==3567908== Memcheck, a memory error detector ==3567908== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==3567908== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==3567908== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/heart/test/TestExtendedBidomainProblem -malloc_debug -malloc_dump -memory_info ==3567908== Parent PID: 3546972 ==3567908== ==3567908== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==3567908== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==3567908== ==3567908== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==3567908== at 0xA68479E: getsockopt_syscall (getsockopt.c:29) ==3567908== by 0xA68479E: getsockopt (getsockopt.c:94) ==3567908== by 0x14A15157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3567908== by 0x14A1CA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3567908== by 0x14A23DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3567908== by 0x149233C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3567908== by 0x1489CE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==3567908== by 0x1405BE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==3567908== by 0xD6604CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3567908== by 0x9F62418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567908== by 0x9EFBD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567908== by 0xAA15D38: PetscInitialize (pinit.c:924) ==3567908== by 0x9E24717: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3567908== by 0x9E24765: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3567908== by 0x12DB00: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3567908== by 0x128A3D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3567908== by 0x12B846: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3567908== by 0x12B741: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3567908== by 0x12BD55: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3567908== by 0x127240: main (TestExtendedBidomainProblem.cpp:18) ==3567908== Address 0x1ffeffdfac is on thread 1's stack ==3567908== in frame #2, created by pmix_ptl_base_make_connection (???:) ==3567908== { 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 } ==3567908== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==3567908== at 0xA68479E: getsockopt_syscall (getsockopt.c:29) ==3567908== by 0xA68479E: getsockopt (getsockopt.c:94) ==3567908== by 0x14A15157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3567908== by 0x14A1CA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3567908== by 0x14A23DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3567908== by 0x149233C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3567908== by 0x1489CE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==3567908== by 0x1405BE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==3567908== by 0xD6604CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3567908== by 0x9F62418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567908== by 0x9EFBD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567908== by 0xAA15D38: PetscInitialize (pinit.c:924) ==3567908== by 0x9E24717: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3567908== by 0x9E24765: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3567908== by 0x12DB00: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3567908== by 0x128A3D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3567908== by 0x12B846: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3567908== by 0x12B741: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3567908== by 0x12BD55: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3567908== by 0x127240: main (TestExtendedBidomainProblem.cpp:18) ==3567908== Address 0x1ffeffdfac is on thread 1's stack ==3567908== in frame #2, created by pmix_ptl_base_make_connection (???:) ==3567908== { 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 } ==3567908== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==3567908== at 0xA684C7E: setsockopt_syscall (setsockopt.c:29) ==3567908== by 0xA684C7E: setsockopt (setsockopt.c:95) ==3567908== by 0x14A1CBA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3567908== by 0x14A23DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3567908== by 0x149233C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3567908== by 0x1489CE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==3567908== by 0x1405BE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==3567908== by 0xD6604CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3567908== by 0x9F62418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567908== by 0x9EFBD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567908== by 0xAA15D38: PetscInitialize (pinit.c:924) ==3567908== by 0x9E24717: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3567908== by 0x9E24765: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3567908== by 0x12DB00: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3567908== by 0x128A3D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3567908== by 0x12B846: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3567908== by 0x12B741: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3567908== by 0x12BD55: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3567908== by 0x127240: main (TestExtendedBidomainProblem.cpp:18) ==3567908== { 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 } ==3567908== Syscall param pwrite64(buf) points to uninitialised byte(s) ==3567908== at 0xA66F9EF: __libc_pwrite64 (pwrite64.c:25) ==3567908== by 0xA66F9EF: pwrite (pwrite64.c:23) ==3567908== by 0x17E5B9D2: mca_fbtl_posix_pwritev (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_fbtl_posix.so) ==3567908== by 0x17E6B419: mca_common_ompio_file_write (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==3567908== by 0x17E6B79A: mca_common_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==3567908== by 0x17D5689A: mca_io_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_io_ompio.so) ==3567908== by 0x9EEF6A7: PMPI_File_write_at (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567908== by 0xD4BFFEB: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567908== by 0xD2FF4ED: H5FD_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567908== by 0xD2E2313: