==17056== Memcheck, a memory error detector ==17056== Copyright (C) 2002-2024, and GNU GPL'd, by Julian Seward et al. ==17056== Using Valgrind-3.26.0 and LibVEX; rerun with -h for copyright info ==17056== Command: /home/runner/work/Chaste/Chaste/Chaste/chaste-build-dir/global/test/TestCitations -malloc_debug -malloc_dump -memory_info ==17056== Parent PID: 17052 ==17056== ==17056== ==17056== FILE DESCRIPTORS: 11 open (6 inherited) at exit. ==17056== Open file descriptor 10: /dev/shm/open_mpi.0000 ==17056== at 0x4D833B6: __open_nocancel (open64_nocancel.c:39) ==17056== by 0x4D07943: shm_open@@GLIBC_2.34 (shm_open.c:46) ==17056== by 0x719D89E: opal_shmem_posix_shm_open (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==17056== by 0x719DA71: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==17056== by 0x719CC38: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==17056== by 0x719CF97: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==17056== by 0x706C159: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==17056== by 0x4F0A0E7: ompi_rte_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==17056== by 0x4F0F49F: ??? (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==17056== by 0x4F102C3: ompi_mpi_instance_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==17056== by 0x4F0718F: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==17056== by 0x4F41627: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==17056== by 0x5B66446: PetscInitialize (in /usr/lib/x86_64-linux-gnu/libpetsc_real.so.3.24.4) ==17056== by 0x49462F9: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==17056== by 0x4946347: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==17056== by 0x40172BB: TestCitations::TestChasteCitation() (TestCitations.hpp:72) ==17056== by 0x4017BA2: TestDescription_TestCitations_TestChasteCitation::runTest() (TestCitations.cpp:30) ==17056== by 0x40105AA: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==17056== by 0x4013992: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==17056== by 0x4013863: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==17056== by 0x40136F5: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==17056== by 0x4013559: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==17056== by 0x4013C07: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==17056== by 0x400F562: main (TestCitations.cpp:18) ==17056== { 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 } ==17056== Open file descriptor 9: ==17056== at 0x4D9184B: eventfd (syscall-template.S:120) ==17056== by 0x71FD188: evutil_eventfd_ (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==17056== by 0x71FB395: ??? (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==17056== by 0x71FB704: evthread_make_base_notifiable (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==17056== by 0x71FB9F1: event_base_new_with_config (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==17056== by 0x71620D7: opal_event_base_create (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==17056== by 0x71621E8: opal_event_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==17056== by 0x706C120: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==17056== by 0x4F0A0E7: ompi_rte_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==17056== by 0x4F0F49F: ??? (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==17056== by 0x4F102C3: ompi_mpi_instance_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==17056== by 0x4F0718F: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==17056== by 0x4F41627: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==17056== by 0x5B66446: PetscInitialize (in /usr/lib/x86_64-linux-gnu/libpetsc_real.so.3.24.4) ==17056== by 0x49462F9: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==17056== by 0x4946347: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==17056== by 0x40172BB: TestCitations::TestChasteCitation() (TestCitations.hpp:72) ==17056== by 0x4017BA2: TestDescription_TestCitations_TestChasteCitation::runTest() (TestCitations.cpp:30) ==17056== by 0x40105AA: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==17056== by 0x4013992: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==17056== by 0x4013863: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==17056== by 0x40136F5: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==17056== by 0x4013559: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==17056== by 0x4013C07: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==17056== by 0x400F562: main (TestCitations.cpp:18) ==17056== { 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 } ==17056== Open file descriptor 8: ==17056== at 0x4D8213B: pipe2 (syscall-template.S:120) ==17056== by 0x71FCF87: evutil_make_internal_pipe_ (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==17056== by 0x71FF579: evsig_init_ (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==17056== by 0x71FF774: ??? (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==17056== by 0x71FB8AA: event_base_new_with_config (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==17056== by 0x71620D7: opal_event_base_create (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==17056== by 0x71621E8: opal_event_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==17056== by 0x706C120: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==17056== by 0x4F0A0E7: ompi_rte_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==17056== by 0x4F0F49F: ??? (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==17056== by 0x4F102C3: ompi_mpi_instance_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==17056== by 0x4F0718F: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==17056== by 0x4F41627: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==17056== by 0x5B66446: PetscInitialize (in /usr/lib/x86_64-linux-gnu/libpetsc_real.so.3.24.4) ==17056== by 0x49462F9: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==17056== by 0x4946347: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==17056== by 0x40172BB: TestCitations::TestChasteCitation() (TestCitations.hpp:72) ==17056== by 0x4017BA2: TestDescription_TestCitations_TestChasteCitation::runTest() (TestCitations.cpp:30) ==17056== by 0x40105AA: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==17056== by 0x4013992: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==17056== by 0x4013863: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==17056== by 0x40136F5: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==17056== by 0x4013559: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==17056== by 0x4013C07: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==17056== by 0x400F562: main (TestCitations.cpp:18) ==17056== { 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 } ==17056== Open file descriptor 7: ==17056== at 0x4D8213B: pipe2 (syscall-template.S:120) ==17056== by 0x71FCF87: evutil_make_internal_pipe_ (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==17056== by 0x71FF579: evsig_init_ (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==17056== by 0x71FF774: ??? (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==17056== by 0x71FB8AA: event_base_new_with_config (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==17056== by 0x71620D7: opal_event_base_create (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==17056== by 0x71621E8: opal_event_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==17056== by 0x706C120: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==17056== by 0x4F0A0E7: ompi_rte_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==17056== by 0x4F0F49F: ??? (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==17056== by 0x4F102C3: ompi_mpi_instance_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==17056== by 0x4F0718F: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==17056== by 0x4F41627: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==17056== by 0x5B66446: PetscInitialize (in /usr/lib/x86_64-linux-gnu/libpetsc_real.so.3.24.4) ==17056== by 0x49462F9: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==17056== by 0x4946347: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==17056== by 0x40172BB: TestCitations::TestChasteCitation() (TestCitations.hpp:72) ==17056== by 0x4017BA2: TestDescription_TestCitations_TestChasteCitation::runTest() (TestCitations.cpp:30) ==17056== by 0x40105AA: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==17056== by 0x4013992: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==17056== by 0x4013863: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==17056== by 0x40136F5: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==17056== by 0x4013559: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==17056== by 0x4013C07: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==17056== by 0x400F562: main (TestCitations.cpp:18) ==17056== { 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 } ==17056== Open file descriptor 4: ==17056== at 0x4D9234B: epoll_create1 (syscall-template.S:120) ==17056== by 0x71FF6FA: ??? (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==17056== by 0x71FB8AA: event_base_new_with_config (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==17056== by 0x71620D7: opal_event_base_create (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==17056== by 0x71621E8: opal_event_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==17056== by 0x706C120: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==17056== by 0x4F0A0E7: ompi_rte_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==17056== by 0x4F0F49F: ??? (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==17056== by 0x4F102C3: ompi_mpi_instance_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==17056== by 0x4F0718F: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==17056== by 0x4F41627: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==17056== by 0x5B66446: PetscInitialize (in /usr/lib/x86_64-linux-gnu/libpetsc_real.so.3.24.4) ==17056== by 0x49462F9: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==17056== by 0x4946347: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==17056== by 0x40172BB: TestCitations::TestChasteCitation() (TestCitations.hpp:72) ==17056== by 0x4017BA2: TestDescription_TestCitations_TestChasteCitation::runTest() (TestCitations.cpp:30) ==17056== by 0x40105AA: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==17056== by 0x4013992: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==17056== by 0x4013863: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==17056== by 0x40136F5: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==17056== by 0x4013559: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==17056== by 0x4013C07: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==17056== by 0x400F562: main (TestCitations.cpp:18) ==17056== { 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 } ==17056== ==17056== HEAP SUMMARY: ==17056== in use at exit: 124,541 bytes in 897 blocks ==17056== total heap usage: 25,421 allocs, 24,524 frees, 10,262,564 bytes allocated ==17056== ==17056== LEAK SUMMARY: ==17056== definitely lost: 0 bytes in 0 blocks ==17056== indirectly lost: 0 bytes in 0 blocks ==17056== possibly lost: 0 bytes in 0 blocks ==17056== still reachable: 10,073 bytes in 40 blocks ==17056== suppressed: 114,468 bytes in 857 blocks ==17056== Reachable blocks (those to which a pointer was found) are not shown. ==17056== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==17056== ==17056== For lists of detected and suppressed errors, rerun with: -s ==17056== ERROR SUMMARY: 5 errors from 5 contexts (suppressed: 33 from 33)