Adaptive Hybrid Storage Format for Sparse Matrix–Vector Multiplication on Multi-Core SIMD CPUs

Optimizing sparse matrix–vector multiplication (SpMV) is challenging due to the non-uniform distribution of the non-zero elements of the sparse matrix. The best-performing SpMV format changes depending on the input matrix and the underlying architecture, and there is no “one-size-fit-for-all” format. A hybrid scheme combining multiple SpMV storage formats allows one to choose an appropriate format to use for the target matrix and hardware. However, existing hybrid approaches are inadequate for utilizing the SIMD cores of modern multi-core CPUs with SIMDs, and it remains unclear how to best mix different SpMV formats for a given matrix. This paper presents a new hybrid storage format for sparse matrices, specifically targeting multi-core CPUs with SIMDs. Our approach partitions the target sparse matrix into two segmentations based on the regularities of the memory access pattern, where each segmentation is stored in a format suitable for its memory access patterns. Unlike prior hybrid storage schemes that rely on the user to determine the data partition among storage formats, we employ machine learning to build a predictive model to automatically determine the partition threshold on a per matrix basis. Our predictive model is first trained off line, and the trained model can be applied to any new, unseen sparse matrix. We apply our approach to 956 matrices and evaluate its performance on three distinct multi-core CPU platforms: a 72-core Intel Knights Landing (KNL) CPU, a 128-core AMD EPYC CPU, and a 64-core Phytium ARMv8 CPU. Experimental results show that our hybrid scheme, combined with the predictive model, outperforms the best-performing alternative by 2.9%, 17.5% and 16% on average on KNL, AMD, and Phytium, respectively

A performance focused, development friendly and model aided parallelization strategy for scientific applications

The amelioration of high performance computing platforms has provided unprecedented computing power with the evolution of multi-core CPUs, massively parallel architectures such as General Purpose Graphics Processing Units (GPGPUs) and Many Integrated Core (MIC) architectures such as Intel\u27s Xeon phi coprocessor. However, it is a great challenge to leverage capabilities of such advanced supercomputing hardware, as it requires efficient and effective parallelization of scientific applications. This task is difficult mainly due to complexity of scientific algorithms coupled with the variety of available hardware and disparate programming models. To address the aforementioned challenges, this thesis presents a parallelization strategy to accelerate scientific applications that maximizes the opportunities of achieving speedup while minimizing the development efforts. Parallelization is a three step process (1) choose a compatible combination of architecture and parallel programming language, (2) translate base code/algorithm to a parallel language and (3) optimize and tune the application. In this research, a quantitative comparison of run time for various implementations of k-means algorithm, is used to establish that native languages (OpenMP, MPI, CUDA) perform better on respective architectures as opposed to vendor-neutral languages such as OpenCL. A qualitative model is used to select an optimal architecture for a given application by aligning the capabilities of accelerators with characteristics of the application. Once the optimal architecture is chosen, the corresponding native language is employed. This approach provides the best performance with reasonable accuracy (78%) of predicting a fitting combination, while eliminating the need for exploring different architectures individually. It reduces the required development efforts considerably as the application need not be re-written in multiple languages. The focus can be solely on optimization and tuning to achieve the best performance on available architectures with minimized investment in terms of cost and efforts. To verify the prediction accuracy of the qualitative model, the OpenDwarfs benchmark suite, which implements the Berkeley\u27s dwarfs in OpenCL, is used. A dwarf is an algorithmic method that captures a pattern of computation and communication. For the purpose of this research, the focus is on 9 application from various algorithmic domains that cover the seven dwarfs of symbolic computation, which were identified by Phillip Colella, as omnipresent in scientific and engineering applications. To validate the parallelization strategy collectively, a case study is undertaken. This case study involves parallelization of the Lower Upper Decomposition for the Gaussian Elimination algorithm from the linear algebra domain, using conventional trial and error methods as well as the proposed \u27Architecture First, Language Later\u27\u27 strategy. The development efforts incurred are contrasted for both methods. The aforesaid proposed strategy is observed to reduce the development efforts by an average of 50%

Performance Optimization With An Integrated View Of Compiler And Application Knowledge

