==3567863== Memcheck, a memory error detector ==3567863== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==3567863== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==3567863== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/heart/test/TestBidomainWithSvi -malloc_debug -malloc_dump -memory_info ==3567863== Parent PID: 3546972 ==3567863== ==3567863== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==3567863== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==3567863== ==3567863== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==3567863== at 0xA4C679E: getsockopt_syscall (getsockopt.c:29) ==3567863== by 0xA4C679E: getsockopt (getsockopt.c:94) ==3567863== by 0x14A15157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3567863== by 0x14A1CA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3567863== by 0x14A23DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3567863== by 0x149233C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3567863== by 0x1489CE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==3567863== by 0x1405BE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==3567863== by 0xF8674CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3567863== by 0xBBC5418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567863== by 0xBB5ED7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567863== by 0xA855D38: PetscInitialize (pinit.c:924) ==3567863== by 0x9D9D717: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3567863== by 0x9D9D765: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3567863== by 0x12A630: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3567863== by 0x12473D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3567863== by 0x126CF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3567863== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3567863== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3567863== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==3567863== Address 0x1ffeffdfbc is on thread 1's stack ==3567863== in frame #2, created by pmix_ptl_base_make_connection (???:) ==3567863== { 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 } ==3567863== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==3567863== at 0xA4C679E: getsockopt_syscall (getsockopt.c:29) ==3567863== by 0xA4C679E: getsockopt (getsockopt.c:94) ==3567863== by 0x14A15157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3567863== by 0x14A1CA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3567863== by 0x14A23DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3567863== by 0x149233C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3567863== by 0x1489CE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==3567863== by 0x1405BE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==3567863== by 0xF8674CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3567863== by 0xBBC5418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567863== by 0xBB5ED7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567863== by 0xA855D38: PetscInitialize (pinit.c:924) ==3567863== by 0x9D9D717: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3567863== by 0x9D9D765: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3567863== by 0x12A630: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3567863== by 0x12473D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3567863== by 0x126CF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3567863== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3567863== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3567863== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==3567863== Address 0x1ffeffdfbc is on thread 1's stack ==3567863== in frame #2, created by pmix_ptl_base_make_connection (???:) ==3567863== { 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 } ==3567863== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==3567863== at 0xA4C6C7E: setsockopt_syscall (setsockopt.c:29) ==3567863== by 0xA4C6C7E: setsockopt (setsockopt.c:95) ==3567863== by 0x14A1CBA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3567863== by 0x14A23DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3567863== by 0x149233C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3567863== by 0x1489CE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==3567863== by 0x1405BE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==3567863== by 0xF8674CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3567863== by 0xBBC5418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567863== by 0xBB5ED7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567863== by 0xA855D38: PetscInitialize (pinit.c:924) ==3567863== by 0x9D9D717: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3567863== by 0x9D9D765: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3567863== by 0x12A630: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3567863== by 0x12473D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3567863== by 0x126CF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3567863== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3567863== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3567863== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==3567863== { 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 } ==3567863== Syscall param pwrite64(buf) points to uninitialised byte(s) ==3567863== at 0xA4B19EF: __libc_pwrite64 (pwrite64.c:25) ==3567863== by 0xA4B19EF: pwrite (pwrite64.c:23) ==3567863== by 0x186929D2: mca_fbtl_posix_pwritev (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_fbtl_posix.so) ==3567863== by 0x186A2419: mca_common_ompio_file_write (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==3567863== by 0x186A279A: mca_common_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==3567863== by 0x1858D89A: mca_io_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_io_ompio.so) ==3567863== by 0xBB526A7: PMPI_File_write_at (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567863== by 0xF232FEB: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567863== by 