==935155== Memcheck, a memory error detector ==935155== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==935155== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==935155== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/heart/test/TestBidomainWithBathProblem -malloc_debug -malloc_dump -memory_info ==935155== Parent PID: 914403 ==935155== ==935155== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==935155== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==935155== ==935155== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==935155== at 0xA39679E: getsockopt_syscall (getsockopt.c:29) ==935155== by 0xA39679E: getsockopt (getsockopt.c:94) ==935155== by 0x1444D157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935155== by 0x14454A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935155== by 0x1445BDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935155== by 0x1435B3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935155== by 0x142D4E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==935155== by 0x13A93E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==935155== by 0xF29D4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==935155== by 0xBA97418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935155== by 0xBA30D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935155== by 0xA727D38: PetscInitialize (pinit.c:924) ==935155== by 0x9B8658B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==935155== by 0x9B865D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==935155== by 0x14C926: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==935155== by 0x144CB1: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==935155== by 0x1483C4: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==935155== by 0x148264: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==935155== by 0x1488FB: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==935155== by 0x142E40: main (TestBidomainWithBathProblem.cpp:19) ==935155== Address 0x1ffeffdfcc is on thread 1's stack ==935155== in frame #2, created by pmix_ptl_base_make_connection (???:) ==935155== { 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 } ==935155== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==935155== at 0xA39679E: getsockopt_syscall (getsockopt.c:29) ==935155== by 0xA39679E: getsockopt (getsockopt.c:94) ==935155== by 0x1444D157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935155== by 0x14454A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935155== by 0x1445BDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935155== by 0x1435B3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935155== by 0x142D4E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==935155== by 0x13A93E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==935155== by 0xF29D4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==935155== by 0xBA97418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935155== by 0xBA30D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935155== by 0xA727D38: PetscInitialize (pinit.c:924) ==935155== by 0x9B8658B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==935155== by 0x9B865D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==935155== by 0x14C926: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==935155== by 0x144CB1: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==935155== by 0x1483C4: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==935155== by 0x148264: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==935155== by 0x1488FB: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==935155== by 0x142E40: main (TestBidomainWithBathProblem.cpp:19) ==935155== Address 0x1ffeffdfcc is on thread 1's stack ==935155== in frame #2, created by pmix_ptl_base_make_connection (???:) ==935155== { 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 } ==935155== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==935155== at 0xA396C7E: setsockopt_syscall (setsockopt.c:29) ==935155== by 0xA396C7E: setsockopt (setsockopt.c:95) ==935155== by 0x14454BA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935155== by 0x1445BDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935155== by 0x1435B3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==935155== by 0x142D4E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==935155== by 0x13A93E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==935155== by 0xF29D4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==935155== by 0xBA97418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935155== by 0xBA30D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935155== by 0xA727D38: PetscInitialize (pinit.c:924) ==935155== by 0x9B8658B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==935155== by 0x9B865D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==935155== by 0x14C926: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==935155== by 0x144CB1: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==935155== by 0x1483C4: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==935155== by 0x148264: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==935155== by 0x1488FB: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==935155== by 0x142E40: main (TestBidomainWithBathProblem.cpp:19) ==935155== { 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 } ==935155== Syscall param pwrite64(buf) points to uninitialised byte(s) ==935155== at 0xA3819EF: __libc_pwrite64 (pwrite64.c:25) ==935155== by 0xA3819EF: pwrite (pwrite64.c:23) ==935155== by 0x17CCA9D2: mca_fbtl_posix_pwritev (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_fbtl_posix.so) ==935155== by 0x17CDA419: mca_common_ompio_file_write (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==935155== by 0x17CDA79A: mca_common_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==935155== by 0x17BC589A: