==3303571== Memcheck, a memory error detector ==3303571== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==3303571== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==3303571== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/heart/test/TestArchivingExtendedBidomain -malloc_debug -malloc_dump -memory_info ==3303571== Parent PID: 3282641 ==3303571== ==3303571== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==3303571== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==3303571== ==3303571== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==3303571== at 0xB6AC79E: getsockopt_syscall (getsockopt.c:29) ==3303571== by 0xB6AC79E: getsockopt (getsockopt.c:94) ==3303571== by 0x1467E157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3303571== by 0x14685A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3303571== by 0x1468CDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3303571== by 0x1458C3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3303571== by 0x14505E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==3303571== by 0x13CC4E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==3303571== by 0xF47B4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3303571== by 0xAF8A418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3303571== by 0xAF23D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3303571== by 0x9C1AD38: PetscInitialize (pinit.c:924) ==3303571== by 0x9A8A66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3303571== by 0x9A8A6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3303571== by 0x137FD0: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3303571== by 0x132C1D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3303571== by 0x135C1A: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3303571== by 0x135B15: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3303571== by 0x136129: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3303571== by 0x1313D0: main (TestArchivingExtendedBidomain.cpp:18) ==3303571== Address 0x1ffeffdfac is on thread 1's stack ==3303571== in frame #2, created by pmix_ptl_base_make_connection (???:) ==3303571== { 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 } ==3303571== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==3303571== at 0xB6AC79E: getsockopt_syscall (getsockopt.c:29) ==3303571== by 0xB6AC79E: getsockopt (getsockopt.c:94) ==3303571== by 0x1467E157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3303571== by 0x14685A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3303571== by 0x1468CDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3303571== by 0x1458C3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3303571== by 0x14505E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==3303571== by 0x13CC4E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==3303571== by 0xF47B4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3303571== by 0xAF8A418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3303571== by 0xAF23D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3303571== by 0x9C1AD38: PetscInitialize (pinit.c:924) ==3303571== by 0x9A8A66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3303571== by 0x9A8A6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3303571== by 0x137FD0: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3303571== by 0x132C1D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3303571== by 0x135C1A: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3303571== by 0x135B15: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3303571== by 0x136129: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3303571== by 0x1313D0: main (TestArchivingExtendedBidomain.cpp:18) ==3303571== Address 0x1ffeffdfac is on thread 1's stack ==3303571== in frame #2, created by pmix_ptl_base_make_connection (???:) ==3303571== { 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 } ==3303571== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==3303571== at 0xB6ACC7E: setsockopt_syscall (setsockopt.c:29) ==3303571== by 0xB6ACC7E: setsockopt (setsockopt.c:95) ==3303571== by 0x14685BA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3303571== by 0x1468CDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3303571== by 0x1458C3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3303571== by 0x14505E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==3303571== by 0x13CC4E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==3303571== by 0xF47B4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3303571== by 0xAF8A418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3303571== by 0xAF23D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3303571== by 0x9C1AD38: PetscInitialize (pinit.c:924) ==3303571== by 0x9A8A66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3303571== by 0x9A8A6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3303571== by 0x137FD0: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3303571== by 0x132C1D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3303571== by 0x135C1A: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3303571== by 0x135B15: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3303571== by 0x136129: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3303571== by 0x1313D0: main (TestArchivingExtendedBidomain.cpp:18) ==3303571== { 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 } ==3303571== Syscall param pwrite64(buf) points to uninitialised byte(s) ==3303571== at 0xB6979EF: __libc_pwrite64 (pwrite64.c:25) ==3303571== by 0xB6979EF: pwrite (pwrite64.c:23) ==3303571== by 0x176FB9D2: mca_fbtl_posix_pwritev (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_fbtl_posix.so) ==3303571== by 0x1770B419: mca_common_ompio_file_write (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==3303571== by 0x1770B79A: mca_common_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==3303571== by 0x175F689A: mca_io_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_io_ompio.so) ==3303571== by 0xAF176A7: PMPI_File_write_at (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3303571== by 0xD152FEB: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3303571== by 0xCF924ED: