==28844== Memcheck, a memory error detector ==28844== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==28844== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==28844== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/heart/test/TestExtendedBidomainProblem -malloc_debug -malloc_dump -memory_info ==28844== Parent PID: 7893 ==28844== ==28844== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==28844== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==28844== ==28844== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==28844== at 0xA71179E: getsockopt_syscall (getsockopt.c:29) ==28844== by 0xA71179E: getsockopt (getsockopt.c:94) ==28844== by 0x14AA5157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==28844== by 0x14AACA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==28844== by 0x14AB3DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==28844== by 0x149B33C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==28844== by 0x1492CE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==28844== by 0x140EBE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==28844== by 0xD6D34CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==28844== by 0x9FEF418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==28844== by 0x9F88D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==28844== by 0xAAA2D38: PetscInitialize (pinit.c:924) ==28844== by 0x9EB158B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==28844== by 0x9EB15D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==28844== by 0x12DB00: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==28844== by 0x128A3D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==28844== by 0x12B846: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==28844== by 0x12B741: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==28844== by 0x12BD55: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==28844== by 0x127240: main (TestExtendedBidomainProblem.cpp:18) ==28844== Address 0x1ffeffdfac is on thread 1's stack ==28844== in frame #2, created by pmix_ptl_base_make_connection (???:) ==28844== { 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 } ==28844== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==28844== at 0xA71179E: getsockopt_syscall (getsockopt.c:29) ==28844== by 0xA71179E: getsockopt (getsockopt.c:94) ==28844== by 0x14AA5157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==28844== by 0x14AACA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==28844== by 0x14AB3DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==28844== by 0x149B33C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==28844== by 0x1492CE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==28844== by 0x140EBE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==28844== by 0xD6D34CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==28844== by 0x9FEF418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==28844== by 0x9F88D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==28844== by 0xAAA2D38: PetscInitialize (pinit.c:924) ==28844== by 0x9EB158B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==28844== by 0x9EB15D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==28844== by 0x12DB00: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==28844== by 0x128A3D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==28844== by 0x12B846: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==28844== by 0x12B741: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==28844== by 0x12BD55: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==28844== by 0x127240: main (TestExtendedBidomainProblem.cpp:18) ==28844== Address 0x1ffeffdfac is on thread 1's stack ==28844== in frame #2, created by pmix_ptl_base_make_connection (???:) ==28844== { 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 } ==28844== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==28844== at 0xA711C7E: setsockopt_syscall (setsockopt.c:29) ==28844== by 0xA711C7E: setsockopt (setsockopt.c:95) ==28844== by 0x14AACBA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==28844== by 0x14AB3DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==28844== by 0x149B33C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==28844== by 0x1492CE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==28844== by 0x140EBE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==28844== by 0xD6D34CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==28844== by 0x9FEF418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==28844== by 0x9F88D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==28844== by 0xAAA2D38: PetscInitialize (pinit.c:924) ==28844== by 0x9EB158B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==28844== by 0x9EB15D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==28844== by 0x12DB00: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==28844== by 0x128A3D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==28844== by 0x12B846: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==28844== by 0x12B741: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==28844== by 0x12BD55: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==28844== by 0x127240: main (TestExtendedBidomainProblem.cpp:18) ==28844== { 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 } ==28844== Syscall param pwrite64(buf) points to uninitialised byte(s) ==28844== at 0xA6FC9EF: __libc_pwrite64 (pwrite64.c:25) ==28844== by 0xA6FC9EF: pwrite (pwrite64.c:23) ==28844== by 0x183229D2: mca_fbtl_posix_pwritev (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_fbtl_posix.so) ==28844== by 0x18332419: mca_common_ompio_file_write (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==28844== by 0x1833279A: mca_common_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==28844== by 0x1821D89A: mca_io_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_io_ompio.so) ==28844== by 