==1020113== Memcheck, a memory error detector
==1020113== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
==1020113== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info
==1020113== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/cell_based/test/TestCellSrn -malloc_debug -malloc_dump -memory_info
==1020113== Parent PID: 1018986
==1020113== 
==1020113== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later.
==1020113== You should replace [...] by a specific index such as [0] or [1] or [2] or similar
==1020113== 
==1020113== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s)
==1020113==    at 0xD83E79E: getsockopt_syscall (getsockopt.c:29)
==1020113==    by 0xD83E79E: getsockopt (getsockopt.c:94)
==1020113==    by 0x184C6157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==1020113==    by 0x184CDA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==1020113==    by 0x184D4DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==1020113==    by 0x183D43C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==1020113==    by 0x1834DE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so)
==1020113==    by 0x17B0CE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so)
==1020113==    by 0x1205B4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==1020113==    by 0xD47D418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==1020113==    by 0xD416D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==1020113==    by 0xC0EDD38: PetscInitialize (pinit.c:924)
==1020113==    by 0xBFBF58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==1020113==    by 0xBFBF5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==1020113==    by 0x1241EB: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70)
==1020113==    by 0x11E3FD: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==1020113==    by 0x1208DE: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==1020113==    by 0x1207DA: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==1020113==    by 0x120DED: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==1020113==    by 0x11CC00: main (TestCellSrn.cpp:18)
==1020113==  Address 0x1ffeffdfdc is on thread 1's stack
==1020113==  in frame #2, created by pmix_ptl_base_make_connection (???:)
==1020113== 
{
   <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
}
==1020113== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s)
==1020113==    at 0xD83E79E: getsockopt_syscall (getsockopt.c:29)
==1020113==    by 0xD83E79E: getsockopt (getsockopt.c:94)
==1020113==    by 0x184C6157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==1020113==    by 0x184CDA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==1020113==    by 0x184D4DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==1020113==    by 0x183D43C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==1020113==    by 0x1834DE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so)
==1020113==    by 0x17B0CE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so)
==1020113==    by 0x1205B4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==1020113==    by 0xD47D418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==1020113==    by 0xD416D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==1020113==    by 0xC0EDD38: PetscInitialize (pinit.c:924)
==1020113==    by 0xBFBF58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==1020113==    by 0xBFBF5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==1020113==    by 0x1241EB: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70)
==1020113==    by 0x11E3FD: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==1020113==    by 0x1208DE: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==1020113==    by 0x1207DA: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==1020113==    by 0x120DED: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==1020113==    by 0x11CC00: main (TestCellSrn.cpp:18)
==1020113==  Address 0x1ffeffdfdc is on thread 1's stack
==1020113==  in frame #2, created by pmix_ptl_base_make_connection (???:)
==1020113== 
{
   <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
}
==1020113== Syscall param setsockopt(optlen) contains uninitialised byte(s)
==1020113==    at 0xD83EC7E: setsockopt_syscall (setsockopt.c:29)
==1020113==    by 0xD83EC7E: setsockopt (setsockopt.c:95)
==1020113==    by 0x184CDBA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==1020113==    by 0x184D4DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==1020113==    by 0x183D43C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==1020113==    by 0x1834DE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so)
==1020113==    by 0x17B0CE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so)
==1020113==    by 0x1205B4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==1020113==    by 0xD47D418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==1020113==    by 0xD416D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==1020113==    by 0xC0EDD38: PetscInitialize (pinit.c:924)
==1020113==    by 0xBFBF58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==1020113==    by 0xBFBF5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==1020113==    by 0x1241EB: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70)
==1020113==    by 0x11E3FD: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==1020113==    by 0x1208DE: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==1020113==    by 0x1207DA: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==1020113==    by 0x120DED: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==1020113==    by 0x11CC00: main (TestCellSrn.cpp:18)
==1020113== 
{
   <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
}
==1020113== 
==1020113== FILE DESCRIPTORS: 9 open (3 std) at exit.
==1020113== Open file descriptor 12:
==1020113==    at 0xD82C22D: pipe (pipe.c:29)
==1020113==    by 0x17B0D07D: ???
==1020113==    by 0x1205B4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==1020113==    by 0xD47D418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==1020113==    by 0xD416D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==1020113==    by 0xC0EDD38: PetscInitialize (pinit.c:924)
==1020113==    by 0xBFBF58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==1020113==    by 0xBFBF5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==1020113==    by 0x1241EB: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70)
==1020113==    by 0x11E3FD: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==1020113==    by 0x1208DE: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==1020113==    by 0x1207DA: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==1020113==    by 0x120DED: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==1020113==    by 0x11CC00: main (TestCellSrn.cpp:18)
==1020113== 
==1020113== Open file descriptor 8: /dev/shm/open_mpi.0000
==1020113==    at 0xD830BCC: __open_nocancel (open64_nocancel.c:39)
==1020113==    by 0xD7B4C4F: shm_open@@GLIBC_2.34 (shm_open.c:40)
==1020113==    by 0xD377822: ???
