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