Graph analytics and storage

Graph analytics, which explores the relationships among interconnected entities, is becoming increasingly important due to its broad applicability, from machine learning to social sciences. However, due to the irregular data access patterns in graph computations, one major challenge for graph processing systems is performance. The algorithms, softwares, and hardwares that have been tailored for mainstream parallel applications are generally not effective for massive, sparse graphs from the real-world problems, due to their complex and irregular structures. To address the performance issues in large-scale graph analytics, we leverage the exceptional random access performance of the emerging Hybrid Memory Cube (HMC) combined with the flexibility and efficiency of modern FPGAs. In particular, we develop a collaborative software/hardware technique to perform a level-synchronized Breadth First Search (BFS) on a FPGA-HMC platform. From the software perspective, we develop an architecture-aware graph clustering algorithm that exploits the FPGA-HMC platform»s capability to improve data locality and memory access efficiency. From the hardware perspective, we further improve the FPGA-HMC graph processor architecture by designing a memory request merging unit to take advantage of the increased data locality resulting from graph clustering. We evaluate the performance of our BFS implementation using the AC-510 development kit from Micron and achieve $2.8 \times$ average performance improvement compared to the latest FPGA-HMC based graph processing system over a set of benchmarks from a wide range of applications.

Due to the limited capacity of GPU memory, the majority of prior work on graph applications on GPUs has been restricted to graphs of modest sizes that fit in memory. Recent hardware and software advances make it possible to address much larger host memory transparently as a part of a feature known as unified virtual memory. While accessing host memory over an interconnect is understandably slower, the problem space has not been sufficiently explored in the context of a challenging workload with low computational intensity and an irregular data access pattern such as graph traversal. We analyse the performance of breadth first search (BFS) for several large graphs in the context of unified memory and identify the key factors that contribute to slowdowns. Next, we propose a lightweight offline graph reordering algorithm, HALO (Harmonic Locality Ordering), that can be used as a pre-processing step for static graphs. HALO yields speedups of 1.5x-1.9x over baseline in subsequent traversals. Our method specifically aims to cover large directed real world graphs in addition to undirected graphs whereas prior methods only account for the latter. Additionally, we demonstrate ties between the locality ordering problem and graph compression and show that prior methods from graph compression such as recursive graph bisection can be suitably adapted to this problem.

An important component of current research in big data is graph analytics on very large graphs. Of the many problems of interest in this domain, graph pattern matching is both challenging and practically important. The problem is, given a relatively small query graph, finding matching patterns in a large data graph. Algorithms to address this problem are used in large social networks and graph databases. Though fast querying is highly desirable, the scalability of pattern matching algorithms is hindered by the NP-completeness of the subgraph isomorphism problem. This paper presents a conceptually simple, memory-efficient, pruning-based algorithm for the subgraph isomorphism problem that outperforms commonly used algorithms on large graphs. The high performance is due in large part to the effectiveness of the pruning algorithm, which in many cases removes a large percentage of the vertices not found in isomorphic matches. In this paper, the runtime of the algorithm is tested alongside other algorithms on graphs of up to 10 million vertices and 250 million edges.

GPUs provide high-bandwidth/low-latency on-chip shared memory and L1 cache to efficiently service a large number of concurrent memory requests. Specifically, concurrent memory requests accessing contiguous memory space are coalesced into warp-wide accesses. To support such large accesses to L1 cache with low latency, the size of L1 cache line is no smaller than that of warp-wide accesses. However, such L1 cache architecture cannot always be efficiently utilized when applications generate many memory requests with irregular access patterns especially due to branch and memory divergences that make requests uncoalesced and small. Furthermore, unlike L1 cache, the shared memory of GPUs is not often used in many applications, which essentially depends on programmers. In this article, we propose Elastic-Cache, which can efficiently support both fine- and coarse-grained L1 cache line management for applications with both regular and irregular memory access patterns to improve the L1 cache efficiency. Specifically, it can store 32- or 64-byte words in non-contiguous memory space to a single 128-byte cache line. Furthermore, it neither requires an extra memory structure nor reduces the capacity of L1 cache for tag storage, since it stores auxiliary tags for fine-grained L1 cache line managements in the shared memory space that is not fully used in many applications. To improve the bandwidth utilization of L1 cache with Elastic-Cache for fine-grained accesses, we further propose Elastic-Plus to issue 32-byte memory requests in parallel, which can reduce the processing latency of memory instructions and improve the throughput of GPUs. Our experiment result shows that Elastic-Cache improves the geometric-mean performance of applications with irregular memory access patterns by 104% without degrading the performance of applications with regular memory access patterns. Elastic-Plus outperforms Elastic-Cache and improves the performance of applications with irregular memory access patterns by 131%.

