==1977283== Memcheck, a memory error detector ==1977283== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==1977283== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==1977283== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/heart/test/TestBidomainDistributedMesh -malloc_debug -malloc_dump -memory_info ==1977283== Parent PID: 1956552 ==1977283== ==1977283== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==1977283== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==1977283== ==1977283== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==1977283== at 0xB54179E: getsockopt_syscall (getsockopt.c:29) ==1977283== by 0xB54179E: getsockopt (getsockopt.c:94) ==1977283== by 0x1467C157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1977283== by 0x14683A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1977283== by 0x1468ADF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1977283== by 0x1458A3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1977283== by 0x14503E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==1977283== by 0x13CC2E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==1977283== by 0xF4774CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1977283== by 0xAE1F418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1977283== by 0xADB8D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1977283== by 0x9A8FD38: PetscInitialize (pinit.c:924) ==1977283== by 0x996358B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1977283== by 0x99635D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1977283== by 0x1340C8: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1977283== by 0x12D7BD: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1977283== by 0x12FF16: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1977283== by 0x12FE12: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1977283== by 0x130425: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1977283== by 0x12BFC0: main (TestBidomainDistributedMesh.cpp:18) ==1977283== Address 0x1ffeffdfac is on thread 1's stack ==1977283== in frame #2, created by pmix_ptl_base_make_connection (???:) ==1977283== { 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 } ==1977283== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==1977283== at 0xB54179E: getsockopt_syscall (getsockopt.c:29) ==1977283== by 0xB54179E: getsockopt (getsockopt.c:94) ==1977283== by 0x1467C157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1977283== by 0x14683A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1977283== by 0x1468ADF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1977283== by 0x1458A3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1977283== by 0x14503E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==1977283== by 0x13CC2E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==1977283== by 0xF4774CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1977283== by 0xAE1F418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1977283== by 0xADB8D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1977283== by 0x9A8FD38: PetscInitialize (pinit.c:924) ==1977283== by 0x996358B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1977283== by 0x99635D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1977283== by 0x1340C8: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1977283== by 0x12D7BD: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1977283== by 0x12FF16: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1977283== by 0x12FE12: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1977283== by 0x130425: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1977283== by 0x12BFC0: main (TestBidomainDistributedMesh.cpp:18) ==1977283== Address 0x1ffeffdfac is on thread 1's stack ==1977283== in frame #2, created by pmix_ptl_base_make_connection (???:) ==1977283== { 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 } ==1977283== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==1977283== at 0xB541C7E: setsockopt_syscall (setsockopt.c:29) ==1977283== by 0xB541C7E: setsockopt (setsockopt.c:95) ==1977283== by 0x14683BA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1977283== by 0x1468ADF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1977283== by 0x1458A3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1977283== by 0x14503E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==1977283== by 0x13CC2E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==1977283== by 0xF4774CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1977283== by 0xAE1F418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1977283== by 0xADB8D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1977283== by 0x9A8FD38: PetscInitialize (pinit.c:924) ==1977283== by 0x996358B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1977283== by 0x99635D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1977283== by 0x1340C8: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1977283== by 0x12D7BD: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1977283== by 0x12FF16: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1977283== by 0x12FE12: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1977283== by 0x130425: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1977283== by 0x12BFC0: main (TestBidomainDistributedMesh.cpp:18) ==1977283== { 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 } ==1977283== Syscall param pwrite64(buf) points to uninitialised byte(s) ==1977283== at 0xB52C9EF: __libc_pwrite64 (pwrite64.c:25) ==1977283== by 0xB52C9EF: pwrite (pwrite64.c:23) ==1977283== by 0x16EF99D2: mca_fbtl_posix_pwritev (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_fbtl_posix.so) ==1977283== by 0x16F09419: mca_common_ompio_file_write (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==1977283== by 0x16F0979A: mca_common_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==1977283== by 0x16DF489A: mca_io_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_io_ompio.so) ==1977283== by 0xADAC6A7: PMPI_File_write_at (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1977283== by 0xEE40FEB: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977283== by 0xEC804ED: H5FD_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977283== by 0xEC63313: H5F__accum_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977283== by 0xED5E442: H5PB_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977283== by 0xEC6ADEA: H5F_block_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977283== by 0xEBF4E98: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977283== by 0xEE343F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977283== by 0xEE359CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977283== by 0xEE3647E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977283== by 0xEBD154C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977283== by 0xEC69936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977283== by 0xEC6A3FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977283== by 0xEC6DBB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977283== by 0xEC6DEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977283== by 0xECDD51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977283== by 0xECDD5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977283== by 0xEC6A831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977283== by 0xEC5F881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977283== by 0xC11F967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==1977283== by 0xC11A647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==1977283== by 0xC11A6ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==1977283== by 0x687A4F7: AbstractCardiacProblem<2u, 2u, 2u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==1977283== by 0x687A097: AbstractCardiacProblem<2u, 2u, 2u>::Solve() (AbstractCardiacProblem.cpp:582) ==1977283== by 0x134378: TestBidomainDistributedMesh::TestBidomainProblemWithDistributedMesh2D() (TestBidomainDistributedMesh.hpp:83) ==1977283== by 0x13641C: TestDescription_TestBidomainDistributedMesh_TestBidomainProblemWithDistributedMesh2D::runTest() (TestBidomainDistributedMesh.cpp:30) ==1977283== by 0x12CFF4: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==1977283== by 0x1301C4: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==1977283== by 0x1300A9: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==1977283== by 0x12FF4F: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==1977283== by 0x12FE12: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1977283== by 0x130425: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1977283== by 0x12BFC0: main (TestBidomainDistributedMesh.cpp:18) ==1977283== Address 0x16c0cd0e is 62 bytes inside a block of size 320 alloc'd ==1977283== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==1977283== by 0xEBF4E26: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977283== by 0xEE343F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977283== by 0xEE359CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977283== by 0xEE3647E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977283== by 0xEBD154C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977283== by 0xEC69936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977283== by 0xEC6A3FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977283== by 0xEC6DBB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977283== by 0xEC6DEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977283== by 0xECDD51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977283== by 0xECDD5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977283== by 0xEC6A831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977283== by 0xEC5F881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977283== by 0xC11F967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==1977283== by 0xC11A647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==1977283== by 0xC11A6ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==1977283== by 0x687A4F7: AbstractCardiacProblem<2u, 2u, 2u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==1977283== by 0x687A097: AbstractCardiacProblem<2u, 2u, 2u>::Solve() (AbstractCardiacProblem.cpp:582) ==1977283== by 0x134378: TestBidomainDistributedMesh::TestBidomainProblemWithDistributedMesh2D() (TestBidomainDistributedMesh.hpp:83) ==1977283== by 0x13641C: TestDescription_TestBidomainDistributedMesh_TestBidomainProblemWithDistributedMesh2D::runTest() (TestBidomainDistributedMesh.cpp:30) ==1977283== by 0x12CFF4: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==1977283== by 0x1301C4: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==1977283== by 0x1300A9: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==1977283== by 0x12FF4F: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==1977283== by 0x12FE12: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1977283== by 0x130425: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1977283== by 0x12BFC0: main (TestBidomainDistributedMesh.cpp:18) ==1977283== { 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 } ==1977283== ==1977283== FILE DESCRIPTORS: 9 open (3 std) at exit. ==1977283== Open file descriptor 12: ==1977283== at 0xB52F22D: pipe (pipe.c:29) ==1977283== by 0x13CC307D: ??? ==1977283== by 0xF4774CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1977283== by 0xAE1F418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1977283== by 0xADB8D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1977283== by 0x9A8FD38: PetscInitialize (pinit.c:924) ==1977283== by 0x996358B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1977283== by 