This paper studies and compares PNR and rMSATS methods for load balancing in parallel finite element analysis. Both the strengths and weaknesses of two algorithms are discussed. Some possible improvements to the two algorithms are also suggested and studied. A benchmark for evaluating algorithms is described. Direct numerical comparisons among the considered partitioning algorithms are then conducted using this benchmark. In addition, we think different algorithms as vertices of a undirected weighted graph. Choosing an algorithm from different partition methods is a recursive graph partitioning problem when dealing with a certain FEM computations. Choosing algorithm use heuristic algorithm in this paper. The initial value is critical at the heuristic algorithm. Wrong initial value leads to long execution time.