==16667== Memcheck, a memory error detector
==16667== Copyright (C) 2002-2024, and GNU GPL'd, by Julian Seward et al.
==16667== Using Valgrind-3.26.0 and LibVEX; rerun with -h for copyright info
==16667== Command: /home/runner/work/Chaste/Chaste/Chaste/chaste-build-dir/cell_based/test/TestOffLatticeSimulationWithNodeBasedCellPopulationIn3d -malloc_debug -malloc_dump -memory_info
==16667== Parent PID: 15320
==16667== 
==16667== 
==16667== FILE DESCRIPTORS: 11 open (6 inherited) at exit.
==16667== Open file descriptor 10: /dev/shm/open_mpi.0000
==16667==    at 0x11710536: __open_nocancel (open64_nocancel.c:39)
==16667==    by 0x11694BC3: shm_open@@GLIBC_2.34 (shm_open.c:46)
==16667==    by 0x1644889E: opal_shmem_posix_shm_open (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==16667==    by 0x16448A71: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==16667==    by 0x16447C38: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==16667==    by 0x16447F97: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==16667==    by 0x16317159: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==16667==    by 0x11F5C0E7: ompi_rte_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16667==    by 0x11F6149F: ??? (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16667==    by 0x11F622C3: ompi_mpi_instance_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16667==    by 0x11F5918F: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16667==    by 0x11F93627: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16667==    by 0x12BB8446: PetscInitialize (in /usr/lib/x86_64-linux-gnu/libpetsc_real.so.3.24.4)
==16667==    by 0xEF3C2D9: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==16667==    by 0xEF3C327: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==16667==    by 0x402A134: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==16667==    by 0x4024A41: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==16667==    by 0x40276FE: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==16667==    by 0x4027591: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==16667==    by 0x4027C8B: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==16667==    by 0x4022E98: main (TestOffLatticeSimulationWithNodeBasedCellPopulationIn3d.cpp:18)
==16667== 
{
   <insert_a_suppression_name_here>
   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
}
==16667== Open file descriptor 9:
==16667==    at 0x1171E96B: eventfd (syscall-template.S:120)
==16667==    by 0x164AA188: evutil_eventfd_ (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1)
==16667==    by 0x164A8395: ??? (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1)
==16667==    by 0x164A8704: evthread_make_base_notifiable (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1)
==16667==    by 0x164A89F1: event_base_new_with_config (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1)
==16667==    by 0x1640D0D7: opal_event_base_create (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==16667==    by 0x1640D1E8: opal_event_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==16667==    by 0x16317120: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==16667==    by 0x11F5C0E7: ompi_rte_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16667==    by 0x11F6149F: ??? (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16667==    by 0x11F622C3: ompi_mpi_instance_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16667==    by 0x11F5918F: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16667==    by 0x11F93627: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16667==    by 0x12BB8446: PetscInitialize (in /usr/lib/x86_64-linux-gnu/libpetsc_real.so.3.24.4)
==16667==    by 0xEF3C2D9: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==16667==    by 0xEF3C327: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==16667==    by 0x402A134: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==16667==    by 0x4024A41: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==16667==    by 0x40276FE: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==16667==    by 0x4027591: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==16667==    by 0x4027C8B: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==16667==    by 0x4022E98: main (TestOffLatticeSimulationWithNodeBasedCellPopulationIn3d.cpp:18)
==16667== 
{
   <insert_a_suppression_name_here>
   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
}
==16667== Open file descriptor 8:
==16667==    at 0x1170F2BB: pipe2 (syscall-template.S:120)
==16667==    by 0x164A9F87: evutil_make_internal_pipe_ (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1)
==16667==    by 0x164AC579: evsig_init_ (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1)
==16667==    by 0x164AC774: ??? (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1)
==16667==    by 0x164A88AA: event_base_new_with_config (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1)
==16667==    by 0x1640D0D7: opal_event_base_create (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==16667==    by 0x1640D1E8: opal_event_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==16667==    by 0x16317120: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==16667==    by 0x11F5C0E7: ompi_rte_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16667==    by 0x11F6149F: ??? (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16667==    by 0x11F622C3: ompi_mpi_instance_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16667==    by 0x11F5918F: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16667==    by 0x11F93627: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16667==    by 0x12BB8446: PetscInitialize (in /usr/lib/x86_64-linux-gnu/libpetsc_real.so.3.24.4)
