==936989== Memcheck, a memory error detector ==936989== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==936989== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==936989== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/heart/test/TestCheckpointing -malloc_debug -malloc_dump -memory_info ==936989== Parent PID: 914403 ==936989== ==936989== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==936989== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==936989== ==936989== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==936989== at 0x9EE779E: getsockopt_syscall (getsockopt.c:29) ==936989== by 0x9EE779E: getsockopt (getsockopt.c:94) ==936989== by 0x1444D157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936989== by 0x14454A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936989== by 0x1445BDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936989== by 0x1435B3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936989== by 0x142D4E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==936989== by 0x13A93E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==936989== by 0xF2994CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==936989== by 0xB5E6418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936989== by 0xB57FD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936989== by 0xA276D38: PetscInitialize (pinit.c:924) ==936989== by 0x97BE58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==936989== by 0x97BE5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==936989== by 0x12D0CE: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==936989== by 0x12653D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==936989== by 0x128EF4: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==936989== by 0x128DEF: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936989== by 0x129403: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936989== by 0x124D40: main (TestCheckpointing.cpp:18) ==936989== Address 0x1ffeffdfec is on thread 1's stack ==936989== in frame #2, created by pmix_ptl_base_make_connection (???:) ==936989== { 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 } ==936989== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==936989== at 0x9EE779E: getsockopt_syscall (getsockopt.c:29) ==936989== by 0x9EE779E: getsockopt (getsockopt.c:94) ==936989== by 0x1444D157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936989== by 0x14454A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936989== by 0x1445BDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936989== by 0x1435B3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936989== by 0x142D4E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==936989== by 0x13A93E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==936989== by 0xF2994CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==936989== by 0xB5E6418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936989== by 0xB57FD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936989== by 0xA276D38: PetscInitialize (pinit.c:924) ==936989== by 0x97BE58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==936989== by 0x97BE5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==936989== by 0x12D0CE: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==936989== by 0x12653D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==936989== by 0x128EF4: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==936989== by 0x128DEF: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936989== by 0x129403: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936989== by 0x124D40: main (TestCheckpointing.cpp:18) ==936989== Address 0x1ffeffdfec is on thread 1's stack ==936989== in frame #2, created by pmix_ptl_base_make_connection (???:) ==936989== { 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 } ==936989== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==936989== at 0x9EE7C7E: setsockopt_syscall (setsockopt.c:29) ==936989== by 0x9EE7C7E: setsockopt (setsockopt.c:95) ==936989== by 0x14454BA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936989== by 0x1445BDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936989== by 0x1435B3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==936989== by 0x142D4E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==936989== by 0x13A93E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==936989== by 0xF2994CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==936989== by 0xB5E6418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936989== by 0xB57FD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936989== by 0xA276D38: PetscInitialize (pinit.c:924) ==936989== by 0x97BE58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==936989== by 0x97BE5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==936989== by 0x12D0CE: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==936989== by 0x12653D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==936989== by 0x128EF4: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==936989== by 0x128DEF: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936989== by 0x129403: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936989== by 0x124D40: main (TestCheckpointing.cpp:18) ==936989== { 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 } ==936989== Syscall param pwrite64(buf) points to uninitialised byte(s) ==936989== at 0x9ED29EF: __libc_pwrite64 (pwrite64.c:25) ==936989== by 0x9ED29EF: pwrite (pwrite64.c:23) ==936989== by 0x17CCA9D2: mca_fbtl_posix_pwritev (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_fbtl_posix.so) ==936989== by 0x17CDA419: mca_common_ompio_file_write (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==936989== by 0x17CDA79A: mca_common_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==936989== by 0x17BC589A: mca_io_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_io_ompio.so) ==936989== by 