Architectural support for message queue task parallelism

The scaling of threads is an attractive way to exploit task-level parallelism and boost performance. From the perspective of software programming, many applications (e.g., network package processing, SQL queries) could be composite of a set of small tasks. Those tasks are arranged in a data flow graph and each task is undertaken by some threads. Message queues are often used to coordinate the tasks among the threads. On the other side, thread scaling is in favor of the hardware advancing trend that there are more Processing Elements (PE) in modern Chip Multiprocessors (CMP) than ever before. This is because single PE cannot simply run faster due to power and thermal limitations; instead architects have to use more transistors for increasing number of PEs, in order to improve the overall computing power of a processor. Unfortunately, this paradigm using message queues to drive parallel tasks sometime leads to diminishing performance returns due to issues lying in the architecture and system design. Particularly, the conventional coherent shared-memory architectures let task-parallel workloads suffer from unnecessary synchronization overhead and load-to-use latency. For instance, when passing messages through queues, multiple threads could contend for the exclusivity of the cacheline where the shared queue data structure stays. The more threads, the more severe the contention is, because every transition upgrading a cacheline from shared to exclusive state needs to invalidate more copies in the private caches of other cores, and waits for the acknowledgements from more cores. Such a overhead hurts the scalability of threads synchronizing via message queues. Adding to the coherence overhead, the load-to-use latency (from a consumer requesting data until the data being moved to the consumer to use) is often on the critical path, slowing down the computation. This is because the cache hierarchy in modern processors creates some layers of local storage to buffer data separately for different cores. Therefore, serving message queue data in an ondemand manner incurs longer load-to-use latency. It is also challenging to schedule message-driven tasks to use cores efficiently when arrival rate and service rate mismatch. It wastes CPU cycles if a runtime system leaves tasks blocked on full/empty message queues, while switching tasks has additional scheduling overheads. Diverse system topologies further complicate the problem, as the scheduling also needs to take data locality into consideration. This dissertation explores architectural supports for enhancing the scalability of message queue task parallelism, reducing the load-to-use latency, as well as avoiding blocking. Specifically, this dissertation designs and evaluates a message queue architecture that lowers the overhead of synchronization on shared queue states, a speculation technique to hide the load-to-use latency, as well as a locality-aware message queue runtime system with low overhead on scheduling and buffer resizing. The first contribution of the dissertation is Virtual-Link scalable message queue architecture (VL). Instead of having threads access the shared queue state variables (i.e., head, tail, or lock) atomically, VL provides configurable hardware support, providing both data transfer and synchronization. Unlike other hardware queue architectures with dedicated network, VL reuses the existing cache coherence network and delivers a virtualized channel as if there were a direct link (or route) between two arbitrary PEs. VL facilitates efficient synchronized data movement between M:N producers and consumers with several benefits: (i) the number of sharers on synchronization primitives is reduced to zero, eliminating a primary bottleneck of traditional lock-free queues, (ii) memory spills, snoops, and invalidations are reduced, (iii) data stays on the fast path (inside the interconnect) a majority of the time. Another contribution of the dissertation is SPAMeR speculation mechanism. SPAMeR has the capability to speculatively push messages in anticipation of consumer message requests. With the speculation, the latency of moving data from the source to the consumer that needs the data could be partially or fully overlapped with the message processing time. Unlike pre-fetch approaches which predict what addresses to fetch next, with a queue we know exactly what data is needed next but not when it is needed; SPAMeR proposes algorithms to learn from queue operation history in order to predict this. Finally the dissertation contributes ARMQ locality-aware runtime. ARMQ collects a set of approaches that avoids message queue blocking, ranging from the most general yielding, to dynamically resizing the buffer, and to spawning helper tasks. On one hand, ARMQ minimizes the overheads (e.g., wasteful polling, context switch, memory allocation and copying etc.) with a few techniques (e.g., userspace threading, chunk-based ringbuffer etc.) On the other hand, ARMQ schedules the message-driven tasks precisely and opportunely, in order to maximize the data locality preserved (in favor of cache) and balance the resource allocation.Electrical and Computer Engineerin

