Parallel ant colony optimization for the training of cell signaling networks

[Abstract]: Acquiring a functional comprehension of the deregulation of cell signaling networks in disease allows progress in the development of new therapies and drugs. Computational models are becoming increasingly popular as a systematic tool to analyze the functioning of complex biochemical networks, such as those involved in cell signaling. CellNOpt is a framework to build predictive logic-based models of signaling pathways by training a prior knowledge network to biochemical data obtained from perturbation experiments. This training can be formulated as an optimization problem that can be solved using metaheuristics. However, the genetic algorithm used so far in CellNOpt presents limitations in terms of execution time and quality of solutions when applied to large instances. Thus, in order to overcome those issues, in this paper we propose the use of a method based on ant colony optimization, adapted to the problem at hand and parallelized using a hybrid approach. The performance of this novel method is illustrated with several challenging benchmark problems in the study of new therapies for liver cancer

Re-engineering the ant colony optimization for CMP architectures

[EN] The ant colony optimization (ACO) is inspired by the behavior of real ants, and as a bioinspired method, its underlying computation is massively parallel by definition. This paper shows re-engineering strategies to migrate the ACO algorithm applied to the Traveling Salesman Problem to modern Intel-based multi- and many-core architectures in a step-by-step methodology. The paper provides detailed guidelines on how to optimize the algorithm for the intra-node (thread and vector) parallelization, showing the performance scalability along with the number of cores on different Intel architectures, reporting up to 5.5x speedup factor between the Intel Xeon Phi Knights Landing and Intel Xeon v2. Moreover, parallel efficiency is provided for all targeted architectures, finding that core load imbalance, memory bandwidth limitations, and NUMA effects on data placement are some of the key factors limiting performance. Finally, a distributed implementation is also presented, reaching up to 2.96x speedup factor when running the code on 3 nodes over the single-node counterpart version. In the latter case, the parallel efficiency is affected by the synchronization frequency, which also affects the quality of the solution found by the distributed implementation.This work was partially supported by the Fundación Séneca, Agencia de Ciencia y Tecnología de la Región de Murcia under Project 20813/PI/18, and by Spanish Ministry of Science, Innovation and Universities as well as European Commission FEDER funds under Grants TIN2015-66972-C5-3-R, RTI2018-098156-B-C53, TIN2016-78799-P (AEI/FEDER, UE), and RTC-2017-6389-5. We acknowledge the excellent work done by Victor Montesinos while he was doing a research internship supported by the University of Murcia.Cecilia-Canales, JM.; García Carrasco, JM. (2020). Re-engineering the ant colony optimization for CMP architectures. The Journal of Supercomputing (Online). 76(6):4581-4602. https://doi.org/10.1007/s11227-019-02869-8S45814602766Yang XS (2010) Nature-inspired metaheuristic algorithms. Luniver Press, LebanonAkila M, Anusha P, Sindhu M, Selvan Krishnasamy T (2017) Examination of PSO, GA-PSO and ACO algorithms for the design optimization of printed antennas. In: IEEE Applied Electromagnetics Conference (AEMC)Dorigo M, Stützle T (2004) Ant colony optimization. A bradford book. The MIT Press, CambridgeCecilia JM, García JM, Nisbet A, Amos M, Ujaldón M (2013) Enhancing data parallelism for ant colony optimization on GPUs. J Parallel Distrib Comput 73(1):42–51Dawson L, Stewart I (2013) Improving ant colony optimization performance on the GPU using CUDA. In: IEEE Conference on Evolutionary Computation, pp 1901–1908Llanes A, Cecilia JM, Sánchez A, García JM, Amos M, Ujaldón M (2016) Dynamic load balancing on heterogeneous clusters for parallel ant colony