==936806== Memcheck, a memory error detector ==936806== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==936806== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==936806== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/heart/test/TestMonodomainPurkinjeProblem -malloc_debug -malloc_dump -memory_info ==936806== Parent PID: 914403 ==936806== ==936806== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==936806== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==936806== ==936806== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==936806== at 0x9E6079E: getsockopt_syscall (getsockopt.c:29) ==936806== by 0x9E6079E: getsockopt (getsockopt.c:94) ==936806== by 0x1444D157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936806== by 0x14454A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936806== by 0x1445BDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936806== by 0x1435B3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936806== by 0x142D4E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==936806== by 0x13A93E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==936806== by 0xF2994CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==936806== by 0xB55F418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936806== by 0xB4F8D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936806== by 0xA1EFD38: PetscInitialize (pinit.c:924) ==936806== by 0x973758B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==936806== by 0x97375D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==936806== by 0x13526C: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==936806== by 0x12E38F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==936806== by 0x1310E8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==936806== by 0x130F88: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936806== by 0x13161F: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936806== by 0x12C6C0: main (TestMonodomainPurkinjeProblem.cpp:19) ==936806== Address 0x1ffeffdfcc is on thread 1's stack ==936806== in frame #2, created by pmix_ptl_base_make_connection (???:) ==936806== { 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 } ==936806== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==936806== at 0x9E6079E: getsockopt_syscall (getsockopt.c:29) ==936806== by 0x9E6079E: getsockopt (getsockopt.c:94) ==936806== by 0x1444D157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936806== by 0x14454A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936806== by 0x1445BDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936806== by 0x1435B3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936806== by 0x142D4E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==936806== by 0x13A93E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==936806== by 0xF2994CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==936806== by 0xB55F418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936806== by 0xB4F8D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936806== by 0xA1EFD38: PetscInitialize (pinit.c:924) ==936806== by 0x973758B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==936806== by 0x97375D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==936806== by 0x13526C: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==936806== by 0x12E38F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==936806== by 0x1310E8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==936806== by 0x130F88: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936806== by 0x13161F: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936806== by 0x12C6C0: main (TestMonodomainPurkinjeProblem.cpp:19) ==936806== Address 0x1ffeffdfcc is on thread 1's stack ==936806== in frame #2, created by pmix_ptl_base_make_connection (???:) ==936806== { 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 } ==936806== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==936806== at 0x9E60C7E: setsockopt_syscall (setsockopt.c:29) ==936806== by 0x9E60C7E: setsockopt (setsockopt.c:95) ==936806== by 0x14454BA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936806== by 0x1445BDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936806== by 0x1435B3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936806== by 0x142D4E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==936806== by 0x13A93E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==936806== by 0xF2994CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==936806== by 0xB55F418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936806== by 0xB4F8D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936806== by 0xA1EFD38: PetscInitialize (pinit.c:924) ==936806== by 0x973758B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==936806== by 0x97375D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==936806== by 0x13526C: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==936806== by 0x12E38F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==936806== by 0x1310E8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==936806== by 0x130F88: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936806== by 0x13161F: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936806== by 0x12C6C0: main (TestMonodomainPurkinjeProblem.cpp:19) ==936806== { 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 } ==936806== Syscall param pwrite64(buf) points to uninitialised byte(s) ==936806== at 0x9E4B9EF: __libc_pwrite64 (pwrite64.c:25) ==936806== by 0x9E4B9EF: pwrite (pwrite64.c:23) ==936806== by 0x17CCA9D2: mca_fbtl_posix_pwritev (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_fbtl_posix.so) ==936806== by 0x17CDA419: mca_common_ompio_file_write (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==936806== by 0x17CDA79A: