A parallel computer system includes computing nodes to execute a parallel program for generating computing processes that perform computations and monitoring processes and forming a monitoring hierarchical structure, each monitoring process monitors a monitoring process and a computing process arranged immediately lower than the monitoring process, each of the computing nodes operating as the computing process when the computing process is allocated to the computing node and operating as the monitoring process when the monitoring process is allocated to the computing node. Each of the computing nodes allocated to the monitoring process performs processing that changes the hierarchical structure based on a first target value serving as a target value for the total number of subordinate computing processes of the allocated monitoring process and a second target value serving as a target value for the number of monitoring processes and computing processes arranged immediately lower than the allocated monitoring process.