X Windows Freeze but SSH can connect to Ubuntu 10.04

Hi,

I am very new to Linux. I need to run some scientific program which are native linux code, so I chose the Ubuntu 10.04 which supports some architecture required by the code. So most of my install and button meshing are default or as laid out in the guide.

I have a few of the problems found on the wiki page
https://wiki.ubuntu.com/X/Troubleshooting/Freeze#Reporting_GPU_lockup_Bugs
and the problems only occurs when I have successfully finish a run of the tophat program (http://tophat.cbcb.umd.edu/), every run of this program takes around 15-17 hours so I am not sure if I can reproduce this easily, and the freeze has happened on both times I ran this.

In particular, the 4 symptoms below applies to my case.

Symptoms
    X stops responding to input (sometimes mouse cursor can still move, but clicking has no effect)
    The screen displays but does not update. Sometimes there is screen corruption too, sometimes the screen goes black.
    Often, X cannot be killed from the console or if it can, it won't restart properly; only a reboot clears the state
    You can ping the machine and SSH into it remotely

As suggested in the wiki, I have collected the dmesg and X log in the dropbox below
https://www.dropbox.com/sh/sgki44nzos3dyn4/LSArQ4S_98

Any advise with the issue is appreciated, but please do take me as a noob when u are offering advise.