mca_io_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_io_ompio.so) ==935155== by 0xBA246A7: PMPI_File_write_at (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935155== by 0xC21FFEB: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935155== by 0xC05F4ED: H5FD_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935155== by 0xC042313: H5F__accum_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935155== by 0xC13D442: H5PB_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935155== by 0xC049DEA: H5F_block_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935155== by 0xBFD3E98: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935155== by 0xC2133F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935155== by 0xC2149CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935155== by 0xC21547E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935155== by 0xBFB054C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935155== by 0xC048936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935155== by 0xC0493FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935155== by 0xC04CBB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935155== by 0xC04CEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935155== by 0xC0BC51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935155== by 0xC0BC5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935155== by 0xC049831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935155== by 0xC03E881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935155== by 0xBEF3967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==935155== by 0xBEEE647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==935155== by 0xBEEE6ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==935155== by 0x678ABE5: AbstractCardiacProblem<1u, 1u, 2u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==935155== by 0x678A785: AbstractCardiacProblem<1u, 1u, 2u>::Solve() (AbstractCardiacProblem.cpp:582) ==935155== by 0x14E320: TestBidomainWithBathProblem::TestLabellingNodes() (TestBidomainWithBathProblem.hpp:105) ==935155== by 0x15D268: TestDescription_TestBidomainWithBathProblem_TestLabellingNodes::runTest() (TestBidomainWithBathProblem.cpp:31) ==935155== by 0x1442AC: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==935155== by 0x148672: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==935155== by 0x148557: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==935155== by 0x1483FD: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==935155== by 0x148264: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==935155== by 0x1488FB: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==935155== by 0x142E40: main (TestBidomainWithBathProblem.cpp:19) ==935155== Address 0x164befbe is 62 bytes inside a block of size 320 alloc'd ==935155== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==935155== by 0xBFD3E26: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935155== by 0xC2133F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935155== by 0xC2149CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935155== by 0xC21547E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935155== by 0xBFB054C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935155== by 0xC048936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935155== by 0xC0493FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935155== by 0xC04CBB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935155== by 0xC04CEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935155== by 0xC0BC51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935155== by 0xC0BC5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935155== by 0xC049831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935155== by 0xC03E881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==935155== by 0xBEF3967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==935155== by 0xBEEE647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==935155== by 0xBEEE6ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==935155== by 0x678ABE5: AbstractCardiacProblem<1u, 1u, 2u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==935155== by 0x678A785: AbstractCardiacProblem<1u, 1u, 2u>::Solve() (AbstractCardiacProblem.cpp:582) ==935155== by 0x14E320: TestBidomainWithBathProblem::TestLabellingNodes() (TestBidomainWithBathProblem.hpp:105) ==935155== by 0x15D268: TestDescription_TestBidomainWithBathProblem_TestLabellingNodes::runTest() (TestBidomainWithBathProblem.cpp:31) ==935155== by 0x1442AC: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==935155== by 0x148672: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==935155== by 0x148557: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==935155== by 0x1483FD: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==935155== by 0x148264: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==935155== by 0x1488FB: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==935155== by 0x142E40: main (TestBidomainWithBathProblem.cpp:19) ==935155== { 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:_ZN27TestBidomainWithBathProblem18TestLabellingNodesEv fun:_ZN62TestDescription_TestBidomainWithBathProblem_TestLabellingNodes7runTestEv fun:_ZN7CxxTest19RealTestDescription3runEv fun:_ZN7CxxTest10TestRunner7runTestERNS_15TestDescriptionE fun:_ZN7CxxTest10TestRunner8runSuiteERNS_16SuiteDescriptionE fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==935155== ==935155== FILE DESCRIPTORS: 9 open (3 std) at exit. ==935155== Open file descriptor 12: ==935155== at 0xA38422D: pipe (pipe.c:29) ==935155== by 0x13A9407D: ??? ==935155== by 0xF29D4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==935155== by 0xBA97418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935155== by 0xBA30D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935155== by 0xA727D38: PetscInitialize (pinit.c:924) ==935155== by 