==293168== Memcheck, a memory error detector ==293168== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==293168== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==293168== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/cell_based/test/TestImmersedBoundaryCellPopulation -malloc_debug -malloc_dump -memory_info ==293168== Parent PID: 291395 ==293168== ==293168== ==293168== FILE DESCRIPTORS: 9 open (3 std) at exit. ==293168== Open file descriptor 12: ==293168== at 0x10CD022D: pipe (pipe.c:29) ==293168== by 0x1968D07D: ??? ==293168== by 0x14BF04CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==293168== by 0x105D8418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==293168== by 0x10571D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==293168== by 0xF268D38: PetscInitialize (pinit.c:924) ==293168== by 0xF0DD2DF: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==293168== by 0xF0DD32D: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==293168== by 0x16AAB1: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70) ==293168== by 0x162F29: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==293168== by 0x1660DA: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==293168== by 0x165F7A: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==293168== by 0x166611: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==293168== by 0x161345: main (TestImmersedBoundaryCellPopulation.cpp:19) ==293168== ==293168== Open file descriptor 8: /dev/shm/open_mpi.0000 ==293168== at 0x10CD4BCC: __open_nocancel (open64_nocancel.c:39) ==293168== by 0x10C58C4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==293168== by 0xF112822: ??? ==293168== by 0xF11296F: ??? ==293168== by 0x14C956DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==293168== by 0x14C95938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==293168== by 0x14C4B922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==293168== by 0x14BF02DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==293168== by 0x105D8418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==293168== by 0x10571D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==293168== by 0xF268D38: PetscInitialize (pinit.c:924) ==293168== by 0xF0DD2DF: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==293168== by 0xF0DD32D: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==293168== by 0x16AAB1: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70) ==293168== by 0x162F29: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==293168== by 0x1660DA: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==293168== by 0x165F7A: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==293168== by 0x166611: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==293168== by 0x161345: main (TestImmersedBoundaryCellPopulation.cpp:19) ==293168== ==293168== Open file descriptor 115: ==293168== ==293168== ==293168== Open file descriptor 112: ==293168== ==293168== ==293168== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestImmersedBoundaryCellPopulation_valgrind.txt ==293168== ==293168== ==293168== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==293168== ==293168== ==293168== ==293168== HEAP SUMMARY: ==293168== in use at exit: 1,054,748 bytes in 15,477 blocks ==293168== total heap usage: 101,953 allocs, 86,476 frees, 1,373,541,004 bytes allocated ==293168== ==293168== 240 bytes in 6 blocks are possibly lost in loss record 39 of 90 ==293168== at 0x4849013: operator new(unsigned long) (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==293168== by 0xA4EB6C5: __gnu_cxx::new_allocator >::allocate(unsigned long, void const*) (new_allocator.h:127) ==293168== by 0xA4EA4F1: std::allocator_traits > >::allocate(std::allocator >&, unsigned long) (alloc_traits.h:464) ==293168== by 0xA4E8126: std::_Rb_tree, std::less, std::allocator >::_M_get_node() (stl_tree.h:561) ==293168== by 0xA4E6A6F: std::_Rb_tree_node* std::_Rb_tree, std::less, std::allocator >::_M_create_node(unsigned int const&) (stl_tree.h:611) ==293168== by 0xA4E5E28: std::_Rb_tree_node* std::_Rb_tree, std::less, std::allocator >::_Alloc_node::operator()(unsigned int const&) const (stl_tree.h:529) ==293168== by 0xA4E57C3: std::_Rb_tree_iterator std::_Rb_tree, std::less, std::allocator >::_M_insert_, std::less, std::allocator >::_Alloc_node>(std::_Rb_tree_node_base*, std::_Rb_tree_node_base*, unsigned int const&, std::_Rb_tree, std::less, std::allocator >::_Alloc_node&) (stl_tree.h:1784) ==293168== by 0xA4E4E21: std::pair, bool> std::_Rb_tree, std::less, std::allocator >::_M_insert_unique(unsigned int const&) (stl_tree.h:2129) ==293168== by 0xA4E4377: std::set, std::allocator >::insert(unsigned int const&) (stl_set.h:512) ==293168== by 0xE5AD375: Node<2u>::AddElement(unsigned int) (Node.cpp:270) ==293168== by 0xE508EAF: Element<2u, 2u>::RegisterWithNodes() (Element.cpp:69) ==293168== by 0xE508DB9: Element<2u, 2u>::Element(unsigned int, std::vector*, std::allocator*> > const&, bool) (Element.cpp:51) ==293168== by 0xE614D75: TetrahedralMesh<2u, 2u>::ConstructFromMeshReader(AbstractMeshReader<2u, 2u>&) (TetrahedralMesh.cpp:127) ==293168== by 0xA861210: ImmersedBoundaryCellPopulation<2u>::GetTetrahedralMeshForPdeModifier() (ImmersedBoundaryCellPopulation.cpp:886) ==293168== by 0x16CC7A: TestImmersedBoundaryCellPopulation::TestMeshMethods() (TestImmersedBoundaryCellPopulation.hpp:213) ==293168== by 0x17234C: TestDescription_TestImmersedBoundaryCellPopulation_TestMeshMethods::runTest() (TestImmersedBoundaryCellPopulation.cpp:37) ==293168== by 0x16260D: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==293168== by 0x166388: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==293168== by 0x16626D: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==293168== by 0x166113: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==293168== by 0x165F7A: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==293168== by 0x166611: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==293168== by 0x161345: main (TestImmersedBoundaryCellPopulation.cpp:19) ==293168== { Memcheck:Leak match-leak-kinds: possible fun:_Znwm fun:_ZN9__gnu_cxx13new_allocatorISt13_Rb_tree_nodeIjEE8allocateEmPKv fun:_ZNSt16allocator_traitsISaISt13_Rb_tree_nodeIjEEE8allocateERS2_m fun:_ZNSt8_Rb_treeIjjSt9_IdentityIjESt4lessIjESaIjEE11_M_get_nodeEv fun:_ZNSt8_Rb_treeIjjSt9_IdentityIjESt4lessIjESaIjEE14_M_create_nodeIJRKjEEEPSt13_Rb_tree_nodeIjEDpOT_ fun:_ZNKSt8_Rb_treeIjjSt9_IdentityIjESt4lessIjESaIjEE11_Alloc_nodeclIRKjEEPSt13_Rb_tree_nodeIjEOT_ fun:_ZNSt8_Rb_treeIjjSt9_IdentityIjESt4lessIjESaIjEE10_M_insert_IRKjNS5_11_Alloc_nodeEEESt17_Rb_tree_iteratorIjEPSt18_Rb_tree_node_baseSD_OT_RT0_ fun:_ZNSt8_Rb_treeIjjSt9_IdentityIjESt4lessIjESaIjEE16_M_insert_uniqueIRKjEESt4pairISt17_Rb_tree_iteratorIjEbEOT_ fun:_ZNSt3setIjSt4lessIjESaIjEE6insertERKj fun:_ZN4NodeILj2EE10AddElementEj fun:_ZN7ElementILj2ELj2EE17RegisterWithNodesEv fun:_ZN7ElementILj2ELj2EEC1EjRKSt6vectorIP4NodeILj2EESaIS4_EEb fun:_ZN15TetrahedralMeshILj2ELj2EE23ConstructFromMeshReaderER18AbstractMeshReaderILj2ELj2EE fun:_ZN30ImmersedBoundaryCellPopulationILj2EE32GetTetrahedralMeshForPdeModifierEv fun:_ZN34TestImmersedBoundaryCellPopulation15TestMeshMethodsEv fun:_ZN66TestDescription_TestImmersedBoundaryCellPopulation_TestMeshMethods7runTestEv fun:_ZN7CxxTest19RealTestDescription3runEv fun:_ZN7CxxTest10TestRunner7runTestERNS_15TestDescriptionE fun:_ZN7CxxTest10TestRunner8runSuiteERNS_16SuiteDescriptionE fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==293168== 240 bytes in 6 blocks are possibly lost in loss record 40 of 90 ==293168== at 0x4849013: operator new(unsigned long) (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==293168== by 0xA4EB6C5: __gnu_cxx::new_allocator >::allocate(unsigned long, void const*) (new_allocator.h:127) ==293168== by 0xA4EA4F1: std::allocator_traits > >::allocate(std::allocator >&, unsigned long) (alloc_traits.h:464) ==293168== by 0xA4E8126: std::_Rb_tree, std::less, std::allocator >::_M_get_node() (stl_tree.h:561) ==293168== by 0xA4E6A6F: std::_Rb_tree_node* std::_Rb_tree, std::less, std::allocator >::_M_create_node(unsigned int const&) (stl_tree.h:611) ==293168== by 0xA4E5E28: std::_Rb_tree_node* std::_Rb_tree, std::less, std::allocator >::_Alloc_node::operator()(unsigned int const&) const (stl_tree.h:529) ==293168== by 0xA4E57C3: std::_Rb_tree_iterator std::_Rb_tree, std::less, std::allocator >::_M_insert_, std::less, std::allocator >::_Alloc_node>(std::_Rb_tree_node_base*, std::_Rb_tree_node_base*, unsigned int const&, std::_Rb_tree, std::less, std::allocator >::_Alloc_node&) (stl_tree.h:1784) ==293168== by 0xA4E4E21: std::pair, bool> std::_Rb_tree, std::less, std::allocator >::_M_insert_unique(unsigned int const&) (stl_tree.h:2129) ==293168== by 0xA4E4377: std::set, std::allocator >::insert(unsigned int const&) (stl_set.h:512) ==293168== by 0xE5AD75B: Node<2u>::AddBoundaryElement(unsigned int) (Node.cpp:296) ==293168== by 0xE615075: TetrahedralMesh<2u, 2u>::ConstructFromMeshReader(AbstractMeshReader<2u, 2u>&) (TetrahedralMesh.cpp:169) ==293168== by 0xA861210: ImmersedBoundaryCellPopulation<2u>::GetTetrahedralMeshForPdeModifier() (ImmersedBoundaryCellPopulation.cpp:886) ==293168== by 0x16CC7A: TestImmersedBoundaryCellPopulation::TestMeshMethods() (TestImmersedBoundaryCellPopulation.hpp:213) ==293168== by 0x17234C: TestDescription_TestImmersedBoundaryCellPopulation_TestMeshMethods::runTest() (TestImmersedBoundaryCellPopulation.cpp:37) ==293168== by 0x16260D: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==293168== by 0x166388: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==293168== by 0x16626D: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==293168== by 0x166113: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==293168== by 0x165F7A: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==293168== by 0x166611: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==293168== by 0x161345: main (TestImmersedBoundaryCellPopulation.cpp:19) ==293168== { Memcheck:Leak match-leak-kinds: possible fun:_Znwm fun:_ZN9__gnu_cxx13new_allocatorISt13_Rb_tree_nodeIjEE8allocateEmPKv fun:_ZNSt16allocator_traitsISaISt13_Rb_tree_nodeIjEEE8allocateERS2_m fun:_ZNSt8_Rb_treeIjjSt9_IdentityIjESt4lessIjESaIjEE11_M_get_nodeEv fun:_ZNSt8_Rb_treeIjjSt9_IdentityIjESt4lessIjESaIjEE14_M_create_nodeIJRKjEEEPSt13_Rb_tree_nodeIjEDpOT_ fun:_ZNKSt8_Rb_treeIjjSt9_IdentityIjESt4lessIjESaIjEE11_Alloc_nodeclIRKjEEPSt13_Rb_tree_nodeIjEOT_ fun:_ZNSt8_Rb_treeIjjSt9_IdentityIjESt4lessIjESaIjEE10_M_insert_IRKjNS5_11_Alloc_nodeEEESt17_Rb_tree_iteratorIjEPSt18_Rb_tree_node_baseSD_OT_RT0_ fun:_ZNSt8_Rb_treeIjjSt9_IdentityIjESt4lessIjESaIjEE16_M_insert_uniqueIRKjEESt4pairISt17_Rb_tree_iteratorIjEbEOT_ fun:_ZNSt3setIjSt4lessIjESaIjEE6insertERKj fun:_ZN4NodeILj2EE18AddBoundaryElementEj fun:_ZN15TetrahedralMeshILj2ELj2EE23ConstructFromMeshReaderER18AbstractMeshReaderILj2ELj2EE fun:_ZN30ImmersedBoundaryCellPopulationILj2EE32GetTetrahedralMeshForPdeModifierEv fun:_ZN34TestImmersedBoundaryCellPopulation15TestMeshMethodsEv fun:_ZN66TestDescription_TestImmersedBoundaryCellPopulation_TestMeshMethods7runTestEv fun:_ZN7CxxTest19RealTestDescription3runEv fun:_ZN7CxxTest10TestRunner7runTestERNS_15TestDescriptionE fun:_ZN7CxxTest10TestRunner8runSuiteERNS_16SuiteDescriptionE fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==293168== 432 bytes in 3 blocks are possibly lost in loss record 43 of 90 ==293168== at 0x4849013: operator new(unsigned long) (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==293168== by 0xE614AB9: TetrahedralMesh<2u, 