==2305995== Memcheck, a memory error detector ==2305995== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==2305995== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==2305995== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/heart/test/TestCardiacElectroMechanicsProblem -malloc_debug -malloc_dump -memory_info ==2305995== Parent PID: 2283975 ==2305995== ==2305995== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==2305995== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==2305995== ==2305995== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==2305995== at 0xA56C79E: getsockopt_syscall (getsockopt.c:29) ==2305995== by 0xA56C79E: getsockopt (getsockopt.c:94) ==2305995== by 0x1467E157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2305995== by 0x14685A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2305995== by 0x1468CDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2305995== by 0x1458C3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2305995== by 0x14505E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==2305995== by 0x13CC4E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==2305995== by 0xD2D34CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2305995== by 0x9D63418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2305995== by 0x9CFCD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2305995== by 0xA762D38: PetscInitialize (pinit.c:924) ==2305995== by 0x9C2366F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2305995== by 0x9C236BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2305995== by 0x13DC96: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2305995== by 0x13542F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2305995== by 0x1389B2: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2305995== by 0x138852: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2305995== by 0x138EE9: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2305995== by 0x133760: main (TestCardiacElectroMechanicsProblem.cpp:19) ==2305995== Address 0x1ffeffdf8c is on thread 1's stack ==2305995== in frame #2, created by pmix_ptl_base_make_connection (???:) ==2305995== { 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 } ==2305995== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==2305995== at 0xA56C79E: getsockopt_syscall (getsockopt.c:29) ==2305995== by 0xA56C79E: getsockopt (getsockopt.c:94) ==2305995== by 0x1467E157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2305995== by 0x14685A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2305995== by 0x1468CDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2305995== by 0x1458C3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2305995== by 0x14505E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==2305995== by 0x13CC4E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==2305995== by 0xD2D34CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2305995== by 0x9D63418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2305995== by 0x9CFCD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2305995== by 0xA762D38: PetscInitialize (pinit.c:924) ==2305995== by 0x9C2366F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2305995== by 0x9C236BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2305995== by 0x13DC96: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2305995== by 0x13542F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2305995== by 0x1389B2: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2305995== by 0x138852: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2305995== by 0x138EE9: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2305995== by 0x133760: main (TestCardiacElectroMechanicsProblem.cpp:19) ==2305995== Address 0x1ffeffdf8c is on thread 1's stack ==2305995== in frame #2, created by pmix_ptl_base_make_connection (???:) ==2305995== { 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 } ==2305995== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==2305995== at 0xA56CC7E: setsockopt_syscall (setsockopt.c:29) ==2305995== by 0xA56CC7E: setsockopt (setsockopt.c:95) ==2305995== by 0x14685BA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2305995== by 0x1468CDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2305995== by 0x1458C3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2305995== by 0x14505E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==2305995== by 0x13CC4E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==2305995== by 0xD2D34CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2305995== by 0x9D63418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2305995== by 0x9CFCD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2305995== by 0xA762D38: PetscInitialize (pinit.c:924) ==2305995== by 0x9C2366F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2305995== by 0x9C236BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2305995== by 0x13DC96: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2305995== by 0x13542F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2305995== by 0x1389B2: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2305995== by 0x138852: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2305995== by 0x138EE9: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2305995== by 0x133760: main (TestCardiacElectroMechanicsProblem.cpp:19) ==2305995== { 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 } ==2305995== Syscall param pwrite64(buf) points to uninitialised byte(s) ==2305995== at 0xA5579EF: __libc_pwrite64 (pwrite64.c:25) ==2305995== by 0xA5579EF: pwrite (pwrite64.c:23) ==2305995== by 0x176FB9D2: mca_fbtl_posix_pwritev (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_fbtl_posix.so) ==2305995== by 0x1770B419: mca_common_ompio_file_write (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==2305995== by 0x1770B79A: mca_common_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==2305995== by 0x175F689A: mca_io_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_io_ompio.so) ==2305995== by 0x9CF06A7: PMPI_File_write_at (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2305995== by 0xD152FEB: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2305995== by 0xCF924ED: H5FD_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2305995== by 0xCF75313: H5F__accum_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2305995== by 0xD070442: H5PB_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2305995== by 0xCF7CDEA: H5F_block_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2305995== by 0xCF06E98: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2305995== by 0xD1463F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2305995== by 0xD1479CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2305995== by 0xD14847E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2305995== by 0xCEE354C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2305995== by 0xCF7B936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2305995== by 