0xF0724ED: H5FD_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567863== by 0xF055313: H5F__accum_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567863== by 0xF150442: H5PB_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567863== by 0xF05CDEA: H5F_block_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567863== by 0xEFE6E98: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567863== by 0xF2263F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567863== by 0xF2279CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567863== by 0xF22847E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567863== by 0xEFC354C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567863== by 0xF05B936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567863== by 0xF05C3FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567863== by 0xF05FBB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567863== by 0xF05FEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567863== by 0xF0CF51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567863== by 0xF0CF5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567863== by 0xF05C831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567863== by 0xF051881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567863== by 0xC4BA967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==3567863== by 0xC4B5647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==3567863== by 0xC4B56ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==3567863== by 0x68749DF: AbstractCardiacProblem<1u, 1u, 2u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==3567863== by 0x687457F: AbstractCardiacProblem<1u, 1u, 2u>::Solve() (AbstractCardiacProblem.cpp:582) ==3567863== by 0x12ADEF: TestBidomainWithSvi::TestConductionVelocityConvergesFasterWithSvi1d() (TestBidomainWithSvi.hpp:157) ==3567863== by 0x12CDE8: TestDescription_TestBidomainWithSvi_TestConductionVelocityConvergesFasterWithSvi1d::runTest() (TestBidomainWithSvi.cpp:30) ==3567863== by 0x123F74: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==3567863== by 0x126FA6: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==3567863== by 0x126E8B: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==3567863== by 0x126D31: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==3567863== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3567863== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3567863== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==3567863== Address 0x16ae5dae is 62 bytes inside a block of size 320 alloc'd ==3567863== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==3567863== by 0xEFE6E26: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567863== by 0xF2263F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567863== by 0xF2279CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567863== by 0xF22847E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567863== by 0xEFC354C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567863== by 0xF05B936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567863== by 0xF05C3FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567863== by 0xF05FBB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567863== by 0xF05FEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567863== by 0xF0CF51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567863== by 0xF0CF5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567863== by 0xF05C831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567863== by 0xF051881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3567863== by 0xC4BA967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==3567863== by 0xC4B5647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==3567863== by 0xC4B56ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==3567863== by 0x68749DF: AbstractCardiacProblem<1u, 1u, 2u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==3567863== by 0x687457F: AbstractCardiacProblem<1u, 1u, 2u>::Solve() (AbstractCardiacProblem.cpp:582) ==3567863== by 0x12ADEF: TestBidomainWithSvi::TestConductionVelocityConvergesFasterWithSvi1d() (TestBidomainWithSvi.hpp:157) ==3567863== by 0x12CDE8: TestDescription_TestBidomainWithSvi_TestConductionVelocityConvergesFasterWithSvi1d::runTest() (TestBidomainWithSvi.cpp:30) ==3567863== by 0x123F74: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==3567863== by 0x126FA6: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==3567863== by 0x126E8B: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==3567863== by 0x126D31: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==3567863== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3567863== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3567863== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==3567863== { 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 } ==3567863== ==3567863== FILE DESCRIPTORS: 9 open (3 std) at exit. ==3567863== Open file descriptor 12: ==3567863== at 0xA4B422D: pipe (pipe.c:29) ==3567863== by 0x1405C07D: ??? ==3567863== by 0xF8674CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3567863== by 0xBBC5418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567863== by 0xBB5ED7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567863== by 0xA855D38: PetscInitialize (pinit.c:924) ==3567863== by 0x9D9D717: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3567863== by 0x9D9D765: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3567863== by 0x12A630: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3567863== by 0x12473D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3567863== by 0x126CF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3567863== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3567863== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3567863== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==3567863== ==3567863== Open file descriptor 8: /dev/shm/open_mpi.0000 ==3567863== at 0xA4B8BCC: __open_nocancel (open64_nocancel.c:39) ==3567863== by 0xA43CC4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==3567863== by 