==1586887== Memcheck, a memory error detector ==1586887== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==1586887== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==1586887== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/pde/test/TestSimpleLinearParabolicSolver -malloc_debug -malloc_dump -memory_info ==1586887== Parent PID: 1586025 ==1586887== ==1586887== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==1586887== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==1586887== ==1586887== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==1586887== at 0x7E9079E: getsockopt_syscall (getsockopt.c:29) ==1586887== by 0x7E9079E: getsockopt (getsockopt.c:94) ==1586887== by 0x107D5157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1586887== by 0x107DCA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1586887== by 0x107E3DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1586887== by 0x106E33C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1586887== by 0x1065CE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==1586887== by 0xFE1BE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==1586887== by 0xBCB64CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1586887== by 0x8471418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1586887== by 0x840AD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1586887== by 0x6448D38: PetscInitialize (pinit.c:924) ==1586887== by 0x631C58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1586887== by 0x631C5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1586887== by 0x15FBB0: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1586887== by 0x158BAF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1586887== by 0x15C0EA: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1586887== by 0x15BF8A: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1586887== by 0x15C621: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1586887== by 0x156EE0: main (TestSimpleLinearParabolicSolver.cpp:19) ==1586887== Address 0x1ffeffdf9c is on thread 1's stack ==1586887== in frame #2, created by pmix_ptl_base_make_connection (???:) ==1586887== { 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 } ==1586887== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==1586887== at 0x7E9079E: getsockopt_syscall (getsockopt.c:29) ==1586887== by 0x7E9079E: getsockopt (getsockopt.c:94) ==1586887== by 0x107D5157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1586887== by 0x107DCA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1586887== by 0x107E3DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1586887== by 0x106E33C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1586887== by 0x1065CE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==1586887== by 0xFE1BE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==1586887== by 0xBCB64CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1586887== by 0x8471418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1586887== by 0x840AD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1586887== by 0x6448D38: PetscInitialize (pinit.c:924) ==1586887== by 0x631C58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1586887== by 0x631C5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1586887== by 0x15FBB0: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1586887== by 0x158BAF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1586887== by 0x15C0EA: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1586887== by 0x15BF8A: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1586887== by 0x15C621: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1586887== by 0x156EE0: main (TestSimpleLinearParabolicSolver.cpp:19) ==1586887== Address 0x1ffeffdf9c is on thread 1's stack ==1586887== in frame #2, created by pmix_ptl_base_make_connection (???:) ==1586887== { 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 } ==1586887== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==1586887== at 0x7E90C7E: setsockopt_syscall (setsockopt.c:29) ==1586887== by 0x7E90C7E: setsockopt (setsockopt.c:95) ==1586887== by 0x107DCBA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1586887== by 0x107E3DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1586887== by 0x106E33C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1586887== by 0x1065CE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==1586887== by 0xFE1BE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==1586887== by 0xBCB64CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1586887== by 0x8471418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1586887== by 0x840AD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1586887== by 0x6448D38: PetscInitialize (pinit.c:924) ==1586887== by 0x631C58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1586887== by 0x631C5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1586887== by 0x15FBB0: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1586887== by 0x158BAF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1586887== by 0x15C0EA: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1586887== by 0x15BF8A: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1586887== by 0x15C621: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1586887== by 0x156EE0: main (TestSimpleLinearParabolicSolver.cpp:19) ==1586887== { 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 } ==1586887== Syscall param pwrite64(buf) points to uninitialised byte(s) ==1586887== at 0x7E7B9EF: __libc_pwrite64 (pwrite64.c:25) ==1586887== by 0x7E7B9EF: pwrite (pwrite64.c:23) ==1586887== by 0x137289D2: mca_fbtl_posix_pwritev (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_fbtl_posix.so) ==1586887== by 0x13708419: mca_common_ompio_file_write (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==1586887== by 0x1370879A: mca_common_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==1586887== by 0x136D789A: mca_io_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_io_ompio.so) ==1586887== by 