==3161418== Memcheck, a memory error detector
==3161418== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
==3161418== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info
==3161418== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/cell_based/test/TestCellWriters -malloc_debug -malloc_dump -memory_info
==3161418== Parent PID: 3159762
==3161418== 
==3161418== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later.
==3161418== You should replace [...] by a specific index such as [0] or [1] or [2] or similar
==3161418== 
==3161418== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s)
==3161418==    at 0xED3979E: getsockopt_syscall (getsockopt.c:29)
==3161418==    by 0xED3979E: getsockopt (getsockopt.c:94)
==3161418==    by 0x192CB157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==3161418==    by 0x192D2A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==3161418==    by 0x192D9DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==3161418==    by 0x191D93C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==3161418==    by 0x19152E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so)
==3161418==    by 0x18911E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so)
==3161418==    by 0x13F124CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==3161418==    by 0x106D8418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==3161418==    by 0x10671D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==3161418==    by 0xF366D38: PetscInitialize (pinit.c:924)
==3161418==    by 0xE5E858B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==3161418==    by 0xE5E85D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==3161418==    by 0x14F23A: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==3161418==    by 0x145EFF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==3161418==    by 0x1492F2: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==3161418==    by 0x149192: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==3161418==    by 0x149829: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==3161418==    by 0x144230: main (TestCellWriters.cpp:19)
==3161418==  Address 0x1ffeffdfac is on thread 1's stack
==3161418==  in frame #2, created by pmix_ptl_base_make_connection (???:)
==3161418== 
{
   <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
}
==3161418== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s)
==3161418==    at 0xED3979E: getsockopt_syscall (getsockopt.c:29)
==3161418==    by 0xED3979E: getsockopt (getsockopt.c:94)
==3161418==    by 0x192CB157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==3161418==    by 0x192D2A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==3161418==    by 0x192D9DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==3161418==    by 0x191D93C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==3161418==    by 0x19152E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so)
==3161418==    by 0x18911E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so)
==3161418==    by 0x13F124CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==3161418==    by 0x106D8418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==3161418==    by 0x10671D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==3161418==    by 0xF366D38: PetscInitialize (pinit.c:924)
==3161418==    by 0xE5E858B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==3161418==    by 0xE5E85D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==3161418==    by 0x14F23A: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==3161418==    by 0x145EFF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==3161418==    by 0x1492F2: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==3161418==    by 0x149192: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==3161418==    by 0x149829: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==3161418==    by 0x144230: main (TestCellWriters.cpp:19)
==3161418==  Address 0x1ffeffdfac is on thread 1's stack
==3161418==  in frame #2, created by pmix_ptl_base_make_connection (???:)
==3161418== 
{
   <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
}
==3161418== Syscall param setsockopt(optlen) contains uninitialised byte(s)
==3161418==    at 0xED39C7E: setsockopt_syscall (setsockopt.c:29)
==3161418==    by 0xED39C7E: setsockopt (setsockopt.c:95)
==3161418==    by 0x192D2BA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==3161418==    by 0x192D9DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==3161418==    by 0x191D93C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==3161418==    by 0x19152E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so)
==3161418==    by 0x18911E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so)
==3161418==    by 0x13F124CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==3161418==    by 0x106D8418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==3161418==    by 0x10671D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==3161418==    by 0xF366D38: PetscInitialize (pinit.c:924)
==3161418==    by 0xE5E858B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==3161418==    by 0xE5E85D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==3161418==    by 0x14F23A: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==3161418==    by 0x145EFF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==3161418==    by 0x1492F2: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==3161418==    by 0x149192: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==3161418==    by 0x149829: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==3161418==    by 0x144230: main (TestCellWriters.cpp:19)
==3161418== 
{
   <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
}
==3161418== 
==3161418== FILE DESCRIPTORS: 9 open (3 std) at exit.
==3161418== Open file descriptor 12:
==3161418==    at 0xED2722D: pipe (pipe.c:29)
==3161418==    by 0x1891207D: ???
==3161418==    by 0x13F124CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==3161418==    by 0x106D8418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==3161418==    by 0x10671D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==3161418==    by 0xF366D38: PetscInitialize (pinit.c:924)
==3161418==    by 0xE5E858B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==3161418==    by 0xE5E85D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==3161418==    by 0x14F23A: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==3161418==    by 0x145EFF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==3161418==    by 0x1492F2: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==3161418==    by 0x149192: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==3161418==    by 0x149829: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==3161418==    by 0x144230: main (TestCellWriters.cpp:19)
==3161418== 
==3161418== Open file descriptor 8: /dev/shm/open_mpi.0000
==3161418==    at 0xED2BBCC: __open_nocancel (open64_nocancel.c:39)
==3161418==    by 0xECAFC4F: shm_open@@GLIBC_2.34 (shm_open.c:40)
==3161418==    by 0xE620822: ???