mca_common_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==936806== by 0x17BC589A: mca_io_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_io_ompio.so) ==936806== by 0xB4EC6A7: PMPI_File_write_at (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936806== by 0xEC64FEB: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936806== by 0xEAA44ED: H5FD_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936806== by 0xEA87313: H5F__accum_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936806== by 0xEB82442: H5PB_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936806== by 0xEA8EDEA: H5F_block_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936806== by 0xEA18E98: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936806== by 0xEC583F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936806== by 0xEC599CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936806== by 0xEC5A47E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936806== by 0xE9F554C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936806== by 0xEA8D936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936806== by 0xEA8E3FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936806== by 0xEA91BB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936806== by 0xEA91EFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936806== by 0xEB0151F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936806== by 0xEB015EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936806== by 0xEA8E831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936806== by 0xEA83881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936806== by 0xBEF3967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==936806== by 0xBEEE647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==936806== by 0xBEEE6ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==936806== by 0x677F5E9: AbstractCardiacProblem<2u, 2u, 1u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==936806== by 0x677F189: AbstractCardiacProblem<2u, 2u, 1u>::Solve() (AbstractCardiacProblem.cpp:582) ==936806== by 0x137F66: TestMonodomainPurkinjeProblem::TestMonodomainPurkinjeProblemRunning() (TestMonodomainPurkinjeProblem.hpp:270) ==936806== by 0x141F76: TestDescription_TestMonodomainPurkinjeProblem_TestMonodomainPurkinjeProblemRunning::runTest() (TestMonodomainPurkinjeProblem.cpp:31) ==936806== by 0x12D98A: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==936806== by 0x131396: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==936806== by 0x13127B: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==936806== by 0x131121: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==936806== by 0x130F88: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936806== by 0x13161F: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936806== by 0x12C6C0: main (TestMonodomainPurkinjeProblem.cpp:19) ==936806== Address 0x16b489be is 62 bytes inside a block of size 320 alloc'd ==936806== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==936806== by 0xEA18E26: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936806== by 0xEC583F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936806== by 0xEC599CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936806== by 0xEC5A47E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936806== by 0xE9F554C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936806== by 0xEA8D936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936806== by 0xEA8E3FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936806== by 0xEA91BB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936806== by 0xEA91EFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936806== by 0xEB0151F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936806== by 0xEB015EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936806== by 0xEA8E831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936806== by 0xEA83881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936806== by 0xBEF3967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==936806== by 0xBEEE647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==936806== by 0xBEEE6ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==936806== by 0x677F5E9: AbstractCardiacProblem<2u, 2u, 1u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==936806== by 0x677F189: AbstractCardiacProblem<2u, 2u, 1u>::Solve() (AbstractCardiacProblem.cpp:582) ==936806== by 0x137F66: TestMonodomainPurkinjeProblem::TestMonodomainPurkinjeProblemRunning() (TestMonodomainPurkinjeProblem.hpp:270) ==936806== by 0x141F76: TestDescription_TestMonodomainPurkinjeProblem_TestMonodomainPurkinjeProblemRunning::runTest() (TestMonodomainPurkinjeProblem.cpp:31) ==936806== by 0x12D98A: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==936806== by 0x131396: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==936806== by 0x13127B: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==936806== by 0x131121: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==936806== by 0x130F88: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936806== by 0x13161F: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936806== by 0x12C6C0: main (TestMonodomainPurkinjeProblem.cpp:19) ==936806== { 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 } ==936806== ==936806== FILE DESCRIPTORS: 9 open (3 std) at exit. ==936806== Open file descriptor 12: ==936806== at 0x9E4E22D: pipe (pipe.c:29) ==936806== by 0x13A9407D: ??? ==936806== by 0xF2994CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==936806== by 0xB55F418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936806== by 0xB4F8D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936806== by 0xA1EFD38: PetscInitialize (pinit.c:924) ==936806== by 0x973758B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==936806== by 