[petsc-users] MatSetValues on same column multiple times

[Matthew Knepley]

On Tue, Sep 25, 2012 at 5:56 PM, John Mousel <john.mousel at gmail.com> wrote:

> To be more clear, I do the following:
>
> <preallocate>
> <insert 0's where I want columns>
> <flush>
> <insert real entries>
> <flush>
> <clean up special rows by adding corrections to coefficients>
>
> What I want to clarify is if I touch the same column more than once, say
> I'm looping over neighbors in an octree mesh, and it's just easier to
> insert them multiple times as I find them for fluxes in different
> directions instead of finding one exact coefficient for each neighbor, how
> much preallocation would I need to specify? The number of times it gets
> touched, or just one?
>

Just once. This is exactly how we operate with DMCreateMatrix(). You can
test it in any of the examples, like SNES ex5.

    Matt


> John
>
>
> On Tue, Sep 25, 2012 at 4:50 PM, Matthew Knepley <knepley at gmail.com>wrote:
>
>> On Tue, Sep 25, 2012 at 5:44 PM, John Mousel <john.mousel at gmail.com>wrote:
>>
>>>
>>> If I'm adding to a particular column in multiple passes, do I need to
>>> preallocate enough memory for each pass, or just 1 for each column in the
>>> row?
>>> Right now I'm drastically over-allocating, and I'm trying to reduce
>>> this. If I give the true number of columns in the row, I keep getting new
>>> entry errors.
>>>
>>> New nonzero at (8045,60) caused a malloc!
>>>
>>
>> You have to be more specific. It sounds like what you are doing is
>>
>> <preallocate>
>> <put in some nonzeros>
>> <assemble>
>> <try to put in more nonzeros>
>>
>> This will not work since assembly squeezes out extra space. Why are you
>> assembling in between?
>> If you need to clear buffers, you can just to MAT_ASSEMBLY_FLUSH.
>>
>>    Matt
>>
>>
>>> I have it spit into phases where I set zeros in the non-zero pattern,
>>> then I come back and fill in entries in a bulk pass, and then do a second
>>> pass to clean up entries in special rows.
>>> Could someone clarify how this works.
>>>
>>> John
>>>
>>
>>
>>
>> --
>> 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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