==934490== Memcheck, a memory error detector ==934490== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==934490== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==934490== Command: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/crypt/test/TestCryptSimulation2dWithVertexBasedCellPopulation -malloc_debug -malloc_dump -memory_info ==934490== Parent PID: 914403 ==934490== ==934490== WARNING: pwritev(vector[...]) is an obsolete suppression line not supported in valgrind 3.15 or later. ==934490== You should replace [...] by a specific index such as [0] or [1] or [2] or similar ==934490== ==934490== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==934490== at 0x109E079E: getsockopt_syscall (getsockopt.c:29) ==934490== by 0x109E079E: getsockopt (getsockopt.c:94) ==934490== by 0x19DA5157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==934490== by 0x19DACA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==934490== by 0x19DB3DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==934490== by 0x19CB33C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==934490== by 0x19C2CE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==934490== by 0x193EBE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==934490== by 0x149504CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==934490== by 0x102D8418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==934490== by 0x10271D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==934490== by 0xEF68D38: PetscInitialize (pinit.c:924) ==934490== by 0xEDDA58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==934490== by 0xEDDA5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==934490== by 0x232E47: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70) ==934490== by 0x229013: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==934490== by 0x22CCD6: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==934490== by 0x22CB76: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==934490== by 0x22D20D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==934490== by 0x227300: main (TestCryptSimulation2dWithVertexBasedCellPopulation.cpp:19) ==934490== Address 0x1ffeffdf8c is on thread 1's stack ==934490== in frame #2, created by pmix_ptl_base_make_connection (???:) ==934490== { 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 } ==934490== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==934490== at 0x109E079E: getsockopt_syscall (getsockopt.c:29) ==934490== by 0x109E079E: getsockopt (getsockopt.c:94) ==934490== by 0x19DA5157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==934490== by 0x19DACA1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==934490== by 0x19DB3DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==934490== by 0x19CB33C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==934490== by 0x19C2CE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==934490== by 0x193EBE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==934490== by 0x149504CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==934490== by 0x102D8418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==934490== by 0x10271D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==934490== by 0xEF68D38: PetscInitialize (pinit.c:924) ==934490== by 0xEDDA58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==934490== by 0xEDDA5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==934490== by 0x232E47: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70) ==934490== by 0x229013: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==934490== by 0x22CCD6: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==934490== by 0x22CB76: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==934490== by 0x22D20D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==934490== by 0x227300: main (TestCryptSimulation2dWithVertexBasedCellPopulation.cpp:19) ==934490== Address 0x1ffeffdf8c is on thread 1's stack ==934490== in frame #2, created by pmix_ptl_base_make_connection (???:) ==934490== { 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 } ==934490== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==934490== at 0x109E0C7E: setsockopt_syscall (setsockopt.c:29) ==934490== by 0x109E0C7E: setsockopt (setsockopt.c:95) ==934490== by 0x19DACBA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==934490== by 0x19DB3DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==934490== by 0x19CB33C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==934490== by 0x19C2CE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==934490== by 0x193EBE6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==934490== by 0x149504CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==934490== by 0x102D8418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==934490== by 0x10271D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==934490== by 0xEF68D38: PetscInitialize (pinit.c:924) ==934490== by 0xEDDA58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==934490== by 0xEDDA5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==934490== by 0x232E47: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70) ==934490== by 0x229013: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==934490== by 0x22CCD6: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==934490== by 0x22CB76: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==934490== by 0x22D20D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==934490== by 0x227300: main (TestCryptSimulation2dWithVertexBasedCellPopulation.cpp:19) ==934490== { 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 } ==934490== ==934490== FILE DESCRIPTORS: 9 open (3 std) at exit. ==934490== Open file descriptor 12: ==934490== at 0x109CE22D: pipe (pipe.c:29) ==934490== by 0x193EC07D: ??? ==934490== by 0x149504CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==934490== by 0x102D8418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==934490== by 0x10271D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==934490== by 0xEF68D38: PetscInitialize (pinit.c:924) ==934490== by 0xEDDA58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==934490== by 0xEDDA5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==934490== by 