[petsc-users] Trying to modify petrbf to use custom text file

[Matthew Knepley]

On Sun, Mar 31, 2013 at 12:42 AM, Matthew Knepley <knepley at gmail.com> wrote:

> On Sat, Mar 30, 2013 at 7:26 PM, Anil . <dasans at gmail.com> wrote:
>
>> Matt,
>>
>> PetRBF runs properly on my system. But is the dev branch still required
>> to run petRBF?
>> Could my issues be associated with this?
>>
>
> No.
>

You should

1) Look at the matrix to check that connections are short range with
-mat_view draw

2) Reduce the number of blocks until convergence

    Matt


>    Matt
>
>
>> On Wed, Mar 27, 2013 at 9:50 AM, Matthew Knepley <knepley at gmail.com>wrote:
>>
>>> On Wed, Mar 27, 2013 at 3:13 PM, Anil . <dasans at gmail.com> wrote:
>>>
>>>> Matt,
>>>>
>>>> Petsc Options I use to run are....
>>>> mpirun -np 4 ./reader -pc_type asm -sub_pc_type lu -sub_mat_type dense
>>>> -ksp_monitor -ksp_rtol 1e-13 -ksp_max_it 100 -vecscatter_alltoall
>>>> -log_summary
>>>>
>>>
>>> 1) Always run with -ksp_view.
>>>
>>> 2) The relative tolerance is probably too tight, but that is secondary
>>>
>>> 3) Something is really wrong here. I am guessing something in the input
>>> not what you want. If the interaction is
>>>     truly short range, you would see significant drop in the residual on
>>> the first iteration. First, take a look at the
>>>     matrix using -mat_view draw:: -draw_pause -1. It should be banded.
>>>
>>>     Matt
>>>
>>>  Attached is the output..It also contains my petsc configuration
>>>>
>>>>
>>>>
>>>> On Wed, Mar 27, 2013 at 7:59 AM, Matthew Knepley <knepley at gmail.com>wrote:
>>>>
>>>>> On Wed, Mar 27, 2013 at 11:58 AM, Anil . <dasans at gmail.com> wrote:
>>>>>
>>>>>> Matt,
>>>>>>
>>>>>> I am having around 3481 particles that are placed in an unstructured
>>>>>> manner.
>>>>>> Attached is the image showing the distribution.
>>>>>>
>>>>>
>>>>>  Show me your PETSc options, and try playing with the number of
>>>>> blocks. If you look
>>>>> at the PetRBF paper, we give guidance for choosing the sizes.
>>>>>
>>>>>    Matt
>>>>>
>>>>>
>>>>>>
>>>>>> On Tue, Mar 26, 2013 at 11:45 PM, Matthew Knepley <knepley at gmail.com>wrote:
>>>>>>
>>>>>>> On Mon, Mar 25, 2013 at 10:38 PM, Anil . <dasans at gmail.com> wrote:
>>>>>>>
>>>>>>>> 1) Could not find the petrbf mailing list
>>>>>>>> 2) Petrbf runs perfectly
>>>>>>>> 3) Attached is the output with -ksp_view -ksp_monitor
>>>>>>>>
>>>>>>>> Just point me in the right direction. Issues might be very basic as
>>>>>>>> I am starting to use Petsc
>>>>>>>>
>>>>>>>
>>>>>>> This output is a little strange. Some partitions have 0 entries. I
>>>>>>> am guessing this problem is very
>>>>>>> small. For PeRBF, it does turn out to be optimal to use small
>>>>>>> blocks, but the block size depends
>>>>>>> on your interaction scale. Right now you have 75 blocks, which might
>>>>>>> be too many for your small
>>>>>>> problem.
>>>>>>>
>>>>>>>    Matt
>>>>>>>
>>>>>>>
>>>>>>>> On Sat, Mar 23, 2013 at 2:18 AM, Matthew Knepley <knepley at gmail.com
>>>>>>>> > wrote:
>>>>>>>>
>>>>>>>>> On Fri, Mar 22, 2013 at 10:58 PM, Anil . <dasans at gmail.com> wrote:
>>>>>>>>>
>>>>>>>>>> Hi,
>>>>>>>>>>
>>>>>>>>>> I have a text file containing N rows.
>>>>>>>>>> Each row with x,y,omega values.
>>>>>>>>>> I am trying to interpolate this data onto a regular grid using
>>>>>>>>>> petrbf
>>>>>>>>>> But the KSP does not converge and am not able to find the reason.
>>>>>>>>>>
>>>>>>>>>> The code is available with the text files at
>>>>>>>>>> https://www.dropbox.com/s/cypuwugbxo07kx0/rbf-interpolation.tar.gz
>>>>>>>>>>
>>>>>>>>>> I am very new to petsc and any direction how o proceed would be
>>>>>>>>>> helpful.
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>> 1) Did you mail the petrbf list?
>>>>>>>>>
>>>>>>>>> 2) Could you run the petrbf examples?
>>>>>>>>>
>>>>>>>>> 3) We cannot tell anything about convergence without the output of
>>>>>>>>> -ksp_view -ksp_monitor.
>>>>>>>>>
>>>>>>>>>    Matt
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> Sincerely
>>>>>>>>>> Anil Das P V
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> 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
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> Sincerely
>>>>>>>> Anil Das P V
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> 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
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Sincerely
>>>>>> Anil Das P V
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> 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
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Sincerely
>>>> Anil Das P V
>>>>
>>>
>>>
>>>
>>> --
>>> 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
>>>
>>
>>
>>
>> --
>> Sincerely
>> Anil Das P V
>>
>
>
>
> --
> 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20130331/6983eba5/attachment-0001.html>