==2304739== Memcheck, a memory error detector ==2304739== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==2304739== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==2304739== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/heart/test/TestBidomainWithSvi -malloc_debug -malloc_dump -memory_info ==2304739== Parent PID: 2283975 ==2304739== ==2304739== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==2304739== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==2304739== ==2304739== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==2304739== at 0xA12C79E: getsockopt_syscall (getsockopt.c:29) ==2304739== by 0xA12C79E: getsockopt (getsockopt.c:94) ==2304739== by 0x1467C157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2304739== by 0x14683A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2304739== by 0x1468ADF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2304739== by 0x1458A3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2304739== by 0x14503E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==2304739== by 0x13CC2E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==2304739== by 0xF4C84CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2304739== by 0xB82B418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2304739== by 0xB7C4D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2304739== by 0xA4BBD38: PetscInitialize (pinit.c:924) ==2304739== by 0x9A0366F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2304739== by 0x9A036BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2304739== by 0x12A630: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2304739== by 0x12473D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2304739== by 0x126CF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2304739== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2304739== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2304739== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==2304739== Address 0x1ffeffdfbc is on thread 1's stack ==2304739== in frame #2, created by pmix_ptl_base_make_connection (???:) ==2304739== { 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 } ==2304739== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==2304739== at 0xA12C79E: getsockopt_syscall (getsockopt.c:29) ==2304739== by 0xA12C79E: getsockopt (getsockopt.c:94) ==2304739== by 0x1467C157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2304739== by 0x14683A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2304739== by 0x1468ADF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2304739== by 0x1458A3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2304739== by 0x14503E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==2304739== by 0x13CC2E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==2304739== by 0xF4C84CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2304739== by 0xB82B418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2304739== by 0xB7C4D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2304739== by 0xA4BBD38: PetscInitialize (pinit.c:924) ==2304739== by 0x9A0366F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2304739== by 0x9A036BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2304739== by 0x12A630: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2304739== by 0x12473D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2304739== by 0x126CF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2304739== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2304739== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2304739== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==2304739== Address 0x1ffeffdfbc is on thread 1's stack ==2304739== in frame #2, created by pmix_ptl_base_make_connection (???:) ==2304739== { 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 } ==2304739== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==2304739== at 0xA12CC7E: setsockopt_syscall (setsockopt.c:29) ==2304739== by 0xA12CC7E: setsockopt (setsockopt.c:95) ==2304739== by 0x14683BA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2304739== by 0x1468ADF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2304739== by 0x1458A3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==2304739== by 0x14503E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==2304739== by 0x13CC2E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==2304739== by 0xF4C84CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2304739== by 0xB82B418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2304739== by 0xB7C4D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2304739== by 0xA4BBD38: PetscInitialize (pinit.c:924) ==2304739== by 0x9A0366F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2304739== by 0x9A036BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2304739== by 0x12A630: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2304739== by 0x12473D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2304739== by 0x126CF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2304739== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2304739== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2304739== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==2304739== { 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 } ==2304739== Syscall param pwrite64(buf) points to uninitialised byte(s) ==2304739== at 0xA1179EF: __libc_pwrite64 (pwrite64.c:25) ==2304739== by 0xA1179EF: pwrite (pwrite64.c:23) ==2304739== by 0x16EF99D2: mca_fbtl_posix_pwritev (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_fbtl_posix.so) ==2304739== by 0x16F09419: mca_common_ompio_file_write (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==2304739== by 0x16F0979A: mca_common_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==2304739== by 0x16DF489A: mca_io_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_io_ompio.so) ==2304739== by 0xB7B86A7: PMPI_File_write_at (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2304739== by 0xEEA5FEB: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304739== by 0xECE54ED: H5FD_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304739== by 0xECC8313: H5F__accum_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304739== by 0xEDC3442: H5PB_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304739== by 0xECCFDEA: H5F_block_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304739== by 0xEC59E98: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304739== by 0xEE993F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304739== by 0xEE9A9CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304739== by 0xEE9B47E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304739== by 0xEC3654C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304739== by 0xECCE936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304739== by 0xECCF3FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304739== by 0xECD2BB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304739== by 0xECD2EFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304739== by 0xED4251F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304739== by 0xED425EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304739== by 0xECCF831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304739== by 0xECC4881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304739== by 0xC120855: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==2304739== by 0xC11B535: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==2304739== by 0xC11B5DB: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==2304739== by 0x6874A3D: AbstractCardiacProblem<1u, 1u, 2u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==2304739== by 0x68745DD: AbstractCardiacProblem<1u, 1u, 2u>::Solve() (AbstractCardiacProblem.cpp:582) ==2304739== by 0x12ADEF: TestBidomainWithSvi::TestConductionVelocityConvergesFasterWithSvi1d() (TestBidomainWithSvi.hpp:157) ==2304739== by 0x12CDE8: TestDescription_TestBidomainWithSvi_TestConductionVelocityConvergesFasterWithSvi1d::runTest() (TestBidomainWithSvi.cpp:30) ==2304739== by 0x123F74: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==2304739== by 0x126FA6: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==2304739== by 0x126E8B: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==2304739== by 0x126D31: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==2304739== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2304739== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2304739== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==2304739== Address 0x165f35ee is 62 bytes inside a block of size 320 alloc'd ==2304739== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==2304739== by 0xEC59E26: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304739== by 0xEE993F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304739== by 0xEE9A9CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304739== by 0xEE9B47E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304739== by 0xEC3654C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304739== by 0xECCE936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304739== by 0xECCF3FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304739== by 0xECD2BB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304739== by 0xECD2EFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304739== by 0xED4251F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304739== by 0xED425EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304739== by 0xECCF831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304739== by 0xECC4881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==2304739== by 0xC120855: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==2304739== by 0xC11B535: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==2304739== by 0xC11B5DB: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==2304739== by 0x6874A3D: AbstractCardiacProblem<1u, 1u, 2u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==2304739== by 0x68745DD: AbstractCardiacProblem<1u, 1u, 2u>::Solve() (AbstractCardiacProblem.cpp:582) ==2304739== by 0x12ADEF: TestBidomainWithSvi::TestConductionVelocityConvergesFasterWithSvi1d() (TestBidomainWithSvi.hpp:157) ==2304739== by 0x12CDE8: TestDescription_TestBidomainWithSvi_TestConductionVelocityConvergesFasterWithSvi1d::runTest() (TestBidomainWithSvi.cpp:30) ==2304739== by 0x123F74: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==2304739== by 0x126FA6: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==2304739== by 0x126E8B: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==2304739== by 0x126D31: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==2304739== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2304739== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2304739== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==2304739== { 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:_ZN22AbstractCardiacProblemILj1ELj1ELj2EE24CloseFilesAndPostProcessEv fun:_ZN22AbstractCardiacProblemILj1ELj1ELj2EE5SolveEv fun:_ZN19TestBidomainWithSvi46TestConductionVelocityConvergesFasterWithSvi1dEv fun:_ZN82TestDescription_TestBidomainWithSvi_TestConductionVelocityConvergesFasterWithSvi1d7runTestEv fun:_ZN7CxxTest19RealTestDescription3runEv fun:_ZN7CxxTest10TestRunner7runTestERNS_15TestDescriptionE fun:_ZN7CxxTest10TestRunner8runSuiteERNS_16SuiteDescriptionE fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==2304739== ==2304739== FILE DESCRIPTORS: 9 open (3 std) at exit. ==2304739== Open file descriptor 12: ==2304739== at 0xA11A22D: pipe (pipe.c:29) ==2304739== by 0x13CC307D: ??? ==2304739== by 0xF4C84CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2304739== by 0xB82B418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2304739== by 