optimization. Cluster Comput 19(1):1–11Cecilia JM, Llanes A, Abellán JL, Gómez-Luna J, Chang L, Hwu WW (2018) High-throughput ant colony optimization on graphics processing units. J Parallel Distrib Comput 113:261–274Lloyd H, Amos M (2016) A Highly Parallelized and Vectorized Implementation of Max–Min Ant System on Intel Xeon Phi. In: IEEE computational intelligenceTirado F, Barrientos RJ, González P, Mora M (2017) Efficient exploitation of the Xeon Phi architecture for the ant colony optimization (ACO) metaheuristic. J Supercomput 73(11):5053–5070Montesinos V, García JM (2018) Vectorization strategies for ant colony optimization on intel architectures. Parallel Computing is Everywhere. IOS Press, Amsterdam, pp 400–409Lawler E, Lenstra J, Kan A, Shmoys D (1987) The Traveling salesman problem. Wiley, New YorkMontesinos V (June 2018) Performance analysis of ant colony optimization on intel architectures. Master’s Thesis, University of Murcia (Spain)Lloyd H, Amos M (2017) Analysis of independent roulette selection in parallel ant colony optimization. In: Genetic and Evolutionary Computation Conference, ACM, pp 19–26Dorigo M (1992) Optimization, learning and natural algorithms. Ph.D. Thesis, Politecnico di Milano, ItalyDuran A, Klemm M (2012) The intel many integrated core architecture. In: Internal Conference on High Performance Computing and Simulation (HPCS), pp 365–366The OpenMP API specification for parallel programming. URL: https://www.openmp.org . [Last accessed 14 June 2018]The Message Passing Interface (MPI) standard. URL: http://www.mcs.anl.gov/research/projects/mpi/ . [Last accessed 15 June 2018]Vladimirov A, Asai R (2016) Clustering modes in Knights landing processors: developer’s guide. Colfax international. URL: https://colfaxresearch.com/knl-numa/ . [Last accessed: 16 June 2018]Intel Developer Zone. URL: https://software.intel.com/en-us/modern-code . [Last accessed 02 Oct 2018]Pearce M (2018) What is code modernization? Intel developer zone. URL: http://software.intel.com/en-us/articles/what-is-code-modernization . [Last accessed 15 Feb 2018]Stützle T ACOTSP v1.03. Last accessed 15 Feb 2018. URL: http://iridia.ulb.ac.be/~mdorigo/ACO/downloads/ACOTSP-1.03.tgzReinelt G (1991) TSPLIB—a traveling salesman problem library. ORSA J Comput 3:376–384Crainic TG, Toulouse M (2003) Parallel strategies for meta-heuristics. State-of-the-art handbook in metaheuristics. Kluwer Academic Publishers, Dordrecht, pp 475–513Delévacq A, Delisle P, Gravel M, Krajecki M (2013) Parallel ant colony optimization on graphics processing units. J Parallel Distrib Comput 73(1):52–61Skinderowicz R (2016) The GPU-based parallel ant colony system. J Parallel Distrib Comput 98:48–60Zhou Y, He F, Hou N, Qiu Y (2018) Parallel ant colony optimization on multi-core SIMD CPUs. Future Gener Comput Syst 79:473–487Peake J, Amos M, Yiapanis P, Lloyd H (2018) Vectorized candidate set selection for parallel ant colony optimization. In: Genetic and Evolutionary Computation Conference, ACM, pp 1300–1306Stützle T (1998) Parallelization strategies for ant colony optimization. In: Eiben AE, Bäck T, Schoenauer M, Schwefel HP (eds) Parallel problem solving from nature—PPSN V. PPSN. Lecture Notes in Computer Science, vol 1498. Springer, Berlin, HeidelbergAbdelkafi O, Lepagnot J, Idoumghar L (2014) Multi-level parallelization for hybrid ACO. In: Siarry P, Idoumghar L, Lepagnot J (eds) Swarm Intelligence Based Optimization. ICSIBO 2014. Lecture Notes in Computer Science, vol 8472. Springer, ChamMichel R, Middendorf M (1998) An island model based ant system with lookahead for the shortest super sequence problem. In: Eiben AE, Bäck T, Schoenauer M, Schwefel HP (eds) Parallel problem solving from nature— PPSN V. PPSN. Lecture Notes in Computer Science, vol 1498. Springer, Berlin, HeidelbergChen L, Sun H, Wang S (2008) Parallel implementation of ant colony optimization on MPP. In: International Conference on Machine Learning and CyberneticsLin Y, Cai H, Xiao J, Zhang J (2007) Pseudo parallel ant colony optimization for continuous functions. In: International Conference on Natural Computatio

