==2814226== Memcheck, a memory error detector ==2814226== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==2814226== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==2814226== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/heart/test/TestBidomainDistributedMesh -malloc_debug -malloc_dump -memory_info ==2814226== Parent PID: 2793356 ==2814226== ==2814226== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==2814226== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==2814226== ==2814226== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==2814226== at 0xB96779E: getsockopt_syscall (getsockopt.c:29) ==2814226== by 0xB96779E: getsockopt (getsockopt.c:94) ==2814226== by 0x14AA3157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2814226== by 0x14AAAA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2814226== by 0x14AB1DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2814226== by 0x149B13C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2814226== by 0x1492AE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==2814226== by 0x140E9E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==2814226== by 0xF89E4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2814226== by 0xB245418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2814226== by 0xB1DED7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2814226== by 0x9EB5D38: PetscInitialize (pinit.c:924) ==2814226== by 0x9D8958B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2814226== by 0x9D895D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2814226== by 0x1340C8: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2814226== by 0x12D7BD: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2814226== by 0x12FF16: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2814226== by 0x12FE12: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2814226== by 0x130425: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2814226== by 0x12BFC0: main (TestBidomainDistributedMesh.cpp:18) ==2814226== Address 0x1ffeffdfac is on thread 1's stack ==2814226== in frame #2, created by pmix_ptl_base_make_connection (???:) ==2814226== { 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 } ==2814226== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==2814226== at 0xB96779E: getsockopt_syscall (getsockopt.c:29) ==2814226== by 0xB96779E: getsockopt (getsockopt.c:94) ==2814226== by 0x14AA3157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2814226== by 0x14AAAA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2814226== by 0x14AB1DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2814226== by 0x149B13C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2814226== by 0x1492AE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==2814226== by 0x140E9E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==2814226== by 0xF89E4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2814226== by 0xB245418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2814226== by 0xB1DED7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2814226== by 0x9EB5D38: PetscInitialize (pinit.c:924) ==2814226== by 0x9D8958B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2814226== by 0x9D895D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2814226== by 0x1340C8: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2814226== by 0x12D7BD: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2814226== by 0x12FF16: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2814226== by 0x12FE12: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2814226== by 0x130425: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2814226== by 0x12BFC0: main (TestBidomainDistributedMesh.cpp:18) ==2814226== Address 0x1ffeffdfac is on thread 1's stack ==2814226== in frame #2, created by pmix_ptl_base_make_connection (???:) ==2814226== { 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 } ==2814226== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==2814226== at 0xB967C7E: setsockopt_syscall (setsockopt.c:29) ==2814226== by 0xB967C7E: setsockopt (setsockopt.c:95) ==2814226== by 0x14AAABA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2814226== by 0x14AB1DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2814226== by 0x149B13C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2814226== by 0x1492AE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==2814226== by 0x140E9E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==2814226== by 0xF89E4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2814226== by 0xB245418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2814226== by 0xB1DED7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2814226== by 0x9EB5D38: PetscInitialize (pinit.c:924) ==2814226== by 0x9D8958B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2814226== by 0x9D895D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2814226== by 0x1340C8: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2814226== by 0x12D7BD: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2814226== by 0x12FF16: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2814226== by 0x12FE12: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2814226== by 0x130425: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2814226== by 0x12BFC0: main (TestBidomainDistributedMesh.cpp:18) ==2814226== { 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 } ==2814226== Syscall param pwrite64(buf) points to uninitialised byte(s) ==2814226== at 0xB9529EF: __libc_pwrite64 (pwrite64.c:25) ==2814226== by 0xB9529EF: pwrite (pwrite64.c:23) ==2814226== by 0x183209D2: mca_fbtl_posix_pwritev (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_fbtl_posix.so) ==2814226== by 0x18330419: mca_common_ompio_file_write (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==2814226== by 0x1833079A: mca_common_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==2814226== by 0x1821B89A: mca_io_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_io_ompio.so) ==2814226== by 0xB1D26A7: PMPI_File_write_at (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2814226== by 0xF267FEB: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2814226== by 0xF0A74ED: H5FD_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2814226== by 0xF08A313: H5F__accum_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2814226== by 0xF185442: H5PB_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2814226== by 0xF091DEA: H5F_block_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2814226== by 0xF01BE98: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2814226== by 0xF25B3F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2814226== by 0xF25C9CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2814226== by 0xF25D47E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2814226== by 0xEFF854C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2814226== by 0xF090936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2814226== by 0xF0913FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2814226== by 0xF094BB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2814226== by 0xF094EFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2814226== by 0xF10451F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2814226== by 0xF1045EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2814226== by 0xF091831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2814226== by 0xF086881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2814226== by 0xC545967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==2814226== by 0xC540647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==2814226== by 0xC5406ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==2814226== by 0x687A51B: AbstractCardiacProblem<2u, 2u, 2u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==2814226== by 0x687A0BB: AbstractCardiacProblem<2u, 2u, 2u>::Solve() (AbstractCardiacProblem.cpp:582) ==2814226== by 0x134378: TestBidomainDistributedMesh::TestBidomainProblemWithDistributedMesh2D() (TestBidomainDistributedMesh.hpp:83) ==2814226== by 0x13641C: TestDescription_TestBidomainDistributedMesh_TestBidomainProblemWithDistributedMesh2D::runTest() (TestBidomainDistributedMesh.cpp:30) ==2814226== by 0x12CFF4: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==2814226== by 0x1301C4: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==2814226== by 0x1300A9: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==2814226== by 0x12FF4F: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==2814226== by 0x12FE12: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2814226== by 0x130425: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2814226== by 0x12BFC0: main (TestBidomainDistributedMesh.cpp:18) ==2814226== Address 0x16570a8e is 62 bytes inside a block of size 320 alloc'd ==2814226== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==2814226== by 0xF01BE26: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2814226== by 0xF25B3F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2814226== by 0xF25C9CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2814226== by 0xF25D47E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2814226== by 0xEFF854C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2814226== by 0xF090936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2814226== by 0xF0913FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2814226== by 0xF094BB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2814226== by 0xF094EFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2814226== by 0xF10451F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2814226== by 0xF1045EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2814226== by 0xF091831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2814226== by 0xF086881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2814226== by 0xC545967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==2814226== by 0xC540647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==2814226== by 0xC5406ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==2814226== by 0x687A51B: AbstractCardiacProblem<2u, 2u, 2u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==2814226== by 0x687A0BB: AbstractCardiacProblem<2u, 2u, 2u>::Solve() (AbstractCardiacProblem.cpp:582) ==2814226== by 0x134378: TestBidomainDistributedMesh::TestBidomainProblemWithDistributedMesh2D() (TestBidomainDistributedMesh.hpp:83) ==2814226== by 0x13641C: TestDescription_TestBidomainDistributedMesh_TestBidomainProblemWithDistributedMesh2D::runTest() (TestBidomainDistributedMesh.cpp:30) ==2814226== by 0x12CFF4: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==2814226== by 0x1301C4: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==2814226== by 0x1300A9: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==2814226== by 0x12FF4F: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==2814226== by 0x12FE12: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2814226== by 0x130425: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2814226== by 0x12BFC0: main (TestBidomainDistributedMesh.cpp:18) ==2814226== { 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:_ZN22AbstractCardiacProblemILj2ELj2ELj2EE24CloseFilesAndPostProcessEv fun:_ZN22AbstractCardiacProblemILj2ELj2ELj2EE5SolveEv fun:_ZN27TestBidomainDistributedMesh40TestBidomainProblemWithDistributedMesh2DEv fun:_ZN84TestDescription_TestBidomainDistributedMesh_TestBidomainProblemWithDistributedMesh2D7runTestEv fun:_ZN7CxxTest19RealTestDescription3runEv fun:_ZN7CxxTest10TestRunner7runTestERNS_15TestDescriptionE fun:_ZN7CxxTest10TestRunner8runSuiteERNS_16SuiteDescriptionE fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==2814226== ==2814226== FILE DESCRIPTORS: 9 open (3 std) at exit. ==2814226== Open file descriptor 12: ==2814226== at 0xB95522D: pipe (pipe.c:29) ==2814226== by 0x140EA07D: ??? ==2814226== by 0xF89E4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2814226== by 0xB245418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2814226== by 