==3547218== Memcheck, a memory error detector ==3547218== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==3547218== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==3547218== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/io/test/TestHdf5DataWriter -malloc_debug -malloc_dump -memory_info ==3547218== Parent PID: 3546972 ==3547218== ==3547218== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==3547218== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==3547218== ==3547218== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==3547218== at 0x65C879E: getsockopt_syscall (getsockopt.c:29) ==3547218== by 0x65C879E: getsockopt (getsockopt.c:94) ==3547218== by 0xB919157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3547218== by 0xB920A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3547218== by 0xB927DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3547218== by 0xB8273C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3547218== by 0xB7A0E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==3547218== by 0xAF5FE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==3547218== by 0x8F804CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3547218== by 0x6207418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3547218== by 0x61A0D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3547218== by 0x4AC0D38: PetscInitialize (pinit.c:924) ==3547218== by 0x4994717: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3547218== by 0x4994765: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3547218== by 0x126698: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3547218== by 0x11FFCF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3547218== by 0x123098: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3547218== by 0x122F38: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3547218== by 0x1235CF: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3547218== by 0x11E300: main (TestHdf5DataWriter.cpp:19) ==3547218== Address 0x1ffeffdfbc is on thread 1's stack ==3547218== in frame #2, created by pmix_ptl_base_make_connection (???:) ==3547218== { 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 } ==3547218== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==3547218== at 0x65C879E: getsockopt_syscall (getsockopt.c:29) ==3547218== by 0x65C879E: getsockopt (getsockopt.c:94) ==3547218== by 0xB919157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3547218== by 0xB920A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3547218== by 0xB927DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3547218== by 0xB8273C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3547218== by 0xB7A0E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==3547218== by 0xAF5FE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==3547218== by 0x8F804CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3547218== by 0x6207418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3547218== by 0x61A0D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3547218== by 0x4AC0D38: PetscInitialize (pinit.c:924) ==3547218== by 0x4994717: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3547218== by 0x4994765: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3547218== by 0x126698: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3547218== by 0x11FFCF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3547218== by 0x123098: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3547218== by 0x122F38: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3547218== by 0x1235CF: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3547218== by 0x11E300: main (TestHdf5DataWriter.cpp:19) ==3547218== Address 0x1ffeffdfbc is on thread 1's stack ==3547218== in frame #2, created by pmix_ptl_base_make_connection (???:) ==3547218== { 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 } ==3547218== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==3547218== at 0x65C8C7E: setsockopt_syscall (setsockopt.c:29) ==3547218== by 0x65C8C7E: setsockopt (setsockopt.c:95) ==3547218== by 0xB920BA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3547218== by 0xB927DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3547218== by 0xB8273C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3547218== by 0xB7A0E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==3547218== by 0xAF5FE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==3547218== by 0x8F804CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3547218== by 0x6207418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3547218== by 0x61A0D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3547218== by 0x4AC0D38: PetscInitialize (pinit.c:924) ==3547218== by 0x4994717: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3547218== by 0x4994765: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3547218== by 0x126698: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3547218== by 0x11FFCF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3547218== by 0x123098: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3547218== by 0x122F38: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3547218== by 0x1235CF: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3547218== by 0x11E300: main (TestHdf5DataWriter.cpp:19) ==3547218== { 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 } ==3547218== Syscall param pwrite64(buf) points to uninitialised byte(s) ==3547218== at 0x65B39EF: __libc_pwrite64 (pwrite64.c:25) ==3547218== by 0x65B39EF: pwrite (pwrite64.c:23) ==3547218== by 0x10C519D2: mca_fbtl_posix_pwritev (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_fbtl_posix.so) ==3547218== by 