==434627== Memcheck, a memory error detector
==434627== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
==434627== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info
==434627== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/mesh/test/TestVertexMeshReader -malloc_debug -malloc_dump -memory_info
==434627== Parent PID: 433953
==434627== 
==434627== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later.
==434627== You should replace [...] by a specific index such as [0] or [1] or [2] or similar
==434627== 
==434627== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s)
==434627==    at 0x663779E: getsockopt_syscall (getsockopt.c:29)
==434627==    by 0x663779E: getsockopt (getsockopt.c:94)
==434627==    by 0x107C7157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==434627==    by 0x107CEA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==434627==    by 0x107D5DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==434627==    by 0x106D53C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==434627==    by 0x1064EE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so)
==434627==    by 0xFE0DE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so)
==434627==    by 0xB7464CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==434627==    by 0x7C80418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==434627==    by 0x7C19D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==434627==    by 0x690ED38: PetscInitialize (pinit.c:924)
==434627==    by 0x626D58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==434627==    by 0x626D5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==434627==    by 0x11F542: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==434627==    by 0x11A4E5: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==434627==    by 0x11D584: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==434627==    by 0x11D424: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==434627==    by 0x11DABB: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==434627==    by 0x118815: main (TestVertexMeshReader.cpp:19)
==434627==  Address 0x1ffeffdfac is on thread 1's stack
==434627==  in frame #2, created by pmix_ptl_base_make_connection (???:)
==434627== 
{
   <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
}
==434627== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s)
==434627==    at 0x663779E: getsockopt_syscall (getsockopt.c:29)
==434627==    by 0x663779E: getsockopt (getsockopt.c:94)
==434627==    by 0x107C7157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==434627==    by 0x107CEA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==434627==    by 0x107D5DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==434627==    by 0x106D53C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==434627==    by 0x1064EE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so)
==434627==    by 0xFE0DE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so)
==434627==    by 0xB7464CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==434627==    by 0x7C80418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==434627==    by 0x7C19D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==434627==    by 0x690ED38: PetscInitialize (pinit.c:924)
==434627==    by 0x626D58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==434627==    by 0x626D5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==434627==    by 0x11F542: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==434627==    by 0x11A4E5: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==434627==    by 0x11D584: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==434627==    by 0x11D424: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==434627==    by 0x11DABB: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==434627==    by 0x118815: main (TestVertexMeshReader.cpp:19)
==434627==  Address 0x1ffeffdfac is on thread 1's stack
==434627==  in frame #2, created by pmix_ptl_base_make_connection (???:)
==434627== 
{
   <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
}
==434627== Syscall param setsockopt(optlen) contains uninitialised byte(s)
==434627==    at 0x6637C7E: setsockopt_syscall (setsockopt.c:29)
==434627==    by 0x6637C7E: setsockopt (setsockopt.c:95)
==434627==    by 0x107CEBA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==434627==    by 0x107D5DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==434627==    by 0x106D53C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==434627==    by 0x1064EE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so)
==434627==    by 0xFE0DE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so)
==434627==    by 0xB7464CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==434627==    by 0x7C80418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==434627==    by 0x7C19D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==434627==    by 0x690ED38: PetscInitialize (pinit.c:924)
==434627==    by 0x626D58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==434627==    by 0x626D5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==434627==    by 0x11F542: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==434627==    by 0x11A4E5: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==434627==    by 0x11D584: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==434627==    by 0x11D424: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==434627==    by 0x11DABB: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==434627==    by 0x118815: main (TestVertexMeshReader.cpp:19)
==434627== 
{
   <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
}
==434627== 
==434627== FILE DESCRIPTORS: 9 open (3 std) at exit.
==434627== Open file descriptor 12:
==434627==    at 0x662522D: pipe (pipe.c:29)
==434627==    by 0xFE0E07D: ???
==434627==    by 0xB7464CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==434627==    by 0x7C80418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==434627==    by 0x7C19D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==434627==    by 0x690ED38: PetscInitialize (pinit.c:924)
==434627==    by 0x626D58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==434627==    by 0x626D5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==434627==    by 0x11F542: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==434627==    by 0x11A4E5: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==434627==    by 0x11D584: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==434627==    by 0x11D424: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==434627==    by 0x11DABB: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==434627==    by 0x118815: main (TestVertexMeshReader.cpp:19)
==434627== 
==434627== Open file descriptor 8: /dev/shm/open_mpi.0000
==434627==    at 0x6629BCC: __open_nocancel (open64_nocancel.c:39)
==434627==    by 0x65ADC4F: shm_open@@GLIBC_2.34 (shm_open.c:40)
==434627==    by 0x62A5822: ???
