Characterization of applications in new architectures

English: Computer science is continuously evolving to improve the development of applications, and to allow programmers to achieve better productivity. One key issue to solve is the ability to reuse the work previously done by others. Currently, the same or similar algorithms and libraries are used in many different kinds of applications (weather forecasting, physics simulations, artificial intelligence decision, entertainment programs, etc.), despite of which kind of input data is processed and how. The increasing number of requirements are the reason that only one processor is not enough for high performance applications, forcing processors to cooperate in a synchronized way. For this, there is the idea of granularity: a program must be divided in subtasks (a.k.a. threads) which need to communicate to exchange data and coordinate their activities in order to distribute workload and improve application performance. So, when those requirements are high enough, migration of the application to a new and more powerful platform is needed, with inappreciable modifications or without any changes either in the algorithm or in the source code. Throughout this document we show how to achieve that goal and what techniques, resources and steps have been chosen around application and platform Kratos and Mare Nostrum would be the main elements in this document in order to help make easier future migrations, either with others applications on similar or different platforms

A Domain-Specific Language and Editor for Parallel Particle Methods

Domain-specific languages (DSLs) are of increasing importance in scientific high-performance computing to reduce development costs, raise the level of abstraction and, thus, ease scientific programming. However, designing and implementing DSLs is not an easy task, as it requires knowledge of the application domain and experience in language engineering and compilers. Consequently, many DSLs follow a weak approach using macros or text generators, which lack many of the features that make a DSL a comfortable for programmers. Some of these features---e.g., syntax highlighting, type inference, error reporting, and code completion---are easily provided by language workbenches, which combine language engineering techniques and tools in a common ecosystem. In this paper, we present the Parallel Particle-Mesh Environment (PPME), a DSL and development environment for numerical simulations based on particle methods and hybrid particle-mesh methods. PPME uses the meta programming system (MPS), a projectional language workbench. PPME is the successor of the Parallel Particle-Mesh Language (PPML), a Fortran-based DSL that used conventional implementation strategies. We analyze and compare both languages and demonstrate how the programmer's experience can be improved using static analyses and projectional editing. Furthermore, we present an explicit domain model for particle abstractions and the first formal type system for particle methods.Comment: Submitted to ACM Transactions on Mathematical Software on Dec. 25, 201

Automatische Codegenerierung für Massiv Parallele Applikationen in der Numerischen Strömungsmechanik

Solving partial differential equations (PDEs) is a fundamental challenge in many application domains in industry and academia alike. With increasingly large problems, efficient and highly scalable implementations become more and more crucial. Today, facing this challenge is more difficult than ever due to the increasingly heterogeneous hardware landscape. One promising approach is developing domain‐specific languages (DSLs) for a set of applications. Using code generation techniques then allows targeting a range of hardware platforms while concurrently applying domain‐specific optimizations in an automated fashion. The present work aims to further the state of the art in this field. As domain, we choose PDE solvers and, in particular, those from the group of geometric multigrid methods. To avoid having a focus too broad, we restrict ourselves to methods working on structured and patch‐structured grids. We face the challenge of handling a domain as complex as ours, while providing different abstractions for diverse user groups, by splitting our external DSL ExaSlang into multiple layers, each specifying different aspects of the final application. Layer 1 is designed to resemble LaTeX and allows inputting continuous equations and functions. Their discretization is expressed on layer 2. It is complemented by algorithmic components which can be implemented in a Matlab‐like syntax on layer 3. All information provided to this point is summarized on layer 4, enriched with particulars about data structures and the employed parallelization. Additionally, we support automated progression between the different layers. All ExaSlang input is processed by our jointly developed Scala code generation framework to ultimately emit C++ code. We particularly focus on how to generate applications parallelized with, e.g., MPI and OpenMP that are able to run on workstations and large‐scale cluster alike. We showcase the applicability of our approach by implementing simple test problems, like Poisson’s equation, as well as relevant applications from the field of computational fluid dynamics (CFD). In particular, we implement scalable solvers for the Stokes, Navier‐Stokes and shallow water equations (SWE) discretized using finite differences (FD) and finite volumes (FV). For the case of Navier‐Stokes, we also extend our implementation towards non‐uniform grids, thereby enabling static mesh refinement, and advanced effects such as the simulated fluid being non‐Newtonian and non‐isothermal

The OpenModelica integrated environment for modeling, simulation, and model-based development