Analysis of age and gender associated N-glycoproteome in human whole saliva

BACKGROUND: Glycoproteins comprise a large portion of the salivary proteome and have great potential for biomarker discovery and disease diagnosis. However, the rate of production and the concentration of whole saliva change with age, gender and physiological states of the human body. Therefore, a thorough understanding of the salivary glycoproteome of healthy individuals of different ages and genders is a prerequisite for saliva to have clinical utility. METHODS: Formerly N-linked glycopeptides were isolated from the pooled whole saliva of six age and gender groups by hydrazide chemistry and hydrophilic affinity methods followed by mass spectrometry identification. Selected physiochemical characteristics of salivary glycoproteins were analyzed, and the salivary glycoproteomes of different age and gender groups were compared based on their glycoprotein components and gene ontology. RESULTS AND DISCUSSION: Among 85 N-glycoproteins identified in healthy human saliva, the majority were acidic proteins with low molecular weight. The numbers of salivary N-glycoproteins increased with age. Fifteen salivary glycoproteins were identified as potential age- or gender-associated glycoproteins, and many of them have functions related to innate immunity against microorganisms and oral cavity protection. Moreover, many salivary glycoproteins have been previously reported as disease related glycoproteins. This study reveals the important role of salivary glycoproteins in the maintenance of oral health and homeostasis and the great potential of saliva for biomarker discovery and disease diagnosis

NextGen-Malloc: Giving Memory Allocator Its Own Room in the House

Article describes how memory allocation and management have a significant impact on performance and energy of modern applications. The authors observe that performance can vary by as much as 72% in some applications based on which memory allocator is used, and in this paper, the authors make a case for offloading memory allocation (and other similar management functions) from main processing cores to other processing units to boost performance, reduce energy consumption, and customize services to specific applications or application domains

Prediction of Biological Functions on Glycosylation Site Migrations in Human Influenza H1N1 Viruses

Protein glycosylation alteration is typically employed by various viruses for escaping immune pressures from their hosts. Our previous work had shown that not only the increase of glycosylation sites (glycosites) numbers, but also glycosite migration might be involved in the evolution of human seasonal influenza H1N1 viruses. More importantly, glycosite migration was likely a more effectively alteration way for the host adaption of human influenza H1N1 viruses. In this study, we provided more bioinformatics and statistic evidences for further predicting the significant biological functions of glycosite migration in the host adaptation of human influenza H1N1 viruses, by employing homology modeling and in silico protein glycosylation of representative HA and NA proteins as well as amino acid variability analysis at antigenic sites of HA and NA. The results showed that glycosite migrations in human influenza viruses have at least five possible functions: to more effectively mask the antigenic sites, to more effectively protect the enzymatic cleavage sites of neuraminidase (NA), to stabilize the polymeric structures, to regulate the receptor binding and catalytic activities and to balance the binding activity of hemagglutinin (HA) with the release activity of NA. The information here can provide some constructive suggestions for the function research related to protein glycosylation of influenza viruses, although these predictions still need to be supported by experimental data

Glycosylation Site Alteration in the Evolution of Influenza A (H1N1) Viruses

Influenza virus typically alters protein glycosylation in order to escape immune pressure from hosts and hence to facilitate survival in different host environments. In this study, the patterns and conservation of glycosylation sites on HA and NA of influenza A/H1N1 viruses isolated from various hosts at different time periods were systematically analyzed, by employing a new strategy combining genome-based glycosylation site prediction and 3D modeling of glycoprotein structures, for elucidation of the modes and laws of glycosylation site alteration in the evolution of influenza A/H1N1 viruses. The results showed that influenza H1N1 viruses underwent different alterations of protein glycosylation in different hosts. Two alternative modes of glycosylation site alteration were involved in the evolution of human influenza virus: One was an increase in glycosylation site numbers, which mainly occurred with high frequency in the early stages of evolution. The other was a change in the positional conversion of the glycosylation sites, which was the dominating mode with relatively low frequency in the later evolutionary stages. The mechanisms and possibly biological functions of glycosylation site alteration for the evolution of influenza A/H1N1 viruses were also discussed. Importantly, the significant role of positional alteration of glycosylation sites in the host adaptation of influenza virus was elucidated. Although the results still need to be supported by experimental data, the information here may provide some constructive suggestions for research into the glycosylation of influenza viruses as well as even the design of surveillance and the production of viral vaccines