==395919== Memcheck, a memory error detector
==395919== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
==395919== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info
==395919== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/heart/test/TestHeartGeometryInformation -malloc_debug -malloc_dump -memory_info
==395919== Parent PID: 368214
==395919== 
==395919== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later.
==395919== You should replace [...] by a specific index such as [0] or [1] or [2] or similar
==395919== 
==395919== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s)
==395919==    at 0xA26679E: getsockopt_syscall (getsockopt.c:29)
==395919==    by 0xA26679E: getsockopt (getsockopt.c:94)
==395919==    by 0x14AA5157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==395919==    by 0x14AACA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==395919==    by 0x14AB3DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==395919==    by 0x149B33C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==395919==    by 0x1492CE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so)
==395919==    by 0x140EBE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so)
==395919==    by 0xF8ED4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==395919==    by 0xB967418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==395919==    by 0xB900D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==395919==    by 0xA5F7D38: PetscInitialize (pinit.c:924)
==395919==    by 0x9B3F58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==395919==    by 0x9B3F5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==395919==    by 0x127E74: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==395919==    by 0x121BEF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==395919==    by 0x124830: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==395919==    by 0x1246D0: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==395919==    by 0x124D67: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==395919==    by 0x11FF20: main (TestHeartGeometryInformation.cpp:19)
==395919==  Address 0x1ffeffdf9c is on thread 1's stack
==395919==  in frame #2, created by pmix_ptl_base_make_connection (???:)
==395919== 
{
   <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
}
==395919== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s)
==395919==    at 0xA26679E: getsockopt_syscall (getsockopt.c:29)
==395919==    by 0xA26679E: getsockopt (getsockopt.c:94)
==395919==    by 0x14AA5157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==395919==    by 0x14AACA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==395919==    by 0x14AB3DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==395919==    by 0x149B33C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==395919==    by 0x1492CE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so)
==395919==    by 0x140EBE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so)
==395919==    by 0xF8ED4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==395919==    by 0xB967418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==395919==    by 0xB900D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==395919==    by 0xA5F7D38: PetscInitialize (pinit.c:924)
==395919==    by 0x9B3F58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==395919==    by 0x9B3F5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==395919==    by 0x127E74: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==395919==    by 0x121BEF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==395919==    by 0x124830: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==395919==    by 0x1246D0: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==395919==    by 0x124D67: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==395919==    by 0x11FF20: main (TestHeartGeometryInformation.cpp:19)
==395919==  Address 0x1ffeffdf9c is on thread 1's stack
==395919==  in frame #2, created by pmix_ptl_base_make_connection (???:)
==395919== 
{
   <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
}
==395919== Syscall param setsockopt(optlen) contains uninitialised byte(s)
==395919==    at 0xA266C7E: setsockopt_syscall (setsockopt.c:29)
==395919==    by 0xA266C7E: setsockopt (setsockopt.c:95)
==395919==    by 0x14AACBA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==395919==    by 0x14AB3DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==395919==    by 0x149B33C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==395919==    by 0x1492CE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so)
==395919==    by 0x140EBE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so)
==395919==    by 0xF8ED4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==395919==    by 0xB967418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==395919==    by 0xB900D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==395919==    by 0xA5F7D38: PetscInitialize (pinit.c:924)
==395919==    by 0x9B3F58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==395919==    by 0x9B3F5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==395919==    by 0x127E74: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==395919==    by 0x121BEF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==395919==    by 0x124830: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==395919==    by 0x1246D0: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==395919==    by 0x124D67: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==395919==    by 0x11FF20: main (TestHeartGeometryInformation.cpp:19)
==395919== 
{
   <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
}
==395919== 
==395919== FILE DESCRIPTORS: 9 open (3 std) at exit.
==395919== Open file descriptor 12:
==395919==    at 0xA25422D: pipe (pipe.c:29)
==395919==    by 0x140EC07D: ???
==395919==    by 0xF8ED4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==395919==    by 0xB967418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==395919==    by 0xB900D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==395919==    by 0xA5F7D38: PetscInitialize (pinit.c:924)
==395919==    by 0x9B3F58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==395919==    by 0x9B3F5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==395919==    by 0x127E74: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==395919==    by 0x121BEF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==395919==    by 0x124830: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==395919==    by 0x1246D0: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==395919==    by 0x124D67: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==395919==    by 0x11FF20: main (TestHeartGeometryInformation.cpp:19)
==395919== 
==395919== Open file descriptor 8: /dev/shm/open_mpi.0000
==395919==    at 0xA258BCC: __open_nocancel (open64_nocancel.c:39)
==395919==    by 0xA1DCC4F: shm_open@@GLIBC_2.34 (shm_open.c:40)
==395919==    by 0x9B77822: ???
