==17216== Memcheck, a memory error detector
==17216== Copyright (C) 2002-2024, and GNU GPL'd, by Julian Seward et al.
==17216== Using Valgrind-3.26.0 and LibVEX; rerun with -h for copyright info
==17216== Command: /home/runner/work/Chaste/Chaste/Chaste/chaste-build-dir/cell_based/test/TestAlarcon2004OxygenBasedCellCycleOdeSystem -malloc_debug -malloc_dump -memory_info
==17216== Parent PID: 16731
==17216== 
==17216== 
==17216== FILE DESCRIPTORS: 11 open (6 inherited) at exit.
==17216== Open file descriptor 10: /dev/shm/open_mpi.0000
==17216==    at 0xF7173B6: __open_nocancel (open64_nocancel.c:39)
==17216==    by 0xF69B943: shm_open@@GLIBC_2.34 (shm_open.c:46)
==17216==    by 0x16A4F89E: opal_shmem_posix_shm_open (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==17216==    by 0x16A4FA71: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==17216==    by 0x16A4EC38: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==17216==    by 0x16A4EF97: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==17216==    by 0x1691E159: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==17216==    by 0xEFB00E7: ompi_rte_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==17216==    by 0xEFB549F: ??? (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==17216==    by 0xEFB62C3: ompi_mpi_instance_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==17216==    by 0xEFAD18F: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==17216==    by 0xEFE7627: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==17216==    by 0xDFB1446: PetscInitialize (in /usr/lib/x86_64-linux-gnu/libpetsc_real.so.3.24.4)
==17216==    by 0xD67F2F9: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==17216==    by 0xD67F347: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==17216==    by 0x4024313: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70)
==17216==    by 0x401F6C3: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==17216==    by 0x4021D60: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==17216==    by 0x4021BFE: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==17216==    by 0x40222AB: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==17216==    by 0x401DEB2: main (TestAlarcon2004OxygenBasedCellCycleOdeSystem.cpp:18)
==17216== 
{
   <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
}
==17216== Open file descriptor 9:
==17216==    at 0xF72584B: eventfd (syscall-template.S:120)
==17216==    by 0x16AAF188: evutil_eventfd_ (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1)
==17216==    by 0x16AAD395: ??? (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1)
==17216==    by 0x16AAD704: evthread_make_base_notifiable (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1)
==17216==    by 0x16AAD9F1: event_base_new_with_config (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1)
==17216==    by 0x16A140D7: opal_event_base_create (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==17216==    by 0x16A141E8: opal_event_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==17216==    by 0x1691E120: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==17216==    by 0xEFB00E7: ompi_rte_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==17216==    by 0xEFB549F: ??? (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==17216==    by 0xEFB62C3: ompi_mpi_instance_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==17216==    by 0xEFAD18F: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==17216==    by 0xEFE7627: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==17216==    by 0xDFB1446: PetscInitialize (in /usr/lib/x86_64-linux-gnu/libpetsc_real.so.3.24.4)
==17216==    by 0xD67F2F9: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==17216==    by 0xD67F347: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==17216==    by 0x4024313: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70)
==17216==    by 0x401F6C3: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==17216==    by 0x4021D60: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==17216==    by 0x4021BFE: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==17216==    by 0x40222AB: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==17216==    by 0x401DEB2: main (TestAlarcon2004OxygenBasedCellCycleOdeSystem.cpp:18)
==17216== 
{
   <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
}
==17216== Open file descriptor 8:
==17216==    at 0xF71613B: pipe2 (syscall-template.S:120)
==17216==    by 0x16AAEF87: evutil_make_internal_pipe_ (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1)
==17216==    by 0x16AB1579: evsig_init_ (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1)
==17216==    by 0x16AB1774: ??? (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1)
==17216==    by 0x16AAD8AA: event_base_new_with_config (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1)
==17216==    by 0x16A140D7: opal_event_base_create (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==17216==    by 0x16A141E8: opal_event_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==17216==    by 0x1691E120: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==17216==    by 0xEFB00E7: ompi_rte_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==17216==    by 0xEFB549F: ??? (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==17216==    by 0xEFB62C3: ompi_mpi_instance_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==17216==    by 0xEFAD18F: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==17216==    by 0xEFE7627: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==17216==    by 0xDFB1446: PetscInitialize (in /usr/lib/x86_64-linux-gnu/libpetsc_real.so.3.24.4)