0x9F7C6A7: PMPI_File_write_at (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==28844== by 0xD552FEB: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28844== by 0xD3924ED: H5FD_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28844== by 0xD375313: H5F__accum_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28844== by 0xD470442: H5PB_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28844== by 0xD37CDEA: H5F_block_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28844== by 0xD306E98: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28844== by 0xD5463F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28844== by 0xD5479CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28844== by 0xD54847E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28844== by 0xD2E354C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28844== by 0xD37B936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28844== by 0xD37C3FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28844== by 0xD37FBB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28844== by 0xD37FEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28844== by 0xD3EF51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28844== by 0xD3EF5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28844== by 0xD37C831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28844== by 0xD371881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28844== by 0x9DE0967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==28844== by 0x9DDB647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==28844== by 0x9DDB6ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==28844== by 0x6885B17: AbstractCardiacProblem<1u, 1u, 3u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==28844== by 0x68856B7: AbstractCardiacProblem<1u, 1u, 3u>::Solve() (AbstractCardiacProblem.cpp:582) ==28844== by 0x12FC1C: TestExtendedBidomainProblem::TestExtendedProblemVsMartincCode() (TestExtendedBidomainProblem.hpp:168) ==28844== by 0x1313BC: TestDescription_TestExtendedBidomainProblem_TestExtendedProblemVsMartincCode::runTest() (TestExtendedBidomainProblem.cpp:30) ==28844== by 0x128274: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==28844== by 0x12BAF4: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==28844== by 0x12B9D9: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==28844== by 0x12B87F: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==28844== by 0x12B741: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==28844== by 0x12BD55: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==28844== by 0x127240: main (TestExtendedBidomainProblem.cpp:18) ==28844== Address 0x1748274e is 62 bytes inside a block of size 320 alloc'd ==28844== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==28844== by 0xD306E26: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28844== by 0xD5463F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28844== by 0xD5479CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28844== by 0xD54847E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28844== by 0xD2E354C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28844== by 0xD37B936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28844== by 0xD37C3FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28844== by 0xD37FBB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28844== by 0xD37FEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28844== by 0xD3EF51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28844== by 0xD3EF5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28844== by 0xD37C831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28844== by 0xD371881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==28844== by 0x9DE0967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==28844== by 0x9DDB647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==28844== by 0x9DDB6ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==28844== by 0x6885B17: AbstractCardiacProblem<1u, 1u, 3u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==28844== by 0x68856B7: AbstractCardiacProblem<1u, 1u, 3u>::Solve() (AbstractCardiacProblem.cpp:582) ==28844== by 0x12FC1C: TestExtendedBidomainProblem::TestExtendedProblemVsMartincCode() (TestExtendedBidomainProblem.hpp:168) ==28844== by 0x1313BC: TestDescription_TestExtendedBidomainProblem_TestExtendedProblemVsMartincCode::runTest() (TestExtendedBidomainProblem.cpp:30) ==28844== by 0x128274: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==28844== by 0x12BAF4: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==28844== by 0x12B9D9: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==28844== by 0x12B87F: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==28844== by 0x12B741: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==28844== by 0x12BD55: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==28844== by 0x127240: main (TestExtendedBidomainProblem.cpp:18) ==28844== { 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:_ZN22AbstractCardiacProblemILj1ELj1ELj3EE24CloseFilesAndPostProcessEv fun:_ZN22AbstractCardiacProblemILj1ELj1ELj3EE5SolveEv fun:_ZN27TestExtendedBidomainProblem32TestExtendedProblemVsMartincCodeEv fun:_ZN76TestDescription_TestExtendedBidomainProblem_TestExtendedProblemVsMartincCode7runTestEv fun:_ZN7CxxTest19RealTestDescription3runEv fun:_ZN7CxxTest10TestRunner7runTestERNS_15TestDescriptionE fun:_ZN7CxxTest10TestRunner8runSuiteERNS_16SuiteDescriptionE fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==28844== ==28844== FILE DESCRIPTORS: 9 open (3 std) at exit. ==28844== Open file descriptor 12: ==28844== at 0xA6FF22D: pipe (pipe.c:29) ==28844== by 0x140EC07D: ??? ==28844== by 0xD6D34CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==28844== by 0x9FEF418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==28844== by 0x9F88D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==28844== by 