==935153== Memcheck, a memory error detector ==935153== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==935153== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==935153== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/heart/test/TestBidomainProblem -malloc_debug -malloc_dump -memory_info ==935153== Parent PID: 914403 ==935153== ==935153== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==935153== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==935153== ==935153== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==935153== at 0xB82F79E: getsockopt_syscall (getsockopt.c:29) ==935153== by 0xB82F79E: getsockopt (getsockopt.c:94) ==935153== by 0x1444E157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935153== by 0x14455A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935153== by 0x1445CDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935153== by 0x1435C3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935153== by 0x142D5E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==935153== by 0x13A94E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==935153== by 0xF24B4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==935153== by 0xB10D418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935153== by 0xB0A6D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935153== by 0x9D9DD38: PetscInitialize (pinit.c:924) ==935153== by 0x9C0D58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==935153== by 0x9C0D5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==935153== by 0x14AE64: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==935153== by 0x1430E1: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==935153== by 0x146866: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==935153== by 0x146706: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==935153== by 0x146D9D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==935153== by 0x141270: main (TestBidomainProblem.cpp:19) ==935153== Address 0x1ffeffdfdc is on thread 1's stack ==935153== in frame #2, created by pmix_ptl_base_make_connection (???:) ==935153== { 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 } ==935153== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==935153== at 0xB82F79E: getsockopt_syscall (getsockopt.c:29) ==935153== by 0xB82F79E: getsockopt (getsockopt.c:94) ==935153== by 0x1444E157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935153== by 0x14455A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935153== by 0x1445CDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935153== by 0x1435C3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935153== by 0x142D5E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==935153== by 0x13A94E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==935153== by 0xF24B4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==935153== by 0xB10D418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935153== by 0xB0A6D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935153== by 0x9D9DD38: PetscInitialize (pinit.c:924) ==935153== by 0x9C0D58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==935153== by 0x9C0D5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==935153== by 0x14AE64: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==935153== by 0x1430E1: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==935153== by 0x146866: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==935153== by 0x146706: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==935153== by 0x146D9D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==935153== by 0x141270: main (TestBidomainProblem.cpp:19) ==935153== Address 0x1ffeffdfdc is on thread 1's stack ==935153== in frame #2, created by pmix_ptl_base_make_connection (???:) ==935153== { 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 } ==935153== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==935153== at 0xB82FC7E: setsockopt_syscall (setsockopt.c:29) ==935153== by 0xB82FC7E: setsockopt (setsockopt.c:95) ==935153== by 0x14455BA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935153== by 0x1445CDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935153== by 0x1435C3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935153== by 0x142D5E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==935153== by 0x13A94E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==935153== by 0xF24B4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==935153== by 0xB10D418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935153== by 0xB0A6D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935153== by 0x9D9DD38: PetscInitialize (pinit.c:924) ==935153== by 0x9C0D58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==935153== by 0x9C0D5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==935153== by 0x14AE64: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==935153== by 0x1430E1: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==935153== by 0x146866: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==935153== by 0x146706: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==935153== by 0x146D9D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==935153== by 0x141270: main (TestBidomainProblem.cpp:19) ==935153== { 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 } ==935153== Syscall param pwrite64(buf) points to uninitialised byte(s) ==935153== at 0xB81A9EF: __libc_pwrite64 (pwrite64.c:25) ==935153== by 0xB81A9EF: pwrite (pwrite64.c:23) ==935153== by 0x17CCB9D2: mca_fbtl_posix_pwritev (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_fbtl_posix.so) ==935153== by 0x17CDB419: mca_common_ompio_file_write (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==935153== by 0x17CDB79A: mca_common_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==935153== by 0x17BC689A: mca_io_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_io_ompio.so) ==935153== by 0xB09A6A7: PMPI_File_write_at (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935153== by 0xC21FFEB: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935153== by 0xC05F4ED: H5FD_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935153== by 0xC042313: H5F__accum_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935153== by 0xC13D442: H5PB_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935153== by 0xC049DEA: H5F_block_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935153== by 0xBFD3E98: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935153== by 0xC2133F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935153== by 0xC2149CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935153== by 0xC21547E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935153== by 0xBFB054C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935153== by 0xC048936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935153== by 0xC0493FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935153== by 0xC04CBB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935153== by 0xC04CEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935153== by 0xC0BC51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935153== by 0xC0BC5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935153== by 0xC049831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935153== by 0xC03E881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935153== by 0x9B3C967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==935153== by 0x9B37647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==935153== by 0x9B376ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==935153== by 0x678ABE5: AbstractCardiacProblem<1u, 1u, 2u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==935153== by 0x678AA71: AbstractCardiacProblem<1u, 1u, 2u>::Solve() (AbstractCardiacProblem.cpp:527) ==935153== by 0x14E102: TestBidomainProblem::TestBidomainErrorHandling() (TestBidomainProblem.hpp:209) ==935153== by 0x169134: TestDescription_TestBidomainProblem_TestBidomainErrorHandling::runTest() (TestBidomainProblem.cpp:31) ==935153== by 0x1426DC: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==935153== by 0x146B14: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==935153== by 0x1469F9: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==935153== by 0x14689F: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==935153== by 0x146706: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==935153== by 0x146D9D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==935153== by 0x141270: main (TestBidomainProblem.cpp:19) ==935153== Address 0x1648812e is 62 bytes inside a block of size 320 alloc'd ==935153== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==935153== by 0xBFD3E26: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935153== by 0xC2133F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935153== by 0xC2149CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935153== by 0xC21547E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935153== by 0xBFB054C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935153== by 0xC048936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935153== by 0xC0493FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935153== by 0xC04CBB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935153== by 0xC04CEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935153== by 0xC0BC51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935153== by 0xC0BC5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935153== by 0xC049831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935153== by 0xC03E881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935153== by 0x9B3C967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==935153== by 0x9B37647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==935153== by 0x9B376ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==935153== by 0x678ABE5: AbstractCardiacProblem<1u, 1u, 2u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==935153== by 0x678AA71: AbstractCardiacProblem<1u, 1u, 2u>::Solve() (AbstractCardiacProblem.cpp:527) ==935153== by 0x14E102: TestBidomainProblem::TestBidomainErrorHandling() (TestBidomainProblem.hpp:209) ==935153== by 0x169134: TestDescription_TestBidomainProblem_TestBidomainErrorHandling::runTest() (TestBidomainProblem.cpp:31) ==935153== by 0x1426DC: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==935153== by 0x146B14: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==935153== by 0x1469F9: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==935153== by 0x14689F: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==935153== by 0x146706: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==935153== by 0x146D9D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==935153== by 0x141270: main (TestBidomainProblem.cpp:19) ==935153== { 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:_ZN19TestBidomainProblem25TestBidomainErrorHandlingEv fun:_ZN61TestDescription_TestBidomainProblem_TestBidomainErrorHandling7runTestEv fun:_ZN7CxxTest19RealTestDescription3runEv fun:_ZN7CxxTest10TestRunner7runTestERNS_15TestDescriptionE fun:_ZN7CxxTest10TestRunner8runSuiteERNS_16SuiteDescriptionE fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==935153== ==935153== FILE DESCRIPTORS: 9 open (3 std) at exit. ==935153== Open file descriptor 12: ==935153== at 0xB81D22D: pipe (pipe.c:29) ==935153== by 0x13A9507D: ??? ==935153== by 0xF24B4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==935153== by 0xB10D418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935153== by 0xB0A6D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935153== by 0x9D9DD38: PetscInitialize (pinit.c:924) ==935153== by 