0x10C61419: mca_common_ompio_file_write (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==3547218== by 0x10C6179A: mca_common_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==3547218== by 0x10B4C89A: mca_io_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_io_ompio.so) ==3547218== by 0x61946A7: PMPI_File_write_at (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3547218== by 0x6033FEB: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3547218== by 0x5E734ED: H5FD_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3547218== by 0x5E56313: H5F__accum_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3547218== by 0x5F51442: H5PB_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3547218== by 0x5E5DDEA: H5F_block_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3547218== by 0x5DE7E98: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3547218== by 0x60273F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3547218== by 0x60289CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3547218== by 0x602947E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3547218== by 0x5DC454C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3547218== by 0x5E5C936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3547218== by 0x5E5D3FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3547218== by 0x5E60BB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3547218== by 0x5E60EFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3547218== by 0x5ED051F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3547218== by 0x5ED05EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3547218== by 0x5E5D831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3547218== by 0x5E52881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3547218== by 0x126CA2: TestHdf5DataWriter::TestSimpleParallelWriteDirectlyWithHdf5() (TestHdf5DataWriter.hpp:149) ==3547218== by 0x153266: TestDescription_TestHdf5DataWriter_TestSimpleParallelWriteDirectlyWithHdf5::runTest() (TestHdf5DataWriter.cpp:31) ==3547218== by 0x11F5CA: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==3547218== by 0x123346: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==3547218== by 0x12322B: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==3547218== by 0x1230D1: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==3547218== by 0x122F38: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3547218== by 0x1235CF: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3547218== by 0x11E300: main (TestHdf5DataWriter.cpp:19) ==3547218== Address 0xfda69c3 is 83 bytes inside a block of size 168 alloc'd ==3547218== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==3547218== by 0x5DE7E26: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3547218== by 0x60273F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3547218== by 0x60289CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3547218== by 0x602947E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3547218== by 0x5DC454C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3547218== by 0x5E5C936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3547218== by 0x5E5D3FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3547218== by 0x5E60BB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3547218== by 0x5E60EFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3547218== by 0x5ED051F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3547218== by 0x5ED05EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3547218== by 0x5E5D831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3547218== by 0x5E52881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3547218== by 0x126CA2: TestHdf5DataWriter::TestSimpleParallelWriteDirectlyWithHdf5() (TestHdf5DataWriter.hpp:149) ==3547218== by 0x153266: TestDescription_TestHdf5DataWriter_TestSimpleParallelWriteDirectlyWithHdf5::runTest() (TestHdf5DataWriter.cpp:31) ==3547218== by 0x11F5CA: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==3547218== by 0x123346: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==3547218== by 0x12322B: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==3547218== by 0x1230D1: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==3547218== by 0x122F38: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3547218== by 0x1235CF: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3547218== by 0x11E300: main (TestHdf5DataWriter.cpp:19) ==3547218== { 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:_ZN18TestHdf5DataWriter39TestSimpleParallelWriteDirectlyWithHdf5Ev fun:_ZN74TestDescription_TestHdf5DataWriter_TestSimpleParallelWriteDirectlyWithHdf57runTestEv fun:_ZN7CxxTest19RealTestDescription3runEv fun:_ZN7CxxTest10TestRunner7runTestERNS_15TestDescriptionE fun:_ZN7CxxTest10TestRunner8runSuiteERNS_16SuiteDescriptionE fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==3547218== Warning: invalid file descriptor -1 in syscall close() ==3547218== ==3547218== FILE DESCRIPTORS: 9 open (3 std) at exit. ==3547218== Open file descriptor 12: ==3547218== at 0x65B622D: pipe (pipe.c:29) ==3547218== by 0xAF6007D: ??? ==3547218== by 0x8F804CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3547218== by 0x6207418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3547218== by 0x61A0D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3547218== by 0x4AC0D38: PetscInitialize (pinit.c:924) ==3547218== by 0x4994717: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3547218== by 0x4994765: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3547218== by 0x126698: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3547218== by 