On Monday February 21 2011 15:14:59 Garth N. Wells wrote: > On 21/02/11 20:52, Johan Hake wrote: > > On Monday February 21 2011 12:47:51 Garth N. Wells wrote: > >> On 21/02/11 20:36, Johan Hake wrote: > >>> On Monday February 21 2011 12:31:18 Garth N. Wells wrote: > >>>> On 21/02/11 18:00, Johan Hake wrote: > >>>>> On Monday February 21 2011 08:18:18 Garth N. Wells wrote: > >>>>>> On 17/02/11 21:28, Johan Hake wrote: > >>>>>>> Hello! > >>>>>>> > >>>>>>> I have a not so large 3D mesh of some 50K vertices, generated from > >>>>>>> some geometry (not UnitCube). > >>>>>>> > >>>>>>> When I set > >>>>>>> > >>>>>>> parameters.num_threads = 2 > >>>>>>> > >>>>>>> and try to assemble I just get: > >>>>>>> Coloring mesh. > >>>>>>> > >>>>>>> and then it seems it wont find a solution... I had to break it > >>>>>>> because it nearly hang the computer for some 5 min. > >>>>>>> > >>>>>>> Have anyone experience the same? Is there any way to controll the > >>>>>>> coloring? > >>>>>> > >>>>>> It's had minimal testing, so issues can be expected. Can you post > >>>>>> your solver? 50k vertices is not very big, so I would expect it to > >>>>>> be pretty fast. > >>>>> > >>>>> Yes I would expect that too. I have used the coloring on other meshes > >>>>> with success. > >>>>> > >>>>> The mesh can be downloaded from here: > >>>>> <http://folk.uio.no/hake/trouble.xml.gz> > >>>>> > >>>>> To reproduce the trouble just run: > >>>>> from dolfin import * > >>>>> mesh = Mesh('trouble.xml.gz') > >>>>> V = FunctionSpace(mesh, "CG", 1) > >>>>> assemble(Function(V)*dx) > >>>>> parameters.num_threads = 2 > >>>>> assemble(Function(V)*dx) > >>>>> > >>>>> The mesh has two distinct domains, but that shouldnto be causing the > >>>>> trouble, as other I have successfully colored other such meshes. > > > > The language is a bit hasty put together, but I meant to say here that I > > have succesfully tried it with other disconnected meshes. > > > >>>>> I > >>>>> guess it can be the particular mesh that causes coloring to stall. It > >>>>> is generated using tetgen. > > > > Here I meant to say that the particular mesh might cause the problem. > > > >>>> I don't think that I've tested multi-threaded assembly for > >>>> functionals. > >>>> > >>>> When we get around to implementing it, assembling functionals > >>>> shouldn't require colouring. It should just involve OpenMP > >>>> parallelising the assembly loop, and then each thread adds its > >>>> contribution to the result once it's processed its bunch of cells > >>>> (while avoiding a race condition). > >>> > >>> I just used a Functional so I could stick with a shorter example ;) > >>> > >>> The above code works fine with another mesh. Changing the form to a > >>> linear or bilinear form triggers the same coloring (right?), which > >>> stalls on this particular mesh. > >> > >> You didn't bother to mention that the mesh is special! > > > > I tried! > > > >> The mesh is disconnected, which I suspect is the problem. My limited > >> understanding of the Boost colouring algorithm is that it starts at one > >> graph node and advances from there by moving along edges. Obviously this > >> will break down for a disconnected meshes since there is no way for the > >> algorithm to move from one graph (mesh) to the next. > > > > I thought that too. But as I tried to tell you, I have succesfully tried > > other disconnected meshes. > > I've made it possible to choose between Boost and Zoltan for colouring > via the parameter system. Zoltan seems to handle your mesh (it runs - I > haven't checked the result further).
Thanks! Will look further into it. Johan > Garth > > > Johan > > > >> Garth > >> > >>> Johan > >>> > >>>> Garth > >>>> > >>>>> At the end of the day I have to wait untill we support subdomains in > >>>>> the OpenMPAssembler as I am heavily using these... > >>>>> > >>>>> Johan > >>>>> > >>>>>> Garth > >>>>>> > >>>>>>> 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
