==2599675== Memcheck, a memory error detector ==2599675== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==2599675== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==2599675== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/heart/test/TestMonodomainPurkinjeProblem -malloc_debug -malloc_dump -memory_info ==2599675== Parent PID: 2577069 ==2599675== ==2599675== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==2599675== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==2599675== ==2599675== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==2599675== at 0xA4B279E: getsockopt_syscall (getsockopt.c:29) ==2599675== by 0xA4B279E: getsockopt (getsockopt.c:94) ==2599675== by 0x14AA3157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2599675== by 0x14AAAA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2599675== by 0x14AB1DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2599675== by 0x149B13C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2599675== by 0x1492AE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==2599675== by 0x140E9E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==2599675== by 0xF8EB4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2599675== by 0xBBB1418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2599675== by 0xBB4AD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2599675== by 0xA841D38: PetscInitialize (pinit.c:924) ==2599675== by 0x9D8958B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2599675== by 0x9D895D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2599675== by 0x13526C: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2599675== by 0x12E38F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2599675== by 0x1310E8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2599675== by 0x130F88: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2599675== by 0x13161F: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2599675== by 0x12C6C0: main (TestMonodomainPurkinjeProblem.cpp:19) ==2599675== Address 0x1ffeffdf9c is on thread 1's stack ==2599675== in frame #2, created by pmix_ptl_base_make_connection (???:) ==2599675== { 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 } ==2599675== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==2599675== at 0xA4B279E: getsockopt_syscall (getsockopt.c:29) ==2599675== by 0xA4B279E: getsockopt (getsockopt.c:94) ==2599675== by 0x14AA3157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2599675== by 0x14AAAA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2599675== by 0x14AB1DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2599675== by 0x149B13C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2599675== by 0x1492AE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==2599675== by 0x140E9E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==2599675== by 0xF8EB4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2599675== by 0xBBB1418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2599675== by 0xBB4AD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2599675== by 0xA841D38: PetscInitialize (pinit.c:924) ==2599675== by 0x9D8958B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2599675== by 0x9D895D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2599675== by 0x13526C: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2599675== by 0x12E38F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2599675== by 0x1310E8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2599675== by 0x130F88: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2599675== by 0x13161F: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2599675== by 0x12C6C0: main (TestMonodomainPurkinjeProblem.cpp:19) ==2599675== Address 0x1ffeffdf9c is on thread 1's stack ==2599675== in frame #2, created by pmix_ptl_base_make_connection (???:) ==2599675== { 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 } ==2599675== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==2599675== at 0xA4B2C7E: setsockopt_syscall (setsockopt.c:29) ==2599675== by 0xA4B2C7E: setsockopt (setsockopt.c:95) ==2599675== by 0x14AAABA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2599675== by 0x14AB1DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2599675== by 0x149B13C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2599675== by 0x1492AE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==2599675== by 0x140E9E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==2599675== by 0xF8EB4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2599675== by 0xBBB1418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2599675== by 0xBB4AD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2599675== by 0xA841D38: PetscInitialize (pinit.c:924) ==2599675== by 0x9D8958B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2599675== by 0x9D895D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2599675== by 0x13526C: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2599675== by 0x12E38F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2599675== by 0x1310E8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2599675== by 0x130F88: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2599675== by 0x13161F: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2599675== by 0x12C6C0: main (TestMonodomainPurkinjeProblem.cpp:19) ==2599675== { 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 } ==2599675== Syscall param pwrite64(buf) points to uninitialised byte(s) ==2599675== at 0xA49D9EF: __libc_pwrite64 (pwrite64.c:25) ==2599675== by 0xA49D9EF: pwrite (pwrite64.c:23) ==2599675== by 0x183209D2: mca_fbtl_posix_pwritev (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_fbtl_posix.so) ==2599675== by 0x18330419: mca_common_ompio_file_write (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==2599675== by 0x1833079A: mca_common_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==2599675== by 0x1821B89A: mca_io_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_io_ompio.so) ==2599675== by 0xBB3E6A7: PMPI_File_write_at (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2599675== by 0xF2B4FEB: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2599675== by 0xF0F44ED: H5FD_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2599675== by 0xF0D7313: H5F__accum_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2599675== by 0xF1D2442: H5PB_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2599675== by 0xF0DEDEA: H5F_block_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2599675== by 0xF068E98: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2599675== by 0xF2A83F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2599675== by 0xF2A99CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2599675== by 0xF2AA47E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2599675== by 0xF04554C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2599675== by 0xF0DD936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2599675== by 0xF0DE3FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2599675== by 0xF0E1BB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2599675== by 0xF0E1EFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2599675== by 0xF15151F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2599675== by 0xF1515EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2599675== by 0xF0DE831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2599675== by 0xF0D3881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2599675== by 0xC545967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==2599675== by 0xC540647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==2599675== by 0xC5406ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==2599675== by 0x6869407: AbstractCardiacProblem<2u, 2u, 1u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==2599675== by 0x6868FA7: AbstractCardiacProblem<2u, 2u, 1u>::Solve() (AbstractCardiacProblem.cpp:582) ==2599675== by 0x137F66: TestMonodomainPurkinjeProblem::TestMonodomainPurkinjeProblemRunning() (TestMonodomainPurkinjeProblem.hpp:270) ==2599675== by 0x141F7A: TestDescription_TestMonodomainPurkinjeProblem_TestMonodomainPurkinjeProblemRunning::runTest() (TestMonodomainPurkinjeProblem.cpp:31) ==2599675== by 0x12D98A: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==2599675== by 0x131396: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==2599675== by 0x13127B: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==2599675== by 0x131121: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==2599675== by 0x130F88: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2599675== by 0x13161F: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2599675== by 0x12C6C0: main (TestMonodomainPurkinjeProblem.cpp:19) ==2599675== Address 0x162adcce is 62 bytes inside a block of size 320 alloc'd ==2599675== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==2599675== by 0xF068E26: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2599675== by 0xF2A83F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2599675== by 0xF2A99CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2599675== by 0xF2AA47E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2599675== by 0xF04554C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2599675== by 0xF0DD936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2599675== by 0xF0DE3FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2599675== by 0xF0E1BB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2599675== by 0xF0E1EFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2599675== by 0xF15151F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2599675== by 0xF1515EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2599675== by 0xF0DE831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2599675== by 0xF0D3881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2599675== by 0xC545967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==2599675== by 0xC540647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==2599675== by 0xC5406ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==2599675== by 0x6869407: AbstractCardiacProblem<2u, 2u, 1u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==2599675== by 0x6868FA7: AbstractCardiacProblem<2u, 2u, 1u>::Solve() (AbstractCardiacProblem.cpp:582) ==2599675== by 0x137F66: TestMonodomainPurkinjeProblem::TestMonodomainPurkinjeProblemRunning() (TestMonodomainPurkinjeProblem.hpp:270) ==2599675== by 0x141F7A: TestDescription_TestMonodomainPurkinjeProblem_TestMonodomainPurkinjeProblemRunning::runTest() (TestMonodomainPurkinjeProblem.cpp:31) ==2599675== by 0x12D98A: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==2599675== by 0x131396: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==2599675== by 0x13127B: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==2599675== by 0x131121: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==2599675== by 0x130F88: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2599675== by 0x13161F: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2599675== by 0x12C6C0: main (TestMonodomainPurkinjeProblem.cpp:19) ==2599675== { 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:_ZN22AbstractCardiacProblemILj2ELj2ELj1EE24CloseFilesAndPostProcessEv fun:_ZN22AbstractCardiacProblemILj2ELj2ELj1EE5SolveEv fun:_ZN29TestMonodomainPurkinjeProblem36TestMonodomainPurkinjeProblemRunningEv fun:_ZN82TestDescription_TestMonodomainPurkinjeProblem_TestMonodomainPurkinjeProblemRunning7runTestEv fun:_ZN7CxxTest19RealTestDescription3runEv fun:_ZN7CxxTest10TestRunner7runTestERNS_15TestDescriptionE fun:_ZN7CxxTest10TestRunner8runSuiteERNS_16SuiteDescriptionE fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==2599675== ==2599675== FILE DESCRIPTORS: 9 open (3 std) at exit. ==2599675== Open file descriptor 12: ==2599675== at 0xA4A022D: pipe (pipe.c:29) ==2599675== by 0x140EA07D: ??? ==2599675== by 0xF8EB4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2599675== by 0xBBB1418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2599675== by 