AirLift is the first read remapping tool that enables users to quickly and comprehensively map a read set, that had been previously mapped to one reference genome, to another similar reference. Users can then quickly run a downstream analysis of read sets for each latest reference release. Compared to the state-of-the-art method for remapping reads (i.e., full mapping), AirLift reduces the overall execution time to remap read sets between two reference genome versions by up to 27.4×. We validate our remapping results with GATK and find that AirLift provides high accuracy in identifying ground truth SNP/INDEL variants.

Conventional virtual memory (VM) frameworks enable a virtual address to flexibly map to any physical address. This flexibility necessitates large data structures to store virtual-to-physical mappings, which leads to high address translation latency and large translation-induced interference in the memory hierarchy, especially in data-intensive workloads. On the other hand, restricting the address mapping so that a virtual address can only map to a specific set of physical addresses can significantly reduce address translation overheads by making use of compact and efficient translation structures. However, restricting the address mapping flexibility across the entire main memory severely limits data sharing across different processes and increases data accesses to the swap space of the storage device even in the presence of free memory.

Hybrid storage systems (HSS) use multiple different storage devices to provide high and scalable storage capacity at high performance. Data placement across different devices is critical to maximize the benefits of such a hybrid system. Recent research proposes various techniques that aim to accurately identify performance-critical data to place it in a "best-fit" storage device. Unfortunately, most of these techniques are rigid, which (1) limits their adaptivity to perform well for a wide range of workloads and storage device configurations, and (2) makes it difficult for designers to extend these techniques to different storage system configurations (e.g., with a different number or different types of storage devices) than the configuration they are designed for. Our goal is to design a new data placement technique for hybrid storage systems that overcomes these issues and provides: (1) adaptivity, by continuously learning from and adapting to the workload and the storage device characteristics, and (2) easy extensibility to a wide range of workloads and HSS configurations.

Processing-using-DRAM has been proposed for a limited set of basic operations (i.e., logic operations, addition). However, in order to enable full adoption of processing-using-DRAM, it is necessary to provide support for more complex operations. In this paper, we propose SIMDRAM, a flexible general-purpose processing-using-DRAM framework that (1) enables the efficient implementation of complex operations, and (2) provides a flexible mechanism tosupport the implementation of arbitrary user-defined operations. The SIMDRAM framework comprises three key steps. The first step builds an efficient MAJ/NOT representation of a given desired operation. The second step allocates DRAM rows that are reserved for computation to the operation’s input and output operands, and generates the required sequence of DRAM commands to perform the MAJ/NOT implementation of the desired operation in DRAM. The third step uses the SIMDRAM control unit located inside the memory controller to manage the computation of the operation from start to end, by executing the DRAM commands generated in the second step of the framework. We design the hardware and ISA support for SIMDRAM framework to (1) address key system integration challenges, and (2) allow programmers to employ new SIMDRAM operations without hardware changes.

Computers continue to diversify with respect to system designs, emerging memory technologies, and application memory demands. Unfortunately, continually adapting the conventional virtual memory framework to each possible system configuration is challenging, and often results in performance loss or requires non-trivial workarounds. To address these challenges, we propose a new virtual memory framework, the Virtual Block Interface (VBI). We design VBI based on the key idea that delegating memory management duties to hardware can reduce the overheads and software complexity associated with virtual memory. VBI introduces a set of variable-sized virtual blocks (VBs) to applications. Each VB is a contiguous region of the globally-visible VBI address space, and an application can allocate each semantically meaningful unit of information (e.g., a data structure) in a separate VB. VBI decouples access protection from memory allocation and address translation. While the OS controls which programs have access to which VBs, dedicated hardware in the memory controller manages the physical memory allocation and address translation of the VBs. This approach enables several architectural optimizations to (1) efficiently and flexibly cater to different and increasingly diverse system configurations, and (2) eliminate key inefficiencies of conventional virtual memory. We demonstrate the benefits of VBI with two important use cases: (1) reducing the overheads of address translation (for both native execution and virtual machine environments), as VBI reduces the number of translation requests and associated memory accesses; and (2) two heterogeneous main memory architectures, where VBI increases the effectiveness of managing fast memory regions. For both cases, VBI significantly improves performance over conventional virtual memory.

Specialized on-chip accelerators are widely used to improve the energy efficiency of computing systems. Recent advances in memory technology have enabled near-data accelerators (NDAs), which reside off-chip close to main memory and can yield further benefits than on-chip accelerators. However, enforcing coherence with the rest of the system, which is already a major challenge for accelerators, becomes more difficult for NDAs. This is because (1) the cost of communication between NDAs and CPUs is high, and (2) NDA applications generate a lot of off-chip data movement. As a result, as we show in this work, existing coherence mechanisms eliminate most of the benefits of NDAs. We extensively analyze these mechanisms, and observe that (1) the majority of off-chip coherence traffic is unnecessary, and (2) much of the off-chip traffic can be eliminated if a coherence mechanism has insight into the memory accesses performed by the NDA.

This paper makes a case for a new cross-layer interface, Expressive Memory (XMem), to communicate higher-level program semantics from the application to the system software and hardware architecture. XMem provides (i) a flexible and extensible abstraction, called an Atom, enabling the application to express key program semantics in terms of how the program accesses data and the attributes of the data itself, and (ii) new cross-layer interfaces to make the expressed higher-level information available to the underlying OS and architecture. By providing key information that is otherwise unavailable, XMem exposes a new, rich view of the program data to the OS and the different architectural components that optimize memory system performance (e.g., caches, memory controllers). By bridging the semantic gap between the application and the underlying memory resources, XMem provides two key benefits. First, it enables architectural/system-level techniques to leverage key program semantics that are challenging to predict or infer. Second, it improves the efficacy and portability of software optimizations by alleviating the need to tune code for specific hardware resources (e.g., cache space). While XMem is designed to enhance and enable a wide range of memory optimizations, we demonstrate the benefits of XMem using two use cases: (i) improving the performance portability of software-based cache optimization by expressing the semantics of data locality in the optimization and (ii) improving the performance of OS-based page placement in DRAM by leveraging the semantics of data structures and their access properties.