Error with Show() in pvpython but works on different system

ParaView Support
1

Hello,

I have some Python 3 code that runs perfectly on my personal system (using Ubuntu 18), but when I try to run the same code on a server (using CentOS 7) it gets stuck on Show() and about 5-10 seconds later displays ‘Killed’ and quits. Running it via slurm shows no error and simply gets stuck at Show() and never exits. I have ParaView-5.8.0-osmesa-MPI-Linux-Python3.7-64bit.tar.gz installed on both systems. I’ve been searching around but have not been able to find any errors similar to this. I have not been able to see the error message that occurs nor do I know how to force pvpython to output error messages. This is also a separate question, but how do I force pvpython to display the error that causes the program to terminate.

Here is the code up to where it fails - also fails if Show() is given no inputs

file_info = Xdmf3ReaderS(FileName=[file_location])
print('read')
temp_view = GetActiveView()
print('active view')
Show(file_info, temp_view)
print('shown')

Thank you!

Carter

2

Does the following works ?

Wavelet()
Show()
Render()
3

Yes, that seems to work on both systems, and saving an image on both systems shows the same thing (just the white edge of the bounding box in this case).

After some more debugging, it seems like the xdmf data being read in is corrupted somehow.

Here is some of the debugging code:

with open(file_location, 'r') as f:
    print(f.read())
file_info = Xdmf3ReaderS(FileName=[file_location])
print(file_info)
print(file_info.CellData.keys())

On my computer (the one where the code fully runs), This prints the .xdmf file text (to show the file is being read correctly), prints <paraview.servermanager.Xdmf3ReaderS object at 0x7fe9e0a736d0>, and finally prints the cell names.
On the server, this still prints the entire .xdmf file (so its definitely the right file location), then prints the same paraview.servermanager.Xdmf3ReaderS but fails on the last print statement. So it seems like the reader is failing at reading the file. If I use just XDMFReader, it still runs on my computer but fails on the server when printing the file_info data from the xdmf reader.

4

Just for anyone in the future.

My issue ended up being an issue with HDF5 versions. I had a different version of HDF5 in my LD_LIBRARY_PATH and when ParaView was reading my HDF5 file it would run out of memory and crash. I used the --enable-bt flag with pvpython to figure out what was happening when the code failed. Depending on the reader I used ParaView would either crash when reading the file, or would essentially read in nothing and then crash when it tried to display that.