0xBB4AD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2599675== by 0xA841D38: PetscInitialize (pinit.c:924) ==2599675== by 0x9D8958B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2599675== by 0x9D895D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2599675== by 0x13526C: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2599675== by 0x12E38F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2599675== by 0x1310E8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2599675== by 0x130F88: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2599675== by 0x13161F: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2599675== by 0x12C6C0: main (TestMonodomainPurkinjeProblem.cpp:19) ==2599675== ==2599675== Open file descriptor 8: /dev/shm/open_mpi.0000 ==2599675== at 0xA4A4BCC: __open_nocancel (open64_nocancel.c:39) ==2599675== by 0xA428C4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==2599675== by 0x9DC1822: ??? ==2599675== by 0x9DC196F: ??? ==2599675== by 0xF9906DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2599675== by 0xF990938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2599675== by 0xF946922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2599675== by 0xF8EB2DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2599675== by 0xBBB1418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2599675== by 0xBB4AD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2599675== by 0xA841D38: PetscInitialize (pinit.c:924) ==2599675== by 0x9D8958B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2599675== by 0x9D895D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2599675== by 0x13526C: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2599675== by 0x12E38F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2599675== by 0x1310E8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2599675== by 0x130F88: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2599675== by 0x13161F: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2599675== by 0x12C6C0: main (TestMonodomainPurkinjeProblem.cpp:19) ==2599675== ==2599675== Open file descriptor 117: ==2599675== ==2599675== ==2599675== Open file descriptor 110: ==2599675== ==2599675== ==2599675== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestMonodomainPurkinjeProblem_valgrind.txt ==2599675== ==2599675== ==2599675== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==2599675== ==2599675== ==2599675== ==2599675== HEAP SUMMARY: ==2599675== in use at exit: 701,168 bytes in 9,383 blocks ==2599675== total heap usage: 1,148,979 allocs, 1,139,596 frees, 2,594,277,575 bytes allocated ==2599675== ==2599675== 552 bytes in 1 blocks are definitely lost in loss record 40 of 63 ==2599675== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==2599675== by 0x149B8C13: ??? ==2599675== by 0x149B922C: ??? ==2599675== by 0x1492C4B7: ??? ==2599675== by 0xBB1715A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2599675== by 0xBBB1A97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2599675== by 0xBB4AD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2599675== by 0xA841D38: PetscInitialize (pinit.c:924) ==2599675== by 0x9D8958B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2599675== by 0x9D895D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2599675== by 0x13526C: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2599675== by 0x12E38F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2599675== by 0x1310E8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2599675== by 0x130F88: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2599675== by 0x13161F: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2599675== by 0x12C6C0: main (TestMonodomainPurkinjeProblem.cpp:19) ==2599675== { 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 } ==2599675== 685,252 (136 direct, 685,116 indirect) bytes in 1 blocks are definitely lost in loss record 63 of 63 ==2599675== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==2599675== by 0x15B2B74E: ??? ==2599675== by 0x15B2BE0B: ??? ==2599675== by 0x15B2EF56: ??? ==2599675== by 0x15B2465D: ??? ==2599675== by 0x15B24FA3: ??? ==2599675== by 0xF9FCF05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==2599675== by 0xF9D8AE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==2599675== by 0xF989CB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2599675== by 0xF8B6EF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2599675== by 0x140EAF03: ??? ==2599675== by 0xF8EB4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2599675== by 0xBBB1418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2599675== by 0xBB4AD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2599675== by 0xA841D38: PetscInitialize (pinit.c:924) ==2599675== by 0x9D8958B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2599675== by 0x9D895D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2599675== by 0x13526C: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2599675== by 0x12E38F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2599675== by 0x1310E8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2599675== by 0x130F88: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2599675== by 0x13161F: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2599675== by 0x12C6C0: main (TestMonodomainPurkinjeProblem.cpp:19) ==2599675== { 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 } ==2599675== LEAK SUMMARY: ==2599675== definitely lost: 688 bytes in 2 blocks ==2599675== indirectly lost: 1,760 bytes in 16 blocks ==2599675== possibly lost: 0 bytes in 0 blocks ==2599675== still reachable: 1,531 bytes in 6 blocks ==2599675== suppressed: 697,189 bytes in 9,359 blocks ==2599675== Reachable blocks (those to which a pointer was found) are not shown. ==2599675== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==2599675== ==2599675== Use --track-origins=yes to see where uninitialised values come from ==2599675== For lists of detected and suppressed errors, rerun with: -s ==2599675== ERROR SUMMARY: 38 errors from 6 contexts (suppressed: 26 from 26)