==4080183== Memcheck, a memory error detector
==4080183== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
==4080183== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info
==4080183== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/mesh/test/TestToroidal2dMesh -malloc_debug -malloc_dump -memory_info
==4080183== Parent PID: 4079680
==4080183== 
==4080183== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later.
==4080183== You should replace [...] by a specific index such as [0] or [1] or [2] or similar
==4080183== 
==4080183== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s)
==4080183==    at 0x7F5B79E: getsockopt_syscall (getsockopt.c:29)
==4080183==    by 0x7F5B79E: getsockopt (getsockopt.c:94)
==4080183==    by 0x107C6157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==4080183==    by 0x107CDA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==4080183==    by 0x107D4DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==4080183==    by 0x106D43C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==4080183==    by 0x1064DE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so)
==4080183==    by 0xFE0CE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so)
==4080183==    by 0xB74E4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==4080183==    by 0x776C418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==4080183==    by 0x7705D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==4080183==    by 0x63FCD38: PetscInitialize (pinit.c:924)
==4080183==    by 0x626C58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==4080183==    by 0x626C5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==4080183==    by 0x12CC97: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70)
==4080183==    by 0x1269AD: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==4080183==    by 0x129366: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==4080183==    by 0x129262: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==4080183==    by 0x129875: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==4080183==    by 0x1251B0: main (TestToroidal2dMesh.cpp:18)
==4080183==  Address 0x1ffeffdfbc is on thread 1's stack
==4080183==  in frame #2, created by pmix_ptl_base_make_connection (???:)
==4080183== 
{
   <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
}
==4080183== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s)
==4080183==    at 0x7F5B79E: getsockopt_syscall (getsockopt.c:29)
==4080183==    by 0x7F5B79E: getsockopt (getsockopt.c:94)
==4080183==    by 0x107C6157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==4080183==    by 0x107CDA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==4080183==    by 0x107D4DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==4080183==    by 0x106D43C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==4080183==    by 0x1064DE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so)
==4080183==    by 0xFE0CE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so)
==4080183==    by 0xB74E4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==4080183==    by 0x776C418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==4080183==    by 0x7705D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==4080183==    by 0x63FCD38: PetscInitialize (pinit.c:924)
==4080183==    by 0x626C58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==4080183==    by 0x626C5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==4080183==    by 0x12CC97: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70)
==4080183==    by 0x1269AD: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==4080183==    by 0x129366: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==4080183==    by 0x129262: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==4080183==    by 0x129875: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==4080183==    by 0x1251B0: main (TestToroidal2dMesh.cpp:18)
==4080183==  Address 0x1ffeffdfbc is on thread 1's stack
==4080183==  in frame #2, created by pmix_ptl_base_make_connection (???:)
==4080183== 
{
   <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
}
==4080183== Syscall param setsockopt(optlen) contains uninitialised byte(s)
==4080183==    at 0x7F5BC7E: setsockopt_syscall (setsockopt.c:29)
==4080183==    by 0x7F5BC7E: setsockopt (setsockopt.c:95)
==4080183==    by 0x107CDBA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==4080183==    by 0x107D4DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==4080183==    by 0x106D43C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==4080183==    by 0x1064DE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so)
==4080183==    by 0xFE0CE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so)
==4080183==    by 0xB74E4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==4080183==    by 0x776C418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==4080183==    by 0x7705D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==4080183==    by 0x63FCD38: PetscInitialize (pinit.c:924)
==4080183==    by 0x626C58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==4080183==    by 0x626C5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==4080183==    by 0x12CC97: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70)
==4080183==    by 0x1269AD: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==4080183==    by 0x129366: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==4080183==    by 0x129262: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==4080183==    by 0x129875: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==4080183==    by 0x1251B0: main (TestToroidal2dMesh.cpp:18)
==4080183== 
{
   <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
}
==4080183== 
==4080183== FILE DESCRIPTORS: 9 open (3 std) at exit.
==4080183== Open file descriptor 12:
==4080183==    at 0x7F4922D: pipe (pipe.c:29)
==4080183==    by 0xFE0D07D: ???
==4080183==    by 0xB74E4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==4080183==    by 0x776C418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==4080183==    by 0x7705D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==4080183==    by 0x63FCD38: PetscInitialize (pinit.c:924)
==4080183==    by 0x626C58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==4080183==    by 0x626C5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==4080183==    by 0x12CC97: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70)
==4080183==    by 0x1269AD: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==4080183==    by 0x129366: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==4080183==    by 0x129262: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==4080183==    by 0x129875: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==4080183==    by 0x1251B0: main (TestToroidal2dMesh.cpp:18)
==4080183== 
==4080183== Open file descriptor 8: /dev/shm/open_mpi.0000
==4080183==    at 0x7F4DBCC: __open_nocancel (open64_nocancel.c:39)
==4080183==    by 0x7ED1C4F: shm_open@@GLIBC_2.34 (shm_open.c:40)
==4080183==    by 0x62A4822: ???