==16667==    by 0xEF3C2D9: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==16667==    by 0xEF3C327: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==16667==    by 0x402A134: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==16667==    by 0x4024A41: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==16667==    by 0x40276FE: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==16667==    by 0x4027591: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==16667==    by 0x4027C8B: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==16667==    by 0x4022E98: main (TestOffLatticeSimulationWithNodeBasedCellPopulationIn3d.cpp:18)
==16667== 
{
   <insert_a_suppression_name_here>
   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
}
==16667== Open file descriptor 7:
==16667==    at 0x1170F2BB: pipe2 (syscall-template.S:120)
==16667==    by 0x164A9F87: evutil_make_internal_pipe_ (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1)
==16667==    by 0x164AC579: evsig_init_ (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1)
==16667==    by 0x164AC774: ??? (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1)
==16667==    by 0x164A88AA: event_base_new_with_config (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1)
==16667==    by 0x1640D0D7: opal_event_base_create (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==16667==    by 0x1640D1E8: opal_event_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==16667==    by 0x16317120: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==16667==    by 0x11F5C0E7: ompi_rte_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16667==    by 0x11F6149F: ??? (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16667==    by 0x11F622C3: ompi_mpi_instance_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16667==    by 0x11F5918F: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16667==    by 0x11F93627: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16667==    by 0x12BB8446: PetscInitialize (in /usr/lib/x86_64-linux-gnu/libpetsc_real.so.3.24.4)
==16667==    by 0xEF3C2D9: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==16667==    by 0xEF3C327: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==16667==    by 0x402A134: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==16667==    by 0x4024A41: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==16667==    by 0x40276FE: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==16667==    by 0x4027591: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==16667==    by 0x4027C8B: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==16667==    by 0x4022E98: main (TestOffLatticeSimulationWithNodeBasedCellPopulationIn3d.cpp:18)
==16667== 
{
   <insert_a_suppression_name_here>
   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
}
==16667== Open file descriptor 6:
==16667==    at 0x1171F46B: epoll_create1 (syscall-template.S:120)
==16667==    by 0x164AC6FA: ??? (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1)
==16667==    by 0x164A88AA: event_base_new_with_config (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1)
==16667==    by 0x1640D0D7: opal_event_base_create (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==16667==    by 0x1640D1E8: opal_event_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==16667==    by 0x16317120: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==16667==    by 0x11F5C0E7: ompi_rte_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16667==    by 0x11F6149F: ??? (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16667==    by 0x11F622C3: ompi_mpi_instance_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16667==    by 0x11F5918F: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16667==    by 0x11F93627: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16667==    by 0x12BB8446: PetscInitialize (in /usr/lib/x86_64-linux-gnu/libpetsc_real.so.3.24.4)
==16667==    by 0xEF3C2D9: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==16667==    by 0xEF3C327: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==16667==    by 0x402A134: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==16667==    by 0x4024A41: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==16667==    by 0x40276FE: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==16667==    by 0x4027591: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==16667==    by 0x4027C8B: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==16667==    by 0x4022E98: main (TestOffLatticeSimulationWithNodeBasedCellPopulationIn3d.cpp:18)
==16667== 
{
   <insert_a_suppression_name_here>
   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
}
==16667== 
==16667== HEAP SUMMARY:
==16667==     in use at exit: 128,892 bytes in 930 blocks
==16667==   total heap usage: 7,126,564 allocs, 7,125,634 frees, 7,713,571,151 bytes allocated
==16667== 
==16667== LEAK SUMMARY:
==16667==    definitely lost: 0 bytes in 0 blocks
==16667==    indirectly lost: 0 bytes in 0 blocks
==16667==      possibly lost: 0 bytes in 0 blocks
==16667==    still reachable: 11,981 bytes in 45 blocks
==16667==         suppressed: 116,911 bytes in 885 blocks
==16667== Reachable blocks (those to which a pointer was found) are not shown.
==16667== To see them, rerun with: --leak-check=full --show-leak-kinds=all
==16667== 
==16667== For lists of detected and suppressed errors, rerun with: -s
==16667== ERROR SUMMARY: 5 errors from 5 contexts (suppressed: 33 from 33)