==1167334== Memcheck, a memory error detector ==1167334== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==1167334== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==1167334== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/heart/test/TestMonodomainMassLumping -malloc_debug -malloc_dump -memory_info ==1167334== Parent PID: 1144851 ==1167334== ==1167334== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==1167334== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==1167334== ==1167334== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==1167334== at 0xA1C379E: getsockopt_syscall (getsockopt.c:29) ==1167334== by 0xA1C379E: getsockopt (getsockopt.c:94) ==1167334== by 0x1467A157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1167334== by 0x14681A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1167334== by 0x14688DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1167334== by 0x145883C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1167334== by 0x14501E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==1167334== by 0x13CC0E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==1167334== by 0xCF1E4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1167334== by 0x9AA1418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1167334== by 0x9A3AD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1167334== by 0xA552D38: PetscInitialize (pinit.c:924) ==1167334== by 0x996358B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1167334== by 0x99635D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1167334== by 0x125B66: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1167334== by 0x11F5FD: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1167334== by 0x1222E8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1167334== by 0x1221E3: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1167334== by 0x1227F7: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1167334== by 0x11DE00: main (TestMonodomainMassLumping.cpp:18) ==1167334== Address 0x1ffeffdfbc is on thread 1's stack ==1167334== in frame #2, created by pmix_ptl_base_make_connection (???:) ==1167334== { 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 } ==1167334== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==1167334== at 0xA1C379E: getsockopt_syscall (getsockopt.c:29) ==1167334== by 0xA1C379E: getsockopt (getsockopt.c:94) ==1167334== by 0x1467A157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1167334== by 0x14681A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1167334== by 0x14688DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1167334== by 0x145883C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1167334== by 0x14501E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==1167334== by 0x13CC0E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==1167334== by 0xCF1E4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1167334== by 0x9AA1418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1167334== by 0x9A3AD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1167334== by 0xA552D38: PetscInitialize (pinit.c:924) ==1167334== by 0x996358B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1167334== by 0x99635D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1167334== by 0x125B66: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1167334== by 0x11F5FD: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1167334== by 0x1222E8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1167334== by 0x1221E3: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1167334== by 0x1227F7: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1167334== by 0x11DE00: main (TestMonodomainMassLumping.cpp:18) ==1167334== Address 0x1ffeffdfbc is on thread 1's stack ==1167334== in frame #2, created by pmix_ptl_base_make_connection (???:) ==1167334== { 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 } ==1167334== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==1167334== at 0xA1C3C7E: setsockopt_syscall (setsockopt.c:29) ==1167334== by 0xA1C3C7E: setsockopt (setsockopt.c:95) ==1167334== by 0x14681BA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1167334== by 0x14688DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1167334== by 0x145883C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1167334== by 0x14501E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==1167334== by 0x13CC0E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==1167334== by 0xCF1E4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1167334== by 0x9AA1418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1167334== by 0x9A3AD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1167334== by 0xA552D38: PetscInitialize (pinit.c:924) ==1167334== by 0x996358B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1167334== by 0x99635D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1167334== by 0x125B66: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1167334== by 0x11F5FD: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1167334== by 0x1222E8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1167334== by 0x1221E3: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1167334== by 0x1227F7: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1167334== by 0x11DE00: main (TestMonodomainMassLumping.cpp:18) ==1167334== { 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 } ==1167334== Syscall param pwrite64(buf) points to uninitialised byte(s) ==1167334== at 0xA1AE9EF: __libc_pwrite64 (pwrite64.c:25) ==1167334== by 0xA1AE9EF: pwrite (pwrite64.c:23) ==1167334== by 0x171CD9D2: mca_fbtl_posix_pwritev (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_fbtl_posix.so) ==1167334== by 0x171AD419: mca_common_ompio_file_write (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==1167334== by 0x171AD79A: mca_common_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==1167334== by 0x1717C89A: mca_io_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_io_ompio.so) ==1167334== by 