dolfin team mailing list archive

[Johan Hake <hake@xxxxxxxxx>]

On Tuesday 22 September 2009 15:06:22 Garth N. Wells wrote:
> Johan Hake wrote:
> > On Tuesday 22 September 2009 14:57:16 DOLFIN wrote:
> >> One or more new changesets pushed to the primary dolfin repository.
> >> A short summary of the last three changesets is included below.
> >>
> >> changeset:   7134:18c7e560897b
> >> tag:         tip
> >> user:        "Johan Hake <hake@xxxxxxxxx>"
> >> date:        Tue Sep 22 14:57:13 2009 +0200
> >> files:       test/memory/dolfin_valgrind.supp
> >> description:
> >> A try to suppress some more annoying mpi valgrind complaints
> >
> > In the memtest on the jaunty-amd64 buildbot there are some complaints
> > related to gts and petsc:
> >
> > GTS:
> >
> > 72 bytes in 1 blocks are still reachable in loss record 40 of 67
> >    at 0x4C278AE: malloc (vg_replace_malloc.c:207)
> >    by 0x9077A12: g_malloc (in /usr/lib/libglib-2.0.so.0.2000.1)
> >    by 0x908DB07: g_slice_alloc (in /usr/lib/libglib-2.0.so.0.2000.1)
> >    by 0x9061812: g_hash_table_new_full (in
> > /usr/lib/libglib-2.0.so.0.2000.1) by 0x87D0E82: gts_object_class_new (in
> > /usr/lib/libgts-0.7.so.5.0.1) by 0x87D0F3E: gts_object_class (in
> > /usr/lib/libgts-0.7.so.5.0.1) by 0x87DCD0D: gts_bbox_class (in
> > /usr/lib/libgts-0.7.so.5.0.1) by 0x5043E1E:
> > dolfin::GTSInterface::create_box(dolfin::Cell const&)
> > (GTSInterface.cpp:186)
> >    by 0x5043FFD: dolfin::GTSInterface::buildCellTree()
> > (GTSInterface.cpp:198) by 0x5044134:
> > dolfin::GTSInterface::GTSInterface(dolfin::Mesh const&)
> > (GTSInterface.cpp:34)
> >    by 0x502DDA0:
> > dolfin::IntersectionDetector::IntersectionDetector(dolfin::Mesh const&)
> > (IntersectionDetector.cpp:30)
> >    by 0x4F67F67: dolfin::FunctionSpace::eval(double*, double const*,
> > dolfin::Function const&) const (FunctionSpace.cpp:122)
> >
> > +++
> >
> > PETSc:
> >
> > 96 bytes in 2 blocks are indirectly lost in loss record 55 of 67
> >    at 0x4C278AE: malloc (vg_replace_malloc.c:207)
> >    by 0xC6A5059: (within /usr/lib/openmpi/lib/libmpi.so.0.0.0)
> >    by 0xC6D1503: PMPI_Attr_put (in /usr/lib/openmpi/lib/libmpi.so.0.0.0)
> >    by 0x76C6F1D: PetscCommDuplicate(ompi_communicator_t*,
> > ompi_communicator_t**, int*) (tagm.c:233)
> >    by 0x764612F: PetscHeaderCreate_Private(_p_PetscObject*, int, int,
> > char const*, ompi_communicator_t*, int (*)(_p_PetscObject*), int (*)
> > (_p_PetscObject*, _p_PetscViewer*)) (inherit.c:44)
> >    by 0x7318595: VecCreate(ompi_communicator_t*, _p_Vec**)
> > (veccreate.c:39) by 0x7379278: VecCreateSeq(ompi_communicator_t*, int,
> > _p_Vec**) (vseqcr.c:38)
> >    by 0x4FE7B82: dolfin::PETScVector::init(unsigned int, unsigned int,
> > std::string) (PETScVector.cpp:520)
> >    by 0x4FE884B: dolfin::PETScVector::PETScVector(std::string)
> > (PETScVector.cpp:50)
> >    by 0x5016EEE: dolfin::PETScFactory::create_vector() const
> > (PETScFactory.cpp:27)
> >    by 0x4F4C2E8:
> > dolfin::VariationalProblem::solve_linear(dolfin::Function&) (Vector.h:32)
> >    by 0x438CB7: Eval::testArbitraryEval() (test.cpp:73)
> >
> > +++
> >
> > Are these real leaks or false positives? Can someone with more knowledge
> > of PETSc and/or GTS look at it?
> 
> I believe that the first is a libgts issue. The second I don't know. I
> had a look but I don't see any problems.
> 
> The supression files are of limited used because they depend on the
> library versions - the valgrind messages I get on my desktop are
> slightly different the valgrind messages on the buildbots. This makes
> sorting out leaks clumsy.

For sure!

However there are ways of expressing general suppressions with the use of *. 
We have tried to do that, but as you say, it is tedious and certainly not fail 
proof.

Should we only run the memtest on one buildbot? The problem are all the 
different configurations we have, which we then do not test.

Johan

> Garth
> 
> > Johan
> >
> >> changeset:   7133:5498ce4cf5fb
> >> user:        Anders Logg <logg@xxxxxxxxx>
> >> date:        Tue Sep 22 14:19:00 2009 +0200
> >> files:       test/system/parallel-assembly-solve/solver.py
> >> description:
> >> Keep tolerance 1e-10 in parallel system test but use as relative
> >> tolerance. Should make buildbot happy.
> >>
> >>
> >> changeset:   7132:0152cc635793
> >> user:        "Garth N. Wells <gnw20@xxxxxxxxx>"
> >> date:        Tue Sep 22 12:04:07 2009 +0100
> >> files:       test/regression/test.py
> >> description:
> >> Remove elastodynamics demo from regression tests (too slow).
> >>
> >> ----------------------------------------------------------------------
> >> For more details, visit http://www.fenics.org/hg/dolfin
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> >
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