==3284975== Memcheck, a memory error detector
==3284975== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
==3284975== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info
==3284975== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/cell_based/test/TestOffLatticeSimulationWithPdes -malloc_debug -malloc_dump -memory_info
==3284975== Parent PID: 3282641
==3284975== 
==3284975== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later.
==3284975== You should replace [...] by a specific index such as [0] or [1] or [2] or similar
==3284975== 
==3284975== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s)
==3284975==    at 0xE0E379E: getsockopt_syscall (getsockopt.c:29)
==3284975==    by 0xE0E379E: getsockopt (getsockopt.c:94)
==3284975==    by 0x184C7157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==3284975==    by 0x184CEA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==3284975==    by 0x184D5DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==3284975==    by 0x183D53C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==3284975==    by 0x1834EE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so)
==3284975==    by 0x17B0DE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so)
==3284975==    by 0x131104CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==3284975==    by 0xF9BD418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==3284975==    by 0xF956D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==3284975==    by 0xE64DD38: PetscInitialize (pinit.c:924)
==3284975==    by 0xD8AB66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==3284975==    by 0xD8AB6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==3284975==    by 0x234CAC: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==3284975==    by 0x22CD2B: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==3284975==    by 0x230952: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==3284975==    by 0x2307F2: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==3284975==    by 0x230E89: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==3284975==    by 0x22AFE0: main (TestOffLatticeSimulationWithPdes.cpp:19)
==3284975==  Address 0x1ffeffdf8c is on thread 1's stack
==3284975==  in frame #2, created by pmix_ptl_base_make_connection (???:)
==3284975== 
{
   <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
}
==3284975== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s)
==3284975==    at 0xE0E379E: getsockopt_syscall (getsockopt.c:29)
==3284975==    by 0xE0E379E: getsockopt (getsockopt.c:94)
==3284975==    by 0x184C7157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==3284975==    by 0x184CEA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==3284975==    by 0x184D5DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==3284975==    by 0x183D53C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==3284975==    by 0x1834EE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so)
==3284975==    by 0x17B0DE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so)
==3284975==    by 0x131104CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==3284975==    by 0xF9BD418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==3284975==    by 0xF956D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==3284975==    by 0xE64DD38: PetscInitialize (pinit.c:924)
==3284975==    by 0xD8AB66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==3284975==    by 0xD8AB6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==3284975==    by 0x234CAC: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==3284975==    by 0x22CD2B: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==3284975==    by 0x230952: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==3284975==    by 0x2307F2: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==3284975==    by 0x230E89: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==3284975==    by 0x22AFE0: main (TestOffLatticeSimulationWithPdes.cpp:19)
==3284975==  Address 0x1ffeffdf8c is on thread 1's stack
==3284975==  in frame #2, created by pmix_ptl_base_make_connection (???:)
==3284975== 
{
   <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
}
==3284975== Syscall param setsockopt(optlen) contains uninitialised byte(s)
==3284975==    at 0xE0E3C7E: setsockopt_syscall (setsockopt.c:29)
==3284975==    by 0xE0E3C7E: setsockopt (setsockopt.c:95)
==3284975==    by 0x184CEBA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==3284975==    by 0x184D5DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==3284975==    by 0x183D53C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==3284975==    by 0x1834EE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so)
==3284975==    by 0x17B0DE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so)
==3284975==    by 0x131104CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==3284975==    by 0xF9BD418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==3284975==    by 0xF956D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==3284975==    by 0xE64DD38: PetscInitialize (pinit.c:924)
==3284975==    by 0xD8AB66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==3284975==    by 0xD8AB6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==3284975==    by 0x234CAC: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==3284975==    by 0x22CD2B: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==3284975==    by 0x230952: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==3284975==    by 0x2307F2: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==3284975==    by 0x230E89: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==3284975==    by 0x22AFE0: main (TestOffLatticeSimulationWithPdes.cpp:19)
==3284975== 
{
   <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
}
==3284975== 
==3284975== FILE DESCRIPTORS: 9 open (3 std) at exit.
==3284975== Open file descriptor 12:
==3284975==    at 0xE0D122D: pipe (pipe.c:29)
==3284975==    by 0x17B0E07D: ???
==3284975==    by 0x131104CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==3284975==    by 0xF9BD418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==3284975==    by 0xF956D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==3284975==    by 0xE64DD38: PetscInitialize (pinit.c:924)
==3284975==    by 0xD8AB66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==3284975==    by 0xD8AB6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==3284975==    by 0x234CAC: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==3284975==    by 0x22CD2B: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==3284975==    by 0x230952: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==3284975==    by 0x2307F2: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==3284975==    by 0x230E89: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==3284975==    by 0x22AFE0: main (TestOffLatticeSimulationWithPdes.cpp:19)
==3284975== 
==3284975== Open file descriptor 8: /dev/shm/open_mpi.0000
==3284975==    at 0xE0D5BCC: __open_nocancel (open64_nocancel.c:39)
==3284975==    by 0xE059C4F: shm_open@@GLIBC_2.34 (shm_open.c:40)
==3284975==    by 0xD8E3822: ???