0x9A2E6A7: PMPI_File_write_at (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1167334== by 0xF071FEB: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1167334== by 0xEEB14ED: H5FD_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1167334== by 0xEE94313: H5F__accum_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1167334== by 0xEF8F442: H5PB_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1167334== by 0xEE9BDEA: H5F_block_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1167334== by 0xEE25E98: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1167334== by 0xF0653F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1167334== by 0xF0669CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1167334== by 0xF06747E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1167334== by 0xEE0254C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1167334== by 0xEE9A936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1167334== by 0xEE9B3FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1167334== by 0xEE9EBB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1167334== by 0xEE9EEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1167334== by 0xEF0E51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1167334== by 0xEF0E5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1167334== by 0xEE9B831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1167334== by 0xEE90881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1167334== by 0xC11F967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==1167334== by 0xC11A647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==1167334== by 0xC11A6ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==1167334== by 0x686EEC7: AbstractCardiacProblem<3u, 3u, 1u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==1167334== by 0x686EA67: AbstractCardiacProblem<3u, 3u, 1u>::Solve() (AbstractCardiacProblem.cpp:582) ==1167334== by 0x125DA9: TestMonodomainMassLumping::TestCompareCubePlaneStimulus() (TestMonodomainMassLumping.hpp:69) ==1167334== by 0x126822: TestDescription_TestMonodomainMassLumping_TestCompareCubePlaneStimulus::runTest() (TestMonodomainMassLumping.cpp:30) ==1167334== by 0x11EE34: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==1167334== by 0x122596: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==1167334== by 0x12247B: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==1167334== by 0x122321: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==1167334== by 0x1221E3: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1167334== by 0x1227F7: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1167334== by 0x11DE00: main (TestMonodomainMassLumping.cpp:18) ==1167334== Address 0x1616ab5e is 62 bytes inside a block of size 320 alloc'd ==1167334== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==1167334== by 0xEE25E26: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1167334== by 0xF0653F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1167334== by 0xF0669CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1167334== by 0xF06747E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1167334== by 0xEE0254C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1167334== by 0xEE9A936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1167334== by 0xEE9B3FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1167334== by 0xEE9EBB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1167334== by 0xEE9EEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1167334== by 0xEF0E51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1167334== by 0xEF0E5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1167334== by 0xEE9B831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1167334== by 0xEE90881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1167334== by 0xC11F967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==1167334== by 0xC11A647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==1167334== by 0xC11A6ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==1167334== by 0x686EEC7: AbstractCardiacProblem<3u, 3u, 1u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==1167334== by 0x686EA67: AbstractCardiacProblem<3u, 3u, 1u>::Solve() (AbstractCardiacProblem.cpp:582) ==1167334== by 0x125DA9: TestMonodomainMassLumping::TestCompareCubePlaneStimulus() (TestMonodomainMassLumping.hpp:69) ==1167334== by 0x126822: TestDescription_TestMonodomainMassLumping_TestCompareCubePlaneStimulus::runTest() (TestMonodomainMassLumping.cpp:30) ==1167334== by 0x11EE34: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==1167334== by 0x122596: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==1167334== by 0x12247B: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==1167334== by 0x122321: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==1167334== by 0x1221E3: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1167334== by 0x1227F7: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1167334== by 0x11DE00: main (TestMonodomainMassLumping.cpp:18) ==1167334== { 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:_ZN22AbstractCardiacProblemILj3ELj3ELj1EE24CloseFilesAndPostProcessEv fun:_ZN22AbstractCardiacProblemILj3ELj3ELj1EE5SolveEv fun:_ZN25TestMonodomainMassLumping28TestCompareCubePlaneStimulusEv fun:_ZN70TestDescription_TestMonodomainMassLumping_TestCompareCubePlaneStimulus7runTestEv fun:_ZN7CxxTest19RealTestDescription3runEv fun:_ZN7CxxTest10TestRunner7runTestERNS_15TestDescriptionE fun:_ZN7CxxTest10TestRunner8runSuiteERNS_16SuiteDescriptionE fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==1167334== ==1167334== FILE DESCRIPTORS: 9 open (3 std) at exit. ==1167334== Open file descriptor 12: ==1167334== at 0xA1B122D: pipe (pipe.c:29) ==1167334== by 0x13CC107D: ??? ==1167334== by 0xCF1E4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1167334== by 0x9AA1418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1167334== by 0x9A3AD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1167334== by 