Compiler optimization is a long-standing research field that enhances program performance with a set of rigorous code analyses and transformations. Traditional compiler optimization focuses on general programs or program structures without considering too much high-level application operations or data structure knowledge. In this thesis, we claim that an integrated view of the application and compiler is helpful to further improve program performance. Particularly, we study integrated optimization opportunities for three kinds of applications: irregular tree-based query processing systems such as B+ tree, security enhancement such as buffer overflow protection, and tensor/matrix-based linear algebra computation. The performance of B+ tree query processing is important for many applications, such as file systems and databases. Latch-free B+ tree query processing is efficient since the queries are processed in batches without locks. To avoid long latency, the batch size can not be very large. However, modern processors provide opportunities to process larger batches parallel with acceptable latency. From studying real-world data, we find that there are many redundant and unnecessary queries especially when the real-world data is highly skewed. We develop a query sequence transformation framework Qtrans to reduce the redundancies in queries by applying classic dataflow analysis to queries. To further confirm the effectiveness, we integrate Qtrans into an existing BSP-based B+ tree query processing system, PALM tree. The evaluations show that the throughput can be improved up to 16X. Heap overflows are still the most common vulnerabilities in C/C++ programs. Common approaches incur high overhead since it checks every memory access. By analyzing dozens of bugs, we find that all heap overflows are related to arrays. We only need to check array-related memory accesses. We propose Prober to efficiently detect and prevent heap overflows. It contains Prober-Static to identify the array-related allocations and Prober-Dynamic to protect objects at runtime. In this thesis, our contributions lie on the Prober-Static side. The key challenge is to correctly identify the array-related allocations. We propose a hybrid method. Some objects can be identified as array-related (or not) by static analysis. For the remaining ones, we instrument the basic allocation type size statically and then determine the real allocation size at runtime. The evaluations show Prober-Static is effective. Tensor algebra is widely used in many applications, such as machine learning and data analytics. Tensors representing real-world data are usually large and sparse. There are many sparse tensor storage formats, and the kernels are different with varied formats. These different kernels make performance optimization for sparse tensor algebra challenging. We propose a tensor algebra domain-specific language and a compiler to automatically generate kernels for sparse tensor algebra computations, called SPACe. This compiler supports a wide range of sparse tensor formats. To further improve the performance, we integrate the data reordering into SPACe to improve data locality. The evaluations show that the code generated by SPACe outperforms state-of-the-art sparse tensor algebra compilers

Reducing Waste in Memory Hierarchies

Memory hierarchies play an important role in microarchitectural design to bridge the performance gap between modern microprocessors and main memory. However, memory hierarchies are inefficient due to storing waste. This dissertation quantifies two types of waste, dead blocks and data redundancy. This dissertation studies waste in diverse memory hierarchies and proposes techniques to reduce waste to improve performance with limited overhead. This dissertation observes that waste of dead blocks in an inclusive last level cache consists of two kinds of blocks: blocks that are highly accessed in core caches and blocks that have low temporal locality in both core caches and the last-level cache. Blindly replacing all dead blocks in an inclusive last level cache may degrade performance. This dissertation proposes temporal-based multilevel correlating cache replacement to improve performance of inclusive cache hierarchies. This dissertation observes that waste exists in private caches of graphics processing units (GPUs) as zero-reuse blocks. This dissertation defines zero-reuse blocks as blocks that are dead after being inserted into caches. This dissertation proposes adaptive GPU cache bypassing technique to improve performance as well as reducing power consumption by dynamically bypassing zero-reuse blocks. This dissertation exploits waste of data redundancy at the block-level granularity and finds that conventional cache design wastes capacity because it stores duplicate data. This dissertation quantifies the percentage of data duplication and analyze causes. This dissertation proposes a practical cache deduplication technique to increase the effectiveness of the cache with limited area and power consumption

Performance Evaluation of In-storage Processing Architectures for Diverse Applications and Benchmarks