0x232E47: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70) ==934490== by 0x229013: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==934490== by 0x22CCD6: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==934490== by 0x22CB76: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==934490== by 0x22D20D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==934490== by 0x227300: main (TestCryptSimulation2dWithVertexBasedCellPopulation.cpp:19) ==934490== ==934490== Open file descriptor 8: /dev/shm/open_mpi.0000 ==934490== at 0x109D2BCC: __open_nocancel (open64_nocancel.c:39) ==934490== by 0x10956C4F: shm_open@@GLIBC_2.34 (shm_open.c:40) ==934490== by 0xEE12822: ??? ==934490== by 0xEE1296F: ??? ==934490== by 0x149F56DC: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==934490== by 0x149F5938: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==934490== by 0x149AB922: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==934490== by 0x149502DB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==934490== by 0x102D8418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==934490== by 0x10271D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==934490== by 0xEF68D38: PetscInitialize (pinit.c:924) ==934490== by 0xEDDA58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==934490== by 0xEDDA5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==934490== by 0x232E47: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70) ==934490== by 0x229013: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==934490== by 0x22CCD6: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==934490== by 0x22CB76: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==934490== by 0x22D20D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==934490== by 0x227300: main (TestCryptSimulation2dWithVertexBasedCellPopulation.cpp:19) ==934490== ==934490== Open file descriptor 111: ==934490== ==934490== ==934490== Open file descriptor 108: ==934490== ==934490== ==934490== Open file descriptor 4: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/memtest/TestCryptSimulation2dWithVertexBasedCellPopulation_valgrind.txt ==934490== ==934490== ==934490== Open file descriptor 3: /home/github/actions-runner/_work/Chaste/Chaste/Chaste/chaste-build-dir/Testing/Temporary/LastTest.log.tmp ==934490== ==934490== ==934490== ==934490== HEAP SUMMARY: ==934490== in use at exit: 700,718 bytes in 9,374 blocks ==934490== total heap usage: 3,331,411 allocs, 3,322,037 frees, 1,615,401,760 bytes allocated ==934490== ==934490== 552 bytes in 1 blocks are definitely lost in loss record 36 of 62 ==934490== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==934490== by 0x19CBAC13: ??? ==934490== by 0x19CBB22C: ??? ==934490== by 0x19C2E4B7: ??? ==934490== by 0x1023E15A: ompi_proc_complete_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==934490== by 0x102D8A97: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==934490== by 0x10271D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==934490== by 0xEF68D38: PetscInitialize (pinit.c:924) ==934490== by 0xEDDA58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==934490== by 0xEDDA5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==934490== by 0x232E47: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70) ==934490== by 0x229013: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==934490== by 0x22CCD6: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==934490== by 0x22CB76: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==934490== by 0x22D20D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==934490== by 0x227300: main (TestCryptSimulation2dWithVertexBasedCellPopulation.cpp:19) ==934490== { 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 } ==934490== 84,459 (136 direct, 84,323 indirect) bytes in 1 blocks are definitely lost in loss record 59 of 62 ==934490== at 0x484DA83: calloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==934490== by 0x1B22D74E: ??? ==934490== by 0x1B22DE0B: ??? ==934490== by 0x1B230F56: ??? ==934490== by 0x1B22665D: ??? ==934490== by 0x1B226FA3: ??? ==934490== by 0x14A61F05: ??? (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==934490== by 0x14A3DAE8: hwloc_topology_load (in /usr/lib/x86_64-linux-gnu/libhwloc.so.15.5.2) ==934490== by 0x149EECB5: opal_hwloc_base_get_topology (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.40.30.2) ==934490== by 0x1491BEF6: orte_ess_base_proc_binding (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==934490== by 0x193ECF03: ??? ==934490== by 0x149504CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==934490== by 0x102D8418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==934490== by 0x10271D7A: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==934490== by 0xEF68D38: PetscInitialize (pinit.c:924) ==934490== by 0xEDDA58B: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==934490== by 0xEDDA5D9: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==934490== by 0x232E47: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70) ==934490== by 0x229013: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==934490== by 0x22CCD6: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==934490== by 0x22CB76: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==934490== by 0x22D20D: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==934490== by 0x227300: main (TestCryptSimulation2dWithVertexBasedCellPopulation.cpp:19) ==934490== { 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 } ==934490== LEAK SUMMARY: ==934490== definitely lost: 688 bytes in 2 blocks ==934490== indirectly lost: 1,760 bytes in 16 blocks ==934490== possibly lost: 0 bytes in 0 blocks ==934490== still reachable: 1,563 bytes in 7 blocks ==934490== suppressed: 696,707 bytes in 9,349 blocks ==934490== Reachable blocks (those to which a pointer was found) are not shown. ==934490== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==934490== ==934490== Use --track-origins=yes to see where uninitialised values come from ==934490== For lists of detected and suppressed errors, rerun with: -s ==934490== ERROR SUMMARY: 5 errors from 5 contexts (suppressed: 28 from 28)