==936980== Memcheck, a memory error detector ==936980== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==936980== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==936980== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/heart/test/TestCardiacSimulation -malloc_debug -malloc_dump -memory_info ==936980== Parent PID: 914403 ==936980== ==936980== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==936980== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==936980== ==936980== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==936980== at 0x876179E: getsockopt_syscall (getsockopt.c:29) ==936980== by 0x876179E: getsockopt (getsockopt.c:94) ==936980== by 0x1444F157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936980== by 0x14456A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936980== by 0x1445DDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936980== by 0x1435D3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936980== by 0x142D6E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==936980== by 0x13A95E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==936980== by 0xE5DA4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==936980== by 0x9E62418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936980== by 0x9DFBD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936980== by 0x8AF2D38: PetscInitialize (pinit.c:924) ==936980== by 0x803A58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==936980== by 0x803A5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==936980== by 0x12AA12: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==936980== by 0x123ACF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==936980== by 0x127372: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==936980== by 0x127212: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936980== by 0x1278A9: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936980== by 0x121E00: main (TestCardiacSimulation.cpp:19) ==936980== Address 0x1ffeffdfdc is on thread 1's stack ==936980== in frame #2, created by pmix_ptl_base_make_connection (???:) ==936980== { 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 } ==936980== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==936980== at 0x876179E: getsockopt_syscall (getsockopt.c:29) ==936980== by 0x876179E: getsockopt (getsockopt.c:94) ==936980== by 0x1444F157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936980== by 0x14456A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936980== by 0x1445DDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936980== by 0x1435D3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936980== by 0x142D6E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==936980== by 0x13A95E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==936980== by 0xE5DA4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==936980== by 0x9E62418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936980== by 0x9DFBD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936980== by 0x8AF2D38: PetscInitialize (pinit.c:924) ==936980== by 0x803A58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==936980== by 0x803A5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==936980== by 0x12AA12: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==936980== by 0x123ACF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==936980== by 0x127372: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==936980== by 0x127212: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936980== by 0x1278A9: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936980== by 0x121E00: main (TestCardiacSimulation.cpp:19) ==936980== Address 0x1ffeffdfdc is on thread 1's stack ==936980== in frame #2, created by pmix_ptl_base_make_connection (???:) ==936980== { 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 } ==936980== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==936980== at 0x8761C7E: setsockopt_syscall (setsockopt.c:29) ==936980== by 0x8761C7E: setsockopt (setsockopt.c:95) ==936980== by 0x14456BA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936980== by 0x1445DDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936980== by 0x1435D3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936980== by 0x142D6E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==936980== by 0x13A95E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==936980== by 0xE5DA4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==936980== by 0x9E62418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936980== by 0x9DFBD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936980== by 0x8AF2D38: PetscInitialize (pinit.c:924) ==936980== by 0x803A58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==936980== by 0x803A5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==936980== by 0x12AA12: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==936980== by 0x123ACF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==936980== by 0x127372: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==936980== by 0x127212: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936980== by 0x1278A9: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936980== by 0x121E00: main (TestCardiacSimulation.cpp:19) ==936980== { 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 } ==936980== Syscall param pwrite64(buf) points to uninitialised byte(s) ==936980== at 0x874C9EF: __libc_pwrite64 (pwrite64.c:25) ==936980== by 0x874C9EF: pwrite (pwrite64.c:23) ==936980== by 0x17CCC9D2: mca_fbtl_posix_pwritev (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_fbtl_posix.so) ==936980== by 0x17CDC419: mca_common_ompio_file_write (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==936980== by 0x17CDC79A: mca_common_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==936980== by 0x17BC789A: mca_io_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_io_ompio.so) ==936980== by 0x9DEF6A7: