==2304781== Memcheck, a memory error detector ==2304781== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==2304781== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==2304781== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/heart/test/TestExtendedBidomainProblem -malloc_debug -malloc_dump -memory_info ==2304781== Parent PID: 2283975 ==2304781== ==2304781== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==2304781== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==2304781== ==2304781== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==2304781== at 0xA2EA79E: getsockopt_syscall (getsockopt.c:29) ==2304781== by 0xA2EA79E: getsockopt (getsockopt.c:94) ==2304781== by 0x1467E157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2304781== by 0x14685A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2304781== by 0x1468CDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2304781== by 0x1458C3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2304781== by 0x14505E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==2304781== by 0x13CC4E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==2304781== by 0xD2D34CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2304781== by 0x9BC8418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2304781== by 0x9B61D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2304781== by 0xA67BD38: PetscInitialize (pinit.c:924) ==2304781== by 0x9A8A66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2304781== by 0x9A8A6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2304781== by 0x12DB00: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2304781== by 0x128A3D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2304781== by 0x12B846: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2304781== by 0x12B741: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2304781== by 0x12BD55: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2304781== by 0x127240: main (TestExtendedBidomainProblem.cpp:18) ==2304781== Address 0x1ffeffdfac is on thread 1's stack ==2304781== in frame #2, created by pmix_ptl_base_make_connection (???:) ==2304781== { 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 } ==2304781== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==2304781== at 0xA2EA79E: getsockopt_syscall (getsockopt.c:29) ==2304781== by 0xA2EA79E: getsockopt (getsockopt.c:94) ==2304781== by 0x1467E157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2304781== by 0x14685A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2304781== by 0x1468CDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2304781== by 0x1458C3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2304781== by 0x14505E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==2304781== by 0x13CC4E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==2304781== by 0xD2D34CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2304781== by 0x9BC8418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2304781== by 0x9B61D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2304781== by 0xA67BD38: PetscInitialize (pinit.c:924) ==2304781== by 0x9A8A66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2304781== by 0x9A8A6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2304781== by 0x12DB00: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2304781== by 0x128A3D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2304781== by 0x12B846: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2304781== by 0x12B741: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2304781== by 0x12BD55: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2304781== by 0x127240: main (TestExtendedBidomainProblem.cpp:18) ==2304781== Address 0x1ffeffdfac is on thread 1's stack ==2304781== in frame #2, created by pmix_ptl_base_make_connection (???:) ==2304781== { 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 } ==2304781== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==2304781== at 0xA2EAC7E: setsockopt_syscall (setsockopt.c:29) ==2304781== by 0xA2EAC7E: setsockopt (setsockopt.c:95) ==2304781== by 0x14685BA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2304781== by 0x1468CDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2304781== by 0x1458C3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2304781== by 0x14505E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==2304781== by 0x13CC4E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==2304781== by 0xD2D34CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2304781== by 0x9BC8418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2304781== by 0x9B61D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2304781== by 0xA67BD38: PetscInitialize (pinit.c:924) ==2304781== by 0x9A8A66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2304781== by 0x9A8A6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2304781== by 0x12DB00: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2304781== by 0x128A3D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2304781== by 0x12B846: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2304781== by 0x12B741: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2304781== by 0x12BD55: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2304781== by 0x127240: main (TestExtendedBidomainProblem.cpp:18) ==2304781== { 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 } ==2304781== Syscall param pwrite64(buf) points to uninitialised byte(s) ==2304781== at 0xA2D59EF: __libc_pwrite64 (pwrite64.c:25) ==2304781== by 0xA2D59EF: pwrite (pwrite64.c:23) ==2304781== by 0x176FB9D2: mca_fbtl_posix_pwritev (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_fbtl_posix.so) ==2304781== by 0x1770B419: mca_common_ompio_file_write (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==2304781== by 0x1770B79A: mca_common_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==2304781== by 0x175F689A: mca_io_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_io_ompio.so) ==2304781== by 0x9B556A7: PMPI_File_write_at (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2304781== by 0xD152FEB: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304781== by 0xCF924ED: H5FD_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304781== by 0xCF75313: H5F__accum_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304781== by 0xD070442: H5PB_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304781== by 0xCF7CDEA: H5F_block_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304781== by 0xCF06E98: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304781== by 0xD1463F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304781== by 0xD1479CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304781== by 0xD14847E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304781== by 0xCEE354C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304781== by 