[petsc-users] Strange error(?) message

[Matthew Knepley]

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
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