1. A non-transitory computer-readable medium containing a program which, when executed, performs an operation of generating a visual representation of performance data for an application running on a plurality of compute nodes of a parallel computing system, wherein instances of the application communicate with one another using a first network, the operation comprising: receiving a value for each of one or more dedicated hardware performance counters present on the plurality of compute nodes, wherein the values are received without disrupting the performance of the application running on the plurality of compute nodes by using a second network that is separate from the first network, and wherein at least one of the dedicated hardware performance counters is configured to count a number of packets that pass through a plurality of network ports coupled to one of the plurality of compute nodes; determining a maximum value for each of the dedicated hardware performance counters and a minimum value for each of the dedicated hardware performance counters, wherein the maximum value represents the maximum value for the dedicated hardware performance counter across all of the plurality of compute nodes, and wherein the minimum value represents the minimum value for the dedicated hardware performance counter across all of the plurality of compute nodes; for each of the plurality of compute nodes, determining a weighted color value relative to the received values for the other compute nodes in the plurality of compute nodes, wherein the weighted color value is based on the received value for each respective compute node, the respective maximum value for the performance counter, and the respective minimum value for the performance counter; and generating a three-dimensional visual display representing the plurality of compute nodes, wherein the three-dimensional visual display depicts a network topology of the plurality of compute nodes, and wherein the three-dimensional visual display is colored based on the weighted color value determined for each of the plurality of compute nodes.