[petsc-users] Strange error(?) message

[Matthew Knepley]

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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