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). 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
