[Paraview] Running Paraview on an HPC machine with multiple processes?

Jake Gerard jake.a.gerard at gmail.com
Thu Jul 13 14:15:39 EDT 2017 

I tried a newer version of Paraview (5.2.0) and still had the same problem.
Why would this be able to run on one process but not on multiple? The
velocity still shows up and can be split based on process id. Should I put
the scalar data into the xmf in a different format?

On Thu, Jul 13, 2017 at 8:49 AM, Jake Gerard <jake.a.gerard at gmail.com>
wrote:

> I will download a newer version and try again this morning.  Will let you
> know how it goes.
>
> On Wed, Jul 12, 2017 at 3:16 PM, Andy Smith <agsmith424 at gmail.com> wrote:
>
>> How many processors are you attempting to run on?
>> Is it possible to try a newer version of ParaView?  The oldest that I
>> have on my system is 4.4.0.
>>
>> On Wed, Jul 12, 2017 at 3:33 PM, Jake Gerard <jake.a.gerard at gmail.com>
>> wrote:
>>
>>> Andy,
>>>
>>> I wasn't setting up the server or anything. I have just been connecting
>>> to one of my preset configurations. The velocity data shows up fine but for
>>> some reason when there is more than one processor working on the
>>> visualization Paraview can't read it.
>>>
>>> Here is the error:
>>>
>>> ERROR: In /p/home/angel/PV/4.3.1/Build_4.3.1_osmesa/paraview/src/parav
>>> iew/VTK/IO/Xdmf2/vtkXdmfHeavyData.cxx, line 1128
>>>
>>> vtkXdmfReader (0x104ae20): Failed to read attribute data
>>>
>>>
>>> The setup has just been clicking the connect icon, the system, and
>>> choosing the number of nodes and processors per node. If it helps I'm on
>>> Paraview 4.3.1 64-bit. Sorry I am pretty new to all of this stuff. Slowly
>>> getting the hang of things.
>>>
>>>
>>> Jake
>>>
>>> On Wed, Jul 12, 2017 at 1:48 PM, Andy Smith <agsmith424 at gmail.com>
>>> wrote:
>>>
>>>> Jake,
>>>>
>>>> If I start up the remote server in parallel using something like:
>>>> mpiexec.hydra -n 8 pvserver -sp=11111
>>>>
>>>> and then connect from my workstation I am able to read an XDMF file
>>>> like the one you posted using ParaView 5.4.0.  Can you post how you are
>>>> starting your server and the exact error that you receive?
>>>>
>>>> I've attached the .xmf file and a Python script to generate dummy data
>>>> in a .h5 file that corresponds to your data structure.
>>>>
>>>> Note that I am using the xdmf2 reader for my testing.  The xdmf3 reader
>>>> fails to read the file (even locally in serial) with the following error:
>>>>
>>>> Type not one of accepted values: INTEGER in XdmfArrayType::New
>>>> terminate called after throwing an instance of 'XdmfError'
>>>>   what():  Type not one of accepted values: INTEGER in
>>>> XdmfArrayType::New
>>>> Aborted
>>>>
>>>>
>>>> -Andy
>>>>
>>>> On Wed, Jul 12, 2017 at 1:31 PM, Jake Gerard <jake.a.gerard at gmail.com>
>>>> wrote:
>>>>
>>>>> Alessandro,
>>>>>
>>>>> Paraview says that it failed to read the attribute data. I just mean
>>>>> that when I connect Paraview to the machine, the pressure data does not
>>>>> load if I select more than 1 node or process/node.
>>>>>
>>>>> Jake
>>>>>
>>>>> On Wed, Jul 12, 2017 at 11:00 AM, Alessandro De Maio <
>>>>> demaio.a at gmail.com> wrote:
>>>>>
>>>>>> Hi Jake,
>>>>>>      when you talk about running in multi-processing are you talking
>>>>>> about the solver that produces the data or about running Paraview in
>>>>>> mpi-mode?
>>>>>> Which is the error you get?
>>>>>>
>>>>>> Alessandro
>>>>>>
>>>>>> On Wed, Jul 12, 2017 at 5:28 PM, Jake Gerard <jake.a.gerard at gmail.com
>>>>>> > wrote:
>>>>>>
