==447338== Memcheck, a memory error detector
==447338== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
==447338== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info
==447338== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/cell_based/test/TestRunningDeltaNotchSimulationsTutorial -malloc_debug -malloc_dump -memory_info
==447338== Parent PID: 433953
==447338== 
==447338== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later.
==447338== You should replace [...] by a specific index such as [0] or [1] or [2] or similar
==447338== 
==447338== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s)
==447338==    at 0xEA0D79E: getsockopt_syscall (getsockopt.c:29)
==447338==    by 0xEA0D79E: getsockopt (getsockopt.c:94)
==447338==    by 0x192CE157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==447338==    by 0x192D5A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==447338==    by 0x192DCDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==447338==    by 0x191DC3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==447338==    by 0x19155E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so)
==447338==    by 0x18914E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so)
==447338==    by 0x13F154CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==447338==    by 0x106DB418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==447338==    by 0x10674D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==447338==    by 0xF36BD38: PetscInitialize (pinit.c:924)
==447338==    by 0xE30058B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==447338==    by 0xE3005D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==447338==    by 0x12E496: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==447338==    by 0x12863D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==447338==    by 0x12AAF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==447338==    by 0x12A9F4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==447338==    by 0x12B007: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==447338==    by 0x126E40: main (TestRunningDeltaNotchSimulationsTutorial.cpp:18)
==447338==  Address 0x1ffeffdf8c is on thread 1's stack
==447338==  in frame #2, created by pmix_ptl_base_make_connection (???:)
==447338== 
{
   <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
}
==447338== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s)
==447338==    at 0xEA0D79E: getsockopt_syscall (getsockopt.c:29)
==447338==    by 0xEA0D79E: getsockopt (getsockopt.c:94)
==447338==    by 0x192CE157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==447338==    by 0x192D5A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==447338==    by 0x192DCDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==447338==    by 0x191DC3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==447338==    by 0x19155E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so)
==447338==    by 0x18914E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so)
==447338==    by 0x13F154CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==447338==    by 0x106DB418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==447338==    by 0x10674D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==447338==    by 0xF36BD38: PetscInitialize (pinit.c:924)
==447338==    by 0xE30058B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==447338==    by 0xE3005D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==447338==    by 0x12E496: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==447338==    by 0x12863D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==447338==    by 0x12AAF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==447338==    by 0x12A9F4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==447338==    by 0x12B007: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==447338==    by 0x126E40: main (TestRunningDeltaNotchSimulationsTutorial.cpp:18)
==447338==  Address 0x1ffeffdf8c is on thread 1's stack
==447338==  in frame #2, created by pmix_ptl_base_make_connection (???:)
==447338== 
{
   <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
}
==447338== Syscall param setsockopt(optlen) contains uninitialised byte(s)
==447338==    at 0xEA0DC7E: setsockopt_syscall (setsockopt.c:29)
==447338==    by 0xEA0DC7E: setsockopt (setsockopt.c:95)
==447338==    by 0x192D5BA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==447338==    by 0x192DCDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==447338==    by 0x191DC3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==447338==    by 0x19155E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so)
==447338==    by 0x18914E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so)
==447338==    by 0x13F154CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==447338==    by 0x106DB418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==447338==    by 0x10674D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==447338==    by 0xF36BD38: PetscInitialize (pinit.c:924)
==447338==    by 0xE30058B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==447338==    by 0xE3005D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==447338==    by 0x12E496: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==447338==    by 0x12863D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==447338==    by 0x12AAF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==447338==    by 0x12A9F4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==447338==    by 0x12B007: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==447338==    by 0x126E40: main (TestRunningDeltaNotchSimulationsTutorial.cpp:18)
==447338== 
{
   <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
}
==447338== 
==447338== FILE DESCRIPTORS: 9 open (3 std) at exit.
==447338== Open file descriptor 12:
==447338==    at 0xE9FB22D: pipe (pipe.c:29)
==447338==    by 0x1891507D: ???
==447338==    by 0x13F154CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==447338==    by 0x106DB418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==447338==    by 0x10674D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==447338==    by 0xF36BD38: PetscInitialize (pinit.c:924)
==447338==    by 0xE30058B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==447338==    by 0xE3005D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==447338==    by 0x12E496: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==447338==    by 0x12863D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==447338==    by 0x12AAF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==447338==    by 0x12A9F4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==447338==    by 0x12B007: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==447338==    by 0x126E40: main (TestRunningDeltaNotchSimulationsTutorial.cpp:18)
==447338== 
==447338== Open file descriptor 8: /dev/shm/open_mpi.0000
==447338==    at 0xE9FFBCC: __open_nocancel (open64_nocancel.c:39)
==447338==    by 0xE983C4F: shm_open@@GLIBC_2.34 (shm_open.c:40)
==447338==    by 0xE338822: ???
