==936786== Memcheck, a memory error detector ==936786== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==936786== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==936786== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/heart/test/TestMonodomainProblem -malloc_debug -malloc_dump -memory_info ==936786== Parent PID: 914403 ==936786== ==936786== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==936786== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==936786== ==936786== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==936786== at 0xB83479E: getsockopt_syscall (getsockopt.c:29) ==936786== by 0xB83479E: getsockopt (getsockopt.c:94) ==936786== by 0x1444E157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936786== by 0x14455A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936786== by 0x1445CDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936786== by 0x1435C3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936786== by 0x142D5E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==936786== by 0x13A94E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==936786== by 0xF7574CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==936786== by 0xB112418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936786== by 0xB0ABD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936786== by 0x99EDD38: PetscInitialize (pinit.c:924) ==936786== by 0x985D58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==936786== by 0x985D5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==936786== by 0x154BCC: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==936786== by 0x14A8EF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==936786== by 0x14DB8A: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==936786== by 0x14DA2A: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936786== by 0x14E0C1: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936786== by 0x148BD0: main (TestMonodomainProblem.cpp:19) ==936786== Address 0x1ffeffdfdc is on thread 1's stack ==936786== in frame #2, created by pmix_ptl_base_make_connection (???:) ==936786== { 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 } ==936786== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==936786== at 0xB83479E: getsockopt_syscall (getsockopt.c:29) ==936786== by 0xB83479E: getsockopt (getsockopt.c:94) ==936786== by 0x1444E157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936786== by 0x14455A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936786== by 0x1445CDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936786== by 0x1435C3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936786== by 0x142D5E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==936786== by 0x13A94E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==936786== by 0xF7574CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==936786== by 0xB112418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936786== by 0xB0ABD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936786== by 0x99EDD38: PetscInitialize (pinit.c:924) ==936786== by 0x985D58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==936786== by 0x985D5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==936786== by 0x154BCC: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==936786== by 0x14A8EF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==936786== by 0x14DB8A: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==936786== by 0x14DA2A: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936786== by 0x14E0C1: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936786== by 0x148BD0: main (TestMonodomainProblem.cpp:19) ==936786== Address 0x1ffeffdfdc is on thread 1's stack ==936786== in frame #2, created by pmix_ptl_base_make_connection (???:) ==936786== { 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 } ==936786== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==936786== at 0xB834C7E: setsockopt_syscall (setsockopt.c:29) ==936786== by 0xB834C7E: setsockopt (setsockopt.c:95) ==936786== by 0x14455BA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936786== by 0x1445CDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936786== by 0x1435C3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936786== by 0x142D5E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==936786== by 0x13A94E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==936786== by 0xF7574CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==936786== by 0xB112418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936786== by 0xB0ABD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936786== by 0x99EDD38: PetscInitialize (pinit.c:924) ==936786== by 0x985D58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==936786== by 0x985D5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==936786== by 0x154BCC: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==936786== by 0x14A8EF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==936786== by 0x14DB8A: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==936786== by 0x14DA2A: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936786== by 0x14E0C1: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936786== by 0x148BD0: main (TestMonodomainProblem.cpp:19) ==936786== { 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 } ==936786== Syscall param pwrite64(buf) points to uninitialised byte(s) ==936786== at 0xB81F9EF: __libc_pwrite64 (pwrite64.c:25) ==936786== by 0xB81F9EF: pwrite (pwrite64.c:23) ==936786== by 0x17CCB9D2: mca_fbtl_posix_pwritev (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_fbtl_posix.so) ==936786== by 0x17CDB419: mca_common_ompio_file_write (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==936786== by 0x17CDB79A: mca_common_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==936786== by 0x17BC689A: mca_io_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_io_ompio.so) ==936786== by 0xB09F6A7: