[petsc-users] Strange error(?) message

[Mohammad Mirzadeh]

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!

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?




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/410/485but 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
>
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