Improving DRAM Performance by Parallelizing Refreshes with Accesses

Modern DRAM cells are periodically refreshed to prevent data loss due to leakage. Commodity DDR DRAM refreshes cells at the rank level. This degrades performance significantly because it prevents an entire rank from serving memory requests while being refreshed. DRAM designed for mobile platforms, LPDDR DRAM, supports an enhanced mode, called per-bank refresh, that refreshes cells at the bank level. This enables a bank to be accessed while another in the same rank is being refreshed, alleviating part of the negative performance impact of refreshes. However, there are two shortcomings of per-bank refresh. First, the per-bank refresh scheduling scheme does not exploit the full potential of overlapping refreshes with accesses across banks because it restricts the banks to be refreshed in a sequential round-robin order. Second, accesses to a bank that is being refreshed have to wait. To mitigate the negative performance impact of DRAM refresh, we propose two complementary mechanisms, DARP (Dynamic Access Refresh Parallelization) and SARP (Subarray Access Refresh Parallelization). The goal is to address the drawbacks of per-bank refresh by building more efficient techniques to parallelize refreshes and accesses within DRAM. First, instead of issuing per-bank refreshes in a round-robin order, DARP issues per-bank refreshes to idle banks in an out-of-order manner. Furthermore, DARP schedules refreshes during intervals when a batch of writes are draining to DRAM. Second, SARP exploits the existence of mostly-independent subarrays within a bank. With minor modifications to DRAM organization, it allows a bank to serve memory accesses to an idle subarray while another subarray is being refreshed. Extensive evaluations show that our mechanisms improve system performance and energy efficiency compared to state-of-the-art refresh policies and the benefit increases as DRAM density increases.Comment: The original paper published in the International Symposium on High-Performance Computer Architecture (HPCA) contains an error. The arxiv version has an erratum that describes the error and the fix for i

Common DNA sequence variation influences 3-dimensional conformation of the human genome.

BACKGROUND:The 3-dimensional (3D) conformation of chromatin inside the nucleus is integral to a variety of nuclear processes including transcriptional regulation, DNA replication, and DNA damage repair. Aberrations in 3D chromatin conformation have been implicated in developmental abnormalities and cancer. Despite the importance of 3D chromatin conformation to cellular function and human health, little is known about how 3D chromatin conformation varies in the human population, or whether DNA sequence variation between individuals influences 3D chromatin conformation. RESULTS:To address these questions, we perform Hi-C on lymphoblastoid cell lines from 20 individuals. We identify thousands of regions across the genome where 3D chromatin conformation varies between individuals and find that this variation is often accompanied by variation in gene expression, histone modifications, and transcription factor binding. Moreover, we find that DNA sequence variation influences several features of 3D chromatin conformation including loop strength, contact insulation, contact directionality, and density of local cis contacts. We map hundreds of quantitative trait loci associated with 3D chromatin features and find evidence that some of these same variants are associated at modest levels with other molecular phenotypes as well as complex disease risk. CONCLUSION:Our results demonstrate that common DNA sequence variants can influence 3D chromatin conformation, pointing to a more pervasive role for 3D chromatin conformation in human phenotypic variation than previously recognized

Wellington : a novel method for the accurate identification of digital genomic footprints from DNase-seq data

The expression of eukaryotic genes is regulated by cis-regulatory elements such as promoters and enhancers, which bind sequence-specific DNA-binding proteins. One of the great challenges in the gene regulation field is to characterise these elements. This involves the identification of transcription factor (TF) binding sites within regulatory elements that are occupied in a defined regulatory context. Digestion with DNase and the subsequent analysis of regions protected from cleavage (DNase footprinting) has for many years been used to identify specific binding sites occupied by TFs at individual cis-elements with high resolution. This methodology has recently been adapted for high-throughput sequencing (DNase-seq). In this study, we describe an imbalance in the DNA strand-specific alignment information of DNase-seq data surrounding protein–DNA interactions that allows accurate prediction of occupied TF binding sites. Our study introduces a novel algorithm, Wellington, which considers the imbalance in this strand-specific information to efficiently identify DNA footprints. This algorithm significantly enhances specificity by reducing the proportion of false positives and requires significantly fewer predictions than previously reported methods to recapitulate an equal amount of ChIP-seq data. We also provide an open-source software package, pyDNase, which implements the Wellington algorithm to interface with DNase-seq data and expedite analyses

Subtle changes in chromatin loop contact propensity are associated with differential gene regulation and expression.

While genetic variation at chromatin loops is relevant for human disease, the relationships between contact propensity (the probability that loci at loops physically interact), genetics, and gene regulation are unclear. We quantitatively interrogate these relationships by comparing Hi-C and molecular phenotype data across cell types and haplotypes. While chromatin loops consistently form across different cell types, they have subtle quantitative differences in contact frequency that are associated with larger changes in gene expression and H3K27ac. For the vast majority of loci with quantitative differences in contact frequency across haplotypes, the changes in magnitude are smaller than those across cell types; however, the proportional relationships between contact propensity, gene expression, and H3K27ac are consistent. These findings suggest that subtle changes in contact propensity have a biologically meaningful role in gene regulation and could be a mechanism by which regulatory genetic variants in loop anchors mediate effects on expression

Omphale: Streamlining the Communication for Jobs in a Multi Processor System on Chip

Our Multi Processor System on Chip (MPSoC) template provides processing tiles that are connected via a network on chip. A processing tile contains a processing unit and a Scratch Pad Memory (SPM). This paper presents the Omphale tool that performs the first step in mapping a job, represented by a task graph, to such an MPSoC, given the SPM sizes as constraints. Furthermore a memory tile is introduced. The result of Omphale is a Cyclo Static DataFlow (CSDF) model and a task graph where tasks communicate via sliding windows that are located in circular buffers. The CSDF model is used to determine the size of the buffers and the communication pattern of the data. A buffer must fit in the SPM of the processing unit that is reading from it, such that low latency access is realized with a minimized number of stall cycles. If a task and its buffer exceed the size of the SPM, the task is examined for additional parallelism or the circular buffer is partly located in a memory tile. This results in an extended task graph that satisfies the SPM size constraints