[Paraview] paraview display issue on parallel files

Thu Sep 7 16:44:46 EDT 2017

Dear Kenneth and Andy,

Thanks so much.

This works fine. It is truly the simplest way for me to post-processing the
data.  In this way, almost all the serial algorithm can be applied to
multi-files.

Thanks again for your kind help.

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 16:18 GMT-04:00 Moreland, Kenneth <kmorel at sandia.gov>:

> Rilin,
>
>
>
> I think I found a solution for you that will work at least most of the
> time. The solution is to simply write out .vtm files instead of .pvtu
> files. vtm, which is the multiblock file format, is similar to the pvt*
> format. The main difference is that when VTK reads in vtm files it keeps
> the data from different files in different blocks, and that will prevent
> ParaView from removing what it thinks are internal faces. I’ve attached an
> example vtkm file to this email.
>
>
>
> A bit more explanation and a description of where this will fail. As Andy
> said the problem is that the files in your dataset have overlapping cells.
> When ParaView reads in a pvtu file, it combines all the cells from all
> files into a single mesh, and this mesh will have duplicates of the
> overlapping cells. By definition, these overlapping cells will share all of
> their faces. ParaView’s external faces algorithm assumes that if two cells
> have the same face, that face must be internal and can be removed (which is
> true in conforming meshes but not when there are duplicate cells). When you
> first load your mesh into ParaView, everything seems to be working fine
> because the reader is also creating duplicate points so index-wise the
> duplicate cells register as different. But many operations (like merge
> cells, clip, and D3) will find coincident points and merge them together.
> That’s when ParaView removes all the faces of all duplicate cells.
>
>
>
> When ParaView reads the vtm file, it keeps the data from each file in a
> separate mesh. When ParaView runs algorithms like external faces, it does
> so independently from each other. So even if the cells are sharing faces,
> they will be across blocks and will still be considered external. The
> multiblock structure should remain intact as long as you don’t run a filter
> that merges them together like D3 or Merge Blocks.
>
>
>
> Hope that helps.
>
>
>
> -Ken
>
>
>
> *From:* ParaView [mailto:paraview-bounces at paraview.org] *On Behalf Of *Rilin
> Shen
> *Sent:* Thursday, September 7, 2017 1:38 PM
> *To:* Bauer, Andy (External Contacts) <andy.bauer at kitware.com>
> *Cc:* paraview at paraview.org
> *Subject:* [EXTERNAL] Re: [Paraview] paraview display issue on parallel
> files
>
>
>
> 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 <+1%20646-200-2122>
>
> 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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