0xB5736A7: PMPI_File_write_at (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936989== by 0xCEF1FEB: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936989== by 0xCD314ED: H5FD_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936989== by 0xCD14313: H5F__accum_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936989== by 0xCE0F442: H5PB_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936989== by 0xCD1BDEA: H5F_block_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936989== by 0xCCA5E98: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936989== by 0xCEE53F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936989== by 0xCEE69CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936989== by 0xCEE747E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936989== by 0xCC8254C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936989== by 0xCD1A936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936989== by 0xCD1B3FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936989== by 0xCD1EBB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936989== by 0xCD1EEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936989== by 0xCD8E51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936989== by 0xCD8E5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936989== by 0xCD1B831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936989== by 0xCD10881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936989== by 0x96ED967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==936989== by 0x96E8647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==936989== by 0x96E86ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==936989== by 0x6796215: AbstractCardiacProblem<3u, 3u, 2u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==936989== by 0x6795DB5: AbstractCardiacProblem<3u, 3u, 2u>::Solve() (AbstractCardiacProblem.cpp:582) ==936989== by 0x12D323: TestCheckpointing::TestMultipleCallsToProblemSolve() (TestCheckpointing.hpp:72) ==936989== by 0x12EB44: TestDescription_TestCheckpointing_TestMultipleCallsToProblemSolve::runTest() (TestCheckpointing.cpp:30) ==936989== by 0x125D74: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==936989== by 0x1291A2: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==936989== by 0x129087: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==936989== by 0x128F2D: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==936989== by 0x128DEF: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936989== by 0x129403: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936989== by 0x124D40: main (TestCheckpointing.cpp:18) ==936989== Address 0x159f993e is 62 bytes inside a block of size 320 alloc'd ==936989== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==936989== by 0xCCA5E26: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936989== by 0xCEE53F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936989== by 0xCEE69CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936989== by 0xCEE747E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936989== by 0xCC8254C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936989== by 0xCD1A936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936989== by 0xCD1B3FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936989== by 0xCD1EBB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936989== by 0xCD1EEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936989== by 0xCD8E51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936989== by 0xCD8E5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936989== by 0xCD1B831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936989== by 0xCD10881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==936989== by 0x96ED967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==936989== by 0x96E8647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==936989== by 0x96E86ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==936989== by 0x6796215: AbstractCardiacProblem<3u, 3u, 2u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==936989== by 0x6795DB5: AbstractCardiacProblem<3u, 3u, 2u>::Solve() (AbstractCardiacProblem.cpp:582) ==936989== by 0x12D323: TestCheckpointing::TestMultipleCallsToProblemSolve() (TestCheckpointing.hpp:72) ==936989== by 0x12EB44: TestDescription_TestCheckpointing_TestMultipleCallsToProblemSolve::runTest() (TestCheckpointing.cpp:30) ==936989== by 0x125D74: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==936989== by 0x1291A2: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==936989== by 0x129087: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==936989== by 0x128F2D: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==936989== by 0x128DEF: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936989== by 0x129403: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936989== by 0x124D40: main (TestCheckpointing.cpp:18) ==936989== { 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:_ZN22AbstractCardiacProblemILj3ELj3ELj2EE24CloseFilesAndPostProcessEv fun:_ZN22AbstractCardiacProblemILj3ELj3ELj2EE5SolveEv fun:_ZN17TestCheckpointing31TestMultipleCallsToProblemSolveEv fun:_ZN65TestDescription_TestCheckpointing_TestMultipleCallsToProblemSolve7runTestEv fun:_ZN7CxxTest19RealTestDescription3runEv fun:_ZN7CxxTest10TestRunner7runTestERNS_15TestDescriptionE fun:_ZN7CxxTest10TestRunner8runSuiteERNS_16SuiteDescriptionE fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==936989== ==936989== FILE DESCRIPTORS: 9 open (3 std) at exit. ==936989== Open file descriptor 12: ==936989== at 0x9ED522D: pipe (pipe.c:29) ==936989== by 0x13A9407D: ??? ==936989== by 0xF2994CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==936989== by 0xB5E6418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936989== by 0xB57FD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936989== by 