==935190== Memcheck, a memory error detector ==935190== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==935190== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==935190== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/heart/test/TestExtendedVsBidomainProblem -malloc_debug -malloc_dump -memory_info ==935190== Parent PID: 914403 ==935190== ==935190== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==935190== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==935190== ==935190== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==935190== at 0xA33679E: getsockopt_syscall (getsockopt.c:29) ==935190== by 0xA33679E: getsockopt (getsockopt.c:94) ==935190== by 0x1444F157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935190== by 0x14456A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935190== by 0x1445DDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935190== by 0x1435D3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935190== by 0x142D6E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==935190== by 0x13A95E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==935190== by 0xF29D4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==935190== by 0xBA37418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935190== by 0xB9D0D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935190== by 0xA6C7D38: PetscInitialize (pinit.c:924) ==935190== by 0x9C0D58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==935190== by 0x9C0D5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==935190== by 0x1374BE: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==935190== by 0x13200F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==935190== by 0x13546E: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==935190== by 0x13530E: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==935190== by 0x1359A5: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==935190== by 0x130340: main (TestExtendedVsBidomainProblem.cpp:19) ==935190== Address 0x1ffeffdfcc is on thread 1's stack ==935190== in frame #2, created by pmix_ptl_base_make_connection (???:) ==935190== { 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 } ==935190== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==935190== at 0xA33679E: getsockopt_syscall (getsockopt.c:29) ==935190== by 0xA33679E: getsockopt (getsockopt.c:94) ==935190== by 0x1444F157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935190== by 0x14456A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935190== by 0x1445DDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935190== by 0x1435D3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935190== by 0x142D6E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==935190== by 0x13A95E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==935190== by 0xF29D4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==935190== by 0xBA37418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935190== by 0xB9D0D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935190== by 0xA6C7D38: PetscInitialize (pinit.c:924) ==935190== by 0x9C0D58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==935190== by 0x9C0D5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==935190== by 0x1374BE: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==935190== by 0x13200F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==935190== by 0x13546E: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==935190== by 0x13530E: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==935190== by 0x1359A5: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==935190== by 0x130340: main (TestExtendedVsBidomainProblem.cpp:19) ==935190== Address 0x1ffeffdfcc is on thread 1's stack ==935190== in frame #2, created by pmix_ptl_base_make_connection (???:) ==935190== { 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 } ==935190== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==935190== at 0xA336C7E: setsockopt_syscall (setsockopt.c:29) ==935190== by 0xA336C7E: setsockopt (setsockopt.c:95) ==935190== by 0x14456BA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935190== by 0x1445DDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935190== by 0x1435D3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935190== by 0x142D6E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==935190== by 0x13A95E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==935190== by 0xF29D4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==935190== by 0xBA37418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935190== by 0xB9D0D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935190== by 0xA6C7D38: PetscInitialize (pinit.c:924) ==935190== by 0x9C0D58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==935190== by 0x9C0D5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==935190== by 0x1374BE: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==935190== by 0x13200F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==935190== by 0x13546E: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==935190== by 0x13530E: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==935190== by 0x1359A5: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==935190== by 0x130340: main (TestExtendedVsBidomainProblem.cpp:19) ==935190== { 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 } ==935190== Syscall param pwrite64(buf) points to uninitialised byte(s) ==935190== at 0xA3219EF: __libc_pwrite64 (pwrite64.c:25) ==935190== by 0xA3219EF: pwrite (pwrite64.c:23) ==935190== by 0x17CCC9D2: mca_fbtl_posix_pwritev (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_fbtl_posix.so) ==935190== by 0x17CDC419: mca_common_ompio_file_write (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==935190== by 0x17CDC79A: mca_common_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==935190== by 0x17BC789A: mca_io_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_io_ompio.so) ==935190== by 0xB9C46A7: PMPI_File_write_at (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935190== by 