0xCF7B936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304781== by 0xCF7C3FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304781== by 0xCF7FBB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304781== by 0xCF7FEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304781== by 0xCFEF51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304781== by 0xCFEF5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304781== by 0xCF7C831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304781== by 0xCF71881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304781== by 0x99B8855: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==2304781== by 0x99B3535: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==2304781== by 0x99B35DB: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==2304781== by 0x6885B51: AbstractCardiacProblem<1u, 1u, 3u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==2304781== by 0x68856F1: AbstractCardiacProblem<1u, 1u, 3u>::Solve() (AbstractCardiacProblem.cpp:582) ==2304781== by 0x12FC1C: TestExtendedBidomainProblem::TestExtendedProblemVsMartincCode() (TestExtendedBidomainProblem.hpp:168) ==2304781== by 0x1313BC: TestDescription_TestExtendedBidomainProblem_TestExtendedProblemVsMartincCode::runTest() (TestExtendedBidomainProblem.cpp:30) ==2304781== by 0x128274: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==2304781== by 0x12BAF4: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==2304781== by 0x12B9D9: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==2304781== by 0x12B87F: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==2304781== by 0x12B741: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2304781== by 0x12BD55: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2304781== by 0x127240: main (TestExtendedBidomainProblem.cpp:18) ==2304781== Address 0x166fbe3e is 62 bytes inside a block of size 320 alloc'd ==2304781== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==2304781== by 0xCF06E26: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304781== by 0xD1463F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304781== by 0xD1479CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304781== by 0xD14847E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304781== by 0xCEE354C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304781== by 0xCF7B936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304781== by 0xCF7C3FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304781== by 0xCF7FBB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304781== by 0xCF7FEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304781== by 0xCFEF51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304781== by 0xCFEF5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304781== by 0xCF7C831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304781== by 0xCF71881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304781== by 0x99B8855: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==2304781== by 0x99B3535: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==2304781== by 0x99B35DB: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==2304781== by 0x6885B51: AbstractCardiacProblem<1u, 1u, 3u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==2304781== by 0x68856F1: AbstractCardiacProblem<1u, 1u, 3u>::Solve() (AbstractCardiacProblem.cpp:582) ==2304781== by 0x12FC1C: TestExtendedBidomainProblem::TestExtendedProblemVsMartincCode() (TestExtendedBidomainProblem.hpp:168) ==2304781== by 0x1313BC: TestDescription_TestExtendedBidomainProblem_TestExtendedProblemVsMartincCode::runTest() (TestExtendedBidomainProblem.cpp:30) ==2304781== by 0x128274: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==2304781== by 0x12BAF4: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==2304781== by 0x12B9D9: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==2304781== by 0x12B87F: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==2304781== by 0x12B741: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2304781== by 0x12BD55: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2304781== by 0x127240: main (TestExtendedBidomainProblem.cpp:18) ==2304781== { 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 } ==2304781== ==2304781== FILE DESCRIPTORS: 9 open (3 std) at exit. ==2304781== Open file descriptor 12: ==2304781== at 0xA2D822D: pipe (pipe.c:29) ==2304781== by 0x13CC507D: ??? ==2304781== by 0xD2D34CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2304781== by 0x9BC8418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2304781== by 0x9B61D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2304781== by 0xA67BD38: PetscInitialize (pinit.c:924) ==2304781== by 0x9A8A66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2304781== by 0x9A8A6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2304781== by 0x12DB00: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2304781== by 0x128A3D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2304781== by 0x12B846: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2304781== by 0x12B741: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2304781== by 0x12BD55: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2304781== by 0x127240: main (TestExtendedBidomainProblem.cpp:18) ==2304781== ==2304781== Open file descriptor 8: /dev/shm/open_mpi.0000 ==2304781== at 0xA2DCBCC: __open_nocancel (open64_nocancel.c:39) ==2304781== by 0xA260C4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==2304781== by 0x9AC2822: ??? ==2304781== by 0x9AC296F: ??? ==2304781== by 0xD3786DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2304781== by 0xD378938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2304781== by 0xD32E922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2304781== by 0xD2D32DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2304781== by 0x9BC8418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2304781== by 0x9B61D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2304781== by 0xA67BD38: PetscInitialize (pinit.c:924) ==2304781== by 0x9A8A66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2304781== by 0x9A8A6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2304781== by 0x12DB00: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2304781== by 0x128A3D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2304781== by 0x12B846: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2304781== by 0x12B741: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2304781== by 0x12BD55: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2304781== by 0x127240: main (TestExtendedBidomainProblem.cpp:18) ==2304781== ==2304781== Open file descriptor 117: ==2304781== ==2304781== ==2304781== Open file descriptor 110: ==2304781== ==2304781== ==2304781== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestExtendedBidomainProblem_valgrind.txt ==2304781== ==2304781== ==2304781== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==2304781== ==2304781== ==2304781== ==2304781== HEAP SUMMARY: ==2304781== in use at exit: 701,168 bytes in 9,383 blocks ==2304781== total heap usage: 2,374,749 allocs, 2,365,366 frees, 2,483,205,949 bytes allocated ==2304781== ==2304781== 32 bytes in 1 blocks are possibly lost in loss record 13 of 68 ==2304781== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==2304781== by 0x1570671E: ??? ==2304781== by 0x15706E0B: ??? ==2304781== by 0x15709F56: ??? ==2304781== by 0x156FF65D: ??? ==2304781== by 0x156FFFA3: ??? ==2304781== by 0xD3E4F05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==2304781== by 0xD3C0AE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==2304781== by 0xD371CB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2304781== by 0xD29EEF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2304781== by 0x13CC5F03: ??? ==2304781== by 0xD2D34CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2304781== by 0x9BC8418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2304781== by 0x9B61D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2304781== by 0xA67BD38: PetscInitialize (pinit.c:924) ==2304781== by 0x9A8A66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2304781== by 0x9A8A6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2304781== by 0x12DB00: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2304781== by 0x128A3D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2304781== by 0x12B846: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2304781== by 0x12B741: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2304781== by 0x12BD55: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2304781== by 0x127240: main (TestExtendedBidomainProblem.cpp:18) ==2304781== { Memcheck:Leak match-leak-kinds: possible 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 } ==2304781== 136 bytes in 1 blocks are possibly lost in loss record 35 of 68 ==2304781== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==2304781== by 0x157066E8: ??? ==2304781== by 0x15706E0B: ??? ==2304781== by 0x15709F56: ??? ==2304781== by 0x156FF65D: ??? ==2304781== by 0x156FFFA3: ??? ==2304781== by 0xD3E4F05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==2304781== by 0xD3C0AE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==2304781== by 0xD371CB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2304781== by 0xD29EEF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2304781== by 0x13CC5F03: ??? ==2304781== by 0xD2D34CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2304781== by 0x9BC8418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2304781== by 0x9B61D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2304781== by 0xA67BD38: PetscInitialize (pinit.c:924) ==2304781== by 0x9A8A66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2304781== by 0x9A8A6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2304781== by 0x12DB00: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2304781== by 0x128A3D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2304781== by 0x12B846: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2304781== by 0x12B741: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2304781== by 0x12BD55: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2304781== by 0x127240: main (TestExtendedBidomainProblem.cpp:18) ==2304781== { Memcheck:Leak match-leak-kinds: possible 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 } ==2304781== 552 bytes in 1 blocks are definitely lost in loss record 42 of 68 ==2304781== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==2304781== by 0x14593C13: ??? ==2304781== by 0x1459422C: ??? ==2304781== by 0x145074B7: ??? ==2304781== by 0x9B2E15A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2304781== by 0x9BC8A97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2304781== by 0x9B61D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2304781== by 0xA67BD38: PetscInitialize (pinit.c:924) ==2304781== by 0x9A8A66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2304781== by 0x9A8A6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2304781== by 0x12DB00: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2304781== by 0x128A3D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2304781== by 0x12B846: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2304781== by 0x12B741: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2304781== by 0x12BD55: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2304781== by 0x127240: main (TestExtendedBidomainProblem.cpp:18) ==2304781== { 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 } ==2304781== 23,137 (136 direct, 23,001 indirect) bytes in 1 blocks are definitely lost in loss record 65 of 68 ==2304781== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==2304781== by 0x1570674E: ??? ==2304781== by 0x15706E0B: ??? ==2304781== by 0x15709F56: ??? ==2304781== by 0x156FF65D: ??? ==2304781== by 0x156FFFA3: ??? ==2304781== by 0xD3E4F05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==2304781== by 0xD3C0AE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==2304781== by 0xD371CB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2304781== by 0xD29EEF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2304781== by 0x13CC5F03: ??? ==2304781== by 0xD2D34CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2304781== by 0x9BC8418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2304781== by 0x9B61D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2304781== by 0xA67BD38: PetscInitialize (pinit.c:924) ==2304781== by 0x9A8A66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2304781== by 0x9A8A6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2304781== by 0x12DB00: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2304781== by 0x128A3D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2304781== by 0x12B846: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2304781== by 0x12B741: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2304781== by 0x12BD55: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2304781== by 0x127240: main (TestExtendedBidomainProblem.cpp:18) ==2304781== { 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 } ==2304781== LEAK SUMMARY: ==2304781== definitely lost: 688 bytes in 2 blocks ==2304781== indirectly lost: 1,592 bytes in 14 blocks ==2304781== possibly lost: 168 bytes in 2 blocks ==2304781== still reachable: 1,531 bytes in 6 blocks ==2304781== suppressed: 697,189 bytes in 9,359 blocks ==2304781== Reachable blocks (those to which a pointer was found) are not shown. ==2304781== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==2304781== ==2304781== Use --track-origins=yes to see where uninitialised values come from ==2304781== For lists of detected and suppressed errors, rerun with: -s ==2304781== ERROR SUMMARY: 13 errors from 8 contexts (suppressed: 29 from 29)