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

Sobre el papel de la programación paralela en los nuevos planes de estudios de informática

La difusión reciente de los sistemas paralelos hace que la programación paralela haya adquirido gran importancia, y dentro del proceso de reforma de los planes de estudios deberíamos plantearnos darle la importancia que realmente tiene. Los ingenieros en informática trabajan con estos sistemas y tienen que desarrollar software para ellos, por lo que no puede aducirse que es un tipo de programación complejo para no incluirlo o relegarlo de los estudios. Además, para obtener las máximas prestaciones de estos sistemas es necesario estudiar análisis y diseño de algoritmos paralelos. Este trabajo pretende motivar la discusión sobre cómo incluir los contenidos de programación y algoritmos paralelos. En nuestra opinión una buena opción sería incluir la programación paralela como parte de asignaturas de programación, junto con alguna asignatura específica de paralelismo.Peer Reviewe

Exploiting hybrid parallelism in the kinematic analysis of multibody systems based on group equations

Computational kinematics is a fundamental tool for the design, simulation, control, optimization and dynamic analysis of multibody systems. The analysis of complex multibody systems and the need for real time solutions requires the development of kinematic and dynamic formulations that reduces computational cost, the selection and efficient use of the most appropriated solvers and the exploiting of all the computer resources using parallel computing techniques. The topological approach based on group equations and natural coordinates reduces the computation time in comparison with well-known global formulations and enables the use of parallelism techniques which can be applied at different levels: simultaneous solution of equations, use of multithreading routines, or a combination of both. This paper studies and compares these topological formulation and parallel techniques to ascertain which combination performs better in two applications. The first application uses dedicated systems for the real time control of small multibody systems, defined by a few number of equations and small linear systems, so shared-memory parallelism in combination with linear algebra routines is analyzed in a small multicore and in Raspberry Pi. The control of a Stewart platform is used as a case study. The second application studies large multibody systems in which the kinematic analysis must be performed several times during the design of multibody systems. A simulator which allows us to control the formulation, the solver, the parallel techniques and size of the problem has been developed and tested in more powerful computational systems with larger multicores and GPU.This work was supported by the Spanish MINECO, as well as European Commission FEDER funds, under grant TIN2015-66972-C5-3-

Letras premiadas y no mencionadas en las Crónicas del Festival Internacional del Cante de las Minas

El Festival del Cante de las Minas de La Unión convocó concursos de letras de distintas modalidades entre 1971 y 2004. No hay una publicación específica dedicada a estos concursos, y la relación más detallada sobre ellos se puede encontrar en las Crónicas del Festival Internacional del Cante de las Minas, con cinco ediciones (la última en 2010). Las sucesivas ediciones contienen algunas lagunas en lo que se refiere a los premios de letras, con algunas de estas o de los autores ausentes o erróneas. En este trabajo se completa la información sobre los premios de letras que aparece errónea o incompletaThe “Festival del Cante de las Minas” in La Unión included between 1971 and 2004 lyric contests of different modalities. There is no publication dedicated to these contests, and the most detailed relation is in the Crónicas del Festival Internacional del Cante de las Minas, with five editions (the last one in 2010). The successive editions contain some mistakes, with some of the lyrics or authors absent or wrong. In this work we complete the information that appears erroneous or incomplet

Mujeres premiadas en concursos de letras flamencas

En el presente trabajo se analiza la participación de mujeres en concursos de letras flamencas, los premios y menciones conseguidos así como la evolución de la participación femenina en dichos eventos.This paper analyzes the participation of women in flamenco literary competitions, the awards and mentions achieved, as well as the evolution of female participation in these events

Revisiting Strassen’s Matrix Multiplication for Multicore Systems

Strassen’s matrix multiplication reduces the computational cost of multiplying matrices of size n × n from the O(n3) cost of a typical three-loop implementation to approximately O(n2.81). The reduction is made at the expense of additional operations of cost O(n2), and additional memory is needed for temporary results of recursive calls. The advantage of Strassen’s algorithm is therefore only apparent for larger matrices and it requires careful implementation. The increase in the speed of computational systems with several cores which share a common memory space also makes it more difficult for the algorithm to compete against highly optimized three-loop multiplications. This paper discusses various aspects which need to be addressed when designing Strassen multiplications for today’s multicore systems

Modelling parallel metaheuristics and hyperheuristics for auto-tuning

This paper studies the auto-tuning of parallel metaheuristics and hyperheuristics. The modelling of the shared-memory scheme is considered for both types of algorithms, and a first study of message-passing metaheuristic schemes is introduced. A theoretical model of the execution time of a parametrized metaheuristic scheme is empirically adapted for a particular metaheuristic through experimentation. The parallelization of the shared-memory scheme is achieved through the independent parallelization of the basic functions in the metaheuristic scheme. The model is used to decide at running time the number of threads to obtain a reduced execution time. The number of threads is different for the different basic functions in the scheme, and depends on the problem to be solved, the metaheuristic or hyperheuristic scheme, the implementation of the basic functions and the computational system where the problem is solved. The auto-tuning methodology for shared-memory parametrized metaheuristic schemes can in turn be applied to shared-memory hyperheuristics developed on top of them. In the case of the message-passing scheme, an island model implemented with the master-slave scheme is used, and new metaheuristic-parallelism parameters representing the migration frequency, the size of the migration and the number of processes are introduced. The applicability of the proposal is shown with a minimization of electricity consumption in exploitation of wells problem and with the problem of obtaining satisfactory metaheuristics for that problem. Experimental results with these two problems show that satisfactory execution times can be achieved in metaheuristics with auto-tuning techniques based on theoretical-empirical models of the execution time