0xCF7C3FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2305995== by 0xCF7FBB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2305995== by 0xCF7FEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2305995== by 0xCFEF51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2305995== by 0xCFEF5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2305995== by 0xCF7C831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2305995== by 0xCF71881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2305995== by 0x9B51855: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==2305995== by 0x699A19D: CardiacElectroMechanicsProblem<2u, 1u>::Solve() (CardiacElectroMechanicsProblem.cpp:889) ==2305995== by 0x13EDEB: TestCardiacElectroMechanicsProblem::TestWithHomogeneousEverythingCompressible() (TestCardiacElectroMechanicsProblem.hpp:185) ==2305995== by 0x147F56: TestDescription_TestCardiacElectroMechanicsProblem_TestWithHomogeneousEverythingCompressible::runTest() (TestCardiacElectroMechanicsProblem.cpp:37) ==2305995== by 0x134A2A: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==2305995== by 0x138C60: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==2305995== by 0x138B45: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==2305995== by 0x1389EB: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==2305995== by 0x138852: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2305995== by 0x138EE9: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2305995== by 0x133760: main (TestCardiacElectroMechanicsProblem.cpp:19) ==2305995== Address 0x13a684be is 62 bytes inside a block of size 320 alloc'd ==2305995== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==2305995== by 0xCF06E26: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2305995== by 0xD1463F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2305995== by 0xD1479CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2305995== by 0xD14847E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2305995== by 0xCEE354C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2305995== by 0xCF7B936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2305995== by 0xCF7C3FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2305995== by 0xCF7FBB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2305995== by 0xCF7FEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2305995== by 0xCFEF51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2305995== by 0xCFEF5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2305995== by 0xCF7C831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2305995== by 0xCF71881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2305995== by 0x9B51855: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==2305995== by 0x699A19D: CardiacElectroMechanicsProblem<2u, 1u>::Solve() (CardiacElectroMechanicsProblem.cpp:889) ==2305995== by 0x13EDEB: TestCardiacElectroMechanicsProblem::TestWithHomogeneousEverythingCompressible() (TestCardiacElectroMechanicsProblem.hpp:185) ==2305995== by 0x147F56: TestDescription_TestCardiacElectroMechanicsProblem_TestWithHomogeneousEverythingCompressible::runTest() (TestCardiacElectroMechanicsProblem.cpp:37) ==2305995== by 0x134A2A: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==2305995== by 0x138C60: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==2305995== by 0x138B45: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==2305995== by 0x1389EB: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==2305995== by 0x138852: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2305995== by 0x138EE9: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2305995== by 0x133760: main (TestCardiacElectroMechanicsProblem.cpp:19) ==2305995== { 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:_ZN30CardiacElectroMechanicsProblemILj2ELj1EE5SolveEv fun:_ZN34TestCardiacElectroMechanicsProblem41TestWithHomogeneousEverythingCompressibleEv fun:_ZN92TestDescription_TestCardiacElectroMechanicsProblem_TestWithHomogeneousEverythingCompressible7runTestEv fun:_ZN7CxxTest19RealTestDescription3runEv fun:_ZN7CxxTest10TestRunner7runTestERNS_15TestDescriptionE fun:_ZN7CxxTest10TestRunner8runSuiteERNS_16SuiteDescriptionE fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==2305995== ==2305995== FILE DESCRIPTORS: 9 open (3 std) at exit. ==2305995== Open file descriptor 12: ==2305995== at 0xA55A22D: pipe (pipe.c:29) ==2305995== by 0x13CC507D: ??? ==2305995== by 0xD2D34CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2305995== by 0x9D63418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2305995== by 0x9CFCD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2305995== by 0xA762D38: PetscInitialize (pinit.c:924) ==2305995== by 0x9C2366F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2305995== by 0x9C236BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2305995== by 0x13DC96: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2305995== by 0x13542F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2305995== by 0x1389B2: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2305995== by 0x138852: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2305995== by 0x138EE9: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2305995== by 0x133760: main (TestCardiacElectroMechanicsProblem.cpp:19) ==2305995== ==2305995== Open file descriptor 8: /dev/shm/open_mpi.0000 ==2305995== at 0xA55EBCC: __open_nocancel (open64_nocancel.c:39) ==2305995== by 0xA4E2C4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==2305995== by 0x9C5B822: ??? ==2305995== by 0x9C5B96F: ??? ==2305995== by 0xD3786DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2305995== by 0xD378938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2305995== by 0xD32E922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2305995== by 0xD2D32DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2305995== by 0x9D63418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2305995== by 0x9CFCD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2305995== by 0xA762D38: PetscInitialize (pinit.c:924) ==2305995== by 0x9C2366F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2305995== by 0x9C236BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2305995== by 0x13DC96: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2305995== by 0x13542F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2305995== by 0x1389B2: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2305995== by 0x138852: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2305995== by 0x138EE9: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2305995== by 0x133760: main (TestCardiacElectroMechanicsProblem.cpp:19) ==2305995== ==2305995== Open file descriptor 117: ==2305995== ==2305995== ==2305995== Open file descriptor 110: ==2305995== ==2305995== ==2305995== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestCardiacElectroMechanicsProblem_valgrind.txt ==2305995== ==2305995== ==2305995== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==2305995== ==2305995== ==2305995== ==2305995== HEAP SUMMARY: ==2305995== in use at exit: 701,239 bytes in 9,387 blocks ==2305995== total heap usage: 571,771 allocs, 562,384 frees, 1,495,948,364 bytes allocated ==2305995== ==2305995== 32 bytes in 1 blocks are possibly lost in loss record 16 of 72 ==2305995== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==2305995== by 0x1570671E: ??? ==2305995== by 0x15706E0B: ??? ==2305995== by 0x15709F56: ??? ==2305995== by 0x156FF65D: ??? ==2305995== by 0x156FFFA3: ??? ==2305995== by 0xD3E4F05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==2305995== by 0xD3C0AE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==2305995== by 0xD371CB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2305995== by 0xD29EEF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2305995== by 0x13CC5F03: ??? ==2305995== by 0xD2D34CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2305995== by 0x9D63418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2305995== by 0x9CFCD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2305995== by 0xA762D38: PetscInitialize (pinit.c:924) ==2305995== by 0x9C2366F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2305995== by 0x9C236BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2305995== by 0x13DC96: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2305995== by 0x13542F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2305995== by 0x1389B2: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2305995== by 0x138852: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2305995== by 0x138EE9: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2305995== by 0x133760: main (TestCardiacElectroMechanicsProblem.cpp:19) ==2305995== { Memcheck:Leak match-leak-kinds: possible 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 } ==2305995== 272 bytes in 2 blocks are possibly lost in loss record 43 of 72 ==2305995== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==2305995== by 0x157066E8: ??? ==2305995== by 0x15706E0B: ??? ==2305995== by 0x15709F56: ??? ==2305995== by 0x156FF65D: ??? ==2305995== by 0x156FFFA3: ??? ==2305995== by 0xD3E4F05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==2305995== by 0xD3C0AE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==2305995== by 0xD371CB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2305995== by 0xD29EEF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2305995== by 0x13CC5F03: ??? ==2305995== by 0xD2D34CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2305995== by 0x9D63418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2305995== by 0x9CFCD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2305995== by 0xA762D38: PetscInitialize (pinit.c:924) ==2305995== by 0x9C2366F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2305995== by 0x9C236BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2305995== by 0x13DC96: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2305995== by 0x13542F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2305995== by 0x1389B2: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2305995== by 0x138852: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2305995== by 0x138EE9: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2305995== by 0x133760: main (TestCardiacElectroMechanicsProblem.cpp:19) ==2305995== { Memcheck:Leak match-leak-kinds: possible 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 } ==2305995== 552 bytes in 1 blocks are definitely lost in loss record 46 of 72 ==2305995== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==2305995== by 0x14593C13: ??? ==2305995== by 0x1459422C: ??? ==2305995== by 0x145074B7: ??? ==2305995== by 0x9CC915A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2305995== by 0x9D63A97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2305995== by 0x9CFCD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2305995== by 0xA762D38: PetscInitialize (pinit.c:924) ==2305995== by 0x9C2366F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2305995== by 0x9C236BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2305995== by 0x13DC96: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2305995== by 0x13542F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2305995== by 0x1389B2: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2305995== by 0x138852: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2305995== by 0x138EE9: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2305995== by 0x133760: main (TestCardiacElectroMechanicsProblem.cpp:19) ==2305995== { 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 } ==2305995== 23,001 (136 direct, 22,865 indirect) bytes in 1 blocks are definitely lost in loss record 69 of 72 ==2305995== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==2305995== by 0x1570674E: ??? ==2305995== by 0x15706E0B: ??? ==2305995== by 0x15709F56: ??? ==2305995== by 0x156FF65D: ??? ==2305995== by 0x156FFFA3: ??? ==2305995== by 0xD3E4F05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==2305995== by 0xD3C0AE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==2305995== by 0xD371CB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2305995== by 0xD29EEF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2305995== by 0x13CC5F03: ??? ==2305995== by 0xD2D34CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2305995== by 0x9D63418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2305995== by 0x9CFCD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2305995== by 0xA762D38: PetscInitialize (pinit.c:924) ==2305995== by 0x9C2366F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2305995== by 0x9C236BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2305995== by 0x13DC96: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2305995== by 0x13542F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2305995== by 0x1389B2: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2305995== by 0x138852: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2305995== by 0x138EE9: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2305995== by 0x133760: main (TestCardiacElectroMechanicsProblem.cpp:19) ==2305995== { 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 } ==2305995== LEAK SUMMARY: ==2305995== definitely lost: 688 bytes in 2 blocks ==2305995== indirectly lost: 1,456 bytes in 13 blocks ==2305995== possibly lost: 304 bytes in 3 blocks ==2305995== still reachable: 1,531 bytes in 6 blocks ==2305995== suppressed: 697,260 bytes in 9,363 blocks ==2305995== Reachable blocks (those to which a pointer was found) are not shown. ==2305995== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==2305995== ==2305995== Use --track-origins=yes to see where uninitialised values come from ==2305995== For lists of detected and suppressed errors, rerun with: -s ==2305995== ERROR SUMMARY: 49 errors from 8 contexts (suppressed: 33 from 33)