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

Jake Gerard jake.a.gerard at gmail.com
Thu Jul 13 09:49:23 EDT 2017 

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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>>
>
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