==3305354== Memcheck, a memory error detector ==3305354== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==3305354== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==3305354== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/heart/test/TestSpiralWaveAndPhase -malloc_debug -malloc_dump -memory_info ==3305354== Parent PID: 3282641 ==3305354== ==3305354== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==3305354== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==3305354== ==3305354== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==3305354== at 0x7DF379E: getsockopt_syscall (getsockopt.c:29) ==3305354== by 0x7DF379E: getsockopt (getsockopt.c:94) ==3305354== by 0x107D7157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3305354== by 0x107DEA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3305354== by 0x107E5DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3305354== by 0x106E53C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3305354== by 0x1065EE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==3305354== by 0xFE1DE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==3305354== by 0xBCB64CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3305354== by 0x8473418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3305354== by 0x840CD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3305354== by 0x63ABD38: PetscInitialize (pinit.c:924) ==3305354== by 0x627F66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3305354== by 0x627F6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3305354== by 0x1236A2: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3305354== by 0x11D81D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3305354== by 0x120128: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3305354== by 0x120023: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3305354== by 0x120637: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3305354== by 0x11C020: main (TestSpiralWaveAndPhase.cpp:18) ==3305354== Address 0x1ffeffdfbc is on thread 1's stack ==3305354== in frame #2, created by pmix_ptl_base_make_connection (???:) ==3305354== { 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 } ==3305354== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==3305354== at 0x7DF379E: getsockopt_syscall (getsockopt.c:29) ==3305354== by 0x7DF379E: getsockopt (getsockopt.c:94) ==3305354== by 0x107D7157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3305354== by 0x107DEA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3305354== by 0x107E5DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3305354== by 0x106E53C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3305354== by 0x1065EE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==3305354== by 0xFE1DE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==3305354== by 0xBCB64CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3305354== by 0x8473418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3305354== by 0x840CD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3305354== by 0x63ABD38: PetscInitialize (pinit.c:924) ==3305354== by 0x627F66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3305354== by 0x627F6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3305354== by 0x1236A2: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3305354== by 0x11D81D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3305354== by 0x120128: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3305354== by 0x120023: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3305354== by 0x120637: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3305354== by 0x11C020: main (TestSpiralWaveAndPhase.cpp:18) ==3305354== Address 0x1ffeffdfbc is on thread 1's stack ==3305354== in frame #2, created by pmix_ptl_base_make_connection (???:) ==3305354== { 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 } ==3305354== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==3305354== at 0x7DF3C7E: setsockopt_syscall (setsockopt.c:29) ==3305354== by 0x7DF3C7E: setsockopt (setsockopt.c:95) ==3305354== by 0x107DEBA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3305354== by 0x107E5DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3305354== by 0x106E53C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==3305354== by 0x1065EE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==3305354== by 0xFE1DE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==3305354== by 0xBCB64CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3305354== by 0x8473418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3305354== by 0x840CD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3305354== by 0x63ABD38: PetscInitialize (pinit.c:924) ==3305354== by 0x627F66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3305354== by 0x627F6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3305354== by 0x1236A2: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3305354== by 0x11D81D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3305354== by 0x120128: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3305354== by 0x120023: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3305354== by 0x120637: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3305354== by 0x11C020: main (TestSpiralWaveAndPhase.cpp:18) ==3305354== { 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 } ==3305354== Syscall param pwrite64(buf) points to uninitialised byte(s) ==3305354== at 0x7DDE9EF: __libc_pwrite64 (pwrite64.c:25) ==3305354== by 0x7DDE9EF: pwrite (pwrite64.c:23) ==3305354== by 0x190549D2: mca_fbtl_posix_pwritev (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_fbtl_posix.so) ==3305354== by 