University of Minnesota Ph.D. dissertation.June 2018. Major: Electrical/Computer Engineering. Advisor: David Lilja. 1 computer file (PDF); vii, 100 pages.As we inch towards the future, the storage needs of the world are going to be massive and diversied. To tackle the needs of the next generation, the storage systems are required to be studied and require innovative solutions. These solutions need to solve multitude of issues involving high power consumption of traditional systems, manageability, easy scaling out, and integration into existing systems. Therefore, we need to rethink the new technologies from the ground up. To keep the energy signature under control we devised a new architecture called Storage Processing Unit (SPU). For the modeling of this architecture we incorporate a processing element inside the storage medium to limit the data movement between the storage device and the host processor. This resulted in a hierarchal architecture which required an extensive design space exploration along with in-depth study of the applications. We found this new architecture to provide energy savings from 11-423X and gave performance gains from 4-66X for applications including k-means, Sparse BLAS, and others. Moreover, to understand the diverse nature of the applications and newer technologies, we tried the concept of in-storage processing for unstructured data. This type of data is demonstrating huge amount of growth and would continue to do so. Seagate's new class of drives - Kinetic Drives, address the rise of unstructured data. They have a processing element inside disk drives that execute LevelDB, a key-value store. We evaluated this off-the-shelf device using micro and macro benchmarks for an in-depth throughput and latency benchmarking. We observed sequential write throughput of 63 MB/sec and sequential read throughput of 78 MB/sec for 1 MB value sizes. We tested several unique features including P2P transfer that takes place in a Kinetic Drive. These new class of drives outperformed traditional servers workloads for several test cases. Finally, large number of these devices are needed for huge amounts of data. To demonstrate that Kinetic Drives reduce the management complexity for large-scale deployment, we conducted a study. We allocated large amounts of data on Kinetic Drives and then evaluated the performance of the system for migration of data amongst drives. Previously developed key indexing schemes were evaluated which gave important insights into their performance differences. Based on this study we can conclude that efficient mapping of key-value pairs to drives could be obtained. This lead to an understanding of the trade-offs between the number of empty drives and mapping of different key ranges to different drives. In conclusion, in-storage processing architectures bring an interesting aspect where processing is moved closer to the data. This leads to a paradigm shift which often results in a major software and hardware architectural changes. Furthermore, the new architectures have the potential to perform better than the traditional systems but require easy integration with the existing systems

Doctor of Philosophy

dissertationThe internet-based information infrastructure that has powered the growth of modern personal/mobile computing is composed of powerful, warehouse-scale computers or datacenters. These heavily subscribed datacenters perform data-processing jobs under intense quality of service guarantees. Further, high-performance compute platforms are being used to model and analyze increasingly complex scientific problems and natural phenomena. To ensure that the high-performance needs of these machines are met, it is necessary to increase the efficiency of the memory system that supplies data to the processing cores. Many of the microarchitectural innovations that were designed to scale the memory wall (e.g., out-of-order instruction execution, on-chip caches) are being rendered less effective due to several emerging trends (e.g., increased emphasis on energy consumption, limited access locality). This motivates the optimization of the main memory system itself. The key to an efficient main memory system is the memory controller. In particular, the scheduling algorithm in the memory controller greatly influences its performance. This dissertation explores this hypothesis in several contexts. It develops tools to better understand memory scheduling and develops scheduling innovations for CPUs and GPUs. We propose novel memory scheduling techniques that are strongly aware of the access patterns of the clients as well as the microarchitecture of the memory device. Based on these, we present (i) a Dynamic Random Access Memory (DRAM) chip microarchitecture optimized for reducing write-induced slowdown, (ii) a memory scheduling algorithm that exploits these features, (iii) several memory scheduling algorithms to reduce the memory-related stall experienced by irregular General Purpose Graphics Processing Unit (GPGPU) applications, and (iv) the Utah Simulated Memory Module (USIMM), a detailed, validated simulator for DRAM main memory that we use for analyzing and proposing scheduler algorithms

