[Paraview] Cannot get parallelism working in paraview 4.2.0 on our clusters (works with 4.1.0)

Wed Nov 26 18:53:53 EST 2014

Thanks Rich. The molecule data gets into the range that requires parallel
visualization extremely rarely. However, this may affect others, such as
those loading large vtu files. We'll make sure that this is fixed very soon.

-berk

On Tue, Nov 25, 2014 at 5:15 PM, Cook, Rich <cook47 at llnl.gov> wrote:

>  I do not have an urgent need to view this data.  However, be advised that
> I got it from what appears to be the PDB canonical source, so I assumed our
> molecular people would appreciate being able to visualize their stuff. This
> kind of model doesn’t usually get that big, though, probably.
>
> http://www.rcsb.org/pdb/explore.do?structureId=1lmb
>
>  Thank you kindly.  No workaround is needed.
> — Rich
>
>  On Nov 25, 2014, at 12:55 PM, Berk Geveci <berk.geveci at kitware.com>
> wrote:
>
>  Marcus will investigate the errors.
>
>  They are not related to why the dataset is no longer distributed. There
> was code in 4.1 that automatically redistributed data from serial readers
> using a very naive approach. That code is no longer there. We are
> investigating various options of improving on the 4.1 functionality. I
> would normally say that you can use the D3 filter to distribute the data
> but I was cautious and tried it first. It crashes :-( This dataset has
> string arrays in it, which it seems D3 does not handle.
>
>  Do you have a particular use case driving parallel PDB capability? If
> you do, I can find some workarounds of these issues. If not, D3 should
> nicely work on most polydata and unstructured grid sources. We are working
> on better ways of redistributing the other data types.
>
>  Best,
> -berk
>
> On Tue, Nov 25, 2014 at 9:44 AM, Marcus D. Hanwell <
> marcus.hanwell at kitware.com> wrote:
>
>>  Hi,
>>
>>  I think I know the cause, the PDB reader was modified to produce a
>> vtkMolecule in addition to the vtkPolyData I think it has always produced.
>> It looks like there is a packaging issue, and the XML file cannot be found.
>> We should probably just statically compile the file in, or convert it to a
>> header as the data is pretty static - atomic radii, colors, etc.
>>
>>  Marcus
>>
>>
>>  On Tue, Nov 25, 2014 at 9:06 AM, Berk Geveci <berk.geveci at kitware.com>
>> wrote:
>>
>>> Hey Rich,
>>>
>>>  Can you send me the dataset?
>>>
>>>  Best,
>>> -berk
>>>
>>>  On Mon, Nov 24, 2014 at 7:25 PM, Cook, Rich <cook47 at llnl.gov> wrote:
>>>
>>>>  Hi,
>>>> I have recently compiled paraview 4.2.0 on our clusters in the same way
>>>> I compile with 4.1.0 and am getting some errors.
>>>> I run pvserver in parallel, and it does not give any weird outputs.
>>>> I connect with it from my desktop (Mac OS X).  I can see in the desktop
>>>> GUI that four remote servers are connected.
>>>> I open up a PDB dataset and it is different.  I see two “Output”
>>>> objects in the pipeline browser.  This is different than the behavior in
>>>> 4.1.0.
>>>>
>>>>  <Voila_Capture 2014-11-24_04-23-27_PM.png>
>>>>
>>>>  I click Apply and get smacked in the face with an error dialog.
>>>>
>>>>  ERROR: In
>>>> /Users/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release-Python27/paraview/src/paraview/VTK/Domains/Chemistry/vtkBlueObeliskDataParser.cxx,
>>>> line 68
>>>> vtkBlueObeliskDataParser (0x7fea5e2a9980): Cannot find elements.xml.
>>>> Checked
>>>> /Users/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release-Python27/paraview/src/paraview-build/CMakeFiles/__macos_install/share/paraview-4.2/vtkDomainsChemistry
>>>> and
>>>> /Users/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release-Python27/paraview/src/paraview/VTK/Domains/Chemistry
>>>>
>>>>
>>>>  ERROR: In
>>>> /Users/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release-Python27/paraview/src/paraview/VTK/IO/XMLParser/vtkXMLParser.cxx,
>>>> line 382
>>>> vtkBlueObeliskDataParser (0x7fea5e2a9980): Parse() called with no
>>>> Stream set.
>>>>
>>>>
>>>>  ERROR: In
>>>> /Users/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release-Python27/paraview/src/paraview/VTK/Common/ExecutionModel/vtkDemandDrivenPipeline.cxx,
>>>> line 710
>>>> vtkPVDataRepresentationPipeline (0x7fea5e2a4d80): Input port 0 of
>>>> algorithm vtkMoleculeRepresentation(0x7fea56c005d0) has 0 connections but
>>>> is not optional.
>>>>
>>>>
>>>>   I’m unable to color by process scalar ID, or more precisely, the
>>>> Filter seems to get applied but the color does not change.  Appears all
>>>> work is done on process 0.
>>>>
>>>>  Something is vewwwy scwewwy.
>>>>
>>>>  Help?
>>>>
>>>>
>>>>  --
>>>> ✐Richard Cook
>>>> ✇ Lawrence Livermore National Laboratory
>>>> Bldg-453 Rm-4024, Mail Stop L-557
>>>> 7000 East Avenue,  Livermore, CA, 94550, USA
>>>> ☎ (office) (925) 423-9605
>>>> ☎ (fax) (925) 423-6961
>>>> ---
>>>> Information Management & Graphics Grp., Services & Development Div.,
>>>> Integrated Computing & Communications Dept.
>>>> (opinions expressed herein are mine and not those of LLNL)
>>>>
>>>>
>>>>
>>>>
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>>>
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>>
>
>  --
> ✐Richard Cook
> ✇ Lawrence Livermore National Laboratory
> Bldg-453 Rm-4024, Mail Stop L-557
> 7000 East Avenue,  Livermore, CA, 94550, USA
> ☎ (office) (925) 423-9605
> ☎ (fax) (925) 423-6961
> ---
> Information Management & Graphics Grp., Services & Development Div.,
> Integrated Computing & Communications Dept.
> (opinions expressed herein are mine and not those of LLNL)
>
>
>
>
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