==3161418==    by 0xE62096F: ???
==3161418==    by 0x13FB76DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==3161418==    by 0x13FB7938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==3161418==    by 0x13F6D922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==3161418==    by 0x13F122DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==3161418==    by 0x106D8418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==3161418==    by 0x10671D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==3161418==    by 0xF366D38: PetscInitialize (pinit.c:924)
==3161418==    by 0xE5E858B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==3161418==    by 0xE5E85D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==3161418==    by 0x14F23A: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==3161418==    by 0x145EFF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==3161418==    by 0x1492F2: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==3161418==    by 0x149192: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==3161418==    by 0x149829: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==3161418==    by 0x144230: main (TestCellWriters.cpp:19)
==3161418== 
==3161418== Open file descriptor 117:
==3161418==    <inherited from parent>
==3161418== 
==3161418== Open file descriptor 99:
==3161418==    <inherited from parent>
==3161418== 
==3161418== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestCellWriters_valgrind.txt
==3161418==    <inherited from parent>
==3161418== 
==3161418== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp
==3161418==    <inherited from parent>
==3161418== 
==3161418== 
==3161418== HEAP SUMMARY:
==3161418==     in use at exit: 700,775 bytes in 9,378 blocks
==3161418==   total heap usage: 66,057 allocs, 56,679 frees, 1,355,849,195 bytes allocated
==3161418== 
==3161418== 552 bytes in 1 blocks are definitely lost in loss record 40 of 66
==3161418==    at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==3161418==    by 0x191E0C13: ???
==3161418==    by 0x191E122C: ???
==3161418==    by 0x191544B7: ???
==3161418==    by 0x1063E15A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==3161418==    by 0x106D8A97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==3161418==    by 0x10671D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==3161418==    by 0xF366D38: PetscInitialize (pinit.c:924)
==3161418==    by 0xE5E858B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==3161418==    by 0xE5E85D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==3161418==    by 0x14F23A: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==3161418==    by 0x145EFF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==3161418==    by 0x1492F2: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==3161418==    by 0x149192: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==3161418==    by 0x149829: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==3161418==    by 0x144230: main (TestCellWriters.cpp:19)
==3161418== 
{
   <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
}
==3161418== 23,323 (136 direct, 23,187 indirect) bytes in 1 blocks are definitely lost in loss record 63 of 66
==3161418==    at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==3161418==    by 0x1A75374E: ???
==3161418==    by 0x1A753E0B: ???
==3161418==    by 0x1A756F56: ???
==3161418==    by 0x1A74C65D: ???
==3161418==    by 0x1A74CFA3: ???
==3161418==    by 0x14023F05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2)
==3161418==    by 0x13FFFAE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2)
==3161418==    by 0x13FB0CB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==3161418==    by 0x13EDDEF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==3161418==    by 0x18912F03: ???
==3161418==    by 0x13F124CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==3161418==    by 0x106D8418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==3161418==    by 0x10671D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==3161418==    by 0xF366D38: PetscInitialize (pinit.c:924)
==3161418==    by 0xE5E858B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==3161418==    by 0xE5E85D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==3161418==    by 0x14F23A: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==3161418==    by 0x145EFF: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==3161418==    by 0x1492F2: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==3161418==    by 0x149192: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==3161418==    by 0x149829: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==3161418==    by 0x144230: main (TestCellWriters.cpp:19)
==3161418== 
{
   <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
}
==3161418== LEAK SUMMARY:
==3161418==    definitely lost: 688 bytes in 2 blocks
==3161418==    indirectly lost: 1,760 bytes in 16 blocks
==3161418==      possibly lost: 0 bytes in 0 blocks
==3161418==    still reachable: 1,563 bytes in 7 blocks
==3161418==         suppressed: 696,764 bytes in 9,353 blocks
==3161418== Reachable blocks (those to which a pointer was found) are not shown.
==3161418== To see them, rerun with: --leak-check=full --show-leak-kinds=all
==3161418== 
==3161418== Use --track-origins=yes to see where uninitialised values come from
==3161418== For lists of detected and suppressed errors, rerun with: -s
==3161418== ERROR SUMMARY: 5 errors from 5 contexts (suppressed: 32 from 32)