==1827334== Memcheck, a memory error detector ==1827334== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==1827334== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==1827334== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/heart/test/TestSpiralWaveAndPhase -malloc_debug -malloc_dump -memory_info ==1827334== Parent PID: 1804739 ==1827334== ==1827334== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==1827334== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==1827334== ==1827334== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==1827334== at 0x7DF179E: getsockopt_syscall (getsockopt.c:29) ==1827334== by 0x7DF179E: getsockopt (getsockopt.c:94) ==1827334== by 0x107D5157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1827334== by 0x107DCA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1827334== by 0x107E3DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1827334== by 0x106E33C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1827334== by 0x1065CE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==1827334== by 0xFE1BE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==1827334== by 0xBCB64CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1827334== by 0x8471418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1827334== by 0x840AD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1827334== by 0x63A9D38: PetscInitialize (pinit.c:924) ==1827334== by 0x627D58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1827334== by 0x627D5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1827334== by 0x1236A2: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1827334== by 0x11D81D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1827334== by 0x120128: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1827334== by 0x120023: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1827334== by 0x120637: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1827334== by 0x11C020: main (TestSpiralWaveAndPhase.cpp:18) ==1827334== Address 0x1ffeffdfac is on thread 1's stack ==1827334== in frame #2, created by pmix_ptl_base_make_connection (???:) ==1827334== { 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 } ==1827334== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==1827334== at 0x7DF179E: getsockopt_syscall (getsockopt.c:29) ==1827334== by 0x7DF179E: getsockopt (getsockopt.c:94) ==1827334== by 0x107D5157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1827334== by 0x107DCA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1827334== by 0x107E3DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1827334== by 0x106E33C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1827334== by 0x1065CE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==1827334== by 0xFE1BE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==1827334== by 0xBCB64CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1827334== by 0x8471418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1827334== by 0x840AD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1827334== by 0x63A9D38: PetscInitialize (pinit.c:924) ==1827334== by 0x627D58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1827334== by 0x627D5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1827334== by 0x1236A2: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1827334== by 0x11D81D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1827334== by 0x120128: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1827334== by 0x120023: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1827334== by 0x120637: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1827334== by 0x11C020: main (TestSpiralWaveAndPhase.cpp:18) ==1827334== Address 0x1ffeffdfac is on thread 1's stack ==1827334== in frame #2, created by pmix_ptl_base_make_connection (???:) ==1827334== { 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 } ==1827334== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==1827334== at 0x7DF1C7E: setsockopt_syscall (setsockopt.c:29) ==1827334== by 0x7DF1C7E: setsockopt (setsockopt.c:95) ==1827334== by 0x107DCBA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1827334== by 0x107E3DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1827334== by 0x106E33C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1827334== by 0x1065CE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==1827334== by 0xFE1BE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==1827334== by 0xBCB64CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1827334== by 0x8471418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1827334== by 0x840AD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1827334== by 0x63A9D38: PetscInitialize (pinit.c:924) ==1827334== by 0x627D58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1827334== by 0x627D5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1827334== by 0x1236A2: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1827334== by 0x11D81D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1827334== by 0x120128: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1827334== by 0x120023: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1827334== by 0x120637: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1827334== by 0x11C020: main (TestSpiralWaveAndPhase.cpp:18) ==1827334== { 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 } ==1827334== Syscall param pwrite64(buf) points to uninitialised byte(s) ==1827334== at 0x7DDC9EF: __libc_pwrite64 (pwrite64.c:25) ==1827334== by 0x7DDC9EF: pwrite (pwrite64.c:23) ==1827334== by 0x190529D2: mca_fbtl_posix_pwritev (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_fbtl_posix.so) ==1827334== by 0x19062419: mca_common_ompio_file_write (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==1827334== by 0x1906279A: mca_common_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==1827334== by 0x13B4D89A: mca_io_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_io_ompio.so) ==1827334== by 0x83FE6A7: PMPI_File_write_at (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1827334== by 0x829BFEB: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1827334== by 0x80DB4ED: H5FD_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1827334== by 0x80BE313: H5F__accum_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1827334== by 0x81B9442: H5PB_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1827334== by 0x80C5DEA: H5F_block_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1827334== by 0x804FE98: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1827334== by 0x828F3F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1827334== by 0x82909CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1827334== by 0x829147E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1827334== by 0x802C54C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1827334== by 0x80C4936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1827334== by 0x80C53FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1827334== by 0x80C8BB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1827334== by 0x80C8EFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1827334== by 0x813851F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1827334== by 0x81385EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1827334== by 0x80C5831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1827334== by 0x80BA881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1827334== by 0x61AC967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==1827334== by 0x125A46: TestSpiralWaveAndPhase::TestPhaseCalculation() (TestSpiralWaveAndPhase.hpp:210) ==1827334== by 0x12651C: TestDescription_TestSpiralWaveAndPhase_TestPhaseCalculation::runTest() (TestSpiralWaveAndPhase.cpp:30) ==1827334== by 0x11D054: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==1827334== by 0x1203D6: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==1827334== by 0x1202BB: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==1827334== by 0x120161: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==1827334== by 0x120023: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1827334== by 0x120637: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1827334== by 0x11C020: main (TestSpiralWaveAndPhase.cpp:18) ==1827334== Address 0x1290f11e is 62 bytes inside a block