==935169== Memcheck, a memory error detector ==935169== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==935169== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==935169== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/heart/test/TestBidomainWithSvi -malloc_debug -malloc_dump -memory_info ==935169== Parent PID: 914403 ==935169== ==935169== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==935169== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==935169== ==935169== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==935169== at 0x9EFF79E: getsockopt_syscall (getsockopt.c:29) ==935169== by 0x9EFF79E: getsockopt (getsockopt.c:94) ==935169== by 0x1444D157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935169== by 0x14454A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935169== by 0x1445BDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935169== by 0x1435B3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935169== by 0x142D4E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==935169== by 0x13A93E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==935169== by 0xF2994CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==935169== by 0xB5FE418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935169== by 0xB597D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935169== by 0xA28ED38: PetscInitialize (pinit.c:924) ==935169== by 0x97D658B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==935169== by 0x97D65D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==935169== by 0x12A630: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==935169== by 0x12473D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==935169== by 0x126CF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==935169== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==935169== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==935169== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==935169== Address 0x1ffeffdfec is on thread 1's stack ==935169== in frame #2, created by pmix_ptl_base_make_connection (???:) ==935169== { 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 } ==935169== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==935169== at 0x9EFF79E: getsockopt_syscall (getsockopt.c:29) ==935169== by 0x9EFF79E: getsockopt (getsockopt.c:94) ==935169== by 0x1444D157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935169== by 0x14454A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935169== by 0x1445BDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935169== by 0x1435B3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935169== by 0x142D4E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==935169== by 0x13A93E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==935169== by 0xF2994CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==935169== by 0xB5FE418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935169== by 0xB597D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935169== by 0xA28ED38: PetscInitialize (pinit.c:924) ==935169== by 0x97D658B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==935169== by 0x97D65D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==935169== by 0x12A630: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==935169== by 0x12473D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==935169== by 0x126CF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==935169== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==935169== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==935169== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==935169== Address 0x1ffeffdfec is on thread 1's stack ==935169== in frame #2, created by pmix_ptl_base_make_connection (???:) ==935169== { 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 } ==935169== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==935169== at 0x9EFFC7E: setsockopt_syscall (setsockopt.c:29) ==935169== by 0x9EFFC7E: setsockopt (setsockopt.c:95) ==935169== by 0x14454BA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935169== by 0x1445BDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935169== by 0x1435B3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935169== by 0x142D4E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==935169== by 0x13A93E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==935169== by 0xF2994CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==935169== by 0xB5FE418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935169== by 0xB597D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935169== by 0xA28ED38: PetscInitialize (pinit.c:924) ==935169== by 0x97D658B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==935169== by 0x97D65D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==935169== by 0x12A630: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==935169== by 0x12473D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==935169== by 0x126CF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==935169== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==935169== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==935169== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==935169== { 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 } ==935169== Syscall param pwrite64(buf) points to uninitialised byte(s) ==935169== at 0x9EEA9EF: __libc_pwrite64 (pwrite64.c:25) ==935169== by 0x9EEA9EF: pwrite (pwrite64.c:23) ==935169== by 0x17CCA9D2: mca_fbtl_posix_pwritev (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_fbtl_posix.so) ==935169== by 0x17CDA419: mca_common_ompio_file_write (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==935169== by 0x17CDA79A: mca_common_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==935169== by 0x17BC589A: mca_io_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_io_ompio.so) ==935169== by 0xB58B6A7: PMPI_File_write_at (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935169== by 0xEC64FEB: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935169== by 0xEAA44ED: H5FD_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935169== by 0xEA87313: H5F__accum_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935169== by 0xEB82442: H5PB_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935169== by 0xEA8EDEA: H5F_block_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935169== by 0xEA18E98: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935169== by 0xEC583F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935169== by 0xEC599CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935169== by 0xEC5A47E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935169== by 0xE9F554C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935169== by 0xEA8D936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935169== by 0xEA8E3FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935169== by 0xEA91BB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935169== by 0xEA91EFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935169== by 0xEB0151F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935169== by 0xEB015EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935169== by 0xEA8E831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935169== by 0xEA83881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935169== by 0xBEF3967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==935169== by 0xBEEE647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==935169== by 0xBEEE6ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==935169== by 0x678ABE5: AbstractCardiacProblem<1u, 1u, 2u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==935169== by 0x678A785: AbstractCardiacProblem<1u, 1u, 2u>::Solve() (AbstractCardiacProblem.cpp:582) ==935169== by 0x12ADEF: TestBidomainWithSvi::TestConductionVelocityConvergesFasterWithSvi1d() (TestBidomainWithSvi.hpp:157) ==935169== by 0x12CDE8: TestDescription_TestBidomainWithSvi_TestConductionVelocityConvergesFasterWithSvi1d::runTest() (TestBidomainWithSvi.cpp:30) ==935169== by 0x123F74: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==935169== by 0x126FA6: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==935169== by 0x126E8B: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==935169== by 0x126D31: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==935169== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==935169== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==935169== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==935169== Address 0x1608338e is 62 bytes inside a