The emergence of many non-volatile memory (NVM) techniques is poised to revolutionize main memory systems because of the relatively high capacity and low lifetime power consumption of NVM. However, to avoid the typical limitation of NVM as the main memory, NVM is usually combined with DRAM to form a hybrid NVM/DRAM system to gain the benefits of each. However, this integrated memory system raises a question on how to manage data placement and movement across NVM and DRAM, which is critical for maximizing the benefits of this integration. The existing solutions have several limitations, which obstruct adoption of these solutions in the high performance computing (HPC) domain. In particular, they cannot take advantage of application semantics, thus losing critical optimization opportunities and demanding extensive hardware extensions; they implement persistent semantics for resilience purpose while suffering large performance and energy overhead. In this paper, we re-examine the current hybrid memory designs from the HPC perspective, and aim to leverage the knowledge of numerical algorithms to direct data placement. With explicit algorithm management and limited hardware support, we optimize data movement between NVM and DRAM, improve data locality, and implement a relaxed memory persistency scheme in NVM. Our work demonstrates significant benefits of integrating algorithm knowledge into the hybrid memory design to achieve multi-dimensional optimization (performance, energy, and resilience) in HPC.