0x11FFCF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3547218== by 0x123098: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3547218== by 0x122F38: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3547218== by 0x1235CF: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3547218== by 0x11E300: main (TestHdf5DataWriter.cpp:19) ==3547218== ==3547218== Open file descriptor 8: /dev/shm/open_mpi.0000 ==3547218== at 0x65BABCC: __open_nocancel (open64_nocancel.c:39) ==3547218== by 0x653EC4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==3547218== by 0x5D4A822: ??? ==3547218== by 0x5D4A96F: ??? ==3547218== by 0x90256DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==3547218== by 0x9025938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==3547218== by 0x8FDB922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==3547218== by 0x8F802DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3547218== by 0x6207418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3547218== by 0x61A0D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3547218== by 0x4AC0D38: PetscInitialize (pinit.c:924) ==3547218== by 0x4994717: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3547218== by 0x4994765: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3547218== by 0x126698: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3547218== by 0x11FFCF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3547218== by 0x123098: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3547218== by 0x122F38: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3547218== by 0x1235CF: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3547218== by 0x11E300: main (TestHdf5DataWriter.cpp:19) ==3547218== ==3547218== Open file descriptor 117: ==3547218== ==3547218== ==3547218== Open file descriptor 110: ==3547218== ==3547218== ==3547218== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestHdf5DataWriter_valgrind.txt ==3547218== ==3547218== ==3547218== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==3547218== ==3547218== ==3547218== ==3547218== HEAP SUMMARY: ==3547218== in use at exit: 700,775 bytes in 9,387 blocks ==3547218== total heap usage: 115,935 allocs, 106,548 frees, 1,427,387,336 bytes allocated ==3547218== ==3547218== 552 bytes in 1 blocks are definitely lost in loss record 43 of 66 ==3547218== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==3547218== by 0xB82EC13: ??? ==3547218== by 0xB82F22C: ??? ==3547218== by 0xB7A24B7: ??? ==3547218== by 0x616D15A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3547218== by 0x6207A97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3547218== by 0x61A0D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3547218== by 0x4AC0D38: PetscInitialize (pinit.c:924) ==3547218== by 0x4994717: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3547218== by 0x4994765: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3547218== by 0x126698: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3547218== by 0x11FFCF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3547218== by 0x123098: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3547218== by 0x122F38: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3547218== by 0x1235CF: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3547218== by 0x11E300: main (TestHdf5DataWriter.cpp:19) ==3547218== { 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 } ==3547218== 685,300 (136 direct, 685,164 indirect) bytes in 1 blocks are definitely lost in loss record 66 of 66 ==3547218== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==3547218== by 0xCA4374E: ??? ==3547218== by 0xCA43E0B: ??? ==3547218== by 0xCA46F56: ??? ==3547218== by 0xCA3C65D: ??? ==3547218== by 0xCA3CFA3: ??? ==3547218== by 0x9093F05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==3547218== by 0x906FAE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==3547218== by 0x901ECB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==3547218== by 0x8F4BEF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3547218== by 0xAF60F03: ??? ==3547218== by 0x8F804CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3547218== by 0x6207418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3547218== by 0x61A0D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3547218== by 0x4AC0D38: PetscInitialize (pinit.c:924) ==3547218== by 0x4994717: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3547218== by 0x4994765: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3547218== by 0x126698: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3547218== by 0x11FFCF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3547218== by 0x123098: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3547218== by 0x122F38: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3547218== by 0x1235CF: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3547218== by 0x11E300: main (TestHdf5DataWriter.cpp:19) ==3547218== { 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 } ==3547218== LEAK SUMMARY: ==3547218== definitely lost: 688 bytes in 2 blocks ==3547218== indirectly lost: 1,760 bytes in 16 blocks ==3547218== possibly lost: 0 bytes in 0 blocks ==3547218== still reachable: 1,531 bytes in 6 blocks ==3547218== suppressed: 696,796 bytes in 9,363 blocks ==3547218== Reachable blocks (those to which a pointer was found) are not shown. ==3547218== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==3547218== ==3547218== Use --track-origins=yes to see where uninitialised values come from ==3547218== For lists of detected and suppressed errors, rerun with: -s ==3547218== ERROR SUMMARY: 69 errors from 6 contexts (suppressed: 29 from 29)