==395919==    by 0x9B7796F: ???
==395919==    by 0xF9926DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==395919==    by 0xF992938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==395919==    by 0xF948922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==395919==    by 0xF8ED2DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==395919==    by 0xB967418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==395919==    by 0xB900D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==395919==    by 0xA5F7D38: PetscInitialize (pinit.c:924)
==395919==    by 0x9B3F58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==395919==    by 0x9B3F5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==395919==    by 0x127E74: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==395919==    by 0x121BEF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==395919==    by 0x124830: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==395919==    by 0x1246D0: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==395919==    by 0x124D67: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==395919==    by 0x11FF20: main (TestHeartGeometryInformation.cpp:19)
==395919== 
==395919== Open file descriptor 116:
==395919==    <inherited from parent>
==395919== 
==395919== Open file descriptor 111:
==395919==    <inherited from parent>
==395919== 
==395919== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestHeartGeometryInformation_valgrind.txt
==395919==    <inherited from parent>
==395919== 
==395919== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp
==395919==    <inherited from parent>
==395919== 
==395919== 
==395919== HEAP SUMMARY:
==395919==     in use at exit: 700,686 bytes in 9,373 blocks
==395919==   total heap usage: 2,625,023 allocs, 2,615,650 frees, 1,668,061,950 bytes allocated
==395919== 
==395919== 552 bytes in 1 blocks are definitely lost in loss record 37 of 60
==395919==    at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==395919==    by 0x149BAC13: ???
==395919==    by 0x149BB22C: ???
==395919==    by 0x1492E4B7: ???
==395919==    by 0xB8CD15A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==395919==    by 0xB967A97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==395919==    by 0xB900D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==395919==    by 0xA5F7D38: PetscInitialize (pinit.c:924)
==395919==    by 0x9B3F58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==395919==    by 0x9B3F5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==395919==    by 0x127E74: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==395919==    by 0x121BEF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==395919==    by 0x124830: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==395919==    by 0x1246D0: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==395919==    by 0x124D67: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==395919==    by 0x11FF20: main (TestHeartGeometryInformation.cpp:19)
==395919== 
{
   <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
}
==395919== 685,143 (136 direct, 685,007 indirect) bytes in 1 blocks are definitely lost in loss record 60 of 60
==395919==    at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==395919==    by 0x15B2D74E: ???
==395919==    by 0x15B2DE0B: ???
==395919==    by 0x15B30F56: ???
==395919==    by 0x15B2665D: ???
==395919==    by 0x15B26FA3: ???
==395919==    by 0xFA00F05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2)
==395919==    by 0xF9DCAE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2)
==395919==    by 0xF98BCB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==395919==    by 0xF8B8EF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==395919==    by 0x140ECF03: ???
==395919==    by 0xF8ED4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==395919==    by 0xB967418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==395919==    by 0xB900D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==395919==    by 0xA5F7D38: PetscInitialize (pinit.c:924)
==395919==    by 0x9B3F58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==395919==    by 0x9B3F5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==395919==    by 0x127E74: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==395919==    by 0x121BEF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==395919==    by 0x124830: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==395919==    by 0x1246D0: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==395919==    by 0x124D67: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==395919==    by 0x11FF20: main (TestHeartGeometryInformation.cpp:19)
==395919== 
{
   <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
}
==395919== LEAK SUMMARY:
==395919==    definitely lost: 688 bytes in 2 blocks
==395919==    indirectly lost: 1,760 bytes in 16 blocks
==395919==      possibly lost: 0 bytes in 0 blocks
==395919==    still reachable: 1,531 bytes in 6 blocks
==395919==         suppressed: 696,707 bytes in 9,349 blocks
==395919== Reachable blocks (those to which a pointer was found) are not shown.
==395919== To see them, rerun with: --leak-check=full --show-leak-kinds=all
==395919== 
==395919== Use --track-origins=yes to see where uninitialised values come from
==395919== For lists of detected and suppressed errors, rerun with: -s
==395919== ERROR SUMMARY: 5 errors from 5 contexts (suppressed: 27 from 27)