System Workbench for STM32 installation and configuration on Linux
searching around, I saw there someone has mentioned that “SWT_GTK3=0 /yourpath/eclipse &”
to fix one of GTK related issue.
I tried it and it fix my problem.
Now I can change the project properties and run debugging my STM32F0Discovery board through OpenOCD/STLinkv2 .
Hope this will help someone.