>>>>>>> Any help here would be greatly appreciated.
>>>>>>>
>>>>>>> On Tue, Jul 11, 2017 at 2:37 PM, Jake Gerard <
>>>>>>> jake.a.gerard at gmail.com> wrote:
>>>>>>>
>>>>>>>> Good Afternoon,
>>>>>>>>
>>>>>>>> I have been moving to an HDF5/XDMF system for analyzing big data
>>>>>>>> from a computational fluid model. I finally got all the basic components
>>>>>>>> working on my local machine but have run into problems when trying to run
>>>>>>>> on an HPC system. Here is the XDMF file:
>>>>>>>>
>>>>>>>> <?xml version="1.0" ?>
>>>>>>>> <!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
>>>>>>>> <Xdmf xmlns:xi="http://www.w3.org/2003/XInclude" Version="2.1">
>>>>>>>>   <Domain>
>>>>>>>>     <Grid Name="my_Grid" GridType="Uniform">
>>>>>>>>       <Topology TopologyType="3DCoRectMesh" Dimensions="91 19 19">
>>>>>>>>       </Topology>
>>>>>>>>       <Geometry GeometryType="Origin_DxDyDz">
>>>>>>>>         <DataItem Dimensions="3" NumberType="Integer" Format="XML">
>>>>>>>>           0 0 0
>>>>>>>>         </DataItem>
>>>>>>>>         <DataItem Dimensions="3" NumberType="Integer" Format="XML">
>>>>>>>>           1 1 1
>>>>>>>>         </DataItem>
>>>>>>>>       </Geometry>
>>>>>>>>       <Attribute Name="pressure" AttributeType="Scalar"
>>>>>>>> Center="Node">
>>>>>>>>         <DataItem Dimensions="91 19 19" NumberType="Float"
>>>>>>>> Format="HDF">
>>>>>>>>           out.h5:/pres_group/presmag
>>>>>>>>         </DataItem>
>>>>>>>>       </Attribute>
>>>>>>>>       <Attribute Name="velocity" AttributeType="Vector"
>>>>>>>> Center="Node">
>>>>>>>>         <DataItem ItemType="Function" Function="JOIN($0, $1, $2)"
>>>>>>>> Dimensions="91 19 19 3">
>>>>>>>>           <DataItem Dimensions="91 19 19" NumberType="Float"
>>>>>>>> Format="HDF">
>>>>>>>>             out.h5:/velo_group/x_velo
>>>>>>>>           </DataItem>
>>>>>>>>           <DataItem Dimensions="91 19 19" NumberType="Float"
>>>>>>>> Format="HDF">
>>>>>>>>             out.h5:/velo_group/y_velo
>>>>>>>>           </DataItem>
>>>>>>>>           <DataItem Dimensions="91 19 19" NumberType="Float"
>>>>>>>> Format="HDF">
>>>>>>>>             out.h5:/velo_group/z_velo
>>>>>>>>           </DataItem>
>>>>>>>>         </DataItem>
>>>>>>>>       </Attribute>
>>>>>>>>     </Grid>
>>>>>>>>   </Domain>
>>>>>>>> </Xdmf>
>>>>>>>>
>>>>>>>> This has worked properly on my machine. However, when I was getting
>>>>>>>> an error of failing to read the pressure data when I tried this on multiple
>>>>>>>> processes. The vector data for velocity was fine, but the pressure data
>>>>>>>> could not be read. I narrowed the problem down to something regarding the
>>>>>>>> number of processes because the pressure data worked fine on the HPC
>>>>>>>> machine if I only ran it on 1 process. Is there anything that sticks out
>>>>>>>> that could be causing this problem? For instance, is there a different
>>>>>>>> format for these files when they are run on multiple processes?
>>>>>>>>
>>>>>>>> Respectfully,
>>>>>>>>
>>>>>>>> Jacob Gerard
>>>>>>>>
>>>>>>>
>>>>>>>
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>>>>>>
>>>>>
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>>>>> Powered by www.kitware.com
>>>>>
>>>>> Visit other Kitware open-source projects at
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>>>>>
>>>>> Please keep messages on-topic and check the ParaView Wiki at:
>>>>> http://paraview.org/Wiki/ParaView
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>>>>>
>>>>
>>>
>>
>
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