==3567840== Memcheck, a memory error detector ==3567840== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==3567840== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==3567840== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/heart/test/TestBidomainProblem -malloc_debug -malloc_dump -memory_info ==3567840== Parent PID: 3546972 ==3567840== ==3567840== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==3567840== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==3567840== ==3567840== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==3567840== at 0xBDF679E: getsockopt_syscall (getsockopt.c:29) ==3567840== by 0xBDF679E: getsockopt (getsockopt.c:94) ==3567840== by 0x14A17157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3567840== by 0x14A1EA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3567840== by 0x14A25DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3567840== by 0x149253C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3567840== by 0x1489EE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==3567840== by 0x1405DE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==3567840== by 0xF8164CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3567840== by 0xB6D4418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567840== by 0xB66DD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567840== by 0xA364D38: PetscInitialize (pinit.c:924) ==3567840== by 0xA1D4717: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3567840== by 0xA1D4765: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3567840== by 0x14AE64: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3567840== by 0x1430E1: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3567840== by 0x146866: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3567840== by 0x146706: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3567840== by 0x146D9D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3567840== by 0x141270: main (TestBidomainProblem.cpp:19) ==3567840== Address 0x1ffeffdfac is on thread 1's stack ==3567840== in frame #2, created by pmix_ptl_base_make_connection (???:) ==3567840== { 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 } ==3567840== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==3567840== at 0xBDF679E: getsockopt_syscall (getsockopt.c:29) ==3567840== by 0xBDF679E: getsockopt (getsockopt.c:94) ==3567840== by 0x14A17157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3567840== by 0x14A1EA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3567840== by 0x14A25DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3567840== by 0x149253C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3567840== by 0x1489EE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==3567840== by 0x1405DE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==3567840== by 0xF8164CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3567840== by 0xB6D4418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567840== by 0xB66DD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567840== by 0xA364D38: PetscInitialize (pinit.c:924) ==3567840== by 0xA1D4717: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3567840== by 0xA1D4765: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3567840== by 0x14AE64: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3567840== by 0x1430E1: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3567840== by 0x146866: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3567840== by 0x146706: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3567840== by 0x146D9D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3567840== by 0x141270: main (TestBidomainProblem.cpp:19) ==3567840== Address 0x1ffeffdfac is on thread 1's stack ==3567840== in frame #2, created by pmix_ptl_base_make_connection (???:) ==3567840== { 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 } ==3567840== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==3567840== at 0xBDF6C7E: setsockopt_syscall (setsockopt.c:29) ==3567840== by 0xBDF6C7E: setsockopt (setsockopt.c:95) ==3567840== by 0x14A1EBA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3567840== by 0x14A25DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3567840== by 0x149253C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3567840== by 0x1489EE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==3567840== by 0x1405DE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==3567840== by 0xF8164CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3567840== by 0xB6D4418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567840== by 0xB66DD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567840== by 0xA364D38: PetscInitialize (pinit.c:924) ==3567840== by 0xA1D4717: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3567840== by 0xA1D4765: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3567840== by 0x14AE64: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3567840== by 0x1430E1: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3567840== by 0x146866: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3567840== by 0x146706: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3567840== by 0x146D9D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3567840== by 0x141270: main (TestBidomainProblem.cpp:19) ==3567840== { 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 } ==3567840== Syscall param pwrite64(buf) points to uninitialised byte(s) ==3567840== at 0xBDE19EF: __libc_pwrite64 (pwrite64.c:25) ==3567840== by 0xBDE19EF: pwrite (pwrite64.c:23) ==3567840== by 0x186949D2: mca_fbtl_posix_pwritev (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_fbtl_posix.so) ==3567840== by 0x186A4419: mca_common_ompio_file_write (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==3567840== by 0x186A479A: mca_common_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==3567840== by 0x1858F89A: mca_io_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_io_ompio.so) ==3567840== by 0xB6616A7: PMPI_File_write_at (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567840== by 0xC7E6FEB: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567840== by 0xC6264ED: H5FD_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567840== by 