==3305424== Memcheck, a memory error detector ==3305424== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==3305424== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==3305424== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/heart/test/TestCardiacSimulation -malloc_debug -malloc_dump -memory_info ==3305424== Parent PID: 3282641 ==3305424== ==3305424== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==3305424== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==3305424== ==3305424== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==3305424== at 0x898E79E: getsockopt_syscall (getsockopt.c:29) ==3305424== by 0x898E79E: getsockopt (getsockopt.c:94) ==3305424== by 0x1467E157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3305424== by 0x14685A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3305424== by 0x1468CDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3305424== by 0x1458C3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3305424== by 0x14505E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==3305424== by 0x13CC4E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==3305424== by 0xE8084CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3305424== by 0xA08F418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3305424== by 0xA028D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3305424== by 0x8D1FD38: PetscInitialize (pinit.c:924) ==3305424== by 0x826766F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3305424== by 0x82676BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3305424== by 0x12AA32: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3305424== by 0x123AEF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3305424== by 0x127392: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3305424== by 0x127232: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3305424== by 0x1278C9: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3305424== by 0x121E20: main (TestCardiacSimulation.cpp:19) ==3305424== Address 0x1ffeffdfac is on thread 1's stack ==3305424== in frame #2, created by pmix_ptl_base_make_connection (???:) ==3305424== { 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 } ==3305424== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==3305424== at 0x898E79E: getsockopt_syscall (getsockopt.c:29) ==3305424== by 0x898E79E: getsockopt (getsockopt.c:94) ==3305424== by 0x1467E157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3305424== by 0x14685A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3305424== by 0x1468CDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3305424== by 0x1458C3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3305424== by 0x14505E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==3305424== by 0x13CC4E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==3305424== by 0xE8084CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3305424== by 0xA08F418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3305424== by 0xA028D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3305424== by 0x8D1FD38: PetscInitialize (pinit.c:924) ==3305424== by 0x826766F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3305424== by 0x82676BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3305424== by 0x12AA32: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3305424== by 0x123AEF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3305424== by 0x127392: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3305424== by 0x127232: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3305424== by 0x1278C9: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3305424== by 0x121E20: main (TestCardiacSimulation.cpp:19) ==3305424== Address 0x1ffeffdfac is on thread 1's stack ==3305424== in frame #2, created by pmix_ptl_base_make_connection (???:) ==3305424== { 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 } ==3305424== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==3305424== at 0x898EC7E: setsockopt_syscall (setsockopt.c:29) ==3305424== by 0x898EC7E: setsockopt (setsockopt.c:95) ==3305424== by 0x14685BA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3305424== by 0x1468CDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3305424== by 0x1458C3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3305424== by 0x14505E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==3305424== by 0x13CC4E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==3305424== by 0xE8084CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3305424== by 0xA08F418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3305424== by 0xA028D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3305424== by 0x8D1FD38: PetscInitialize (pinit.c:924) ==3305424== by 0x826766F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3305424== by 0x82676BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3305424== by 0x12AA32: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3305424== by 0x123AEF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3305424== by 0x127392: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3305424== by 0x127232: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3305424== by 0x1278C9: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3305424== by 0x121E20: main (TestCardiacSimulation.cpp:19) ==3305424== { 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 } ==3305424== Syscall param pwrite64(buf) points to uninitialised byte(s) ==3305424== at 0x89799EF: __libc_pwrite64 (pwrite64.c:25) ==3305424== by 0x89799EF: pwrite (pwrite64.c:23) ==3305424== by 0x17AFB9D2: mca_fbtl_posix_pwritev (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_fbtl_posix.so) ==3305424== by 0x17B0B419: mca_common_ompio_file_write (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==3305424== by 0x17B0B79A: mca_common_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==3305424== by 0x175F689A: mca_io_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_io_ompio.so) ==3305424== by 0xA01C6A7: PMPI_File_write_at (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3305424== by 0xC44DFEB: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305424== by 0xC28D4ED: H5FD_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305424== by 