==1977360== Memcheck, a memory error detector ==1977360== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==1977360== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==1977360== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/heart/test/TestExtendedBidomainProblem -malloc_debug -malloc_dump -memory_info ==1977360== Parent PID: 1956552 ==1977360== ==1977360== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==1977360== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==1977360== ==1977360== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==1977360== at 0xA2E979E: getsockopt_syscall (getsockopt.c:29) ==1977360== by 0xA2E979E: getsockopt (getsockopt.c:94) ==1977360== by 0x1467A157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1977360== by 0x14681A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1977360== by 0x14688DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1977360== by 0x145883C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1977360== by 0x14501E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==1977360== by 0x13CC0E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==1977360== by 0xD2D34CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1977360== by 0x9BC7418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1977360== by 0x9B60D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1977360== by 0xA67AD38: PetscInitialize (pinit.c:924) ==1977360== by 0x9A8958B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1977360== by 0x9A895D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1977360== by 0x12DB00: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1977360== by 0x128A3D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1977360== by 0x12B846: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1977360== by 0x12B741: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1977360== by 0x12BD55: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1977360== by 0x127240: main (TestExtendedBidomainProblem.cpp:18) ==1977360== Address 0x1ffeffdfac is on thread 1's stack ==1977360== in frame #2, created by pmix_ptl_base_make_connection (???:) ==1977360== { 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 } ==1977360== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==1977360== at 0xA2E979E: getsockopt_syscall (getsockopt.c:29) ==1977360== by 0xA2E979E: getsockopt (getsockopt.c:94) ==1977360== by 0x1467A157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1977360== by 0x14681A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1977360== by 0x14688DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1977360== by 0x145883C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1977360== by 0x14501E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==1977360== by 0x13CC0E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==1977360== by 0xD2D34CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1977360== by 0x9BC7418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1977360== by 0x9B60D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1977360== by 0xA67AD38: PetscInitialize (pinit.c:924) ==1977360== by 0x9A8958B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1977360== by 0x9A895D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1977360== by 0x12DB00: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1977360== by 0x128A3D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1977360== by 0x12B846: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1977360== by 0x12B741: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1977360== by 0x12BD55: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1977360== by 0x127240: main (TestExtendedBidomainProblem.cpp:18) ==1977360== Address 0x1ffeffdfac is on thread 1's stack ==1977360== in frame #2, created by pmix_ptl_base_make_connection (???:) ==1977360== { 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 } ==1977360== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==1977360== at 0xA2E9C7E: setsockopt_syscall (setsockopt.c:29) ==1977360== by 0xA2E9C7E: setsockopt (setsockopt.c:95) ==1977360== by 0x14681BA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1977360== by 0x14688DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1977360== by 0x145883C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1977360== by 0x14501E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==1977360== by 0x13CC0E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==1977360== by 0xD2D34CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1977360== by 0x9BC7418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1977360== by 0x9B60D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1977360== by 0xA67AD38: PetscInitialize (pinit.c:924) ==1977360== by 0x9A8958B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1977360== by 0x9A895D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1977360== by 0x12DB00: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1977360== by 0x128A3D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1977360== by 0x12B846: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1977360== by 0x12B741: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1977360== by 0x12BD55: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1977360== by 0x127240: main (TestExtendedBidomainProblem.cpp:18) ==1977360== { 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 } ==1977360== Syscall param pwrite64(buf) points to uninitialised byte(s) ==1977360== at 0xA2D49EF: __libc_pwrite64 (pwrite64.c:25) ==1977360== by 0xA2D49EF: pwrite (pwrite64.c:23) ==1977360== by 0x16EF79D2: mca_fbtl_posix_pwritev (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_fbtl_posix.so) ==1977360== by 0x16F07419: mca_common_ompio_file_write (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==1977360== by 0x16F0779A: mca_common_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/libmca_common_ompio.so.41.29.2) ==1977360== by 0x16DF289A: mca_io_ompio_file_write_at (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_io_ompio.so) ==1977360== by 0x9B546A7: PMPI_File_write_at (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1977360== by 0xD152FEB: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977360== by 0xCF924ED: H5FD_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977360== by 0xCF75313: H5F__accum_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977360== by 0xD070442: H5PB_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977360== by 0xCF7CDEA: H5F_block_write (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977360== by 0xCF06E98: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977360== by 0xD1463F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977360== by 0xD1479CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977360== by 0xD14847E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977360== by 0xCEE354C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977360== by 0xCF7B936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977360== by 0xCF7C3FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977360== by 0xCF7FBB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977360== by 0xCF7FEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977360== by 0xCFEF51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977360== by 0xCFEF5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977360== by 0xCF7C831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977360== by 0xCF71881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977360== by 0x99B8967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==1977360== by 0x99B3647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==1977360== by 0x99B36ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==1977360== by 0x6885AF3: AbstractCardiacProblem<1u, 1u, 3u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==1977360== by 0x6885693: AbstractCardiacProblem<1u, 1u, 3u>::Solve() (AbstractCardiacProblem.cpp:582) ==1977360== by 0x12FC1C: TestExtendedBidomainProblem::TestExtendedProblemVsMartincCode() (TestExtendedBidomainProblem.hpp:168) ==1977360== by 0x1313BC: TestDescription_TestExtendedBidomainProblem_TestExtendedProblemVsMartincCode::runTest() (TestExtendedBidomainProblem.cpp:30) ==1977360== by 0x128274: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==1977360== by 0x12BAF4: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==1977360== by 0x12B9D9: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==1977360== by 0x12B87F: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==1977360== by 0x12B741: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1977360== by 0x12BD55: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1977360== by 0x127240: main (TestExtendedBidomainProblem.cpp:18) ==1977360== Address 0x1668899e is 62 bytes inside a block of size 320 alloc'd ==1977360== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==1977360== by 0xCF06E26: H5C__flush_single_entry (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977360== by 0xD1463F9: H5C_apply_candidate_list (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977360== by 0xD1479CA: H5AC__run_sync_point (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977360== by 0xD14847E: H5AC__flush_entries (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977360== by 0xCEE354C: H5AC_flush (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977360== by 0xCF7B936: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977360== by 0xCF7C3FE: H5F__dest (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977360== by 0xCF7FBB2: H5F_try_close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977360== by 0xCF7FEFB: H5F__close_cb (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977360== by 0xCFEF51F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977360== by 0xCFEF5EA: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977360== by 0xCF7C831: H5F__close (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977360== by 0xCF71881: H5Fclose (in /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0) ==1977360== by 0x99B8967: Hdf5DataWriter::Close() (Hdf5DataWriter.cpp:1100) ==1977360== by 0x99B3647: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:273) ==1977360== by 0x99B36ED: Hdf5DataWriter::~Hdf5DataWriter() (Hdf5DataWriter.cpp:283) ==1977360== by 0x6885AF3: AbstractCardiacProblem<1u, 1u, 3u>::CloseFilesAndPostProcess() (AbstractCardiacProblem.cpp:597) ==1977360== by 0x6885693: AbstractCardiacProblem<1u, 1u, 3u>::Solve() (AbstractCardiacProblem.cpp:582) ==1977360== by 0x12FC1C: TestExtendedBidomainProblem::TestExtendedProblemVsMartincCode() (TestExtendedBidomainProblem.hpp:168) ==1977360== by 0x1313BC: TestDescription_TestExtendedBidomainProblem_TestExtendedProblemVsMartincCode::runTest() (TestExtendedBidomainProblem.cpp:30) ==1977360== by 0x128274: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==1977360== by 0x12BAF4: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==1977360== by 0x12B9D9: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==1977360== by 0x12B87F: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==1977360== by 0x12B741: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1977360== by 0x12BD55: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1977360== by 0x127240: main (TestExtendedBidomainProblem.cpp:18) ==1977360== { Memcheck:Param pwrite64(buf) fun:__libc_pwrite64 fun:pwrite fun:mca_fbtl_posix_pwritev fun:mca_common_ompio_file_write fun:mca_common_ompio_file_write_at fun:mca_io_ompio_file_write_at fun:PMPI_File_write_at obj:/usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0 fun:H5FD_write fun:H5F__accum_write fun:H5PB_write fun:H5F_block_write fun:H5C__flush_single_entry fun:H5C_apply_candidate_list fun:H5AC__run_sync_point fun:H5AC__flush_entries fun:H5AC_flush obj:/usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103.3.0 fun:H5F__dest fun:H5F_try_close fun:H5F__close_cb fun:H5I_dec_ref fun:H5I_dec_app_ref fun:H5F__close fun:H5Fclose fun:_ZN14Hdf5DataWriter5CloseEv fun:_ZN14Hdf5DataWriterD1Ev fun:_ZN14Hdf5DataWriterD0Ev fun:_ZN22AbstractCardiacProblemILj1ELj1ELj3EE24CloseFilesAndPostProcessEv fun:_ZN22AbstractCardiacProblemILj1ELj1ELj3EE5SolveEv fun:_ZN27TestExtendedBidomainProblem32TestExtendedProblemVsMartincCodeEv fun:_ZN76TestDescription_TestExtendedBidomainProblem_TestExtendedProblemVsMartincCode7runTestEv fun:_ZN7CxxTest19RealTestDescription3runEv fun:_ZN7CxxTest10TestRunner7runTestERNS_15TestDescriptionE fun:_ZN7CxxTest10TestRunner8runSuiteERNS_16SuiteDescriptionE fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==1977360== ==1977360== FILE DESCRIPTORS: 9 open (3 std) at exit. ==1977360== Open