==17216==    by 0xD67F2F9: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==17216==    by 0xD67F347: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==17216==    by 0x4024313: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70)
==17216==    by 0x401F6C3: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==17216==    by 0x4021D60: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==17216==    by 0x4021BFE: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==17216==    by 0x40222AB: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==17216==    by 0x401DEB2: main (TestAlarcon2004OxygenBasedCellCycleOdeSystem.cpp:18)
==17216== 
{
   <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
}
==17216== Open file descriptor 7:
==17216==    at 0xF71613B: pipe2 (syscall-template.S:120)
==17216==    by 0x16AAEF87: evutil_make_internal_pipe_ (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1)
==17216==    by 0x16AB1579: evsig_init_ (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1)
==17216==    by 0x16AB1774: ??? (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1)
==17216==    by 0x16AAD8AA: event_base_new_with_config (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1)
==17216==    by 0x16A140D7: opal_event_base_create (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==17216==    by 0x16A141E8: opal_event_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==17216==    by 0x1691E120: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==17216==    by 0xEFB00E7: ompi_rte_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==17216==    by 0xEFB549F: ??? (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==17216==    by 0xEFB62C3: ompi_mpi_instance_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==17216==    by 0xEFAD18F: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==17216==    by 0xEFE7627: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==17216==    by 0xDFB1446: PetscInitialize (in /usr/lib/x86_64-linux-gnu/libpetsc_real.so.3.24.4)
==17216==    by 0xD67F2F9: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==17216==    by 0xD67F347: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==17216==    by 0x4024313: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70)
==17216==    by 0x401F6C3: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==17216==    by 0x4021D60: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==17216==    by 0x4021BFE: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==17216==    by 0x40222AB: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==17216==    by 0x401DEB2: main (TestAlarcon2004OxygenBasedCellCycleOdeSystem.cpp:18)
==17216== 
{
   <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
}
==17216== Open file descriptor 6:
==17216==    at 0xF72634B: epoll_create1 (syscall-template.S:120)
==17216==    by 0x16AB16FA: ??? (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1)
==17216==    by 0x16AAD8AA: event_base_new_with_config (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1)
==17216==    by 0x16A140D7: opal_event_base_create (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==17216==    by 0x16A141E8: opal_event_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==17216==    by 0x1691E120: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==17216==    by 0xEFB00E7: ompi_rte_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==17216==    by 0xEFB549F: ??? (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==17216==    by 0xEFB62C3: ompi_mpi_instance_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==17216==    by 0xEFAD18F: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==17216==    by 0xEFE7627: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==17216==    by 0xDFB1446: PetscInitialize (in /usr/lib/x86_64-linux-gnu/libpetsc_real.so.3.24.4)
==17216==    by 0xD67F2F9: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==17216==    by 0xD67F347: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==17216==    by 0x4024313: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70)
==17216==    by 0x401F6C3: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==17216==    by 0x4021D60: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==17216==    by 0x4021BFE: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==17216==    by 0x40222AB: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==17216==    by 0x401DEB2: main (TestAlarcon2004OxygenBasedCellCycleOdeSystem.cpp:18)
==17216== 
{
   <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
}
==17216== 
==17216== HEAP SUMMARY:
==17216==     in use at exit: 126,441 bytes in 901 blocks
==17216==   total heap usage: 146,436 allocs, 145,535 frees, 21,649,800 bytes allocated
==17216== 
==17216== LEAK SUMMARY:
==17216==    definitely lost: 0 bytes in 0 blocks
==17216==    indirectly lost: 0 bytes in 0 blocks
==17216==      possibly lost: 0 bytes in 0 blocks
==17216==    still reachable: 11,941 bytes in 44 blocks
==17216==         suppressed: 114,500 bytes in 857 blocks
==17216== Reachable blocks (those to which a pointer was found) are not shown.
==17216== To see them, rerun with: --leak-check=full --show-leak-kinds=all
==17216== 
==17216== For lists of detected and suppressed errors, rerun with: -s
==17216== ERROR SUMMARY: 5 errors from 5 contexts (suppressed: 33 from 33)