PMPI_File_write_at (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936980== by 0xC21FFEB: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936980== by 0xC05F4ED: H5FD_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936980== by 0xC042313: H5F__accum_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936980== by 0xC13D442: H5PB_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936980== by 0xC049DEA: H5F_block_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936980== by 0xBFD3E98: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936980== by 0xC2133F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936980== by 0xC2149CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936980== by 0xC21547E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936980== by 0xBFB054C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936980== by 0xC048936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936980== by 0xC0493FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936980== by 0xC04CBB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936980== by 0xC04CEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936980== by 0xC0BC51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936980== by 0xC0BC5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936980== by 0xC049831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936980== by 0xC03E881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936980== by 0x7F67967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==936980== by 0x7F62647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==936980== by 0x7F626ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==936980== by 0x676E53D: AbstractCardiacProblem<1u, 1u, 1u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==936980== by 0x676E0DD: AbstractCardiacProblem<1u, 1u, 1u>::Solve() (AbstractCardiacProblem.cpp:582) ==936980== by 0x68E3CA0: void CardiacSimulation::CreateAndRun, 1u>() (CardiacSimulation.hpp:136) ==936980== by 0x68DEA87: CardiacSimulation::Run() (CardiacSimulation.cpp:178) ==936980== by 0x68DE362: CardiacSimulation::CardiacSimulation(std::__cxx11::basic_string, std::allocator >, bool, bool) (CardiacSimulation.cpp:106) ==936980== by 0x12AB87: TestCardiacSimulation::TestMono1dSmall() (TestCardiacSimulation.hpp:78) ==936980== by 0x13CD76: TestDescription_TestCardiacSimulation_TestMono1dSmall::runTest() (TestCardiacSimulation.cpp:31) ==936980== by 0x1230CA: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==936980== by 0x127620: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==936980== by 0x127505: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==936980== by 0x1273AB: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==936980== by 0x127212: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936980== by 0x1278A9: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936980== by 0x121E00: main (TestCardiacSimulation.cpp:19) ==936980== Address 0x161b0abe is 62 bytes inside a block of size 320 alloc'd ==936980== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==936980== by 0xBFD3E26: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936980== by 0xC2133F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936980== by 0xC2149CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936980== by 0xC21547E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936980== by 0xBFB054C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936980== by 0xC048936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936980== by 0xC0493FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936980== by 0xC04CBB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936980== by 0xC04CEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936980== by 0xC0BC51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936980== by 0xC0BC5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936980== by 0xC049831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936980== by 0xC03E881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936980== by 0x7F67967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==936980== by 0x7F62647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==936980== by 0x7F626ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==936980== by 0x676E53D: AbstractCardiacProblem<1u, 1u, 1u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==936980== by 0x676E0DD: AbstractCardiacProblem<1u, 1u, 1u>::Solve() (AbstractCardiacProblem.cpp:582) ==936980== by 0x68E3CA0: void CardiacSimulation::CreateAndRun, 1u>() (CardiacSimulation.hpp:136) ==936980== by 0x68DEA87: CardiacSimulation::Run() (CardiacSimulation.cpp:178) ==936980== by 0x68DE362: CardiacSimulation::CardiacSimulation(std::__cxx11::basic_string, std::allocator >, bool, bool) (CardiacSimulation.cpp:106) ==936980== by 0x12AB87: TestCardiacSimulation::TestMono1dSmall() (TestCardiacSimulation.hpp:78) ==936980== by 0x13CD76: TestDescription_TestCardiacSimulation_TestMono1dSmall::runTest() (TestCardiacSimulation.cpp:31) ==936980== by 0x1230CA: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==936980== by 0x127620: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==936980== by 0x127505: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==936980== by 0x1273AB: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==936980== by 0x127212: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936980== by 0x1278A9: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936980== by 0x121E00: main (TestCardiacSimulation.cpp:19) ==936980== { 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 } ==936980== ==936980== FILE DESCRIPTORS: 9 open (3 std) at exit. ==936980== Open file descriptor 12: ==936980== at 0x874F22D: pipe (pipe.c:29) ==936980== by 0x13A9607D: ??? ==936980== by 0xE5DA4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==936980== by 0x9E62418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936980== by 0x9DFBD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936980== by 