==605162== Memcheck, a memory error detector
==605162== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
==605162== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info
==605162== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/heart/test/TestHdf5ToVisualizerConverters -malloc_debug -malloc_dump -memory_info
==605162== Parent PID: 582436
==605162== 
==605162== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later.
==605162== You should replace [...] by a specific index such as [0] or [1] or [2] or similar
==605162== 
==605162== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s)
==605162==    at 0xA61979E: getsockopt_syscall (getsockopt.c:29)
==605162==    by 0xA61979E: getsockopt (getsockopt.c:94)
==605162==    by 0x14AA3157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==605162==    by 0x14AAAA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==605162==    by 0x14AB1DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==605162==    by 0x149B13C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==605162==    by 0x1492AE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so)
==605162==    by 0x140E9E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so)
==605162==    by 0xF8EF4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==605162==    by 0xBD18418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==605162==    by 0xBCB1D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==605162==    by 0xA9A8D38: PetscInitialize (pinit.c:924)
==605162==    by 0x9EF058B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==605162==    by 0x9EF05D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==605162==    by 0x12ED48: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==605162==    by 0x126C8F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==605162==    by 0x1297F8: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==605162==    by 0x129698: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==605162==    by 0x129D2F: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==605162==    by 0x124FC0: main (TestHdf5ToVisualizerConverters.cpp:19)
==605162==  Address 0x1ffeffdf9c is on thread 1's stack
==605162==  in frame #2, created by pmix_ptl_base_make_connection (???:)
==605162== 
{
   <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
}
==605162== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s)
==605162==    at 0xA61979E: getsockopt_syscall (getsockopt.c:29)
==605162==    by 0xA61979E: getsockopt (getsockopt.c:94)
==605162==    by 0x14AA3157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==605162==    by 0x14AAAA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==605162==    by 0x14AB1DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==605162==    by 0x149B13C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==605162==    by 0x1492AE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so)
==605162==    by 0x140E9E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so)
==605162==    by 0xF8EF4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==605162==    by 0xBD18418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==605162==    by 0xBCB1D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==605162==    by 0xA9A8D38: PetscInitialize (pinit.c:924)
==605162==    by 0x9EF058B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==605162==    by 0x9EF05D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==605162==    by 0x12ED48: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==605162==    by 0x126C8F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==605162==    by 0x1297F8: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==605162==    by 0x129698: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==605162==    by 0x129D2F: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==605162==    by 0x124FC0: main (TestHdf5ToVisualizerConverters.cpp:19)
==605162==  Address 0x1ffeffdf9c is on thread 1's stack
==605162==  in frame #2, created by pmix_ptl_base_make_connection (???:)
==605162== 
{
   <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
}
==605162== Syscall param setsockopt(optlen) contains uninitialised byte(s)
==605162==    at 0xA619C7E: setsockopt_syscall (setsockopt.c:29)
==605162==    by 0xA619C7E: setsockopt (setsockopt.c:95)
==605162==    by 0x14AAABA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==605162==    by 0x14AB1DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==605162==    by 0x149B13C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==605162==    by 0x1492AE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so)
==605162==    by 0x140E9E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so)
==605162==    by 0xF8EF4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==605162==    by 0xBD18418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==605162==    by 0xBCB1D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==605162==    by 0xA9A8D38: PetscInitialize (pinit.c:924)
==605162==    by 0x9EF058B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==605162==    by 0x9EF05D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==605162==    by 0x12ED48: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==605162==    by 0x126C8F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==605162==    by 0x1297F8: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==605162==    by 0x129698: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==605162==    by 0x129D2F: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==605162==    by 0x124FC0: main (TestHdf5ToVisualizerConverters.cpp:19)
==605162== 
{
   <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
}
==605162== 
==605162== FILE DESCRIPTORS: 9 open (3 std) at exit.
==605162== Open file descriptor 12:
==605162==    at 0xA60722D: pipe (pipe.c:29)
==605162==    by 0x140EA07D: ???
==605162==    by 0xF8EF4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==605162==    by 0xBD18418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==605162==    by 0xBCB1D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==605162==    by 0xA9A8D38: PetscInitialize (pinit.c:924)
==605162==    by 0x9EF058B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==605162==    by 0x9EF05D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==605162==    by 0x12ED48: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==605162==    by 0x126C8F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==605162==    by 0x1297F8: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==605162==    by 0x129698: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==605162==    by 0x129D2F: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==605162==    by 0x124FC0: main (TestHdf5ToVisualizerConverters.cpp:19)
==605162== 
==605162== Open file descriptor 8: /dev/shm/open_mpi.0000
==605162==    at 0xA60BBCC: __open_nocancel (open64_nocancel.c:39)
==605162==    by 0xA58FC4F: shm_open@@GLIBC_2.34 (shm_open.c:40)
==605162==    by 0x9F28822: ???
