==914742== Memcheck, a memory error detector
==914742== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
==914742== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info
==914742== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/linalg/test/TestUblasCustomFunctions -malloc_debug -malloc_dump -memory_info
==914742== Parent PID: 914403
==914742== 
==914742== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later.
==914742== You should replace [...] by a specific index such as [0] or [1] or [2] or similar
==914742== 
==914742== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s)
==914742==    at 0x4E5C79E: getsockopt_syscall (getsockopt.c:29)
==914742==    by 0x4E5C79E: getsockopt (getsockopt.c:94)
==914742==    by 0xB934157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==914742==    by 0xB93BA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==914742==    by 0xB942DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==914742==    by 0xB8423C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==914742==    by 0xB7BBE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so)
==914742==    by 0xAF7AE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so)
==914742==    by 0x8A8C4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==914742==    by 0x6426418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==914742==    by 0x63BFD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==914742==    by 0x5094D38: PetscInitialize (pinit.c:924)
==914742==    by 0x49AB58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==914742==    by 0x49AB5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==914742==    by 0x11B1D2: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==914742==    by 0x1164A5: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==914742==    by 0x118EC4: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==914742==    by 0x118D64: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==914742==    by 0x1193FB: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==914742==    by 0x1147D5: main (TestUblasCustomFunctions.cpp:19)
==914742==  Address 0x1ffeffdfcc is on thread 1's stack
==914742==  in frame #2, created by pmix_ptl_base_make_connection (???:)
==914742== 
{
   <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
}
==914742== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s)
==914742==    at 0x4E5C79E: getsockopt_syscall (getsockopt.c:29)
==914742==    by 0x4E5C79E: getsockopt (getsockopt.c:94)
==914742==    by 0xB934157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==914742==    by 0xB93BA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==914742==    by 0xB942DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==914742==    by 0xB8423C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==914742==    by 0xB7BBE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so)
==914742==    by 0xAF7AE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so)
==914742==    by 0x8A8C4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==914742==    by 0x6426418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==914742==    by 0x63BFD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==914742==    by 0x5094D38: PetscInitialize (pinit.c:924)
==914742==    by 0x49AB58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==914742==    by 0x49AB5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==914742==    by 0x11B1D2: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==914742==    by 0x1164A5: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==914742==    by 0x118EC4: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==914742==    by 0x118D64: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==914742==    by 0x1193FB: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==914742==    by 0x1147D5: main (TestUblasCustomFunctions.cpp:19)
==914742==  Address 0x1ffeffdfcc is on thread 1's stack
==914742==  in frame #2, created by pmix_ptl_base_make_connection (???:)
==914742== 
{
   <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
}
==914742== Syscall param setsockopt(optlen) contains uninitialised byte(s)
==914742==    at 0x4E5CC7E: setsockopt_syscall (setsockopt.c:29)
==914742==    by 0x4E5CC7E: setsockopt (setsockopt.c:95)
==914742==    by 0xB93BBA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==914742==    by 0xB942DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==914742==    by 0xB8423C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==914742==    by 0xB7BBE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so)
==914742==    by 0xAF7AE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so)
==914742==    by 0x8A8C4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==914742==    by 0x6426418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==914742==    by 0x63BFD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==914742==    by 0x5094D38: PetscInitialize (pinit.c:924)
==914742==    by 0x49AB58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==914742==    by 0x49AB5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==914742==    by 0x11B1D2: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==914742==    by 0x1164A5: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==914742==    by 0x118EC4: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==914742==    by 0x118D64: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==914742==    by 0x1193FB: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==914742==    by 0x1147D5: main (TestUblasCustomFunctions.cpp:19)
==914742== 
{
   <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
}
==914742== 
==914742== FILE DESCRIPTORS: 9 open (3 std) at exit.
==914742== Open file descriptor 12:
==914742==    at 0x4E4A22D: pipe (pipe.c:29)
==914742==    by 0xAF7B07D: ???
==914742==    by 0x8A8C4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==914742==    by 0x6426418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==914742==    by 0x63BFD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==914742==    by 0x5094D38: PetscInitialize (pinit.c:924)
==914742==    by 0x49AB58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==914742==    by 0x49AB5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==914742==    by 0x11B1D2: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==914742==    by 0x1164A5: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==914742==    by 0x118EC4: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==914742==    by 0x118D64: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==914742==    by 0x1193FB: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==914742==    by 0x1147D5: main (TestUblasCustomFunctions.cpp:19)
==914742== 
==914742== Open file descriptor 8: /dev/shm/open_mpi.0000
==914742==    at 0x4E4EBCC: __open_nocancel (open64_nocancel.c:39)
==914742==    by 0x4DD2C4F: shm_open@@GLIBC_2.34 (shm_open.c:40)
==914742==    by 0x49E3822: ???