0xC270313: H5F__accum_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305424== by 0xC36B442: H5PB_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305424== by 0xC277DEA: H5F_block_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305424== by 0xC201E98: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305424== by 0xC4413F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305424== by 0xC4429CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305424== by 0xC44347E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305424== by 0xC1DE54C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305424== by 0xC276936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305424== by 0xC2773FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305424== by 0xC27ABB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305424== by 0xC27AEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305424== by 0xC2EA51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305424== by 0xC2EA5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305424== by 0xC277831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305424== by 0xC26C881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305424== by 0x81938E7: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==3305424== by 0x818E5C7: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==3305424== by 0x818E66D: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==3305424== by 0x6858427: AbstractCardiacProblem<1u, 1u, 1u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==3305424== by 0x6857FC7: AbstractCardiacProblem<1u, 1u, 1u>::Solve() (AbstractCardiacProblem.cpp:582) ==3305424== by 0x69CDBA2: void CardiacSimulation::CreateAndRun, 1u>() (CardiacSimulation.hpp:136) ==3305424== by 0x69C8989: CardiacSimulation::Run() (CardiacSimulation.cpp:178) ==3305424== by 0x69C8264: CardiacSimulation::CardiacSimulation(std::__cxx11::basic_string, std::allocator >, bool, bool) (CardiacSimulation.cpp:106) ==3305424== by 0x12ABA7: TestCardiacSimulation::TestMono1dSmall() (TestCardiacSimulation.hpp:78) ==3305424== by 0x13CDA8: TestDescription_TestCardiacSimulation_TestMono1dSmall::runTest() (TestCardiacSimulation.cpp:31) ==3305424== by 0x1230EA: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==3305424== by 0x127640: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==3305424== by 0x127525: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==3305424== by 0x1273CB: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==3305424== by 0x127232: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3305424== by 0x1278C9: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3305424== by 0x121E20: main (TestCardiacSimulation.cpp:19) ==3305424== Address 0x15f4ad9e is 62 bytes inside a block of size 320 alloc'd ==3305424== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==3305424== by 0xC201E26: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305424== by 0xC4413F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305424== by 0xC4429CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305424== by 0xC44347E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305424== by 0xC1DE54C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305424== by 0xC276936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305424== by 0xC2773FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305424== by 0xC27ABB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305424== by 0xC27AEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305424== by 0xC2EA51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305424== by 0xC2EA5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305424== by 0xC277831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305424== by 0xC26C881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305424== by 0x81938E7: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==3305424== by 0x818E5C7: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==3305424== by 0x818E66D: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==3305424== by 0x6858427: AbstractCardiacProblem<1u, 1u, 1u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==3305424== by 0x6857FC7: AbstractCardiacProblem<1u, 1u, 1u>::Solve() (AbstractCardiacProblem.cpp:582) ==3305424== by 0x69CDBA2: void CardiacSimulation::CreateAndRun, 1u>() (CardiacSimulation.hpp:136) ==3305424== by 0x69C8989: CardiacSimulation::Run() (CardiacSimulation.cpp:178) ==3305424== by 0x69C8264: CardiacSimulation::CardiacSimulation(std::__cxx11::basic_string, std::allocator >, bool, bool) (CardiacSimulation.cpp:106) ==3305424== by 0x12ABA7: TestCardiacSimulation::TestMono1dSmall() (TestCardiacSimulation.hpp:78) ==3305424== by 0x13CDA8: TestDescription_TestCardiacSimulation_TestMono1dSmall::runTest() (TestCardiacSimulation.cpp:31) ==3305424== by 0x1230EA: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==3305424== by 0x127640: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==3305424== by 0x127525: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==3305424== by 0x1273CB: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==3305424== by 0x127232: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3305424== by 0x1278C9: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3305424== by 0x121E20: main (TestCardiacSimulation.cpp:19) ==3305424== { 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:_ZN22AbstractCardiacProblemILj1ELj1ELj1EE24CloseFilesAndPostProcessEv fun:_ZN22AbstractCardiacProblemILj1ELj1ELj1EE5SolveEv fun:_ZN17CardiacSimulation12CreateAndRunI17MonodomainProblemILj1ELj1EELj1EEEvv fun:_ZN17CardiacSimulation3RunEv fun:_ZN17CardiacSimulationC1ENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEbb fun:_ZN21TestCardiacSimulation15TestMono1dSmallEv fun:_ZN53TestDescription_TestCardiacSimulation_TestMono1dSmall7runTestEv fun:_ZN7CxxTest19RealTestDescription3runEv fun:_ZN7CxxTest10TestRunner7runTestERNS_15TestDescriptionE fun:_ZN7CxxTest10TestRunner8runSuiteERNS_16SuiteDescriptionE fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==3305424== ==3305424== FILE DESCRIPTORS: 9 open (3 std) at exit. ==3305424== Open file descriptor 12: ==3305424== at 0x897C22D: pipe (pipe.c:29) ==3305424== by 