Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS

GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest supercomputers in the world. Here, we describe some of the ways we have been able to realize this through the use of parallelization on all levels, combined with a constant focus on absolute performance. Release 4.6 of GROMACS uses SIMD acceleration on a wide range of architectures, GPU offloading acceleration, and both OpenMP and MPI parallelism within and between nodes, respectively. The recent work on acceleration made it necessary to revisit the fundamental algorithms of molecular simulation, including the concept of neighborsearching, and we discuss the present and future challenges we see for exascale simulation - in particular a very fine-grained task parallelism. We also discuss the software management, code peer review and continuous integration testing required for a project of this complexity.Comment: EASC 2014 conference proceedin

Designing a scalable dynamic load -balancing algorithm for pipelined single program multiple data applications on a non-dedicated heterogeneous network of workstations

Dynamic load balancing strategies have been shown to be the most critical part of an efficient implementation of various applications on large distributed computing systems. The need for dynamic load balancing strategies increases when the underlying hardware is a non-dedicated heterogeneous network of workstations (HNOW). This research focuses on the single program multiple data (SPMD) programming model as it has been extensively used in parallel programming for its simplicity and scalability in terms of computational power and memory size.;This dissertation formally defines and addresses the problem of designing a scalable dynamic load-balancing algorithm for pipelined SPMD applications on non-dedicated HNOW. During this process, the HNOW parameters, SPMD application characteristics, and load-balancing performance parameters are identified.;The dissertation presents a taxonomy that categorizes general load balancing algorithms and a methodology that facilitates creating new algorithms that can harness the HNOW computing power and still preserve the scalability of the SPMD application.;The dissertation devises a new algorithm, DLAH (Dynamic Load-balancing Algorithm for HNOW). DLAH is based on a modified diffusion technique, which incorporates the HNOW parameters. Analytical performance bound for the worst-case scenario of the diffusion technique has been derived.;The dissertation develops and utilizes an HNOW simulation model to conduct extensive simulations. These simulations were used to validate DLAH and compare its performance to related dynamic algorithms. The simulations results show that DLAH algorithm is scalable and performs well for both homogeneous and heterogeneous networks. Detailed sensitivity analysis was conducted to study the effects of key parameters on performance

Factores de rendimiento asociados a SPMD

Actualmente existen muchas aplicaciones paralelas/distribuidas en las cuales SPMD es el paradigma más usado. Obtener un buen rendimiento en una aplicación paralela de este tipo es uno de los principales desafíos dada la gran cantidad de aplicaciones existentes. Este objetivo no es fácil de resolver ya que existe una gran variedad de configuraciones de hardware, y también la naturaleza de los problemas pueden ser variados así como la forma de implementarlos. En consecuencia, si no se considera adecuadamente la combinación "software/hardware" pueden aparecer problemas inherentes a una aplicación iterativa sin una jerarquía de control definida de acuerdo a este paradigma. En SPMD todos los procesos ejecutan el mismo código pero computan una sección diferente de los datos de entrada. Una solución a un posible problema del rendimiento es proponer una estrategia de balance de carga para homogeneizar el cómputo entre los diferentes procesos. En este trabajo analizamos el benchmark CG con cargas heterogéneas con la finalidad de detectar los posibles problemas de rendimiento en una aplicación real. Un factor que determina el rendimiento en esta aplicación es la cantidad de elementos nonzero contenida en la sección de matriz asignada a cada proceso. Determinamos que es posible definir una estrategia de balance de carga que puede ser implementada de forma dinámica y demostramos experimentalmente que el rendimiento de la aplicación puede mejorarse de forma significativa con dicha estrategia.There currently are many 'parallel/distributed' applications that use the SPMD paradigm. Getting a good performance in a parallel application of this type is a major challenge because of the large number of existing applications. This objective is not easily achieved because there are many hardware configurations possible, and also the nature of the problems can be varied as well as its implementation. Consequently, if not adequately consider the combination 'software/hardware' inherent problems can occur without an iterative application defined control hierarchy according to this paradigm. In SPMD all processes execute the same code but they compute a different section of the input data. In this paper we analyze the benchmark CG with heterogeneous loads in order to detect possible performance problems in a real application. One factor that determines the performance in this application is the number of elements nonzero contained in the array section assigned to each process. We determined that it is possible to define a load balancing strategy, which can be implemented dynamically, and we demonstrate experimentally that the application performance can be significantly improved with this approach.Actualment existeixen moltes aplicacions paral·leles/distribuïdes en les quals SPMD és el paradigma més emprat. Obtenir un bon rendiment en una aplicació paral·lela d'aquest tipus és un dels principals reptes donada la gran quantitat d'aplicacions existents. Aquest objectiu no és fàcil de resoldre donat que existeixen una gran varietat de configuracions de hardware, i també la naturalesa dels problemes pot ser variada així com la forma d'implementar-los. En conseqüència, si no es considera adequadament la combinació "software/hardware" poden aparèixer problemes inherents a una aplicació iterativa sense una jerarquia de control definida d'acord a aquest paradigma. En SPMD tots els processos executen el mateix codi però computen una secció diferent de les dades d'entrada. Una solució a un possible problema de rendiment es proposar una estratègia de balanceig de càrrega per homogeneïtzar el còmput entre els diferents processos. En aquest treball analitzem el benchmark CG amb càrregues heterogènies amb la finalitat de detectar els possibles problemes de rendiment en una aplicació real. Un factor que determina el rendiment en aquesta aplicació és la quantitat d'elements nonzero continguda en la secció de la matriu assignada a cada procés. Es determina que és possible definir una estratègia de balanceig de càrrega que pot ser implementada de forma dinàmica i es demostra de forma experimental que el rendiment de la aplicació pot millorar-se de forma significativa amb aquesta estratègia