==914742==    by 0x49E396F: ???
==914742==    by 0x8B316DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==914742==    by 0x8B31938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==914742==    by 0x8AE7922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==914742==    by 0x8A8C2DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==914742==    by 0x6426418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==914742==    by 0x63BFD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==914742==    by 0x5094D38: PetscInitialize (pinit.c:924)
==914742==    by 0x49AB58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==914742==    by 0x49AB5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==914742==    by 0x11B1D2: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==914742==    by 0x1164A5: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==914742==    by 0x118EC4: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==914742==    by 0x118D64: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==914742==    by 0x1193FB: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==914742==    by 0x1147D5: main (TestUblasCustomFunctions.cpp:19)
==914742== 
==914742== Open file descriptor 111:
==914742==    <inherited from parent>
==914742== 
==914742== Open file descriptor 108:
==914742==    <inherited from parent>
==914742== 
==914742== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestUblasCustomFunctions_valgrind.txt
==914742==    <inherited from parent>
==914742== 
==914742== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp
==914742==    <inherited from parent>
==914742== 
==914742== 
==914742== HEAP SUMMARY:
==914742==     in use at exit: 700,290 bytes in 9,377 blocks
==914742==   total heap usage: 47,166 allocs, 37,789 frees, 1,353,176,268 bytes allocated
==914742== 
==914742== 552 bytes in 1 blocks are definitely lost in loss record 40 of 63
==914742==    at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==914742==    by 0xB849C13: ???
==914742==    by 0xB84A22C: ???
==914742==    by 0xB7BD4B7: ???
==914742==    by 0x638C15A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==914742==    by 0x6426A97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==914742==    by 0x63BFD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==914742==    by 0x5094D38: PetscInitialize (pinit.c:924)
==914742==    by 0x49AB58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==914742==    by 0x49AB5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==914742==    by 0x11B1D2: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==914742==    by 0x1164A5: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==914742==    by 0x118EC4: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==914742==    by 0x118D64: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==914742==    by 0x1193FB: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==914742==    by 0x1147D5: main (TestUblasCustomFunctions.cpp:19)
==914742== 
{
   <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
}
==914742== 685,273 (136 direct, 685,137 indirect) bytes in 1 blocks are definitely lost in loss record 63 of 63
==914742==    at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==914742==    by 0xCA5D74E: ???
==914742==    by 0xCA5DE0B: ???
==914742==    by 0xCA60F56: ???
==914742==    by 0xCA5665D: ???
==914742==    by 0xCA56FA3: ???
==914742==    by 0x8B9DF05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2)
==914742==    by 0x8B79AE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2)
==914742==    by 0x8B2ACB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==914742==    by 0x8A57EF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==914742==    by 0xAF7BF03: ???
==914742==    by 0x8A8C4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==914742==    by 0x6426418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==914742==    by 0x63BFD7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==914742==    by 0x5094D38: PetscInitialize (pinit.c:924)
==914742==    by 0x49AB58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==914742==    by 0x49AB5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==914742==    by 0x11B1D2: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==914742==    by 0x1164A5: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==914742==    by 0x118EC4: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==914742==    by 0x118D64: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==914742==    by 0x1193FB: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==914742==    by 0x1147D5: main (TestUblasCustomFunctions.cpp:19)
==914742== 
{
   <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
}
==914742== LEAK SUMMARY:
==914742==    definitely lost: 688 bytes in 2 blocks
==914742==    indirectly lost: 1,760 bytes in 16 blocks
==914742==      possibly lost: 0 bytes in 0 blocks
==914742==    still reachable: 1,531 bytes in 6 blocks
==914742==         suppressed: 696,311 bytes in 9,353 blocks
==914742== Reachable blocks (those to which a pointer was found) are not shown.
==914742== To see them, rerun with: --leak-check=full --show-leak-kinds=all
==914742== 
==914742== Use --track-origins=yes to see where uninitialised values come from
==914742== For lists of detected and suppressed errors, rerun with: -s
==914742== ERROR SUMMARY: 5 errors from 5 contexts (suppressed: 30 from 30)