==936845== Memcheck, a memory error detector ==936845== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==936845== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==936845== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/heart/test/TestMonodomainWithTimeAdaptivity -malloc_debug -malloc_dump -memory_info ==936845== Parent PID: 914403 ==936845== ==936845== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==936845== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==936845== ==936845== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==936845== at 0xB31579E: getsockopt_syscall (getsockopt.c:29) ==936845== by 0xB31579E: getsockopt (getsockopt.c:94) ==936845== by 0x1444F157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936845== by 0x14456A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936845== by 0x1445DDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936845== by 0x1435D3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936845== by 0x142D6E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==936845== by 0x13A95E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==936845== by 0xF24C4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==936845== by 0xABF3418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936845== by 0xAB8CD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936845== by 0x9863D38: PetscInitialize (pinit.c:924) ==936845== by 0x973758B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==936845== by 0x97375D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==936845== by 0x130FA0: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==936845== by 0x129C0F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==936845== by 0x12CDC6: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==936845== by 0x12CC66: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936845== by 0x12D2FD: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936845== by 0x127F40: main (TestMonodomainWithTimeAdaptivity.cpp:19) ==936845== Address 0x1ffeffdfbc is on thread 1's stack ==936845== in frame #2, created by pmix_ptl_base_make_connection (???:) ==936845== { 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 } ==936845== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==936845== at 0xB31579E: getsockopt_syscall (getsockopt.c:29) ==936845== by 0xB31579E: getsockopt (getsockopt.c:94) ==936845== by 0x1444F157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936845== by 0x14456A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936845== by 0x1445DDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936845== by 0x1435D3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936845== by 0x142D6E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==936845== by 0x13A95E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==936845== by 0xF24C4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==936845== by 0xABF3418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936845== by 0xAB8CD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936845== by 0x9863D38: PetscInitialize (pinit.c:924) ==936845== by 0x973758B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==936845== by 0x97375D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==936845== by 0x130FA0: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==936845== by 0x129C0F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==936845== by 0x12CDC6: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==936845== by 0x12CC66: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936845== by 0x12D2FD: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936845== by 0x127F40: main (TestMonodomainWithTimeAdaptivity.cpp:19) ==936845== Address 0x1ffeffdfbc is on thread 1's stack ==936845== in frame #2, created by pmix_ptl_base_make_connection (???:) ==936845== { 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 } ==936845== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==936845== at 0xB315C7E: setsockopt_syscall (setsockopt.c:29) ==936845== by 0xB315C7E: setsockopt (setsockopt.c:95) ==936845== by 0x14456BA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936845== by 0x1445DDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936845== by 0x1435D3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936845== by 0x142D6E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==936845== by 0x13A95E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==936845== by 0xF24C4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==936845== by 0xABF3418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936845== by 0xAB8CD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936845== by 0x9863D38: PetscInitialize (pinit.c:924) ==936845== by 0x973758B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==936845== by 0x97375D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==936845== by 0x130FA0: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==936845== by 0x129C0F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==936845== by 0x12CDC6: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==936845== by 0x12CC66: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936845== by 0x12D2FD: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936845== by 0x127F40: main (TestMonodomainWithTimeAdaptivity.cpp:19) ==936845== { 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 } ==936845== Syscall param pwrite64(buf) points to uninitialised byte(s) ==936845== at 0xB3009EF: __libc_pwrite64 (pwrite64.c:25) ==936845== by 0xB3009EF: pwrite (pwrite64.c:23) ==936845== by 0x17CCC9D2: mca_fbtl_posix_pwritev (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_fbtl_posix.so) ==936845== by 0x17CDC419: mca_common_ompio_file_write (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==936845== by 0x17CDC79A: mca_common_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==936845== by 0x17BC789A: mca_io_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_io_ompio.so) ==936845== by 