TensorFlow Doing HPC

TensorFlow is a popular emerging open-source programming framework supporting the execution of distributed applications on heterogeneous hardware. While TensorFlow has been initially designed for developing Machine Learning (ML) applications, in fact TensorFlow aims at supporting the development of a much broader range of application kinds that are outside the ML domain and can possibly include HPC applications. However, very few experiments have been conducted to evaluate TensorFlow performance when running HPC workloads on supercomputers. This work addresses this lack by designing four traditional HPC benchmark applications: STREAM, matrix-matrix multiply, Conjugate Gradient (CG) solver and Fast Fourier Transform (FFT). We analyze their performance on two supercomputers with accelerators and evaluate the potential of TensorFlow for developing HPC applications. Our tests show that TensorFlow can fully take advantage of high performance networks and accelerators on supercomputers. Running our TensorFlow STREAM benchmark, we obtain over 50% of theoretical communication bandwidth on our testing platform. We find an approximately 2x, 1.7x and 1.8x performance improvement when increasing the number of GPUs from two to four in the matrix-matrix multiply, CG and FFT applications respectively. All our performance results demonstrate that TensorFlow has high potential of emerging also as HPC programming framework for heterogeneous supercomputers.Comment: Accepted for publication at The Ninth International Workshop on Accelerators and Hybrid Exascale Systems (AsHES'19

Selective Vectorization for Short-Vector Instructions

Multimedia extensions are nearly ubiquitous in today's general-purpose processors. These extensions consist primarily of a set of short-vector instructions that apply the same opcode to a vector of operands. Vector instructions introduce a data-parallel component to processors that exploit instruction-level parallelism, and present an opportunity for increased performance. In fact, ignoring a processor's vector opcodes can leave a significant portion of the available resources unused. In order for software developers to find short-vector instructions generally useful, however, the compiler must target these extensions with complete transparency and consistent performance. This paper describes selective vectorization, a technique for balancing computation across a processor's scalar and vector units. Current approaches for targeting short-vector instructions directly adopt vectorizing technology first developed for supercomputers. Traditional vectorization, however, can lead to a performance degradation since it fails to account for a processor's scalar resources. We formulate selective vectorization in the context of software pipelining. Our approach creates software pipelines with shorter initiation intervals, and therefore, higher performance. A key aspect of selective vectorization is its ability to manage transfer of operands between vector and scalar instructions. Even when operand transfer is expensive, our technique is sufficiently sophisticated to achieve significant performance gains. We evaluate selective vectorization on a set of SPEC FP benchmarks. On a realistic VLIW processor model, the approach achieves whole-program speedups of up to 1.35x over existing approaches. For individual loops, it provides speedups of up to 1.75x

Dynamic Systolization for Developing Multiprocessor Supercomputers

A dynamic network approach is introduced for developing reconfigurable, systolic arrays or wavefront processors; This allows one to design very powerful and flexible processors to be used in a general-purpose, reconfigurable, and fault-tolerant, multiprocessor computer system. The concepts of macro-dataflow and multitasking can be integrated to handle variable-resolution granularities in computationally intensive algorithms. A multiprocessor architecture, Remps, is proposed based on these design methodologies. The Remps architecture is generalized from the Cedar, HEP, Cray X- MP, Trac, NYU ultracomputer, S-l, Pumps, Chip, and SAM projects. Our goal is to provide a multiprocessor research model for developing design methodologies, multiprocessing and multitasking supports, dynamic systolic/wavefront array processors, interconnection networks, reconfiguration techniques, and performance analysis tools. These system design and operational techniques should be useful to those who are developing or evaluating multiprocessor supercomputers

A bibliography on parallel and vector numerical algorithms

This is a bibliography of numerical methods. It also includes a number of other references on machine architecture, programming language, and other topics of interest to scientific computing. Certain conference proceedings and anthologies which have been published in book form are listed also

Workshop proceedings: Information Systems for Space Astrophysics in the 21st Century, volume 1

The Astrophysical Information Systems Workshop was one of the three Integrated Technology Planning workshops. Its objectives were to develop an understanding of future mission requirements for information systems, the potential role of technology in meeting these requirements, and the areas in which NASA investment might have the greatest impact. Workshop participants were briefed on the astrophysical mission set with an emphasis on those missions that drive information systems technology, the existing NASA space-science operations infrastructure, and the ongoing and planned NASA information systems technology programs. Program plans and recommendations were prepared in five technical areas: Mission Planning and Operations; Space-Borne Data Processing; Space-to-Earth Communications; Science Data Systems; and Data Analysis, Integration, and Visualization

High Performance Computing Algorithms for Accelerating Peptide Identification from Mass-Spectrometry Data Using Heterogeneous Supercomputers

Fast and accurate identification of peptides and proteins from the mass spectrometry (MS) data is a critical problem in modern systems biology. Database peptide search is the most commonly used computational method to identify peptide sequences from the MS data. In this method, giga-bytes of experimentally generated MS data are compared against tera-byte sized databases of theoretically simulated MS data resulting in a compute- and data-intensive problem requiring days or weeks of computational times on desktop machines. Existing serial and high performance computing (HPC) algorithms strive to accelerate and improve the computational efficiency of the search, but exhibit sub-optimal performances due to their inefficient parallelization models, low resource utilization and high overhead costs

Integrated risk/cost planning models for the US Air Traffic system

A prototype network planning model for the U.S. Air Traffic control system is described. The model encompasses the dual objectives of managing collision risks and transportation costs where traffic flows can be related to these objectives. The underlying structure is a network graph with nonseparable convex costs; the model is solved efficiently by capitalizing on its intrinsic characteristics. Two specialized algorithms for solving the resulting problems are described: (1) truncated Newton, and (2) simplicial decomposition. The feasibility of the approach is demonstrated using data collected from a control center in the Midwest. Computational results with different computer systems are presented, including a vector supercomputer (CRAY-XMP). The risk/cost model has two primary uses: (1) as a strategic planning tool using aggregate flight information, and (2) as an integrated operational system for forecasting congestion and monitoring (controlling) flow throughout the U.S. In the latter case, access to a supercomputer is required due to the model's enormous size

Computing and data processing

The applications of computers and data processing to astronomy are discussed. Among the topics covered are the emerging national information infrastructure, workstations and supercomputers, supertelescopes, digital astronomy, astrophysics in a numerical laboratory, community software, archiving of ground-based observations, dynamical simulations of complex systems, plasma astrophysics, and the remote control of fourth dimension supercomputers

Exploiting the Parallelism Exposed by Partial Evaluation

We describe an approach to parallel compilation that seeks to harness the vast amount of fine-grain parallelism that is exposed through partial evaluation of numerically-intensive scientific programs. We have constructed a compiler for the Supercomputer Toolkit parallel processor that uses partial evaluation to break down data abstractions and program structure, producing huge basic blocks that contain large amounts of fine-grain parallelism. We show that this fine-grain prarllelism can be effectively utilized even on coarse-grain parallel architectures by selectively grouping operations together so as to adjust the parallelism grain-size to match the inter-processor communication capabilities of the target architecture