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... 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 > > > > > > > > _______________________________________________ > > > > Mailing list: https://launchpad.net/~dolfin > > > > Post to : dolfin@lists.launchpad.net > > > > Unsubscribe : https://launchpad.net/~dolfin > > > > More help : https://help.launchpad.net/ListHelp > > > > > > _______________________________________________ > > > Mailing list: https://launchpad.net/~dolfin > > > Post to : dolfin@lists.launchpad.net > > > Unsubscribe : https://launchpad.net/~dolfin > > > More help : https://help.launchpad.net/ListHelp > > > > _______________________________________________ > > Mailing list: https://launchpad.net/~dolfin > > Post to : dolfin@lists.launchpad.net > > Unsubscribe : https://launchpad.net/~dolfin > > More help : https://help.launchpad.net/ListHelp _______________________________________________ Mailing list: https://launchpad.net/~dolfin Post to : dolfin@lists.launchpad.net Unsubscribe : https://launchpad.net/~dolfin More help : https://help.launchpad.net/ListHelp
