I did not find to root cause of my problem with this specific application (questasim). But what i found is a bug on the mailing list that is exactly what i have . the bug is #475
https://bugs.x2go.org/cgi-bin/bugreport.cgi?bug=475 When starting this application i got realy high CPU load on the x2goagent process. One thing i have notice is that it is only append when it is running in published application. When running is desktop mode (MATE) the tool run fine. But we need to run in published application mode. We have try Xpra and this application run fine. But Xpra seem a bit slower in refreshing display(blurryness) and tool interation seem a bit slower also. So again any help would be appreciated. I can do some test but i do not know where to look and what to look for.