0xA552D38: PetscInitialize (pinit.c:924) ==1167334== by 0x996358B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1167334== by 0x99635D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1167334== by 0x125B66: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1167334== by 0x11F5FD: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1167334== by 0x1222E8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1167334== by 0x1221E3: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1167334== by 0x1227F7: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1167334== by 0x11DE00: main (TestMonodomainMassLumping.cpp:18) ==1167334== ==1167334== Open file descriptor 8: /dev/shm/open_mpi.0000 ==1167334== at 0xA1B5BCC: __open_nocancel (open64_nocancel.c:39) ==1167334== by 0xA139C4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==1167334== by 0x999B822: ??? ==1167334== by 0x999B96F: ??? ==1167334== by 0xCFC36DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==1167334== by 0xCFC3938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==1167334== by 0xCF79922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==1167334== by 0xCF1E2DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1167334== by 0x9AA1418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1167334== by 0x9A3AD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1167334== by 0xA552D38: PetscInitialize (pinit.c:924) ==1167334== by 0x996358B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1167334== by 0x99635D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1167334== by 0x125B66: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1167334== by 0x11F5FD: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1167334== by 0x1222E8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1167334== by 0x1221E3: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1167334== by 0x1227F7: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1167334== by 0x11DE00: main (TestMonodomainMassLumping.cpp:18) ==1167334== ==1167334== Open file descriptor 115: ==1167334== ==1167334== ==1167334== Open file descriptor 108: ==1167334== ==1167334== ==1167334== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestMonodomainMassLumping_valgrind.txt ==1167334== ==1167334== ==1167334== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==1167334== ==1167334== ==1167334== ==1167334== HEAP SUMMARY: ==1167334== in use at exit: 701,168 bytes in 9,383 blocks ==1167334== total heap usage: 405,904 allocs, 396,521 frees, 1,554,737,368 bytes allocated ==1167334== ==1167334== 552 bytes in 1 blocks are definitely lost in loss record 39 of 65 ==1167334== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==1167334== by 0x1458FC13: ??? ==1167334== by 0x1459022C: ??? ==1167334== by 0x145034B7: ??? ==1167334== by 0x9A0715A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1167334== by 0x9AA1A97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1167334== by 0x9A3AD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1167334== by 0xA552D38: PetscInitialize (pinit.c:924) ==1167334== by 0x996358B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1167334== by 0x99635D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1167334== by 0x125B66: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1167334== by 0x11F5FD: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1167334== by 0x1222E8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1167334== by 0x1221E3: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1167334== by 0x1227F7: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1167334== by 0x11DE00: main (TestMonodomainMassLumping.cpp:18) ==1167334== { 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 } ==1167334== 84,459 (136 direct, 84,323 indirect) bytes in 1 blocks are definitely lost in loss record 62 of 65 ==1167334== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==1167334== by 0x1570274E: ??? ==1167334== by 0x15702E0B: ??? ==1167334== by 0x15705F56: ??? ==1167334== by 0x156FB65D: ??? ==1167334== by 0x156FBFA3: ??? ==1167334== by 0xD02FF05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==1167334== by 0xD00BAE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==1167334== by 0xCFBCCB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==1167334== by 0xCEE9EF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1167334== by 0x13CC1F03: ??? ==1167334== by 0xCF1E4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1167334== by 0x9AA1418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1167334== by 0x9A3AD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1167334== by 0xA552D38: PetscInitialize (pinit.c:924) ==1167334== by 0x996358B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1167334== by 0x99635D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1167334== by 0x125B66: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1167334== by 0x11F5FD: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1167334== by 0x1222E8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1167334== by 0x1221E3: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1167334== by 0x1227F7: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1167334== by 0x11DE00: main (TestMonodomainMassLumping.cpp:18) ==1167334== { 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 } ==1167334== LEAK SUMMARY: ==1167334== definitely lost: 688 bytes in 2 blocks ==1167334== indirectly lost: 1,760 bytes in 16 blocks ==1167334== possibly lost: 0 bytes in 0 blocks ==1167334== still reachable: 1,531 bytes in 6 blocks ==1167334== suppressed: 697,189 bytes in 9,359 blocks ==1167334== Reachable blocks (those to which a pointer was found) are not shown. ==1167334== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==1167334== ==1167334== Use --track-origins=yes to see where uninitialised values come from ==1167334== For lists of detected and suppressed errors, rerun with: -s ==1167334== ERROR SUMMARY: 17 errors from 6 contexts (suppressed: 28 from 28)