2u>::ConstructFromMeshReader(AbstractMeshReader<2u, 2u>&) (TetrahedralMesh.cpp:93) ==293168== by 0xA861210: ImmersedBoundaryCellPopulation<2u>::GetTetrahedralMeshForPdeModifier() (ImmersedBoundaryCellPopulation.cpp:886) ==293168== by 0x16CC7A: TestImmersedBoundaryCellPopulation::TestMeshMethods() (TestImmersedBoundaryCellPopulation.hpp:213) ==293168== by 0x17234C: TestDescription_TestImmersedBoundaryCellPopulation_TestMeshMethods::runTest() (TestImmersedBoundaryCellPopulation.cpp:37) ==293168== by 0x16260D: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==293168== by 0x166388: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==293168== by 0x16626D: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==293168== by 0x166113: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==293168== by 0x165F7A: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==293168== by 0x166611: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==293168== by 0x161345: main (TestImmersedBoundaryCellPopulation.cpp:19) ==293168== { Memcheck:Leak match-leak-kinds: possible fun:_Znwm fun:_ZN15TetrahedralMeshILj2ELj2EE23ConstructFromMeshReaderER18AbstractMeshReaderILj2ELj2EE fun:_ZN30ImmersedBoundaryCellPopulationILj2EE32GetTetrahedralMeshForPdeModifierEv fun:_ZN34TestImmersedBoundaryCellPopulation15TestMeshMethodsEv fun:_ZN66TestDescription_TestImmersedBoundaryCellPopulation_TestMeshMethods7runTestEv fun:_ZN7CxxTest19RealTestDescription3runEv fun:_ZN7CxxTest10TestRunner7runTestERNS_15TestDescriptionE fun:_ZN7CxxTest10TestRunner8runSuiteERNS_16SuiteDescriptionE fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==293168== 353,082 (320 direct, 352,762 indirect) bytes in 1 blocks are definitely lost in loss record 90 of 90 ==293168== at 0x4849013: operator new(unsigned long) (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==293168== by 0xA861180: ImmersedBoundaryCellPopulation<2u>::GetTetrahedralMeshForPdeModifier() (ImmersedBoundaryCellPopulation.cpp:881) ==293168== by 0x16CC7A: TestImmersedBoundaryCellPopulation::TestMeshMethods() (TestImmersedBoundaryCellPopulation.hpp:213) ==293168== by 0x17234C: TestDescription_TestImmersedBoundaryCellPopulation_TestMeshMethods::runTest() (TestImmersedBoundaryCellPopulation.cpp:37) ==293168== by 0x16260D: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==293168== by 0x166388: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==293168== by 0x16626D: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==293168== by 0x166113: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==293168== by 0x165F7A: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==293168== by 0x166611: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==293168== by 0x161345: main (TestImmersedBoundaryCellPopulation.cpp:19) ==293168== { Memcheck:Leak match-leak-kinds: definite fun:_Znwm fun:_ZN30ImmersedBoundaryCellPopulationILj2EE32GetTetrahedralMeshForPdeModifierEv fun:_ZN34TestImmersedBoundaryCellPopulation15TestMeshMethodsEv fun:_ZN66TestDescription_TestImmersedBoundaryCellPopulation_TestMeshMethods7runTestEv fun:_ZN7CxxTest19RealTestDescription3runEv fun:_ZN7CxxTest10TestRunner7runTestERNS_15TestDescriptionE fun:_ZN7CxxTest10TestRunner8runSuiteERNS_16SuiteDescriptionE fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==293168== LEAK SUMMARY: ==293168== definitely lost: 320 bytes in 1 blocks ==293168== indirectly lost: 352,762 bytes in 6,083 blocks ==293168== possibly lost: 912 bytes in 15 blocks ==293168== still reachable: 56 bytes in 3 blocks ==293168== suppressed: 700,698 bytes in 9,375 blocks ==293168== Reachable blocks (those to which a pointer was found) are not shown. ==293168== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==293168== ==293168== For lists of detected and suppressed errors, rerun with: -s ==293168== ERROR SUMMARY: 4 errors from 4 contexts (suppressed: 38 from 38)