UPDATE: I cleaned up my configure, the error still exists on at least two
of our build boxes in opt, oprof and dbg modes. (that's a good sign -
repeatable). Jason, is going to rebuild one of the build boxes itself with
a clean software stack and try once more, we are still not able to make it
fail on our developer test box (called "rod"). I am unable to see any bugs
in the compute_periodic_constraints method so this is still open:
../configure --with-methods=opt oprof dbg
--prefix=/home/moosetest/permcj/moose/scripts/../libmesh/installed
--enable-silent-rules --enable-unique-id --disable-warnings --disable-cxx11
--enable-openmp --enable-shared --disable-static
On Mon, Jul 7, 2014 at 11:59 AM, Cody Permann <codyperm...@gmail.com> wrote:
> Devs,
>
> We updated the MOOSE users to a new revision of libMesh last week and
> picked up a Valgrind error in the process. John spent a good portion of the
> day on Thursday just trying to reproduce it on one of our development Linux
> boxes without success. Towards the end of the day he finally logged into
> one of the build boxes (hpcbuild5) where we are actually seeing the error
> and he was finally able to replicate the error on that box with his own
> build of libMesh+MOOSE. What differences exist between the two boxes is
> still under investigation and I hope to be able to reproduce the error on
> the rest of our boxes. I took his progress one step further by reproducing
> the error using pure libMesh.
>
> As of now, I can grab a fresh copy of libMesh, configure and build with
> the normal set of options that we use for MOOSE and reproduce the error
> with "adaptivity example 5". I'll paste the error here so you can see it
> in case anyone might know what has changed in this code without we pulling
> up my sleeves. I'll continue to dig for more answers. In fact, I just
> noticed that we are using the default-comm-world option still on our build
> boxes which isn't right.
>
> Thanks,
> Cody
>
> Here's my configure from config.log which admittedly is a huge mess:
>
> $ ../configure --with-methods=opt oprof dbg
> --prefix=/home/moosetest/permcj/moose/scripts/../libmesh/installed
> --enable-silent-rules --enable-openmp --enable-shared --disable-static
> --enable-unique-id --disable-warnings --enable-default-comm-world
> --disable-cxx11 CXX=mpicxx CC=mpicc FC=mpif90 F77=mpif77 METHODS=opt oprof
> dbg PETSC_DIR=/opt/moose/petsc/mpich_petsc-3.4.3/gcc-opt --disable-netcdf-4
> --disable-testsets CXX=mpicxx CC=mpicc F77=mpif77 FC=mpif90 CPPFLAGS=
> LIBS= --no-create --no-recursion
>
> Valgrind Error:
> [moosetest][~/permcj/moose/libmesh/installed/examples/adaptivity/ex5]>
> valgrind --leak-check=full --track-origins=yes ./example-opt
> -init_timestep 0 -n_timesteps 5
>
> ==28408== Memcheck, a memory error detector
>
> ==28408== Copyright (C) 2002-2011, and GNU GPL'd, by Julian Seward et al.
>
> ==28408== Using Valgrind-3.7.0 and LibVEX; rerun with -h for copyright info
>
> ==28408== Command: ./example-opt -init_timestep 0 -n_timesteps 5
>
> ==28408==
>
> Usage:
>
> ./example-opt -init_timestep 0
>
> OR
>
> ./example-opt -read_solution -init_timestep 26
>
>
> Running: ./example-opt -init_timestep 0 -n_timesteps 5
>
>
> Mesh Information:
>
> mesh_dimension()=2
>
> spatial_dimension()=3
>
> n_nodes()=4225
>
> n_local_nodes()=4225
>
> n_elem()=5460
>
> n_local_elem()=5460
>
> n_active_elem()=4096
>
> n_subdomains()=1
>
> n_partitions()=1
>
> n_processors()=1
>
> n_threads()=1
>
> processor_id()=0
>
>
> ==28408== Conditional jump or move depends on uninitialised value(s)
>
> ==28408== at 0x72B1D30: rml::internal::isLargeObject(void*)
> (frontend.cpp:2163)
>
> ==28408== by 0x72B2A14: scalable_free (frontend.cpp:2564)
>
> ==28408== by 0x55FECD7: std::_Rb_tree<unsigned int, std::pair<unsigned
> int const, double>, std::_Select1st<std::pair<unsigned int const, double>
> >, std::less<unsigned int>,
> libMesh::Threads::scalable_allocator<std::pair<unsigned int const, double>
> > >::_M_erase_aux(std::_Rb_tree_const_iterator<std::pair<unsigned int
