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

Wed Jul 12 16:16:20 EDT 2017

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/
> paraview/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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