Enabling the “Easy Button” for Broad, Parallel Optimization of Functions Evaluated by Simulation

Java Optimization by Simulation (JOBS) is presented: an open-source, object-oriented Java library designed to enable the study, research, and use of optimization for models evaluated by simulation. JOBS includes several novel design features that make it easy for a simulation modeler, without extensive expertise in optimization or parallel computation, to define an optimization model with deterministic and/or stochastic constraints, choose one or more metaheuristics to solve it and run, using massively parallel function evaluation to reduce wall-clock times. JOBS is supported by a new language independent, application programming interface (API) for remote simulation model evaluation and a serverless computing environment to provide massively parallel function evaluation, on demand. Dynamic loop scheduling methods are evaluated in the serverless environment with the opportunity for significant resource contention for master node computing power and network bandwidth. JOBS implements several population-based and single-solution improvement metaheuristics (solvers) for real, discrete, and mixed problems. The object-oriented design is extendible with classes that drastically reduce the amount of code required to implement a new solver and encourage re-use of solvers as building blocks for creating new multi-stage solvers or memetic algorithms

Message passing interface implementation for Concordia parallel programming environment

In this report, we present the design and implementation of a Message Passing interface (MPI) [1] for the Concordia Parallel Programming Environment (CPPE), an environment for parallel computing simulation. The purpose of this project is to provide Message Passing Interface (MPI) support for CPPE, so that user can get access to MPI programming with CPPE. Also the CPPE environment, which allows users to study impacts of the system and software factors on program performance and locate performance bottlenecks in parallel programming [2], in turn, benefits the developing of the MPI applications with all of its advanced features. Parallel computing offers the potential to push the perfomance of computer systems into new dimensions. One of the main obstacles for a broad application of the parallel technology is the lack of parallel programming standards. The Message Passing Interface (MPI) is just such a portable message passing standard that facilitates the development of parallel applications and libraries. The goal of MPI is to achieve efficient communication, portability and rich functionality. This report outlines the development and implementation of MPI for CPPE. As a development tool, this implementation enables MPI parallel software developing easy and inexpensive. As a learning tool, it provides a larger group of computer users with the opportunity to gain experience with MPI programming on their personal computers. We also discuss the MPI standard in detail, and furthermore illustrate the MPI parallel programming with some example programs. We focus on design and implementation issues for MPI, as well as the simulation procedure under CPPE virtual parallel machine. Special consideration is given to confirm the correctness of this implementation by comparing the running of a series of MPI applications on CPPE with that of MPICH implementation on UNIX

The Oceanographic Multipurpose Software Environment (OMUSE v1.0)

In this paper we present the Oceanographic Multipurpose Software Environment (OMUSE). OMUSE aims to provide a homogeneous environment for existing or newly developed numerical ocean simulation codes, simplifying their use and deployment. In this way, numerical experiments that combine ocean models representing different physics or spanning different ranges of physical scales can be easily designed. Rapid development of simulation models is made possible through the creation of simple high-level scripts. The low-level core of the abstraction in OMUSE is designed to deploy these simulations efficiently on heterogeneous high-performance computing resources. Cross-verification of simulation models with different codes and numerical methods is facilitated by the unified interface that OMUSE provides. Reproducibility in numerical experiments is fostered by allowing complex numerical experiments to be expressed in portable scripts that conform to a common OMUSE interface. Here, we present the design of OMUSE as well as the modules and model components currently included, which range from a simple conceptual quasi-geostrophic solver to the global circulation model POP (Parallel Ocean Program). The uniform access to the codes' simulation state and the extensive automation of data transfer and conversion operations aids the implementation of model couplings. We discuss the types of couplings that can be implemented using OMUSE. We also present example applications that demonstrate the straightforward model initialization and the concurrent use of data analysis tools on a running model. We give examples of multiscale and multiphysics simulations by embedding a regional ocean model into a global ocean model and by coupling a surface wave propagation model with a coastal circulation model

MOLNs: A cloud platform for interactive, reproducible and scalable spatial stochastic computational experiments in systems biology using PyURDME

Computational experiments using spatial stochastic simulations have led to important new biological insights, but they require specialized tools, a complex software stack, as well as large and scalable compute and data analysis resources due to the large computational cost associated with Monte Carlo computational workflows. The complexity of setting up and managing a large-scale distributed computation environment to support productive and reproducible modeling can be prohibitive for practitioners in systems biology. This results in a barrier to the adoption of spatial stochastic simulation tools, effectively limiting the type of biological questions addressed by quantitative modeling. In this paper, we present PyURDME, a new, user-friendly spatial modeling and simulation package, and MOLNs, a cloud computing appliance for distributed simulation of stochastic reaction-diffusion models. MOLNs is based on IPython and provides an interactive programming platform for development of sharable and reproducible distributed parallel computational experiments

Leveraging legacy codes to distributed problem solving environments: A web service approach

This paper describes techniques used to leverage high performance legacy codes as CORBA components to a distributed problem solving environment. It first briefly introduces the software architecture adopted by the environment. Then it presents a CORBA oriented wrapper generator (COWG) which can be used to automatically wrap high performance legacy codes as CORBA components. Two legacy codes have been wrapped with COWG. One is an MPI-based molecular dynamic simulation (MDS) code, the other is a finite element based computational fluid dynamics (CFD) code for simulating incompressible Navier-Stokes flows. Performance comparisons between runs of the MDS CORBA component and the original MDS legacy code on a cluster of workstations and on a parallel computer are also presented. Wrapped as CORBA components, these legacy codes can be reused in a distributed computing environment. The first case shows that high performance can be maintained with the wrapped MDS component. The second case shows that a Web user can submit a task to the wrapped CFD component through a Web page without knowing the exact implementation of the component. In this way, a user’s desktop computing environment can be extended to a high performance computing environment using a cluster of workstations or a parallel computer

VirtFogSim: A parallel toolbox for dynamic energy-delay performance testing and optimization of 5G Mobile-Fog-Cloud virtualized platforms

It is expected that the pervasive deployment of multi-tier 5G-supported Mobile-Fog-Cloudtechnological computing platforms will constitute an effective means to support the real-time execution of future Internet applications by resource- and energy-limited mobile devices. Increasing interest in this emerging networking-computing technology demands the optimization and performance evaluation of several parts of the underlying infrastructures. However, field trials are challenging due to their operational costs, and in every case, the obtained results could be difficult to repeat and customize. These emergingMobile-Fog-Cloud ecosystems still lack, indeed, customizable software tools for the performance simulation of their computing-networking building blocks. Motivated by these considerations, in this contribution, we present VirtFogSim. It is aMATLAB-supported software toolbox that allows the dynamic joint optimization and tracking of the energy and delay performance of Mobile-Fog-Cloud systems for the execution of applications described by general Directed Application Graphs (DAGs). In a nutshell, the main peculiar features of the proposed VirtFogSim toolbox are that: (i) it allows the joint dynamic energy-aware optimization of the placement of the application tasks and the allocation of the needed computing-networking resources under hard constraints on acceptable overall execution times, (ii) it allows the repeatable and customizable simulation of the resulting energy-delay performance of the overall system; (iii) it allows the dynamic tracking of the performed resource allocation under time-varying operational environments, as those typically featuring mobile applications; (iv) it is equipped with a user-friendly Graphic User Interface (GUI) that supports a number of graphic formats for data rendering, and (v) itsMATLAB code is optimized for running atop multi-core parallel execution platforms. To check both the actual optimization and scalability capabilities of the VirtFogSim toolbox, a number of experimental setups featuring different use cases and operational environments are simulated, and their performances are compared