> const, double> >) (in
> /home/moosetest/permcj/moose/libmesh/installed/lib/libmesh_opt.so.0.0.0)
>
> ==28408== by 0x55FED58: std::_Rb_tree<unsigned int, std::pair<unsigned
> int const, double>, std::_Select1st<std::pair<unsigned int const, double>
> >, std::less<unsigned int>,
> libMesh::Threads::scalable_allocator<std::pair<unsigned int const, double>
> > >::erase(unsigned int const&) (in
> /home/moosetest/permcj/moose/libmesh/installed/lib/libmesh_opt.so.0.0.0)
>
> ==28408== by 0x55F6F51:
> libMesh::DofMap::process_constraints(libMesh::MeshBase&) (in
> /home/moosetest/permcj/moose/libmesh/installed/lib/libmesh_opt.so.0.0.0)
>
> ==28408== by 0x5B859AF: libMesh::System::init_data() (in
> /home/moosetest/permcj/moose/libmesh/installed/lib/libmesh_opt.so.0.0.0)
>
> ==28408== by 0x5B6B8F2: libMesh::ImplicitSystem::init_data() (in
> /home/moosetest/permcj/moose/libmesh/installed/lib/libmesh_opt.so.0.0.0)
>
> ==28408== by 0x5B734D8: libMesh::LinearImplicitSystem::init_data() (in
> /home/moosetest/permcj/moose/libmesh/installed/lib/libmesh_opt.so.0.0.0)
>
> ==28408== by 0x5BBF794:
> libMesh::TransientSystem<libMesh::LinearImplicitSystem>::init_data() (in
> /home/moosetest/permcj/moose/libmesh/installed/lib/libmesh_opt.so.0.0.0)
>
> ==28408== by 0x5B85C38: libMesh::System::init() (in
> /home/moosetest/permcj/moose/libmesh/installed/lib/libmesh_opt.so.0.0.0)
>
> ==28408== by 0x5B493ED: libMesh::EquationSystems::init() (in
> /home/moosetest/permcj/moose/libmesh/installed/lib/libmesh_opt.so.0.0.0)
>
> ==28408== by 0x40DB8D: main (in
> /home/moosetest/permcj/moose/libmesh/installed/examples/adaptivity/ex5/example-opt)
>
> ==28408== Uninitialised value was created by a stack allocation
>
> ==28408== at 0x5707D00:
> libMesh::FEGenericBase<double>::compute_periodic_constraints(libMesh::DofConstraints&,
> libMesh::DofMap&, libMesh::PeriodicBoundaries const&, libMesh::MeshBase
> const&, libMesh::PointLocatorBase const*, unsigned int, libMesh::Elem
> const*) (in
> /home/moosetest/permcj/moose/libmesh/installed/lib/libmesh_opt.so.0.0.0)
>
> ==28408==
>
> ==28408== Conditional jump or move depends on uninitialised value(s)
>
> ==28408== at 0x72B1D30: rml::internal::isLargeObject(void*)
> (frontend.cpp:2163)
>
> ==28408== by 0x72B2A14: scalable_free (frontend.cpp:2564)
>
> ==28408== by 0x56187AA: libMesh::SparsityPattern::Build::~Build() (in
> /home/moosetest/permcj/moose/libmesh/installed/lib/libmesh_opt.so.0.0.0)
>
> ==28408== by 0x55CB575:
> libMesh::DofMap::compute_sparsity(libMesh::MeshBase const&) (in
> /home/moosetest/permcj/moose/libmesh/installed/lib/libmesh_opt.so.0.0.0)
>
> ==28408== by 0x5B68824: libMesh::ImplicitSystem::init_matrices() (in
> /home/moosetest/permcj/moose/libmesh/installed/lib/libmesh_opt.so.0.0.0)
>
> ==28408== by 0x5B734D8: libMesh::LinearImplicitSystem::init_data() (in
> /home/moosetest/permcj/moose/libmesh/installed/lib/libmesh_opt.so.0.0.0)
>
> ==28408== by 0x5BBF794:
> libMesh::TransientSystem<libMesh::LinearImplicitSystem>::init_data() (in
> /home/moosetest/permcj/moose/libmesh/installed/lib/libmesh_opt.so.0.0.0)
>
> ==28408== by 0x5B85C38: libMesh::System::init() (in
> /home/moosetest/permcj/moose/libmesh/installed/lib/libmesh_opt.so.0.0.0)
>
> ==28408== by 0x5B493ED: libMesh::EquationSystems::init() (in
> /home/moosetest/permcj/moose/libmesh/installed/lib/libmesh_opt.so.0.0.0)
>
> ==28408== by 0x40DB8D: main (in
> /home/moosetest/permcj/moose/libmesh/installed/examples/adaptivity/ex5/example-opt)
>
> ==28408== Uninitialised value was created by a stack allocation
>
> ==28408== at 0x5707D00:
> libMesh::FEGenericBase<double>::compute_periodic_constraints(libMesh::DofConstraints&,
> libMesh::DofMap&, libMesh::PeriodicBoundaries const&, libMesh::MeshBase
> const&, libMesh::PointLocatorBase const*, unsigned int, libMesh::Elem
> const*) (in
> /home/moosetest/permcj/moose/libmesh/installed/lib/libmesh_opt.so.0.0.0)
>
> ==28408==
>
> Initial H1 norm = 1.74175
>
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