==28798== Memcheck, a memory error detector ==28798== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==28798== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==28798== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/heart/test/TestBidomainWithSvi -malloc_debug -malloc_dump -memory_info ==28798== Parent PID: 7893 ==28798== ==28798== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==28798== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==28798== ==28798== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==28798== at 0xA55379E: getsockopt_syscall (getsockopt.c:29) ==28798== by 0xA55379E: getsockopt (getsockopt.c:94) ==28798== by 0x14AA5157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==28798== by 0x14AACA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==28798== by 0x14AB3DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==28798== by 0x149B33C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==28798== by 0x1492CE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==28798== by 0x140EBE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==28798== by 0xF8ED4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==28798== by 0xBC52418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==28798== by 0xBBEBD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==28798== by 0xA8E2D38: PetscInitialize (pinit.c:924) ==28798== by 0x9E2A58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==28798== by 0x9E2A5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==28798== by 0x12A630: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==28798== by 0x12473D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==28798== by 0x126CF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==28798== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==28798== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==28798== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==28798== Address 0x1ffeffdfbc is on thread 1's stack ==28798== in frame #2, created by pmix_ptl_base_make_connection (???:) ==28798== { 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 } ==28798== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==28798== at 0xA55379E: getsockopt_syscall (getsockopt.c:29) ==28798== by 0xA55379E: getsockopt (getsockopt.c:94) ==28798== by 0x14AA5157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==28798== by 0x14AACA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==28798== by 0x14AB3DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==28798== by 0x149B33C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==28798== by 0x1492CE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==28798== by 0x140EBE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==28798== by 0xF8ED4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==28798== by 0xBC52418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==28798== by 0xBBEBD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==28798== by 0xA8E2D38: PetscInitialize (pinit.c:924) ==28798== by 0x9E2A58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==28798== by 0x9E2A5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==28798== by 0x12A630: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==28798== by 0x12473D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==28798== by 0x126CF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==28798== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==28798== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==28798== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==28798== Address 0x1ffeffdfbc is on thread 1's stack ==28798== in frame #2, created by pmix_ptl_base_make_connection (???:) ==28798== { 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 } ==28798== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==28798== at 0xA553C7E: setsockopt_syscall (setsockopt.c:29) ==28798== by 0xA553C7E: setsockopt (setsockopt.c:95) ==28798== by 0x14AACBA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==28798== by 0x14AB3DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==28798== by 0x149B33C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==28798== by 0x1492CE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==28798== by 0x140EBE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==28798== by 0xF8ED4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==28798== by 0xBC52418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==28798== by 0xBBEBD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==28798== by 0xA8E2D38: PetscInitialize (pinit.c:924) ==28798== by 0x9E2A58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==28798== by 0x9E2A5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==28798== by 0x12A630: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==28798== by 0x12473D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==28798== by 0x126CF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==28798== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==28798== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==28798== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==28798== { 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 } ==28798== Syscall param pwrite64(buf) points to uninitialised byte(s) ==28798== at 0xA53E9EF: __libc_pwrite64 (pwrite64.c:25) ==28798== by 0xA53E9EF: pwrite (pwrite64.c:23) ==28798== by 0x17F229D2: mca_fbtl_posix_pwritev (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_fbtl_posix.so) ==28798== by 0x17F32419: mca_common_ompio_file_write (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==28798== by 0x17F3279A: mca_common_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==28798== by 0x17E1D89A: mca_io_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_io_ompio.so) ==28798== by 0xBBDF6A7: PMPI_File_write_at (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==28798== by 0xF2B6FEB: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28798== by 0xF0F64ED: H5FD_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28798== by 0xF0D9313: H5F__accum_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28798== by 0xF1D4442: H5PB_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28798== by 0xF0E0DEA: H5F_block_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28798== by 0xF06AE98: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28798== by 0xF2AA3F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28798== by 0xF2AB9CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28798== by 0xF2AC47E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28798== by 0xF04754C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28798== by 0xF0DF936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28798== by 0xF0E03FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28798== by 0xF0E3BB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28798== by 0xF0E3EFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28798== by 0xF15351F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28798== by 0xF1535EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28798== by 0xF0E0831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28798== by 0xF0D5881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28798== by 0xC547967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==28798== by 0xC542647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==28798== by 0xC5426ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==28798== by 0x6874A03: AbstractCardiacProblem<1u, 1u, 2u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==28798== by 0x68745A3: AbstractCardiacProblem<1u, 1u, 2u>::Solve() (AbstractCardiacProblem.cpp:582) ==28798== by 0x12ADEF: TestBidomainWithSvi::TestConductionVelocityConvergesFasterWithSvi1d() (TestBidomainWithSvi.hpp:157) ==28798== by 0x12CDE8: TestDescription_TestBidomainWithSvi_TestConductionVelocityConvergesFasterWithSvi1d::runTest() (TestBidomainWithSvi.cpp:30) ==28798== by 0x123F74: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==28798== by 0x126FA6: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==28798== by 0x126E8B: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==28798== by 0x126D31: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==28798== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==28798== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==28798== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==28798== Address 