==4080183==    by 0x62A496F: ???
==4080183==    by 0xB7F36DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==4080183==    by 0xB7F3938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==4080183==    by 0xB7A9922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==4080183==    by 0xB74E2DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==4080183==    by 0x776C418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==4080183==    by 0x7705D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==4080183==    by 0x63FCD38: PetscInitialize (pinit.c:924)
==4080183==    by 0x626C58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==4080183==    by 0x626C5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==4080183==    by 0x12CC97: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70)
==4080183==    by 0x1269AD: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==4080183==    by 0x129366: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==4080183==    by 0x129262: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==4080183==    by 0x129875: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==4080183==    by 0x1251B0: main (TestToroidal2dMesh.cpp:18)
==4080183== 
==4080183== Open file descriptor 115:
==4080183==    <inherited from parent>
==4080183== 
==4080183== Open file descriptor 110:
==4080183==    <inherited from parent>
==4080183== 
==4080183== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestToroidal2dMesh_valgrind.txt
==4080183==    <inherited from parent>
==4080183== 
==4080183== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp
==4080183==    <inherited from parent>
==4080183== 
==4080183== 
==4080183== HEAP SUMMARY:
==4080183==     in use at exit: 700,647 bytes in 9,377 blocks
==4080183==   total heap usage: 166,351 allocs, 156,974 frees, 1,367,921,522 bytes allocated
==4080183== 
==4080183== 552 bytes in 1 blocks are definitely lost in loss record 39 of 65
==4080183==    at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==4080183==    by 0x106DBC13: ???
==4080183==    by 0x106DC22C: ???
==4080183==    by 0x1064F4B7: ???
==4080183==    by 0x76D215A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==4080183==    by 0x776CA97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==4080183==    by 0x7705D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==4080183==    by 0x63FCD38: PetscInitialize (pinit.c:924)
==4080183==    by 0x626C58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==4080183==    by 0x626C5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==4080183==    by 0x12CC97: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70)
==4080183==    by 0x1269AD: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==4080183==    by 0x129366: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==4080183==    by 0x129262: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==4080183==    by 0x129875: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==4080183==    by 0x1251B0: main (TestToroidal2dMesh.cpp:18)
==4080183== 
{
   <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
}
==4080183== 84,459 (136 direct, 84,323 indirect) bytes in 1 blocks are definitely lost in loss record 62 of 65
==4080183==    at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==4080183==    by 0x1184E74E: ???
==4080183==    by 0x1184EE0B: ???
==4080183==    by 0x11851F56: ???
==4080183==    by 0x1184765D: ???
==4080183==    by 0x11847FA3: ???
==4080183==    by 0xB85FF05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2)
==4080183==    by 0xB83BAE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2)
==4080183==    by 0xB7ECCB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==4080183==    by 0xB719EF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==4080183==    by 0xFE0DF03: ???
==4080183==    by 0xB74E4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==4080183==    by 0x776C418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==4080183==    by 0x7705D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==4080183==    by 0x63FCD38: PetscInitialize (pinit.c:924)
==4080183==    by 0x626C58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==4080183==    by 0x626C5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==4080183==    by 0x12CC97: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70)
==4080183==    by 0x1269AD: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==4080183==    by 0x129366: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==4080183==    by 0x129262: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==4080183==    by 0x129875: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==4080183==    by 0x1251B0: main (TestToroidal2dMesh.cpp:18)
==4080183== 
{
   <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
}
==4080183== LEAK SUMMARY:
==4080183==    definitely lost: 688 bytes in 2 blocks
==4080183==    indirectly lost: 1,760 bytes in 16 blocks
==4080183==      possibly lost: 0 bytes in 0 blocks
==4080183==    still reachable: 1,531 bytes in 6 blocks
==4080183==         suppressed: 696,668 bytes in 9,353 blocks
==4080183== Reachable blocks (those to which a pointer was found) are not shown.
==4080183== To see them, rerun with: --leak-check=full --show-leak-kinds=all
==4080183== 
==4080183== Use --track-origins=yes to see where uninitialised values come from
==4080183== For lists of detected and suppressed errors, rerun with: -s
==4080183== ERROR SUMMARY: 5 errors from 5 contexts (suppressed: 32 from 32)