A parallel computer system includes a plurality of calculation nodes and a job management apparatus to allocate jobs to the plurality of calculation nodes. The job management apparatus includes a controller to execute a process including searching a vacant resource generated as a result of job allocation, the vacant resource including one or more of the plurality of calculation nodes each having a vacant state in a range between current time and a scheduled start time point of a certain allocated job, retrieving the job allocatable to the vacant resource, from the unallocated jobs when the vacant resource is found, and allocating the retrieved job to the vacant resource.