==16039== Memcheck, a memory error detector ==16039== Copyright (C) 2002-2024, and GNU GPL'd, by Julian Seward et al. ==16039== Using Valgrind-3.26.0 and LibVEX; rerun with -h for copyright info ==16039== Command: /home/runner/work/Chaste/Chaste/Chaste/chaste-build-dir/global/test/TestCitations -malloc_debug -malloc_dump -memory_info ==16039== Parent PID: 16035 ==16039== ==16039== ==16039== FILE DESCRIPTORS: 11 open (6 inherited) at exit. ==16039== Open file descriptor 10: /dev/shm/open_mpi.0000 ==16039== at 0x4D933B6: __open_nocancel (open64_nocancel.c:39) ==16039== by 0x4D17943: shm_open@@GLIBC_2.34 (shm_open.c:46) ==16039== by 0x71AD89E: opal_shmem_posix_shm_open (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==16039== by 0x71ADA71: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==16039== by 0x71ACC38: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==16039== by 0x71ACF97: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==16039== by 0x707C159: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==16039== by 0x4F1A0E7: ompi_rte_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==16039== by 0x4F1F49F: ??? (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==16039== by 0x4F202C3: ompi_mpi_instance_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==16039== by 0x4F1718F: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==16039== by 0x4F51627: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==16039== by 0x5B76446: PetscInitialize (in /usr/lib/x86_64-linux-gnu/libpetsc_real.so.3.24.4) ==16039== by 0x4951610: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==16039== by 0x495165F: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==16039== by 0x40172BD: TestCitations::TestChasteCitation() (TestCitations.hpp:72) ==16039== by 0x4017BA4: TestDescription_TestCitations_TestChasteCitation::runTest() (TestCitations.cpp:30) ==16039== by 0x40105AC: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==16039== by 0x4013994: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==16039== by 0x4013865: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==16039== by 0x40136F7: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==16039== by 0x401355B: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==16039== by 0x4013C09: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==16039== by 0x400F563: main (TestCitations.cpp:18) ==16039== { 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:_ZN13TestCitations18TestChasteCitationEv fun:_ZN48TestDescription_TestCitations_TestChasteCitation7runTestEv fun:_ZN7CxxTest19RealTestDescription3runEv fun:_ZN7CxxTest10TestRunner7runTestERNS_15TestDescriptionE fun:_ZN7CxxTest10TestRunner8runSuiteERNS_16SuiteDescriptionE fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==16039== Open file descriptor 9: ==16039== at 0x4DA184B: eventfd (syscall-template.S:120) ==16039== by 0x720D188: evutil_eventfd_ (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==16039== by 0x720B395: ??? (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==16039== by 0x720B704: evthread_make_base_notifiable (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==16039== by 0x720B9F1: event_base_new_with_config (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==16039== by 0x71720D7: opal_event_base_create (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==16039== by 0x71721E8: opal_event_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==16039== by 0x707C120: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==16039== by 0x4F1A0E7: ompi_rte_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==16039== by 0x4F1F49F: ??? (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==16039== by 0x4F202C3: ompi_mpi_instance_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==16039== by 0x4F1718F: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==16039== by 0x4F51627: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==16039== by 0x5B76446: PetscInitialize (in /usr/lib/x86_64-linux-gnu/libpetsc_real.so.3.24.4) ==16039== by 0x4951610: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==16039== by 0x495165F: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==16039== by 0x40172BD: TestCitations::TestChasteCitation() (TestCitations.hpp:72) ==16039== by 0x4017BA4: TestDescription_TestCitations_TestChasteCitation::runTest() (TestCitations.cpp:30) ==16039== by 0x40105AC: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==16039== by 0x4013994: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==16039== by 0x4013865: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==16039== by 0x40136F7: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==16039== by 0x401355B: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==16039== by 0x4013C09: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==16039== by 0x400F563: main (TestCitations.cpp:18) ==16039== { 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:_ZN13TestCitations18TestChasteCitationEv fun:_ZN48TestDescription_TestCitations_TestChasteCitation7runTestEv fun:_ZN7CxxTest19RealTestDescription3runEv fun:_ZN7CxxTest10TestRunner7runTestERNS_15TestDescriptionE fun:_ZN7CxxTest10TestRunner8runSuiteERNS_16SuiteDescriptionE fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==16039== Open file descriptor 8: ==16039== at 0x4D9213B: pipe2 (syscall-template.S:120) ==16039== by 0x720CF87: evutil_make_internal_pipe_ (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==16039== by 0x720F579: evsig_init_ (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==16039== by 0x720F774: ??? (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==16039== by 0x720B8AA: event_base_new_with_config (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==16039== by 0x71720D7: opal_event_base_create (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==16039== by 0x71721E8: opal_event_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==16039== by 0x707C120: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==16039== by 0x4F1A0E7: ompi_rte_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==16039== by 0x4F1F49F: ??? (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==16039== by 0x4F202C3: ompi_mpi_instance_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==16039== by 0x4F1718F: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==16039== by 0x4F51627: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==16039== by 0x5B76446: PetscInitialize (in /usr/lib/x86_64-linux-gnu/libpetsc_real.so.3.24.4) ==16039== by 0x4951610: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==16039== by 