==2062998== Memcheck, a memory error detector ==2062998== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==2062998== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==2062998== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/heart/test/TestPostProcessingWriter -malloc_debug -malloc_dump -memory_info ==2062998== Parent PID: 2040441 ==2062998== ==2062998== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==2062998== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==2062998== ==2062998== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==2062998== at 0xB8E079E: getsockopt_syscall (getsockopt.c:29) ==2062998== by 0xB8E079E: getsockopt (getsockopt.c:94) ==2062998== by 0x1467D157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2062998== by 0x14684A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2062998== by 0x1468BDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2062998== by 0x1458B3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2062998== by 0x14504E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==2062998== by 0x13CC3E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==2062998== by 0xF4C54CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2062998== by 0xBC63418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2062998== by 0xBBFCD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2062998== by 0x9F67D38: PetscInitialize (pinit.c:924) ==2062998== by 0x9E3958B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2062998== by 0x9E395D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2062998== by 0x131AC6: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2062998== by 0x12A13D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2062998== by 0x12CE00: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2062998== by 0x12CCFB: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2062998== by 0x12D30F: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2062998== by 0x128940: main (TestPostProcessingWriter.cpp:18) ==2062998== Address 0x1ffeffdfdc is on thread 1's stack ==2062998== in frame #2, created by pmix_ptl_base_make_connection (???:) ==2062998== { 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 } ==2062998== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==2062998== at 0xB8E079E: getsockopt_syscall (getsockopt.c:29) ==2062998== by 0xB8E079E: getsockopt (getsockopt.c:94) ==2062998== by 0x1467D157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2062998== by 0x14684A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2062998== by 0x1468BDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2062998== by 0x1458B3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2062998== by 0x14504E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==2062998== by 0x13CC3E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==2062998== by 0xF4C54CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2062998== by 0xBC63418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2062998== by 0xBBFCD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2062998== by 0x9F67D38: PetscInitialize (pinit.c:924) ==2062998== by 0x9E3958B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2062998== by 0x9E395D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2062998== by 0x131AC6: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2062998== by 0x12A13D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2062998== by 0x12CE00: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2062998== by 0x12CCFB: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2062998== by 0x12D30F: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2062998== by 0x128940: main (TestPostProcessingWriter.cpp:18) ==2062998== Address 0x1ffeffdfdc is on thread 1's stack ==2062998== in frame #2, created by pmix_ptl_base_make_connection (???:) ==2062998== { 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 } ==2062998== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==2062998== at 0xB8E0C7E: setsockopt_syscall (setsockopt.c:29) ==2062998== by 0xB8E0C7E: setsockopt (setsockopt.c:95) ==2062998== by 0x14684BA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2062998== by 0x1468BDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2062998== by 0x1458B3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2062998== by 0x14504E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==2062998== by 0x13CC3E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==2062998== by 0xF4C54CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2062998== by 0xBC63418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2062998== by 0xBBFCD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2062998== by 0x9F67D38: PetscInitialize (pinit.c:924) ==2062998== by 0x9E3958B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2062998== by 0x9E395D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2062998== by 0x131AC6: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2062998== by 0x12A13D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2062998== by 0x12CE00: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2062998== by 0x12CCFB: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2062998== by 0x12D30F: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2062998== by 0x128940: main (TestPostProcessingWriter.cpp:18) ==2062998== { 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 } ==2062998== Syscall param pwrite64(buf) points to uninitialised byte(s) ==2062998== at 0xB8CB9EF: __libc_pwrite64 (pwrite64.c:25) ==2062998== by 0xB8CB9EF: pwrite (pwrite64.c:23) ==2062998== by 0x176FA9D2: mca_fbtl_posix_pwritev (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_fbtl_posix.so) ==2062998== by 0x1770A419: mca_common_ompio_file_write (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==2062998== by 0x1770A79A: mca_common_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==2062998== by 0x175F589A: mca_io_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_io_ompio.so) ==2062998== by 