Memory Subsystems for Security, Consistency, and Scalability

In response to the continuous demand for the ability to process ever larger datasets, as well as discoveries in next-generation memory technologies, researchers have been vigorously studying memory-driven computing architectures that shall allow data-intensive applications to access enormous amounts of pooled non-volatile memory. As applications continue to interact with increasing amounts of components and datasets, existing systems struggle to eÿciently enforce the principle of least privilege for security. While non-volatile memory can retain data even after a power loss and allow for large main memory capacity, programmers have to bear the burdens of maintaining the consistency of program memory for fault tolerance as well as handling huge datasets with traditional yet expensive memory management interfaces for scalability. Today’s computer systems have become too sophisticated for existing memory subsystems to handle many design requirements. In this dissertation, we introduce three memory subsystems to address challenges in terms of security, consistency, and scalability. Specifcally, we propose SMVs to provide threads with fne-grained control over access privileges for a partially shared address space for security, NVthreads to allow programmers to easily leverage nonvolatile memory with automatic persistence for consistency, and PetaMem to enable memory-centric applications to freely access memory beyond the traditional process boundary with support for memory isolation and crash recovery for security, consistency, and scalability

Distributed Logless Atomic Durability with Persistent Memory

Datacenter operators have started deploying Persistent Memory (PM), leveraging its combination of fast access and persistence for significant performance gains. A key challenge for PM-aware software is to maintain high performance while achieving atomic durability. The latter typically requires the use of logging, which introduces considerable overhead with additional CPU cycles, write traffic, and ordering requirements. In this paper, we exploit the data multiversioning inherent in the memory hierarchy to achieve atomic durability without logging. Our design, LAD, relies on persistent buffering space at the memory controllers (MCs)—already present in modern CPUs—to speculatively accumulate all of a transaction’s updates before they are all atomically committed to PM. LAD employs an on-chip distributed commit protocol in hardware to manage the distributed speculative state each transaction accumulates across multiple MCs. We demonstrate that LAD is a practical design relying on modest hardware modifications to provide atomically durable transactions, while delivering up to 80% of ideal—i.e., PM-oblivious software’s—performance

Novel Genetic Variants Associated With Increased Vertebral Volumetric BMD, Reduced Vertebral Fracture Risk, and Increased Expression of SLC1A3 and EPHB2.

Genome-wide association studies (GWASs) have revealed numerous loci for areal bone mineral density (aBMD). We completed the first GWAS meta-analysis (n = 15,275) of lumbar spine volumetric BMD (vBMD) measured by quantitative computed tomography (QCT), allowing for examination of the trabecular bone compartment. SNPs that were significantly associated with vBMD were also examined in two GWAS meta-analyses to determine associations with morphometric vertebral fracture (n = 21,701) and clinical vertebral fracture (n = 5893). Expression quantitative trait locus (eQTL) analyses of iliac crest biopsies were performed in 84 postmenopausal women, and murine osteoblast expression of genes implicated by eQTL or by proximity to vBMD-associated SNPs was examined. We identified significant vBMD associations with five loci, including: 1p36.12, containing WNT4 and ZBTB40; 8q24, containing TNFRSF11B; and 13q14, containing AKAP11 and TNFSF11. Two loci (5p13 and 1p36.12) also contained associations with radiographic and clinical vertebral fracture, respectively. In 5p13, rs2468531 (minor allele frequency [MAF] = 3%) was associated with higher vBMD (β = 0.22, p = 1.9 × 10-8 ) and decreased risk of radiographic vertebral fracture (odds ratio [OR] = 0.75; false discovery rate [FDR] p = 0.01). In 1p36.12, rs12742784 (MAF = 21%) was associated with higher vBMD (β = 0.09, p = 1.2 × 10-10 ) and decreased risk of clinical vertebral fracture (OR = 0.82; FDR p = 7.4 × 10-4 ). Both SNPs are noncoding and were associated with increased mRNA expression levels in human bone biopsies: rs2468531 with SLC1A3 (β = 0.28, FDR p = 0.01, involved in glutamate signaling and osteogenic response to mechanical loading) and rs12742784 with EPHB2 (β = 0.12, FDR p = 1.7 × 10-3 , functions in bone-related ephrin signaling). Both genes are expressed in murine osteoblasts. This is the first study to link SLC1A3 and EPHB2 to clinically relevant vertebral osteoporosis phenotypes. These results may help elucidate vertebral bone biology and novel approaches to reducing vertebral fracture incidence. © 2016 American Society for Bone and Mineral Research

Nine loci for ocular axial length identified through genome-wide association studies, including shared loci with refractive error

10.1016/j.ajhg.2013.06.016American Journal of Human Genetics932264-277AJHG