0x495165F: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==16039== by 0x40172BD: TestCitations::TestChasteCitation() (TestCitations.hpp:72) ==16039== by 0x4017BA4: TestDescription_TestCitations_TestChasteCitation::runTest() (TestCitations.cpp:30) ==16039== by 0x40105AC: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==16039== by 0x4013994: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==16039== by 0x4013865: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==16039== by 0x40136F7: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==16039== by 0x401355B: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==16039== by 0x4013C09: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==16039== by 0x400F563: main (TestCitations.cpp:18) ==16039== { 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:_ZN13TestCitations18TestChasteCitationEv fun:_ZN48TestDescription_TestCitations_TestChasteCitation7runTestEv fun:_ZN7CxxTest19RealTestDescription3runEv fun:_ZN7CxxTest10TestRunner7runTestERNS_15TestDescriptionE fun:_ZN7CxxTest10TestRunner8runSuiteERNS_16SuiteDescriptionE fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==16039== Open file descriptor 7: ==16039== at 0x4D9213B: pipe2 (syscall-template.S:120) ==16039== by 0x720CF87: evutil_make_internal_pipe_ (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==16039== by 0x720F579: evsig_init_ (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==16039== by 0x720F774: ??? (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==16039== by 0x720B8AA: event_base_new_with_config (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==16039== by 0x71720D7: opal_event_base_create (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==16039== by 0x71721E8: opal_event_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==16039== by 0x707C120: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==16039== by 0x4F1A0E7: ompi_rte_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==16039== by 0x4F1F49F: ??? (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==16039== by 0x4F202C3: ompi_mpi_instance_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==16039== by 0x4F1718F: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==16039== by 0x4F51627: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==16039== by 0x5B76446: PetscInitialize (in /usr/lib/x86_64-linux-gnu/libpetsc_real.so.3.24.4) ==16039== by 0x4951610: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==16039== by 0x495165F: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==16039== by 0x40172BD: TestCitations::TestChasteCitation() (TestCitations.hpp:72) ==16039== by 0x4017BA4: TestDescription_TestCitations_TestChasteCitation::runTest() (TestCitations.cpp:30) ==16039== by 0x40105AC: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==16039== by 0x4013994: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==16039== by 0x4013865: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==16039== by 0x40136F7: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==16039== by 0x401355B: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==16039== by 0x4013C09: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==16039== by 0x400F563: main (TestCitations.cpp:18) ==16039== { 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:_ZN13TestCitations18TestChasteCitationEv fun:_ZN48TestDescription_TestCitations_TestChasteCitation7runTestEv fun:_ZN7CxxTest19RealTestDescription3runEv fun:_ZN7CxxTest10TestRunner7runTestERNS_15TestDescriptionE fun:_ZN7CxxTest10TestRunner8runSuiteERNS_16SuiteDescriptionE fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==16039== Open file descriptor 6: ==16039== at 0x4DA234B: epoll_create1 (syscall-template.S:120) ==16039== by 0x720F6FA: ??? (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==16039== by 0x720B8AA: event_base_new_with_config (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==16039== by 0x71720D7: opal_event_base_create (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==16039== by 0x71721E8: opal_event_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==16039== by 0x707C120: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==16039== by 0x4F1A0E7: ompi_rte_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==16039== by 0x4F1F49F: ??? (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==16039== by 0x4F202C3: ompi_mpi_instance_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==16039== by 0x4F1718F: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==16039== by 0x4F51627: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==16039== by 0x5B76446: PetscInitialize (in /usr/lib/x86_64-linux-gnu/libpetsc_real.so.3.24.4) ==16039== by 0x4951610: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==16039== by 0x495165F: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==16039== by 0x40172BD: TestCitations::TestChasteCitation() (TestCitations.hpp:72) ==16039== by 0x4017BA4: TestDescription_TestCitations_TestChasteCitation::runTest() (TestCitations.cpp:30) ==16039== by 0x40105AC: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==16039== by 0x4013994: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==16039== by 0x4013865: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==16039== by 0x40136F7: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==16039== by 0x401355B: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==16039== by 0x4013C09: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==16039== by 0x400F563: main (TestCitations.cpp:18) ==16039== { 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:_ZN13TestCitations18TestChasteCitationEv fun:_ZN48TestDescription_TestCitations_TestChasteCitation7runTestEv fun:_ZN7CxxTest19RealTestDescription3runEv fun:_ZN7CxxTest10TestRunner7runTestERNS_15TestDescriptionE fun:_ZN7CxxTest10TestRunner8runSuiteERNS_16SuiteDescriptionE fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==16039== ==16039== HEAP SUMMARY: ==16039== in use at exit: 102,033 bytes in 626 blocks ==16039== total heap usage: 24,939 allocs, 24,313 frees, 8,273,542 bytes allocated ==16039== ==16039== LEAK SUMMARY: ==16039== definitely lost: 0 bytes in 0 blocks ==16039== indirectly lost: 0 bytes in 0 blocks ==16039== possibly lost: 0 bytes in 0 blocks ==16039== still reachable: 10,185 bytes in 41 blocks ==16039== suppressed: 91,848 bytes in 585 blocks ==16039== Reachable blocks (those to which a pointer was found) are not shown. ==16039== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==16039== ==16039== For lists of detected and suppressed errors, rerun with: -s ==16039== ERROR SUMMARY: 5 errors from 5 contexts (suppressed: 33 from 33)