0xBBF06A7: PMPI_File_write_at (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2062998== by 0xC44BFEB: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2062998== by 0xC28B4ED: H5FD_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2062998== by 0xC26E313: H5F__accum_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2062998== by 0xC369442: H5PB_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2062998== by 0xC275DEA: H5F_block_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2062998== by 0xC1FFE98: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2062998== by 0xC43F3F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2062998== by 0xC4409CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2062998== by 0xC44147E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2062998== by 0xC1DC54C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2062998== by 0xC274936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2062998== by 0xC2753FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2062998== by 0xC278BB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2062998== by 0xC278EFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2062998== by 0xC2E851F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2062998== by 0xC2E85EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2062998== by 0xC275831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2062998== by 0xC26A881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2062998== by 0x9D68967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==2062998== by 0x682E7D2: PostProcessingWriter<1u, 1u>::WriteOutputDataToHdf5(std::vector >, std::allocator > > > const&, std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_string, std::allocator > const&) (PostProcessingWriter.cpp:244) ==2062998== by 0x682CEFD: PostProcessingWriter<1u, 1u>::WriteApdMapFile(double, double) (PostProcessingWriter.cpp:256) ==2062998== by 0x132126: TestPostProcessingWriter::TestWriterMethods() (TestPostProcessingWriter.hpp:107) ==2062998== by 0x139BB6: TestDescription_TestPostProcessingWriter_TestWriterMethods::runTest() (TestPostProcessingWriter.cpp:30) ==2062998== by 0x129974: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==2062998== by 0x12D0AE: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==2062998== by 0x12CF93: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==2062998== by 0x12CE39: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==2062998== by 0x12CCFB: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2062998== by 0x12D30F: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2062998== by 0x128940: main (TestPostProcessingWriter.cpp:18) ==2062998== Address 0x15a86146 is 70 bytes inside a block of size 320 alloc'd ==2062998== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==2062998== by 0xC1FFE26: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2062998== by 0xC43F3F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2062998== by 0xC4409CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2062998== by 0xC44147E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2062998== by 0xC1DC54C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2062998== by 0xC274936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2062998== by 0xC2753FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2062998== by 0xC278BB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2062998== by 0xC278EFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2062998== by 0xC2E851F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2062998== by 0xC2E85EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2062998== by 0xC275831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2062998== by 0xC26A881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2062998== by 0x9D68967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==2062998== by 0x682E7D2: PostProcessingWriter<1u, 1u>::WriteOutputDataToHdf5(std::vector >, std::allocator > > > const&, std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_string, std::allocator > const&) (PostProcessingWriter.cpp:244) ==2062998== by 0x682CEFD: PostProcessingWriter<1u, 1u>::WriteApdMapFile(double, double) (PostProcessingWriter.cpp:256) ==2062998== by 0x132126: TestPostProcessingWriter::TestWriterMethods() (TestPostProcessingWriter.hpp:107) ==2062998== by 0x139BB6: TestDescription_TestPostProcessingWriter_TestWriterMethods::runTest() (TestPostProcessingWriter.cpp:30) ==2062998== by 0x129974: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==2062998== by 0x12D0AE: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==2062998== by 0x12CF93: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==2062998== by 0x12CE39: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==2062998== by 0x12CCFB: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2062998== by 0x12D30F: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2062998== by 0x128940: main (TestPostProcessingWriter.cpp:18) ==2062998== { 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:_ZN20PostProcessingWriterILj1ELj1EE21WriteOutputDataToHdf5ERKSt6vectorIS1_IdSaIdEESaIS3_EERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESF_SF_SF_ fun:_ZN20PostProcessingWriterILj1ELj1EE15WriteApdMapFileEdd fun:_ZN24TestPostProcessingWriter17TestWriterMethodsEv fun:_ZN58TestDescription_TestPostProcessingWriter_TestWriterMethods7runTestEv fun:_ZN7CxxTest19RealTestDescription3runEv fun:_ZN7CxxTest10TestRunner7runTestERNS_15TestDescriptionE fun:_ZN7CxxTest10TestRunner8runSuiteERNS_16SuiteDescriptionE fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==2062998== ==2062998== FILE DESCRIPTORS: 9 open (3 std) at exit. ==2062998== Open file descriptor 12: ==2062998== at 0xB8CE22D: pipe (pipe.c:29) ==2062998== by 0x13CC407D: ??? ==2062998== by 0xF4C54CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2062998== by 0xBC63418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2062998== by 0xBBFCD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2062998== by 