0x8AF2D38: PetscInitialize (pinit.c:924) ==936980== by 0x803A58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==936980== by 0x803A5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==936980== by 0x12AA12: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==936980== by 0x123ACF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==936980== by 0x127372: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==936980== by 0x127212: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936980== by 0x1278A9: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936980== by 0x121E00: main (TestCardiacSimulation.cpp:19) ==936980== ==936980== Open file descriptor 8: /dev/shm/open_mpi.0000 ==936980== at 0x8753BCC: __open_nocancel (open64_nocancel.c:39) ==936980== by 0x86D7C4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==936980== by 0x8072822: ??? ==936980== by 0x807296F: ??? ==936980== by 0xE67F6DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==936980== by 0xE67F938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==936980== by 0xE635922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==936980== by 0xE5DA2DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==936980== by 0x9E62418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936980== by 0x9DFBD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936980== by 0x8AF2D38: PetscInitialize (pinit.c:924) ==936980== by 0x803A58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==936980== by 0x803A5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==936980== by 0x12AA12: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==936980== by 0x123ACF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==936980== by 0x127372: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==936980== by 0x127212: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936980== by 0x1278A9: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936980== by 0x121E00: main (TestCardiacSimulation.cpp:19) ==936980== ==936980== Open file descriptor 111: ==936980== ==936980== ==936980== Open file descriptor 108: ==936980== ==936980== ==936980== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestCardiacSimulation_valgrind.txt ==936980== ==936980== ==936980== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==936980== ==936980== ==936980== ==936980== HEAP SUMMARY: ==936980== in use at exit: 708,586 bytes in 9,399 blocks ==936980== total heap usage: 4,725,508 allocs, 4,716,109 frees, 2,841,976,193 bytes allocated ==936980== ==936980== 552 bytes in 1 blocks are definitely lost in loss record 52 of 79 ==936980== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==936980== by 0x14364C13: ??? ==936980== by 0x1436522C: ??? ==936980== by 0x142D84B7: ??? ==936980== by 0x9DC815A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936980== by 0x9E62A97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936980== by 0x9DFBD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936980== by 0x8AF2D38: PetscInitialize (pinit.c:924) ==936980== by 0x803A58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==936980== by 0x803A5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==936980== by 0x12AA12: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==936980== by 0x123ACF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==936980== by 0x127372: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==936980== by 0x127212: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936980== by 0x1278A9: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936980== by 0x121E00: main (TestCardiacSimulation.cpp:19) ==936980== { 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 } ==936980== 685,266 (136 direct, 685,130 indirect) bytes in 1 blocks are definitely lost in loss record 79 of 79 ==936980== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==936980== by 0x154D774E: ??? ==936980== by 0x154D7E0B: ??? ==936980== by 0x154DAF56: ??? ==936980== by 0x154D065D: ??? ==936980== by 0x154D0FA3: ??? ==936980== by 0xE6EBF05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==936980== by 0xE6C7AE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==936980== by 0xE678CB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==936980== by 0xE5A5EF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==936980== by 0x13A96F03: ??? ==936980== by 0xE5DA4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==936980== by 0x9E62418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936980== by 0x9DFBD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936980== by 0x8AF2D38: PetscInitialize (pinit.c:924) ==936980== by 0x803A58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==936980== by 0x803A5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==936980== by 0x12AA12: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==936980== by 0x123ACF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==936980== by 0x127372: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==936980== by 0x127212: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936980== by 0x1278A9: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936980== by 0x121E00: main (TestCardiacSimulation.cpp:19) ==936980== { 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 } ==936980== LEAK SUMMARY: ==936980== definitely lost: 688 bytes in 2 blocks ==936980== indirectly lost: 1,760 bytes in 16 blocks ==936980== possibly lost: 0 bytes in 0 blocks ==936980== still reachable: 8,951 bytes in 22 blocks ==936980== suppressed: 697,187 bytes in 9,359 blocks ==936980== Reachable blocks (those to which a pointer was found) are not shown. ==936980== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==936980== ==936980== Use --track-origins=yes to see where uninitialised values come from ==936980== For lists of detected and suppressed errors, rerun with: -s ==936980== ERROR SUMMARY: 203 errors from 6 contexts (suppressed: 26 from 26)