0x9B8658B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==935155== by 0x9B865D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==935155== by 0x14C926: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==935155== by 0x144CB1: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==935155== by 0x1483C4: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==935155== by 0x148264: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==935155== by 0x1488FB: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==935155== by 0x142E40: main (TestBidomainWithBathProblem.cpp:19) ==935155== ==935155== Open file descriptor 8: /dev/shm/open_mpi.0000 ==935155== at 0xA388BCC: __open_nocancel (open64_nocancel.c:39) ==935155== by 0xA30CC4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==935155== by 0x9BBE822: ??? ==935155== by 0x9BBE96F: ??? ==935155== by 0xF3426DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==935155== by 0xF342938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==935155== by 0xF2F8922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==935155== by 0xF29D2DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==935155== by 0xBA97418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935155== by 0xBA30D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935155== by 0xA727D38: PetscInitialize (pinit.c:924) ==935155== by 0x9B8658B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==935155== by 0x9B865D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==935155== by 0x14C926: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==935155== by 0x144CB1: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==935155== by 0x1483C4: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==935155== by 0x148264: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==935155== by 0x1488FB: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==935155== by 0x142E40: main (TestBidomainWithBathProblem.cpp:19) ==935155== ==935155== Open file descriptor 111: ==935155== ==935155== ==935155== Open file descriptor 108: ==935155== ==935155== ==935155== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestBidomainWithBathProblem_valgrind.txt ==935155== ==935155== ==935155== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==935155== ==935155== ==935155== ==935155== HEAP SUMMARY: ==935155== in use at exit: 701,166 bytes in 9,383 blocks ==935155== total heap usage: 1,395,457 allocs, 1,386,074 frees, 2,002,434,034 bytes allocated ==935155== ==935155== 552 bytes in 1 blocks are definitely lost in loss record 39 of 62 ==935155== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==935155== by 0x14362C13: ??? ==935155== by 0x1436322C: ??? ==935155== by 0x142D64B7: ??? ==935155== by 0xB9FD15A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935155== by 0xBA97A97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935155== by 0xBA30D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935155== by 0xA727D38: PetscInitialize (pinit.c:924) ==935155== by 0x9B8658B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==935155== by 0x9B865D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==935155== by 0x14C926: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==935155== by 0x144CB1: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==935155== by 0x1483C4: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==935155== by 0x148264: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==935155== by 0x1488FB: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==935155== by 0x142E40: main (TestBidomainWithBathProblem.cpp:19) ==935155== { 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 } ==935155== 685,269 (136 direct, 685,133 indirect) bytes in 1 blocks are definitely lost in loss record 62 of 62 ==935155== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==935155== by 0x154D574E: ??? ==935155== by 0x154D5E0B: ??? ==935155== by 0x154D8F56: ??? ==935155== by 0x154CE65D: ??? ==935155== by 0x154CEFA3: ??? ==935155== by 0xF3AEF05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==935155== by 0xF38AAE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==935155== by 0xF33BCB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==935155== by 0xF268EF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==935155== by 0x13A94F03: ??? ==935155== by 0xF29D4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==935155== by 0xBA97418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935155== by 0xBA30D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==935155== by 0xA727D38: PetscInitialize (pinit.c:924) ==935155== by 0x9B8658B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==935155== by 0x9B865D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==935155== by 0x14C926: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==935155== by 0x144CB1: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==935155== by 0x1483C4: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==935155== by 0x148264: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==935155== by 0x1488FB: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==935155== by 0x142E40: main (TestBidomainWithBathProblem.cpp:19) ==935155== { 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 } ==935155== LEAK SUMMARY: ==935155== definitely lost: 688 bytes in 2 blocks ==935155== indirectly lost: 1,760 bytes in 16 blocks ==935155== possibly lost: 0 bytes in 0 blocks ==935155== still reachable: 1,531 bytes in 6 blocks ==935155== suppressed: 697,187 bytes in 9,359 blocks ==935155== Reachable blocks (those to which a pointer was found) are not shown. ==935155== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==935155== ==935155== Use --track-origins=yes to see where uninitialised values come from ==935155== For lists of detected and suppressed errors, rerun with: -s ==935155== ERROR SUMMARY: 41 errors from 6 contexts (suppressed: 25 from 25)