0x9DD5822: ??? ==3567863== by 0x9DD596F: ??? ==3567863== by 0xF90C6DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==3567863== by 0xF90C938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==3567863== by 0xF8C2922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==3567863== by 0xF8672DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3567863== by 0xBBC5418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567863== by 0xBB5ED7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567863== by 0xA855D38: PetscInitialize (pinit.c:924) ==3567863== by 0x9D9D717: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3567863== by 0x9D9D765: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3567863== by 0x12A630: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3567863== by 0x12473D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3567863== by 0x126CF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3567863== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3567863== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3567863== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==3567863== ==3567863== Open file descriptor 117: ==3567863== ==3567863== ==3567863== Open file descriptor 110: ==3567863== ==3567863== ==3567863== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestBidomainWithSvi_valgrind.txt ==3567863== ==3567863== ==3567863== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==3567863== ==3567863== ==3567863== ==3567863== HEAP SUMMARY: ==3567863== in use at exit: 707,440 bytes in 9,495 blocks ==3567863== total heap usage: 3,540,382 allocs, 3,530,887 frees, 2,061,413,503 bytes allocated ==3567863== ==3567863== 448 bytes in 8 blocks are definitely lost in loss record 51 of 79 ==3567863== at 0x4849013: operator new(unsigned long) (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==3567863== by 0x90537D5: OpenSimplex2S::initLatticePoints() (OpenSimplex2S.cpp:442) ==3567863== by 0x9051A6E: OpenSimplex2S::Initializer::Initializer() (OpenSimplex2S.cpp:14) ==3567863== by 0x9054A14: __static_initialization_and_destruction_0(int, int) (OpenSimplex2S.cpp:18) ==3567863== by 0x9054A39: _GLOBAL__sub_I_OpenSimplex2S.cpp (OpenSimplex2S.cpp:1064) ==3567863== by 0x400647D: call_init.part.0 (dl-init.c:70) ==3567863== by 0x4006567: call_init (dl-init.c:33) ==3567863== by 0x4006567: _dl_init (dl-init.c:117) ==3567863== by 0x40202E9: ??? (in /usr/lib/x86_64-linux-gnu/ld-linux-x86-64.so.2) ==3567863== by 0x3: ??? ==3567863== by 0x1FFF000322: ??? ==3567863== by 0x1FFF000389: ??? ==3567863== by 0x1FFF000397: ??? ==3567863== by 0x1FFF0003A4: ??? ==3567863== { 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:* } ==3567863== 552 bytes in 1 blocks are definitely lost in loss record 53 of 79 ==3567863== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==3567863== by 0x1492AC13: ??? ==3567863== by 0x1492B22C: ??? ==3567863== by 0x1489E4B7: ??? ==3567863== by 0xBB2B15A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567863== by 0xBBC5A97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567863== by 0xBB5ED7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567863== by 0xA855D38: PetscInitialize (pinit.c:924) ==3567863== by 0x9D9D717: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3567863== by 0x9D9D765: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3567863== by 0x12A630: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3567863== by 0x12473D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3567863== by 0x126CF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3567863== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3567863== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3567863== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==3567863== { 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 } ==3567863== 84,459 (136 direct, 84,323 indirect) bytes in 1 blocks are definitely lost in loss record 76 of 79 ==3567863== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==3567863== by 0x15A9D74E: ??? ==3567863== by 0x15A9DE0B: ??? ==3567863== by 0x15AA0F56: ??? ==3567863== by 0x15A9665D: ??? ==3567863== by 0x15A96FA3: ??? ==3567863== by 0xF978F05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==3567863== by 0xF954AE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==3567863== by 0xF905CB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==3567863== by 0xF832EF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3567863== by 0x1405CF03: ??? ==3567863== by 0xF8674CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3567863== by 0xBBC5418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567863== by 0xBB5ED7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3567863== by 0xA855D38: PetscInitialize (pinit.c:924) ==3567863== by 0x9D9D717: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3567863== by 0x9D9D765: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3567863== by 0x12A630: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3567863== by 0x12473D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3567863== by 0x126CF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3567863== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3567863== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3567863== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==3567863== { 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 } ==3567863== LEAK SUMMARY: ==3567863== definitely lost: 1,136 bytes in 10 blocks ==3567863== indirectly lost: 1,760 bytes in 16 blocks ==3567863== possibly lost: 0 bytes in 0 blocks ==3567863== still reachable: 7,355 bytes in 110 blocks ==3567863== suppressed: 697,189 bytes in 9,359 blocks ==3567863== Reachable blocks (those to which a pointer was found) are not shown. ==3567863== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==3567863== ==3567863== Use --track-origins=yes to see where uninitialised values come from ==3567863== For lists of detected and suppressed errors, rerun with: -s ==3567863== ERROR SUMMARY: 45 errors from 7 contexts (suppressed: 28 from 28)