==865553== Memcheck, a memory error detector ==865553== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==865553== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==865553== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/cell_based/test/TestImmersedBoundaryCellPopulation -malloc_debug -malloc_dump -memory_info ==865553== Parent PID: 863787 ==865553== ==865553== ==865553== FILE DESCRIPTORS: 9 open (3 std) at exit. ==865553== Open file descriptor 12: ==865553== at 0x10CE722D: pipe (pipe.c:29) ==865553== by 0x196A507D: ??? ==865553== by 0x14C134CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==865553== by 0x105EF418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==865553== by 0x10588D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==865553== by 0xF27FD38: PetscInitialize (pinit.c:924) ==865553== by 0xF0F42DF: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==865553== by 0xF0F432D: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==865553== by 0x176E25: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70) ==865553== by 0x16F149: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==865553== by 0x17244E: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==865553== by 0x1722EE: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==865553== by 0x172985: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==865553== by 0x16D565: main (TestImmersedBoundaryCellPopulation.cpp:19) ==865553== ==865553== Open file descriptor 8: /dev/shm/open_mpi.0000 ==865553== at 0x10CEBBCC: __open_nocancel (open64_nocancel.c:39) ==865553== by 0x10C6FC4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==865553== by 0xF129822: ??? ==865553== by 0xF12996F: ??? ==865553== by 0x14CB86DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==865553== by 0x14CB8938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==865553== by 0x14C6E922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==865553== by 0x14C132DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==865553== by 0x105EF418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==865553== by 0x10588D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==865553== by 0xF27FD38: PetscInitialize (pinit.c:924) ==865553== by 0xF0F42DF: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==865553== by 0xF0F432D: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==865553== by 0x176E25: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70) ==865553== by 0x16F149: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==865553== by 0x17244E: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==865553== by 0x1722EE: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==865553== by 0x172985: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==865553== by 0x16D565: main (TestImmersedBoundaryCellPopulation.cpp:19) ==865553== ==865553== Open file descriptor 115: ==865553== ==865553== ==865553== Open file descriptor 112: ==865553== ==865553== ==865553== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestImmersedBoundaryCellPopulation_valgrind.txt ==865553== ==865553== ==865553== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==865553== ==865553== ==865553== ==865553== HEAP SUMMARY: ==865553== in use at exit: 1,054,748 bytes in 15,477 blocks ==865553== total heap usage: 113,282 allocs, 97,805 frees, 1,395,666,369 bytes allocated ==865553== ==865553== 160 bytes in 4 blocks are possibly lost in loss record 37 of 89 ==865553== at 0x4849013: operator new(unsigned long) (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==865553== by 0x1982A7: __gnu_cxx::new_allocator >::allocate(unsigned long, void const*) (new_allocator.h:127) ==865553== by 0x197CE4: std::allocator_traits > >::allocate(std::allocator >&, unsigned long) (alloc_traits.h:464) ==865553== by 0x1973B0: std::_Rb_tree, std::less, std::allocator >::_M_get_node() (stl_tree.h:561) ==865553== by 0x196C21: std::_Rb_tree_node* std::_Rb_tree, std::less, std::allocator >::_M_create_node(unsigned int const&) (stl_tree.h:611) ==865553== by 0x195D26: std::_Rb_tree_node* std::_Rb_tree, std::less, std::allocator >::_Alloc_node::operator()(unsigned int const&) const (stl_tree.h:529) ==865553== by 0xA4EA263: 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) ==865553== by 0xA4E98C1: std::pair, bool> std::_Rb_tree, std::less, std::allocator >::_M_insert_unique(unsigned int const&) (stl_tree.h:2129) ==865553== by 0xA4E8E17: std::set, std::allocator >::insert(unsigned int const&) (stl_set.h:512) ==865553== by 0xE5BF855: Node<2u>::AddElement(unsigned int) (Node.cpp:270) ==865553== by 0xE51B38F: Element<2u, 2u>::RegisterWithNodes() (Element.cpp:69) ==865553== by 0xE51B299: Element<2u, 2u>::Element(unsigned int, std::vector*, std::allocator*> > const&, bool) (Element.cpp:51) ==865553== by 0xE627255: TetrahedralMesh<2u, 2u>::ConstructFromMeshReader(AbstractMeshReader<2u, 2u>&) (TetrahedralMesh.cpp:127) ==865553== by 0xA867402: ImmersedBoundaryCellPopulation<2u>::GetTetrahedralMeshForPdeModifier() (ImmersedBoundaryCellPopulation.cpp:889) ==865553== by 0x178FEE: TestImmersedBoundaryCellPopulation::TestMeshMethods() (TestImmersedBoundaryCellPopulation.hpp:214) ==865553== by 0x182900: TestDescription_TestImmersedBoundaryCellPopulation_TestMeshMethods::runTest() (TestImmersedBoundaryCellPopulation.cpp:37) ==865553== by 0x16E82D: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==865553== by 0x1726FC: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==865553== by 0x1725E1: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==865553== by 0x172487: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==865553== by 0x1722EE: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==865553== by 