[Paraview] Problem when loading parallel data (SOS and XDMF)

Renato N. Elias rnelias at nacad.ufrj.br
Wed Jul 30 13:10:21 EDT 2008 

Some progress here...

Ok, I named all grids with different names and tested with and without 
the XInclude clause.

*Without XInclude* I've got a catastrophic error and PV closed MPI 
connection. The output message was:
ERROR: In ..\..\..\ParaView3_CVS\Servers\Common\vtkServerConnection.cxx, 
line 67

vtkServerConnection (07981BF0): Server Connection Closed!

ERROR: In 
..\..\..\ParaView3_CVS\Servers\ServerManager\vtkSMArraySelectionInformationHelper.cxx, 
line 79

vtkSMArraySelectionInformationHelper (07804578): Error getting array 
settings from server.

ERROR: In 
..\..\..\ParaView3_CVS\Servers\ServerManager\vtkSMXDMFInformationHelper.cxx, 
line 135

vtkSMXDMFInformationHelper (07C7BBD8): Error getting domains from server.

(and much more...)


*Using XInclude* I've got:
XDMF Error in 
..\..\..\..\ParaView3_CVS\Utilities\Xdmf2\vtk\vtkXdmfReader.cxx line 
2129 (Unknown Topology Type = 0)
XDMF Error in 
..\..\..\..\ParaView3_CVS\Utilities\Xdmf2\vtk\vtkXdmfReader.cxx line 
2129 (Unknown Topology Type = 0)
XDMF Error in 
..\..\..\..\ParaView3_CVS\Utilities\Xdmf2\vtk\vtkXdmfReader.cxx line 
2129 (Unknown Topology Type = 0)
XDMF Error in 
..\..\..\..\ParaView3_CVS\Utilities\Xdmf2\vtk\vtkXdmfReader.cxx line 
2129 (Unknown Topology Type = 0)

Easy to understand if we look the source code. vtkXdmfReader.cxx was 
expecting XDMF_TET and my file had Tetrahedron. Quite weird since it 
works fine when running in serial mode, or loading the model pieces one 
by one. In fact, it seems like a bug. Nevertheless, I've made the 
substitutions I tried again. Now, I have the same error message that 
I've got in the first case (without the XInclude).

Jerry, I've made my files available in 
http://www.nacad.ufrj.br/~rnelias/transfer/xdfm-test.zip (13.4 MB). Just 
to make the debug process easier. It seems that the Xdmf support in 
ParaView is still a bit fragile.

Renato.

p.s.: I wildcard would help us a lot when writing transient files ;o)