We developed a parallel algorithm to improve the cache behavior and overall performance for multiplication of sparse matrices with sparse vectors (SpMSpV), an operation used increasingly in large graph analytics, particularly dynamic graphs in social networks and homeland security applications. The proposed algorithm builds upon the two-phase approach of partitioning the multiplication into a scaling phase and an aggregation phase, to achieve more cache-friendly access patterns individually in each phase [6], [3]. However, to handle dynamic graphs and achieve better load balancing for parallel implementation, we use a combination of private and shared bins, with synchronized access to shared bins to exchange the product terms between the two phases. The new algorithm accumulates product terms in private bins for each thread. The algorithm then performs a bulk transfer between a private bin and a shared bin, when the private bin becomes full. Then results are aggregated from the shared bins. In addition, we employ heuristics to decide the best algorithm for SpMSpV based on the number of nonzeros involved in the operation. When the number of nonzeros is large, it may be better to perform the operation as SpMV (sparse matrix times dense vector) despite the added conversion cost. Also, if the number of nonzeros is low it is advantageous to use a simplified algorithm. We compared our algorithm with existing algorithms for SpMSpV, and our evaluation shows that execution time is reduced by several times when large graphs are considered.

Graph analytics applications often target large-scale web and social networks, which are typically power-law graphs. Graph algorithms can often be recast as generalized Sparse Matrix-Vector multiplication (SpMV) operations, making SpMV optimization important for graph analytics. However, executing SpMV on large-scale power-law graphs results in highly irregular memory access patterns with poor cache utilization. Worse, we find that existing SpMV locality and vectorization optimizations are largely ineffective on modern out-of-order (OOO) processors-they are not faster (or only marginally so) than the standard Compressed Sparse Row (CSR) SpMV implementation. To improve performance for power-law graphs on modern OOO processors, we propose Locality-Aware Vectorization (LAV). LAV is a new approach that leverages a graph's power-law nature to extract locality and enable effective vectorization for SpMV-like memory access patterns. LAV splits the input matrix into a dense and a sparse portion. The dense portion is stored in a new representation, which is vectorization-friendly and exploits data locality. The sparse portion is processed using the standard CSR algorithm. We evaluate LAV with several graphs on an Intel Skylake-SP processor, and find that it is faster than CSR (and prior approaches) by an average of 1.5x. LAV reduces the number of DRAM accesses by 35% on average, with only a 3.3% memory overhead.

We have entered the age of big data. Massive datasets are now common in science, government and enterprises. Yet, making sense of these data remains a fundamental challenge. Where do we start our analysis? Where to go next? How to visualize our findings? We answers these questions by bridging Data Mining and Human- Computer Interaction (HCI) to create tools for making sense of graphs with billions of nodes and edges, focusing on: (1) Attention Routing: we introduce this idea, based on anomaly detection, that automatically draws people’s attention to interesting areas of the graph to start their analyses. We present three examples: Polonium unearths malware from 37 billion machine-file relationships; NetProbe fingers bad guys who commit auction fraud. (2) Mixed-Initiative Sensemaking: we present two examples that combine machine inference and visualization to help users locate next areas of interest: Apolo guides users to explore large graphs by learning from few examples of user interest; Graphite finds interesting subgraphs, based on only fuzzy descriptions drawn graphically. (3) Scaling Up: we show how to enable interactive analytics of large graphs by leveraging Hadoop, staging of operations, and approximate computation. This thesis contributes to data mining, HCI, and importantly their intersection, including: interactive systems and algorithms that scale; theories that unify graph mining approaches; and paradigms that overcome fundamental challenges in visual analytics. Our work is making impact to academia and society: Polonium protects 120 million people worldwide from malware; NetProbe made headlines on CNN, WSJ and USA Today; Pegasus won an opensource software award; Apolo helps DARPA detect insider threats and prevent exfiltration. We hope our Big Data Mantra “Machine for Attention Routing, Human for Interaction” will inspire more innovations at the crossroad of data mining and HCI.