==434627==    by 0x62A596F: ???
==434627==    by 0xB7EB6DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==434627==    by 0xB7EB938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==434627==    by 0xB7A1922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==434627==    by 0xB7462DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==434627==    by 0x7C80418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==434627==    by 0x7C19D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==434627==    by 0x690ED38: PetscInitialize (pinit.c:924)
==434627==    by 0x626D58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==434627==    by 0x626D5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==434627==    by 0x11F542: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==434627==    by 0x11A4E5: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==434627==    by 0x11D584: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==434627==    by 0x11D424: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==434627==    by 0x11DABB: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==434627==    by 0x118815: main (TestVertexMeshReader.cpp:19)
==434627== 
==434627== Open file descriptor 116:
==434627==    <inherited from parent>
==434627== 
==434627== Open file descriptor 111:
==434627==    <inherited from parent>
==434627== 
==434627== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestVertexMeshReader_valgrind.txt
==434627==    <inherited from parent>
==434627== 
==434627== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp
==434627==    <inherited from parent>
==434627== 
==434627== 
==434627== HEAP SUMMARY:
==434627==     in use at exit: 700,642 bytes in 9,377 blocks
==434627==   total heap usage: 49,943 allocs, 40,566 frees, 1,353,786,292 bytes allocated
==434627== 
==434627== 552 bytes in 1 blocks are definitely lost in loss record 40 of 63
==434627==    at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==434627==    by 0x106DCC13: ???
==434627==    by 0x106DD22C: ???
==434627==    by 0x106504B7: ???
==434627==    by 0x7BE615A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==434627==    by 0x7C80A97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==434627==    by 0x7C19D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==434627==    by 0x690ED38: PetscInitialize (pinit.c:924)
==434627==    by 0x626D58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==434627==    by 0x626D5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==434627==    by 0x11F542: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==434627==    by 0x11A4E5: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==434627==    by 0x11D584: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==434627==    by 0x11D424: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==434627==    by 0x11DABB: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==434627==    by 0x118815: main (TestVertexMeshReader.cpp:19)
==434627== 
{
   <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
}
==434627== 685,257 (136 direct, 685,121 indirect) bytes in 1 blocks are definitely lost in loss record 63 of 63
==434627==    at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==434627==    by 0x1184F74E: ???
==434627==    by 0x1184FE0B: ???
==434627==    by 0x11852F56: ???
==434627==    by 0x1184865D: ???
==434627==    by 0x11848FA3: ???
==434627==    by 0xB857F05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2)
==434627==    by 0xB833AE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2)
==434627==    by 0xB7E4CB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==434627==    by 0xB711EF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==434627==    by 0xFE0EF03: ???
==434627==    by 0xB7464CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==434627==    by 0x7C80418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==434627==    by 0x7C19D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==434627==    by 0x690ED38: PetscInitialize (pinit.c:924)
==434627==    by 0x626D58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==434627==    by 0x626D5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==434627==    by 0x11F542: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==434627==    by 0x11A4E5: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==434627==    by 0x11D584: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==434627==    by 0x11D424: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==434627==    by 0x11DABB: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==434627==    by 0x118815: main (TestVertexMeshReader.cpp:19)
==434627== 
{
   <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
}
==434627== LEAK SUMMARY:
==434627==    definitely lost: 688 bytes in 2 blocks
==434627==    indirectly lost: 1,760 bytes in 16 blocks
==434627==      possibly lost: 0 bytes in 0 blocks
==434627==    still reachable: 1,531 bytes in 6 blocks
==434627==         suppressed: 696,663 bytes in 9,353 blocks
==434627== Reachable blocks (those to which a pointer was found) are not shown.
==434627== To see them, rerun with: --leak-check=full --show-leak-kinds=all
==434627== 
==434627== Use --track-origins=yes to see where uninitialised values come from
==434627== For lists of detected and suppressed errors, rerun with: -s
==434627== ERROR SUMMARY: 5 errors from 5 contexts (suppressed: 30 from 30)