Jerry Clarke wrote:
> Renato,
>
> I think it is a bug .... If the Collection Grid does not have
> a "Name" nothing is read. Just give your Collection Grid a Name
> and it should work.
>
> Here's an example that works :
>
> Spatial.xmf :::
> <?xml version="1.0" ?>
> <Xdmf xmlns:xi="http://www.w3.org/2001/XInclude" Version="2.0">
>     <Domain>
>     <Grid Name="MyCollection" GridType="Collection" 
> CollectionType="Spatial" >
>         <xi:include href="cube1.xmf" 
> xpointer="xpointer(//Xdmf/Domain/Grid)" />
>         <xi:include href="cube2.xmf" 
> xpointer="xpointer(//Xdmf/Domain/Grid)" />
>     </Grid>
>     </Domain>
> </Xdmf>
> ---------------------------------------------------
> cube1.xmf :::
> <?xml version="1.0" ?>
> <Xdmf>
>    <Domain>
>       <Grid Name="one">
>          <Topology  Type="3DCORECTMESH" Dimensions="2 2 2"/>
>          <Geometry Type="ORIGIN_DXDYDZ">
>             <DataItem DataType="Float" Dimensions="3" Format="XML">
>                0.0 0.0 0.0
>             </DataItem>
>             <DataItem DataType="Float" Dimensions="3" Format="XML">
>                1.0 1.0 1.0
>             </DataItem>
>          </Geometry>
>       </Grid>
>    </Domain>
> </Xdmf>
> --------------------------------------------------------
> cube2.xmf :::
> <?xml version="1.0" ?>
> <Xdmf>
>    <Domain>
>       <Grid Name="two">
>          <Topology  Type="3DCORECTMESH" Dimensions="2 2 2"/>
>          <Geometry Type="ORIGIN_DXDYDZ">
>             <DataItem DataType="Float" Dimensions="3" Format="XML">
>                5.0 0.0 0.0
>             </DataItem>
>             <DataItem DataType="Float" Dimensions="3" Format="XML">
>                1.0 1.0 1.0
>             </DataItem>
>          </Geometry>
>       </Grid>
>    </Domain>
> </Xdmf>
>
> Renato N. Elias wrote:
>>
>> So, I suppose it's not possible to load parallel xdmf files in PV 
>> yet  :o(
>>
>> Renato.
>>
>> Jerry Clarke wrote:
>>> I think what is happening is that the Xinclude/XPointer interfaces 
>>> are more particular. Technically, if the
>>> XML specifies a DTD it should be there, but it had been ignored in the
>>> past. So I guess we're all doing it wrong, technically.
>>>
>>> Jerry
>>>
>>> Renato N. Elias wrote:
>>>>
>>>> Ok, I commented all <!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []> clauses 
>>>> and now PV does not complain about DTD anymore but nothing is 
>>>> loaded :o(
>>>>
>>>> Am I doing something wrong? I can load the domain pieces 
>>>> individually which make me believe that the XDMF files are correct.
>>>>
>>>> Renato.
>>>>
>>>>
>>>> Jerry Clarke wrote:
>>>>> Renato,
>>>>>
>>>>> I think I've seen this before. The XML parser is trying to validate
>>>>> the XML.
>>>>>
>>>>> As a test, try removing "<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>" 
>>>>> from the
>>>>> xml file or creating an empty Xdmf.dtd (I'll dig up the actual DTD).
>>>>>
>>>>> Jerry
>>>>>
>>>>>
>>>>> Renato N. Elias wrote:
>>>>>>
>>>>>> Oops, my mistake Berk. It's not the first time I mismatch 
>>>>>> versions... (it's easy to get confused when you have 6 different 
>>>>>> PV versions installed).
>>>>>>
>>>>>> Ok, now I can load SOS but it seems that time support is not 
>>>>>> available yet (besides some important parallel filters such as 
>>>>>> "clean to grid"). Is it correct?!
>>>>>>
>>>>>> For the XDMF file I've had no success. I've tried to load the 
>>>>>> following file:
>>>>>>
>>>>>> <?xml version="1.0" ?>
>>>>>> <!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
>>>>>> <Xdmf xmlns:xi="http://www.w3.org/2001/XInclude" Version="2.0">
>>>>>>   <Domain>
>>>>>>      <Grid GridType="Collection" CollectionType="Spatial">