Enhancing the performance of malleable MPI applications by using performance-aware dynamic reconfiguration

The work in this paper focuses on providing malleability to MPI applications by using a novel performance-aware dynamic reconfiguration technique. This paper describes the design and implementation of Flex-MPI, an MPI library extension which can automatically monitor and predict the performance of applications, balance and redistribute the workload, and reconfigure the application at runtime by changing the number of processes. Unlike existent approaches, our reconfiguring policy is guided by user-defined performance criteria. We focus on iterative SPMD programs, a class of applications with critical mass within the scientific community. Extensive experiments show that Flex-MPI can improve the performance, parallel efficiency, and cost-efficiency of MPI programs with a minimal effort from the programmer.This work has been partially supported by the Spanish Ministry of Economy and Competitiveness under the project TIN2013- 41350-P, Scalable Data Management Techniques for High-End Computing Systems, and EU under the COST Program Action IC1305, Network for Sustainable Ultrascale Computing (NESUS)Peer ReviewedPostprint (author's final draft

ReSHAPE: A Framework for Dynamic Resizing and Scheduling of Homogeneous Applications in a Parallel Environment

Applications in science and engineering often require huge computational resources for solving problems within a reasonable time frame. Parallel supercomputers provide the computational infrastructure for solving such problems. A traditional application scheduler running on a parallel cluster only supports static scheduling where the number of processors allocated to an application remains fixed throughout the lifetime of execution of the job. Due to the unpredictability in job arrival times and varying resource requirements, static scheduling can result in idle system resources thereby decreasing the overall system throughput. In this paper we present a prototype framework called ReSHAPE, which supports dynamic resizing of parallel MPI applications executed on distributed memory platforms. The framework includes a scheduler that supports resizing of applications, an API to enable applications to interact with the scheduler, and a library that makes resizing viable. Applications executed using the ReSHAPE scheduler framework can expand to take advantage of additional free processors or can shrink to accommodate a high priority application, without getting suspended. In our research, we have mainly focused on structured applications that have two-dimensional data arrays distributed across a two-dimensional processor grid. The resize library includes algorithms for processor selection and processor mapping. Experimental results show that the ReSHAPE framework can improve individual job turn-around time and overall system throughput.Comment: 15 pages, 10 figures, 5 tables Submitted to International Conference on Parallel Processing (ICPP'07

Flexible language constructs for large parallel programs

The goal of the research described is to develop flexible language constructs for writing large data parallel numerical programs for distributed memory (MIMD) multiprocessors. Previously, several models have been developed to support synchronization and communication. Models for global synchronization include SIMD (Single Instruction Multiple Data), SPMD (Single Program Multiple Data), and sequential programs annotated with data distribution statements. The two primary models for communication include implicit communication based on shared memory and explicit communication based on messages. None of these models by themselves seem sufficient to permit the natural and efficient expression of the variety of algorithms that occur in large scientific computations. An overview of a new language that combines many of these programming models in a clean manner is given. This is done in a modular fashion such that different models can be combined to support large programs. Within a module, the selection of a model depends on the algorithm and its efficiency requirements. An overview of the language and discussion of some of the critical implementation details is given

Massively Parallel Simulation of Structured Connectionist Networks: An Interim Report

We map structured connectionist models of knowledge representation and reasoning onto existing general purpose massively parallel architectures with the objective of developing and implementing practical, real-time knowledge base systems. Shruti, a connectionist knowledge representation and reasoning system which attempts to model reflexive reasoning, will serve as our representative connectionist model. Efficient simulation systems for shruti are developed on the Connection Machine CM-2 - an SIMD architecture - and on the Connection Machine CM-5 - an MIMD architecture. The resulting simulators are evaluated and tested using large, random knowledge bases with up to half a million rules and facts. Though SIMD simulations on the CM-2 are reasonably fast - requiring a few seconds to tens of seconds for answering simple queries - experiments indicate that MIMD simulations are vastly superior to SIMD simulations and offer hundred- to thousand-fold speedups. This work provides new insights into the simulation of structured connectionist networks on massively parallel machines and is a step toward developing large yet efficient knowledge representation and reasoning systems

An approach for an efficient execution of SPMD applications on Multi-core environments

Executing traditional Message Passing Interface (MPI) applications on multi-core cluster balancing speed and computational efficiency is a difficult task that parallel programmers have to deal with. For this reason, communications on multi-core clusters ought to be handled carefully in order to improve performance metrics such as efficiency, speedup, execution time and scalability. In this paper we focus our attention on SPMD (Single Program Multiple Data) applications with high communication volume and synchronicity and also following characteristics such as: static, local and regular. This work proposes a method for SPMD applications, which is focused on managing the communication heterogeneity (different cache level, RAM memory, network, etc.) on homogeneous multi-core computing platform in order to improve the application efficiency. In this sense, the main objective of this work is to find analytically the ideal number of cores necessary that allows us to obtain the maximum speedup, while the computational efficiency is maintained over a defined threshold (strong scalability). This method also allows us to determine how the problem size must be increased in order to maintain an execution time constant while the number of cores are expanded (weak scalability) considering the tradeoff between speed and efficiency. This methodology has been tested with different benchmarks and applications and we achieved an average improvement around 30.35% of efficiency in applications tested using different problems sizes and multi-core clusters. In addition, results show that maximum speedup with a defined efficiency is located close to the values calculated with our analytical model with an error rate lower than 5% for the applications tested.This research has been supported by the MINECO (MICINN) Spain under contracts TIN2011-24384 and TIN2014- 53172-PPeer ReviewedPostprint (author's final draft