0x169b655e is 62 bytes inside a block of size 320 alloc'd ==28798== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==28798== by 0xF06AE26: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28798== by 0xF2AA3F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28798== by 0xF2AB9CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28798== by 0xF2AC47E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28798== by 0xF04754C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28798== by 0xF0DF936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28798== by 0xF0E03FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28798== by 0xF0E3BB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28798== by 0xF0E3EFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28798== by 0xF15351F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28798== by 0xF1535EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28798== by 0xF0E0831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28798== by 0xF0D5881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28798== by 0xC547967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==28798== by 0xC542647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==28798== by 0xC5426ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==28798== by 0x6874A03: AbstractCardiacProblem<1u, 1u, 2u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==28798== by 0x68745A3: AbstractCardiacProblem<1u, 1u, 2u>::Solve() (AbstractCardiacProblem.cpp:582) ==28798== by 0x12ADEF: TestBidomainWithSvi::TestConductionVelocityConvergesFasterWithSvi1d() (TestBidomainWithSvi.hpp:157) ==28798== by 0x12CDE8: TestDescription_TestBidomainWithSvi_TestConductionVelocityConvergesFasterWithSvi1d::runTest() (TestBidomainWithSvi.cpp:30) ==28798== by 0x123F74: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==28798== by 0x126FA6: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==28798== by 0x126E8B: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==28798== by 0x126D31: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==28798== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==28798== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==28798== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==28798== { 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 } ==28798== ==28798== FILE DESCRIPTORS: 9 open (3 std) at exit. ==28798== Open file descriptor 12: ==28798== at 0xA54122D: pipe (pipe.c:29) ==28798== by 0x140EC07D: ??? ==28798== by 0xF8ED4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==28798== by 0xBC52418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==28798== by 0xBBEBD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==28798== by 0xA8E2D38: PetscInitialize (pinit.c:924) ==28798== by 0x9E2A58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==28798== by 0x9E2A5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==28798== by 0x12A630: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==28798== by 0x12473D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==28798== by 0x126CF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==28798== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==28798== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==28798== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==28798== ==28798== Open file descriptor 8: /dev/shm/open_mpi.0000 ==28798== at 0xA545BCC: __open_nocancel (open64_nocancel.c:39) ==28798== by 0xA4C9C4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==28798== by 0x9E62822: ??? ==28798== by 0x9E6296F: ??? ==28798== by 0xF9926DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==28798== by 0xF992938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==28798== by 0xF948922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==28798== by 0xF8ED2DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==28798== by 0xBC52418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==28798== by 0xBBEBD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==28798== by 0xA8E2D38: PetscInitialize (pinit.c:924) ==28798== by 0x9E2A58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==28798== by 0x9E2A5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==28798== by 0x12A630: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==28798== by 0x12473D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==28798== by 0x126CF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==28798== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==28798== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==28798== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==28798== ==28798== Open file descriptor 115: ==28798== ==28798== ==28798== Open file descriptor 110: ==28798== ==28798== ==28798== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestBidomainWithSvi_valgrind.txt ==28798== ==28798== ==28798== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==28798== ==28798== ==28798== ==28798== HEAP SUMMARY: ==28798== in use at exit: 701,164 bytes in 9,383 blocks ==28798== total heap usage: 3,540,257 allocs, 3,530,874 frees, 2,061,505,052 bytes allocated ==28798== ==28798== 552 bytes in 1 blocks are definitely lost in loss record 39 of 65 ==28798== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==28798== by 0x149BAC13: ??? ==28798== by 0x149BB22C: ??? ==28798== by 0x1492E4B7: ??? ==28798== by 0xBBB815A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==28798== by 0xBC52A97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==28798== by 0xBBEBD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==28798== by 0xA8E2D38: PetscInitialize (pinit.c:924) ==28798== by 0x9E2A58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==28798== by 0x9E2A5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==28798== by 0x12A630: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==28798== by 0x12473D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==28798== by 0x126CF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==28798== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==28798== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==28798== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==28798== { 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 } ==28798== 84,459 (136 direct, 84,323 indirect) bytes in 1 blocks are definitely lost in loss record 62 of 65 ==28798== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==28798== by 0x15B2D74E: ??? ==28798== by 0x15B2DE0B: ??? ==28798== by 0x15B30F56: ??? ==28798== by 0x15B2665D: ??? ==28798== by 0x15B26FA3: ??? ==28798== by 0xF9FEF05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==28798== by 0xF9DAAE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==28798== by 0xF98BCB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==28798== by 0xF8B8EF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==28798== by 0x140ECF03: ??? ==28798== by 0xF8ED4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==28798== by 0xBC52418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==28798== by 0xBBEBD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==28798== by 0xA8E2D38: PetscInitialize (pinit.c:924) ==28798== by 0x9E2A58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==28798== by 0x9E2A5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==28798== by 0x12A630: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==28798== by 0x12473D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==28798== by 0x126CF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==28798== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==28798== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==28798== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==28798== { 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 } ==28798== LEAK SUMMARY: ==28798== definitely lost: 688 bytes in 2 blocks ==28798== indirectly lost: 1,760 bytes in 16 blocks ==28798== possibly lost: 0 bytes in 0 blocks ==28798== still reachable: 1,531 bytes in 6 blocks ==28798== suppressed: 697,185 bytes in 9,359 blocks ==28798== Reachable blocks (those to which a pointer was found) are not shown. ==28798== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==28798== ==28798== Use --track-origins=yes to see where uninitialised values come from ==28798== For lists of detected and suppressed errors, rerun with: -s ==28798== ERROR SUMMARY: 44 errors from 6 contexts (suppressed: 28 from 28)