0xA25F5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==811881== by 0x1374BE: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==811881== by 0x13200F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==811881== by 0x13546E: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==811881== by 0x13530E: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==811881== by 0x1359A5: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==811881== by 0x130340: main (TestExtendedVsBidomainProblem.cpp:19) ==811881== { 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 } ==811881== 84,459 (136 direct, 84,323 indirect) bytes in 1 blocks are definitely lost in loss record 66 of 69 ==811881== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==811881== by 0x15B2974E: ??? ==811881== by 0x15B29E0B: ??? ==811881== by 0x15B2CF56: ??? ==811881== by 0x15B2265D: ??? ==811881== by 0x15B22FA3: ??? ==811881== by 0xFA00F05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==811881== by 0xF9DCAE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==811881== by 0xF98DCB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==811881== by 0xF8BAEF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==811881== by 0x140E8F03: ??? ==811881== by 0xF8EF4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==811881== by 0xC089418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==811881== by 0xC022D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==811881== by 0xAD19D38: PetscInitialize (pinit.c:924) ==811881== by 0xA25F58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==811881== by 0xA25F5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==811881== by 0x1374BE: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==811881== by 0x13200F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==811881== by 0x13546E: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==811881== by 0x13530E: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==811881== by 0x1359A5: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==811881== by 0x130340: main (TestExtendedVsBidomainProblem.cpp:19) ==811881== { 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 } ==811881== LEAK SUMMARY: ==811881== definitely lost: 688 bytes in 2 blocks ==811881== indirectly lost: 1,760 bytes in 16 blocks ==811881== possibly lost: 0 bytes in 0 blocks ==811881== still reachable: 1,531 bytes in 6 blocks ==811881== suppressed: 697,255 bytes in 9,363 blocks ==811881== Reachable blocks (those to which a pointer was found) are not shown. ==811881== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==811881== ==811881== Use --track-origins=yes to see where uninitialised values come from ==811881== For lists of detected and suppressed errors, rerun with: -s ==811881== ERROR SUMMARY: 32 errors from 6 contexts (suppressed: 32 from 32)