==1825518== Memcheck, a memory error detector ==1825518== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==1825518== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==1825518== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/heart/test/TestBidomainWithSvi -malloc_debug -malloc_dump -memory_info ==1825518== Parent PID: 1804739 ==1825518== ==1825518== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==1825518== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==1825518== ==1825518== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==1825518== at 0xA12B79E: getsockopt_syscall (getsockopt.c:29) ==1825518== by 0xA12B79E: getsockopt (getsockopt.c:94) ==1825518== by 0x1467C157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1825518== by 0x14683A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1825518== by 0x1468ADF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1825518== by 0x1458A3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1825518== by 0x14503E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==1825518== by 0x13CC2E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==1825518== by 0xF4C44CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1825518== by 0xB82A418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1825518== by 0xB7C3D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1825518== by 0xA4BAD38: PetscInitialize (pinit.c:924) ==1825518== by 0x9A0258B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1825518== by 0x9A025D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1825518== by 0x12A630: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1825518== by 0x12473D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1825518== by 0x126CF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1825518== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1825518== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1825518== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==1825518== Address 0x1ffeffdfbc is on thread 1's stack ==1825518== in frame #2, created by pmix_ptl_base_make_connection (???:) ==1825518== { 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 } ==1825518== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==1825518== at 0xA12B79E: getsockopt_syscall (getsockopt.c:29) ==1825518== by 0xA12B79E: getsockopt (getsockopt.c:94) ==1825518== by 0x1467C157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1825518== by 0x14683A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1825518== by 0x1468ADF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1825518== by 0x1458A3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1825518== by 0x14503E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==1825518== by 0x13CC2E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==1825518== by 0xF4C44CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1825518== by 0xB82A418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1825518== by 0xB7C3D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1825518== by 0xA4BAD38: PetscInitialize (pinit.c:924) ==1825518== by 0x9A0258B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1825518== by 0x9A025D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1825518== by 0x12A630: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1825518== by 0x12473D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1825518== by 0x126CF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1825518== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1825518== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1825518== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==1825518== Address 0x1ffeffdfbc is on thread 1's stack ==1825518== in frame #2, created by pmix_ptl_base_make_connection (???:) ==1825518== { 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 } ==1825518== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==1825518== at 0xA12BC7E: setsockopt_syscall (setsockopt.c:29) ==1825518== by 0xA12BC7E: setsockopt (setsockopt.c:95) ==1825518== by 0x14683BA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1825518== by 0x1468ADF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1825518== by 0x1458A3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1825518== by 0x14503E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==1825518== by 0x13CC2E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==1825518== by 0xF4C44CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1825518== by 0xB82A418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1825518== by 0xB7C3D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1825518== by 0xA4BAD38: PetscInitialize (pinit.c:924) ==1825518== by 0x9A0258B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1825518== by 0x9A025D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1825518== by 0x12A630: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1825518== by 0x12473D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1825518== by 0x126CF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1825518== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1825518== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1825518== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==1825518== { 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 } ==1825518== Syscall param pwrite64(buf) points to uninitialised byte(s) ==1825518== at 0xA1169EF: __libc_pwrite64 (pwrite64.c:25) ==1825518== by 0xA1169EF: pwrite (pwrite64.c:23) ==1825518== by 0x176F99D2: mca_fbtl_posix_pwritev (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_fbtl_posix.so) ==1825518== by 0x17709419: mca_common_ompio_file_write (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==1825518== by 0x1770979A: mca_common_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==1825518== by 0x175F489A: mca_io_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_io_ompio.so) ==1825518== by 0xB7B76A7: PMPI_File_write_at (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1825518== by 0xEE8DFEB: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1825518== by 0xECCD4ED: H5FD_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1825518== by 0xECB0313: H5F__accum_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1825518== by 0xEDAB442: H5PB_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1825518== by 0xECB7DEA: H5F_block_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1825518== by 0xEC41E98: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1825518== by 0xEE813F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1825518== by 0xEE829CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1825518== by 0xEE8347E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1825518== by 0xEC1E54C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1825518== by 0xECB6936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1825518== by 0xECB73FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1825518== by 0xECBABB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1825518== by 0xECBAEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1825518== by 0xED2A51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1825518== by 0xED2A5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1825518== by 0xECB7831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1825518== by 0xECAC881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1825518== by 0xC11F967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==1825518== by 0xC11A647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==1825518== by 0xC11A6ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==1825518== by 0x68749DF: AbstractCardiacProblem<1u, 1u, 2u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==1825518== by 0x687457F: AbstractCardiacProblem<1u, 1u, 2u>::Solve() (AbstractCardiacProblem.cpp:582) ==1825518== by 0x12ADEF: TestBidomainWithSvi::TestConductionVelocityConvergesFasterWithSvi1d() (TestBidomainWithSvi.hpp:157) ==1825518== by 0x12CDE8: TestDescription_TestBidomainWithSvi_TestConductionVelocityConvergesFasterWithSvi1d::runTest() (TestBidomainWithSvi.cpp:30) ==1825518== by 0x123F74: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==1825518== by 0x126FA6: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==1825518== by 0x126E8B: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==1825518== by 0x126D31: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==1825518== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1825518== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1825518== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==1825518== Address 0x16a7859e is 62 bytes