block of size 320 alloc'd ==935169== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==935169== by 0xEA18E26: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935169== by 0xEC583F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935169== by 0xEC599CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935169== by 0xEC5A47E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935169== by 0xE9F554C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935169== by 0xEA8D936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935169== by 0xEA8E3FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935169== by 0xEA91BB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935169== by 0xEA91EFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935169== by 0xEB0151F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935169== by 0xEB015EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935169== by 0xEA8E831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935169== by 0xEA83881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935169== by 0xBEF3967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==935169== by 0xBEEE647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==935169== by 0xBEEE6ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==935169== by 0x678ABE5: AbstractCardiacProblem<1u, 1u, 2u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==935169== by 0x678A785: AbstractCardiacProblem<1u, 1u, 2u>::Solve() (AbstractCardiacProblem.cpp:582) ==935169== by 0x12ADEF: TestBidomainWithSvi::TestConductionVelocityConvergesFasterWithSvi1d() (TestBidomainWithSvi.hpp:157) ==935169== by 0x12CDE8: TestDescription_TestBidomainWithSvi_TestConductionVelocityConvergesFasterWithSvi1d::runTest() (TestBidomainWithSvi.cpp:30) ==935169== by 0x123F74: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==935169== by 0x126FA6: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==935169== by 0x126E8B: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==935169== by 0x126D31: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==935169== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==935169== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==935169== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==935169== { 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 } ==935169== ==935169== FILE DESCRIPTORS: 9 open (3 std) at exit. ==935169== Open file descriptor 12: ==935169== at 0x9EED22D: pipe (pipe.c:29) ==935169== by 0x13A9407D: ??? ==935169== by 0xF2994CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==935169== by 0xB5FE418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935169== by 0xB597D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935169== by 0xA28ED38: PetscInitialize (pinit.c:924) ==935169== by 0x97D658B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==935169== by 0x97D65D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==935169== by 0x12A630: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==935169== by 0x12473D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==935169== by 0x126CF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==935169== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==935169== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==935169== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==935169== ==935169== Open file descriptor 8: /dev/shm/open_mpi.0000 ==935169== at 0x9EF1BCC: __open_nocancel (open64_nocancel.c:39) ==935169== by 0x9E75C4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==935169== by 0x980E822: ??? ==935169== by 0x980E96F: ??? ==935169== by 0xF33E6DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==935169== by 0xF33E938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==935169== by 0xF2F4922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==935169== by 0xF2992DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==935169== by 0xB5FE418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935169== by 0xB597D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935169== by 0xA28ED38: PetscInitialize (pinit.c:924) ==935169== by 0x97D658B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==935169== by 0x97D65D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==935169== by 0x12A630: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==935169== by 0x12473D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==935169== by 0x126CF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==935169== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==935169== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==935169== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==935169== ==935169== Open file descriptor 111: ==935169== ==935169== ==935169== Open file descriptor 108: ==935169== ==935169== ==935169== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestBidomainWithSvi_valgrind.txt ==935169== ==935169== ==935169== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==935169== ==935169== ==935169== ==935169== HEAP SUMMARY: ==935169== in use at exit: 701,166 bytes in 9,383 blocks ==935169== total heap usage: 3,540,067 allocs, 3,530,684 frees, 2,061,211,916 bytes allocated ==935169== ==935169== 552 bytes in 1 blocks are definitely lost in loss record 39 of 62 ==935169== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==935169== by 0x14362C13: ??? ==935169== by 0x1436322C: ??? ==935169== by 0x142D64B7: ??? ==935169== by 0xB56415A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935169== by 0xB5FEA97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935169== by 0xB597D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935169== by 0xA28ED38: PetscInitialize (pinit.c:924) ==935169== by 0x97D658B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==935169== by 0x97D65D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==935169== by 0x12A630: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==935169== by 0x12473D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==935169== by 0x126CF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==935169== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==935169== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==935169== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==935169== { 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 } ==935169== 685,285 (136 direct, 685,149 indirect) bytes in 1 blocks are definitely lost in loss record 62 of 62 ==935169== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==935169== by 0x154D574E: ??? ==935169== by 0x154D5E0B: ??? ==935169== by 0x154D8F56: ??? ==935169== by 0x154CE65D: ??? ==935169== by 0x154CEFA3: ??? ==935169== by 0xF3AAF05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==935169== by 0xF386AE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==935169== by 0xF337CB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==935169== by 0xF264EF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==935169== by 0x13A94F03: ??? ==935169== by 0xF2994CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==935169== by 0xB5FE418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935169== by 0xB597D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935169== by 0xA28ED38: PetscInitialize (pinit.c:924) ==935169== by 0x97D658B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==935169== by 0x97D65D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==935169== by 0x12A630: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==935169== by 0x12473D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==935169== by 0x126CF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==935169== by 0x126BF4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==935169== by 0x127207: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==935169== by 0x122F40: main (TestBidomainWithSvi.cpp:18) ==935169== { 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 } ==935169== LEAK SUMMARY: ==935169== definitely lost: 688 bytes in 2 blocks ==935169== indirectly lost: 1,760 bytes in 16 blocks ==935169== possibly lost: 0 bytes in 0 blocks ==935169== still reachable: 1,531 bytes in 6 blocks ==935169== suppressed: 697,187 bytes in 9,359 blocks ==935169== Reachable blocks (those to which a pointer was found) are not shown. ==935169== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==935169== ==935169== Use --track-origins=yes to see where uninitialised values come from ==935169== For lists of detected and suppressed errors, rerun with: -s ==935169== ERROR SUMMARY: 44 errors from 6 contexts (suppressed: 25 from 25)