PMPI_File_write_at (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936786== by 0xAF3EFEB: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936786== by 0xAD7E4ED: H5FD_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936786== by 0xAD61313: H5F__accum_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936786== by 0xAE5C442: H5PB_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936786== by 0xAD68DEA: H5F_block_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936786== by 0xACF2E98: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936786== by 0xAF323F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936786== by 0xAF339CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936786== by 0xAF3447E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936786== by 0xACCF54C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936786== by 0xAD67936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936786== by 0xAD683FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936786== by 0xAD6BBB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936786== by 0xAD6BEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936786== by 0xADDB51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936786== by 0xADDB5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936786== by 0xAD68831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936786== by 0xAD5D881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936786== by 0x978C967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==936786== by 0x9787647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==936786== by 0x97876ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==936786== by 0x676E53D: AbstractCardiacProblem<1u, 1u, 1u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==936786== by 0x676E0DD: AbstractCardiacProblem<1u, 1u, 1u>::Solve() (AbstractCardiacProblem.cpp:582) ==936786== by 0x1559F5: TestMonodomainProblem::TestMonodomainProblemSimplestMesh1D() (TestMonodomainProblem.hpp:207) ==936786== by 0x17C1A2: TestDescription_TestMonodomainProblem_TestMonodomainProblemSimplestMesh1D::runTest() (TestMonodomainProblem.cpp:31) ==936786== by 0x149EEA: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==936786== by 0x14DE38: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==936786== by 0x14DD1D: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==936786== by 0x14DBC3: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==936786== by 0x14DA2A: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936786== by 0x14E0C1: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936786== by 0x148BD0: main (TestMonodomainProblem.cpp:19) ==936786== Address 0x13a1f7ce is 62 bytes inside a block of size 320 alloc'd ==936786== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==936786== by 0xACF2E26: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936786== by 0xAF323F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936786== by 0xAF339CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936786== by 0xAF3447E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936786== by 0xACCF54C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936786== by 0xAD67936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936786== by 0xAD683FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936786== by 0xAD6BBB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936786== by 0xAD6BEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936786== by 0xADDB51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936786== by 0xADDB5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936786== by 0xAD68831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936786== by 0xAD5D881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936786== by 0x978C967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==936786== by 0x9787647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==936786== by 0x97876ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==936786== by 0x676E53D: AbstractCardiacProblem<1u, 1u, 1u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==936786== by 0x676E0DD: AbstractCardiacProblem<1u, 1u, 1u>::Solve() (AbstractCardiacProblem.cpp:582) ==936786== by 0x1559F5: TestMonodomainProblem::TestMonodomainProblemSimplestMesh1D() (TestMonodomainProblem.hpp:207) ==936786== by 0x17C1A2: TestDescription_TestMonodomainProblem_TestMonodomainProblemSimplestMesh1D::runTest() (TestMonodomainProblem.cpp:31) ==936786== by 0x149EEA: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==936786== by 0x14DE38: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==936786== by 0x14DD1D: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==936786== by 0x14DBC3: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==936786== by 0x14DA2A: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936786== by 0x14E0C1: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936786== by 0x148BD0: main (TestMonodomainProblem.cpp:19) ==936786== { 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:_ZN22AbstractCardiacProblemILj1ELj1ELj1EE24CloseFilesAndPostProcessEv fun:_ZN22AbstractCardiacProblemILj1ELj1ELj1EE5SolveEv fun:_ZN21TestMonodomainProblem35TestMonodomainProblemSimplestMesh1DEv fun:_ZN73TestDescription_TestMonodomainProblem_TestMonodomainProblemSimplestMesh1D7runTestEv fun:_ZN7CxxTest19RealTestDescription3runEv fun:_ZN7CxxTest10TestRunner7runTestERNS_15TestDescriptionE fun:_ZN7CxxTest10TestRunner8runSuiteERNS_16SuiteDescriptionE fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==936786== Warning: invalid file descriptor -1 in syscall close() ==936786== ==936786== FILE DESCRIPTORS: 9 open (3 std) at exit. ==936786== Open file descriptor 12: ==936786== at 0xB82222D: pipe (pipe.c:29) ==936786== by 0x13A9507D: ??? ==936786== by 0xF7574CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==936786== by 0xB112418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936786== by 0xB0ABD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936786== by 