>>>>>>         <xi:include href="cav_4_000.xmf" 
>>>>>> xpointer="xpointer(//Xdmf/Domain/Grid)" />
>>>>>>         <xi:include href="cav_4_001.xmf" 
>>>>>> xpointer="xpointer(//Xdmf/Domain/Grid)" />
>>>>>>         <xi:include href="cav_4_002.xmf" 
>>>>>> xpointer="xpointer(//Xdmf/Domain/Grid)" />
>>>>>>         <xi:include href="cav_4_003.xmf" 
>>>>>> xpointer="xpointer(//Xdmf/Domain/Grid)" />
>>>>>>      </Grid>
>>>>>>   </Domain>
>>>>>> </Xdmf>
>>>>>>
>>>>>> Started PV client and launched PV server with the command 
>>>>>> (mpiexec -n 4 pvserver -rc -ch=localhost) and got the following 
>>>>>> error:
>>>>>>
>>>>>> file:///C%3A/users/Renato/svn/EdgeCFD-HEAD/bin/cav31/P2P/cav_4_000.xmf:2: 
>>>>>> I/O wa
>>>>>> rning : failed to load external entity 
>>>>>> "file:///C%3A/users/Renato/svn/EdgeCFD-HEAD/bin/cav31/P2P/Xdmf.dtd"
>>>>>> <!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
>>>>>>                                    ^
>>>>>> file:///C%3A/users/Renato/svn/EdgeCFD-HEAD/bin/cav31/P2P/cav_4_001.xmf:2: 
>>>>>> I/O wa
>>>>>> rning : failed to load external entity 
>>>>>> "file:///C%3A/users/Renato/svn/EdgeCFD-HEAD/bin/cav31/P2P/Xdmf.dtd"
>>>>>> <!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
>>>>>>                                    ^
>>>>>> file:///C%3A/users/Renato/svn/EdgeCFD-HEAD/bin/cav31/P2P/cav_4_002.xmf:2: 
>>>>>> I/O wa
>>>>>> rning : failed to load external entity 
>>>>>> "file:///C%3A/users/Renato/svn/EdgeCFD-HEAD/bin/cav31/P2P/Xdmf.dtd"
>>>>>> <!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
>>>>>>                                    ^
>>>>>> file:///C%3A/users/Renato/svn/EdgeCFD-HEAD/bin/cav31/P2P/cav_4_003.xmf:2: 
>>>>>> I/O wa
>>>>>> rning : failed to load external entity 
>>>>>> "file:///C%3A/users/Renato/svn/EdgeCFD-HEAD/bin/cav31/P2P/Xdmf.dtd"
>>>>>> <!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
>>>>>>                                    ^
>>>>>> file:///C%3A/users/Renato/svn/EdgeCFD-HEAD/bin/cav31/P2P/cav_4_000.xmf:2: 
>>>>>> I/O wa
>>>>>> rning : failed to load external entity 
>>>>>> "file:///C%3A/users/Renato/svn/EdgeCFD-HEAD/bin/cav31/P2P/Xdmf.dtd"
>>>>>> <!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
>>>>>>
>>>>>> ...
>>>>>>
>>>>>> I also tried substituting the "xi:include..." statements by the 
>>>>>> corresponding XML extended portions. The model was not loaded, 
>>>>>> but the error message disappeared ;o)
>>>>>>
>>>>>> Regards
>>>>>>
>>>>>> Renato.
>>>>>>
>>>>>>
>>>>>> Berk Geveci wrote:
>>>>>>> I am pretty sure this is due to client/server version 
>>>>>>> incompatibility.
>>>>>>>
>>>>>>> -berk
>>>>>>>
>>>>>>> On Tue, Jul 29, 2008 at 3:42 PM, Renato N. Elias 
>>>>>>> <rnelias at nacad.ufrj.br> wrote:
>>>>>>>  
>>>>>>>> I'm trying to load XDMF and Ensight SOS parallel data in PV3 
>>>>>>>> (CVS's HEAD)
>>>>>>>> which is returning me the following error message:
>>>>>>>>
>>>>>>>> ERROR: In
>>>>>>>> C:\berk\ReleaseBuilds\ParaView3\Servers\Common\vtkPVDataInformation.cxx, 
>>>>>>>>
>>>>>>>> line 991
>>>>>>>> vtkPVDataInformation (062A6ED8): Error parsing bounds.
>>>>>>>> (...It's funny read error messages pointing to Berk's paths :oD  )
>>>>>>>>
>>>>>>>> The same problem occur with SOS and XDMF as well. Any hint?
>>>>>>>>
>>>>>>>> Regards
>>>>>>>>
>>>>>>>> Renato.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
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>>>>>>>> ParaView at paraview.org
>>>>>>>> http://www.paraview.org/mailman/listinfo/paraview
>>>>>>>>
>>>>>>>>     
>>>>>>>
>>>>>>>   
>>>>>>
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>>>>>
>>>>
>>>
>>
>

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