inside a block of size 320 alloc'd ==1825518== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==1825518== by 0xEC41E26: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1825518== by 0xEE813F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1825518== by 0xEE829CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1825518== by 0xEE8347E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1825518== by 0xEC1E54C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1825518== by 0xECB6936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1825518== by 0xECB73FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1825518== by 0xECBABB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1825518== by 0xECBAEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1825518== by 0xED2A51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1825518== by 0xED2A5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1825518== by 0xECB7831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1825518== by 0xECAC881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1825518== by 0xC11F967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==1825518== by 0xC11A647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==1825518== by 0xC11A6ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==1825518== by 0x68749DF: AbstractCardiacProblem<1u, 1u, 2u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==1825518== by 0x687457F: AbstractCardiacProblem<1u, 1u, 2u>::Solve() (AbstractCardiacProblem.cpp:582) ==1825518== by 0x12ADEF: TestBidomainWithSvi::TestConductionVelocityConvergesFasterWithSvi1d() (TestBidomainWithSvi.hpp:157) ==1825518== by 0x12CDE8: TestDescription_TestBidomainWithSvi_TestConductionVelocityConvergesFasterWithSvi1d::runTest() (TestBidomainWithSvi.cpp:30) ==1825518== by 0x123F74: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==1825518== by 0x126FA6: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==1825518== by 0x126E8B: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==1825518== by 0x126D31: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==1825518== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1825518== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1825518== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==1825518== { 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 } ==1825518== ==1825518== FILE DESCRIPTORS: 9 open (3 std) at exit. ==1825518== Open file descriptor 12: ==1825518== at 0xA11922D: pipe (pipe.c:29) ==1825518== by 0x13CC307D: ??? ==1825518== by 0xF4C44CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1825518== by 0xB82A418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1825518== by 0xB7C3D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1825518== by 0xA4BAD38: PetscInitialize (pinit.c:924) ==1825518== by 0x9A0258B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1825518== by 0x9A025D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1825518== by 0x12A630: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1825518== by 0x12473D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1825518== by 0x126CF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1825518== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1825518== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1825518== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==1825518== ==1825518== Open file descriptor 8: /dev/shm/open_mpi.0000 ==1825518== at 0xA11DBCC: __open_nocancel (open64_nocancel.c:39) ==1825518== by 0xA0A1C4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==1825518== by 0x9A3A822: ??? ==1825518== by 0x9A3A96F: ??? ==1825518== by 0xF5696DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==1825518== by 0xF569938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==1825518== by 0xF51F922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==1825518== by 0xF4C42DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1825518== by 0xB82A418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1825518== by 0xB7C3D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1825518== by 0xA4BAD38: PetscInitialize (pinit.c:924) ==1825518== by 0x9A0258B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1825518== by 0x9A025D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1825518== by 0x12A630: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1825518== by 0x12473D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1825518== by 0x126CF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1825518== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1825518== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1825518== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==1825518== ==1825518== Open file descriptor 117: ==1825518== ==1825518== ==1825518== Open file descriptor 110: ==1825518== ==1825518== ==1825518== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestBidomainWithSvi_valgrind.txt ==1825518== ==1825518== ==1825518== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==1825518== ==1825518== ==1825518== ==1825518== HEAP SUMMARY: ==1825518== in use at exit: 701,168 bytes in 9,383 blocks ==1825518== total heap usage: 3,540,159 allocs, 3,530,776 frees, 2,061,287,665 bytes allocated ==1825518== ==1825518== 552 bytes in 1 blocks are definitely lost in loss record 39 of 65 ==1825518== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==1825518== by 0x14591C13: ??? ==1825518== by 0x1459222C: ??? ==1825518== by 0x145054B7: ??? ==1825518== by 0xB79015A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1825518== by 0xB82AA97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1825518== by 0xB7C3D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1825518== by 0xA4BAD38: PetscInitialize (pinit.c:924) ==1825518== by 0x9A0258B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1825518== by 0x9A025D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1825518== by 0x12A630: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1825518== by 0x12473D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1825518== by 0x126CF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1825518== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1825518== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1825518== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==1825518== { 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 } ==1825518== 23,323 (136 direct, 23,187 indirect) bytes in 1 blocks are definitely lost in loss record 62 of 65 ==1825518== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==1825518== by 0x1570474E: ??? ==1825518== by 0x15704E0B: ??? ==1825518== by 0x15707F56: ??? ==1825518== by 0x156FD65D: ??? ==1825518== by 0x156FDFA3: ??? ==1825518== by 0xF5D5F05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==1825518== by 0xF5B1AE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==1825518== by 0xF562CB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==1825518== by 0xF48FEF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1825518== by 0x13CC3F03: ??? ==1825518== by 0xF4C44CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1825518== by 0xB82A418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1825518== by 0xB7C3D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1825518== by 0xA4BAD38: PetscInitialize (pinit.c:924) ==1825518== by 0x9A0258B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1825518== by 0x9A025D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1825518== by 0x12A630: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1825518== by 0x12473D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1825518== by 0x126CF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1825518== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1825518== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1825518== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==1825518== { 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 } ==1825518== LEAK SUMMARY: ==1825518== definitely lost: 688 bytes in 2 blocks ==1825518== indirectly lost: 1,760 bytes in 16 blocks ==1825518== possibly lost: 0 bytes in 0 blocks ==1825518== still reachable: 1,531 bytes in 6 blocks ==1825518== suppressed: 697,189 bytes in 9,359 blocks ==1825518== Reachable blocks (those to which a pointer was found) are not shown. ==1825518== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==1825518== ==1825518== Use --track-origins=yes to see where uninitialised values come from ==1825518== For lists of detected and suppressed errors, rerun with: -s ==1825518== ERROR SUMMARY: 44 errors from 6 contexts (suppressed: 28 from 28)