==1020113==    by 0xD37796F: ???
==1020113==    by 0x121006DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==1020113==    by 0x12100938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==1020113==    by 0x120B6922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==1020113==    by 0x1205B2DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==1020113==    by 0xD47D418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==1020113==    by 0xD416D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==1020113==    by 0xC0EDD38: PetscInitialize (pinit.c:924)
==1020113==    by 0xBFBF58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==1020113==    by 0xBFBF5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==1020113==    by 0x1241EB: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70)
==1020113==    by 0x11E3FD: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==1020113==    by 0x1208DE: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==1020113==    by 0x1207DA: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==1020113==    by 0x120DED: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==1020113==    by 0x11CC00: main (TestCellSrn.cpp:18)
==1020113== 
==1020113== Open file descriptor 115:
==1020113==    <inherited from parent>
==1020113== 
==1020113== Open file descriptor 108:
==1020113==    <inherited from parent>
==1020113== 
==1020113== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestCellSrn_valgrind.txt
==1020113==    <inherited from parent>
==1020113== 
==1020113== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp
==1020113==    <inherited from parent>
==1020113== 
==1020113== 
==1020113== HEAP SUMMARY:
==1020113==     in use at exit: 700,839 bytes in 9,379 blocks
==1020113==   total heap usage: 64,599 allocs, 55,220 frees, 1,354,311,791 bytes allocated
==1020113== 
==1020113== 552 bytes in 1 blocks are definitely lost in loss record 41 of 67
==1020113==    at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==1020113==    by 0x183DBC13: ???
==1020113==    by 0x183DC22C: ???
==1020113==    by 0x1834F4B7: ???
==1020113==    by 0xD3E315A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==1020113==    by 0xD47DA97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==1020113==    by 0xD416D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==1020113==    by 0xC0EDD38: PetscInitialize (pinit.c:924)
==1020113==    by 0xBFBF58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==1020113==    by 0xBFBF5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==1020113==    by 0x1241EB: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70)
==1020113==    by 0x11E3FD: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==1020113==    by 0x1208DE: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==1020113==    by 0x1207DA: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==1020113==    by 0x120DED: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==1020113==    by 0x11CC00: main (TestCellSrn.cpp:18)
==1020113== 
{
   <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
}
==1020113== 23,297 (136 direct, 23,161 indirect) bytes in 1 blocks are definitely lost in loss record 64 of 67
==1020113==    at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==1020113==    by 0x1994E74E: ???
==1020113==    by 0x1994EE0B: ???
==1020113==    by 0x19951F56: ???
==1020113==    by 0x1994765D: ???
==1020113==    by 0x19947FA3: ???
==1020113==    by 0x1216EF05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2)
==1020113==    by 0x1214AAE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2)
==1020113==    by 0x120F9CB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==1020113==    by 0x12026EF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==1020113==    by 0x17B0DF03: ???
==1020113==    by 0x1205B4CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==1020113==    by 0xD47D418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==1020113==    by 0xD416D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==1020113==    by 0xC0EDD38: PetscInitialize (pinit.c:924)
==1020113==    by 0xBFBF58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==1020113==    by 0xBFBF5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==1020113==    by 0x1241EB: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70)
==1020113==    by 0x11E3FD: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==1020113==    by 0x1208DE: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==1020113==    by 0x1207DA: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==1020113==    by 0x120DED: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==1020113==    by 0x11CC00: main (TestCellSrn.cpp:18)
==1020113== 
{
   <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
}
==1020113== LEAK SUMMARY:
==1020113==    definitely lost: 688 bytes in 2 blocks
==1020113==    indirectly lost: 1,760 bytes in 16 blocks
==1020113==      possibly lost: 0 bytes in 0 blocks
==1020113==    still reachable: 1,627 bytes in 8 blocks
==1020113==         suppressed: 696,764 bytes in 9,353 blocks
==1020113== Reachable blocks (those to which a pointer was found) are not shown.
==1020113== To see them, rerun with: --leak-check=full --show-leak-kinds=all
==1020113== 
==1020113== Use --track-origins=yes to see where uninitialised values come from
==1020113== For lists of detected and suppressed errors, rerun with: -s
==1020113== ERROR SUMMARY: 5 errors from 5 contexts (suppressed: 32 from 32)