==3180683== Memcheck, a memory error detector ==3180683== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==3180683== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==3180683== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/heart/test/TestBidomainWithSvi -malloc_debug -malloc_dump -memory_info ==3180683== Parent PID: 3159762 ==3180683== ==3180683== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==3180683== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==3180683== ==3180683== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==3180683== at 0xA55179E: getsockopt_syscall (getsockopt.c:29) ==3180683== by 0xA55179E: getsockopt (getsockopt.c:94) ==3180683== by 0x14AA3157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3180683== by 0x14AAAA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3180683== by 0x14AB1DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3180683== by 0x149B13C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3180683== by 0x1492AE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==3180683== by 0x140E9E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==3180683== by 0xF8EB4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3180683== by 0xBC50418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3180683== by 0xBBE9D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3180683== by 0xA8E0D38: PetscInitialize (pinit.c:924) ==3180683== by 0x9E2858B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3180683== by 0x9E285D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3180683== by 0x12A630: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3180683== by 0x12473D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3180683== by 0x126CF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3180683== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3180683== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3180683== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==3180683== Address 0x1ffeffdfbc is on thread 1's stack ==3180683== in frame #2, created by pmix_ptl_base_make_connection (???:) ==3180683== { 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 } ==3180683== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==3180683== at 0xA55179E: getsockopt_syscall (getsockopt.c:29) ==3180683== by 0xA55179E: getsockopt (getsockopt.c:94) ==3180683== by 0x14AA3157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3180683== by 0x14AAAA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3180683== by 0x14AB1DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3180683== by 0x149B13C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3180683== by 0x1492AE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==3180683== by 0x140E9E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==3180683== by 0xF8EB4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3180683== by 0xBC50418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3180683== by 0xBBE9D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3180683== by 0xA8E0D38: PetscInitialize (pinit.c:924) ==3180683== by 0x9E2858B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3180683== by 0x9E285D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3180683== by 0x12A630: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3180683== by 0x12473D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3180683== by 0x126CF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3180683== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3180683== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3180683== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==3180683== Address 0x1ffeffdfbc is on thread 1's stack ==3180683== in frame #2, created by pmix_ptl_base_make_connection (???:) ==3180683== { 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 } ==3180683== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==3180683== at 0xA551C7E: setsockopt_syscall (setsockopt.c:29) ==3180683== by 0xA551C7E: setsockopt (setsockopt.c:95) ==3180683== by 0x14AAABA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3180683== by 0x14AB1DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3180683== by 0x149B13C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3180683== by 0x1492AE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==3180683== by 0x140E9E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==3180683== by 0xF8EB4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3180683== by 0xBC50418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3180683== by 0xBBE9D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3180683== by 0xA8E0D38: PetscInitialize (pinit.c:924) ==3180683== by 0x9E2858B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3180683== by 0x9E285D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3180683== by 0x12A630: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3180683== by 0x12473D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3180683== by 0x126CF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3180683== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3180683== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3180683== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==3180683== { 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 } ==3180683== Syscall param pwrite64(buf) points to uninitialised byte(s) ==3180683== at 0xA53C9EF: __libc_pwrite64 (pwrite64.c:25) ==3180683== by 0xA53C9EF: pwrite (pwrite64.c:23) ==3180683== by 0x17F209D2: mca_fbtl_posix_pwritev (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_fbtl_posix.so) ==3180683== by 0x17F30419: mca_common_ompio_file_write (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==3180683== by 0x17F3079A: mca_common_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==3180683== by 0x17E1B89A: mca_io_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_io_ompio.so) ==3180683== by 