0x99635D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1977283== by 0x1340C8: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1977283== by 0x12D7BD: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1977283== by 0x12FF16: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1977283== by 0x12FE12: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1977283== by 0x130425: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1977283== by 0x12BFC0: main (TestBidomainDistributedMesh.cpp:18) ==1977283== ==1977283== Open file descriptor 8: /dev/shm/open_mpi.0000 ==1977283== at 0xB533BCC: __open_nocancel (open64_nocancel.c:39) ==1977283== by 0xB4B7C4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==1977283== by 0xAD19822: ??? ==1977283== by 0xAD1996F: ??? ==1977283== by 0xF51C6DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==1977283== by 0xF51C938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==1977283== by 0xF4D2922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==1977283== by 0xF4772DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1977283== by 0xAE1F418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1977283== by 0xADB8D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1977283== by 0x9A8FD38: PetscInitialize (pinit.c:924) ==1977283== by 0x996358B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1977283== by 0x99635D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1977283== by 0x1340C8: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1977283== by 0x12D7BD: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1977283== by 0x12FF16: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1977283== by 0x12FE12: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1977283== by 0x130425: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1977283== by 0x12BFC0: main (TestBidomainDistributedMesh.cpp:18) ==1977283== ==1977283== Open file descriptor 117: ==1977283== ==1977283== ==1977283== Open file descriptor 110: ==1977283== ==1977283== ==1977283== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestBidomainDistributedMesh_valgrind.txt ==1977283== ==1977283== ==1977283== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==1977283== ==1977283== ==1977283== ==1977283== HEAP SUMMARY: ==1977283== in use at exit: 701,239 bytes in 9,387 blocks ==1977283== total heap usage: 430,032 allocs, 420,645 frees, 1,452,278,377 bytes allocated ==1977283== ==1977283== 552 bytes in 1 blocks are definitely lost in loss record 43 of 69 ==1977283== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==1977283== by 0x14591C13: ??? ==1977283== by 0x1459222C: ??? ==1977283== by 0x145054B7: ??? ==1977283== by 0xAD8515A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1977283== by 0xAE1FA97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1977283== by 0xADB8D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1977283== by 0x9A8FD38: PetscInitialize (pinit.c:924) ==1977283== by 0x996358B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1977283== by 0x99635D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1977283== by 0x1340C8: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1977283== by 0x12D7BD: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1977283== by 0x12FF16: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1977283== by 0x12FE12: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1977283== by 0x130425: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1977283== by 0x12BFC0: main (TestBidomainDistributedMesh.cpp:18) ==1977283== { 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 } ==1977283== 84,459 (136 direct, 84,323 indirect) bytes in 1 blocks are definitely lost in loss record 66 of 69 ==1977283== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==1977283== by 0x1570474E: ??? ==1977283== by 0x15704E0B: ??? ==1977283== by 0x15707F56: ??? ==1977283== by 0x156FD65D: ??? ==1977283== by 0x156FDFA3: ??? ==1977283== by 0xF588F05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==1977283== by 0xF564AE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==1977283== by 0xF515CB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==1977283== by 0xF442EF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1977283== by 0x13CC3F03: ??? ==1977283== by 0xF4774CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1977283== by 0xAE1F418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1977283== by 0xADB8D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1977283== by 0x9A8FD38: PetscInitialize (pinit.c:924) ==1977283== by 0x996358B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1977283== by 0x99635D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1977283== by 0x1340C8: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1977283== by 0x12D7BD: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1977283== by 0x12FF16: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1977283== by 0x12FE12: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1977283== by 0x130425: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1977283== by 0x12BFC0: main (TestBidomainDistributedMesh.cpp:18) ==1977283== { 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 } ==1977283== LEAK SUMMARY: ==1977283== definitely lost: 688 bytes in 2 blocks ==1977283== indirectly lost: 1,760 bytes in 16 blocks ==1977283== possibly lost: 0 bytes in 0 blocks ==1977283== still reachable: 1,531 bytes in 6 blocks ==1977283== suppressed: 697,260 bytes in 9,363 blocks ==1977283== Reachable blocks (those to which a pointer was found) are not shown. ==1977283== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==1977283== ==1977283== Use --track-origins=yes to see where uninitialised values come from ==1977283== For lists of detected and suppressed errors, rerun with: -s ==1977283== ERROR SUMMARY: 23 errors from 6 contexts (suppressed: 32 from 32)