==3284975==    by 0xD8E396F: ???
==3284975==    by 0x131B56DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==3284975==    by 0x131B5938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==3284975==    by 0x1316B922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==3284975==    by 0x131102DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==3284975==    by 0xF9BD418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==3284975==    by 0xF956D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==3284975==    by 0xE64DD38: PetscInitialize (pinit.c:924)
==3284975==    by 0xD8AB66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==3284975==    by 0xD8AB6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==3284975==    by 0x234CAC: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==3284975==    by 0x22CD2B: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==3284975==    by 0x230952: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==3284975==    by 0x2307F2: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==3284975==    by 0x230E89: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==3284975==    by 0x22AFE0: main (TestOffLatticeSimulationWithPdes.cpp:19)
==3284975== 
==3284975== Open file descriptor 117:
==3284975==    <inherited from parent>
==3284975== 
==3284975== Open file descriptor 108:
==3284975==    <inherited from parent>
==3284975== 
==3284975== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestOffLatticeSimulationWithPdes_valgrind.txt
==3284975==    <inherited from parent>
==3284975== 
==3284975== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp
==3284975==    <inherited from parent>
==3284975== 
==3284975== 
==3284975== HEAP SUMMARY:
==3284975==     in use at exit: 700,704 bytes in 9,374 blocks
==3284975==   total heap usage: 7,431,093 allocs, 7,421,719 frees, 2,648,285,123 bytes allocated
==3284975== 
==3284975== 552 bytes in 1 blocks are definitely lost in loss record 36 of 62
==3284975==    at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==3284975==    by 0x183DCC13: ???
==3284975==    by 0x183DD22C: ???
==3284975==    by 0x183504B7: ???
==3284975==    by 0xF92315A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==3284975==    by 0xF9BDA97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==3284975==    by 0xF956D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==3284975==    by 0xE64DD38: PetscInitialize (pinit.c:924)
==3284975==    by 0xD8AB66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==3284975==    by 0xD8AB6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==3284975==    by 0x234CAC: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==3284975==    by 0x22CD2B: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==3284975==    by 0x230952: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==3284975==    by 0x2307F2: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==3284975==    by 0x230E89: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==3284975==    by 0x22AFE0: main (TestOffLatticeSimulationWithPdes.cpp:19)
==3284975== 
{
   <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
}
==3284975== 84,408 (136 direct, 84,272 indirect) bytes in 1 blocks are definitely lost in loss record 59 of 62
==3284975==    at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==3284975==    by 0x1994F74E: ???
==3284975==    by 0x1994FE0B: ???
==3284975==    by 0x19952F56: ???
==3284975==    by 0x1994865D: ???
==3284975==    by 0x19948FA3: ???
==3284975==    by 0x13221F05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2)
==3284975==    by 0x131FDAE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2)
==3284975==    by 0x131AECB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==3284975==    by 0x130DBEF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==3284975==    by 0x17B0EF03: ???
==3284975==    by 0x131104CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==3284975==    by 0xF9BD418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==3284975==    by 0xF956D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==3284975==    by 0xE64DD38: PetscInitialize (pinit.c:924)
==3284975==    by 0xD8AB66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==3284975==    by 0xD8AB6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==3284975==    by 0x234CAC: PetscSetup::setUpWorld() (PetscSetupAndFinalize.hpp:61)
==3284975==    by 0x22CD2B: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==3284975==    by 0x230952: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==3284975==    by 0x2307F2: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==3284975==    by 0x230E89: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==3284975==    by 0x22AFE0: main (TestOffLatticeSimulationWithPdes.cpp:19)
==3284975== 
{
   <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
}
==3284975== LEAK SUMMARY:
==3284975==    definitely lost: 688 bytes in 2 blocks
==3284975==    indirectly lost: 1,760 bytes in 16 blocks
==3284975==      possibly lost: 0 bytes in 0 blocks
==3284975==    still reachable: 1,563 bytes in 7 blocks
==3284975==         suppressed: 696,693 bytes in 9,349 blocks
==3284975== Reachable blocks (those to which a pointer was found) are not shown.
==3284975== To see them, rerun with: --leak-check=full --show-leak-kinds=all
==3284975== 
==3284975== Use --track-origins=yes to see where uninitialised values come from
==3284975== For lists of detected and suppressed errors, rerun with: -s
==3284975== ERROR SUMMARY: 5 errors from 5 contexts (suppressed: 28 from 28)