0xBBDD6A7: PMPI_File_write_at (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3180683== by 0xF2B4FEB: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3180683== by 0xF0F44ED: H5FD_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3180683== by 0xF0D7313: H5F__accum_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3180683== by 0xF1D2442: H5PB_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3180683== by 0xF0DEDEA: H5F_block_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3180683== by 0xF068E98: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3180683== by 0xF2A83F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3180683== by 0xF2A99CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3180683== by 0xF2AA47E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3180683== by 0xF04554C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3180683== by 0xF0DD936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3180683== by 0xF0DE3FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3180683== by 0xF0E1BB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3180683== by 0xF0E1EFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3180683== by 0xF15151F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3180683== by 0xF1515EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3180683== by 0xF0DE831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3180683== by 0xF0D3881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3180683== by 0xC545967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==3180683== by 0xC540647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==3180683== by 0xC5406ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==3180683== by 0x6874A03: AbstractCardiacProblem<1u, 1u, 2u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==3180683== by 0x68745A3: AbstractCardiacProblem<1u, 1u, 2u>::Solve() (AbstractCardiacProblem.cpp:582) ==3180683== by 0x12ADEF: TestBidomainWithSvi::TestConductionVelocityConvergesFasterWithSvi1d() (TestBidomainWithSvi.hpp:157) ==3180683== by 0x12CDE8: TestDescription_TestBidomainWithSvi_TestConductionVelocityConvergesFasterWithSvi1d::runTest() (TestBidomainWithSvi.cpp:30) ==3180683== by 0x123F74: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==3180683== by 0x126FA6: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==3180683== by 0x126E8B: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==3180683== by 0x126D31: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==3180683== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3180683== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3180683== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==3180683== Address 0x1665867e is 62 bytes inside a block of size 320 alloc'd ==3180683== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==3180683== by 0xF068E26: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3180683== by 0xF2A83F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3180683== by 0xF2A99CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3180683== by 0xF2AA47E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3180683== by 0xF04554C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3180683== by 0xF0DD936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3180683== by 0xF0DE3FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3180683== by 0xF0E1BB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3180683== by 0xF0E1EFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3180683== by 0xF15151F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3180683== by 0xF1515EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3180683== by 0xF0DE831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3180683== by 0xF0D3881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3180683== by 0xC545967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==3180683== by 0xC540647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==3180683== by 0xC5406ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==3180683== by 0x6874A03: AbstractCardiacProblem<1u, 1u, 2u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==3180683== by 0x68745A3: AbstractCardiacProblem<1u, 1u, 2u>::Solve() (AbstractCardiacProblem.cpp:582) ==3180683== by 0x12ADEF: TestBidomainWithSvi::TestConductionVelocityConvergesFasterWithSvi1d() (TestBidomainWithSvi.hpp:157) ==3180683== by 0x12CDE8: TestDescription_TestBidomainWithSvi_TestConductionVelocityConvergesFasterWithSvi1d::runTest() (TestBidomainWithSvi.cpp:30) ==3180683== by 0x123F74: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==3180683== by 0x126FA6: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==3180683== by 0x126E8B: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==3180683== by 0x126D31: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==3180683== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3180683== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3180683== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==3180683== { 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:_ZN19TestBidomainWithSvi46TestConductionVelocityConvergesFasterWithSvi1dEv fun:_ZN82TestDescription_TestBidomainWithSvi_TestConductionVelocityConvergesFasterWithSvi1d7runTestEv fun:_ZN7CxxTest19RealTestDescription3runEv fun:_ZN7CxxTest10TestRunner7runTestERNS_15TestDescriptionE fun:_ZN7CxxTest10TestRunner8runSuiteERNS_16SuiteDescriptionE fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==3180683== ==3180683== FILE DESCRIPTORS: 9 open (3 std) at exit. ==3180683== Open file descriptor 12: ==3180683== at 0xA53F22D: pipe (pipe.c:29) ==3180683== by 0x140EA07D: ??? ==3180683== by 0xF8EB4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3180683== by 0xBC50418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3180683== by 0xBBE9D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3180683== by 