0xC21FFEB: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935190== by 0xC05F4ED: H5FD_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935190== by 0xC042313: H5F__accum_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935190== by 0xC13D442: H5PB_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935190== by 0xC049DEA: H5F_block_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935190== by 0xBFD3E98: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935190== by 0xC2133F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935190== by 0xC2149CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935190== by 0xC21547E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935190== by 0xBFB054C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935190== by 0xC048936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935190== by 0xC0493FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935190== by 0xC04CBB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935190== by 0xC04CEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935190== by 0xC0BC51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935190== by 0xC0BC5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935190== by 0xC049831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935190== by 0xC03E881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935190== by 0x9B3C967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==935190== by 0x9B37647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==935190== by 0x9B376ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==935190== by 0x678ABE5: AbstractCardiacProblem<1u, 1u, 2u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==935190== by 0x678A785: AbstractCardiacProblem<1u, 1u, 2u>::Solve() (AbstractCardiacProblem.cpp:582) ==935190== by 0x13A877: TestExtendedVsBidomainProblem::RunBidomain() (TestExtendedVsBidomainProblem.hpp:226) ==935190== by 0x13A9DE: TestExtendedVsBidomainProblem::TestCompareStimulationOfFirstCell() (TestExtendedVsBidomainProblem.hpp:233) ==935190== by 0x147B38: TestDescription_TestExtendedVsBidomainProblem_TestCompareStimulationOfFirstCell::runTest() (TestExtendedVsBidomainProblem.cpp:31) ==935190== by 0x13160A: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==935190== by 0x13571C: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==935190== by 0x135601: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==935190== by 0x1354A7: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==935190== by 0x13530E: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==935190== by 0x1359A5: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==935190== by 0x130340: main (TestExtendedVsBidomainProblem.cpp:19) ==935190== Address 0x15e02f9e is 62 bytes inside a block of size 320 alloc'd ==935190== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==935190== by 0xBFD3E26: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935190== by 0xC2133F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935190== by 0xC2149CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935190== by 0xC21547E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935190== by 0xBFB054C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935190== by 0xC048936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935190== by 0xC0493FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935190== by 0xC04CBB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935190== by 0xC04CEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935190== by 0xC0BC51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935190== by 0xC0BC5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935190== by 0xC049831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935190== by 0xC03E881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935190== by 0x9B3C967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==935190== by 0x9B37647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==935190== by 0x9B376ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==935190== by 0x678ABE5: AbstractCardiacProblem<1u, 1u, 2u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==935190== by 0x678A785: AbstractCardiacProblem<1u, 1u, 2u>::Solve() (AbstractCardiacProblem.cpp:582) ==935190== by 0x13A877: TestExtendedVsBidomainProblem::RunBidomain() (TestExtendedVsBidomainProblem.hpp:226) ==935190== by 0x13A9DE: TestExtendedVsBidomainProblem::TestCompareStimulationOfFirstCell() (TestExtendedVsBidomainProblem.hpp:233) ==935190== by 0x147B38: TestDescription_TestExtendedVsBidomainProblem_TestCompareStimulationOfFirstCell::runTest() (TestExtendedVsBidomainProblem.cpp:31) ==935190== by 0x13160A: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==935190== by 0x13571C: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==935190== by 0x135601: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==935190== by 0x1354A7: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==935190== by 0x13530E: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==935190== by 0x1359A5: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==935190== by 0x130340: main (TestExtendedVsBidomainProblem.cpp:19) ==935190== { 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:_ZN29TestExtendedVsBidomainProblem11RunBidomainEv fun:_ZN29TestExtendedVsBidomainProblem33TestCompareStimulationOfFirstCellEv fun:_ZN79TestDescription_TestExtendedVsBidomainProblem_TestCompareStimulationOfFirstCell7runTestEv fun:_ZN7CxxTest19RealTestDescription3runEv fun:_ZN7CxxTest10TestRunner7runTestERNS_15TestDescriptionE fun:_ZN7CxxTest10TestRunner8runSuiteERNS_16SuiteDescriptionE fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==935190== ==935190== FILE DESCRIPTORS: 9 open (3 std) at exit. ==935190== Open file descriptor 12: ==935190== at 0xA32422D: pipe (pipe.c:29) ==935190== by 0x13A9607D: ??? ==935190== by 0xF29D4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==935190== by 0xBA37418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935190== by 