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. 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
