==15811== Memcheck, a memory error detector ==15811== Copyright (C) 2002-2024, and GNU GPL'd, by Julian Seward et al. ==15811== Using Valgrind-3.26.0 and LibVEX; rerun with -h for copyright info ==15811== Command: /home/runner/work/Chaste/Chaste/Chaste/chaste-build-dir/global/test/TestCitations -malloc_debug -malloc_dump -memory_info ==15811== Parent PID: 15807 ==15811== ==15811== ==15811== FILE DESCRIPTORS: 11 open (6 inherited) at exit. ==15811== Open file descriptor 10: /dev/shm/open_mpi.0000 ==15811== at 0x4D8B536: __open_nocancel (open64_nocancel.c:39) ==15811== by 0x4D0FBC3: shm_open@@GLIBC_2.34 (shm_open.c:46) ==15811== by 0x71A589E: opal_shmem_posix_shm_open (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==15811== by 0x71A5A71: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==15811== by 0x71A4C38: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==15811== by 0x71A4F97: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==15811== by 0x7074159: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==15811== by 0x4F120E7: ompi_rte_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15811== by 0x4F1749F: ??? (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15811== by 0x4F182C3: ompi_mpi_instance_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15811== by 0x4F0F18F: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15811== by 0x4F49627: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15811== by 0x5B6E446: PetscInitialize (in /usr/lib/x86_64-linux-gnu/libpetsc_real.so.3.24.4) ==15811== by 0x492B2D9: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==15811== by 0x492B327: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==15811== by 0x401058B: TestCitations::TestChasteCitation() (TestCitations.hpp:72) ==15811== by 0x4010E72: TestDescription_TestCitations_TestChasteCitation::runTest() (TestCitations.cpp:30) ==15811== by 0x400987A: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==15811== by 0x400CC62: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==15811== by 0x400CB33: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==15811== by 0x400C9C5: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==15811== by 0x400C829: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==15811== by 0x400CED7: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==15811== by 0x4008832: main (TestCitations.cpp:18) ==15811== { 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 } ==15811== Open file descriptor 9: ==15811== at 0x4D9996B: eventfd (syscall-template.S:120) ==15811== by 0x7205188: evutil_eventfd_ (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==15811== by 0x7203395: ??? (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==15811== by 0x7203704: evthread_make_base_notifiable (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==15811== by 0x72039F1: event_base_new_with_config (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==15811== by 0x716A0D7: opal_event_base_create (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==15811== by 0x716A1E8: opal_event_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==15811== by 0x7074120: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==15811== by 0x4F120E7: ompi_rte_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15811== by 0x4F1749F: ??? (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15811== by 0x4F182C3: ompi_mpi_instance_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15811== by 0x4F0F18F: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15811== by 0x4F49627: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15811== by 0x5B6E446: PetscInitialize (in /usr/lib/x86_64-linux-gnu/libpetsc_real.so.3.24.4) ==15811== by 0x492B2D9: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==15811== by 0x492B327: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==15811== by 0x401058B: TestCitations::TestChasteCitation() (TestCitations.hpp:72) ==15811== by 0x4010E72: TestDescription_TestCitations_TestChasteCitation::runTest() (TestCitations.cpp:30) ==15811== by 0x400987A: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==15811== by 0x400CC62: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==15811== by 0x400CB33: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==15811== by 0x400C9C5: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==15811== by 0x400C829: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==15811== by 0x400CED7: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==15811== by 0x4008832: main (TestCitations.cpp:18) ==15811== { 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 } ==15811== Open file descriptor 8: ==15811== at 0x4D8A2BB: pipe2 (syscall-template.S:120) ==15811== by 0x7204F87: evutil_make_internal_pipe_ (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==15811== by 0x7207579: evsig_init_ (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==15811== by 0x7207774: ??? (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==15811== by 0x72038AA: event_base_new_with_config (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==15811== by 0x716A0D7: opal_event_base_create (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==15811== by 0x716A1E8: opal_event_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==15811== by 0x7074120: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==15811== by 0x4F120E7: ompi_rte_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15811== by 0x4F1749F: ??? (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15811== by 0x4F182C3: ompi_mpi_instance_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15811== by 0x4F0F18F: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15811== by 0x4F49627: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15811== by 0x5B6E446: PetscInitialize (in /usr/lib/x86_64-linux-gnu/libpetsc_real.so.3.24.4) ==15811== by 