Distributed-memory clusters are used for in-memory processing of very large graphs with billions of nodes and edges. This requires partitioning the graph among the machines in the cluster. When a graph is partitioned, a node in the graph may be replicated on several machines, and communication is required to keep these replicas synchronized. Good partitioning policies attempt to reduce this synchronization overhead while keeping the computational load balanced across machines. A number of recent studies have looked at ways to control replication of nodes, but these studies are not conclusive because they were performed on small clusters with eight to sixteen machines, did not consider work-efficient data-driven algorithms, or did not optimize communication for the partitioning strategies they studied. This paper presents an experimental study of partitioning strategies for work-efficient graph analytics applications on large KNL and Skylake clusters with up to 256 machines using the Gluon communication runtime which implements partitioning-specific communication optimizations. Evaluation results show that although simple partitioning strategies like Edge-Cuts perform well on a small number of machines, an alternative partitioning strategy called Cartesian Vertex-Cut (CVC) performs better at scale even though paradoxically it has a higher replication factor and performs more communication than Edge-Cut partitioning does. Results from communication micro-benchmarks resolve this paradox by showing that communication overhead depends not only on communication volume but also on the communication pattern among the partitions. These experiments suggest that high-performance graph analytics systems should support multiple partitioning strategies, like Gluon does, as no single graph partitioning strategy is best for all cluster sizes. For such systems, a decision tree for selecting a good partitioning strategy based on characteristics of the computation and the cluster is presented.

We present Ringo, a system for analysis of large graphs. Graphs provide a way to represent and analyze systems of interacting objects (people, proteins, webpages) with edges between the objects denoting interactions (friendships, physical interactions, links). Mining graphs provides valuable insights about individual objects as well as the relationships among them. In building Ringo, we take advantage of the fact that machines with large memory and many cores are widely available and also relatively affordable. This allows us to build an easy-to-use interactive high-performance graph analytics system. Graphs also need to be built from input data, which often resides in the form of relational tables. Thus, Ringo provides rich functionality for manipulating raw input data tables into various kinds of graphs. Furthermore, Ringo also provides over 200 graph analytics functions that can then be applied to constructed graphs. We show that a single big-memory machine provides a very attractive platform for performing analytics on all but the largest graphs as it offers excellent performance and ease of use as compared to alternative approaches. With Ringo, we also demonstrate how to integrate graph analytics with an iterative process of trial-and-error data exploration and rapid experimentation, common in data mining workloads.

Breadth-first search (BFS) is an essential graph traversal strategy widely used in many computing applications. Because of its irregular data access patterns, BFS has become a non-trivial problem hard to parallelize efficiently. In this paper, we introduce a parallelization strategy that allows the load balancing of computation resources as well as the execution of graph traversals in hybrid environments composed of CPUs and GPUs. To achieve that goal, we use a fine-grained task-based parallelization scheme and the OmpSs programming model. We obtain processing rates up to 2.8 billion traversed edges per second with a single GPU and a multi-core processor. Our study shows high processing rates are achievable with hybrid environments despite the GPU communication latency and memory coherence.

B+-trees algorithm is a high efficient and common-used data organization algorithm in database system. But B+-trees algorithm has a disadvantage of low storage utilization. This disadvantage has a bad effect especially on embedded database systems, which have limit storage. To overcome this drawback, this paper presents an improved B+-trees algorithm, and applies it to an embedded database-Berkeley DB. Experimental results show that the improved B+-trees algorithm can attain higher storage utilization at the expense of more execution time than the conventional B+-trees algorithm.