0xC609313: H5F__accum_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567840== by 0xC704442: H5PB_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567840== by 0xC610DEA: H5F_block_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567840== by 0xC59AE98: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567840== by 0xC7DA3F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567840== by 0xC7DB9CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567840== by 0xC7DC47E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567840== by 0xC57754C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567840== by 0xC60F936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567840== by 0xC6103FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567840== by 0xC613BB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567840== by 0xC613EFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567840== by 0xC68351F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567840== by 0xC6835EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567840== by 0xC610831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567840== by 0xC605881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567840== by 0xA102967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==3567840== by 0xA0FD647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==3567840== by 0xA0FD6ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==3567840== by 0x68749DF: AbstractCardiacProblem<1u, 1u, 2u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==3567840== by 0x687486B: AbstractCardiacProblem<1u, 1u, 2u>::Solve() (AbstractCardiacProblem.cpp:527) ==3567840== by 0x14E102: TestBidomainProblem::TestBidomainErrorHandling() (TestBidomainProblem.hpp:209) ==3567840== by 0x169134: TestDescription_TestBidomainProblem_TestBidomainErrorHandling::runTest() (TestBidomainProblem.cpp:31) ==3567840== by 0x1426DC: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==3567840== by 0x146B14: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==3567840== by 0x1469F9: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==3567840== by 0x14689F: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==3567840== by 0x146706: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3567840== by 0x146D9D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3567840== by 0x141270: main (TestBidomainProblem.cpp:19) ==3567840== Address 0x167447de is 62 bytes inside a block of size 320 alloc'd ==3567840== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==3567840== by 0xC59AE26: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567840== by 0xC7DA3F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567840== by 0xC7DB9CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567840== by 0xC7DC47E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567840== by 0xC57754C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567840== by 0xC60F936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567840== by 0xC6103FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567840== by 0xC613BB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567840== by 0xC613EFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567840== by 0xC68351F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567840== by 0xC6835EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567840== by 0xC610831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567840== by 0xC605881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567840== by 0xA102967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==3567840== by 0xA0FD647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==3567840== by 0xA0FD6ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==3567840== by 0x68749DF: AbstractCardiacProblem<1u, 1u, 2u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==3567840== by 0x687486B: AbstractCardiacProblem<1u, 1u, 2u>::Solve() (AbstractCardiacProblem.cpp:527) ==3567840== by 0x14E102: TestBidomainProblem::TestBidomainErrorHandling() (TestBidomainProblem.hpp:209) ==3567840== by 0x169134: TestDescription_TestBidomainProblem_TestBidomainErrorHandling::runTest() (TestBidomainProblem.cpp:31) ==3567840== by 0x1426DC: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==3567840== by 0x146B14: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==3567840== by 0x1469F9: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==3567840== by 0x14689F: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==3567840== by 0x146706: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3567840== by 0x146D9D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3567840== by 0x141270: main (TestBidomainProblem.cpp:19) ==3567840== { 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 } ==3567840== ==3567840== FILE DESCRIPTORS: 9 open (3 std) at exit. ==3567840== Open file descriptor 12: ==3567840== at 0xBDE422D: pipe (pipe.c:29) ==3567840== by 0x1405E07D: ??? ==3567840== by 0xF8164CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3567840== by 0xB6D4418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567840== by 0xB66DD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567840== by 0xA364D38: PetscInitialize (pinit.c:924) ==3567840== by 0xA1D4717: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3567840== by 0xA1D4765: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3567840== by 0x14AE64: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3567840== by 0x1430E1: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3567840== by 0x146866: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3567840== by 0x146706: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3567840== by 0x146D9D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3567840== by 0x141270: main (TestBidomainProblem.cpp:19) ==3567840== ==3567840== Open file descriptor 8: /dev/shm/open_mpi.0000 ==3567840== at 0xBDE8BCC: __open_nocancel (open64_nocancel.c:39) ==3567840== by 0xBD6CC4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==3567840== by 0xA20C822: ??? ==3567840== by 0xA20C96F: ??? ==3567840== by 0xF8BB6DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==3567840== by 0xF8BB938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==3567840== by 