0xA276D38: PetscInitialize (pinit.c:924) ==936989== by 0x97BE58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==936989== by 0x97BE5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==936989== by 0x12D0CE: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==936989== by 0x12653D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==936989== by 0x128EF4: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==936989== by 0x128DEF: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936989== by 0x129403: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936989== by 0x124D40: main (TestCheckpointing.cpp:18) ==936989== ==936989== Open file descriptor 8: /dev/shm/open_mpi.0000 ==936989== at 0x9ED9BCC: __open_nocancel (open64_nocancel.c:39) ==936989== by 0x9E5DC4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==936989== by 0x97F6822: ??? ==936989== by 0x97F696F: ??? ==936989== by 0xF33E6DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==936989== by 0xF33E938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==936989== by 0xF2F4922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==936989== by 0xF2992DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==936989== by 0xB5E6418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936989== by 0xB57FD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936989== by 0xA276D38: PetscInitialize (pinit.c:924) ==936989== by 0x97BE58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==936989== by 0x97BE5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==936989== by 0x12D0CE: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==936989== by 0x12653D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==936989== by 0x128EF4: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==936989== by 0x128DEF: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936989== by 0x129403: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936989== by 0x124D40: main (TestCheckpointing.cpp:18) ==936989== ==936989== Open file descriptor 111: ==936989== ==936989== ==936989== Open file descriptor 108: ==936989== ==936989== ==936989== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestCheckpointing_valgrind.txt ==936989== ==936989== ==936989== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==936989== ==936989== ==936989== ==936989== HEAP SUMMARY: ==936989== in use at exit: 701,234 bytes in 9,387 blocks ==936989== total heap usage: 834,054 allocs, 824,667 frees, 1,457,765,162 bytes allocated ==936989== ==936989== 552 bytes in 1 blocks are definitely lost in loss record 43 of 66 ==936989== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==936989== by 0x14362C13: ??? ==936989== by 0x1436322C: ??? ==936989== by 0x142D64B7: ??? ==936989== by 0xB54C15A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936989== by 0xB5E6A97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936989== by 0xB57FD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936989== by 0xA276D38: PetscInitialize (pinit.c:924) ==936989== by 0x97BE58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==936989== by 0x97BE5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==936989== by 0x12D0CE: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==936989== by 0x12653D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==936989== by 0x128EF4: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==936989== by 0x128DEF: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936989== by 0x129403: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936989== by 0x124D40: main (TestCheckpointing.cpp:18) ==936989== { 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 } ==936989== 685,285 (136 direct, 685,149 indirect) bytes in 1 blocks are definitely lost in loss record 66 of 66 ==936989== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==936989== by 0x154D574E: ??? ==936989== by 0x154D5E0B: ??? ==936989== by 0x154D8F56: ??? ==936989== by 0x154CE65D: ??? ==936989== by 0x154CEFA3: ??? ==936989== by 0xF3AAF05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==936989== by 0xF386AE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==936989== by 0xF337CB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==936989== by 0xF264EF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==936989== by 0x13A94F03: ??? ==936989== by 0xF2994CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==936989== by 0xB5E6418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936989== by 0xB57FD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==936989== by 0xA276D38: PetscInitialize (pinit.c:924) ==936989== by 0x97BE58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==936989== by 0x97BE5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==936989== by 0x12D0CE: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==936989== by 0x12653D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==936989== by 0x128EF4: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==936989== by 0x128DEF: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==936989== by 0x129403: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==936989== by 0x124D40: main (TestCheckpointing.cpp:18) ==936989== { 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 } ==936989== LEAK SUMMARY: ==936989== definitely lost: 688 bytes in 2 blocks ==936989== indirectly lost: 1,760 bytes in 16 blocks ==936989== possibly lost: 0 bytes in 0 blocks ==936989== still reachable: 1,531 bytes in 6 blocks ==936989== suppressed: 697,255 bytes in 9,363 blocks ==936989== Reachable blocks (those to which a pointer was found) are not shown. ==936989== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==936989== ==936989== Use --track-origins=yes to see where uninitialised values come from ==936989== For lists of detected and suppressed errors, rerun with: -s ==936989== ERROR SUMMARY: 32 errors from 6 contexts (suppressed: 29 from 29)