Existing Big Data streams coming from social and other connected sensor networks exhibit intrinsic inter-dependency enabling unique challenges to scalable graph analytics. Data from these graphs is usually collected in different geographically located data servers making it suitable for distributed processing on clouds. While numerous solutions for large scale static graph analysis have been proposed, addressing in real-time the dynamics of social interactions requires novel approaches that leverage incremental stream processing and graph analytics on elastic clouds. We propose a scalable solution based on our stream processing engine, Floe, on top of which we perform real-time data processing and graph updates to enable low latency graph analytics on large evolving social networks. We demonstrate the platform on a large Twitter data set by performing several fast graph and non-graph analytics to extract in real-time the top k influential nodes, with different metrics, during key events such as the US NFL playoffs. This information allows advertisers to maximize their exposure to the public by always targeting the continuously changing set of most influential nodes. Its applicability spans multiple domains including surveillance, counter-terrorism, or disease spread monitoring. The evaluation will be performed on a combination our local cluster of 16 eight-core nodes running Eucalyptus fabric and 100s of virtual machines on the Amazon AWS public cloud. We will showcase the low latency in detecting changes in the graph under variable data streams, and also the efficiency of the platform to utilize resources and to elastically scale to meet demand.

Mining large graphs has now become an important aspect of multiple diverse applications and a number of computer systems have been proposed to provide runtime support. Recent interest in this area has led to the construction of single machine graph computation systems that use solid state drives (SSDs) to store the graph. This approach reduces the cost and simplifies the implementation of graph algorithms, making computations on large graphs available to the average user. However, SSDs are slower than main memory, and making full use of their bandwidth is crucial for executing graph algorithms in a reasonable amount of time. In this paper, we present PrefEdge, a prefetcher for graph algorithms that parallelises requests to derive maximum throughput from SSDs. PrefEdge combines a judicious distribution of graph state between main memory and SSDs with an innovative read-ahead algorithm to prefetch needed data in parallel. This is in contrast to existing approaches that depend on multi-threading the graph algorithms to saturate available bandwidth. Our experiments on graph algorithms using random access show that PrefEdge not only is capable of maximising the throughput from SSDs but is also able to almost hide the effect of I/O latency. The improvements in runtime for graph algorithms is up to 14× when compared to a single threaded baseline. When compared to multi-threaded implementations, PrefEdge performs up to 80% faster without the program complexity and the programmer effort needed for multi-threaded graph algorithms.

Comparison among graphs is ubiquitous in graph analytics. However, it is a\nhard task in terms of the expressiveness of the employed similarity measure and\nthe efficiency of its computation. Ideally, graph comparison should be\ninvariant to the order of nodes and the sizes of compared graphs, adaptive to\nthe scale of graph patterns, and scalable. Unfortunately, these properties have\nnot been addressed together. Graph comparisons still rely on direct approaches,\ngraph kernels, or representation-based methods, which are all inefficient and\nimpractical for large graph collections.\n In this paper, we propose the Network Laplacian Spectral Descriptor (NetLSD):\nthe first, to our knowledge, permutation- and size-invariant, scale-adaptive,\nand efficiently computable graph representation method that allows for\nstraightforward comparisons of large graphs. NetLSD extracts a compact\nsignature that inherits the formal properties of the Laplacian spectrum,\nspecifically its heat or wave kernel; thus, it hears the shape of a graph. Our\nevaluation on a variety of real-world graphs demonstrates that it outperforms\nprevious works in both expressiveness and efficiency.\n

Digital era produces vast amounts of data which leads to advances in data storage and analysis and the emergence of the concept of big data. Big data will be an important resource used in academic research and to make data driven decision making. This paper provides an overview about the big data concept and its application in libraries. This paper aims to create an awareness amongst librarians about big data, its applications and the role of librarian in big data scenario.