==729573== Memcheck, a memory error detector ==729573== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==729573== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==729573== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/heart/test/TestBidomainWithBathProblem -malloc_debug -malloc_dump -memory_info ==729573== Parent PID: 708652 ==729573== ==729573== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==729573== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==729573== ==729573== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==729573== at 0xA9E879E: getsockopt_syscall (getsockopt.c:29) ==729573== by 0xA9E879E: getsockopt (getsockopt.c:94) ==729573== by 0x14AA2157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==729573== by 0x14AA9A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==729573== by 0x14AB0DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==729573== by 0x149B03C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==729573== by 0x14929E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==729573== by 0x140E8E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==729573== by 0xF8EA4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==729573== by 0xC0E9418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==729573== by 0xC082D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==729573== by 0xAD79D38: PetscInitialize (pinit.c:924) ==729573== by 0xA1D858B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==729573== by 0xA1D85D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==729573== by 0x14C926: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==729573== by 0x144CB1: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==729573== by 0x1483C4: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==729573== by 0x148264: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==729573== by 0x1488FB: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==729573== by 0x142E40: main (TestBidomainWithBathProblem.cpp:19) ==729573== Address 0x1ffeffdf9c is on thread 1's stack ==729573== in frame #2, created by pmix_ptl_base_make_connection (???:) ==729573== { 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 } ==729573== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==729573== at 0xA9E879E: getsockopt_syscall (getsockopt.c:29) ==729573== by 0xA9E879E: getsockopt (getsockopt.c:94) ==729573== by 0x14AA2157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==729573== by 0x14AA9A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==729573== by 0x14AB0DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==729573== by 0x149B03C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==729573== by 0x14929E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==729573== by 0x140E8E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==729573== by 0xF8EA4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==729573== by 0xC0E9418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==729573== by 0xC082D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==729573== by 0xAD79D38: PetscInitialize (pinit.c:924) ==729573== by 0xA1D858B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==729573== by 0xA1D85D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==729573== by 0x14C926: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==729573== by 0x144CB1: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==729573== by 0x1483C4: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==729573== by 0x148264: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==729573== by 0x1488FB: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==729573== by 0x142E40: main (TestBidomainWithBathProblem.cpp:19) ==729573== Address 0x1ffeffdf9c is on thread 1's stack ==729573== in frame #2, created by pmix_ptl_base_make_connection (???:) ==729573== { 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 } ==729573== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==729573== at 0xA9E8C7E: setsockopt_syscall (setsockopt.c:29) ==729573== by 0xA9E8C7E: setsockopt (setsockopt.c:95) ==729573== by 0x14AA9BA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==729573== by 0x14AB0DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==729573== by 0x149B03C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==729573== by 0x14929E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==729573== by 0x140E8E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==729573== by 0xF8EA4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==729573== by 0xC0E9418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==729573== by 0xC082D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==729573== by 0xAD79D38: PetscInitialize (pinit.c:924) ==729573== by 0xA1D858B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==729573== by 0xA1D85D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==729573== by 0x14C926: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==729573== by 0x144CB1: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==729573== by 0x1483C4: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==729573== by 0x148264: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==729573== by 0x1488FB: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==729573== by 0x142E40: main (TestBidomainWithBathProblem.cpp:19) ==729573== { 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 } ==729573== Syscall param pwrite64(buf) points to uninitialised byte(s) ==729573== at 0xA9D39EF: __libc_pwrite64 (pwrite64.c:25) ==729573== by 0xA9D39EF: pwrite (pwrite64.c:23) ==729573== by 0x1831F9D2: mca_fbtl_posix_pwritev (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_fbtl_posix.so) ==729573== by 0x1832F419: mca_common_ompio_file_write (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==729573== by 0x1832F79A: mca_common_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==729573== by 0x1821A89A: mca_io_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_io_ompio.so) ==729573== by 0xC0766A7: PMPI_File_write_at (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==729573== by 0xC871FEB: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==729573== by 0xC6B14ED: H5FD_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==729573== by 0xC694313: H5F__accum_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==729573== by 0xC78F442: H5PB_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==729573== by 0xC69BDEA: H5F_block_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==729573== by 0xC625E98: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==729573== by 0xC8653F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==729573== by 0xC8669CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==729573== by 0xC86747E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==729573== by 0xC60254C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==729573== by 0xC69A936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==729573== by 0xC69B3FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==729573== by 0xC69EBB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==729573== by 0xC69EEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==729573== by 0xC70E51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==729573== by 0xC70E5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==729573== by 0xC69B831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==729573== by 0xC690881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==729573== by 0xC545967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==729573== by 0xC540647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==729573== by 0xC5406ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==729573== by 0x6874A03: AbstractCardiacProblem<1u, 1u, 2u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==729573== by 0x68745A3: AbstractCardiacProblem<1u, 1u, 2u>::Solve() (AbstractCardiacProblem.cpp:582) ==729573== by 0x14E320: TestBidomainWithBathProblem::TestLabellingNodes() (TestBidomainWithBathProblem.hpp:105) ==729573== by 0x15D268: TestDescription_TestBidomainWithBathProblem_TestLabellingNodes::runTest() (TestBidomainWithBathProblem.cpp:31) ==729573== by 0x1442AC: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==729573== by 0x148672: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==729573== by 0x148557: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==729573== by 0x1483FD: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==729573== by 0x148264: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==729573== by 0x1488FB: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==729573== by 0x142E40: main (TestBidomainWithBathProblem.cpp:19) ==729573== Address 0x16d35c3e is 62 bytes inside a block of size 320 alloc'd ==729573== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==729573== by 0xC625E26: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==729573== by 0xC8653F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==729573== by 0xC8669CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==729573== by 0xC86747E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==729573== by 0xC60254C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==729573== by 0xC69A936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==729573== by 0xC69B3FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==729573== by 0xC69EBB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==729573== by 0xC69EEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==729573== by 0xC70E51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==729573== by 0xC70E5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==729573== by 0xC69B831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==729573== by 0xC690881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==729573== by 0xC545967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==729573== by 0xC540647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==729573== by 0xC5406ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==729573== by 0x6874A03: AbstractCardiacProblem<1u, 1u, 2u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==729573== by 0x68745A3: AbstractCardiacProblem<1u, 1u, 2u>::Solve() (AbstractCardiacProblem.cpp:582) ==729573== by 0x14E320: TestBidomainWithBathProblem::TestLabellingNodes() (TestBidomainWithBathProblem.hpp:105) ==729573== by 0x15D268: TestDescription_TestBidomainWithBathProblem_TestLabellingNodes::runTest() (TestBidomainWithBathProblem.cpp:31) ==729573== by 0x1442AC: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==729573== by 0x148672: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==729573== by 0x148557: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==729573== by 0x1483FD: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==729573== by 0x148264: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==729573== by 0x1488FB: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==729573== by 0x142E40: main (TestBidomainWithBathProblem.cpp:19) ==729573== { 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:_ZN27TestBidomainWithBathProblem18TestLabellingNodesEv fun:_ZN62TestDescription_TestBidomainWithBathProblem_TestLabellingNodes7runTestEv fun:_ZN7CxxTest19RealTestDescription3runEv fun:_ZN7CxxTest10TestRunner7runTestERNS_15TestDescriptionE fun:_ZN7CxxTest10TestRunner8runSuiteERNS_16SuiteDescriptionE fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==729573== ==729573== FILE DESCRIPTORS: 9 open (3 std) at exit. ==729573== Open file descriptor 12: ==729573== at 0xA9D622D: pipe (pipe.c:29) ==729573== by 0x140E907D: ??? ==729573== by 0xF8EA4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==729573== by 0xC0E9418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==729573== by 0xC082D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==729573== by 0xAD79D38: PetscInitialize (pinit.c:924) ==729573== by 0xA1D858B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==729573== by 0xA1D85D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==729573== by 0x14C926: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==729573== by 0x144CB1: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==729573== by 0x1483C4: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==729573== by 0x148264: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==729573== by 0x1488FB: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==729573== by 0x142E40: main (TestBidomainWithBathProblem.cpp:19) ==729573== ==729573== Open file descriptor 8: /dev/shm/open_mpi.0000 ==729573== at 0xA9DABCC: __open_nocancel (open64_nocancel.c:39) ==729573== by 0xA95EC4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==729573== by 0xA210822: ??? ==729573== by 0xA21096F: ??? ==729573== by 0xF98F6DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==729573== by 0xF98F938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==729573== by 0xF945922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==729573== by 0xF8EA2DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==729573== by 0xC0E9418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==729573== by 0xC082D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==729573== by 0xAD79D38: PetscInitialize (pinit.c:924) ==729573== by 0xA1D858B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==729573== by 0xA1D85D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==729573== by 0x14C926: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==729573== by 0x144CB1: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==729573== by 0x1483C4: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==729573== by 0x148264: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==729573== by 0x1488FB: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==729573== by 0x142E40: main (TestBidomainWithBathProblem.cpp:19) ==729573== ==729573== Open file descriptor 116: ==729573== ==729573== ==729573== Open file descriptor 111: ==729573== ==729573== ==729573== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestBidomainWithBathProblem_valgrind.txt ==729573== ==729573== ==729573== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==729573== ==729573== ==729573== ==729573== HEAP SUMMARY: ==729573== in use at exit: 701,166 bytes in 9,383 blocks ==729573== total heap usage: 1,395,644 allocs, 1,386,261 frees, 2,002,602,877 bytes allocated ==729573== ==729573== 552 bytes in 1 blocks are definitely lost in loss record 39 of 65 ==729573== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==729573== by 0x149B7C13: ??? ==729573== by 0x149B822C: ??? ==729573== by 0x1492B4B7: ??? ==729573== by 0xC04F15A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==729573== by 0xC0E9A97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==729573== by 0xC082D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==729573== by 0xAD79D38: PetscInitialize (pinit.c:924) ==729573== by 0xA1D858B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==729573== by 0xA1D85D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==729573== by 0x14C926: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==729573== by 0x144CB1: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==729573== by 0x1483C4: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==729573== by 0x148264: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==729573== by 0x1488FB: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==729573== by 0x142E40: main (TestBidomainWithBathProblem.cpp:19) ==729573== { 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 } ==729573== 84,459 (136 direct, 84,323 indirect) bytes in 1 blocks are definitely lost in loss record 62 of 65 ==729573== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==729573== by 0x15B2A74E: ??? ==729573== by 0x15B2AE0B: ??? ==729573== by 0x15B2DF56: ??? ==729573== by 0x15B2365D: ??? ==729573== by 0x15B23FA3: ??? ==729573== by 0xF9FDF05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==729573== by 0xF9D9AE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==729573== by 0xF988CB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==729573== by 0xF8B5EF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==729573== by 0x140E9F03: ??? ==729573== by 0xF8EA4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==729573== by 0xC0E9418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==729573== by 0xC082D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==729573== by 0xAD79D38: PetscInitialize (pinit.c:924) ==729573== by 0xA1D858B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==729573== by 0xA1D85D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==729573== by 0x14C926: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==729573== by 0x144CB1: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==729573== by 0x1483C4: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==729573== by 0x148264: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==729573== by 0x1488FB: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==729573== by 0x142E40: main (TestBidomainWithBathProblem.cpp:19) ==729573== { 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 } ==729573== LEAK SUMMARY: ==729573== definitely lost: 688 bytes in 2 blocks ==729573== indirectly lost: 1,760 bytes in 16 blocks ==729573== possibly lost: 0 bytes in 0 blocks ==729573== still reachable: 1,531 bytes in 6 blocks ==729573== suppressed: 697,187 bytes in 9,359 blocks ==729573== Reachable blocks (those to which a pointer was found) are not shown. ==729573== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==729573== ==729573== Use --track-origins=yes to see where uninitialised values come from ==729573== For lists of detected and suppressed errors, rerun with: -s ==729573== ERROR SUMMARY: 41 errors from 6 contexts (suppressed: 28 from 28)