0x13CC507D: ??? ==3305424== by 0xE8084CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3305424== by 0xA08F418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3305424== by 0xA028D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3305424== by 0x8D1FD38: PetscInitialize (pinit.c:924) ==3305424== by 0x826766F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3305424== by 0x82676BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3305424== by 0x12AA32: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3305424== by 0x123AEF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3305424== by 0x127392: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3305424== by 0x127232: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3305424== by 0x1278C9: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3305424== by 0x121E20: main (TestCardiacSimulation.cpp:19) ==3305424== ==3305424== Open file descriptor 8: /dev/shm/open_mpi.0000 ==3305424== at 0x8980BCC: __open_nocancel (open64_nocancel.c:39) ==3305424== by 0x8904C4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==3305424== by 0x829F822: ??? ==3305424== by 0x829F96F: ??? ==3305424== by 0xE8AD6DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==3305424== by 0xE8AD938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==3305424== by 0xE863922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==3305424== by 0xE8082DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3305424== by 0xA08F418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3305424== by 0xA028D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3305424== by 0x8D1FD38: PetscInitialize (pinit.c:924) ==3305424== by 0x826766F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3305424== by 0x82676BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3305424== by 0x12AA32: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3305424== by 0x123AEF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3305424== by 0x127392: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3305424== by 0x127232: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3305424== by 0x1278C9: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3305424== by 0x121E20: main (TestCardiacSimulation.cpp:19) ==3305424== ==3305424== Open file descriptor 117: ==3305424== ==3305424== ==3305424== Open file descriptor 108: ==3305424== ==3305424== ==3305424== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestCardiacSimulation_valgrind.txt ==3305424== ==3305424== ==3305424== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==3305424== ==3305424== ==3305424== ==3305424== HEAP SUMMARY: ==3305424== in use at exit: 708,588 bytes in 9,399 blocks ==3305424== total heap usage: 4,721,838 allocs, 4,712,439 frees, 2,841,246,496 bytes allocated ==3305424== ==3305424== 552 bytes in 1 blocks are definitely lost in loss record 52 of 82 ==3305424== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==3305424== by 0x14593C13: ??? ==3305424== by 0x1459422C: ??? ==3305424== by 0x145074B7: ??? ==3305424== by 0x9FF515A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3305424== by 0xA08FA97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3305424== by 0xA028D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3305424== by 0x8D1FD38: PetscInitialize (pinit.c:924) ==3305424== by 0x826766F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3305424== by 0x82676BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3305424== by 0x12AA32: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3305424== by 0x123AEF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3305424== by 0x127392: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3305424== by 0x127232: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3305424== by 0x1278C9: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3305424== by 0x121E20: main (TestCardiacSimulation.cpp:19) ==3305424== { 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 } ==3305424== 84,459 (136 direct, 84,323 indirect) bytes in 1 blocks are definitely lost in loss record 79 of 82 ==3305424== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==3305424== by 0x1570674E: ??? ==3305424== by 0x15706E0B: ??? ==3305424== by 0x15709F56: ??? ==3305424== by 0x156FF65D: ??? ==3305424== by 0x156FFFA3: ??? ==3305424== by 0xE919F05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==3305424== by 0xE8F5AE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==3305424== by 0xE8A6CB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==3305424== by 0xE7D3EF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3305424== by 0x13CC5F03: ??? ==3305424== by 0xE8084CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3305424== by 0xA08F418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3305424== by 0xA028D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3305424== by 0x8D1FD38: PetscInitialize (pinit.c:924) ==3305424== by 0x826766F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3305424== by 0x82676BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3305424== by 0x12AA32: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3305424== by 0x123AEF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3305424== by 0x127392: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3305424== by 0x127232: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3305424== by 0x1278C9: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3305424== by 0x121E20: main (TestCardiacSimulation.cpp:19) ==3305424== { 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 } ==3305424== LEAK SUMMARY: ==3305424== definitely lost: 688 bytes in 2 blocks ==3305424== indirectly lost: 1,760 bytes in 16 blocks ==3305424== possibly lost: 0 bytes in 0 blocks ==3305424== still reachable: 8,951 bytes in 22 blocks ==3305424== suppressed: 697,189 bytes in 9,359 blocks ==3305424== Reachable blocks (those to which a pointer was found) are not shown. ==3305424== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==3305424== ==3305424== Use --track-origins=yes to see where uninitialised values come from ==3305424== For lists of detected and suppressed errors, rerun with: -s ==3305424== ERROR SUMMARY: 203 errors from 6 contexts (suppressed: 28 from 28)