dolfin team mailing list archive

["Garth N. Wells" <gnw20@xxxxxxxxx>]

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(_ZN6dolfi
>>> n12EpetraMatrixaSERKS0_+0x156) [0x7ff3b983d7a6]
>>> [bamse:25675] [ 5]
>>> /home/hake/bzr/fenics/dolfin/work/build/dolfin/libdolfin.so.0.9(_ZN6dolfi
>>> 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_NonlinearProblem1JERN6dolfin13G
>>> enericMatrixERKNS0_13GenericVectorE+0xfe) [0x7ff3b9d3a3be]
>>> [bamse:25675] [14]
>>> /home/hake/bzr/fenics/dolfin/work/build/dolfin/libdolfin.so.0.9(_ZN6dolfi
>>> n12NewtonSolver5solveERNS_16NonlinearProblemERNS_13GenericVectorE+0x180)
>>> [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.

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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>>>
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> 
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