==16909== Memcheck, a memory error detector
==16909== Copyright (C) 2002-2024, and GNU GPL'd, by Julian Seward et al.
==16909== Using Valgrind-3.26.0 and LibVEX; rerun with -h for copyright info
==16909== Command: /home/runner/work/Chaste/Chaste/Chaste/chaste-build-dir/cell_based/test/TestAlarcon2004OxygenBasedCellCycleOdeSystem -malloc_debug -malloc_dump -memory_info
==16909== Parent PID: 16468
==16909== 
==16909== 
==16909== FILE DESCRIPTORS: 11 open (6 inherited) at exit.
==16909== Open file descriptor 10: /dev/shm/open_mpi.0000
==16909==    at 0xF7173B6: __open_nocancel (open64_nocancel.c:39)
==16909==    by 0xF69B943: shm_open@@GLIBC_2.34 (shm_open.c:46)
==16909==    by 0x16A4F89E: opal_shmem_posix_shm_open (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==16909==    by 0x16A4FA71: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==16909==    by 0x16A4EC38: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==16909==    by 0x16A4EF97: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==16909==    by 0x1691E159: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==16909==    by 0xEFB00E7: ompi_rte_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16909==    by 0xEFB549F: ??? (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16909==    by 0xEFB62C3: ompi_mpi_instance_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16909==    by 0xEFAD18F: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16909==    by 0xEFE7627: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16909==    by 0xDFB1446: PetscInitialize (in /usr/lib/x86_64-linux-gnu/libpetsc_real.so.3.24.4)
==16909==    by 0xD67F27F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==16909==    by 0xD67F2CD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==16909==    by 0x4024313: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70)
==16909==    by 0x401F6C3: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==16909==    by 0x4021D60: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==16909==    by 0x4021BFE: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==16909==    by 0x40222AB: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==16909==    by 0x401DEB2: main (TestAlarcon2004OxygenBasedCellCycleOdeSystem.cpp:18)
==16909== 
{
   <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
}
==16909== Open file descriptor 9:
==16909==    at 0xF72584B: eventfd (syscall-template.S:120)
==16909==    by 0x16AAF188: evutil_eventfd_ (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1)
==16909==    by 0x16AAD395: ??? (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1)
==16909==    by 0x16AAD704: evthread_make_base_notifiable (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1)
==16909==    by 0x16AAD9F1: event_base_new_with_config (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1)
==16909==    by 0x16A140D7: opal_event_base_create (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==16909==    by 0x16A141E8: opal_event_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==16909==    by 0x1691E120: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==16909==    by 0xEFB00E7: ompi_rte_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16909==    by 0xEFB549F: ??? (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16909==    by 0xEFB62C3: ompi_mpi_instance_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16909==    by 0xEFAD18F: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16909==    by 0xEFE7627: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16909==    by 0xDFB1446: PetscInitialize (in /usr/lib/x86_64-linux-gnu/libpetsc_real.so.3.24.4)
==16909==    by 0xD67F27F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==16909==    by 0xD67F2CD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==16909==    by 0x4024313: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70)
==16909==    by 0x401F6C3: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==16909==    by 0x4021D60: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==16909==    by 0x4021BFE: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==16909==    by 0x40222AB: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==16909==    by 0x401DEB2: main (TestAlarcon2004OxygenBasedCellCycleOdeSystem.cpp:18)
==16909== 
{
   <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
}
==16909== Open file descriptor 8:
==16909==    at 0xF71613B: pipe2 (syscall-template.S:120)
==16909==    by 0x16AAEF87: evutil_make_internal_pipe_ (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1)
==16909==    by 0x16AB1579: evsig_init_ (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1)
==16909==    by 0x16AB1774: ??? (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1)
==16909==    by 0x16AAD8AA: event_base_new_with_config (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1)
==16909==    by 0x16A140D7: opal_event_base_create (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==16909==    by 0x16A141E8: opal_event_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==16909==    by 0x1691E120: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==16909==    by 0xEFB00E7: ompi_rte_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16909==    by 0xEFB549F: ??? (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16909==    by 0xEFB62C3: ompi_mpi_instance_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16909==    by 0xEFAD18F: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16909==    by 0xEFE7627: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16909==    by 0xDFB1446: PetscInitialize (in /usr/lib/x86_64-linux-gnu/libpetsc_real.so.3.24.4)