0x492B2D9: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==15811== by 0x492B327: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==15811== by 0x401058B: TestCitations::TestChasteCitation() (TestCitations.hpp:72) ==15811== by 0x4010E72: TestDescription_TestCitations_TestChasteCitation::runTest() (TestCitations.cpp:30) ==15811== by 0x400987A: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==15811== by 0x400CC62: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==15811== by 0x400CB33: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==15811== by 0x400C9C5: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==15811== by 0x400C829: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==15811== by 0x400CED7: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==15811== by 0x4008832: main (TestCitations.cpp:18) ==15811== { 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 } ==15811== Open file descriptor 7: ==15811== at 0x4D8A2BB: pipe2 (syscall-template.S:120) ==15811== by 0x7204F87: evutil_make_internal_pipe_ (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==15811== by 0x7207579: evsig_init_ (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==15811== by 0x7207774: ??? (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==15811== by 0x72038AA: event_base_new_with_config (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==15811== by 0x716A0D7: opal_event_base_create (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==15811== by 0x716A1E8: opal_event_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==15811== by 0x7074120: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==15811== by 0x4F120E7: ompi_rte_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15811== by 0x4F1749F: ??? (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15811== by 0x4F182C3: ompi_mpi_instance_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15811== by 0x4F0F18F: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15811== by 0x4F49627: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15811== by 0x5B6E446: PetscInitialize (in /usr/lib/x86_64-linux-gnu/libpetsc_real.so.3.24.4) ==15811== by 0x492B2D9: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==15811== by 0x492B327: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==15811== by 0x401058B: TestCitations::TestChasteCitation() (TestCitations.hpp:72) ==15811== by 0x4010E72: TestDescription_TestCitations_TestChasteCitation::runTest() (TestCitations.cpp:30) ==15811== by 0x400987A: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==15811== by 0x400CC62: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==15811== by 0x400CB33: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==15811== by 0x400C9C5: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==15811== by 0x400C829: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==15811== by 0x400CED7: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==15811== by 0x4008832: main (TestCitations.cpp:18) ==15811== { 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 } ==15811== Open file descriptor 5: ==15811== at 0x4D9A46B: epoll_create1 (syscall-template.S:120) ==15811== by 0x72076FA: ??? (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==15811== by 0x72038AA: event_base_new_with_config (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==15811== by 0x716A0D7: opal_event_base_create (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==15811== by 0x716A1E8: opal_event_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==15811== by 0x7074120: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==15811== by 0x4F120E7: ompi_rte_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15811== by 0x4F1749F: ??? (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15811== by 0x4F182C3: ompi_mpi_instance_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15811== by 0x4F0F18F: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15811== by 0x4F49627: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15811== by 0x5B6E446: PetscInitialize (in /usr/lib/x86_64-linux-gnu/libpetsc_real.so.3.24.4) ==15811== by 0x492B2D9: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==15811== by 0x492B327: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==15811== by 0x401058B: TestCitations::TestChasteCitation() (TestCitations.hpp:72) ==15811== by 0x4010E72: TestDescription_TestCitations_TestChasteCitation::runTest() (TestCitations.cpp:30) ==15811== by 0x400987A: CxxTest::RealTestDescription::run() (RealDescriptions.cpp:96) ==15811== by 0x400CC62: CxxTest::TestRunner::runTest(CxxTest::TestDescription&) (TestRunner.h:74) ==15811== by 0x400CB33: CxxTest::TestRunner::runSuite(CxxTest::SuiteDescription&) (TestRunner.h:61) ==15811== by 0x400C9C5: CxxTest::TestRunner::runWorld() (TestRunner.h:46) ==15811== by 0x400C829: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==15811== by 0x400CED7: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==15811== by 0x4008832: main (TestCitations.cpp:18) ==15811== { 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 } ==15811== ==15811== HEAP SUMMARY: ==15811== in use at exit: 124,539 bytes in 897 blocks ==15811== total heap usage: 25,422 allocs, 24,525 frees, 10,262,678 bytes allocated ==15811== ==15811== LEAK SUMMARY: ==15811== definitely lost: 0 bytes in 0 blocks ==15811== indirectly lost: 0 bytes in 0 blocks ==15811== possibly lost: 0 bytes in 0 blocks ==15811== still reachable: 10,073 bytes in 40 blocks ==15811== suppressed: 114,466 bytes in 857 blocks ==15811== Reachable blocks (those to which a pointer was found) are not shown. ==15811== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==15811== ==15811== For lists of detected and suppressed errors, rerun with: -s ==15811== ERROR SUMMARY: 5 errors from 5 contexts (suppressed: 33 from 33)