0x97375D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==936806== by 0x13526C: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==936806== by 0x12E38F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==936806== by 0x1310E8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==936806== by 0x130F88: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936806== by 0x13161F: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936806== by 0x12C6C0: main (TestMonodomainPurkinjeProblem.cpp:19) ==936806== ==936806== Open file descriptor 8: /dev/shm/open_mpi.0000 ==936806== at 0x9E52BCC: __open_nocancel (open64_nocancel.c:39) ==936806== by 0x9DD6C4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==936806== by 0x976F822: ??? ==936806== by 0x976F96F: ??? ==936806== by 0xF33E6DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==936806== by 0xF33E938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==936806== by 0xF2F4922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==936806== by 0xF2992DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==936806== by 0xB55F418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936806== by 0xB4F8D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936806== by 0xA1EFD38: PetscInitialize (pinit.c:924) ==936806== by 0x973758B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==936806== by 0x97375D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==936806== by 0x13526C: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==936806== by 0x12E38F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==936806== by 0x1310E8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==936806== by 0x130F88: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936806== by 0x13161F: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936806== by 0x12C6C0: main (TestMonodomainPurkinjeProblem.cpp:19) ==936806== ==936806== Open file descriptor 111: ==936806== ==936806== ==936806== Open file descriptor 108: ==936806== ==936806== ==936806== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestMonodomainPurkinjeProblem_valgrind.txt ==936806== ==936806== ==936806== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==936806== ==936806== ==936806== ==936806== HEAP SUMMARY: ==936806== in use at exit: 701,234 bytes in 9,387 blocks ==936806== total heap usage: 1,148,756 allocs, 1,139,369 frees, 2,594,165,025 bytes allocated ==936806== ==936806== 552 bytes in 1 blocks are definitely lost in loss record 43 of 66 ==936806== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==936806== by 0x14362C13: ??? ==936806== by 0x1436322C: ??? ==936806== by 0x142D64B7: ??? ==936806== by 0xB4C515A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936806== by 0xB55FA97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936806== by 0xB4F8D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936806== by 0xA1EFD38: PetscInitialize (pinit.c:924) ==936806== by 0x973758B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==936806== by 0x97375D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==936806== by 0x13526C: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==936806== by 0x12E38F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==936806== by 0x1310E8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==936806== by 0x130F88: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936806== by 0x13161F: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936806== by 0x12C6C0: main (TestMonodomainPurkinjeProblem.cpp:19) ==936806== { 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 } ==936806== 685,269 (136 direct, 685,133 indirect) bytes in 1 blocks are definitely lost in loss record 66 of 66 ==936806== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==936806== by 0x154D574E: ??? ==936806== by 0x154D5E0B: ??? ==936806== by 0x154D8F56: ??? ==936806== by 0x154CE65D: ??? ==936806== by 0x154CEFA3: ??? ==936806== by 0xF3AAF05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==936806== by 0xF386AE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==936806== by 0xF337CB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==936806== by 0xF264EF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==936806== by 0x13A94F03: ??? ==936806== by 0xF2994CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==936806== by 0xB55F418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936806== by 0xB4F8D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936806== by 0xA1EFD38: PetscInitialize (pinit.c:924) ==936806== by 0x973758B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==936806== by 0x97375D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==936806== by 0x13526C: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==936806== by 0x12E38F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==936806== by 0x1310E8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==936806== by 0x130F88: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936806== by 0x13161F: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936806== by 0x12C6C0: main (TestMonodomainPurkinjeProblem.cpp:19) ==936806== { 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 } ==936806== LEAK SUMMARY: ==936806== definitely lost: 688 bytes in 2 blocks ==936806== indirectly lost: 1,760 bytes in 16 blocks ==936806== possibly lost: 0 bytes in 0 blocks ==936806== still reachable: 1,531 bytes in 6 blocks ==936806== suppressed: 697,255 bytes in 9,363 blocks ==936806== Reachable blocks (those to which a pointer was found) are not shown. ==936806== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==936806== ==936806== Use --track-origins=yes to see where uninitialised values come from ==936806== For lists of detected and suppressed errors, rerun with: -s ==936806== ERROR SUMMARY: 38 errors from 6 contexts (suppressed: 29 from 29)