0x19064419: mca_common_ompio_file_write (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==3305354== by 0x1906479A: mca_common_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==3305354== by 0x13B4F89A: mca_io_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_io_ompio.so) ==3305354== by 0x84006A7: PMPI_File_write_at (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3305354== by 0x829DFEB: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305354== by 0x80DD4ED: H5FD_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305354== by 0x80C0313: H5F__accum_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305354== by 0x81BB442: H5PB_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305354== by 0x80C7DEA: H5F_block_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305354== by 0x8051E98: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305354== by 0x82913F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305354== by 0x82929CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305354== by 0x829347E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305354== by 0x802E54C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305354== by 0x80C6936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305354== by 0x80C73FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305354== by 0x80CABB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305354== by 0x80CAEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305354== by 0x813A51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305354== by 0x813A5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305354== by 0x80C7831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305354== by 0x80BC881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305354== by 0x61AD8E7: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==3305354== by 0x125A16: TestSpiralWaveAndPhase::TestPhaseCalculation() (TestSpiralWaveAndPhase.hpp:210) ==3305354== by 0x1264EC: TestDescription_TestSpiralWaveAndPhase_TestPhaseCalculation::runTest() (TestSpiralWaveAndPhase.cpp:30) ==3305354== by 0x11D054: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==3305354== by 0x1203D6: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==3305354== by 0x1202BB: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==3305354== by 0x120161: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==3305354== by 0x120023: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3305354== by 0x120637: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3305354== by 0x11C020: main (TestSpiralWaveAndPhase.cpp:18) ==3305354== Address 0x11c6305e is 62 bytes inside a block of size 320 alloc'd ==3305354== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==3305354== by 0x8051E26: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305354== by 0x82913F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305354== by 0x82929CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305354== by 0x829347E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305354== by 0x802E54C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305354== by 0x80C6936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305354== by 0x80C73FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305354== by 0x80CABB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305354== by 0x80CAEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305354== by 0x813A51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305354== by 0x813A5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305354== by 0x80C7831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305354== by 0x80BC881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==3305354== by 0x61AD8E7: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==3305354== by 0x125A16: TestSpiralWaveAndPhase::TestPhaseCalculation() (TestSpiralWaveAndPhase.hpp:210) ==3305354== by 0x1264EC: TestDescription_TestSpiralWaveAndPhase_TestPhaseCalculation::runTest() (TestSpiralWaveAndPhase.cpp:30) ==3305354== by 0x11D054: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==3305354== by 0x1203D6: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==3305354== by 0x1202BB: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==3305354== by 0x120161: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==3305354== by 0x120023: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3305354== by 0x120637: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3305354== by 0x11C020: main (TestSpiralWaveAndPhase.cpp:18) ==3305354== { 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:_ZN22TestSpiralWaveAndPhase20TestPhaseCalculationEv fun:_ZN59TestDescription_TestSpiralWaveAndPhase_TestPhaseCalculation7runTestEv fun:_ZN7CxxTest19RealTestDescription3runEv fun:_ZN7CxxTest10TestRunner7runTestERNS_15TestDescriptionE fun:_ZN7CxxTest10TestRunner8runSuiteERNS_16SuiteDescriptionE fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==3305354== ==3305354== FILE DESCRIPTORS: 9 open (3 std) at exit. ==3305354== Open file descriptor 12: ==3305354== at 0x7DE122D: pipe (pipe.c:29) ==3305354== by 0xFE1E07D: ??? ==3305354== by 0xBCB64CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3305354== by 0x8473418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3305354== by 0x840CD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3305354== by 0x63ABD38: PetscInitialize (pinit.c:924) ==3305354== by 0x627F66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3305354== by 0x627F6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3305354== by 0x1236A2: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3305354== by 0x11D81D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3305354== by 