H5FD_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3303571== by 0xCF75313: H5F__accum_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3303571== by 0xD070442: H5PB_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3303571== by 0xCF7CDEA: H5F_block_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3303571== by 0xCF06E98: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3303571== by 0xD1463F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3303571== by 0xD1479CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3303571== by 0xD14847E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3303571== by 0xCEE354C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3303571== by 0xCF7B936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3303571== by 0xCF7C3FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3303571== by 0xCF7FBB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3303571== by 0xCF7FEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3303571== by 0xCFEF51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3303571== by 0xCFEF5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3303571== by 0xCF7C831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3303571== by 0xCF71881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3303571== by 0x99B88E7: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==3303571== by 0x99B35C7: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==3303571== by 0x99B366D: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==3303571== by 0x688B6C7: AbstractCardiacProblem<2u, 2u, 3u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==3303571== by 0x688B267: AbstractCardiacProblem<2u, 2u, 3u>::Solve() (AbstractCardiacProblem.cpp:582) ==3303571== by 0x13BEF2: TestArchivingExtendedBidomain::Run2DSimulationSaveAfterThreemilliSecondsIntraStim(FileFinder, std::__cxx11::basic_string, std::allocator >) (TestArchivingExtendedBidomain.hpp:291) ==3303571== by 0x13A853: TestArchivingExtendedBidomain::TestArchivingProblemIntraStim() (TestArchivingExtendedBidomain.hpp:160) ==3303571== by 0x13DED0: TestDescription_TestArchivingExtendedBidomain_TestArchivingProblemIntraStim::runTest() (TestArchivingExtendedBidomain.cpp:30) ==3303571== by 0x132454: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==3303571== by 0x135EC8: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==3303571== by 0x135DAD: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==3303571== by 0x135C53: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==3303571== by 0x135B15: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3303571== by 0x136129: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3303571== by 0x1313D0: main (TestArchivingExtendedBidomain.cpp:18) ==3303571== Address 0x160b31fe is 62 bytes inside a block of size 320 alloc'd ==3303571== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==3303571== by 0xCF06E26: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3303571== by 0xD1463F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3303571== by 0xD1479CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3303571== by 0xD14847E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3303571== by 0xCEE354C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3303571== by 0xCF7B936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3303571== by 0xCF7C3FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3303571== by 0xCF7FBB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3303571== by 0xCF7FEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3303571== by 0xCFEF51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3303571== by 0xCFEF5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3303571== by 0xCF7C831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3303571== by 0xCF71881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3303571== by 0x99B88E7: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==3303571== by 0x99B35C7: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==3303571== by 0x99B366D: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==3303571== by 0x688B6C7: AbstractCardiacProblem<2u, 2u, 3u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==3303571== by 0x688B267: AbstractCardiacProblem<2u, 2u, 3u>::Solve() (AbstractCardiacProblem.cpp:582) ==3303571== by 0x13BEF2: TestArchivingExtendedBidomain::Run2DSimulationSaveAfterThreemilliSecondsIntraStim(FileFinder, std::__cxx11::basic_string, std::allocator >) (TestArchivingExtendedBidomain.hpp:291) ==3303571== by 0x13A853: TestArchivingExtendedBidomain::TestArchivingProblemIntraStim() (TestArchivingExtendedBidomain.hpp:160) ==3303571== by 0x13DED0: TestDescription_TestArchivingExtendedBidomain_TestArchivingProblemIntraStim::runTest() (TestArchivingExtendedBidomain.cpp:30) ==3303571== by 0x132454: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==3303571== by 0x135EC8: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==3303571== by 0x135DAD: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==3303571== by 0x135C53: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==3303571== by 0x135B15: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3303571== by 0x136129: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3303571== by 0x1313D0: main (TestArchivingExtendedBidomain.cpp:18) ==3303571== { 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:_ZN22AbstractCardiacProblemILj2ELj2ELj3EE24CloseFilesAndPostProcessEv fun:_ZN22AbstractCardiacProblemILj2ELj2ELj3EE5SolveEv fun:_ZN29TestArchivingExtendedBidomain50Run2DSimulationSaveAfterThreemilliSecondsIntraStimE10FileFinderNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE fun:_ZN29TestArchivingExtendedBidomain29TestArchivingProblemIntraStimEv fun:_ZN75TestDescription_TestArchivingExtendedBidomain_TestArchivingProblemIntraStim7runTestEv fun:_ZN7CxxTest19RealTestDescription3runEv fun:_ZN7CxxTest10TestRunner7runTestERNS_15TestDescriptionE fun:_ZN7CxxTest10TestRunner8runSuiteERNS_16SuiteDescriptionE fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==3303571== ==3303571== FILE DESCRIPTORS: 9 open (3 std) at exit. ==3303571== Open file descriptor 12: ==3303571== at 0xB69A22D: pipe (pipe.c:29) ==3303571== by 0x13CC507D: ??? ==3303571== by 