dolfin team mailing list archive

[Johan Hake <johan.hake@xxxxxxxxx>]

On Thursday July 21 2011 01:43:16 Garth N. Wells wrote:
> On 21/07/11 08:18, Johan Hake wrote:
> > On Thursday July 21 2011 00:12:15 Anders Logg wrote:
> >> On Thu, Jul 21, 2011 at 12:02:23AM -0700, Johan Hake wrote:
> >>>>> Hello!
> >>>>> 
> >>>>> I know this has been discussed earlier, but I cannot find a bug or
> >>>>> blueprint reported for it.
> >>>>> 
> >>>>> Let say I have a MixedSpace containing several global dofs (Real
> >>>>> spaces) and one CG. Even if I define a form using functions defined
> >>>>> only on the CG space it takes literally forever to assemble... This
> >>>>> is because for each cell, a bunch of zeros are added to the global
> >>>>> matrix, as the dofmap which defines the element matrix, is based on
> >>>>> the whole MixedSpace. It would be _really_ nice if the size of the
> >>>>> element matrix was based on the actuall dofs that get assembled.
> >>>> 
> >>>> As a quick fix, try using the Epetra backend. My experience is that
> >>>> it's much faster for this type of case. It must use a different search
> >>>> method for insertion than PETSc.
> >>> 
> >>> That helped _a lot_! Unfortunatly it looked like some assert kicked in
> >>> when using the NewtonSolver:
> >>> 
> >>> python: /usr/include/boost/smart_ptr/shared_ptr.hpp:412: typename
> >>> boost::detail::shared_ptr_traits<T>::reference boost::shared_ptr<
> >>> <template- parameter-1-1> >::operator*() const [with T =
> >>> Epetra_FECrsMatrix]: Assertion `px != 0' failed.
> >>> [bamse:25675] *** Process received signal ***
> >>> [bamse:25675] Signal: Aborted (6)
> >>> [bamse:25675] Signal code:  (-6)
> >>> [bamse:25675] [ 0] /lib/libpthread.so.0(+0xfb40) [0x7ff3bf52ab40]
> >>> [bamse:25675] [ 1] /lib/libc.so.6(gsignal+0x35) [0x7ff3be34bba5]
> >>> [bamse:25675] [ 2] /lib/libc.so.6(abort+0x180) [0x7ff3be34f6b0]
> >>> [bamse:25675] [ 3] /lib/libc.so.6(__assert_fail+0xf1) [0x7ff3be344a71]
> >>> [bamse:25675] [ 4]
> >>> /home/hake/bzr/fenics/dolfin/work/build/dolfin/libdolfin.so.0.9(_ZN6dol
> >>> fi n12EpetraMatrixaSERKS0_+0x156) [0x7ff3b983d7a6]
> >>> [bamse:25675] [ 5]
> >>> /home/hake/bzr/fenics/dolfin/work/build/dolfin/libdolfin.so.0.9(_ZN6dol
> >>> fi n12EpetraMatrixaSERKNS_13GenericMatrixE+0x52) [0x7ff3b983da12]
> >>> [bamse:25675] [ 6] /home/hake/local/lib/python2.6/site-
> >>> packages/dolfin/_cpp.so(+0xe0f23) [0x7ff3b9d4df23]
> >>> [bamse:25675] [ 7] python(PyEval_EvalFrameEx+0x5ca4) [0x4a5ce4]
> >>> [bamse:25675] [ 8] python(PyEval_EvalCodeEx+0x911) [0x4a6bd1]
> >>> [bamse:25675] [ 9] python() [0x535b50]
> >>> [bamse:25675] [10] python(PyObject_Call+0x47) [0x41c9d7]
> >>> [bamse:25675] [11] python() [0x42570f]
> >>> [bamse:25675] [12] python(PyObject_CallMethodObjArgs+0x1e4) [0x4209c4]
> >>> [bamse:25675] [13] /home/hake/local/lib/python2.6/site-
> >>> packages/dolfin/_cpp.so(_ZN29SwigDirector_NonlinearProblem1JERN6dolfin1
> >>> 3G enericMatrixERKNS0_13GenericVectorE+0xfe) [0x7ff3b9d3a3be]
> >>> [bamse:25675] [14]
> >>> /home/hake/bzr/fenics/dolfin/work/build/dolfin/libdolfin.so.0.9(_ZN6dol
> >>> fi
> >>> n12NewtonSolver5solveERNS_16NonlinearProblemERNS_13GenericVectorE+0x18
> >>> 0) [0x7ff3b9936b00]
> >>> [bamse:25675] [15] /home/hake/local/lib/python2.6/site-
> >>> packages/dolfin/_cpp.so(+0x1402e8) [0x7ff3b9dad2e8]
> >>> [bamse:25675] [16] python(PyEval_EvalFrameEx+0x5ca4) [0x4a5ce4]
> >>> [bamse:25675] [17] python(PyEval_EvalFrameEx+0x5a70) [0x4a5ab0]
> >>> [bamse:25675] [18] python(PyEval_EvalCodeEx+0x911) [0x4a6bd1]
> >>> [bamse:25675] [19] python(PyEval_EvalFrameEx+0x4d19) [0x4a4d59]
> >>> [bamse:25675] [20] python(PyEval_EvalFrameEx+0x5a70) [0x4a5ab0]
> >>> [bamse:25675] *** End of error message ***
> >>> Aborted
> >>> 
> >>> Have any one used Epetra backend for hand cooked NonlinearProblems in
> >>> Python. It looks like somehting might happen with the director typemap
> >>> here...
> >> 
> >> You should file a bug report. Maybe our Python maintainer will look at
> >> it. He's an expert in typemaps and directors... ;-)
> > 
> > Hmm, maybe I will? :)
> > 
> > I just wonder if anyone else have had the same problem. I also have to
> > work on a minimal example to reproduce the bug and it is starting to get
> > late over here...
> 
> I have had problems in the past, but they seem to be fixed now. The
> nonlinear demos run fine with Epetra.

I updated to latest version and the assert still kicks in. Not sure where the 
bug is hiding. I have no time debugging or file a detailed bug report for now. 
Will return to this issue in two weeks.

Johan
 
> Garth
> 
> > Good night!
> > 
> > Joahn
> > 
> >> --
> >> Anders
> >> 
> >>>>> Garth has previously mentioned that this is done to simplify the
> >>>>> assemble interface, which is understandable. However, beside fixing
> >>>>> assemble of global dofs in paralell this is my biggest wish for
> >>>>> ufc/ffc/dolfin at the moment :)
> >>>>> 
> >>>>> Unfortunatly I know to little about the ufc/ffc part of FEniCS to say
> >>>>> anything useful about what it would take to implement, but I would
> >>>>> like to here what others think.
> >>>> 
> >>>> I vaguely recall a blueprint on identifying in the generated code
> >>>> global dofs. I think that this is necessary in order to handle
> >>>> parallel assembly, etc, of global dofs.
> >>> 
> >>> Me too, but I could not find it.
> >>> 
> >>> Johan
> >>> 
> >>>> Garth
> >>>> 
> >>>>> Best regards,
> >>>>> 
> >>>>> Johan
> >>>>> 
> >>>>> _______________________________________________
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> >>>> 
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