In this talk, I will present our latest work with the Extrae measurement library and the Paraver analysis tool, with respect to performance analysis of the application PFLOTRAN on the Cray XT5. In collaboration with the PERI performance analysis project, we have collected traces of 8184 processes and detected (known and unknown) evidence of load imbalance, and also detected a possible iteration variance with respect to potential operating system noise, which we suspect is related to a preemption issue. We are continuing our investigation of the issue, and will present our ongoing analysis. Time permitting, I will also present recent advances in the Paraver analysis tools, including clustering computation bursts and folding iterations using low-frequency sampling.