==14656== Memcheck, a memory error detector ==14656== Copyright (C) 2002-2024, and GNU GPL'd, by Julian Seward et al. ==14656== Using Valgrind-3.26.0 and LibVEX; rerun with -h for copyright info ==14656== Command: /home/runner/work/Chaste/Chaste/Chaste/chaste-build-dir/cell_based/test/TestCell -malloc_debug -malloc_dump -memory_info ==14656== Parent PID: 14654 ==14656== ==14656== ==14656== FILE DESCRIPTORS: 11 open (6 inherited) at exit. ==14656== Open file descriptor 10: /dev/shm/open_mpi.0000 ==14656== at 0xF380536: __open_nocancel (open64_nocancel.c:39) ==14656== by 0xF304BC3: shm_open@@GLIBC_2.34 (shm_open.c:46) ==14656== by 0x169E689E: opal_shmem_posix_shm_open (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==14656== by 0x169E6A71: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==14656== by 0x169E5C38: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==14656== by 0x169E5F97: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==14656== by 0x168B5159: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==14656== by 0xEC1B0E7: ompi_rte_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==14656== by 0xEC2049F: ??? (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==14656== by 0xEC212C3: ompi_mpi_instance_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==14656== by 0xEC1818F: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==14656== by 0xEC52627: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==14656== by 0xDBF9446: PetscInitialize (in /usr/lib/x86_64-linux-gnu/libpetsc_real.so.3.24.4) ==14656== by 0xD30A2D9: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==14656== by 0xD30A327: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==14656== by 0x401F39D: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70) ==14656== by 0x4019CED: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==14656== by 0x401CDEA: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==14656== by 0x401CC18: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==14656== by 0x401D35D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==14656== by 0x40180B2: main (TestCell.cpp:19) ==14656== { CoreError:FdNotClosed fun:__open_nocancel fun:shm_open@@GLIBC_2.34 fun:opal_shmem_posix_shm_open obj:/usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5 obj:/usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5 fun:opal_shmem_base_select fun:opal_init fun:ompi_rte_init obj:/usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7 fun:ompi_mpi_instance_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 } ==14656== Open file descriptor 9: ==14656== at 0xF38E96B: eventfd (syscall-template.S:120) ==14656== by 0x16A46188: evutil_eventfd_ (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==14656== by 0x16A44395: ??? (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==14656== by 0x16A44704: evthread_make_base_notifiable (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==14656== by 0x16A449F1: event_base_new_with_config (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==14656== by 0x169AB0D7: opal_event_base_create (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==14656== by 0x169AB1E8: opal_event_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==14656== by 0x168B5120: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==14656== by 0xEC1B0E7: ompi_rte_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==14656== by 0xEC2049F: ??? (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==14656== by 0xEC212C3: ompi_mpi_instance_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==14656== by 0xEC1818F: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==14656== by 0xEC52627: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==14656== by 0xDBF9446: PetscInitialize (in /usr/lib/x86_64-linux-gnu/libpetsc_real.so.3.24.4) ==14656== by 0xD30A2D9: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==14656== by 0xD30A327: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==14656== by 0x401F39D: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70) ==14656== by 0x4019CED: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==14656== by 0x401CDEA: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==14656== by 0x401CC18: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==14656== by 0x401D35D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==14656== by 0x40180B2: main (TestCell.cpp:19) ==14656== { CoreError:FdNotClosed fun:eventfd fun:evutil_eventfd_ obj:/usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1 fun:evthread_make_base_notifiable fun:event_base_new_with_config fun:opal_event_base_create fun:opal_event_init fun:opal_init fun:ompi_rte_init obj:/usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7 fun:ompi_mpi_instance_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 } ==14656== Open file descriptor 8: ==14656== at 0xF37F2BB: pipe2 (syscall-template.S:120) ==14656== by 0x16A45F87: evutil_make_internal_pipe_ (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==14656== by 0x16A48579: evsig_init_ (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==14656== by 0x16A48774: ??? (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==14656== by 0x16A448AA: event_base_new_with_config (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==14656== by 0x169AB0D7: opal_event_base_create (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==14656== by 0x169AB1E8: opal_event_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==14656== by 0x168B5120: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==14656== by 0xEC1B0E7: ompi_rte_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==14656== by 0xEC2049F: ??? (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==14656== by 0xEC212C3: ompi_mpi_instance_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==14656== by 0xEC1818F: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==14656== by 0xEC52627: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==14656== by 0xDBF9446: PetscInitialize (in /usr/lib/x86_64-linux-gnu/libpetsc_real.so.3.24.4) ==14656== by 0xD30A2D9: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==14656== by 0xD30A327: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==14656== by 0x401F39D: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70) ==14656== by 0x4019CED: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==14656== by 0x401CDEA: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==14656== by 0x401CC18: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==14656== by 0x401D35D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==14656== by 0x40180B2: main (TestCell.cpp:19) ==14656== { CoreError:FdNotClosed fun:pipe2 fun:evutil_make_internal_pipe_ fun:evsig_init_ obj:/usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1 fun:event_base_new_with_config fun:opal_event_base_create fun:opal_event_init fun:opal_init fun:ompi_rte_init obj:/usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7 fun:ompi_mpi_instance_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 } ==14656== Open file descriptor 7: ==14656== at 0xF37F2BB: pipe2 (syscall-template.S:120) ==14656== by 0x16A45F87: evutil_make_internal_pipe_ (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==14656== by 0x16A48579: evsig_init_ (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==14656== by 0x16A48774: ??? (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==14656== by 0x16A448AA: event_base_new_with_config (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==14656== by 0x169AB0D7: opal_event_base_create (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==14656== by 0x169AB1E8: opal_event_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==14656== by 0x168B5120: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==14656== by 0xEC1B0E7: ompi_rte_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==14656== by 0xEC2049F: ??? (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==14656== by 0xEC212C3: ompi_mpi_instance_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==14656== by 0xEC1818F: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==14656== by 0xEC52627: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==14656== by 0xDBF9446: PetscInitialize (in /usr/lib/x86_64-linux-gnu/libpetsc_real.so.3.24.4) ==14656== by 0xD30A2D9: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==14656== by 0xD30A327: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==14656== by 0x401F39D: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70) ==14656== by 0x4019CED: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==14656== by 0x401CDEA: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==14656== by 0x401CC18: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==14656== by 0x401D35D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==14656== by 0x40180B2: main (TestCell.cpp:19) ==14656== { CoreError:FdNotClosed fun:pipe2 fun:evutil_make_internal_pipe_ fun:evsig_init_ obj:/usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1 fun:event_base_new_with_config fun:opal_event_base_create fun:opal_event_init fun:opal_init fun:ompi_rte_init obj:/usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7 fun:ompi_mpi_instance_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 } ==14656== Open file descriptor 4: ==14656== at 0xF38F46B: epoll_create1 (syscall-template.S:120) ==14656== by 0x16A486FA: ??? (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==14656== by 0x16A448AA: event_base_new_with_config (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==14656== by 0x169AB0D7: opal_event_base_create (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==14656== by 0x169AB1E8: opal_event_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==14656== by 0x168B5120: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==14656== by 0xEC1B0E7: ompi_rte_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==14656== by 0xEC2049F: ??? (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==14656== by 0xEC212C3: ompi_mpi_instance_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==14656== by 0xEC1818F: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==14656== by 0xEC52627: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==14656== by 0xDBF9446: PetscInitialize (in /usr/lib/x86_64-linux-gnu/libpetsc_real.so.3.24.4) ==14656== by 0xD30A2D9: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==14656== by 0xD30A327: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==14656== by 0x401F39D: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70) ==14656== by 0x4019CED: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==14656== by 0x401CDEA: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==14656== by 0x401CC18: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==14656== by 0x401D35D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==14656== by 0x40180B2: main (TestCell.cpp:19) ==14656== { CoreError:FdNotClosed fun:epoll_create1 obj:/usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1 fun:event_base_new_with_config fun:opal_event_base_create fun:opal_event_init fun:opal_init fun:ompi_rte_init obj:/usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7 fun:ompi_mpi_instance_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 } ==14656== ==14656== HEAP SUMMARY: ==14656== in use at exit: 126,498 bytes in 899 blocks ==14656== total heap usage: 5,163,562 allocs, 5,162,663 frees, 504,027,579 bytes allocated ==14656== ==14656== LEAK SUMMARY: ==14656== definitely lost: 0 bytes in 0 blocks ==14656== indirectly lost: 0 bytes in 0 blocks ==14656== possibly lost: 0 bytes in 0 blocks ==14656== still reachable: 12,109 bytes in 46 blocks ==14656== suppressed: 114,389 bytes in 853 blocks ==14656== Reachable blocks (those to which a pointer was found) are not shown. ==14656== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==14656== ==14656== For lists of detected and suppressed errors, rerun with: -s ==14656== ERROR SUMMARY: 5 errors from 5 contexts (suppressed: 33 from 33)