What broke where for distributed and parallel applications — a whodunit story

Detection, diagnosis and mitigation of performance problems in today\u27s large-scale distributed and parallel systems is a difficult task. These large distributed and parallel systems are composed of various complex software and hardware components. When the system experiences some performance or correctness problem, developers struggle to understand the root cause of the problem and fix in a timely manner. In my thesis, I address these three components of the performance problems in computer systems. First, we focus on diagnosing performance problems in large-scale parallel applications running on supercomputers. We developed techniques to localize the performance problem for root-cause analysis. Parallel applications, most of which are complex scientific simulations running in supercomputers, can create up to millions of parallel tasks that run on different machines and communicate using the message passing paradigm. We developed a highly scalable and accurate automated debugging tool called PRODOMETER, which uses sophisticated algorithms to first, create a logical progress dependency graph of the tasks to highlight how the problem spread through the system manifesting as a system-wide performance issue. Second, uses this logical progress dependence graph to identify the task where the problem originated. Finally, PRODOMETER pinpoints the code region corresponding to the origin of the bug. Second, we developed a tool-chain that can detect performance anomaly using machine-learning techniques and can achieve very low false positive rate. Our input-aware performance anomaly detection system consists of a scalable data collection framework to collect performance related metrics from different granularity of code regions, an offline model creation and prediction-error characterization technique, and a threshold based anomaly-detection-engine for production runs. Our system requires few training runs and can handle unknown inputs and parameter combinations by dynamically calibrating the anomaly detection threshold according to the characteristics of the input data and the characteristics of the prediction-error of the models. Third, we developed performance problem mitigation scheme for erasure-coded distributed storage systems. Repair operations of the failed blocks in erasure-coded distributed storage system take really long time in networked constrained data-centers. The reason being, during the repair operation for erasure-coded distributed storage, a lot of data from multiple nodes are gathered into a single node and then a mathematical operation is performed to reconstruct the missing part. This process severely congests the links toward the destination where newly recreated data is to be hosted. We proposed a novel distributed repair technique, called Partial-Parallel-Repair (PPR) that performs this reconstruction in parallel on multiple nodes and eliminates network bottlenecks, and as a result, greatly speeds up the repair process. Fourth, we study how for a class of applications, performance can be improved (or performance problems can be mitigated) by selectively approximating some of the computations. For many applications, the main computation happens inside a loop that can be logically divided into a few temporal segments, we call phases. We found that while approximating the initial phases might severely degrade the quality of the results, approximating the computation for the later phases have very small impact on the final quality of the result. Based on this observation, we developed an optimization framework that for a given budget of quality-loss, would find the best approximation settings for each phase in the execution

Irregular accesses reorder unit: improving GPGPU memory coalescing for graph-based workloads

GPGPU architectures have become the dominant platform for massively parallel workloads, delivering high performance and energy efficiency for popular applications such as machine learning, computer vision or self-driving cars. However, irregular applications, such as graph processing, fail to fully exploit GPGPU resources due to their divergent memory accesses that saturate the memory hierarchy. To reduce the pressure on the memory subsystem for divergent memory-intensive applications, programmers must take into account SIMT execution model and memory coalescing in GPGPUs, devoting significant efforts in complex optimization techniques. Despite these efforts, we show that irregular graph processing still suffers from low GPGPU performance. We observe that in many irregular applications the mapping of data to threads can be safely changed. In other words, it is possible to relax the strict relationship between thread and data processed to reduce memory divergence. Based on this observation, we propose the Irregular accesses Reorder Unit (IRU), a novel hardware extension tightly integrated in the GPGPU pipeline. The IRU reorders data processed by the threads on irregular accesses to improve memory coalescing, i.e., it tries to assign data elements to threads as to produce coalesced accesses in SIMT groups. Furthermore, the IRU is capable of filtering and merging duplicated accesses, significantly reducing the workload. Programmers can easily utilize the IRU with a simple API, or let the compiler issue instructions from our extended ISA. We evaluate our proposal for state-of-the-art graph-based algorithms and a wide selection of applications. Results show that the IRU achieves a memory coalescing improvement of 1.32x and a 46% reduction in the overall traffic in the memory hierarchy, which results in 1.33x speedup and 13% energy savings on average, while incurring in a small 5.6% area overhead.This work has been supported by the CoCoUnit ERC Advanced Grant of the EU’s Horizon 2020 program (grant No 833057), the Spanish State Research Agency (MCIN/AEI) under grant PID2020-113172RB-I00 and the ICREA Academia program.Peer ReviewedPostprint (published version