Pre-exascale High Performance Computers (HPC) can reach more than 400 Pflop/s real perfor-mance according the HPLinpack benchmarks. For nanoscience and quantum biology there are requirements for those program codes based on quantum physics algorithms which is difficult to ideally parallelize. Such parallel codes reach their limitations at terascale performance clus-ters. The standard Amdahl's law suggestions for code parallelization complicates focusing and planning for the next step the parallel code developments. In this report we focused on a three key applications domain which are highly parallelizable: HPC benchmarks, quantum compu-ting simulators and Car-Parinello molecular dynamics. According the results we summarize the Amdahl's Law & Parallel Speedup performance achievements with supercomputer with pre-petascale homogeneous HPC hardware. We conclude as an universal computer the pre-petascale supercomputing performance homogeneous hardware still has the basic challeng-es which must be addressed by the researchers or developer in order efficiently to use them.