==16909==    by 0xD67F27F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==16909==    by 0xD67F2CD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==16909==    by 0x4024313: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70)
==16909==    by 0x401F6C3: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==16909==    by 0x4021D60: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==16909==    by 0x4021BFE: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==16909==    by 0x40222AB: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==16909==    by 0x401DEB2: main (TestAlarcon2004OxygenBasedCellCycleOdeSystem.cpp:18)
==16909== 
{
   <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
}
==16909== Open file descriptor 7:
==16909==    at 0xF71613B: pipe2 (syscall-template.S:120)
==16909==    by 0x16AAEF87: evutil_make_internal_pipe_ (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1)
==16909==    by 0x16AB1579: evsig_init_ (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1)
==16909==    by 0x16AB1774: ??? (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1)
==16909==    by 0x16AAD8AA: event_base_new_with_config (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1)
==16909==    by 0x16A140D7: opal_event_base_create (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==16909==    by 0x16A141E8: opal_event_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==16909==    by 0x1691E120: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==16909==    by 0xEFB00E7: ompi_rte_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16909==    by 0xEFB549F: ??? (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16909==    by 0xEFB62C3: ompi_mpi_instance_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16909==    by 0xEFAD18F: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16909==    by 0xEFE7627: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16909==    by 0xDFB1446: PetscInitialize (in /usr/lib/x86_64-linux-gnu/libpetsc_real.so.3.24.4)
==16909==    by 0xD67F27F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==16909==    by 0xD67F2CD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==16909==    by 0x4024313: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70)
==16909==    by 0x401F6C3: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==16909==    by 0x4021D60: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==16909==    by 0x4021BFE: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==16909==    by 0x40222AB: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==16909==    by 0x401DEB2: main (TestAlarcon2004OxygenBasedCellCycleOdeSystem.cpp:18)
==16909== 
{
   <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
}
==16909== Open file descriptor 5:
==16909==    at 0xF72634B: epoll_create1 (syscall-template.S:120)
==16909==    by 0x16AB16FA: ??? (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1)
==16909==    by 0x16AAD8AA: event_base_new_with_config (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1)
==16909==    by 0x16A140D7: opal_event_base_create (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==16909==    by 0x16A141E8: opal_event_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==16909==    by 0x1691E120: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5)
==16909==    by 0xEFB00E7: ompi_rte_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16909==    by 0xEFB549F: ??? (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16909==    by 0xEFB62C3: ompi_mpi_instance_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16909==    by 0xEFAD18F: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16909==    by 0xEFE7627: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7)
==16909==    by 0xDFB1446: PetscInitialize (in /usr/lib/x86_64-linux-gnu/libpetsc_real.so.3.24.4)
==16909==    by 0xD67F27F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==16909==    by 0xD67F2CD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==16909==    by 0x4024313: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70)
==16909==    by 0x401F6C3: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==16909==    by 0x4021D60: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==16909==    by 0x4021BFE: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==16909==    by 0x40222AB: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==16909==    by 0x401DEB2: main (TestAlarcon2004OxygenBasedCellCycleOdeSystem.cpp:18)
==16909== 
{
   <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
}
==16909== 
==16909== HEAP SUMMARY:
==16909==     in use at exit: 128,914 bytes in 933 blocks
==16909==   total heap usage: 146,333 allocs, 145,400 frees, 21,693,534 bytes allocated
==16909== 
==16909== LEAK SUMMARY:
==16909==    definitely lost: 0 bytes in 0 blocks
==16909==    indirectly lost: 0 bytes in 0 blocks
==16909==      possibly lost: 0 bytes in 0 blocks
==16909==    still reachable: 11,941 bytes in 44 blocks
==16909==         suppressed: 116,973 bytes in 889 blocks
==16909== Reachable blocks (those to which a pointer was found) are not shown.
==16909== To see them, rerun with: --leak-check=full --show-leak-kinds=all
==16909== 
==16909== For lists of detected and suppressed errors, rerun with: -s
==16909== ERROR SUMMARY: 5 errors from 5 contexts (suppressed: 33 from 33)