0xAB806A7: PMPI_File_write_at (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936845== by 0xEC17FEB: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936845== by 0xEA574ED: H5FD_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936845== by 0xEA3A313: H5F__accum_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936845== by 0xEB35442: H5PB_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936845== by 0xEA41DEA: H5F_block_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936845== by 0xE9CBE98: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936845== by 0xEC0B3F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936845== by 0xEC0C9CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936845== by 0xEC0D47E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936845== by 0xE9A854C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936845== by 0xEA40936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936845== by 0xEA413FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936845== by 0xEA44BB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936845== by 0xEA44EFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936845== by 0xEAB451F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936845== by 0xEAB45EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936845== by 0xEA41831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936845== by 0xEA36881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936845== by 0xBEF3967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==936845== by 0xBEEE647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==936845== by 0xBEEE6ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==936845== by 0x67850CD: AbstractCardiacProblem<3u, 3u, 1u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==936845== by 0x6784C6D: AbstractCardiacProblem<3u, 3u, 1u>::Solve() (AbstractCardiacProblem.cpp:582) ==936845== by 0x13127B: TestMonodomainWithTimeAdaptivity::TestWithCube() (TestMonodomainWithTimeAdaptivity.hpp:101) ==936845== by 0x132E8A: TestDescription_TestMonodomainWithTimeAdaptivity_TestWithCube::runTest() (TestMonodomainWithTimeAdaptivity.cpp:31) ==936845== by 0x12920A: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==936845== by 0x12D074: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==936845== by 0x12CF59: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==936845== by 0x12CDFF: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==936845== by 0x12CC66: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936845== by 0x12D2FD: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936845== by 0x127F40: main (TestMonodomainWithTimeAdaptivity.cpp:19) ==936845== Address 0x15a693fe is 62 bytes inside a block of size 320 alloc'd ==936845== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==936845== by 0xE9CBE26: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936845== by 0xEC0B3F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936845== by 0xEC0C9CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936845== by 0xEC0D47E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936845== by 0xE9A854C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936845== by 0xEA40936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936845== by 0xEA413FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936845== by 0xEA44BB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936845== by 0xEA44EFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936845== by 0xEAB451F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936845== by 0xEAB45EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936845== by 0xEA41831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936845== by 0xEA36881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936845== by 0xBEF3967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==936845== by 0xBEEE647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==936845== by 0xBEEE6ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==936845== by 0x67850CD: AbstractCardiacProblem<3u, 3u, 1u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==936845== by 0x6784C6D: AbstractCardiacProblem<3u, 3u, 1u>::Solve() (AbstractCardiacProblem.cpp:582) ==936845== by 0x13127B: TestMonodomainWithTimeAdaptivity::TestWithCube() (TestMonodomainWithTimeAdaptivity.hpp:101) ==936845== by 0x132E8A: TestDescription_TestMonodomainWithTimeAdaptivity_TestWithCube::runTest() (TestMonodomainWithTimeAdaptivity.cpp:31) ==936845== by 0x12920A: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==936845== by 0x12D074: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==936845== by 0x12CF59: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==936845== by 0x12CDFF: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==936845== by 0x12CC66: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936845== by 0x12D2FD: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936845== by 0x127F40: main (TestMonodomainWithTimeAdaptivity.cpp:19) ==936845== { 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:_ZN22AbstractCardiacProblemILj3ELj3ELj1EE24CloseFilesAndPostProcessEv fun:_ZN22AbstractCardiacProblemILj3ELj3ELj1EE5SolveEv fun:_ZN32TestMonodomainWithTimeAdaptivity12TestWithCubeEv fun:_ZN61TestDescription_TestMonodomainWithTimeAdaptivity_TestWithCube7runTestEv fun:_ZN7CxxTest19RealTestDescription3runEv fun:_ZN7CxxTest10TestRunner7runTestERNS_15TestDescriptionE fun:_ZN7CxxTest10TestRunner8runSuiteERNS_16SuiteDescriptionE fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==936845== ==936845== FILE DESCRIPTORS: 9 open (3 std) at exit. ==936845== Open file descriptor 12: ==936845== at 0xB30322D: pipe (pipe.c:29) ==936845== by 0x13A9607D: ??? ==936845== by 0xF24C4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==936845== by 0xABF3418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936845== by 0xAB8CD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936845== by 0x9863D38: PetscInitialize (pinit.c:924) ==936845== by 0x973758B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==936845== by 0x97375D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==936845== by 0x130FA0: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==936845== by 0x129C0F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==936845== by 0x12CDC6: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==936845== by 0x12CC66: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936845== by 0x12D2FD: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936845== by 0x127F40: main (TestMonodomainWithTimeAdaptivity.cpp:19) ==936845== ==936845== Open file descriptor 8: /dev/shm/open_mpi.0000 ==936845== at 0xB307BCC: __open_nocancel (open64_nocancel.c:39) ==936845== by 0xB28BC4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==936845== by 0xAAED822: ??? ==936845== by 0xAAED96F: ??? ==936845== by 0xF2F16DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==936845== by 0xF2F1938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==936845== by 0xF2A7922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==936845== by 0xF24C2DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==936845== by 0xABF3418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936845== by 0xAB8CD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936845== by 0x9863D38: PetscInitialize (pinit.c:924) ==936845== by 0x973758B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==936845== by 0x97375D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==936845== by 0x130FA0: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==936845== by 0x129C0F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==936845== by 0x12CDC6: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==936845== by 0x12CC66: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936845== by 0x12D2FD: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936845== by 0x127F40: main (TestMonodomainWithTimeAdaptivity.cpp:19) ==936845== ==936845== Open file descriptor 111: ==936845== ==936845== ==936845== Open file descriptor 108: ==936845== ==936845== ==936845== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestMonodomainWithTimeAdaptivity_valgrind.txt ==936845== ==936845== ==936845== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==936845== ==936845== ==936845== ==936845== HEAP SUMMARY: ==936845== in use at exit: 701,166 bytes in 9,383 blocks ==936845== total heap usage: 1,146,847 allocs, 1,137,464 frees, 1,415,488,033 bytes allocated ==936845== ==936845== 552 bytes in 1 blocks are definitely lost in loss record 40 of 63 ==936845== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==936845== by 0x14364C13: ??? ==936845== by 0x1436522C: ??? ==936845== by 0x142D84B7: ??? ==936845== by 0xAB5915A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936845== by 0xABF3A97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936845== by 0xAB8CD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936845== by 0x9863D38: PetscInitialize (pinit.c:924) ==936845== by 0x973758B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==936845== by 0x97375D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==936845== by 0x130FA0: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==936845== by 0x129C0F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==936845== by 0x12CDC6: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==936845== by 0x12CC66: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936845== by 0x12D2FD: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936845== by 0x127F40: main (TestMonodomainWithTimeAdaptivity.cpp:19) ==936845== { 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 } ==936845== 685,230 (136 direct, 685,094 indirect) bytes in 1 blocks are definitely lost in loss record 63 of 63 ==936845== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==936845== by 0x154D774E: ??? ==936845== by 0x154D7E0B: ??? ==936845== by 0x154DAF56: ??? ==936845== by 0x154D065D: ??? ==936845== by 0x154D0FA3: ??? ==936845== by 0xF35DF05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==936845== by 0xF339AE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==936845== by 0xF2EACB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==936845== by 0xF217EF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==936845== by 0x13A96F03: ??? ==936845== by 0xF24C4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==936845== by 0xABF3418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936845== by 0xAB8CD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936845== by 0x9863D38: PetscInitialize (pinit.c:924) ==936845== by 0x973758B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==936845== by 0x97375D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==936845== by 0x130FA0: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==936845== by 0x129C0F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==936845== by 0x12CDC6: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==936845== by 0x12CC66: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936845== by 0x12D2FD: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936845== by 0x127F40: main (TestMonodomainWithTimeAdaptivity.cpp:19) ==936845== { 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 } ==936845== LEAK SUMMARY: ==936845== definitely lost: 688 bytes in 2 blocks ==936845== indirectly lost: 1,760 bytes in 16 blocks ==936845== possibly lost: 0 bytes in 0 blocks ==936845== still reachable: 1,531 bytes in 6 blocks ==936845== suppressed: 697,187 bytes in 9,359 blocks ==936845== Reachable blocks (those to which a pointer was found) are not shown. ==936845== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==936845== ==936845== Use --track-origins=yes to see where uninitialised values come from ==936845== For lists of detected and suppressed errors, rerun with: -s ==936845== ERROR SUMMARY: 17 errors from 6 contexts (suppressed: 26 from 26)