Thanks for your interest, I already shutdown preconditioner as shown in notebook with;
solvers.linearPCGSolver.LinearPCGSolver(precon=None, iterations=500, tolerance=1e-15) I think this should turn preconditioner off but still code run completed at around 55 sec with 8 cores (serial was around 41 sec). So I think problem is beyond preconditioner. I paste last version of the code below if you'd like to try. http://pastebin.com/VL4dWCJr I also would like to know is there a decent way to profile parallel run may be it can gave me a clue on problem. Serbulent 2014-09-30 17:43 GMT+03:00 Daniel Wheeler <[email protected]>: > On Mon, Sep 29, 2014 at 4:09 PM, Serbulent UNSAL <[email protected]> > wrote: > >> Thanks for help. >> >> Using LinearPCGSolver gives some more speed but it it still slower than >> serial version ( 41 sec vs. 55 sec ). >> > > Serbulent, > > It seems that in this notebook, > http://nbviewer.ipython.org/github/wd15/fipy-efficiency/blob/master/notebooks/FiPy-IPython.ipynb, > the serial version PCG using Trilinos is faster than the serial version of > PySparse without preconditioning. Preconditioning with Trilinos can often > impact efficiency quite heavily. > > > >> >> I tried to use Gmsh mesh with using workaround defined at >> http://wd15.github.io/2014/01/30/fipy-trilinos-anaconda/ >> But Gmsh is even slower than normal mesh. >> > > I don't think I factored that in when writing up the notebooks. I might > look into that. > > >> >> Since I use a big mesh (400x400) I think, I will have communication issue >> that defined at the end of the first notebook. >> > > Take a look at the second notebook, > http://nbviewer.ipython.org/github/wd15/fipy-efficiency/blob/master/notebooks/cluster.ipynb, > 400x400 should be large enough to get some reasonable scaling. > > > >> >> I'm open for any alternative strategies and suggestions. >> > > I am not sure what to suggest. Certainly disable the preconditioners in > Trilinos and see what happens. It may be that we need to use > preconditioning in a less naive way in FiPy (not precondition at every > sweep, there may be ways to do that with Trilinos). > > -- > Daniel Wheeler > > _______________________________________________ > fipy mailing list > [email protected] > http://www.ctcms.nist.gov/fipy > [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] > >
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