==605162==    by 0x9F2896F: ???
==605162==    by 0xF9946DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==605162==    by 0xF994938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==605162==    by 0xF94A922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==605162==    by 0xF8EF2DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==605162==    by 0xBD18418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==605162==    by 0xBCB1D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==605162==    by 0xA9A8D38: PetscInitialize (pinit.c:924)
==605162==    by 0x9EF058B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==605162==    by 0x9EF05D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==605162==    by 0x12ED48: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==605162==    by 0x126C8F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==605162==    by 0x1297F8: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==605162==    by 0x129698: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==605162==    by 0x129D2F: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==605162==    by 0x124FC0: main (TestHdf5ToVisualizerConverters.cpp:19)
==605162== 
==605162== Open file descriptor 116:
==605162==    <inherited from parent>
==605162== 
==605162== Open file descriptor 111:
==605162==    <inherited from parent>
==605162== 
==605162== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestHdf5ToVisualizerConverters_valgrind.txt
==605162==    <inherited from parent>
==605162== 
==605162== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp
==605162==    <inherited from parent>
==605162== 
==605162== 
==605162== HEAP SUMMARY:
==605162==     in use at exit: 700,754 bytes in 9,377 blocks
==605162==   total heap usage: 122,363 allocs, 112,986 frees, 1,381,276,476 bytes allocated
==605162== 
==605162== 552 bytes in 1 blocks are definitely lost in loss record 39 of 65
==605162==    at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==605162==    by 0x149B8C13: ???
==605162==    by 0x149B922C: ???
==605162==    by 0x1492C4B7: ???
==605162==    by 0xBC7E15A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==605162==    by 0xBD18A97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==605162==    by 0xBCB1D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==605162==    by 0xA9A8D38: PetscInitialize (pinit.c:924)
==605162==    by 0x9EF058B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==605162==    by 0x9EF05D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==605162==    by 0x12ED48: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==605162==    by 0x126C8F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==605162==    by 0x1297F8: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==605162==    by 0x129698: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==605162==    by 0x129D2F: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==605162==    by 0x124FC0: main (TestHdf5ToVisualizerConverters.cpp:19)
==605162== 
{
   <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
}
==605162== 84,459 (136 direct, 84,323 indirect) bytes in 1 blocks are definitely lost in loss record 62 of 65
==605162==    at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==605162==    by 0x15B2B74E: ???
==605162==    by 0x15B2BE0B: ???
==605162==    by 0x15B2EF56: ???
==605162==    by 0x15B2465D: ???
==605162==    by 0x15B24FA3: ???
==605162==    by 0xFA00F05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2)
==605162==    by 0xF9DCAE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2)
==605162==    by 0xF98DCB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==605162==    by 0xF8BAEF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==605162==    by 0x140EAF03: ???
==605162==    by 0xF8EF4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==605162==    by 0xBD18418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==605162==    by 0xBCB1D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==605162==    by 0xA9A8D38: PetscInitialize (pinit.c:924)
==605162==    by 0x9EF058B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==605162==    by 0x9EF05D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==605162==    by 0x12ED48: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==605162==    by 0x126C8F: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==605162==    by 0x1297F8: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==605162==    by 0x129698: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==605162==    by 0x129D2F: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==605162==    by 0x124FC0: main (TestHdf5ToVisualizerConverters.cpp:19)
==605162== 
{
   <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
}
==605162== LEAK SUMMARY:
==605162==    definitely lost: 688 bytes in 2 blocks
==605162==    indirectly lost: 1,760 bytes in 16 blocks
==605162==      possibly lost: 0 bytes in 0 blocks
==605162==    still reachable: 1,531 bytes in 6 blocks
==605162==         suppressed: 696,775 bytes in 9,353 blocks
==605162== Reachable blocks (those to which a pointer was found) are not shown.
==605162== To see them, rerun with: --leak-check=full --show-leak-kinds=all
==605162== 
==605162== Use --track-origins=yes to see where uninitialised values come from
==605162== For lists of detected and suppressed errors, rerun with: -s
==605162== ERROR SUMMARY: 5 errors from 5 contexts (suppressed: 32 from 32)