H5F__accum_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567908== by 0xD3DD442: H5PB_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567908== by 0xD2E9DEA: H5F_block_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567908== by 0xD273E98: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567908== by 0xD4B33F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567908== by 0xD4B49CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567908== by 0xD4B547E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567908== by 0xD25054C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567908== by 0xD2E8936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567908== by 0xD2E93FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567908== by 0xD2ECBB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567908== by 0xD2ECEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567908== by 0xD35C51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567908== by 0xD35C5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567908== by 0xD2E9831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567908== by 0xD2DE881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567908== by 0x9D52967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==3567908== by 0x9D4D647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==3567908== by 0x9D4D6ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==3567908== by 0x6885AF3: AbstractCardiacProblem<1u, 1u, 3u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==3567908== by 0x6885693: AbstractCardiacProblem<1u, 1u, 3u>::Solve() (AbstractCardiacProblem.cpp:582) ==3567908== by 0x12FC1C: TestExtendedBidomainProblem::TestExtendedProblemVsMartincCode() (TestExtendedBidomainProblem.hpp:168) ==3567908== by 0x1313BC: TestDescription_TestExtendedBidomainProblem_TestExtendedProblemVsMartincCode::runTest() (TestExtendedBidomainProblem.cpp:30) ==3567908== by 0x128274: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==3567908== by 0x12BAF4: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==3567908== by 0x12B9D9: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==3567908== by 0x12B87F: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==3567908== by 0x12B741: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3567908== by 0x12BD55: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3567908== by 0x127240: main (TestExtendedBidomainProblem.cpp:18) ==3567908== Address 0x174f8fde is 62 bytes inside a block of size 320 alloc'd ==3567908== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==3567908== by 0xD273E26: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567908== by 0xD4B33F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567908== by 0xD4B49CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567908== by 0xD4B547E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567908== by 0xD25054C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567908== by 0xD2E8936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567908== by 0xD2E93FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567908== by 0xD2ECBB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567908== by 0xD2ECEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567908== by 0xD35C51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567908== by 0xD35C5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567908== by 0xD2E9831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567908== by 0xD2DE881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567908== by 0x9D52967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==3567908== by 0x9D4D647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==3567908== by 0x9D4D6ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==3567908== by 0x6885AF3: AbstractCardiacProblem<1u, 1u, 3u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==3567908== by 0x6885693: AbstractCardiacProblem<1u, 1u, 3u>::Solve() (AbstractCardiacProblem.cpp:582) ==3567908== by 0x12FC1C: TestExtendedBidomainProblem::TestExtendedProblemVsMartincCode() (TestExtendedBidomainProblem.hpp:168) ==3567908== by 0x1313BC: TestDescription_TestExtendedBidomainProblem_TestExtendedProblemVsMartincCode::runTest() (TestExtendedBidomainProblem.cpp:30) ==3567908== by 0x128274: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==3567908== by 0x12BAF4: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==3567908== by 0x12B9D9: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==3567908== by 0x12B87F: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==3567908== by 0x12B741: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3567908== by 0x12BD55: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3567908== by 0x127240: main (TestExtendedBidomainProblem.cpp:18) ==3567908== { 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 } ==3567908== ==3567908== FILE DESCRIPTORS: 9 open (3 std) at exit. ==3567908== Open file descriptor 12: ==3567908== at 0xA67222D: pipe (pipe.c:29) ==3567908== by 0x1405C07D: ??? ==3567908== by 0xD6604CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3567908== by 0x9F62418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567908== by 0x9EFBD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567908== by 0xAA15D38: PetscInitialize (pinit.c:924) ==3567908== by 0x9E24717: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3567908== by 0x9E24765: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3567908== by 0x12DB00: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3567908== by 0x128A3D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3567908== by 0x12B846: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3567908== by 0x12B741: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3567908== by 0x12BD55: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3567908== by 0x127240: main (TestExtendedBidomainProblem.cpp:18) ==3567908== ==3567908== Open file descriptor 8: /dev/shm/open_mpi.0000 ==3567908== at 0xA676BCC: __open_nocancel (open64_nocancel.c:39) ==3567908== by 0xA5FAC4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==3567908== by 0x9E5C822: ??? ==3567908== by 0x9E5C96F: ??? ==3567908== by 0xD7056DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==3567908== by 0xD705938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==3567908== by 