==27909== Memcheck, a memory error detector
==27909== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
==27909== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info
==27909== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/crypt/test/TestMirams2010WntOdeSystem -malloc_debug -malloc_dump -memory_info
==27909== Parent PID: 7893
==27909== 
==27909== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later.
==27909== You should replace [...] by a specific index such as [0] or [1] or [2] or similar
==27909== 
==27909== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s)
==27909==    at 0xE8D679E: getsockopt_syscall (getsockopt.c:29)
==27909==    by 0xE8D679E: getsockopt (getsockopt.c:94)
==27909==    by 0x1ABAD157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==27909==    by 0x1ABB4A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==27909==    by 0x1ABBBDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==27909==    by 0x1AABB3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==27909==    by 0x1AA34E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so)
==27909==    by 0x1A1F3E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so)
==27909==    by 0x157FF4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==27909==    by 0x120A2418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==27909==    by 0x1203BD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==27909==    by 0x10D32D38: PetscInitialize (pinit.c:924)
==27909==    by 0xE4CC58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==27909==    by 0xE4CC5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==27909==    by 0x12F9E4: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==27909==    by 0x129507: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==27909==    by 0x12BE02: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==27909==    by 0x12BCFE: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==27909==    by 0x12C311: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==27909==    by 0x127150: main (TestMirams2010WntOdeSystem.cpp:18)
==27909==  Address 0x1ffeffdfac is on thread 1's stack
==27909==  in frame #2, created by pmix_ptl_base_make_connection (???:)
==27909== 
{
   <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
}
==27909== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s)
==27909==    at 0xE8D679E: getsockopt_syscall (getsockopt.c:29)
==27909==    by 0xE8D679E: getsockopt (getsockopt.c:94)
==27909==    by 0x1ABAD157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==27909==    by 0x1ABB4A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==27909==    by 0x1ABBBDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==27909==    by 0x1AABB3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==27909==    by 0x1AA34E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so)
==27909==    by 0x1A1F3E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so)
==27909==    by 0x157FF4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==27909==    by 0x120A2418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==27909==    by 0x1203BD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==27909==    by 0x10D32D38: PetscInitialize (pinit.c:924)
==27909==    by 0xE4CC58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==27909==    by 0xE4CC5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==27909==    by 0x12F9E4: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==27909==    by 0x129507: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==27909==    by 0x12BE02: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==27909==    by 0x12BCFE: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==27909==    by 0x12C311: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==27909==    by 0x127150: main (TestMirams2010WntOdeSystem.cpp:18)
==27909==  Address 0x1ffeffdfac is on thread 1's stack
==27909==  in frame #2, created by pmix_ptl_base_make_connection (???:)
==27909== 
{
   <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
}
==27909== Syscall param setsockopt(optlen) contains uninitialised byte(s)
==27909==    at 0xE8D6C7E: setsockopt_syscall (setsockopt.c:29)
==27909==    by 0xE8D6C7E: setsockopt (setsockopt.c:95)
==27909==    by 0x1ABB4BA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==27909==    by 0x1ABBBDF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==27909==    by 0x1AABB3C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==27909==    by 0x1AA34E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so)
==27909==    by 0x1A1F3E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so)
==27909==    by 0x157FF4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==27909==    by 0x120A2418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==27909==    by 0x1203BD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==27909==    by 0x10D32D38: PetscInitialize (pinit.c:924)
==27909==    by 0xE4CC58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==27909==    by 0xE4CC5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==27909==    by 0x12F9E4: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==27909==    by 0x129507: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==27909==    by 0x12BE02: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==27909==    by 0x12BCFE: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==27909==    by 0x12C311: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==27909==    by 0x127150: main (TestMirams2010WntOdeSystem.cpp:18)
==27909== 
{
   <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
}
==27909== 
==27909== FILE DESCRIPTORS: 9 open (3 std) at exit.
==27909== Open file descriptor 12:
==27909==    at 0xE8C422D: pipe (pipe.c:29)
==27909==    by 0x1A1F407D: ???
==27909==    by 0x157FF4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==27909==    by 0x120A2418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==27909==    by 0x1203BD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==27909==    by 0x10D32D38: PetscInitialize (pinit.c:924)
==27909==    by 0xE4CC58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==27909==    by 0xE4CC5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==27909==    by 0x12F9E4: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==27909==    by 0x129507: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==27909==    by 0x12BE02: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==27909==    by 0x12BCFE: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==27909==    by 0x12C311: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==27909==    by 0x127150: main (TestMirams2010WntOdeSystem.cpp:18)
==27909== 
==27909== Open file descriptor 8: /dev/shm/open_mpi.0000
==27909==    at 0xE8C8BCC: __open_nocancel (open64_nocancel.c:39)
==27909==    by 0xE84CC4F: shm_open@@GLIBC_2.34 (shm_open.c:40)
==27909==    by 0xE504822: ???
