[Paraview] Problem when loading parallel data (SOS and XDMF)
Jerry Clarke
clarke at arl.army.mil
Wed Jul 30 15:02:20 EDT 2008
Renato,
OK, first mystery is solved. cav_4_full.xmf had wrong dimensions in
grids cav_00[1,2,3]. I copied the first grid from each individual file
and it worked. Also XDMF_TET should have been "Tetrahedron" like it was
in the individual files.
Now on to the XInclude file .....
Here is new car_4_full.xmf that works in Paraview 3.3
--------------------------------------------------------
<?xml version="1.0" ?>
<!-- <!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []> -->
<Xdmf xmlns:xi="http://www.w3.org/2001/XInclude" Version="2.0">
<Domain>
<Grid Name= "cav" GridType="Collection" CollectionType="Spatial">
<Grid Name="cav_000" Type="Uniform">
<Time Type="Single" Value=" 0.00000000"/>
<Topology Type="Tetrahedron" NumberOfElements=" 27215 "
BaseOffset="1">
<DataItem Dimensions=" 108860 " NumberType="Int"
Format="HDF">cav_4_000_00000.h5:/incid</DataItem>
</Topology>
<Geometry Type="XYZ">
<DataItem Dimensions=" 18726" NumberType="Float"
Precision="8" Format="HDF">cav_4_000_00000.h5:/coords</DataItem>
</Geometry>
<Attribute Name="velocity" AttributeType="Vector"
Center="Node">
<DataItem Dimensions=" 18726" NumberType="Float"
Precision="8" Format="HDF">cav_4_000_00000.h5:/velocity</DataItem>
</Attribute>
<Attribute Name="pressure" AttributeType="Scalar"
Center="Node">
<DataItem Dimensions=" 6242" NumberType="Float"
Precision="8" Format="HDF">cav_4_000_00000.h5:/pressure</DataItem>
</Attribute>
</Grid>
<Grid Name="cav_001" Type="Uniform">
<Time Type="Single" Value=" 0.00000000"/>
<Topology Type="Tetrahedron" NumberOfElements=" 26616 "
BaseOffset="1">
<DataItem Dimensions=" 106464 " NumberType="Int"
Format="HDF">cav_4_001_00000.h5:/incid</DataItem>
</Topology>
<Geometry Type="XYZ">
<DataItem Dimensions=" 18510" NumberType="Float"
Precision="8" Format="HDF">cav_4_001_00000.h5:/coords</DataItem>
</Geometry>
<Attribute Name="velocity" AttributeType="Vector"
Center="Node">
<DataItem Dimensions=" 18510" NumberType="Float"
Precision="8" Format="HDF">cav_4_001_00000.h5:/velocity</DataItem>
</Attribute>
<Attribute Name="pressure" AttributeType="Scalar"
Center="Node">
<DataItem Dimensions=" 6170" NumberType="Float"
Precision="8" Format="HDF">cav_4_001_00000.h5:/pressure</DataItem>
</Attribute>
</Grid>
<Grid Name="cav_002" Type="Uniform">
<Time Type="Single" Value=" 0.00000000"/>
<Topology Type="Tetrahedron" NumberOfElements=" 27709 "
BaseOffset="1">
<DataItem Dimensions=" 110836 " NumberType="Int"
Format="HDF">cav_4_002_00000.h5:/incid</DataItem>
</Topology>
<Geometry Type="XYZ">
<DataItem Dimensions=" 18849" NumberType="Float"
Precision="8" Format="HDF">cav_4_002_00000.h5:/coords</DataItem>
</Geometry>
<Attribute Name="velocity" AttributeType="Vector"
Center="Node">
<DataItem Dimensions=" 18849" NumberType="Float"
Precision="8" Format="HDF">cav_4_002_00000.h5:/velocity</DataItem>
</Attribute>
<Attribute Name="pressure" AttributeType="Scalar"
Center="Node">
<DataItem Dimensions=" 6283" NumberType="Float"
Precision="8" Format="HDF">cav_4_002_00000.h5:/pressure</DataItem>
</Attribute>
</Grid>
<Grid Name="cav_003" Type="Uniform">
<Time Type="Single" Value=" 0.00000000"/>
<Topology Type="Tetrahedron" NumberOfElements=" 26564 "
BaseOffset="1">
<DataItem Dimensions=" 106256 " NumberType="Int"
Format="HDF">cav_4_003_00000.h5:/incid</DataItem>
</Topology>
<Geometry Type="XYZ">
<DataItem Dimensions=" 18498" NumberType="Float"
Precision="8" Format="HDF">cav_4_003_00000.h5:/coords</DataItem>
</Geometry>
<Attribute Name="velocity" AttributeType="Vector"
Center="Node">
<DataItem Dimensions=" 18498" NumberType="Float"
Precision="8" Format="HDF">cav_4_003_00000.h5:/velocity</DataItem>
</Attribute>
<Attribute Name="pressure" AttributeType="Scalar"
Center="Node">
<DataItem Dimensions=" 6166" NumberType="Float"
Precision="8" Format="HDF">cav_4_003_00000.h5:/pressure</DataItem>
</Attribute>
</Grid>
</Grid>
</Domain>
</Xdmf>
Renato N. Elias wrote:
> 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.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> ParaView mailing list
>>>>>>>>> ParaView at paraview.org
>>>>>>>>> http://www.paraview.org/mailman/listinfo/paraview
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> ParaView mailing list
>>>>>>> ParaView at paraview.org
>>>>>>> http://www.paraview.org/mailman/listinfo/paraview
>>>>>>
>>>>>
>>>>
>>>
>>
>
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