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/410/485but > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20120411/e8d3968f/attachment.htm>
