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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