[petsc-users] Preallocation (Unstructured FE)

[Matthew Knepley]

On Mon, May 2, 2011 at 8:16 AM, Tabrez Ali <stali at geology.wisc.edu> wrote:

>  Is there a way I can use this and other mesh routines from Fortran? The
> manual doesn't say much on this.
>

Yes, but you are right that nothing is in the manual. DMMESH (in petsc-dev)
now obeys the full DM interface,
so that DMGetMatrix() will return you a properly allocated Mat. So what is
the problem? Of course, it is that
Petsc has no good way to specify what finite element you are dealing with.

The way I was doing this is to encode it using some C++ classes. This turns
out to be a bad way to do things.
I am currently reworking it so that this information is stored in a simple C
struct that you can produce. Should
have this done soon.

Can you mail me a description of an example you would like to run?

  Thanks,

     Matt


>
> Tabrez
>
>
> On 05/01/2011 09:53 AM, Matthew Knepley wrote:
>
> On Sat, Apr 30, 2011 at 12:58 PM, Tabrez Ali <stali at geology.wisc.edu>wrote:
>
>> Petsc Developers/Users
>>
>> I having some performance issues with preallocation in a fully
>> unstructured FE code. It would be very helpful if those using FE codes can
>> comment.
>>
>> For a problem of size 100K nodes and 600K tet elements (on 1 cpu)
>>
>> 1. If I calculate the _exact_ number of non-zeros per row (using a running
>> list in Fortran) by looping over nodes & elements, the code takes 17 mins
>> (to calculate nnz's/per row, assemble and solve).
>> 2. If I dont use a running list and simply get the average of the max
>> number of nodes a node might be connected to (again by looping over nodes &
>> elements but not using a running list) then it takes 8 mins
>> 3. If I just magically guess the right value calculated in 2 and use that
>> as average nnz per row then it only takes 25 secs.
>>
>> Basically in all cases Assembly and Solve are very fast (few seconds) but
>> the nnz calculation itself (in 2 and 3) takes a long time. How can this be
>> cut down? Is there a heuristic way to estimate the number (as done in 3)
>> even if it slightly overestimates the nnz's per row or are efficient ways to
>> do step 1 or 2. Right now I have do i=1,num_nodes; do j=1,num_elements ...
>> which obviously is slow for large number of nodes/elements.
>>
>
>  If you want to see my code doing this, look at
>
>    include/petscdmmesh.hh:preallocateOperatorNew()
>
>  which handles the determination of nonzero structure for a FEM operator.
> It should look mostly
> like your own code.
>
>      Matt
>
>
>> Thanks in advance
>>  Tabrez
>>
>
>
>
> --
> 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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