0xD6BB922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==3567908== by 0xD6602DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3567908== by 0x9F62418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567908== by 0x9EFBD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567908== by 0xAA15D38: PetscInitialize (pinit.c:924) ==3567908== by 0x9E24717: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3567908== by 0x9E24765: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3567908== by 0x12DB00: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3567908== by 0x128A3D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3567908== by 0x12B846: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3567908== by 0x12B741: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3567908== by 0x12BD55: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3567908== by 0x127240: main (TestExtendedBidomainProblem.cpp:18) ==3567908== ==3567908== Open file descriptor 117: ==3567908== ==3567908== ==3567908== Open file descriptor 110: ==3567908== ==3567908== ==3567908== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestExtendedBidomainProblem_valgrind.txt ==3567908== ==3567908== ==3567908== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==3567908== ==3567908== ==3567908== ==3567908== HEAP SUMMARY: ==3567908== in use at exit: 707,440 bytes in 9,495 blocks ==3567908== total heap usage: 2,374,899 allocs, 2,365,404 frees, 2,483,217,430 bytes allocated ==3567908== ==3567908== 448 bytes in 8 blocks are definitely lost in loss record 52 of 77 ==3567908== at 0x4849013: operator new(unsigned long) (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==3567908== by 0x90537D5: OpenSimplex2S::initLatticePoints() (OpenSimplex2S.cpp:442) ==3567908== by 0x9051A6E: OpenSimplex2S::Initializer::Initializer() (OpenSimplex2S.cpp:14) ==3567908== by 0x9054A14: __static_initialization_and_destruction_0(int, int) (OpenSimplex2S.cpp:18) ==3567908== by 0x9054A39: _GLOBAL__sub_I_OpenSimplex2S.cpp (OpenSimplex2S.cpp:1064) ==3567908== by 0x400647D: call_init.part.0 (dl-init.c:70) ==3567908== by 0x4006567: call_init (dl-init.c:33) ==3567908== by 0x4006567: _dl_init (dl-init.c:117) ==3567908== by 0x40202E9: ??? (in /usr/lib/x86_64-linux-gnu/ld-linux-x86-64.so.2) ==3567908== by 0x3: ??? ==3567908== by 0x1FFF000312: ??? ==3567908== by 0x1FFF000381: ??? ==3567908== by 0x1FFF00038F: ??? ==3567908== by 0x1FFF00039C: ??? ==3567908== { Memcheck:Leak match-leak-kinds: definite fun:_Znwm fun:_ZN13OpenSimplex2S17initLatticePointsEv fun:_ZN13OpenSimplex2S11InitializerC1Ev fun:_Z41__static_initialization_and_destruction_0ii fun:_GLOBAL__sub_I_OpenSimplex2S.cpp fun:call_init.part.0 fun:call_init fun:_dl_init obj:/usr/lib/x86_64-linux-gnu/ld-linux-x86-64.so.2 obj:* obj:* obj:* obj:* obj:* } ==3567908== 552 bytes in 1 blocks are definitely lost in loss record 54 of 77 ==3567908== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==3567908== by 0x1492AC13: ??? ==3567908== by 0x1492B22C: ??? ==3567908== by 0x1489E4B7: ??? ==3567908== by 0x9EC815A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567908== by 0x9F62A97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567908== by 0x9EFBD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567908== by 0xAA15D38: PetscInitialize (pinit.c:924) ==3567908== by 0x9E24717: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3567908== by 0x9E24765: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3567908== by 0x12DB00: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3567908== by 0x128A3D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3567908== by 0x12B846: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3567908== by 0x12B741: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3567908== by 0x12BD55: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3567908== by 0x127240: main (TestExtendedBidomainProblem.cpp:18) ==3567908== { 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 } ==3567908== 685,243 (136 direct, 685,107 indirect) bytes in 1 blocks are definitely lost in loss record 77 of 77 ==3567908== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==3567908== by 0x15A9D74E: ??? ==3567908== by 0x15A9DE0B: ??? ==3567908== by 0x15AA0F56: ??? ==3567908== by 0x15A9665D: ??? ==3567908== by 0x15A96FA3: ??? ==3567908== by 0xD771F05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==3567908== by 0xD74DAE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==3567908== by 0xD6FECB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==3567908== by 0xD62BEF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3567908== by 0x1405CF03: ??? ==3567908== by 0xD6604CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3567908== by 0x9F62418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567908== by 0x9EFBD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567908== by 0xAA15D38: PetscInitialize (pinit.c:924) ==3567908== by 0x9E24717: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3567908== by 0x9E24765: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3567908== by 0x12DB00: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3567908== by 0x128A3D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3567908== by 0x12B846: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3567908== by 0x12B741: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3567908== by 0x12BD55: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3567908== by 0x127240: main (TestExtendedBidomainProblem.cpp:18) ==3567908== { 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 } ==3567908== LEAK SUMMARY: ==3567908== definitely lost: 1,136 bytes in 10 blocks ==3567908== indirectly lost: 1,760 bytes in 16 blocks ==3567908== possibly lost: 0 bytes in 0 blocks ==3567908== still reachable: 7,355 bytes in 110 blocks ==3567908== suppressed: 697,189 bytes in 9,359 blocks ==3567908== Reachable blocks (those to which a pointer was found) are not shown. ==3567908== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==3567908== ==3567908== Use --track-origins=yes to see where uninitialised values come from ==3567908== For lists of detected and suppressed errors, rerun with: -s ==3567908== ERROR SUMMARY: 12 errors from 7 contexts (suppressed: 26 from 26)