State-of-the-art in Smith-Waterman Protein Database Search on HPC Platforms

Searching biological sequence database is a common and repeated task in bioinformatics and molecular biology. The Smith–Waterman algorithm is the most accurate method for this kind of search. Unfortunately, this algorithm is computationally demanding and the situation gets worse due to the exponential growth of biological data in the last years. For that reason, the scientific community has made great efforts to accelerate Smith–Waterman biological database searches in a wide variety of hardware platforms. We give a survey of the state-of-the-art in Smith–Waterman protein database search, focusing on four hardware architectures: central processing units, graphics processing units, field programmable gate arrays and Xeon Phi coprocessors. After briefly describing each hardware platform, we analyse temporal evolution, contributions, limitations and experimental work and the results of each implementation. Additionally, as energy efficiency is becoming more important every day, we also survey performance/power consumption works. Finally, we give our view on the future of Smith–Waterman protein searches considering next generations of hardware architectures and its upcoming technologies.Instituto de Investigación en InformáticaUniversidad Complutense de Madri

DPP-PMRF: Rethinking Optimization for a Probabilistic Graphical Model Using Data-Parallel Primitives

We present a new parallel algorithm for probabilistic graphical model optimization. The algorithm relies on data-parallel primitives (DPPs), which provide portable performance over hardware architecture. We evaluate results on CPUs and GPUs for an image segmentation problem. Compared to a serial baseline, we observe runtime speedups of up to 13X (CPU) and 44X (GPU). We also compare our performance to a reference, OpenMP-based algorithm, and find speedups of up to 7X (CPU).Comment: LDAV 2018, October 201

Scaling Monte Carlo Tree Search on Intel Xeon Phi

Many algorithms have been parallelized successfully on the Intel Xeon Phi coprocessor, especially those with regular, balanced, and predictable data access patterns and instruction flows. Irregular and unbalanced algorithms are harder to parallelize efficiently. They are, for instance, present in artificial intelligence search algorithms such as Monte Carlo Tree Search (MCTS). In this paper we study the scaling behavior of MCTS, on a highly optimized real-world application, on real hardware. The Intel Xeon Phi allows shared memory scaling studies up to 61 cores and 244 hardware threads. We compare work-stealing (Cilk Plus and TBB) and work-sharing (FIFO scheduling) approaches. Interestingly, we find that a straightforward thread pool with a work-sharing FIFO queue shows the best performance. A crucial element for this high performance is the controlling of the grain size, an approach that we call Grain Size Controlled Parallel MCTS. Our subsequent comparing with the Xeon CPUs shows an even more comprehensible distinction in performance between different threading libraries. We achieve, to the best of our knowledge, the fastest implementation of a parallel MCTS on the 61 core Intel Xeon Phi using a real application (47 relative to a sequential run).Comment: 8 pages, 9 figure