0x99EDD38: PetscInitialize (pinit.c:924) ==936786== by 0x985D58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==936786== by 0x985D5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==936786== by 0x154BCC: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==936786== by 0x14A8EF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==936786== by 0x14DB8A: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==936786== by 0x14DA2A: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936786== by 0x14E0C1: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936786== by 0x148BD0: main (TestMonodomainProblem.cpp:19) ==936786== ==936786== Open file descriptor 8: /dev/shm/open_mpi.0000 ==936786== at 0xB826BCC: __open_nocancel (open64_nocancel.c:39) ==936786== by 0xB7AAC4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==936786== by 0x9895822: ??? ==936786== by 0x989596F: ??? ==936786== by 0xF7FC6DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==936786== by 0xF7FC938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==936786== by 0xF7B2922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==936786== by 0xF7572DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==936786== by 0xB112418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936786== by 0xB0ABD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936786== by 0x99EDD38: PetscInitialize (pinit.c:924) ==936786== by 0x985D58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==936786== by 0x985D5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==936786== by 0x154BCC: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==936786== by 0x14A8EF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==936786== by 0x14DB8A: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==936786== by 0x14DA2A: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936786== by 0x14E0C1: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936786== by 0x148BD0: main (TestMonodomainProblem.cpp:19) ==936786== ==936786== Open file descriptor 111: ==936786== ==936786== ==936786== Open file descriptor 108: ==936786== ==936786== ==936786== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestMonodomainProblem_valgrind.txt ==936786== ==936786== ==936786== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==936786== ==936786== ==936786== ==936786== HEAP SUMMARY: ==936786== in use at exit: 701,166 bytes in 9,383 blocks ==936786== total heap usage: 6,603,137 allocs, 6,593,754 frees, 4,030,612,447 bytes allocated ==936786== ==936786== 552 bytes in 1 blocks are definitely lost in loss record 39 of 62 ==936786== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==936786== by 0x14363C13: ??? ==936786== by 0x1436422C: ??? ==936786== by 0x142D74B7: ??? ==936786== by 0xB07815A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936786== by 0xB112A97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936786== by 0xB0ABD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936786== by 0x99EDD38: PetscInitialize (pinit.c:924) ==936786== by 0x985D58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==936786== by 0x985D5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==936786== by 0x154BCC: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==936786== by 0x14A8EF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==936786== by 0x14DB8A: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==936786== by 0x14DA2A: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936786== by 0x14E0C1: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936786== by 0x148BD0: main (TestMonodomainProblem.cpp:19) ==936786== { 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 } ==936786== 685,285 (136 direct, 685,149 indirect) bytes in 1 blocks are definitely lost in loss record 62 of 62 ==936786== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==936786== by 0x154D674E: ??? ==936786== by 0x154D6E0B: ??? ==936786== by 0x154D9F56: ??? ==936786== by 0x154CF65D: ??? ==936786== by 0x154CFFA3: ??? ==936786== by 0xF868F05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==936786== by 0xF844AE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==936786== by 0xF7F5CB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==936786== by 0xF722EF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==936786== by 0x13A95F03: ??? ==936786== by 0xF7574CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==936786== by 0xB112418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936786== by 0xB0ABD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936786== by 0x99EDD38: PetscInitialize (pinit.c:924) ==936786== by 0x985D58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==936786== by 0x985D5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==936786== by 0x154BCC: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==936786== by 0x14A8EF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==936786== by 0x14DB8A: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==936786== by 0x14DA2A: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936786== by 0x14E0C1: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936786== by 0x148BD0: main (TestMonodomainProblem.cpp:19) ==936786== { 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 } ==936786== LEAK SUMMARY: ==936786== definitely lost: 688 bytes in 2 blocks ==936786== indirectly lost: 1,760 bytes in 16 blocks ==936786== possibly lost: 0 bytes in 0 blocks ==936786== still reachable: 1,531 bytes in 6 blocks ==936786== suppressed: 697,187 bytes in 9,359 blocks ==936786== Reachable blocks (those to which a pointer was found) are not shown. ==936786== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==936786== ==936786== Use --track-origins=yes to see where uninitialised values come from ==936786== For lists of detected and suppressed errors, rerun with: -s ==936786== ERROR SUMMARY: 100 errors from 6 contexts (suppressed: 25 from 25)