Speedup bioinformatics applications on multicore-based processor using vectorizing and multithreading strategies

Many computational intensive bioinformatics software, such as multiple sequence alignment, population structure analysis, etc., written in C/C++ are not multicore-aware. A multicore processor is an emerging CPU technology that combines two or more independent processors into a single package. The Single Instruction Multiple Data-stream (SIMD) paradigm is heavily utilized in this class of processors. Nevertheless, most popular compilers including Microsoft Visual C/C++ 6.0, x86 gnu C-compiler gcc do not automatically create SIMD code which can fully utilize the advancement of these processors. To harness the power of the new multicore architecture certain compiler techniques must be considered. This paper presents a generic compiling strategy to assist the compiler in improving the performance of bioinformatics applications written in C/C++. The proposed framework contains 2 main steps: multithreading and vectorizing strategies. After following the strategies, the application can achieve higher speedup by taking the advantage of multicore architecture technology. Due to the extremely fast interconnection networking among multiple cores, it is suggested that the proposed optimization could be more appropriate than making use of parallelization on a small cluster computer which has larger network latency and lower bandwidth

Palgol: A High-Level DSL for Vertex-Centric Graph Processing with Remote Data Access

Pregel is a popular distributed computing model for dealing with large-scale graphs. However, it can be tricky to implement graph algorithms correctly and efficiently in Pregel's vertex-centric model, especially when the algorithm has multiple computation stages, complicated data dependencies, or even communication over dynamic internal data structures. Some domain-specific languages (DSLs) have been proposed to provide more intuitive ways to implement graph algorithms, but due to the lack of support for remote access --- reading or writing attributes of other vertices through references --- they cannot handle the above mentioned dynamic communication, causing a class of Pregel algorithms with fast convergence impossible to implement. To address this problem, we design and implement Palgol, a more declarative and powerful DSL which supports remote access. In particular, programmers can use a more declarative syntax called chain access to naturally specify dynamic communication as if directly reading data on arbitrary remote vertices. By analyzing the logic patterns of chain access, we provide a novel algorithm for compiling Palgol programs to efficient Pregel code. We demonstrate the power of Palgol by using it to implement several practical Pregel algorithms, and the evaluation result shows that the efficiency of Palgol is comparable with that of hand-written code.Comment: 12 pages, 10 figures, extended version of APLAS 2017 pape

Topological Quantum Compiling

A method for compiling quantum algorithms into specific braiding patterns for non-Abelian quasiparticles described by the so-called Fibonacci anyon model is developed. The method is based on the observation that a universal set of quantum gates acting on qubits encoded using triplets of these quasiparticles can be built entirely out of three-stranded braids (three-braids). These three-braids can then be efficiently compiled and improved to any required accuracy using the Solovay-Kitaev algorithm.Comment: 20 pages, 20 figures, published versio

Modularizing and Specifying Protocols among Threads

We identify three problems with current techniques for implementing protocols among threads, which complicate and impair the scalability of multicore software development: implementing synchronization, implementing coordination, and modularizing protocols. To mend these deficiencies, we argue for the use of domain-specific languages (DSL) based on existing models of concurrency. To demonstrate the feasibility of this proposal, we explain how to use the model of concurrency Reo as a high-level protocol DSL, which offers appropriate abstractions and a natural separation of protocols and computations. We describe a Reo-to-Java compiler and illustrate its use through examples.Comment: In Proceedings PLACES 2012, arXiv:1302.579

Parallel software for lattice N=4 supersymmetric Yang--Mills theory

We present new parallel software, SUSY LATTICE, for lattice studies of four-dimensional $\mathcal N = 4$ supersymmetric Yang--Mills theory with gauge group SU(N). The lattice action is constructed to exactly preserve a single supersymmetry charge at non-zero lattice spacing, up to additional potential terms included to stabilize numerical simulations. The software evolved from the MILC code for lattice QCD, and retains a similar large-scale framework despite the different target theory. Many routines are adapted from an existing serial code, which SUSY LATTICE supersedes. This paper provides an overview of the new parallel software, summarizing the lattice system, describing the applications that are currently provided and explaining their basic workflow for non-experts in lattice gauge theory. We discuss the parallel performance of the code, and highlight some notable aspects of the documentation for those interested in contributing to its future development.Comment: Code available at https://github.com/daschaich/sus