0xB9D0D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935190== by 0xA6C7D38: PetscInitialize (pinit.c:924) ==935190== by 0x9C0D58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==935190== by 0x9C0D5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==935190== by 0x1374BE: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==935190== by 0x13200F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==935190== by 0x13546E: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==935190== by 0x13530E: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==935190== by 0x1359A5: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==935190== by 0x130340: main (TestExtendedVsBidomainProblem.cpp:19) ==935190== ==935190== Open file descriptor 8: /dev/shm/open_mpi.0000 ==935190== at 0xA328BCC: __open_nocancel (open64_nocancel.c:39) ==935190== by 0xA2ACC4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==935190== by 0x9C45822: ??? ==935190== by 0x9C4596F: ??? ==935190== by 0xF3426DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==935190== by 0xF342938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==935190== by 0xF2F8922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==935190== by 0xF29D2DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==935190== by 0xBA37418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935190== by 0xB9D0D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935190== by 0xA6C7D38: PetscInitialize (pinit.c:924) ==935190== by 0x9C0D58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==935190== by 0x9C0D5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==935190== by 0x1374BE: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==935190== by 0x13200F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==935190== by 0x13546E: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==935190== by 0x13530E: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==935190== by 0x1359A5: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==935190== by 0x130340: main (TestExtendedVsBidomainProblem.cpp:19) ==935190== ==935190== Open file descriptor 111: ==935190== ==935190== ==935190== Open file descriptor 108: ==935190== ==935190== ==935190== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestExtendedVsBidomainProblem_valgrind.txt ==935190== ==935190== ==935190== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==935190== ==935190== ==935190== ==935190== HEAP SUMMARY: ==935190== in use at exit: 701,234 bytes in 9,387 blocks ==935190== total heap usage: 467,616 allocs, 458,229 frees, 1,460,934,586 bytes allocated ==935190== ==935190== 552 bytes in 1 blocks are definitely lost in loss record 44 of 67 ==935190== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==935190== by 0x14364C13: ??? ==935190== by 0x1436522C: ??? ==935190== by 0x142D84B7: ??? ==935190== by 0xB99D15A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935190== by 0xBA37A97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935190== by 0xB9D0D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935190== by 0xA6C7D38: PetscInitialize (pinit.c:924) ==935190== by 0x9C0D58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==935190== by 0x9C0D5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==935190== by 0x1374BE: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==935190== by 0x13200F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==935190== by 0x13546E: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==935190== by 0x13530E: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==935190== by 0x1359A5: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==935190== by 0x130340: main (TestExtendedVsBidomainProblem.cpp:19) ==935190== { 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 } ==935190== 685,226 (136 direct, 685,090 indirect) bytes in 1 blocks are definitely lost in loss record 67 of 67 ==935190== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==935190== by 0x154D774E: ??? ==935190== by 0x154D7E0B: ??? ==935190== by 0x154DAF56: ??? ==935190== by 0x154D065D: ??? ==935190== by 0x154D0FA3: ??? ==935190== by 0xF3AEF05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==935190== by 0xF38AAE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==935190== by 0xF33BCB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==935190== by 0xF268EF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==935190== by 0x13A96F03: ??? ==935190== by 0xF29D4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==935190== by 0xBA37418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935190== by 0xB9D0D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935190== by 0xA6C7D38: PetscInitialize (pinit.c:924) ==935190== by 0x9C0D58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==935190== by 0x9C0D5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==935190== by 0x1374BE: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==935190== by 0x13200F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==935190== by 0x13546E: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==935190== by 0x13530E: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==935190== by 0x1359A5: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==935190== by 0x130340: main (TestExtendedVsBidomainProblem.cpp:19) ==935190== { 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 } ==935190== LEAK SUMMARY: ==935190== definitely lost: 688 bytes in 2 blocks ==935190== indirectly lost: 1,760 bytes in 16 blocks ==935190== possibly lost: 0 bytes in 0 blocks ==935190== still reachable: 1,531 bytes in 6 blocks ==935190== suppressed: 697,255 bytes in 9,363 blocks ==935190== Reachable blocks (those to which a pointer was found) are not shown. ==935190== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==935190== ==935190== Use --track-origins=yes to see where uninitialised values come from ==935190== For lists of detected and suppressed errors, rerun with: -s ==935190== ERROR SUMMARY: 32 errors from 6 contexts (suppressed: 30 from 30)