==1789403== Memcheck, a memory error detector ==1789403== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==1789403== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==1789403== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/cell_based/test/TestImmersedBoundaryCellPopulation -malloc_debug -malloc_dump -memory_info ==1789403== Parent PID: 1787640 ==1789403== ==1789403== ==1789403== FILE DESCRIPTORS: 9 open (3 std) at exit. ==1789403== Open file descriptor 12: ==1789403== at 0x10CE722D: pipe (pipe.c:29) ==1789403== by 0x196A507D: ??? ==1789403== by 0x14C134CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1789403== by 0x105EF418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1789403== by 0x10588D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1789403== by 0xF27FD38: PetscInitialize (pinit.c:924) ==1789403== by 0xF0F42DF: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1789403== by 0xF0F432D: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1789403== by 0x178F57: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70) ==1789403== by 0x171249: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1789403== by 0x174580: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1789403== by 0x174420: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1789403== by 0x174AB7: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1789403== by 0x16F665: main (TestImmersedBoundaryCellPopulation.cpp:19) ==1789403== ==1789403== Open file descriptor 8: /dev/shm/open_mpi.0000 ==1789403== at 0x10CEBBCC: __open_nocancel (open64_nocancel.c:39) ==1789403== by 0x10C6FC4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==1789403== by 0xF129822: ??? ==1789403== by 0xF12996F: ??? ==1789403== by 0x14CB86DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==1789403== by 0x14CB8938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==1789403== by 0x14C6E922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==1789403== by 0x14C132DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1789403== by 0x105EF418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1789403== by 0x10588D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1789403== by 0xF27FD38: PetscInitialize (pinit.c:924) ==1789403== by 0xF0F42DF: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==1789403== by 0xF0F432D: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==1789403== by 0x178F57: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70) ==1789403== by 0x171249: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==1789403== by 0x174580: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==1789403== by 0x174420: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1789403== by 0x174AB7: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1789403== by 0x16F665: main (TestImmersedBoundaryCellPopulation.cpp:19) ==1789403== ==1789403== Open file descriptor 116: ==1789403== ==1789403== ==1789403== Open file descriptor 112: ==1789403== ==1789403== ==1789403== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestImmersedBoundaryCellPopulation_valgrind.txt ==1789403== ==1789403== ==1789403== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==1789403== ==1789403== ==1789403== ==1789403== HEAP SUMMARY: ==1789403== in use at exit: 1,054,754 bytes in 15,477 blocks ==1789403== total heap usage: 113,700 allocs, 98,223 frees, 1,395,478,856 bytes allocated ==1789403== ==1789403== 4,000 bytes in 1 blocks are possibly lost in loss record 61 of 86 ==1789403== at 0x4849013: operator new(unsigned long) (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==1789403== by 0x1A7C1B: __gnu_cxx::new_allocator::allocate(unsigned long, void const*) (new_allocator.h:127) ==1789403== by 0x1A774F: std::allocator_traits >::allocate(std::allocator&, unsigned long) (alloc_traits.h:464) ==1789403== by 0x1A72BD: std::_Vector_base >::_M_allocate(unsigned long) (stl_vector.h:346) ==1789403== by 0x1A7879: std::vector >::_M_default_append(unsigned long) (vector.tcc:635) ==1789403== by 0x1A7350: std::vector >::resize(unsigned long) (stl_vector.h:940) ==1789403== by 0xE62943D: TetrahedralMesh<2u, 2u>::RefreshJacobianCachedData() (TetrahedralMesh.cpp:685) ==1789403== by 