==2303993== Memcheck, a memory error detector
==2303993== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
==2303993== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info
==2303993== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/crypt/test/TestCryptSimulation1d -malloc_debug -malloc_dump -memory_info
==2303993== Parent PID: 2283975
==2303993== 
==2303993== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later.
==2303993== You should replace [...] by a specific index such as [0] or [1] or [2] or similar
==2303993== 
==2303993== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s)
==2303993==    at 0x109E179E: getsockopt_syscall (getsockopt.c:29)
==2303993==    by 0x109E179E: getsockopt (getsockopt.c:94)
==2303993==    by 0x19DA9157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==2303993==    by 0x19DB0A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==2303993==    by 0x19DB7DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==2303993==    by 0x19CB73C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==2303993==    by 0x19C30E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so)
==2303993==    by 0x193EFE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so)
==2303993==    by 0x149524CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==2303993==    by 0x102D9418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==2303993==    by 0x10272D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==2303993==    by 0xEF69D38: PetscInitialize (pinit.c:924)
==2303993==    by 0xEDDB66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==2303993==    by 0xEDDB6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==2303993==    by 0x233B09: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70)
==2303993==    by 0x229C01: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==2303993==    by 0x22D79A: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==2303993==    by 0x22D695: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==2303993==    by 0x22DCA9: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==2303993==    by 0x2283C0: main (TestCryptSimulation1d.cpp:18)
==2303993==  Address 0x1ffeffdfac is on thread 1's stack
==2303993==  in frame #2, created by pmix_ptl_base_make_connection (???:)
==2303993== 
{
   <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
}
==2303993== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s)
==2303993==    at 0x109E179E: getsockopt_syscall (getsockopt.c:29)
==2303993==    by 0x109E179E: getsockopt (getsockopt.c:94)
==2303993==    by 0x19DA9157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==2303993==    by 0x19DB0A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==2303993==    by 0x19DB7DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==2303993==    by 0x19CB73C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==2303993==    by 0x19C30E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so)
==2303993==    by 0x193EFE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so)
==2303993==    by 0x149524CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==2303993==    by 0x102D9418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==2303993==    by 0x10272D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==2303993==    by 0xEF69D38: PetscInitialize (pinit.c:924)
==2303993==    by 0xEDDB66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==2303993==    by 0xEDDB6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==2303993==    by 0x233B09: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70)
==2303993==    by 0x229C01: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==2303993==    by 0x22D79A: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==2303993==    by 0x22D695: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==2303993==    by 0x22DCA9: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==2303993==    by 0x2283C0: main (TestCryptSimulation1d.cpp:18)
==2303993==  Address 0x1ffeffdfac is on thread 1's stack
==2303993==  in frame #2, created by pmix_ptl_base_make_connection (???:)
==2303993== 
{
   <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
}
==2303993== Syscall param setsockopt(optlen) contains uninitialised byte(s)
==2303993==    at 0x109E1C7E: setsockopt_syscall (setsockopt.c:29)
==2303993==    by 0x109E1C7E: setsockopt (setsockopt.c:95)
==2303993==    by 0x19DB0BA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==2303993==    by 0x19DB7DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==2303993==    by 0x19CB73C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2)
==2303993==    by 0x19C30E4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so)
==2303993==    by 0x193EFE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so)
==2303993==    by 0x149524CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==2303993==    by 0x102D9418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==2303993==    by 0x10272D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==2303993==    by 0xEF69D38: PetscInitialize (pinit.c:924)
==2303993==    by 0xEDDB66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==2303993==    by 0xEDDB6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==2303993==    by 0x233B09: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70)
==2303993==    by 0x229C01: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==2303993==    by 0x22D79A: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==2303993==    by 0x22D695: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==2303993==    by 0x22DCA9: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==2303993==    by 0x2283C0: main (TestCryptSimulation1d.cpp:18)
==2303993== 
{
   <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
}
==2303993== 
==2303993== FILE DESCRIPTORS: 9 open (3 std) at exit.
==2303993== Open file descriptor 12:
==2303993==    at 0x109CF22D: pipe (pipe.c:29)
==2303993==    by 0x193F007D: ???
==2303993==    by 0x149524CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==2303993==    by 0x102D9418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==2303993==    by 0x10272D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==2303993==    by 0xEF69D38: PetscInitialize (pinit.c:924)
==2303993==    by 0xEDDB66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==2303993==    by 0xEDDB6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==2303993==    by 0x233B09: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70)
==2303993==    by 0x229C01: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==2303993==    by 0x22D79A: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==2303993==    by 0x22D695: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==2303993==    by 0x22DCA9: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==2303993==    by 0x2283C0: main (TestCryptSimulation1d.cpp:18)
==2303993== 
==2303993== Open file descriptor 8: /dev/shm/open_mpi.0000
==2303993==    at 0x109D3BCC: __open_nocancel (open64_nocancel.c:39)
==2303993==    by 0x10957C4F: shm_open@@GLIBC_2.34 (shm_open.c:40)
==2303993==    by 0xEE13822: ???
