==2306614== Memcheck, a memory error detector ==2306614== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==2306614== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==2306614== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/heart/test/TestCardiacSimulationArchiver -malloc_debug -malloc_dump -memory_info ==2306614== Parent PID: 2283975 ==2306614== ==2306614== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==2306614== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==2306614== ==2306614== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==2306614== at 0xB92579E: getsockopt_syscall (getsockopt.c:29) ==2306614== by 0xB92579E: getsockopt (getsockopt.c:94) ==2306614== by 0x1467D157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2306614== by 0x14684A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2306614== by 0x1468BDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2306614== by 0x1458B3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2306614== by 0x14504E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==2306614== by 0x13CC3E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==2306614== by 0xF4C54CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2306614== by 0xBCA6418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2306614== by 0xBC3FD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2306614== by 0x9FCAD38: PetscInitialize (pinit.c:924) ==2306614== by 0x9E3A66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2306614== by 0x9E3A6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2306614== by 0x2144D2: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2306614== by 0x20C095: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2306614== by 0x20FC26: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2306614== by 0x20FAC6: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2306614== by 0x21015D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2306614== by 0x20A1E0: main (TestCardiacSimulationArchiver.cpp:19) ==2306614== Address 0x1ffeffdf9c is on thread 1's stack ==2306614== in frame #2, created by pmix_ptl_base_make_connection (???:) ==2306614== { 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 } ==2306614== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==2306614== at 0xB92579E: getsockopt_syscall (getsockopt.c:29) ==2306614== by 0xB92579E: getsockopt (getsockopt.c:94) ==2306614== by 0x1467D157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2306614== by 0x14684A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2306614== by 0x1468BDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2306614== by 0x1458B3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2306614== by 0x14504E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==2306614== by 0x13CC3E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==2306614== by 0xF4C54CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2306614== by 0xBCA6418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2306614== by 0xBC3FD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2306614== by 0x9FCAD38: PetscInitialize (pinit.c:924) ==2306614== by 0x9E3A66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2306614== by 0x9E3A6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2306614== by 0x2144D2: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2306614== by 0x20C095: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2306614== by 0x20FC26: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2306614== by 0x20FAC6: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2306614== by 0x21015D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2306614== by 0x20A1E0: main (TestCardiacSimulationArchiver.cpp:19) ==2306614== Address 0x1ffeffdf9c is on thread 1's stack ==2306614== in frame #2, created by pmix_ptl_base_make_connection (???:) ==2306614== { 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 } ==2306614== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==2306614== at 0xB925C7E: setsockopt_syscall (setsockopt.c:29) ==2306614== by 0xB925C7E: setsockopt (setsockopt.c:95) ==2306614== by 0x14684BA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2306614== by 0x1468BDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2306614== by 0x1458B3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2306614== by 0x14504E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==2306614== by 0x13CC3E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==2306614== by 0xF4C54CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2306614== by 0xBCA6418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2306614== by 0xBC3FD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2306614== by 0x9FCAD38: PetscInitialize (pinit.c:924) ==2306614== by 0x9E3A66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2306614== by 0x9E3A6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2306614== by 0x2144D2: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2306614== by 0x20C095: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2306614== by 0x20FC26: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2306614== by 0x20FAC6: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2306614== by 0x21015D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2306614== by 0x20A1E0: main (TestCardiacSimulationArchiver.cpp:19) ==2306614== { 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 } ==2306614== Syscall param pwrite64(buf) points to uninitialised byte(s) ==2306614== at 0xB9109EF: __libc_pwrite64 (pwrite64.c:25) ==2306614== by 0xB9109EF: pwrite (pwrite64.c:23) ==2306614== by 0x16EC39D2: mca_fbtl_posix_pwritev (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_fbtl_posix.so) ==2306614== by 0x16ED3419: mca_common_ompio_file_write (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==2306614== by 0x16ED379A: mca_common_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==2306614== by 0x16DBE89A: mca_io_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_io_ompio.so) ==2306614== by 