==4100575== Memcheck, a memory error detector ==4100575== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==4100575== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==4100575== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/heart/test/TestBidomainProblem -malloc_debug -malloc_dump -memory_info ==4100575== Parent PID: 4079680 ==4100575== ==4100575== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==4100575== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==4100575== ==4100575== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==4100575== at 0xBE8379E: getsockopt_syscall (getsockopt.c:29) ==4100575== by 0xBE8379E: getsockopt (getsockopt.c:94) ==4100575== by 0x14AA5157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==4100575== by 0x14AACA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==4100575== by 0x14AB3DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==4100575== by 0x149B33C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==4100575== by 0x1492CE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==4100575== by 0x140EBE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==4100575== by 0xF8A24CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==4100575== by 0xB761418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==4100575== by 0xB6FAD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==4100575== by 0xA3F1D38: PetscInitialize (pinit.c:924) ==4100575== by 0xA26158B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==4100575== by 0xA2615D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==4100575== by 0x14AE64: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==4100575== by 0x1430E1: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==4100575== by 0x146866: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==4100575== by 0x146706: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==4100575== by 0x146D9D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==4100575== by 0x141270: main (TestBidomainProblem.cpp:19) ==4100575== Address 0x1ffeffdfac is on thread 1's stack ==4100575== in frame #2, created by pmix_ptl_base_make_connection (???:) ==4100575== { 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 } ==4100575== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==4100575== at 0xBE8379E: getsockopt_syscall (getsockopt.c:29) ==4100575== by 0xBE8379E: getsockopt (getsockopt.c:94) ==4100575== by 0x14AA5157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==4100575== by 0x14AACA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==4100575== by 0x14AB3DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==4100575== by 0x149B33C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==4100575== by 0x1492CE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==4100575== by 0x140EBE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==4100575== by 0xF8A24CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==4100575== by 0xB761418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==4100575== by 0xB6FAD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==4100575== by 0xA3F1D38: PetscInitialize (pinit.c:924) ==4100575== by 0xA26158B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==4100575== by 0xA2615D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==4100575== by 0x14AE64: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==4100575== by 0x1430E1: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==4100575== by 0x146866: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==4100575== by 0x146706: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==4100575== by 0x146D9D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==4100575== by 0x141270: main (TestBidomainProblem.cpp:19) ==4100575== Address 0x1ffeffdfac is on thread 1's stack ==4100575== in frame #2, created by pmix_ptl_base_make_connection (???:) ==4100575== { 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 } ==4100575== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==4100575== at 0xBE83C7E: setsockopt_syscall (setsockopt.c:29) ==4100575== by 0xBE83C7E: setsockopt (setsockopt.c:95) ==4100575== by 0x14AACBA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==4100575== by 0x14AB3DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==4100575== by 0x149B33C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==4100575== by 0x1492CE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==4100575== by 0x140EBE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==4100575== by 0xF8A24CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==4100575== by 0xB761418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==4100575== by 0xB6FAD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==4100575== by 0xA3F1D38: PetscInitialize (pinit.c:924) ==4100575== by 0xA26158B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==4100575== by 0xA2615D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==4100575== by 0x14AE64: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==4100575== by 0x1430E1: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==4100575== by 0x146866: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==4100575== by 0x146706: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==4100575== by 0x146D9D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==4100575== by 0x141270: main (TestBidomainProblem.cpp:19) ==4100575== { 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 } ==4100575== Syscall param pwrite64(buf) points to uninitialised byte(s) ==4100575== at 0xBE6E9EF: __libc_pwrite64 (pwrite64.c:25) ==4100575== by 0xBE6E9EF: pwrite (pwrite64.c:23) ==4100575== by 0x183229D2: mca_fbtl_posix_pwritev (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_fbtl_posix.so) ==4100575== by 0x18332419: mca_common_ompio_file_write (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==4100575== by 0x1833279A: mca_common_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==4100575== by 0x1821D89A: mca_io_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_io_ompio.so) ==4100575== by 0xB6EE6A7: PMPI_File_write_at (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==4100575== by 0xC873FEB: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==4100575== by 0xC6B34ED: H5FD_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==4100575== by 0xC696313: H5F__accum_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==4100575== by 0xC791442: H5PB_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==4100575== by 0xC69DDEA: H5F_block_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==4100575== by 0xC627E98: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==4100575== by 0xC8673F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==4100575== by 0xC8689CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==4100575== by 0xC86947E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==4100575== by 0xC60454C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==4100575== by 0xC69C936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==4100575== by 0xC69D3FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==4100575== by 0xC6A0BB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==4100575== by 0xC6A0EFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==4100575== by 0xC71051F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==4100575== by 0xC7105EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==4100575== by 0xC69D831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==4100575== by 0xC692881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==4100575== by 0xA190967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==4100575== by 0xA18B647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==4100575== by 0xA18B6ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==4100575== by 0x6874A03: AbstractCardiacProblem<1u, 1u, 2u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==4100575== by 0x687488F: AbstractCardiacProblem<1u, 1u, 2u>::Solve() (AbstractCardiacProblem.cpp:527) ==4100575== by 0x14E102: TestBidomainProblem::TestBidomainErrorHandling() (TestBidomainProblem.hpp:209) ==4100575== by 0x169134: TestDescription_TestBidomainProblem_TestBidomainErrorHandling::runTest() (TestBidomainProblem.cpp:31) ==4100575== by 0x1426DC: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==4100575== by 0x146B14: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==4100575== by 0x1469F9: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==4100575== by 0x14689F: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==4100575== by 0x146706: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==4100575== by 0x146D9D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==4100575== by 0x141270: main (TestBidomainProblem.cpp:19) ==4100575== Address 0x16d38e6e is 62 bytes inside a block of size 320 alloc'd ==4100575== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==4100575== by 0xC627E26: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==4100575== by 0xC8673F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==4100575== by 0xC8689CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==4100575== by 0xC86947E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==4100575== by 0xC60454C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==4100575== by 0xC69C936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==4100575== by 0xC69D3FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==4100575== by 0xC6A0BB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==4100575== by 0xC6A0EFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==4100575== by 0xC71051F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==4100575== by 0xC7105EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==4100575== by 0xC69D831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==4100575== by 0xC692881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==4100575== by 0xA190967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==4100575== by 0xA18B647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==4100575== by 0xA18B6ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==4100575== by 0x6874A03: AbstractCardiacProblem<1u, 1u, 2u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==4100575== by 0x687488F: AbstractCardiacProblem<1u, 1u, 2u>::Solve() (AbstractCardiacProblem.cpp:527) ==4100575== by 0x14E102: TestBidomainProblem::TestBidomainErrorHandling() (TestBidomainProblem.hpp:209) ==4100575== by 0x169134: TestDescription_TestBidomainProblem_TestBidomainErrorHandling::runTest() (TestBidomainProblem.cpp:31) ==4100575== by 0x1426DC: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==4100575== by 0x146B14: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==4100575== by 0x1469F9: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==4100575== by 0x14689F: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==4100575== by 0x146706: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==4100575== by 0x146D9D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==4100575== by 0x141270: main (TestBidomainProblem.cpp:19) ==4100575== { 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:_ZN19TestBidomainProblem25TestBidomainErrorHandlingEv fun:_ZN61TestDescription_TestBidomainProblem_TestBidomainErrorHandling7runTestEv fun:_ZN7CxxTest19RealTestDescription3runEv fun:_ZN7CxxTest10TestRunner7runTestERNS_15TestDescriptionE fun:_ZN7CxxTest10TestRunner8runSuiteERNS_16SuiteDescriptionE fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==4100575== ==4100575== FILE DESCRIPTORS: 9 open (3 std) at exit. ==4100575== Open file descriptor 12: ==4100575== at 0xBE7122D: pipe (pipe.c:29) ==4100575== by 0x140EC07D: ??? ==4100575== by 0xF8A24CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==4100575== by 0xB761418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==4100575== by 0xB6FAD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==4100575== by 0xA3F1D38: PetscInitialize (pinit.c:924) ==4100575== by 