0x9F67D38: PetscInitialize (pinit.c:924) ==2062998== by 0x9E3958B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2062998== by 0x9E395D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2062998== by 0x131AC6: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2062998== by 0x12A13D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2062998== by 0x12CE00: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2062998== by 0x12CCFB: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2062998== by 0x12D30F: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2062998== by 0x128940: main (TestPostProcessingWriter.cpp:18) ==2062998== ==2062998== Open file descriptor 8: /dev/shm/open_mpi.0000 ==2062998== at 0xB8D2BCC: __open_nocancel (open64_nocancel.c:39) ==2062998== by 0xB856C4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==2062998== by 0xB1F1822: ??? ==2062998== by 0xB1F196F: ??? ==2062998== by 0xF56C6DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2062998== by 0xF56C938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2062998== by 0xF522922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2062998== by 0xF4C52DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2062998== by 0xBC63418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2062998== by 0xBBFCD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2062998== by 0x9F67D38: PetscInitialize (pinit.c:924) ==2062998== by 0x9E3958B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2062998== by 0x9E395D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2062998== by 0x131AC6: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2062998== by 0x12A13D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2062998== by 0x12CE00: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2062998== by 0x12CCFB: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2062998== by 0x12D30F: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2062998== by 0x128940: main (TestPostProcessingWriter.cpp:18) ==2062998== ==2062998== Open file descriptor 117: ==2062998== ==2062998== ==2062998== Open file descriptor 110: ==2062998== ==2062998== ==2062998== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestPostProcessingWriter_valgrind.txt ==2062998== ==2062998== ==2062998== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==2062998== ==2062998== ==2062998== ==2062998== HEAP SUMMARY: ==2062998== in use at exit: 701,168 bytes in 9,383 blocks ==2062998== total heap usage: 10,856,617 allocs, 10,847,234 frees, 11,731,214,570 bytes allocated ==2062998== ==2062998== 552 bytes in 1 blocks are definitely lost in loss record 39 of 62 ==2062998== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==2062998== by 0x14592C13: ??? ==2062998== by 0x1459322C: ??? ==2062998== by 0x145064B7: ??? ==2062998== by 0xBBC915A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2062998== by 0xBC63A97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2062998== by 0xBBFCD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2062998== by 0x9F67D38: PetscInitialize (pinit.c:924) ==2062998== by 0x9E3958B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2062998== by 0x9E395D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2062998== by 0x131AC6: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2062998== by 0x12A13D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2062998== by 0x12CE00: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2062998== by 0x12CCFB: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2062998== by 0x12D30F: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2062998== by 0x128940: main (TestPostProcessingWriter.cpp:18) ==2062998== { 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 } ==2062998== 685,269 (136 direct, 685,133 indirect) bytes in 1 blocks are definitely lost in loss record 62 of 62 ==2062998== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==2062998== by 0x1570574E: ??? ==2062998== by 0x15705E0B: ??? ==2062998== by 0x15708F56: ??? ==2062998== by 0x156FE65D: ??? ==2062998== by 0x156FEFA3: ??? ==2062998== by 0xF5D8F05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==2062998== by 0xF5B4AE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==2062998== by 0xF565CB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2062998== by 0xF490EF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2062998== by 0x13CC4F03: ??? ==2062998== by 0xF4C54CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2062998== by 0xBC63418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2062998== by 0xBBFCD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2062998== by 0x9F67D38: PetscInitialize (pinit.c:924) ==2062998== by 0x9E3958B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2062998== by 0x9E395D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2062998== by 0x131AC6: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2062998== by 0x12A13D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2062998== by 0x12CE00: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2062998== by 0x12CCFB: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2062998== by 0x12D30F: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2062998== by 0x128940: main (TestPostProcessingWriter.cpp:18) ==2062998== { 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 } ==2062998== LEAK SUMMARY: ==2062998== definitely lost: 688 bytes in 2 blocks ==2062998== indirectly lost: 1,760 bytes in 16 blocks ==2062998== possibly lost: 0 bytes in 0 blocks ==2062998== still reachable: 1,531 bytes in 6 blocks ==2062998== suppressed: 697,189 bytes in 9,359 blocks ==2062998== Reachable blocks (those to which a pointer was found) are not shown. ==2062998== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==2062998== ==2062998== Use --track-origins=yes to see where uninitialised values come from ==2062998== For lists of detected and suppressed errors, rerun with: -s ==2062998== ERROR SUMMARY: 73 errors from 6 contexts (suppressed: 25 from 25)