0xA8E0D38: PetscInitialize (pinit.c:924) ==3180683== by 0x9E2858B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3180683== by 0x9E285D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3180683== by 0x12A630: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3180683== by 0x12473D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3180683== by 0x126CF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3180683== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3180683== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3180683== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==3180683== ==3180683== Open file descriptor 8: /dev/shm/open_mpi.0000 ==3180683== at 0xA543BCC: __open_nocancel (open64_nocancel.c:39) ==3180683== by 0xA4C7C4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==3180683== by 0x9E60822: ??? ==3180683== by 0x9E6096F: ??? ==3180683== by 0xF9906DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==3180683== by 0xF990938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==3180683== by 0xF946922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==3180683== by 0xF8EB2DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3180683== by 0xBC50418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3180683== by 0xBBE9D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3180683== by 0xA8E0D38: PetscInitialize (pinit.c:924) ==3180683== by 0x9E2858B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3180683== by 0x9E285D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3180683== by 0x12A630: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3180683== by 0x12473D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3180683== by 0x126CF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3180683== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3180683== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3180683== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==3180683== ==3180683== Open file descriptor 117: ==3180683== ==3180683== ==3180683== Open file descriptor 99: ==3180683== ==3180683== ==3180683== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestBidomainWithSvi_valgrind.txt ==3180683== ==3180683== ==3180683== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==3180683== ==3180683== ==3180683== ==3180683== HEAP SUMMARY: ==3180683== in use at exit: 701,168 bytes in 9,383 blocks ==3180683== total heap usage: 3,540,245 allocs, 3,530,862 frees, 2,061,504,761 bytes allocated ==3180683== ==3180683== 552 bytes in 1 blocks are definitely lost in loss record 39 of 65 ==3180683== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==3180683== by 0x149B8C13: ??? ==3180683== by 0x149B922C: ??? ==3180683== by 0x1492C4B7: ??? ==3180683== by 0xBBB615A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3180683== by 0xBC50A97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3180683== by 0xBBE9D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3180683== by 0xA8E0D38: PetscInitialize (pinit.c:924) ==3180683== by 0x9E2858B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3180683== by 0x9E285D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3180683== by 0x12A630: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3180683== by 0x12473D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3180683== by 0x126CF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3180683== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3180683== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3180683== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==3180683== { 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 } ==3180683== 84,459 (136 direct, 84,323 indirect) bytes in 1 blocks are definitely lost in loss record 62 of 65 ==3180683== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==3180683== by 0x15B2B74E: ??? ==3180683== by 0x15B2BE0B: ??? ==3180683== by 0x15B2EF56: ??? ==3180683== by 0x15B2465D: ??? ==3180683== by 0x15B24FA3: ??? ==3180683== by 0xF9FCF05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==3180683== by 0xF9D8AE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==3180683== by 0xF989CB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==3180683== by 0xF8B6EF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3180683== by 0x140EAF03: ??? ==3180683== by 0xF8EB4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3180683== by 0xBC50418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3180683== by 0xBBE9D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3180683== by 0xA8E0D38: PetscInitialize (pinit.c:924) ==3180683== by 0x9E2858B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3180683== by 0x9E285D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3180683== by 0x12A630: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3180683== by 0x12473D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3180683== by 0x126CF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3180683== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3180683== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3180683== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==3180683== { 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 } ==3180683== LEAK SUMMARY: ==3180683== definitely lost: 688 bytes in 2 blocks ==3180683== indirectly lost: 1,760 bytes in 16 blocks ==3180683== possibly lost: 0 bytes in 0 blocks ==3180683== still reachable: 1,531 bytes in 6 blocks ==3180683== suppressed: 697,189 bytes in 9,359 blocks ==3180683== Reachable blocks (those to which a pointer was found) are not shown. ==3180683== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==3180683== ==3180683== Use --track-origins=yes to see where uninitialised values come from ==3180683== For lists of detected and suppressed errors, rerun with: -s ==3180683== ERROR SUMMARY: 44 errors from 6 contexts (suppressed: 28 from 28)