0x172985: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==865553== by 0x16D565: main (TestImmersedBoundaryCellPopulation.cpp:19) ==865553== { 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 } ==865553== 160 bytes in 4 blocks are possibly lost in loss record 38 of 89 ==865553== at 0x4849013: operator new(unsigned long) (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==865553== by 0x1982A7: __gnu_cxx::new_allocator >::allocate(unsigned long, void const*) (new_allocator.h:127) ==865553== by 0x197CE4: std::allocator_traits > >::allocate(std::allocator >&, unsigned long) (alloc_traits.h:464) ==865553== by 0x1973B0: std::_Rb_tree, std::less, std::allocator >::_M_get_node() (stl_tree.h:561) ==865553== by 0x196C21: std::_Rb_tree_node* std::_Rb_tree, std::less, std::allocator >::_M_create_node(unsigned int const&) (stl_tree.h:611) ==865553== by 0x195D26: std::_Rb_tree_node* std::_Rb_tree, std::less, std::allocator >::_Alloc_node::operator()(unsigned int const&) const (stl_tree.h:529) ==865553== by 0xA4EA263: 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) ==865553== by 0xA4E98C1: std::pair, bool> std::_Rb_tree, std::less, std::allocator >::_M_insert_unique(unsigned int const&) (stl_tree.h:2129) ==865553== by 0xA4E8E17: std::set, std::allocator >::insert(unsigned int const&) (stl_set.h:512) ==865553== by 0xE5BFC3B: Node<2u>::AddBoundaryElement(unsigned int) (Node.cpp:296) ==865553== by 0xE627555: TetrahedralMesh<2u, 2u>::ConstructFromMeshReader(AbstractMeshReader<2u, 2u>&) (TetrahedralMesh.cpp:169) ==865553== by 0xA867402: ImmersedBoundaryCellPopulation<2u>::GetTetrahedralMeshForPdeModifier() (ImmersedBoundaryCellPopulation.cpp:889) ==865553== by 0x178FEE: TestImmersedBoundaryCellPopulation::TestMeshMethods() (TestImmersedBoundaryCellPopulation.hpp:214) ==865553== by 0x182900: TestDescription_TestImmersedBoundaryCellPopulation_TestMeshMethods::runTest() (TestImmersedBoundaryCellPopulation.cpp:37) ==865553== by 0x16E82D: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==865553== by 0x1726FC: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==865553== by 0x1725E1: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==865553== by 0x172487: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==865553== by 0x1722EE: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==865553== by 0x172985: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==865553== by 0x16D565: main (TestImmersedBoundaryCellPopulation.cpp:19) ==865553== { 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 } ==865553== 432 bytes in 3 blocks are possibly lost in loss record 42 of 89 ==865553== at 0x4849013: operator new(unsigned long) (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==865553== by 0xE626F99: TetrahedralMesh<2u, 2u>::ConstructFromMeshReader(AbstractMeshReader<2u, 2u>&) (TetrahedralMesh.cpp:93) ==865553== by 0xA867402: ImmersedBoundaryCellPopulation<2u>::GetTetrahedralMeshForPdeModifier() (ImmersedBoundaryCellPopulation.cpp:889) ==865553== by 0x178FEE: TestImmersedBoundaryCellPopulation::TestMeshMethods() (TestImmersedBoundaryCellPopulation.hpp:214) ==865553== by 0x182900: TestDescription_TestImmersedBoundaryCellPopulation_TestMeshMethods::runTest() (TestImmersedBoundaryCellPopulation.cpp:37) ==865553== by 0x16E82D: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==865553== by 0x1726FC: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==865553== by 0x1725E1: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==865553== by 0x172487: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==865553== by 0x1722EE: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==865553== by 0x172985: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==865553== by 0x16D565: main (TestImmersedBoundaryCellPopulation.cpp:19) ==865553== { 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 } ==865553== 353,242 (320 direct, 352,922 indirect) bytes in 1 blocks are definitely lost in loss record 89 of 89 ==865553== at 0x4849013: operator new(unsigned long) (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==865553== by 0xA867372: ImmersedBoundaryCellPopulation<2u>::GetTetrahedralMeshForPdeModifier() (ImmersedBoundaryCellPopulation.cpp:884) ==865553== by 0x178FEE: TestImmersedBoundaryCellPopulation::TestMeshMethods() (TestImmersedBoundaryCellPopulation.hpp:214) ==865553== by 0x182900: TestDescription_TestImmersedBoundaryCellPopulation_TestMeshMethods::runTest() (TestImmersedBoundaryCellPopulation.cpp:37) ==865553== by 0x16E82D: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==865553== by 0x1726FC: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==865553== by 0x1725E1: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==865553== by 0x172487: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==865553== by 0x1722EE: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==865553== by 0x172985: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==865553== by 0x16D565: main (TestImmersedBoundaryCellPopulation.cpp:19) ==865553== { 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 } ==865553== LEAK SUMMARY: ==865553== definitely lost: 320 bytes in 1 blocks ==865553== indirectly lost: 352,922 bytes in 6,087 blocks ==865553== possibly lost: 752 bytes in 11 blocks ==865553== still reachable: 56 bytes in 3 blocks ==865553== suppressed: 700,698 bytes in 9,375 blocks ==865553== Reachable blocks (those to which a pointer was found) are not shown. ==865553== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==865553== ==865553== For lists of detected and suppressed errors, rerun with: -s ==865553== ERROR SUMMARY: 4 errors from 4 contexts (suppressed: 37 from 37)