==447338==    by 0xE33896F: ???
==447338==    by 0x13FBA6DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==447338==    by 0x13FBA938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==447338==    by 0x13F70922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==447338==    by 0x13F152DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==447338==    by 0x106DB418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==447338==    by 0x10674D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==447338==    by 0xF36BD38: PetscInitialize (pinit.c:924)
==447338==    by 0xE30058B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==447338==    by 0xE3005D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==447338==    by 0x12E496: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==447338==    by 0x12863D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==447338==    by 0x12AAF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==447338==    by 0x12A9F4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==447338==    by 0x12B007: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==447338==    by 0x126E40: main (TestRunningDeltaNotchSimulationsTutorial.cpp:18)
==447338== 
==447338== Open file descriptor 116:
==447338==    <inherited from parent>
==447338== 
==447338== Open file descriptor 111:
==447338==    <inherited from parent>
==447338== 
==447338== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestRunningDeltaNotchSimulationsTutorial_valgrind.txt
==447338==    <inherited from parent>
==447338== 
==447338== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp
==447338==    <inherited from parent>
==447338== 
==447338== 
==447338== HEAP SUMMARY:
==447338==     in use at exit: 700,702 bytes in 9,374 blocks
==447338==   total heap usage: 5,184,906 allocs, 5,175,532 frees, 1,794,596,929 bytes allocated
==447338== 
==447338== 552 bytes in 1 blocks are definitely lost in loss record 36 of 62
==447338==    at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==447338==    by 0x191E3C13: ???
==447338==    by 0x191E422C: ???
==447338==    by 0x191574B7: ???
==447338==    by 0x1064115A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==447338==    by 0x106DBA97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==447338==    by 0x10674D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==447338==    by 0xF36BD38: PetscInitialize (pinit.c:924)
==447338==    by 0xE30058B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==447338==    by 0xE3005D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==447338==    by 0x12E496: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==447338==    by 0x12863D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==447338==    by 0x12AAF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==447338==    by 0x12A9F4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==447338==    by 0x12B007: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==447338==    by 0x126E40: main (TestRunningDeltaNotchSimulationsTutorial.cpp:18)
==447338== 
{
   <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
}
==447338== 84,459 (136 direct, 84,323 indirect) bytes in 1 blocks are definitely lost in loss record 59 of 62
==447338==    at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==447338==    by 0x1A75674E: ???
==447338==    by 0x1A756E0B: ???
==447338==    by 0x1A759F56: ???
==447338==    by 0x1A74F65D: ???
==447338==    by 0x1A74FFA3: ???
==447338==    by 0x14026F05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2)
==447338==    by 0x14002AE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2)
==447338==    by 0x13FB3CB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==447338==    by 0x13EE0EF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==447338==    by 0x18915F03: ???
==447338==    by 0x13F154CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==447338==    by 0x106DB418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==447338==    by 0x10674D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==447338==    by 0xF36BD38: PetscInitialize (pinit.c:924)
==447338==    by 0xE30058B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==447338==    by 0xE3005D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==447338==    by 0x12E496: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==447338==    by 0x12863D: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==447338==    by 0x12AAF8: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==447338==    by 0x12A9F4: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==447338==    by 0x12B007: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==447338==    by 0x126E40: main (TestRunningDeltaNotchSimulationsTutorial.cpp:18)
==447338== 
{
   <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
}
==447338== LEAK SUMMARY:
==447338==    definitely lost: 688 bytes in 2 blocks
==447338==    indirectly lost: 1,760 bytes in 16 blocks
==447338==      possibly lost: 0 bytes in 0 blocks
==447338==    still reachable: 1,563 bytes in 7 blocks
==447338==         suppressed: 696,691 bytes in 9,349 blocks
==447338== Reachable blocks (those to which a pointer was found) are not shown.
==447338== To see them, rerun with: --leak-check=full --show-leak-kinds=all
==447338== 
==447338== Use --track-origins=yes to see where uninitialised values come from
==447338== For lists of detected and suppressed errors, rerun with: -s
==447338== ERROR SUMMARY: 5 errors from 5 contexts (suppressed: 28 from 28)