file descriptor 12: ==1977360== at 0xA2D722D: pipe (pipe.c:29) ==1977360== by 0x13CC107D: ??? ==1977360== by 0xD2D34CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1977360== by 0x9BC7418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1977360== by 0x9B60D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1977360== by 0xA67AD38: PetscInitialize (pinit.c:924) ==1977360== by 0x9A8958B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1977360== by 0x9A895D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1977360== by 0x12DB00: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1977360== by 0x128A3D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1977360== by 0x12B846: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1977360== by 0x12B741: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1977360== by 0x12BD55: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1977360== by 0x127240: main (TestExtendedBidomainProblem.cpp:18) ==1977360== ==1977360== Open file descriptor 8: /dev/shm/open_mpi.0000 ==1977360== at 0xA2DBBCC: __open_nocancel (open64_nocancel.c:39) ==1977360== by 0xA25FC4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==1977360== by 0x9AC1822: ??? ==1977360== by 0x9AC196F: ??? ==1977360== by 0xD3786DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==1977360== by 0xD378938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==1977360== by 0xD32E922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==1977360== by 0xD2D32DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1977360== by 0x9BC7418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1977360== by 0x9B60D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1977360== by 0xA67AD38: PetscInitialize (pinit.c:924) ==1977360== by 0x9A8958B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1977360== by 0x9A895D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1977360== by 0x12DB00: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1977360== by 0x128A3D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1977360== by 0x12B846: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1977360== by 0x12B741: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1977360== by 0x12BD55: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1977360== by 0x127240: main (TestExtendedBidomainProblem.cpp:18) ==1977360== ==1977360== Open file descriptor 117: ==1977360== ==1977360== ==1977360== Open file descriptor 110: ==1977360== ==1977360== ==1977360== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestExtendedBidomainProblem_valgrind.txt ==1977360== ==1977360== ==1977360== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==1977360== ==1977360== ==1977360== ==1977360== HEAP SUMMARY: ==1977360== in use at exit: 701,168 bytes in 9,383 blocks ==1977360== total heap usage: 2,374,805 allocs, 2,365,422 frees, 2,483,257,349 bytes allocated ==1977360== ==1977360== 552 bytes in 1 blocks are definitely lost in loss record 39 of 65 ==1977360== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==1977360== by 0x1458FC13: ??? ==1977360== by 0x1459022C: ??? ==1977360== by 0x145034B7: ??? ==1977360== by 0x9B2D15A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1977360== by 0x9BC7A97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1977360== by 0x9B60D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1977360== by 0xA67AD38: PetscInitialize (pinit.c:924) ==1977360== by 0x9A8958B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1977360== by 0x9A895D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1977360== by 0x12DB00: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1977360== by 0x128A3D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1977360== by 0x12B846: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1977360== by 0x12B741: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1977360== by 0x12BD55: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1977360== by 0x127240: main (TestExtendedBidomainProblem.cpp:18) ==1977360== { 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 } ==1977360== 84,459 (136 direct, 84,323 indirect) bytes in 1 blocks are definitely lost in loss record 62 of 65 ==1977360== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==1977360== by 0x1570274E: ??? ==1977360== by 0x15702E0B: ??? ==1977360== by 0x15705F56: ??? ==1977360== by 0x156FB65D: ??? ==1977360== by 0x156FBFA3: ??? ==1977360== by 0xD3E4F05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==1977360== by 0xD3C0AE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==1977360== by 0xD371CB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==1977360== by 0xD29EEF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1977360== by 0x13CC1F03: ??? ==1977360== by 0xD2D34CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1977360== by 0x9BC7418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1977360== by 0x9B60D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1977360== by 0xA67AD38: PetscInitialize (pinit.c:924) ==1977360== by 0x9A8958B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1977360== by 0x9A895D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1977360== by 0x12DB00: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61) ==1977360== by 0x128A3D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1977360== by 0x12B846: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1977360== by 0x12B741: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1977360== by 0x12BD55: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1977360== by 0x127240: main (TestExtendedBidomainProblem.cpp:18) ==1977360== { 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 } ==1977360== LEAK SUMMARY: ==1977360== definitely lost: 688 bytes in 2 blocks ==1977360== indirectly lost: 1,760 bytes in 16 blocks ==1977360== possibly lost: 0 bytes in 0 blocks ==1977360== still reachable: 1,531 bytes in 6 blocks ==1977360== suppressed: 697,189 bytes in 9,359 blocks ==1977360== Reachable blocks (those to which a pointer was found) are not shown. ==1977360== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==1977360== ==1977360== Use --track-origins=yes to see where uninitialised values come from ==1977360== For lists of detected and suppressed errors, rerun with: -s ==1977360== ERROR SUMMARY: 11 errors from 6 contexts (suppressed: 28 from 28)