0xB7C4D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2304739== by 0xA4BBD38: PetscInitialize (pinit.c:924) ==2304739== by 0x9A0366F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2304739== by 0x9A036BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2304739== by 0x12A630: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2304739== by 0x12473D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2304739== by 0x126CF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2304739== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2304739== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2304739== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==2304739== ==2304739== Open file descriptor 8: /dev/shm/open_mpi.0000 ==2304739== at 0xA11EBCC: __open_nocancel (open64_nocancel.c:39) ==2304739== by 0xA0A2C4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==2304739== by 0x9A3B822: ??? ==2304739== by 0x9A3B96F: ??? ==2304739== by 0xF56D6DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2304739== by 0xF56D938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2304739== by 0xF523922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2304739== by 0xF4C82DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2304739== by 0xB82B418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2304739== by 0xB7C4D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2304739== by 0xA4BBD38: PetscInitialize (pinit.c:924) ==2304739== by 0x9A0366F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2304739== by 0x9A036BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2304739== by 0x12A630: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2304739== by 0x12473D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2304739== by 0x126CF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2304739== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2304739== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2304739== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==2304739== ==2304739== Open file descriptor 117: ==2304739== ==2304739== ==2304739== Open file descriptor 110: ==2304739== ==2304739== ==2304739== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestBidomainWithSvi_valgrind.txt ==2304739== ==2304739== ==2304739== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==2304739== ==2304739== ==2304739== ==2304739== HEAP SUMMARY: ==2304739== in use at exit: 701,168 bytes in 9,383 blocks ==2304739== total heap usage: 3,538,714 allocs, 3,529,331 frees, 2,061,121,451 bytes allocated ==2304739== ==2304739== 552 bytes in 1 blocks are definitely lost in loss record 39 of 62 ==2304739== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==2304739== by 0x14591C13: ??? ==2304739== by 0x1459222C: ??? ==2304739== by 0x145054B7: ??? ==2304739== by 0xB79115A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2304739== by 0xB82BA97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2304739== by 0xB7C4D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2304739== by 0xA4BBD38: PetscInitialize (pinit.c:924) ==2304739== by 0x9A0366F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2304739== by 0x9A036BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2304739== by 0x12A630: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2304739== by 0x12473D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2304739== by 0x126CF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2304739== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2304739== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2304739== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==2304739== { 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 } ==2304739== 685,263 (136 direct, 685,127 indirect) bytes in 1 blocks are definitely lost in loss record 62 of 62 ==2304739== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==2304739== by 0x1570474E: ??? ==2304739== by 0x15704E0B: ??? ==2304739== by 0x15707F56: ??? ==2304739== by 0x156FD65D: ??? ==2304739== by 0x156FDFA3: ??? ==2304739== by 0xF5D9F05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==2304739== by 0xF5B5AE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==2304739== by 0xF566CB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==2304739== by 0xF493EF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2304739== by 0x13CC3F03: ??? ==2304739== by 0xF4C84CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==2304739== by 0xB82B418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2304739== by 0xB7C4D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==2304739== by 0xA4BBD38: PetscInitialize (pinit.c:924) ==2304739== by 0x9A0366F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==2304739== by 0x9A036BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==2304739== by 0x12A630: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==2304739== by 0x12473D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==2304739== by 0x126CF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==2304739== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==2304739== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==2304739== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==2304739== { 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 } ==2304739== LEAK SUMMARY: ==2304739== definitely lost: 688 bytes in 2 blocks ==2304739== indirectly lost: 1,760 bytes in 16 blocks ==2304739== possibly lost: 0 bytes in 0 blocks ==2304739== still reachable: 1,531 bytes in 6 blocks ==2304739== suppressed: 697,189 bytes in 9,359 blocks ==2304739== Reachable blocks (those to which a pointer was found) are not shown. ==2304739== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==2304739== ==2304739== Use --track-origins=yes to see where uninitialised values come from ==2304739== For lists of detected and suppressed errors, rerun with: -s ==2304739== ERROR SUMMARY: 44 errors from 6 contexts (suppressed: 25 from 25)