METADOCK: A parallel metaheuristic schema for virtual screening methods

Virtual screening through molecular docking can be translated into an optimization problem, which can be tackled with metaheuristic methods. The interaction between two chemical compounds (typically a protein, enzyme or receptor, and a small molecule, or ligand) is calculated by using highly computationally demanding scoring functions that are computed at several binding spots located throughout the protein surface. This paper introduces METADOCK, a novel molecular docking methodology based on parameterized and parallel metaheuristics and designed to leverage heterogeneous computers based on heterogeneous architectures. The application decides the optimization technique at running time by setting a configuration schema. Our proposed solution finds a good workload balance via dynamic assignment of jobs to heterogeneous resources which perform independent metaheuristic executions when computing different molecular interactions required by the scoring functions in use. A cooperative scheduling of jobs optimizes the quality of the solution and the overall performance of the simulation, so opening a new path for further developments of virtual screening methods on high-performance contemporary heterogeneous platforms.Ingeniería, Industria y Construcció

A General Framework for Accelerating Swarm Intelligence Algorithms on FPGAs, GPUs and Multi-core CPUs

Swarm intelligence algorithms (SIAs) have demonstrated excellent performance when solving optimization problems including many real-world problems. However, because of their expensive computational cost for some complex problems, SIAs need to be accelerated effectively for better performance. This paper presents a high-performance general framework to accelerate SIAs (FASI). Different from the previous work which accelerate SIAs through enhancing the parallelization only, FASI considers both the memory architectures of hardware platforms and the dataflow of SIAs, and it reschedules the framework of SIAs as a converged dataflow to improve the memory access efficiency. FASI achieves higher acceleration ability by matching the algorithm framework to the hardware architectures. We also design deep optimized structures of the parallelization and convergence of FASI based on the characteristics of specific hardware platforms. We take the quantum behaved particle swarm optimization algorithm (QPSO) as a case to evaluate FASI. The results show that FASI improves the throughput of SIAs and provides better performance through optimizing the hardware implementations. In our experiments, FASI achieves a maximum of 290.7Mbit/s throughput which is higher than several existing systems, and FASI on FPGAs achieves a better speedup than that on GPUs and multi-core CPUs. FASI is up to 123 times and not less than 1.45 times faster in terms of optimization time on Xilinx Kintex Ultrascale xcku040 when compares to Intel Core i7-6700 CPU/ NVIDIA GTX1080 GPU. Finally, we compare the differences of deploying FASI on hardware platforms and provide some guidelines for promoting the acceleration performance according to the hardware architectures

Optimal Communication Structures for Concurrent Computing

This research focuses on communicative solvers that run concurrently and exchange information to improve performance. This “team of solvers” enables individual algorithms to communicate information regarding their progress and intermediate solutions, and allows them to synchronize memory structures with more “successful” counterparts. The result is that fewer nodes spend computational resources on “struggling” processes. The research is focused on optimization of communication structures that maximize algorithmic efficiency using the theoretical framework of Markov chains. Existing research addressing communication between the cooperative solvers on parallel systems lacks generality: Most studies consider a limited number of communication topologies and strategies, while the evaluation of different configurations is mostly limited to empirical testing. Currently, there is no theoretical framework for tuning communication between cooperative solvers to match the underlying hardware and software. Our goal is to provide such functionality by mapping solvers’ dynamics to Markov processes, and formulating the automatic tuning of communication as a well-defined optimization problem with an objective to maximize solvers’ performance metrics

Surfing the optimization space of a multiple-GPU parallel implementation of a X-ray tomography reconstruction algorithm

The increasing popularity of massively parallel architectures based on accelerators have opened up the possibility of significantly improving the performance of X-ray computed tomography (CT) applications towards achieving real-time imaging. However, achieving this goal is a challenging process, as most CT applications have not been designed for exploiting the amount of parallelism existing in these architectures. In this paper we present the massively parallel implementation and optimization of Mangoose(++), a CT application for reconstructing 3D volumes from 20 images collected by scanners based on cone-beam geometry. The main contribution of this paper are the following. First, we develop a modular application design that allows to exploit the functional parallelism inside the application and to facilitate the parallelization of individual application phases. Second, we identify a set of optimizations that can be applied individually and in combination for optimally deploying the application on a massively parallel multi-GPU system. Third, we present a study of surfing the optimization space of the modularized application and demonstrate that a significant benefit can be obtained from employing the adequate combination of application optimizations. (C) 2014 Elsevier Inc. All rights reserved.This work was partially funded by the Spanish Ministry of Science and Technology under the grant TIN2010-16497, the AMIT project (CEN-20101014) from the CDTI-CENIT program, RECAVA-RETIC Network (RD07/0014/2009), projects TEC2010-21619-C04-01, TEC2011-28972-C02-01, and PI11/00616 from the Spanish Ministerio de Ciencia e Innovacion, ARTEMIS program (S2009/DPI-1802), from the Comunidad de Madrid

Accelerating supply chains with Ant Colony Optimization across range of hardware solutions