0xBC336A7: PMPI_File_write_at (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2306614== by 0xC44CFEB: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2306614== by 0xC28C4ED: H5FD_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2306614== by 0xC26F313: H5F__accum_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2306614== by 0xC36A442: H5PB_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2306614== by 0xC276DEA: H5F_block_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2306614== by 0xC200E98: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2306614== by 0xC4403F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2306614== by 0xC4419CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2306614== by 0xC44247E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2306614== by 0xC1DD54C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2306614== by 0xC275936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2306614== by 0xC2763FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2306614== by 0xC279BB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2306614== by 0xC279EFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2306614== by 0xC2E951F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2306614== by 0xC2E95EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2306614== by 0xC276831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2306614== by 0xC26B881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2306614== by 0x9D68855: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==2306614== by 0x9D63535: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==2306614== by 0x9D635DB: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==2306614== by 0x6874A3D: AbstractCardiacProblem<1u, 1u, 2u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==2306614== by 0x68745DD: AbstractCardiacProblem<1u, 1u, 2u>::Solve() (AbstractCardiacProblem.cpp:582) ==2306614== by 0x21722A: TestCardiacSimulationArchiver::TestSimpleBidomain1D() (TestCardiacSimulationArchiver.hpp:115) ==2306614== by 0x22E566: TestDescription_TestCardiacSimulationArchiver_TestSimpleBidomain1D::runTest() (TestCardiacSimulationArchiver.cpp:31) ==2306614== by 0x20B690: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==2306614== by 0x20FED4: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==2306614== by 0x20FDB9: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==2306614== by 0x20FC5F: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==2306614== by 0x20FAC6: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2306614== by 0x21015D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2306614== by 0x20A1E0: main (TestCardiacSimulationArchiver.cpp:19) ==2306614== Address 0x173bfa1e is 62 bytes inside a block of size 320 alloc'd ==2306614== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==2306614== by 0xC200E26: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2306614== by 0xC4403F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2306614== by 0xC4419CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2306614== by 0xC44247E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2306614== by 0xC1DD54C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2306614== by 0xC275936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2306614== by 0xC2763FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2306614== by 0xC279BB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2306614== by 0xC279EFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2306614== by 0xC2E951F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2306614== by 0xC2E95EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2306614== by 0xC276831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2306614== by 0xC26B881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2306614== by 0x9D68855: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==2306614== by 0x9D63535: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==2306614== by 0x9D635DB: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==2306614== by 0x6874A3D: AbstractCardiacProblem<1u, 1u, 2u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==2306614== by 0x68745DD: AbstractCardiacProblem<1u, 1u, 2u>::Solve() (AbstractCardiacProblem.cpp:582) ==2306614== by 0x21722A: TestCardiacSimulationArchiver::TestSimpleBidomain1D() (TestCardiacSimulationArchiver.hpp:115) ==2306614== by 0x22E566: TestDescription_TestCardiacSimulationArchiver_TestSimpleBidomain1D::runTest() (TestCardiacSimulationArchiver.cpp:31) ==2306614== by 0x20B690: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==2306614== by 0x20FED4: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==2306614== by 0x20FDB9: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==2306614== by 0x20FC5F: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==2306614== by 0x20FAC6: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2306614== by 0x21015D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2306614== by 0x20A1E0: main (TestCardiacSimulationArchiver.cpp:19) ==2306614== { 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:_ZN29TestCardiacSimulationArchiver20TestSimpleBidomain1DEv fun:_ZN66TestDescription_TestCardiacSimulationArchiver_TestSimpleBidomain1D7runTestEv fun:_ZN7CxxTest19RealTestDescription3runEv fun:_ZN7CxxTest10TestRunner7runTestERNS_15TestDescriptionE fun:_ZN7CxxTest10TestRunner8runSuiteERNS_16SuiteDescriptionE fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==2306614== ==2306614== FILE DESCRIPTORS: 9 open (3 std) at exit. ==2306614== Open file descriptor 12: ==2306614== at 0xB91322D: pipe (pipe.c:29) ==2306614== by 0x13CC407D: ??? ==2306614== by 0xF4C54CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2306614== by 0xBCA6418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2306614== by 0xBC3FD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2306614== by 0x9FCAD38: PetscInitialize (pinit.c:924) ==2306614== by 0x9E3A66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2306614== by 0x9E3A6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2306614== by 0x2144D2: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2306614== by 0x20C095: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2306614== by 0x20FC26: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2306614== by 0x20FAC6: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2306614== by 0x21015D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2306614== by 0x20A1E0: main (TestCardiacSimulationArchiver.cpp:19) ==2306614== ==2306614== Open file descriptor 8: /dev/shm/open_mpi.0000 ==2306614== at 0xB917BCC: __open_nocancel (open64_nocancel.c:39) ==2306614== by 0xB89BC4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==2306614== by 0x9E72822: ??? ==2306614== by 0x9E7296F: ??? ==2306614== by 0xF56C6DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2306614== by 0xF56C938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2306614== by 0xF522922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2306614== by 0xF4C52DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2306614== by 0xBCA6418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2306614== by 0xBC3FD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2306614== by 0x9FCAD38: PetscInitialize (pinit.c:924) ==2306614== by 0x9E3A66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2306614== by 0x9E3A6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2306614== by 0x2144D2: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2306614== by 0x20C095: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2306614== by 0x20FC26: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2306614== by 0x20FAC6: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2306614== by 0x21015D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2306614== by 0x20A1E0: main (TestCardiacSimulationArchiver.cpp:19) ==2306614== ==2306614== Open file descriptor 117: ==2306614== ==2306614== ==2306614== Open file descriptor 110: ==2306614== ==2306614== ==2306614== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestCardiacSimulationArchiver_valgrind.txt ==2306614== ==2306614== ==2306614== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==2306614== ==2306614== ==2306614== ==2306614== HEAP SUMMARY: ==2306614== in use at exit: 701,168 bytes in 9,383 blocks ==2306614== total heap usage: 2,886,897 allocs, 2,877,514 frees, 2,321,670,636 bytes allocated ==2306614== ==2306614== 552 bytes in 1 blocks are definitely lost in loss record 39 of 62 ==2306614== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==2306614== by 0x14592C13: ??? ==2306614== by 0x1459322C: ??? ==2306614== by 0x145064B7: ??? ==2306614== by 0xBC0C15A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2306614== by 0xBCA6A97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2306614== by 0xBC3FD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2306614== by 0x9FCAD38: PetscInitialize (pinit.c:924) ==2306614== by 0x9E3A66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2306614== by 0x9E3A6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2306614== by 0x2144D2: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2306614== by 0x20C095: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2306614== by 0x20FC26: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2306614== by 0x20FAC6: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2306614== by 0x21015D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2306614== by 0x20A1E0: main (TestCardiacSimulationArchiver.cpp:19) ==2306614== { 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 } ==2306614== 685,275 (136 direct, 685,139 indirect) bytes in 1 blocks are definitely lost in loss record 62 of 62 ==2306614== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==2306614== by 0x1570574E: ??? ==2306614== by 0x15705E0B: ??? ==2306614== by 0x15708F56: ??? ==2306614== by 0x156FE65D: ??? ==2306614== by 0x156FEFA3: ??? ==2306614== by 0xF5D8F05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==2306614== by 0xF5B4AE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==2306614== by 0xF565CB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2306614== by 0xF490EF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2306614== by 0x13CC4F03: ??? ==2306614== by 0xF4C54CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2306614== by 0xBCA6418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2306614== by 0xBC3FD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2306614== by 0x9FCAD38: PetscInitialize (pinit.c:924) ==2306614== by 0x9E3A66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2306614== by 0x9E3A6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2306614== by 0x2144D2: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2306614== by 0x20C095: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2306614== by 0x20FC26: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2306614== by 0x20FAC6: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2306614== by 0x21015D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2306614== by 0x20A1E0: main (TestCardiacSimulationArchiver.cpp:19) ==2306614== { 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 } ==2306614== LEAK SUMMARY: ==2306614== definitely lost: 688 bytes in 2 blocks ==2306614== indirectly lost: 1,760 bytes in 16 blocks ==2306614== possibly lost: 0 bytes in 0 blocks ==2306614== still reachable: 1,531 bytes in 6 blocks ==2306614== suppressed: 697,189 bytes in 9,359 blocks ==2306614== Reachable blocks (those to which a pointer was found) are not shown. ==2306614== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==2306614== ==2306614== Use --track-origins=yes to see where uninitialised values come from ==2306614== For lists of detected and suppressed errors, rerun with: -s ==2306614== ERROR SUMMARY: 110 errors from 6 contexts (suppressed: 25 from 25)