Error installing ovito on Linux cluster

Quote from Betim Bahtiri on January 13, 2021, 6:56 pm

Quote from Alexander Stukowski on January 13, 2021, 5:27 pm

Please check if the PySide2 module is fully functional (without loading the OVITO module):

>>>import PySide2.QtCore

Does that work or do you get the same error?

import PySide2.QtCore
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ImportError: /usr/lib/x86_64-linux-gnu/libgssapi_krb5.so.2: symbol krb5_ser_cont ext_init, version krb5_3_MIT not defined in file libkrb5.so.3 with link time ref erence

 

seems like not

Quote from Jacob Gruber on January 14, 2021, 8:10 am

Hello, I just tried to install the python ovito package on my laptop (Ubuntu 20.04) and I ran into a similar error, when importing both ovito and PySide2.QtCore:

ImportError: /lib/x86_64-linux-gnu/libgssapi_krb5.so.2: undefined symbol: krb5_ser_context_init, version krb5_3_MIT

This appears to have been caused by a version mismatch of the krb5 library between PySide2 and the system packages. A workaround I was able to find was to compile krb5 from source and then change LD_LIBRARY_PATH when starting python. This allowed me to import ovito without error. Perhaps this may help you solve your problem.

I'm not sure if this belongs in this thread, as my issue is a little different, but I could not find many occurences of this specific error so I thought it might be useful.

Quote from Alexander Stukowski on January 14, 2021, 8:48 am

Quote from Jacob Gruber on January 14, 2021, 8:10 am

Hello, I just tried to install the python ovito package on my laptop (Ubuntu 20.04) and I ran into a similar error, when importing both ovito and PySide2.QtCore:

Thanks for letting us know that you had a similar problem. Which Python interpreter did you use in this case? The standard interpreter from Ubuntu 20.04 or one from an Anaconda environment? And from which source did you install the PySide2 module (or the ovito module)?

I am asking, because the error message seems to be typical for situations where users had installed the PySide2 pip package into an Anaconda interpreter environment. See here for example.

Quote from Betim Bahtiri on January 14, 2021, 9:42 am

Quote from Alexander Stukowski on January 14, 2021, 8:48 am

Quote from Jacob Gruber on January 14, 2021, 8:10 am

Hello, I just tried to install the python ovito package on my laptop (Ubuntu 20.04) and I ran into a similar error, when importing both ovito and PySide2.QtCore:

Thanks for letting us know that you had a similar problem. Which Python interpreter did you use in this case? The standard interpreter from Ubuntu 20.04 or one from an Anaconda environment? And from which source did you install the PySide2 module (or the ovito module)?

I am asking, because the error message seems to be typical for situations where users had installed the PySide2 pip package into an Anaconda interpreter environment. See here for example.

i installed both with pip and i am using the interpreter from anaconda

Quote from Jacob Gruber on January 14, 2021, 8:04 pm

I used a separately installed Python 3.8.5 interpreter (i.e. neither Anaconda nor standard Ubuntu package). All packages installed using pip.