0xA26158B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==4100575== by 0xA2615D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==4100575== by 0x14AE64: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==4100575== by 0x1430E1: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==4100575== by 0x146866: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==4100575== by 0x146706: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==4100575== by 0x146D9D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==4100575== by 0x141270: main (TestBidomainProblem.cpp:19) ==4100575== ==4100575== Open file descriptor 8: /dev/shm/open_mpi.0000 ==4100575== at 0xBE75BCC: __open_nocancel (open64_nocancel.c:39) ==4100575== by 0xBDF9C4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==4100575== by 0xA299822: ??? ==4100575== by 0xA29996F: ??? ==4100575== by 0xF9476DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==4100575== by 0xF947938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==4100575== by 0xF8FD922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==4100575== by 0xF8A22DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==4100575== by 0xB761418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==4100575== by 0xB6FAD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==4100575== by 0xA3F1D38: PetscInitialize (pinit.c:924) ==4100575== by 0xA26158B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==4100575== by 0xA2615D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==4100575== by 0x14AE64: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==4100575== by 0x1430E1: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==4100575== by 0x146866: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==4100575== by 0x146706: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==4100575== by 0x146D9D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==4100575== by 0x141270: main (TestBidomainProblem.cpp:19) ==4100575== ==4100575== Open file descriptor 115: ==4100575== ==4100575== ==4100575== Open file descriptor 110: ==4100575== ==4100575== ==4100575== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestBidomainProblem_valgrind.txt ==4100575== ==4100575== ==4100575== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==4100575== ==4100575== ==4100575== ==4100575== HEAP SUMMARY: ==4100575== in use at exit: 701,239 bytes in 9,387 blocks ==4100575== total heap usage: 585,844 allocs, 576,457 frees, 1,563,767,608 bytes allocated ==4100575== ==4100575== 552 bytes in 1 blocks are definitely lost in loss record 44 of 67 ==4100575== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==4100575== by 0x149BAC13: ??? ==4100575== by 0x149BB22C: ??? ==4100575== by 0x1492E4B7: ??? ==4100575== by 0xB6C715A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==4100575== by 0xB761A97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==4100575== by 0xB6FAD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==4100575== by 0xA3F1D38: PetscInitialize (pinit.c:924) ==4100575== by 0xA26158B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==4100575== by 0xA2615D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==4100575== by 0x14AE64: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==4100575== by 0x1430E1: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==4100575== by 0x146866: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==4100575== by 0x146706: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==4100575== by 0x146D9D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==4100575== by 0x141270: main (TestBidomainProblem.cpp:19) ==4100575== { 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 } ==4100575== 685,173 (136 direct, 685,037 indirect) bytes in 1 blocks are definitely lost in loss record 67 of 67 ==4100575== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==4100575== by 0x15B2D74E: ??? ==4100575== by 0x15B2DE0B: ??? ==4100575== by 0x15B30F56: ??? ==4100575== by 0x15B2665D: ??? ==4100575== by 0x15B26FA3: ??? ==4100575== by 0xF9B3F05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==4100575== by 0xF98FAE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==4100575== by 0xF940CB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==4100575== by 0xF86DEF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==4100575== by 0x140ECF03: ??? ==4100575== by 0xF8A24CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==4100575== by 0xB761418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==4100575== by 0xB6FAD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==4100575== by 0xA3F1D38: PetscInitialize (pinit.c:924) ==4100575== by 0xA26158B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==4100575== by 0xA2615D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==4100575== by 0x14AE64: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==4100575== by 0x1430E1: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==4100575== by 0x146866: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==4100575== by 0x146706: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==4100575== by 0x146D9D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==4100575== by 0x141270: main (TestBidomainProblem.cpp:19) ==4100575== { 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 } ==4100575== LEAK SUMMARY: ==4100575== definitely lost: 688 bytes in 2 blocks ==4100575== indirectly lost: 1,760 bytes in 16 blocks ==4100575== possibly lost: 0 bytes in 0 blocks ==4100575== still reachable: 1,531 bytes in 6 blocks ==4100575== suppressed: 697,260 bytes in 9,363 blocks ==4100575== Reachable blocks (those to which a pointer was found) are not shown. ==4100575== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==4100575== ==4100575== Use --track-origins=yes to see where uninitialised values come from ==4100575== For lists of detected and suppressed errors, rerun with: -s ==4100575== ERROR SUMMARY: 71 errors from 6 contexts (suppressed: 30 from 30)