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 > >>>>> > >>>>> _______________________________________________ > >>>>> Mailing list: https://launchpad.net/~dolfin > >>>>> Post to : [email protected] > >>>>> Unsubscribe : https://launchpad.net/~dolfin > >>>>> More help : https://help.launchpad.net/ListHelp > >>>> > >>>> _______________________________________________ > >>>> Mailing list: https://launchpad.net/~dolfin > >>>> Post to : [email protected] > >>>> Unsubscribe : https://launchpad.net/~dolfin > >>>> More help : https://help.launchpad.net/ListHelp > >>> > >>> _______________________________________________ > >>> Mailing list: https://launchpad.net/~dolfin > >>> Post to : [email protected] > >>> Unsubscribe : https://launchpad.net/~dolfin > >>> More help : https://help.launchpad.net/ListHelp > > > > _______________________________________________ > > Mailing list: https://launchpad.net/~dolfin > > Post to : [email protected] > > Unsubscribe : https://launchpad.net/~dolfin > > More help : https://help.launchpad.net/ListHelp > > _______________________________________________ > Mailing list: https://launchpad.net/~dolfin > Post to : [email protected] > Unsubscribe : https://launchpad.net/~dolfin > More help : https://help.launchpad.net/ListHelp _______________________________________________ Mailing list: https://launchpad.net/~dolfin Post to : [email protected] Unsubscribe : https://launchpad.net/~dolfin More help : https://help.launchpad.net/ListHelp