0xB1DED7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2814226== by 0x9EB5D38: PetscInitialize (pinit.c:924) ==2814226== by 0x9D8958B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2814226== by 0x9D895D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2814226== by 0x1340C8: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2814226== by 0x12D7BD: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2814226== by 0x12FF16: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2814226== by 0x12FE12: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2814226== by 0x130425: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2814226== by 0x12BFC0: main (TestBidomainDistributedMesh.cpp:18) ==2814226== ==2814226== Open file descriptor 8: /dev/shm/open_mpi.0000 ==2814226== at 0xB959BCC: __open_nocancel (open64_nocancel.c:39) ==2814226== by 0xB8DDC4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==2814226== by 0xB13F822: ??? ==2814226== by 0xB13F96F: ??? ==2814226== by 0xF9436DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2814226== by 0xF943938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2814226== by 0xF8F9922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2814226== by 0xF89E2DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2814226== by 0xB245418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2814226== by 0xB1DED7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2814226== by 0x9EB5D38: PetscInitialize (pinit.c:924) ==2814226== by 0x9D8958B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2814226== by 0x9D895D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2814226== by 0x1340C8: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2814226== by 0x12D7BD: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2814226== by 0x12FF16: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2814226== by 0x12FE12: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2814226== by 0x130425: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2814226== by 0x12BFC0: main (TestBidomainDistributedMesh.cpp:18) ==2814226== ==2814226== Open file descriptor 117: ==2814226== ==2814226== ==2814226== Open file descriptor 110: ==2814226== ==2814226== ==2814226== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestBidomainDistributedMesh_valgrind.txt ==2814226== ==2814226== ==2814226== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==2814226== ==2814226== ==2814226== ==2814226== HEAP SUMMARY: ==2814226== in use at exit: 701,239 bytes in 9,387 blocks ==2814226== total heap usage: 430,120 allocs, 420,733 frees, 1,452,393,818 bytes allocated ==2814226== ==2814226== 552 bytes in 1 blocks are definitely lost in loss record 43 of 69 ==2814226== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==2814226== by 0x149B8C13: ??? ==2814226== by 0x149B922C: ??? ==2814226== by 0x1492C4B7: ??? ==2814226== by 0xB1AB15A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2814226== by 0xB245A97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2814226== by 0xB1DED7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2814226== by 0x9EB5D38: PetscInitialize (pinit.c:924) ==2814226== by 0x9D8958B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2814226== by 0x9D895D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2814226== by 0x1340C8: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2814226== by 0x12D7BD: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2814226== by 0x12FF16: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2814226== by 0x12FE12: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2814226== by 0x130425: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2814226== by 0x12BFC0: main (TestBidomainDistributedMesh.cpp:18) ==2814226== { 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 } ==2814226== 84,459 (136 direct, 84,323 indirect) bytes in 1 blocks are definitely lost in loss record 66 of 69 ==2814226== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==2814226== by 0x15B2B74E: ??? ==2814226== by 0x15B2BE0B: ??? ==2814226== by 0x15B2EF56: ??? ==2814226== by 0x15B2465D: ??? ==2814226== by 0x15B24FA3: ??? ==2814226== by 0xF9AFF05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==2814226== by 0xF98BAE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==2814226== by 0xF93CCB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2814226== by 0xF869EF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2814226== by 0x140EAF03: ??? ==2814226== by 0xF89E4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2814226== by 0xB245418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2814226== by 0xB1DED7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2814226== by 0x9EB5D38: PetscInitialize (pinit.c:924) ==2814226== by 0x9D8958B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2814226== by 0x9D895D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2814226== by 0x1340C8: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2814226== by 0x12D7BD: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2814226== by 0x12FF16: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2814226== by 0x12FE12: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2814226== by 0x130425: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2814226== by 0x12BFC0: main (TestBidomainDistributedMesh.cpp:18) ==2814226== { 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 } ==2814226== LEAK SUMMARY: ==2814226== definitely lost: 688 bytes in 2 blocks ==2814226== indirectly lost: 1,760 bytes in 16 blocks ==2814226== possibly lost: 0 bytes in 0 blocks ==2814226== still reachable: 1,531 bytes in 6 blocks ==2814226== suppressed: 697,260 bytes in 9,363 blocks ==2814226== Reachable blocks (those to which a pointer was found) are not shown. ==2814226== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==2814226== ==2814226== Use --track-origins=yes to see where uninitialised values come from ==2814226== For lists of detected and suppressed errors, rerun with: -s ==2814226== ERROR SUMMARY: 23 errors from 6 contexts (suppressed: 32 from 32)