0xAAA2D38: PetscInitialize (pinit.c:924) ==28844== by 0x9EB158B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==28844== by 0x9EB15D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==28844== by 0x12DB00: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==28844== by 0x128A3D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==28844== by 0x12B846: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==28844== by 0x12B741: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==28844== by 0x12BD55: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==28844== by 0x127240: main (TestExtendedBidomainProblem.cpp:18) ==28844== ==28844== Open file descriptor 8: /dev/shm/open_mpi.0000 ==28844== at 0xA703BCC: __open_nocancel (open64_nocancel.c:39) ==28844== by 0xA687C4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==28844== by 0x9EE9822: ??? ==28844== by 0x9EE996F: ??? ==28844== by 0xD77A6DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==28844== by 0xD77A938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==28844== by 0xD730922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==28844== by 0xD6D32DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==28844== by 0x9FEF418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==28844== by 0x9F88D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==28844== by 0xAAA2D38: PetscInitialize (pinit.c:924) ==28844== by 0x9EB158B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==28844== by 0x9EB15D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==28844== by 0x12DB00: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==28844== by 0x128A3D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==28844== by 0x12B846: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==28844== by 0x12B741: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==28844== by 0x12BD55: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==28844== by 0x127240: main (TestExtendedBidomainProblem.cpp:18) ==28844== ==28844== Open file descriptor 115: ==28844== ==28844== ==28844== Open file descriptor 110: ==28844== ==28844== ==28844== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestExtendedBidomainProblem_valgrind.txt ==28844== ==28844== ==28844== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==28844== ==28844== ==28844== ==28844== HEAP SUMMARY: ==28844== in use at exit: 701,164 bytes in 9,383 blocks ==28844== total heap usage: 2,374,898 allocs, 2,365,515 frees, 2,483,277,180 bytes allocated ==28844== ==28844== 552 bytes in 1 blocks are definitely lost in loss record 40 of 63 ==28844== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==28844== by 0x149BAC13: ??? ==28844== by 0x149BB22C: ??? ==28844== by 0x1492E4B7: ??? ==28844== by 0x9F5515A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==28844== by 0x9FEFA97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==28844== by 0x9F88D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==28844== by 0xAAA2D38: PetscInitialize (pinit.c:924) ==28844== by 0x9EB158B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==28844== by 0x9EB15D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==28844== by 0x12DB00: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==28844== by 0x128A3D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==28844== by 0x12B846: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==28844== by 0x12B741: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==28844== by 0x12BD55: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==28844== by 0x127240: main (TestExtendedBidomainProblem.cpp:18) ==28844== { 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 } ==28844== 685,233 (136 direct, 685,097 indirect) bytes in 1 blocks are definitely lost in loss record 63 of 63 ==28844== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==28844== by 0x15B2D74E: ??? ==28844== by 0x15B2DE0B: ??? ==28844== by 0x15B30F56: ??? ==28844== by 0x15B2665D: ??? ==28844== by 0x15B26FA3: ??? ==28844== by 0xD7E6F05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==28844== by 0xD7C2AE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==28844== by 0xD773CB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==28844== by 0xD69EEF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==28844== by 0x140ECF03: ??? ==28844== by 0xD6D34CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==28844== by 0x9FEF418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==28844== by 0x9F88D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==28844== by 0xAAA2D38: PetscInitialize (pinit.c:924) ==28844== by 0x9EB158B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==28844== by 0x9EB15D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==28844== by 0x12DB00: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==28844== by 0x128A3D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==28844== by 0x12B846: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==28844== by 0x12B741: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==28844== by 0x12BD55: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==28844== by 0x127240: main (TestExtendedBidomainProblem.cpp:18) ==28844== { 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 } ==28844== LEAK SUMMARY: ==28844== definitely lost: 688 bytes in 2 blocks ==28844== indirectly lost: 1,760 bytes in 16 blocks ==28844== possibly lost: 0 bytes in 0 blocks ==28844== still reachable: 1,531 bytes in 6 blocks ==28844== suppressed: 697,185 bytes in 9,359 blocks ==28844== Reachable blocks (those to which a pointer was found) are not shown. ==28844== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==28844== ==28844== Use --track-origins=yes to see where uninitialised values come from ==28844== For lists of detected and suppressed errors, rerun with: -s ==28844== ERROR SUMMARY: 11 errors from 6 contexts (suppressed: 26 from 26)