IBMs Blue Gene supercomputer architecture has evolved through three successive generations each providing increased levels of power-efficiency and system densities. From the original Blue Gene/L to P to Q, a higher level of integration has enabled higher single-core performance, larger concurrency per compute node, and a higher level of system integration. Although these changes have brought with them a higher overall system peak-performance, no study has examined in detail the evolution of performance across system generations. In this work we make two significant contributions that of providing a comparative performance analysis across Blue Gene generations using a consistent set of tests, and also in providing a validated performance model of the NEK-Bone proxy application from the DOE CESAR Exascale Co-Design Center. The combination of empirical analysis and the predictive capabilities of the NEK-Bone performance model enable us to not only directly compare measured performance but also allow for a comparison of system configurations that cannot currently be measured. We provide insights into how the changing architectural performance characteristics of Blue Gene have impacted on the application performance, as well as providing insight into what future systems may be able to achieve. © 2013 World Scientific Publishing Company.