of size 320 alloc'd ==1827334== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==1827334== by 0x804FE26: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1827334== by 0x828F3F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1827334== by 0x82909CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1827334== by 0x829147E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1827334== by 0x802C54C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1827334== by 0x80C4936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1827334== by 0x80C53FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1827334== by 0x80C8BB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1827334== by 0x80C8EFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1827334== by 0x813851F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1827334== by 0x81385EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1827334== by 0x80C5831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1827334== by 0x80BA881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1827334== by 0x61AC967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==1827334== by 0x125A46: TestSpiralWaveAndPhase::TestPhaseCalculation() (TestSpiralWaveAndPhase.hpp:210) ==1827334== by 0x12651C: TestDescription_TestSpiralWaveAndPhase_TestPhaseCalculation::runTest() (TestSpiralWaveAndPhase.cpp:30) ==1827334== by 0x11D054: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==1827334== by 0x1203D6: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==1827334== by 0x1202BB: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==1827334== by 0x120161: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==1827334== by 0x120023: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1827334== by 0x120637: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1827334== by 0x11C020: main (TestSpiralWaveAndPhase.cpp:18) ==1827334== { 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 } ==1827334== ==1827334== FILE DESCRIPTORS: 9 open (3 std) at exit. ==1827334== Open file descriptor 12: ==1827334== at 0x7DDF22D: pipe (pipe.c:29) ==1827334== by 0xFE1C07D: ??? ==1827334== by 0xBCB64CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1827334== by 0x8471418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1827334== by 0x840AD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1827334== by 0x63A9D38: PetscInitialize (pinit.c:924) ==1827334== by 0x627D58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1827334== by 0x627D5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1827334== by 0x1236A2: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1827334== by 0x11D81D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1827334== by 0x120128: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1827334== by 0x120023: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1827334== by 0x120637: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1827334== by 0x11C020: main (TestSpiralWaveAndPhase.cpp:18) ==1827334== ==1827334== Open file descriptor 8: /dev/shm/open_mpi.0000 ==1827334== at 0x7DE3BCC: __open_nocancel (open64_nocancel.c:39) ==1827334== by 0x7D67C4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==1827334== by 0x7633822: ??? ==1827334== by 0x763396F: ??? ==1827334== by 0xBD5B6DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==1827334== by 0xBD5B938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==1827334== by 0xBD11922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==1827334== by 0xBCB62DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1827334== by 0x8471418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1827334== by 0x840AD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1827334== by 0x63A9D38: PetscInitialize (pinit.c:924) ==1827334== by 0x627D58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1827334== by 0x627D5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1827334== by 0x1236A2: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1827334== by 0x11D81D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1827334== by 0x120128: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1827334== by 0x120023: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1827334== by 0x120637: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1827334== by 0x11C020: main (TestSpiralWaveAndPhase.cpp:18) ==1827334== ==1827334== Open file descriptor 117: ==1827334== ==1827334== ==1827334== Open file descriptor 110: ==1827334== ==1827334== ==1827334== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestSpiralWaveAndPhase_valgrind.txt ==1827334== ==1827334== ==1827334== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==1827334== ==1827334== ==1827334== ==1827334== HEAP SUMMARY: ==1827334== in use at exit: 701,088 bytes in 9,383 blocks ==1827334== total heap usage: 4,193,446 allocs, 4,184,063 frees, 1,909,550,544 bytes allocated ==1827334== ==1827334== 552 bytes in 1 blocks are definitely lost in loss record 39 of 62 ==1827334== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==1827334== by 0x106EAC13: ??? ==1827334== by 0x106EB22C: ??? ==1827334== by 0x1065E4B7: ??? ==1827334== by 0x83D715A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1827334== by 0x8471A97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1827334== by 0x840AD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1827334== by 0x63A9D38: PetscInitialize (pinit.c:924) ==1827334== by 0x627D58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1827334== by 0x627D5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1827334== by 0x1236A2: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1827334== by 0x11D81D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1827334== by 0x120128: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1827334== by 0x120023: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1827334== by 0x120637: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1827334== by 0x11C020: main (TestSpiralWaveAndPhase.cpp:18) ==1827334== { 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 } ==1827334== 685,269 (136 direct, 685,133 indirect) bytes in 1 blocks are definitely lost in loss record 62 of 62 ==1827334== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==1827334== by 0x1185D74E: ??? ==1827334== by 0x1185DE0B: ??? ==1827334== by 0x11860F56: ??? ==1827334== by 0x1185665D: ??? ==1827334== by 0x11856FA3: ??? ==1827334== by 0xBDC7F05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==1827334== by 0xBDA3AE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==1827334== by 0xBD54CB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==1827334== by 0xBC81EF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1827334== by 0xFE1CF03: ??? ==1827334== by 0xBCB64CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1827334== by 0x8471418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1827334== by 0x840AD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1827334== by 0x63A9D38: PetscInitialize (pinit.c:924) ==1827334== by 0x627D58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1827334== by 0x627D5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1827334== by 0x1236A2: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1827334== by 0x11D81D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1827334== by 0x120128: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1827334== by 0x120023: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1827334== by 0x120637: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1827334== by 0x11C020: main (TestSpiralWaveAndPhase.cpp:18) ==1827334== { 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 } ==1827334== LEAK SUMMARY: ==1827334== definitely lost: 688 bytes in 2 blocks ==1827334== indirectly lost: 1,760 bytes in 16 blocks ==1827334== possibly lost: 0 bytes in 0 blocks ==1827334== still reachable: 1,531 bytes in 6 blocks ==1827334== suppressed: 697,109 bytes in 9,359 blocks ==1827334== Reachable blocks (those to which a pointer was found) are not shown. ==1827334== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==1827334== ==1827334== Use --track-origins=yes to see where uninitialised values come from ==1827334== For lists of detected and suppressed errors, rerun with: -s ==1827334== ERROR SUMMARY: 8 errors from 6 contexts (suppressed: 25 from 25)