Scientific workflows are often composed of compute-intensive simulations and data-intensive analysis and visualization, both equally important for productivity. High-performance computers run the compute-intensive phases efficiently, but data-intensive processing is still getting less attention. Dense non-volatile memory integrated into super-computers can help address this problem. In addition to density, it offers significantly finer-grained I/O than disk-based I/O systems. We present a way to exploit the fundamental capabilities of Storage-Class Memories (SCM), such as Flash, by using scalable key-value (KV) I/O methods instead of traditional file I/O calls commonly used in HPC systems. Our objective is to enable higher performance for on-line and near-line storage for analysis and visualization of very high resolution, but correspondingly transient, simulation results. In this paper, we describe 1) the adaptation of a scalable key-value store to a BlueGene/Q system with integrated Flash memory, 2) a novel key-value aggregation module which implements coalesced, function-shipped calls between the clients and the servers, and 3) the refactoring of a scientific workflow to use application-relevant keys for fine-grained data subsets. The resulting implementation is analogous to function-shipping of POSIX I/O calls but shows an order of magnitude increase in read and a factor 2.5x increase in write IOPS performance (11 million read IOPS, 2.5 million write IOPS from 4096 compute nodes) when compared to a classical file system on the same system. It represents an innovative approach for the integration of SCM within an HPC system at scale.