==914646== Memcheck, a memory error detector ==914646== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==914646== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==914646== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/io/test/TestHdf5DataWriter -malloc_debug -malloc_dump -memory_info ==914646== Parent PID: 914403 ==914646== ==914646== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==914646== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==914646== ==914646== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==914646== at 0x65C779E: getsockopt_syscall (getsockopt.c:29) ==914646== by 0x65C779E: getsockopt (getsockopt.c:94) ==914646== by 0xB917157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==914646== by 0xB91EA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==914646== by 0xB925DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==914646== by 0xB8253C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==914646== by 0xB79EE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==914646== by 0xAF5DE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==914646== by 0x8F7E4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==914646== by 0x6206418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==914646== by 0x619FD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==914646== by 0x4ABFD38: PetscInitialize (pinit.c:924) ==914646== by 0x499358B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==914646== by 0x49935D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==914646== by 0x126698: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==914646== by 0x11FFCF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==914646== by 0x123098: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==914646== by 0x122F38: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==914646== by 0x1235CF: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==914646== by 0x11E300: main (TestHdf5DataWriter.cpp:19) ==914646== Address 0x1ffeffdfdc is on thread 1's stack ==914646== in frame #2, created by pmix_ptl_base_make_connection (???:) ==914646== { 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 } ==914646== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==914646== at 0x65C779E: getsockopt_syscall (getsockopt.c:29) ==914646== by 0x65C779E: getsockopt (getsockopt.c:94) ==914646== by 0xB917157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==914646== by 0xB91EA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==914646== by 0xB925DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==914646== by 0xB8253C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==914646== by 0xB79EE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==914646== by 0xAF5DE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==914646== by 0x8F7E4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==914646== by 0x6206418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==914646== by 0x619FD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==914646== by 0x4ABFD38: PetscInitialize (pinit.c:924) ==914646== by 0x499358B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==914646== by 0x49935D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==914646== by 0x126698: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==914646== by 0x11FFCF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==914646== by 0x123098: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==914646== by 0x122F38: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==914646== by 0x1235CF: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==914646== by 0x11E300: main (TestHdf5DataWriter.cpp:19) ==914646== Address 0x1ffeffdfdc is on thread 1's stack ==914646== in frame #2, created by pmix_ptl_base_make_connection (???:) ==914646== { 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 } ==914646== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==914646== at 0x65C7C7E: setsockopt_syscall (setsockopt.c:29) ==914646== by 0x65C7C7E: setsockopt (setsockopt.c:95) ==914646== by 0xB91EBA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==914646== by 0xB925DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==914646== by 0xB8253C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==914646== by 0xB79EE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==914646== by 0xAF5DE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==914646== by 0x8F7E4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==914646== by 0x6206418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==914646== by 0x619FD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==914646== by 0x4ABFD38: PetscInitialize (pinit.c:924) ==914646== by 0x499358B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==914646== by 0x49935D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==914646== by 0x126698: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==914646== by 0x11FFCF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==914646== by 0x123098: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==914646== by 0x122F38: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==914646== by 0x1235CF: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==914646== by 0x11E300: main (TestHdf5DataWriter.cpp:19) ==914646== { 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 } ==914646== Syscall param pwrite64(buf) points to uninitialised byte(s) ==914646== at 0x65B29EF: __libc_pwrite64 (pwrite64.c:25) ==914646== by 0x65B29EF: pwrite (pwrite64.c:23) ==914646== by 0x10C4E9D2: mca_fbtl_posix_pwritev (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_fbtl_posix.so) ==914646== by 0x10C5E419: mca_common_ompio_file_write (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==914646== by 0x10C5E79A: mca_common_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==914646== by 0x10B4989A: mca_io_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_io_ompio.so) ==914646== by 0x61936A7: PMPI_File_write_at (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==914646== by 0x6032FEB: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==914646== by 0x5E724ED: H5FD_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==914646== by 0x5E55313: H5F__accum_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==914646== by 0x5F50442: H5PB_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==914646== by 0x5E5CDEA: H5F_block_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==914646== by 0x5DE6E98: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==914646== by 0x60263F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==914646== by 0x60279CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==914646== by 0x602847E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==914646== by 0x5DC354C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==914646== by 0x5E5B936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==914646== by 0x5E5C3FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==914646== by 0x5E5FBB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==914646== by 0x5E5FEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==914646== by 0x5ECF51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==914646== by 0x5ECF5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==914646== by 0x5E5C831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==914646== by 0x5E51881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==914646== by 0x126CA2: TestHdf5DataWriter::TestSimpleParallelWriteDirectlyWithHdf5() (TestHdf5DataWriter.hpp:149) ==914646== by 0x153266: TestDescription_TestHdf5DataWriter_TestSimpleParallelWriteDirectlyWithHdf5::runTest() (TestHdf5DataWriter.cpp:31) ==914646== by 0x11F5CA: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==914646== by 0x123346: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==914646== by 0x12322B: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==914646== by 0x1230D1: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==914646== by 0x122F38: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==914646== by 0x1235CF: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==914646== by 0x11E300: main (TestHdf5DataWriter.cpp:19) ==914646== Address 0xfca1be3 is 83 bytes inside a block of size 168 alloc'd ==914646== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==914646== by 0x5DE6E26: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==914646== by 0x60263F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==914646== by 0x60279CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==914646== by 0x602847E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==914646== by 0x5DC354C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==914646== by 0x5E5B936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==914646== by 0x5E5C3FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==914646== by 0x5E5FBB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==914646== by 0x5E5FEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==914646== by 0x5ECF51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==914646== by 0x5ECF5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==914646== by 0x5E5C831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==914646== by 0x5E51881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==914646== by 0x126CA2: TestHdf5DataWriter::TestSimpleParallelWriteDirectlyWithHdf5() (TestHdf5DataWriter.hpp:149) ==914646== by 0x153266: TestDescription_TestHdf5DataWriter_TestSimpleParallelWriteDirectlyWithHdf5::runTest() (TestHdf5DataWriter.cpp:31) ==914646== by 0x11F5CA: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==914646== by 0x123346: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==914646== by 0x12322B: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==914646== by 0x1230D1: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==914646== by 0x122F38: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==914646== by 0x1235CF: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==914646== by 0x11E300: main (TestHdf5DataWriter.cpp:19) ==914646== { 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 } ==914646== Warning: invalid file descriptor -1 in syscall close() ==914646== ==914646== FILE DESCRIPTORS: 9 open (3 std) at exit. ==914646== Open file descriptor 12: ==914646== at 0x65B522D: pipe (pipe.c:29) ==914646== by 0xAF5E07D: ??? ==914646== by 0x8F7E4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==914646== by 0x6206418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==914646== by 0x619FD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==914646== by 0x4ABFD38: PetscInitialize (pinit.c:924) ==914646== by 0x499358B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==914646== by 0x49935D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==914646== by 0x126698: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==914646== by 0x11FFCF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==914646== by 0x123098: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==914646== by 0x122F38: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==914646== by 0x1235CF: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==914646== by 0x11E300: main (TestHdf5DataWriter.cpp:19) ==914646== ==914646== Open file descriptor 8: /dev/shm/open_mpi.0000 ==914646== at 0x65B9BCC: __open_nocancel (open64_nocancel.c:39) ==914646== by 0x653DC4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==914646== by 0x5D49822: ??? ==914646== by 0x5D4996F: ??? ==914646== by 0x90236DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==914646== by 0x9023938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==914646== by 0x8FD9922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==914646== by 0x8F7E2DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==914646== by 0x6206418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==914646== by 0x619FD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==914646== by 0x4ABFD38: PetscInitialize (pinit.c:924) ==914646== by 0x499358B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==914646== by 0x49935D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==914646== by 0x126698: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==914646== by 0x11FFCF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==914646== by 0x123098: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==914646== by 0x122F38: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==914646== by 0x1235CF: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==914646== by 0x11E300: main (TestHdf5DataWriter.cpp:19) ==914646== ==914646== Open file descriptor 111: ==914646== ==914646== ==914646== Open file descriptor 108: ==914646== ==914646== ==914646== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestHdf5DataWriter_valgrind.txt ==914646== ==914646== ==914646== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==914646== ==914646== ==914646== ==914646== HEAP SUMMARY: ==914646== in use at exit: 700,770 bytes in 9,387 blocks ==914646== total heap usage: 115,967 allocs, 106,580 frees, 1,427,378,763 bytes allocated ==914646== ==914646== 552 bytes in 1 blocks are definitely lost in loss record 43 of 66 ==914646== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==914646== by 0xB82CC13: ??? ==914646== by 0xB82D22C: ??? ==914646== by 0xB7A04B7: ??? ==914646== by 0x616C15A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==914646== by 0x6206A97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==914646== by 0x619FD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==914646== by 0x4ABFD38: PetscInitialize (pinit.c:924) ==914646== by 0x499358B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==914646== by 0x49935D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==914646== by 0x126698: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==914646== by 0x11FFCF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==914646== by 0x123098: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==914646== by 0x122F38: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==914646== by 0x1235CF: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==914646== by 0x11E300: main (TestHdf5DataWriter.cpp:19) ==914646== { 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 } ==914646== 685,300 (136 direct, 685,164 indirect) bytes in 1 blocks are definitely lost in loss record 66 of 66 ==914646== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==914646== by 0xCA4074E: ??? ==914646== by 0xCA40E0B: ??? ==914646== by 0xCA43F56: ??? ==914646== by 0xCA3965D: ??? ==914646== by 0xCA39FA3: ??? ==914646== by 0x9091F05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==914646== by 0x906DAE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==914646== by 0x901CCB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==914646== by 0x8F49EF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==914646== by 0xAF5EF03: ??? ==914646== by 0x8F7E4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==914646== by 0x6206418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==914646== by 0x619FD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==914646== by 0x4ABFD38: PetscInitialize (pinit.c:924) ==914646== by 0x499358B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==914646== by 0x49935D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==914646== by 0x126698: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==914646== by 0x11FFCF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==914646== by 0x123098: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==914646== by 0x122F38: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==914646== by 0x1235CF: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==914646== by 0x11E300: main (TestHdf5DataWriter.cpp:19) ==914646== { 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 } ==914646== LEAK SUMMARY: ==914646== definitely lost: 688 bytes in 2 blocks ==914646== indirectly lost: 1,760 bytes in 16 blocks ==914646== possibly lost: 0 bytes in 0 blocks ==914646== still reachable: 1,531 bytes in 6 blocks ==914646== suppressed: 696,791 bytes in 9,363 blocks ==914646== Reachable blocks (those to which a pointer was found) are not shown. ==914646== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==914646== ==914646== Use --track-origins=yes to see where uninitialised values come from ==914646== For lists of detected and suppressed errors, rerun with: -s ==914646== ERROR SUMMARY: 69 errors from 6 contexts (suppressed: 29 from 29)