==390567== Memcheck, a memory error detector
==390567== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
==390567== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info
==390567== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/cell_based/test/TestRunningPottsBasedSimulationsTutorial -malloc_debug -malloc_dump -memory_info
==390567== Parent PID: 368214
==390567== 
==390567== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later.
==390567== You should replace [...] by a specific index such as [0] or [1] or [2] or similar
==390567== 
==390567== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s)
==390567==    at 0xD0AC79E: getsockopt_syscall (getsockopt.c:29)
==390567==    by 0xD0AC79E: getsockopt (getsockopt.c:94)
==390567==    by 0x192CA157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==390567==    by 0x192D1A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==390567==    by 0x192D8DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==390567==    by 0x191D83C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==390567==    by 0x19151E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so)
==390567==    by 0x18910E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so)
==390567==    by 0x13F154CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==390567==    by 0x106DA418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==390567==    by 0x10673D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==390567==    by 0xF36AD38: PetscInitialize (pinit.c:924)
==390567==    by 0xC99D58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==390567==    by 0xC99D5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==390567==    by 0x12EAC6: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==390567==    by 0x129E6F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==390567==    by 0x12C62E: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==390567==    by 0x12C4CF: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==390567==    by 0x12CB65: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==390567==    by 0x1281A0: main (TestRunningPottsBasedSimulationsTutorial.cpp:19)
==390567==  Address 0x1ffeffdf7c is on thread 1's stack
==390567==  in frame #2, created by pmix_ptl_base_make_connection (???:)
==390567== 
{
   <insert_a_suppression_name_here>
   Memcheck:Param
   socketcall.getsockopt(optlen)
   fun:getsockopt_syscall
   fun:getsockopt
   fun:pmix_ptl_base_set_timeout
   fun:pmix_ptl_base_make_connection
   obj:/usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2
   fun:PMIx_Init
   fun:ext3x_client_init
   obj:/usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so
   fun:orte_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
}
==390567== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s)
==390567==    at 0xD0AC79E: getsockopt_syscall (getsockopt.c:29)
==390567==    by 0xD0AC79E: getsockopt (getsockopt.c:94)
==390567==    by 0x192CA157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==390567==    by 0x192D1A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==390567==    by 0x192D8DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==390567==    by 0x191D83C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==390567==    by 0x19151E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so)
==390567==    by 0x18910E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so)
==390567==    by 0x13F154CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==390567==    by 0x106DA418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==390567==    by 0x10673D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==390567==    by 0xF36AD38: PetscInitialize (pinit.c:924)
==390567==    by 0xC99D58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==390567==    by 0xC99D5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==390567==    by 0x12EAC6: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==390567==    by 0x129E6F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==390567==    by 0x12C62E: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==390567==    by 0x12C4CF: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==390567==    by 0x12CB65: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==390567==    by 0x1281A0: main (TestRunningPottsBasedSimulationsTutorial.cpp:19)
==390567==  Address 0x1ffeffdf7c is on thread 1's stack
==390567==  in frame #2, created by pmix_ptl_base_make_connection (???:)
==390567== 
{
   <insert_a_suppression_name_here>
   Memcheck:Param
   socketcall.getsockopt(optlen_out)
   fun:getsockopt_syscall
   fun:getsockopt
   fun:pmix_ptl_base_set_timeout
   fun:pmix_ptl_base_make_connection
   obj:/usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2
   fun:PMIx_Init
   fun:ext3x_client_init
   obj:/usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so
   fun:orte_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
}
==390567== Syscall param setsockopt(optlen) contains uninitialised byte(s)
==390567==    at 0xD0ACC7E: setsockopt_syscall (setsockopt.c:29)
==390567==    by 0xD0ACC7E: setsockopt (setsockopt.c:95)
==390567==    by 0x192D1BA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==390567==    by 0x192D8DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==390567==    by 0x191D83C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==390567==    by 0x19151E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so)
==390567==    by 0x18910E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so)
==390567==    by 0x13F154CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==390567==    by 0x106DA418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==390567==    by 0x10673D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==390567==    by 0xF36AD38: PetscInitialize (pinit.c:924)
==390567==    by 0xC99D58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==390567==    by 0xC99D5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==390567==    by 0x12EAC6: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==390567==    by 0x129E6F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==390567==    by 0x12C62E: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==390567==    by 0x12C4CF: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==390567==    by 0x12CB65: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==390567==    by 0x1281A0: main (TestRunningPottsBasedSimulationsTutorial.cpp:19)
==390567== 
{
   <insert_a_suppression_name_here>
   Memcheck:Param
   setsockopt(optlen)
   fun:setsockopt_syscall
   fun:setsockopt
   fun:pmix_ptl_base_make_connection
   obj:/usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2
   fun:PMIx_Init
   fun:ext3x_client_init
   obj:/usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so
   fun:orte_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
}
==390567== 
==390567== FILE DESCRIPTORS: 9 open (3 std) at exit.
==390567== Open file descriptor 12:
==390567==    at 0xD09A22D: pipe (pipe.c:29)
==390567==    by 0x1891107D: ???