0xF47B4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3303571== by 0xAF8A418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3303571== by 0xAF23D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3303571== by 0x9C1AD38: PetscInitialize (pinit.c:924) ==3303571== by 0x9A8A66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3303571== by 0x9A8A6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3303571== by 0x137FD0: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3303571== by 0x132C1D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3303571== by 0x135C1A: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3303571== by 0x135B15: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3303571== by 0x136129: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3303571== by 0x1313D0: main (TestArchivingExtendedBidomain.cpp:18) ==3303571== ==3303571== Open file descriptor 8: /dev/shm/open_mpi.0000 ==3303571== at 0xB69EBCC: __open_nocancel (open64_nocancel.c:39) ==3303571== by 0xB622C4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==3303571== by 0x9AC2822: ??? ==3303571== by 0x9AC296F: ??? ==3303571== by 0xF5206DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==3303571== by 0xF520938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==3303571== by 0xF4D6922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==3303571== by 0xF47B2DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3303571== by 0xAF8A418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3303571== by 0xAF23D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3303571== by 0x9C1AD38: PetscInitialize (pinit.c:924) ==3303571== by 0x9A8A66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3303571== by 0x9A8A6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3303571== by 0x137FD0: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3303571== by 0x132C1D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3303571== by 0x135C1A: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3303571== by 0x135B15: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3303571== by 0x136129: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3303571== by 0x1313D0: main (TestArchivingExtendedBidomain.cpp:18) ==3303571== ==3303571== Open file descriptor 117: ==3303571== ==3303571== ==3303571== Open file descriptor 108: ==3303571== ==3303571== ==3303571== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestArchivingExtendedBidomain_valgrind.txt ==3303571== ==3303571== ==3303571== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==3303571== ==3303571== ==3303571== ==3303571== HEAP SUMMARY: ==3303571== in use at exit: 701,239 bytes in 9,387 blocks ==3303571== total heap usage: 353,822 allocs, 344,435 frees, 1,454,971,697 bytes allocated ==3303571== ==3303571== 552 bytes in 1 blocks are definitely lost in loss record 43 of 66 ==3303571== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==3303571== by 0x14593C13: ??? ==3303571== by 0x1459422C: ??? ==3303571== by 0x145074B7: ??? ==3303571== by 0xAEF015A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3303571== by 0xAF8AA97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3303571== by 0xAF23D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3303571== by 0x9C1AD38: PetscInitialize (pinit.c:924) ==3303571== by 0x9A8A66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3303571== by 0x9A8A6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3303571== by 0x137FD0: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3303571== by 0x132C1D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3303571== by 0x135C1A: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3303571== by 0x135B15: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3303571== by 0x136129: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3303571== by 0x1313D0: main (TestArchivingExtendedBidomain.cpp:18) ==3303571== { 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 } ==3303571== 685,269 (136 direct, 685,133 indirect) bytes in 1 blocks are definitely lost in loss record 66 of 66 ==3303571== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==3303571== by 0x1570674E: ??? ==3303571== by 0x15706E0B: ??? ==3303571== by 0x15709F56: ??? ==3303571== by 0x156FF65D: ??? ==3303571== by 0x156FFFA3: ??? ==3303571== by 0xF58CF05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==3303571== by 0xF568AE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==3303571== by 0xF519CB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==3303571== by 0xF446EF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3303571== by 0x13CC5F03: ??? ==3303571== by 0xF47B4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3303571== by 0xAF8A418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3303571== by 0xAF23D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3303571== by 0x9C1AD38: PetscInitialize (pinit.c:924) ==3303571== by 0x9A8A66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3303571== by 0x9A8A6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3303571== by 0x137FD0: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3303571== by 0x132C1D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3303571== by 0x135C1A: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3303571== by 0x135B15: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3303571== by 0x136129: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3303571== by 0x1313D0: main (TestArchivingExtendedBidomain.cpp:18) ==3303571== { 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 } ==3303571== LEAK SUMMARY: ==3303571== definitely lost: 688 bytes in 2 blocks ==3303571== indirectly lost: 1,760 bytes in 16 blocks ==3303571== possibly lost: 0 bytes in 0 blocks ==3303571== still reachable: 1,531 bytes in 6 blocks ==3303571== suppressed: 697,260 bytes in 9,363 blocks ==3303571== Reachable blocks (those to which a pointer was found) are not shown. ==3303571== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==3303571== ==3303571== Use --track-origins=yes to see where uninitialised values come from ==3303571== For lists of detected and suppressed errors, rerun with: -s ==3303571== ERROR SUMMARY: 23 errors from 6 contexts (suppressed: 29 from 29)