==2303993==    by 0xEE1396F: ???
==2303993==    by 0x149F76DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==2303993==    by 0x149F7938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==2303993==    by 0x149AD922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==2303993==    by 0x149522DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==2303993==    by 0x102D9418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==2303993==    by 0x10272D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==2303993==    by 0xEF69D38: PetscInitialize (pinit.c:924)
==2303993==    by 0xEDDB66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==2303993==    by 0xEDDB6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==2303993==    by 0x233B09: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70)
==2303993==    by 0x229C01: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==2303993==    by 0x22D79A: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==2303993==    by 0x22D695: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==2303993==    by 0x22DCA9: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==2303993==    by 0x2283C0: main (TestCryptSimulation1d.cpp:18)
==2303993== 
==2303993== Open file descriptor 117:
==2303993==    <inherited from parent>
==2303993== 
==2303993== Open file descriptor 110:
==2303993==    <inherited from parent>
==2303993== 
==2303993== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestCryptSimulation1d_valgrind.txt
==2303993==    <inherited from parent>
==2303993== 
==2303993== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp
==2303993==    <inherited from parent>
==2303993== 
==2303993== 
==2303993== HEAP SUMMARY:
==2303993==     in use at exit: 700,720 bytes in 9,374 blocks
==2303993==   total heap usage: 4,059,208 allocs, 4,049,834 frees, 1,967,881,265 bytes allocated
==2303993== 
==2303993== 552 bytes in 1 blocks are definitely lost in loss record 36 of 62
==2303993==    at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==2303993==    by 0x19CBEC13: ???
==2303993==    by 0x19CBF22C: ???
==2303993==    by 0x19C324B7: ???
==2303993==    by 0x1023F15A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==2303993==    by 0x102D9A97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==2303993==    by 0x10272D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==2303993==    by 0xEF69D38: PetscInitialize (pinit.c:924)
==2303993==    by 0xEDDB66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==2303993==    by 0xEDDB6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==2303993==    by 0x233B09: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70)
==2303993==    by 0x229C01: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==2303993==    by 0x22D79A: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==2303993==    by 0x22D695: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==2303993==    by 0x22DCA9: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==2303993==    by 0x2283C0: main (TestCryptSimulation1d.cpp:18)
==2303993== 
{
   <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
}
==2303993== 84,459 (136 direct, 84,323 indirect) bytes in 1 blocks are definitely lost in loss record 59 of 62
==2303993==    at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
==2303993==    by 0x1B23174E: ???
==2303993==    by 0x1B231E0B: ???
==2303993==    by 0x1B234F56: ???
==2303993==    by 0x1B22A65D: ???
==2303993==    by 0x1B22AFA3: ???
==2303993==    by 0x14A63F05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2)
==2303993==    by 0x14A3FAE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2)
==2303993==    by 0x149F0CB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2)
==2303993==    by 0x1491DEF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==2303993==    by 0x193F0F03: ???
==2303993==    by 0x149524CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2)
==2303993==    by 0x102D9418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==2303993==    by 0x10272D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2)
==2303993==    by 0xEF69D38: PetscInitialize (pinit.c:924)
==2303993==    by 0xEDDB66F: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80)
==2303993==    by 0xEDDB6BD: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88)
==2303993==    by 0x233B09: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70)
==2303993==    by 0x229C01: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266)
==2303993==    by 0x22D79A: CxxTest::TestRunner::runWorld() (TestRunner.h:43)
==2303993==    by 0x22D695: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23)
==2303993==    by 0x22DCA9: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47)
==2303993==    by 0x2283C0: main (TestCryptSimulation1d.cpp:18)
==2303993== 
{
   <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
}
==2303993== LEAK SUMMARY:
==2303993==    definitely lost: 688 bytes in 2 blocks
==2303993==    indirectly lost: 1,760 bytes in 16 blocks
==2303993==      possibly lost: 0 bytes in 0 blocks
==2303993==    still reachable: 1,563 bytes in 7 blocks
==2303993==         suppressed: 696,709 bytes in 9,349 blocks
==2303993== Reachable blocks (those to which a pointer was found) are not shown.
==2303993== To see them, rerun with: --leak-check=full --show-leak-kinds=all
==2303993== 
==2303993== Use --track-origins=yes to see where uninitialised values come from
==2303993== For lists of detected and suppressed errors, rerun with: -s
==2303993== ERROR SUMMARY: 5 errors from 5 contexts (suppressed: 28 from 28)