[Paraview] paraview display issue on parallel files

Thu Sep 7 15:38:09 EDT 2017

Dear Andy,

Thanks very much.

You can remap the point variables back onto the points using the Resample
> with Dataset filter but that won't work for cell data.

I tried the method you advised. Assuming that the original file name is A
and the file after Clean to Grid and Clean Cells to Grid is B, I tried two
different options for the source for Resample with DataSets and both A and
B are not working.  Do I misunderstand something?

I believe that the D3 filter is only available if you have ParaView
> built/installed with MPI. Even then it will only work if you're running
> with more than a single MPI process.

I only use serial paraview to process multi-results generated by other
programs.  I don't use the parallel paraview to deal with large datasets so
I think D3 filter is not suitable for me.

I still suggest writing out the data with either marking the repeated cells
> as ghost cells or not including them in the file as any other thing you do
> to get around that can become fairly expensive and manually intensive as
> you go to bigger datasets.

I would try to not include repeated cells in the original output file. But
how to mark the repeated cells as ghost cells? I think there should a
vtu/pvtu file format to describe it but I didn't find it on the internet.
Could you please share it to me?

BTW,  when I clip a small model with 6700 elements generated by 40
processors, it looks fine. So my question: is there a limit to deal with
the large dataset for paraview?

Best regards,

Rilin Shen
Division of Solid Mechanics, School of Astronautics
*Harbin Institute of Technology*, Harbin 150001, China
Civil Engineering & Engineering Mechanics
*Columbia University*, New York 10027, U.S.
Tel: (+1) 646-200-2122
Email: shenrilin at gmail.com  /  rs3741 at columbia.edu <shenrilin at 126.com>

2017-09-07 15:00 GMT-04:00 Andy Bauer <andy.bauer at kitware.com>:

> Hi,
>
> You can remap the point variables back onto the points using the Resample
> with Dataset filter but that won't work for cell data.
>
> I believe that the D3 filter is only available if you have ParaView
> built/installed with MPI. Even then it will only work if you're running
> with more than a single MPI process.
>
> I still suggest writing out the data with either marking the repeated
> cells as ghost cells or not including them in the file as any other thing
> you do to get around that can become fairly expensive and manually
> intensive as you go to bigger datasets.
>
> Andy
>
> On Wed, Sep 6, 2017 at 3:28 PM, Rilin Shen <shenrilin at gmail.com> wrote:
>
>> Dear all,
>>
>> Thanks for your suggestions. It is exactly what you said.
>>
>> Marking ghost cell would be non-trival work and I tried the second idea.
>> But only cell and points information is left, other field information
>> associated with points seem to be lost. Is that the case? If that is the
>> case, is there an easy way to attach point data to points again?
>>
>> BTW, I searched the internet and found that the D3 filter could be a good
>> option for my unstructured grid information. But I cannot find the D3
>> filter as Filters>Alphabetical>D3. So my second question is how to add D3
>> filter to my paraview?
>>
>> Best regards,
>>
>>
>> Rilin Shen
>> Division of Solid Mechanics, School of Astronautics
>> *Harbin Institute of Technology*, Harbin 150001, China
>> Civil Engineering & Engineering Mechanics
>> *Columbia University*, New York 10027, U.S.
>> Tel: (+1) 646-200-2122 <(646)%20200-2122>
>> Email: shenrilin at gmail.com  /  rs3741 at columbia.edu <shenrilin at 126.com>
>>
>> 2017-09-06 14:50 GMT-04:00 Andy Bauer <andy.bauer at kitware.com>:
>>
>>> Hi,
>>>
>>> Please respond to the entire mailing list so that anyone that wants to
>>> participate or follow along can.
>>>
>>> I think the issue here is that you have the same cell specified in
>>> multiple vtu files and ParaView is getting confused when trying to render
>>> them. These are the overlapping cells at the subdomain boundary. My
>>> recommendation would be to either mark these repeated cells as ghost cells
>>> (see https://blog.kitware.com/ghost-and-blanking-visibility-changes/
>>> for information on that). Other than that, you could use the Clean to Grid
>>> filter to get rid of coincident points and then use the Clean Cells to Grid
>>> filter to get rid of extra copies of the cell.
>>>
>>> Cheers,
>>> Andy
>>>
>>>
>>> On Tue, Sep 5, 2017 at 6:24 PM, Rilin Shen <shenrilin at gmail.com> wrote:
>>>
>>>> 
>>>>  Bone.7z
>>>> <https://drive.google.com/file/d/0B1JLvkeOK5PQVXR3cTBHa2lfQjQ/view?usp=drive_web>
>>>> Dear Andy,
>>>>
>>>> Thanks a lot for your help.
>>>>
>>>> As you said, It looks like a ghost cell issue. I attached my dataset.
>>>> Please check it.
>>>>
>>>> If you need any additional information, please let me know.
>>>>
>>>> Best regards,
>>>>
>>>> Rilin Shen
>>>> Division of Solid Mechanics, School of Astronautics
>>>> *Harbin Institute of Technology*, Harbin 150001, China
>>>> Civil Engineering & Engineering Mechanics
>>>> *Columbia University*, New York 10027, U.S.
>>>> Tel: (+1) 646-200-2122 <(646)%20200-2122>
>>>> Email: shenrilin at gmail.com  /  rs3741 at columbia.edu <shenrilin at 126.com>
>>>>
>>>> 2017-09-05 16:54 GMT-04:00 Andy Bauer <andy.bauer at kitware.com>:
>>>>
>>>>> Hi,
>>>>>
>>>>> This typically happens when ghost cells are marked improperly or the
>>>>> data set has a node/point partitioning and no cells to bridge between the
>>>>> subdomains (though the point partitioning issue usually happens with finite
>>>>> difference simulations instead of FEM simulations). If you could share your
>>>>> dataset it would be easier to diagnose.
>>>>>
>>>>> Best,
>>>>> Andy
>>>>>
>>>>> On Tue, Sep 5, 2017 at 4:23 PM, Rilin Shen <shenrilin at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Dear all,
>>>>>>
>>>>>> I'm very happy to meet all of you in this society.
>>>>>>
>>>>>> I use a finite element software with multiprocessors(40) to solve
>>>>>> problems.
>>>>>>
>>>>>> All the .vtu files. associated with each processor are output and
>>>>>> then a file .pvtu is generated.
>>>>>>
>>>>>> The original file is displayed perfectly as shown in bone.png.
>>>>>> However, when I try to cut it with a plane, it occurs the following issue
>>>>>> as clip.png, It seems not be displayed correctly.
>>>>>>
>>>>>> Would you please tell me what happened to my data?
>>>>>>
>>>>>> Best regards,
>>>>>>
>>>>>> Rilin Shen
>>>>>> Division of Solid Mechanics, School of Astronautics
>>>>>> *Harbin Institute of Technology*, Harbin 150001, China
>>>>>> Civil Engineering & Engineering Mechanics
>>>>>> *Columbia University*, New York 10027, U.S.
>>>>>> Tel: (+1) 646-200-2122 <(646)%20200-2122>
>>>>>> Email: shenrilin at gmail.com  /  rs3741 at columbia.edu
>>>>>> <shenrilin at 126.com>
>>>>>>
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>>>>>
>>>>
>>>
>>
>
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