==27909==    by 0xE50496F: ???
==27909==    by 0x158A46DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==27909==    by 0x158A4938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==27909==    by 0x1585A922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==27909==    by 0x157FF2DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==27909==    by 0x120A2418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==27909==    by 0x1203BD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==27909==    by 0x10D32D38: PetscInitialize (pinit.c:924)
==27909==    by 0xE4CC58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==27909==    by 0xE4CC5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==27909==    by 0x12F9E4: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==27909==    by 0x129507: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==27909==    by 0x12BE02: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==27909==    by 0x12BCFE: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==27909==    by 0x12C311: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==27909==    by 0x127150: main (TestMirams2010WntOdeSystem.cpp:18)
==27909== 
==27909== Open file descriptor 115:
==27909==    <inherited from parent>
==27909== 
==27909== Open file descriptor 110:
==27909==    <inherited from parent>
==27909== 
==27909== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestMirams2010WntOdeSystem_valgrind.txt
==27909==    <inherited from parent>
==27909== 
==27909== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp
==27909==    <inherited from parent>
==27909== 
==27909== 
==27909== HEAP SUMMARY:
==27909==     in use at exit: 700,781 bytes in 9,378 blocks
==27909==   total heap usage: 68,446 allocs, 59,068 frees, 1,355,326,265 bytes allocated
==27909== 
==27909== 552 bytes in 1 blocks are definitely lost in loss record 40 of 66
==27909==    at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==27909==    by 0x1AAC2C13: ???
==27909==    by 0x1AAC322C: ???
==27909==    by 0x1AA364B7: ???
==27909==    by 0x1200815A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==27909==    by 0x120A2A97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==27909==    by 0x1203BD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==27909==    by 0x10D32D38: PetscInitialize (pinit.c:924)
==27909==    by 0xE4CC58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==27909==    by 0xE4CC5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==27909==    by 0x12F9E4: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==27909==    by 0x129507: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==27909==    by 0x12BE02: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==27909==    by 0x12BCFE: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==27909==    by 0x12C311: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==27909==    by 0x127150: main (TestMirams2010WntOdeSystem.cpp:18)
==27909== 
{
   <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
}
==27909== 84,459 (136 direct, 84,323 indirect) bytes in 1 blocks are definitely lost in loss record 63 of 66
==27909==    at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==27909==    by 0x1C03574E: ???
==27909==    by 0x1C035E0B: ???
==27909==    by 0x1C038F56: ???
==27909==    by 0x1C02E65D: ???
==27909==    by 0x1C02EFA3: ???
==27909==    by 0x15910F05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2)
==27909==    by 0x158ECAE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2)
==27909==    by 0x1589DCB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==27909==    by 0x157CAEF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==27909==    by 0x1A1F4F03: ???
==27909==    by 0x157FF4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==27909==    by 0x120A2418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==27909==    by 0x1203BD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==27909==    by 0x10D32D38: PetscInitialize (pinit.c:924)
==27909==    by 0xE4CC58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==27909==    by 0xE4CC5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==27909==    by 0x12F9E4: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==27909==    by 0x129507: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==27909==    by 0x12BE02: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==27909==    by 0x12BCFE: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==27909==    by 0x12C311: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==27909==    by 0x127150: main (TestMirams2010WntOdeSystem.cpp:18)
==27909== 
{
   <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
}
==27909== LEAK SUMMARY:
==27909==    definitely lost: 688 bytes in 2 blocks
==27909==    indirectly lost: 1,760 bytes in 16 blocks
==27909==      possibly lost: 0 bytes in 0 blocks
==27909==    still reachable: 1,563 bytes in 7 blocks
==27909==         suppressed: 696,770 bytes in 9,353 blocks
==27909== Reachable blocks (those to which a pointer was found) are not shown.
==27909== To see them, rerun with: --leak-check=full --show-leak-kinds=all
==27909== 
==27909== Use --track-origins=yes to see where uninitialised values come from
==27909== For lists of detected and suppressed errors, rerun with: -s
==27909== ERROR SUMMARY: 5 errors from 5 contexts (suppressed: 32 from 32)