0xE6276E3: TetrahedralMesh<2u, 2u>::ConstructFromMeshReader(AbstractMeshReader<2u, 2u>&) (TetrahedralMesh.cpp:184) ==1789403== by 0xA867402: ImmersedBoundaryCellPopulation<2u>::GetTetrahedralMeshForPdeModifier() (ImmersedBoundaryCellPopulation.cpp:941) ==1789403== by 0x17B120: TestImmersedBoundaryCellPopulation::TestMeshMethods() (TestImmersedBoundaryCellPopulation.hpp:214) ==1789403== by 0x186A9E: TestDescription_TestImmersedBoundaryCellPopulation_TestMeshMethods::runTest() (TestImmersedBoundaryCellPopulation.cpp:37) ==1789403== by 0x17092D: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==1789403== by 0x17482E: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==1789403== by 0x174713: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==1789403== by 0x1745B9: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==1789403== by 0x174420: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1789403== by 0x174AB7: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1789403== by 0x16F665: main (TestImmersedBoundaryCellPopulation.cpp:19) ==1789403== { Memcheck:Leak match-leak-kinds: possible fun:_Znwm fun:_ZN9__gnu_cxx13new_allocatorIdE8allocateEmPKv fun:_ZNSt16allocator_traitsISaIdEE8allocateERS0_m fun:_ZNSt12_Vector_baseIdSaIdEE11_M_allocateEm fun:_ZNSt6vectorIdSaIdEE17_M_default_appendEm fun:_ZNSt6vectorIdSaIdEE6resizeEm fun:_ZN15TetrahedralMeshILj2ELj2EE25RefreshJacobianCachedDataEv 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 } ==1789403== 24,000 bytes in 1 blocks are possibly lost in loss record 74 of 86 ==1789403== at 0x4849013: operator new(unsigned long) (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==1789403== by 0xE58ED22: __gnu_cxx::new_allocator >::allocate(unsigned long, void const*) (new_allocator.h:127) ==1789403== by 0xE58B092: std::allocator_traits > >::allocate(std::allocator >&, unsigned long) (alloc_traits.h:464) ==1789403== by 0xE586B63: std::_Vector_base, std::allocator > >::_M_allocate(unsigned long) (stl_vector.h:346) ==1789403== by 0xE580C86: std::vector, std::allocator > >::_M_default_append(unsigned long) (vector.tcc:635) ==1789403== by 0xE57B21E: std::vector, std::allocator > >::resize(unsigned long) (stl_vector.h:940) ==1789403== by 0xE6293F2: TetrahedralMesh<2u, 2u>::RefreshJacobianCachedData() (TetrahedralMesh.cpp:675) ==1789403== by 0xE6276E3: TetrahedralMesh<2u, 2u>::ConstructFromMeshReader(AbstractMeshReader<2u, 2u>&) (TetrahedralMesh.cpp:184) ==1789403== by 0xA867402: ImmersedBoundaryCellPopulation<2u>::GetTetrahedralMeshForPdeModifier() (ImmersedBoundaryCellPopulation.cpp:941) ==1789403== by 0x17B120: TestImmersedBoundaryCellPopulation::TestMeshMethods() (TestImmersedBoundaryCellPopulation.hpp:214) ==1789403== by 0x186A9E: TestDescription_TestImmersedBoundaryCellPopulation_TestMeshMethods::runTest() (TestImmersedBoundaryCellPopulation.cpp:37) ==1789403== by 0x17092D: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==1789403== by 0x17482E: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==1789403== by 0x174713: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==1789403== by 0x1745B9: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==1789403== by 0x174420: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1789403== by 0x174AB7: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1789403== by 0x16F665: main (TestImmersedBoundaryCellPopulation.cpp:19) ==1789403== { Memcheck:Leak match-leak-kinds: possible fun:_Znwm fun:_ZN9__gnu_cxx13new_allocatorIN5boost7numeric5ublas8c_matrixIdLm2ELm2EEEE8allocateEmPKv fun:_ZNSt16allocator_traitsISaIN5boost7numeric5ublas8c_matrixIdLm2ELm2EEEEE8allocateERS5_m fun:_ZNSt12_Vector_baseIN5boost7numeric5ublas8c_matrixIdLm2ELm2EEESaIS4_EE11_M_allocateEm fun:_ZNSt6vectorIN5boost7numeric5ublas8c_matrixIdLm2ELm2EEESaIS4_EE17_M_default_appendEm fun:_ZNSt6vectorIN5boost7numeric5ublas8c_matrixIdLm2ELm2EEESaIS4_EE6resizeEm fun:_ZN15TetrahedralMeshILj2ELj2EE25RefreshJacobianCachedDataEv 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 } ==1789403== 24,000 bytes in 1 blocks are possibly lost in loss record 75 of 86 ==1789403== at 0x4849013: operator new(unsigned long) (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==1789403== by 