0x83FE6A7: PMPI_File_write_at (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1586887== by 0x829BFEB: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1586887== by 0x80DB4ED: H5FD_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1586887== by 0x80BE313: H5F__accum_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1586887== by 0x81B9442: H5PB_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1586887== by 0x80C5DEA: H5F_block_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1586887== by 0x804FE98: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1586887== by 0x828F3F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1586887== by 0x82909CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1586887== by 0x829147E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1586887== by 0x802C54C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1586887== by 0x80C4936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1586887== by 0x80C53FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1586887== by 0x80C8BB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1586887== by 0x80C8EFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1586887== by 0x813851F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1586887== by 0x81385EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1586887== by 0x80C5831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1586887== by 0x80BA881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1586887== by 0x624B967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==1586887== by 0x6246647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==1586887== by 0x62466ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==1586887== by 0x16F5A1: AbstractDynamicLinearPdeSolver<2u, 2u, 1u>::Solve() (AbstractDynamicLinearPdeSolver.hpp:474) ==1586887== by 0x1639A4: TestSimpleLinearParabolicSolver::TestSimpleLinearParabolicSolver2DZeroDirich() (TestSimpleLinearParabolicSolver.hpp:386) ==1586887== by 0x16BF9E: TestDescription_TestSimpleLinearParabolicSolver_TestSimpleLinearParabolicSolver2DZeroDirich::runTest() (TestSimpleLinearParabolicSolver.cpp:49) ==1586887== by 0x1581AA: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==1586887== by 0x15C398: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==1586887== by 0x15C27D: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==1586887== by 0x15C123: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==1586887== by 0x15BF8A: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1586887== by 0x15C621: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1586887== by 0x156EE0: main (TestSimpleLinearParabolicSolver.cpp:19) ==1586887== Address 0x11d210a2 is 66 bytes inside a block of size 320 alloc'd ==1586887== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==1586887== by 0x804FE26: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1586887== by 0x828F3F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1586887== by 0x82909CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1586887== by 0x829147E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1586887== by 0x802C54C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1586887== by 0x80C4936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1586887== by 0x80C53FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1586887== by 0x80C8BB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1586887== by 0x80C8EFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1586887== by 0x813851F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1586887== by 0x81385EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1586887== by 0x80C5831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1586887== by 0x80BA881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1586887== by 0x624B967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==1586887== by 0x6246647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==1586887== by 0x62466ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==1586887== by 0x16F5A1: AbstractDynamicLinearPdeSolver<2u, 2u, 1u>::Solve() (AbstractDynamicLinearPdeSolver.hpp:474) ==1586887== by 0x1639A4: TestSimpleLinearParabolicSolver::TestSimpleLinearParabolicSolver2DZeroDirich() (TestSimpleLinearParabolicSolver.hpp:386) ==1586887== by 0x16BF9E: TestDescription_TestSimpleLinearParabolicSolver_TestSimpleLinearParabolicSolver2DZeroDirich::runTest() (TestSimpleLinearParabolicSolver.cpp:49) ==1586887== by 0x1581AA: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==1586887== by 0x15C398: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==1586887== by 0x15C27D: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==1586887== by 0x15C123: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==1586887== by 0x15BF8A: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1586887== by 0x15C621: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1586887== by 0x156EE0: main (TestSimpleLinearParabolicSolver.cpp:19) ==1586887== { 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:_ZN30AbstractDynamicLinearPdeSolverILj2ELj2ELj1EE5SolveEv fun:_ZN31TestSimpleLinearParabolicSolver43TestSimpleLinearParabolicSolver2DZeroDirichEv fun:_ZN91TestDescription_TestSimpleLinearParabolicSolver_TestSimpleLinearParabolicSolver2DZeroDirich7runTestEv fun:_ZN7CxxTest19RealTestDescription3runEv fun:_ZN7CxxTest10TestRunner7runTestERNS_15TestDescriptionE fun:_ZN7CxxTest10TestRunner8runSuiteERNS_16SuiteDescriptionE fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==1586887== ==1586887== FILE DESCRIPTORS: 9 open (3 std) at exit. ==1586887== Open file descriptor 12: ==1586887== at 0x7E7E22D: pipe (pipe.c:29) ==1586887== by 0xFE1C07D: ??? ==1586887== by 0xBCB64CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1586887== by 0x8471418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1586887== by 0x840AD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1586887== by 0x6448D38: PetscInitialize (pinit.c:924) ==1586887== by 0x631C58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1586887== by 0x631C5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1586887== by 0x15FBB0: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1586887== by 0x158BAF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1586887== by 0x15C0EA: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1586887== by 0x15BF8A: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1586887== by 0x15C621: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1586887== by 0x156EE0: main (TestSimpleLinearParabolicSolver.cpp:19) ==1586887== ==1586887== Open file descriptor 8: /dev/shm/open_mpi.0000 ==1586887== at 0x7E82BCC: __open_nocancel (open64_nocancel.c:39) ==1586887== by 0x7E06C4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==1586887== by 0x76D2822: ??? ==1586887== by 0x76D296F: ??? ==1586887== by 0xBD5B6DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==1586887== by 0xBD5B938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==1586887== by 0xBD11922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==1586887== by 0xBCB62DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1586887== by 0x8471418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1586887== by 0x840AD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1586887== by 0x6448D38: PetscInitialize (pinit.c:924) ==1586887== by 0x631C58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1586887== by 0x631C5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1586887== by 0x15FBB0: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1586887== by 0x158BAF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1586887== by 0x15C0EA: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1586887== by 0x15BF8A: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1586887== by 0x15C621: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1586887== by 0x156EE0: main (TestSimpleLinearParabolicSolver.cpp:19) ==1586887== ==1586887== Open file descriptor 117: ==1586887== ==1586887== ==1586887== Open file descriptor 110: ==1586887== ==1586887== ==1586887== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestSimpleLinearParabolicSolver_valgrind.txt ==1586887== ==1586887== ==1586887== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==1586887== ==1586887== ==1586887== ==1586887== HEAP SUMMARY: ==1586887== in use at exit: 701,159 bytes in 9,387 blocks ==1586887== total heap usage: 371,631 allocs, 362,244 frees, 1,444,104,398 bytes allocated ==1586887== ==1586887== 552 bytes in 1 blocks are definitely lost in loss record 43 of 66 ==1586887== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==1586887== by 0x106EAC13: ??? ==1586887== by 0x106EB22C: ??? ==1586887== by 0x1065E4B7: ??? ==1586887== by 0x83D715A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1586887== by 0x8471A97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1586887== by 0x840AD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1586887== by 0x6448D38: PetscInitialize (pinit.c:924) ==1586887== by 0x631C58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1586887== by 0x631C5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1586887== by 0x15FBB0: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1586887== by 0x158BAF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1586887== by 0x15C0EA: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1586887== by 0x15BF8A: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1586887== by 0x15C621: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1586887== by 0x156EE0: main (TestSimpleLinearParabolicSolver.cpp:19) ==1586887== { 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 } ==1586887== 685,289 (136 direct, 685,153 indirect) bytes in 1 blocks are definitely lost in loss record 66 of 66 ==1586887== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==1586887== by 0x1185D74E: ??? ==1586887== by 0x1185DE0B: ??? ==1586887== by 0x11860F56: ??? ==1586887== by 0x1185665D: ??? ==1586887== by 0x11856FA3: ??? ==1586887== by 0xBDC7F05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==1586887== by 0xBDA3AE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==1586887== by 0xBD54CB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==1586887== by 0xBC81EF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1586887== by 0xFE1CF03: ??? ==1586887== by 0xBCB64CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1586887== by 0x8471418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1586887== by 0x840AD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1586887== by 0x6448D38: PetscInitialize (pinit.c:924) ==1586887== by 0x631C58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1586887== by 0x631C5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1586887== by 0x15FBB0: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1586887== by 0x158BAF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1586887== by 0x15C0EA: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1586887== by 0x15BF8A: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1586887== by 0x15C621: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1586887== by 0x156EE0: main (TestSimpleLinearParabolicSolver.cpp:19) ==1586887== { 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 } ==1586887== LEAK SUMMARY: ==1586887== definitely lost: 688 bytes in 2 blocks ==1586887== indirectly lost: 1,760 bytes in 16 blocks ==1586887== possibly lost: 0 bytes in 0 blocks ==1586887== still reachable: 1,531 bytes in 6 blocks ==1586887== suppressed: 697,180 bytes in 9,363 blocks ==1586887== Reachable blocks (those to which a pointer was found) are not shown. ==1586887== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==1586887== ==1586887== Use --track-origins=yes to see where uninitialised values come from ==1586887== For lists of detected and suppressed errors, rerun with: -s ==1586887== ERROR SUMMARY: 11 errors from 6 contexts (suppressed: 29 from 29)