PlinyCompute: A Platform for High-Performance, Distributed, Data-Intensive Tool Development

This paper describes PlinyCompute, a system for development of high-performance, data-intensive, distributed computing tools and libraries. In the large, PlinyCompute presents the programmer with a very high-level, declarative interface, relying on automatic, relational-database style optimization to figure out how to stage distributed computations. However, in the small, PlinyCompute presents the capable systems programmer with a persistent object data model and API (the "PC object model") and associated memory management system that has been designed from the ground-up for high performance, distributed, data-intensive computing. This contrasts with most other Big Data systems, which are constructed on top of the Java Virtual Machine (JVM), and hence must at least partially cede performance-critical concerns such as memory management (including layout and de/allocation) and virtual method/function dispatch to the JVM. This hybrid approach---declarative in the large, trusting the programmer's ability to utilize PC object model efficiently in the small---results in a system that is ideal for the development of reusable, data-intensive tools and libraries. Through extensive benchmarking, we show that implementing complex objects manipulation and non-trivial, library-style computations on top of PlinyCompute can result in a speedup of 2x to more than 50x or more compared to equivalent implementations on Spark.Comment: 48 pages, including references and Appendi

Mangrove: an Inference-based Dynamic Invariant Mining for GPU Architectures

Likely invariants model properties that hold in operating conditions of a computing system. Dynamic mining of invariants aims at extracting logic formulas representing such properties from the system execution traces, and it is widely used for verification of intellectual property (IP) blocks. Although the extracted formulas represent likely invariants that hold in the considered traces, there is no guarantee that they are true in general for the system under verification. As a consequence, to increase the probability that the mined invariants are true in general, dynamic mining has to be performed to large sets of representative execution traces. This makes the execution-based mining process of actual IP blocks very time-consuming due to the trace lengths and to the large sets of monitored signals. This article presents extit{Mangrove}, an efficient implementation of a dynamic invariant mining algorithm for GPU architectures. Mangrove exploits inference rules, which are applied at run time to filter invariants from the execution traces and, thus, to sensibly reduce the problem complexity. Mangrove allows users to define invariant templates and, from these templates, it automatically generates kernels for parallel and efficient mining on GPU architectures. The article presents the tool, the analysis of its performance, and its comparison with the best sequential and parallel implementations at the state of the art

Exploring query execution strategies for JIT vectorization and SIMD

This paper partially explores the design space for efficient query processors on future hardware that is rich in SIMD capabilities. It departs from two well-known approaches: (1) interpreted block-at-a-time execution (a.k.a. "vectorization") and (2) "data-centric" JIT compilation, as in the HyPer system. We argue that in between these two design points in terms of granularity of execution and uni

RAxML-Cell: Parallel Phylogenetic Tree Inference on the Cell Broadband Engine

Phylogenetic tree reconstruction is one of the grand challenge problems in Bioinformatics. The search for a best-scoring tree with 50 organisms, under a reasonable optimality criterion, creates a topological search space which is as large as the number of atoms in the universe. Computational phylogeny is challenging even for the most powerful supercomputers. It is also an ideal candidate for benchmarking emerging multiprocessor architectures, because it exhibits various levels of fine and coarse-grain parallelism. In this paper, we present the porting, optimization, and evaluation of RAxML on the Cell Broadband Engine. RAxML is a provably efficient, hill climbing algorithm for computing phylogenetic trees based on the Maximum Likelihood (ML) method. The algorithm uses an embarrassingly parallel search method, which also exhibits data-level parallelism and control parallelism in the computation of the likelihood functions. We present the optimization of one of the currently fastest tree search algorithms, on a real Cell blade prototype. We also investigate problems and present solutions pertaining to the optimization of floating point code, control flow, communication, scheduling, and multi-level parallelization on the Cell

GeantV: Results from the prototype of concurrent vector particle transport simulation in HEP

Full detector simulation was among the largest CPU consumer in all CERN experiment software stacks for the first two runs of the Large Hadron Collider (LHC). In the early 2010's, the projections were that simulation demands would scale linearly with luminosity increase, compensated only partially by an increase of computing resources. The extension of fast simulation approaches to more use cases, covering a larger fraction of the simulation budget, is only part of the solution due to intrinsic precision limitations. The remainder corresponds to speeding-up the simulation software by several factors, which is out of reach using simple optimizations on the current code base. In this context, the GeantV R&D project was launched, aiming to redesign the legacy particle transport codes in order to make them benefit from fine-grained parallelism features such as vectorization, but also from increased code and data locality. This paper presents extensively the results and achievements of this R&D, as well as the conclusions and lessons learnt from the beta prototype.Comment: 34 pages, 26 figures, 24 table