0xF871922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==3567840== by 0xF8162DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3567840== by 0xB6D4418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567840== by 0xB66DD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567840== by 0xA364D38: PetscInitialize (pinit.c:924) ==3567840== by 0xA1D4717: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3567840== by 0xA1D4765: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3567840== by 0x14AE64: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3567840== by 0x1430E1: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3567840== by 0x146866: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3567840== by 0x146706: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3567840== by 0x146D9D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3567840== by 0x141270: main (TestBidomainProblem.cpp:19) ==3567840== ==3567840== Open file descriptor 117: ==3567840== ==3567840== ==3567840== Open file descriptor 110: ==3567840== ==3567840== ==3567840== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestBidomainProblem_valgrind.txt ==3567840== ==3567840== ==3567840== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==3567840== ==3567840== ==3567840== ==3567840== HEAP SUMMARY: ==3567840== in use at exit: 707,511 bytes in 9,499 blocks ==3567840== total heap usage: 585,795 allocs, 576,296 frees, 1,563,699,110 bytes allocated ==3567840== ==3567840== 448 bytes in 8 blocks are definitely lost in loss record 55 of 83 ==3567840== at 0x4849013: operator new(unsigned long) (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==3567840== by 0x94037D5: OpenSimplex2S::initLatticePoints() (OpenSimplex2S.cpp:442) ==3567840== by 0x9401A6E: OpenSimplex2S::Initializer::Initializer() (OpenSimplex2S.cpp:14) ==3567840== by 0x9404A14: __static_initialization_and_destruction_0(int, int) (OpenSimplex2S.cpp:18) ==3567840== by 0x9404A39: _GLOBAL__sub_I_OpenSimplex2S.cpp (OpenSimplex2S.cpp:1064) ==3567840== by 0x400647D: call_init.part.0 (dl-init.c:70) ==3567840== by 0x4006567: call_init (dl-init.c:33) ==3567840== by 0x4006567: _dl_init (dl-init.c:117) ==3567840== by 0x40202E9: ??? (in /usr/lib/x86_64-linux-gnu/ld-linux-x86-64.so.2) ==3567840== by 0x3: ??? ==3567840== by 0x1FFF000322: ??? ==3567840== by 0x1FFF000389: ??? ==3567840== by 0x1FFF000397: ??? ==3567840== by 0x1FFF0003A4: ??? ==3567840== { Memcheck:Leak match-leak-kinds: definite fun:_Znwm fun:_ZN13OpenSimplex2S17initLatticePointsEv fun:_ZN13OpenSimplex2S11InitializerC1Ev fun:_Z41__static_initialization_and_destruction_0ii fun:_GLOBAL__sub_I_OpenSimplex2S.cpp fun:call_init.part.0 fun:call_init fun:_dl_init obj:/usr/lib/x86_64-linux-gnu/ld-linux-x86-64.so.2 obj:* obj:* obj:* obj:* obj:* } ==3567840== 552 bytes in 1 blocks are definitely lost in loss record 57 of 83 ==3567840== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==3567840== by 0x1492CC13: ??? ==3567840== by 0x1492D22C: ??? ==3567840== by 0x148A04B7: ??? ==3567840== by 0xB63A15A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567840== by 0xB6D4A97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567840== by 0xB66DD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567840== by 0xA364D38: PetscInitialize (pinit.c:924) ==3567840== by 0xA1D4717: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3567840== by 0xA1D4765: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3567840== by 0x14AE64: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3567840== by 0x1430E1: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3567840== by 0x146866: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3567840== by 0x146706: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3567840== by 0x146D9D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3567840== by 0x141270: main (TestBidomainProblem.cpp:19) ==3567840== { 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 } ==3567840== 84,459 (136 direct, 84,323 indirect) bytes in 1 blocks are definitely lost in loss record 80 of 83 ==3567840== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==3567840== by 0x15A9F74E: ??? ==3567840== by 0x15A9FE0B: ??? ==3567840== by 0x15AA2F56: ??? ==3567840== by 0x15A9865D: ??? ==3567840== by 0x15A98FA3: ??? ==3567840== by 0xF927F05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==3567840== by 0xF903AE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==3567840== by 0xF8B4CB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==3567840== by 0xF7E1EF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3567840== by 0x1405EF03: ??? ==3567840== by 0xF8164CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3567840== by 0xB6D4418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567840== by 0xB66DD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567840== by 0xA364D38: PetscInitialize (pinit.c:924) ==3567840== by 0xA1D4717: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3567840== by 0xA1D4765: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3567840== by 0x14AE64: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3567840== by 0x1430E1: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3567840== by 0x146866: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3567840== by 0x146706: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3567840== by 0x146D9D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3567840== by 0x141270: main (TestBidomainProblem.cpp:19) ==3567840== { 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 } ==3567840== LEAK SUMMARY: ==3567840== definitely lost: 1,136 bytes in 10 blocks ==3567840== indirectly lost: 1,760 bytes in 16 blocks ==3567840== possibly lost: 0 bytes in 0 blocks ==3567840== still reachable: 7,355 bytes in 110 blocks ==3567840== suppressed: 697,260 bytes in 9,363 blocks ==3567840== Reachable blocks (those to which a pointer was found) are not shown. ==3567840== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==3567840== ==3567840== Use --track-origins=yes to see where uninitialised values come from ==3567840== For lists of detected and suppressed errors, rerun with: -s ==3567840== ERROR SUMMARY: 72 errors from 7 contexts (suppressed: 32 from 32)