0x9C0D58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==935153== by 0x9C0D5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==935153== by 0x14AE64: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==935153== by 0x1430E1: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==935153== by 0x146866: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==935153== by 0x146706: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==935153== by 0x146D9D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==935153== by 0x141270: main (TestBidomainProblem.cpp:19) ==935153== ==935153== Open file descriptor 8: /dev/shm/open_mpi.0000 ==935153== at 0xB821BCC: __open_nocancel (open64_nocancel.c:39) ==935153== by 0xB7A5C4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==935153== by 0x9C45822: ??? ==935153== by 0x9C4596F: ??? ==935153== by 0xF2F06DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==935153== by 0xF2F0938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==935153== by 0xF2A6922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==935153== by 0xF24B2DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==935153== by 0xB10D418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935153== by 0xB0A6D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935153== by 0x9D9DD38: PetscInitialize (pinit.c:924) ==935153== by 0x9C0D58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==935153== by 0x9C0D5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==935153== by 0x14AE64: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==935153== by 0x1430E1: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==935153== by 0x146866: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==935153== by 0x146706: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==935153== by 0x146D9D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==935153== by 0x141270: main (TestBidomainProblem.cpp:19) ==935153== ==935153== Open file descriptor 111: ==935153== ==935153== ==935153== Open file descriptor 108: ==935153== ==935153== ==935153== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestBidomainProblem_valgrind.txt ==935153== ==935153== ==935153== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==935153== ==935153== ==935153== ==935153== HEAP SUMMARY: ==935153== in use at exit: 701,234 bytes in 9,387 blocks ==935153== total heap usage: 585,655 allocs, 576,268 frees, 1,563,714,372 bytes allocated ==935153== ==935153== 552 bytes in 1 blocks are definitely lost in loss record 44 of 67 ==935153== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==935153== by 0x14363C13: ??? ==935153== by 0x1436422C: ??? ==935153== by 0x142D74B7: ??? ==935153== by 0xB07315A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935153== by 0xB10DA97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935153== by 0xB0A6D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935153== by 0x9D9DD38: PetscInitialize (pinit.c:924) ==935153== by 0x9C0D58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==935153== by 0x9C0D5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==935153== by 0x14AE64: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==935153== by 0x1430E1: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==935153== by 0x146866: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==935153== by 0x146706: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==935153== by 0x146D9D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==935153== by 0x141270: main (TestBidomainProblem.cpp:19) ==935153== { 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 } ==935153== 685,218 (136 direct, 685,082 indirect) bytes in 1 blocks are definitely lost in loss record 67 of 67 ==935153== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==935153== by 0x154D674E: ??? ==935153== by 0x154D6E0B: ??? ==935153== by 0x154D9F56: ??? ==935153== by 0x154CF65D: ??? ==935153== by 0x154CFFA3: ??? ==935153== by 0xF35EF05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==935153== by 0xF33AAE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==935153== by 0xF2E9CB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==935153== by 0xF216EF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==935153== by 0x13A95F03: ??? ==935153== by 0xF24B4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==935153== by 0xB10D418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935153== by 0xB0A6D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935153== by 0x9D9DD38: PetscInitialize (pinit.c:924) ==935153== by 0x9C0D58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==935153== by 0x9C0D5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==935153== by 0x14AE64: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==935153== by 0x1430E1: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==935153== by 0x146866: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==935153== by 0x146706: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==935153== by 0x146D9D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==935153== by 0x141270: main (TestBidomainProblem.cpp:19) ==935153== { 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 } ==935153== LEAK SUMMARY: ==935153== definitely lost: 688 bytes in 2 blocks ==935153== indirectly lost: 1,760 bytes in 16 blocks ==935153== possibly lost: 0 bytes in 0 blocks ==935153== still reachable: 1,531 bytes in 6 blocks ==935153== suppressed: 697,255 bytes in 9,363 blocks ==935153== Reachable blocks (those to which a pointer was found) are not shown. ==935153== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==935153== ==935153== Use --track-origins=yes to see where uninitialised values come from ==935153== For lists of detected and suppressed errors, rerun with: -s ==935153== ERROR SUMMARY: 71 errors from 6 contexts (suppressed: 30 from 30)