This pre-print, arXiv:2001.08102v1 [cs.NE], was published subsequently by Elsevier in Computers and Industrial Engineering, vol. 147, 106610, pp. 1-14 on 29 Jun 2020 and is available at https://doi.org/10.1016/j.cie.2020.106610Ant Colony algorithm has been applied to various optimization problems, however most of the previous work on scaling and parallelism focuses on Travelling Salesman Problems (TSPs). Although, useful for benchmarks and new idea comparison, the algorithmic dynamics does not always transfer to complex real-life problems, where additional meta-data is required during solution construction. This paper looks at real-life outbound supply chain problem using Ant Colony Optimization (ACO) and its scaling dynamics with two parallel ACO architectures - Independent Ant Colonies (IAC) and Parallel Ants (PA). Results showed that PA was able to reach a higher solution quality in fewer iterations as the number of parallel instances increased. Furthermore, speed performance was measured across three different hardware solutions - 16 core CPU, 68 core Xeon Phi and up to 4 Geforce GPUs. State of the art, ACO vectorization techniques such as SS-Roulette were implemented using C++ and CUDA. Although excellent for TSP, it was concluded that for the given supply chain problem GPUs are not suitable due to meta-data access footprint required. Furthermore, compared to their sequential counterpart, vectorized CPU AVX2 implementation achieved 25.4x speedup on CPU while Xeon Phi with its AVX512 instruction set reached 148x on PA with Vectorized (PAwV). PAwV is therefore able to scale at least up to 1024 parallel instances on the supply chain network problem solved

Multipopulation-based multi-level parallel enhanced Jaya algorithms

To solve optimization problems, in the field of engineering optimization, an optimal value of a specific function must be found, in a limited time, within a constrained or unconstrained domain. Metaheuristic methods are useful for a wide range of scientific and engineering applications, which accelerate being able to achieve optimal or near-optimal solutions. The metaheuristic method called Jaya has generated growing interest because of its simplicity and efficiency. We present Jaya-based parallel algorithms to efficiently exploit cluster computing platforms (heterogeneous memory platforms). We propose a multi-level parallel algorithm, in which, to exploit distributed-memory architectures (or multiprocessors), the outermost layer of the Jaya algorithm is parallelized. Moreover, in internal layers, we exploit shared-memory architectures (or multicores) by adding two more levels of parallelization. This two-level internal parallel algorithm is based on both a multipopulation structure and an improved heuristic search path relative to the search path of the sequential algorithm. The multi-level parallel algorithm obtains average efficiency values of 84% using up to 120 and 135 processes, and slightly accelerates the convergence with respect to the sequential Jaya algorithm.This research was supported by the Spanish Ministry of Economy and Competitiveness under Grant TIN2015-66972-C5-4-R and Grant TIN2017-89266-R, co-financed by FEDER funds (MINECO/FEDER/UE)

Refactoring GrPPI:Generic Refactoring for Generic Parallelism in C++

Funding: EU Horizon 2020 project, TeamPlay (https://www.teamplay-xh2020.eu), Grant Number 779882, UK EPSRC Discovery, grant number EP/P020631/1, and Madrid Regional Government, CABAHLA-CM (ConvergenciA Big dAta-Hpc: de Los sensores a las Aplicaciones) Grant Number S2018/TCS-4423.The Generic Reusable Parallel Pattern Interface (GrPPI) is a very useful abstraction over different parallel pattern libraries, allowing the programmer to write generic patterned parallel code that can easily be compiled to different backends such as FastFlow, OpenMP, Intel TBB and C++ threads. However, rewriting legacy code to use GrPPI still involves code transformations that can be highly non-trivial, especially for programmers who are not experts in parallelism. This paper describes software refactorings to semi-automatically introduce instances of GrPPI patterns into sequential C++ code, as well as safety checking static analysis mechanisms which verify that introducing patterns into the code does not introduce concurrency-related bugs such as race conditions. We demonstrate the refactorings and safety-checking mechanisms on four simple benchmark applications, showing that we are able to obtain, with little effort, GrPPI-based parallel versions that accomplish good speedups (comparable to those of manually-produced parallel versions) using different pattern backends.Publisher PDFPeer reviewe

Parallel Improvements of the Jaya Optimization Algorithm

A wide range of applications use optimization algorithms to find an optimal value, often a minimum one, for a given function. Depending on the application, both the optimization algorithm’s behavior, and its computational time, can prove to be critical issues. In this paper, we present our efficient parallel proposals of the Jaya algorithm, a recent optimization algorithm that enables one to solve constrained and unconstrained optimization problems. We tested parallel Jaya algorithms for shared, distributed, and heterogeneous memory platforms, obtaining good parallel performance while leaving Jaya algorithm behavior unchanged. Parallel performance was analyzed using 30 unconstrained functions reaching a speed-up of up to 57.6x using 60 processors. For all tested functions, the parallel distributed memory algorithm obtained parallel efficiencies that were nearly ideal, and combining it with the shared memory algorithm allowed us to obtain good parallel performance. The experimental results show a good parallel performance regardless of the nature of the function to be optimized.This research was supported by the Spanish Ministry of Economy and Competitiveness under Grants TIN2015-66972-C5-4-R and TIN2017-89266-R, co-financed by FEDER funds (MINECO/FEDER/UE)