On Wed, Apr 11, 2012 at 10:49 PM, Mohammad Mirzadeh <mirzadeh at gmail.com>wrote:
> I see. Well the reason for non-symmetry is that I'm using a finite > difference discretization on quadtree AMR grids. When discretizing at a > hanging node, i.e. a node that is missing a direct neighbor, I use > interpolation from nodes of the parent cell. When it comes to discretizing > at those nodes (i.e. nodes of the parent), however, they are on a coarser > grid and will have direct neighbors so they would not see the hanging node > in their discretization. This leads to a non-symmetric discretization > matrix which I was using (structurally) to define the adjacency matrix of > the graph. I think I can fix this by requiring the parent nodes to also > have a link to the hanging node (although they are not used in the > discretization anyway) > > I'm just surprised that ParMetis does not complain about non-symmetric > graphs at lower resolutions and partitions them just fine! > ParMetis does not burden the user with a whole lot of diagnostic output :) > As for the debugger, -start_in_debugger does not start the debugger for me > :(. I'm using mpirun -np 2 ./a.out -start_in_debugger. Is this the correct > way? > Send the entire output. It is likely that at the beginning there are lines showing a failure to open an X window. Matt > > On Wed, Apr 11, 2012 at 3:07 PM, Matthew Knepley <knepley at gmail.com>wrote: > >> On Wed, Apr 11, 2012 at 8:24 PM, Mohammad Mirzadeh <mirzadeh at >> gmail.com>wrote: >> >>> I was reading the FAQ list when I came across the following: >>> >>> http://www.mcs.anl.gov/petsc/documentation/faq.html#key >>> >>> When calling MatPartitioningApply() you get a message Error! Key 16615 >>> not found The graph of the matrix you are using is not symmetric. You >>> must use symmetric matrices for partitioning. >>> >>> Is this a limitation on ParMetis side? I set up the adjacency matrix >>> based on the discretization that I will be performing on the grid which is >>> non-symmetric; both numerically and structurally. What's the solution here? >>> Make an "approximate" adjacency matrix that sort of looks like >>> (structurally) my discretization but is symmetric? What I don't understand >>> is my matrix IS non-symmetric when the code runs on coarser grids! >>> >> >> I don't quite understand how you can have a non-symmetric adjacency >> description. But Metis/ParMetis partitions undirected graphs, which >> by definition have symmetric adjacency matrices. Non-symmetric adjacency >> would seem to imply a directed graph of some sort, or more plainly, >> something is a adjacent to another thing which is not adjacent to it. >> That is a very strange concept. >> >> >>> Also, I was reading the FAQ hoping I can find something regarding using >>> gdb in parallel. I found this: >>> http://scicomp.stackexchange.com/a/410/485 but I'm not sure how I >>> should be using gdb in parallel. Could you (maybe Matt?) please explain a >>> little bit? >>> >> >> -start_in_debugger spawns a gdb windows for EVERY process and attaches it >> >> -debbuger_nodes a,b,c spawns gdb windows ONLY for ranks a, b, and c >> >> Thanks, >> >> Matt >> >> >>> Thanks >>> >>> On Tue, Apr 10, 2012 at 12:08 AM, Mohammad Mirzadeh <mirzadeh at >>> gmail.com>wrote: >>> >>>> Just built petsc-dev and it did not help. I'm going to look into the >>>> code to see if my graph is "ill-formed" in some sense. Just hope the >>>> problem is from my side not a real bug in ParMetis! >>>> >>>> >>>> >>>> On Mon, Apr 9, 2012 at 8:46 PM, Mohammad Mirzadeh <mirzadeh at >>>> gmail.com>wrote: >>>> >>>>> ok. Thanks Jed. I'll try petsc-dev to see if it fixes the problem. >>>>> >>>>> Thanks everyone. >>>>> >>>>> >>>>> On Mon, Apr 9, 2012 at 8:42 PM, Jed Brown <jedbrown at mcs.anl.gov>wrote: >>>>> >>>>>> On Mon, Apr 9, 2012 at 22:37, Mohammad Mirzadeh <mirzadeh at >>>>>> gmail.com>wrote: >>>>>> >>>>>>> Thanks Sean. I'm using Petsc 3.2-p6 along with ParMetis 4.0.2. Since >>>>>>> this was not supported with 3.2-p6, and previous versions had bugs, I >>>>>>> built >>>>>>> parmetis myself and used --with-parmetis-include and --with-parmetis-lib >>>>>>> flags to build petsc. >>>>>>> >>>>>>> Should I switch to petsc-dev? >>>>>>> >>>>>> >>>>>> Yes, and use --download-metis --download-parmetis because the version >>>>>> upstream has some bugs for which the patches have not been applied. >>>>>> >>>>> >>>>> >>>> >>> >> >> >> -- >> What most experimenters take for granted before they begin their >> experiments is infinitely more interesting than any results to which their >> experiments lead. >> -- Norbert Wiener >> > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20120412/eba9df3c/attachment-0001.htm>