0x120128: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3305354== by 0x120023: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3305354== by 0x120637: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3305354== by 0x11C020: main (TestSpiralWaveAndPhase.cpp:18) ==3305354== ==3305354== Open file descriptor 8: /dev/shm/open_mpi.0000 ==3305354== at 0x7DE5BCC: __open_nocancel (open64_nocancel.c:39) ==3305354== by 0x7D69C4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==3305354== by 0x7635822: ??? ==3305354== by 0x763596F: ??? ==3305354== by 0xBD5B6DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==3305354== by 0xBD5B938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==3305354== by 0xBD11922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==3305354== by 0xBCB62DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3305354== by 0x8473418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3305354== by 0x840CD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3305354== by 0x63ABD38: PetscInitialize (pinit.c:924) ==3305354== by 0x627F66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3305354== by 0x627F6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3305354== by 0x1236A2: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3305354== by 0x11D81D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3305354== by 0x120128: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3305354== by 0x120023: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3305354== by 0x120637: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3305354== by 0x11C020: main (TestSpiralWaveAndPhase.cpp:18) ==3305354== ==3305354== Open file descriptor 117: ==3305354== ==3305354== ==3305354== Open file descriptor 108: ==3305354== ==3305354== ==3305354== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestSpiralWaveAndPhase_valgrind.txt ==3305354== ==3305354== ==3305354== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==3305354== ==3305354== ==3305354== ==3305354== HEAP SUMMARY: ==3305354== in use at exit: 701,088 bytes in 9,383 blocks ==3305354== total heap usage: 4,033,454 allocs, 4,024,071 frees, 1,877,745,492 bytes allocated ==3305354== ==3305354== 552 bytes in 1 blocks are definitely lost in loss record 39 of 65 ==3305354== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==3305354== by 0x106ECC13: ??? ==3305354== by 0x106ED22C: ??? ==3305354== by 0x106604B7: ??? ==3305354== by 0x83D915A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3305354== by 0x8473A97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3305354== by 0x840CD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3305354== by 0x63ABD38: PetscInitialize (pinit.c:924) ==3305354== by 0x627F66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3305354== by 0x627F6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3305354== by 0x1236A2: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3305354== by 0x11D81D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3305354== by 0x120128: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3305354== by 0x120023: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3305354== by 0x120637: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3305354== by 0x11C020: main (TestSpiralWaveAndPhase.cpp:18) ==3305354== { 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 } ==3305354== 84,459 (136 direct, 84,323 indirect) bytes in 1 blocks are definitely lost in loss record 62 of 65 ==3305354== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==3305354== by 0x1185F74E: ??? ==3305354== by 0x1185FE0B: ??? ==3305354== by 0x11862F56: ??? ==3305354== by 0x1185865D: ??? ==3305354== by 0x11858FA3: ??? ==3305354== by 0xBDC7F05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==3305354== by 0xBDA3AE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==3305354== by 0xBD54CB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==3305354== by 0xBC81EF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3305354== by 0xFE1EF03: ??? ==3305354== by 0xBCB64CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==3305354== by 0x8473418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3305354== by 0x840CD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==3305354== by 0x63ABD38: PetscInitialize (pinit.c:924) ==3305354== by 0x627F66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==3305354== by 0x627F6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==3305354== by 0x1236A2: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==3305354== by 0x11D81D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==3305354== by 0x120128: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==3305354== by 0x120023: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==3305354== by 0x120637: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==3305354== by 0x11C020: main (TestSpiralWaveAndPhase.cpp:18) ==3305354== { 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 } ==3305354== LEAK SUMMARY: ==3305354== definitely lost: 688 bytes in 2 blocks ==3305354== indirectly lost: 1,760 bytes in 16 blocks ==3305354== possibly lost: 0 bytes in 0 blocks ==3305354== still reachable: 1,531 bytes in 6 blocks ==3305354== suppressed: 697,109 bytes in 9,359 blocks ==3305354== Reachable blocks (those to which a pointer was found) are not shown. ==3305354== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==3305354== ==3305354== Use --track-origins=yes to see where uninitialised values come from ==3305354== For lists of detected and suppressed errors, rerun with: -s ==3305354== ERROR SUMMARY: 8 errors from 6 contexts (suppressed: 28 from 28)