0xE58ED22: __gnu_cxx::new_allocator >::allocate(unsigned long, void const*) (new_allocator.h:127) ==1789403== by 0xE58B092: std::allocator_traits > >::allocate(std::allocator >&, unsigned long) (alloc_traits.h:464) ==1789403== by 0xE586B63: std::_Vector_base, std::allocator > >::_M_allocate(unsigned long) (stl_vector.h:346) ==1789403== by 0xE580C86: std::vector, std::allocator > >::_M_default_append(unsigned long) (vector.tcc:635) ==1789403== by 0xE57B21E: std::vector, std::allocator > >::resize(unsigned long) (stl_vector.h:940) ==1789403== by 0xE62940B: TetrahedralMesh<2u, 2u>::RefreshJacobianCachedData() (TetrahedralMesh.cpp:676) ==1789403== by 0xE6276E3: TetrahedralMesh<2u, 2u>::ConstructFromMeshReader(AbstractMeshReader<2u, 2u>&) (TetrahedralMesh.cpp:184) ==1789403== by 0xA867402: ImmersedBoundaryCellPopulation<2u>::GetTetrahedralMeshForPdeModifier() (ImmersedBoundaryCellPopulation.cpp:941) ==1789403== by 0x17B120: TestImmersedBoundaryCellPopulation::TestMeshMethods() (TestImmersedBoundaryCellPopulation.hpp:214) ==1789403== by 0x186A9E: TestDescription_TestImmersedBoundaryCellPopulation_TestMeshMethods::runTest() (TestImmersedBoundaryCellPopulation.cpp:37) ==1789403== by 0x17092D: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==1789403== by 0x17482E: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==1789403== by 0x174713: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==1789403== by 0x1745B9: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==1789403== by 0x174420: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1789403== by 0x174AB7: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1789403== by 0x16F665: main (TestImmersedBoundaryCellPopulation.cpp:19) ==1789403== { Memcheck:Leak match-leak-kinds: possible fun:_Znwm fun:_ZN9__gnu_cxx13new_allocatorIN5boost7numeric5ublas8c_matrixIdLm2ELm2EEEE8allocateEmPKv fun:_ZNSt16allocator_traitsISaIN5boost7numeric5ublas8c_matrixIdLm2ELm2EEEEE8allocateERS5_m fun:_ZNSt12_Vector_baseIN5boost7numeric5ublas8c_matrixIdLm2ELm2EEESaIS4_EE11_M_allocateEm fun:_ZNSt6vectorIN5boost7numeric5ublas8c_matrixIdLm2ELm2EEESaIS4_EE17_M_default_appendEm fun:_ZNSt6vectorIN5boost7numeric5ublas8c_matrixIdLm2ELm2EEESaIS4_EE6resizeEm fun:_ZN15TetrahedralMeshILj2ELj2EE25RefreshJacobianCachedDataEv 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 } ==1789403== 301,995 (320 direct, 301,675 indirect) bytes in 1 blocks are definitely lost in loss record 85 of 86 ==1789403== at 0x4849013: operator new(unsigned long) (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==1789403== by 0xA867372: ImmersedBoundaryCellPopulation<2u>::GetTetrahedralMeshForPdeModifier() (ImmersedBoundaryCellPopulation.cpp:936) ==1789403== by 0x17B120: TestImmersedBoundaryCellPopulation::TestMeshMethods() (TestImmersedBoundaryCellPopulation.hpp:214) ==1789403== by 0x186A9E: TestDescription_TestImmersedBoundaryCellPopulation_TestMeshMethods::runTest() (TestImmersedBoundaryCellPopulation.cpp:37) ==1789403== by 0x17092D: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==1789403== by 0x17482E: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==1789403== by 0x174713: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==1789403== by 0x1745B9: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==1789403== by 0x174420: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==1789403== by 0x174AB7: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==1789403== by 0x16F665: main (TestImmersedBoundaryCellPopulation.cpp:19) ==1789403== { 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 } ==1789403== LEAK SUMMARY: ==1789403== definitely lost: 320 bytes in 1 blocks ==1789403== indirectly lost: 301,675 bytes in 6,095 blocks ==1789403== possibly lost: 52,000 bytes in 3 blocks ==1789403== still reachable: 56 bytes in 3 blocks ==1789403== suppressed: 700,703 bytes in 9,375 blocks ==1789403== Reachable blocks (those to which a pointer was found) are not shown. ==1789403== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==1789403== ==1789403== For lists of detected and suppressed errors, rerun with: -s ==1789403== ERROR SUMMARY: 4 errors from 4 contexts (suppressed: 37 from 37)