==390567==    by 0x13F154CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==390567==    by 0x106DA418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==390567==    by 0x10673D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==390567==    by 0xF36AD38: PetscInitialize (pinit.c:924)
==390567==    by 0xC99D58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==390567==    by 0xC99D5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==390567==    by 0x12EAC6: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==390567==    by 0x129E6F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==390567==    by 0x12C62E: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==390567==    by 0x12C4CF: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==390567==    by 0x12CB65: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==390567==    by 0x1281A0: main (TestRunningPottsBasedSimulationsTutorial.cpp:19)
==390567== 
==390567== Open file descriptor 8: /dev/shm/open_mpi.0000
==390567==    at 0xD09EBCC: __open_nocancel (open64_nocancel.c:39)
==390567==    by 0xD022C4F: shm_open@@GLIBC_2.34 (shm_open.c:40)
==390567==    by 0xC9D5822: ???
==390567==    by 0xC9D596F: ???
==390567==    by 0x13FBA6DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==390567==    by 0x13FBA938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==390567==    by 0x13F70922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==390567==    by 0x13F152DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==390567==    by 0x106DA418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==390567==    by 0x10673D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==390567==    by 0xF36AD38: PetscInitialize (pinit.c:924)
==390567==    by 0xC99D58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==390567==    by 0xC99D5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==390567==    by 0x12EAC6: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==390567==    by 0x129E6F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==390567==    by 0x12C62E: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==390567==    by 0x12C4CF: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==390567==    by 0x12CB65: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==390567==    by 0x1281A0: main (TestRunningPottsBasedSimulationsTutorial.cpp:19)
==390567== 
==390567== Open file descriptor 116:
==390567==    <inherited from parent>
==390567== 
==390567== Open file descriptor 111:
==390567==    <inherited from parent>
==390567== 
==390567== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestRunningPottsBasedSimulationsTutorial_valgrind.txt
==390567==    <inherited from parent>
==390567== 
==390567== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp
==390567==    <inherited from parent>
==390567== 
==390567== 
==390567== HEAP SUMMARY:
==390567==     in use at exit: 700,702 bytes in 9,374 blocks
==390567==   total heap usage: 40,686,526 allocs, 40,677,152 frees, 3,864,483,994 bytes allocated
==390567== 
==390567== 552 bytes in 1 blocks are definitely lost in loss record 37 of 63
==390567==    at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==390567==    by 0x191DFC13: ???
==390567==    by 0x191E022C: ???
==390567==    by 0x191534B7: ???
==390567==    by 0x1064015A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==390567==    by 0x106DAA97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==390567==    by 0x10673D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==390567==    by 0xF36AD38: PetscInitialize (pinit.c:924)
==390567==    by 0xC99D58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==390567==    by 0xC99D5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==390567==    by 0x12EAC6: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==390567==    by 0x129E6F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==390567==    by 0x12C62E: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==390567==    by 0x12C4CF: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==390567==    by 0x12CB65: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==390567==    by 0x1281A0: main (TestRunningPottsBasedSimulationsTutorial.cpp:19)
==390567== 
{
   <insert_a_suppression_name_here>
   Memcheck:Leak
   match-leak-kinds: definite
   fun:calloc
   obj:*
   obj:*
   obj:*
   fun:ompi_proc_complete_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
}
==390567== 84,445 (136 direct, 84,309 indirect) bytes in 1 blocks are definitely lost in loss record 60 of 63
==390567==    at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==390567==    by 0x1A75274E: ???
==390567==    by 0x1A752E0B: ???
==390567==    by 0x1A755F56: ???
==390567==    by 0x1A74B65D: ???
==390567==    by 0x1A74BFA3: ???
==390567==    by 0x14026F05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2)
==390567==    by 0x14002AE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2)
==390567==    by 0x13FB3CB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==390567==    by 0x13EE0EF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==390567==    by 0x18911F03: ???
==390567==    by 0x13F154CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==390567==    by 0x106DA418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==390567==    by 0x10673D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==390567==    by 0xF36AD38: PetscInitialize (pinit.c:924)
==390567==    by 0xC99D58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==390567==    by 0xC99D5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==390567==    by 0x12EAC6: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==390567==    by 0x129E6F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==390567==    by 0x12C62E: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==390567==    by 0x12C4CF: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==390567==    by 0x12CB65: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==390567==    by 0x1281A0: main (TestRunningPottsBasedSimulationsTutorial.cpp:19)
==390567== 
{
   <insert_a_suppression_name_here>
   Memcheck:Leak
   match-leak-kinds: definite
   fun:calloc
   obj:*
   obj:*
   obj:*
   obj:*
   obj:*
   obj:/usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2
   fun:hwloc_topology_load
   fun:opal_hwloc_base_get_topology
   fun:orte_ess_base_proc_binding
   obj:*
   fun:orte_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
}
==390567== LEAK SUMMARY:
==390567==    definitely lost: 688 bytes in 2 blocks
==390567==    indirectly lost: 1,760 bytes in 16 blocks
==390567==      possibly lost: 0 bytes in 0 blocks
==390567==    still reachable: 1,563 bytes in 7 blocks
==390567==         suppressed: 696,691 bytes in 9,349 blocks
==390567== Reachable blocks (those to which a pointer was found) are not shown.
==390567== To see them, rerun with: --leak-check=full --show-leak-kinds=all
==390567== 
==390567== Use --track-origins=yes to see where uninitialised values come from
==390567== For lists of detected and suppressed errors, rerun with: -s
==390567== ERROR SUMMARY: 5 errors from 5 contexts (suppressed: 28 from 28)