OpenModelica is a unique large-scale integrated open-source Modelica- and FMI-based modeling, simulation, optimization, model-based analysis and development environment. Moreover, the OpenModelica environment provides a number of facilities such as debugging; optimization; visualization and 3D animation; web-based model editing and simulation; scripting from Modelica, Python, Julia, and Matlab; efficient simulation and co-simulation of FMI-based models; compilation for embedded systems; Modelica- UML integration; requirement verification; and generation of parallel code for multi-core architectures. The environment is based on the equation-based object-oriented Modelica language and currently uses the MetaModelica extended version of Modelica for its model compiler implementation. This overview paper gives an up-to-date description of the capabilities of the system, short overviews of used open source symbolic and numeric algorithms with pointers to published literature, tool integration aspects, some lessons learned, and the main vision behind its development.Fil: Fritzson, Peter. Linköping University; SueciaFil: Pop, Adrian. Linköping University; SueciaFil: Abdelhak, Karim. Fachhochschule Bielefeld; AlemaniaFil: Asghar, Adeel. Linköping University; SueciaFil: Bachmann, Bernhard. Fachhochschule Bielefeld; AlemaniaFil: Braun, Willi. Fachhochschule Bielefeld; AlemaniaFil: Bouskela, Daniel. Electricité de France; FranciaFil: Braun, Robert. Linköping University; SueciaFil: Buffoni, Lena. Linköping University; SueciaFil: Casella, Francesco. Politecnico di Milano; ItaliaFil: Castro, Rodrigo Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Investigación en Ciencias de la Computación. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Investigación en Ciencias de la Computación; ArgentinaFil: Franke, Rüdiger. Abb Group; AlemaniaFil: Fritzson, Dag. Linköping University; SueciaFil: Gebremedhin, Mahder. Linköping University; SueciaFil: Heuermann, Andreas. Linköping University; SueciaFil: Lie, Bernt. University of South-Eastern Norway; NoruegaFil: Mengist, Alachew. Linköping University; SueciaFil: Mikelsons, Lars. Linköping University; SueciaFil: Moudgalya, Kannan. Indian Institute Of Technology Bombay; IndiaFil: Ochel, Lennart. Linköping University; SueciaFil: Palanisamy, Arunkumar. Linköping University; SueciaFil: Ruge, Vitalij. Fachhochschule Bielefeld; AlemaniaFil: Schamai, Wladimir. Danfoss Power Solutions GmbH & Co; AlemaniaFil: Sjolund, Martin. Linköping University; SueciaFil: Thiele, Bernhard. Linköping University; SueciaFil: Tinnerholm, John. Linköping University; SueciaFil: Ostlund, Per. Linköping University; Sueci

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

GPU Usage for Parallel Functions and Contacts in Modelica

This thesis investigates two ways of incorporating GPUs in Modelica. The first by automatically generating GPU code for Modelica functions, and the second by using GPU accelerated external code for a contact handling package. Automatic parallelization of functions is desired, as it can potentially accelerate large simulations significantly. Special patterns of nested for-loops in Modelica code are recognized and translated into CUDA kernel functions. Inline integration allows a broader spectrum of models to take advantage of the parallelization, by reducing CPU-GPU transfers. The prototype has been tested and achieved a speed-up factor of up to five compared to the CPU. The contact handling package is capable of handling both complex contact behavior between arbitrarily shaped bodies and large DEM-like simulations, something which Modelica is currently lacking. Attempts to accelerate the package with GPUs were made, with partial success for the broad phase. The package uses Morton encoding for the broad phase, and the narrow phase is based on CSG intersection with BSP trees. Contact response is calculated using a volume dependent method, taking friction, damping and multiple contact points into account. The capability of the package was demonstrated by the fact that both complex contact behavior such as the inversion of the Tippe Top toy and tens of thousands of colliding spheres could be simulated.One of the key components in our modern society is the ability to simulate. By simulations, the industry can design new cars, phones, aircrafts etc., without having to go through prototype after prototype, allowing us the cheap and high-tech products most of us rely on in our day-to-day life. However, good as simulations are today there are still severe limitations on what can be simulated. Two of the largest limiting factors are how hard simulations are to design and how long they take to run. The first of these problems are tackled by the Modelica programming language, which is designed for easy set-up of simulations. We have attacked both these problems by using GPUs to speed-up Modelica simulations more than 5 times, and extending the capability of Modelica to handle collisions between objects

A high-performance open-source framework for multiphysics simulation and adjoint-based shape and topology optimization

The first part of this thesis presents the advances made in the Open-Source software SU2, towards transforming it into a high-performance framework for design and optimization of multiphysics problems. Through this work, and in collaboration with other authors, a tenfold performance improvement was achieved for some problems. More importantly, problems that had previously been impossible to solve in SU2, can now be used in numerical optimization with shape or topology variables. Furthermore, it is now exponentially simpler to study new multiphysics applications, and to develop new numerical schemes taking advantage of modern high-performance-computing systems. In the second part of this thesis, these capabilities allowed the application of topology optimiza- tion to medium scale fluid-structure interaction problems, using high-fidelity models (nonlinear elasticity and Reynolds-averaged Navier-Stokes equations), which had not been done before in the literature. This showed that topology optimization can be used to target aerodynamic objectives, by tailoring the interaction between fluid and structure. However, it also made ev- ident the limitations of density-based methods for this type of problem, in particular, reliably converging to discrete solutions. This was overcome with new strategies to both guarantee and accelerate (i.e. reduce the overall computational cost) the convergence to discrete solutions in fluid-structure interaction problems.Open Acces

PyCUDA and PyOpenCL: A Scripting-Based Approach to GPU Run-Time Code Generation

High-performance computing has recently seen a surge of interest in heterogeneous systems, with an emphasis on modern Graphics Processing Units (GPUs). These devices offer tremendous potential for performance and efficiency in important large-scale applications of computational science. However, exploiting this potential can be challenging, as one must adapt to the specialized and rapidly evolving computing environment currently exhibited by GPUs. One way of addressing this challenge is to embrace better techniques and develop tools tailored to their needs. This article presents one simple technique, GPU run-time code generation (RTCG), along with PyCUDA and PyOpenCL, two open-source toolkits that support this technique. In introducing PyCUDA and PyOpenCL, this article proposes the combination of a dynamic, high-level scripting language with the massive performance of a GPU as a compelling two-tiered computing platform, potentially offering significant performance and productivity advantages over conventional single-tier, static systems. The concept of RTCG is simple and easily implemented using existing, robust infrastructure. Nonetheless it is powerful enough to support (and encourage) the creation of custom application-specific tools by its users. The premise of the paper is illustrated by a wide range of examples where the technique has been applied with considerable success.Comment: Submitted to Parallel Computing, Elsevie

AUTOMATING DATA-LAYOUT DECISIONS IN DOMAIN-SPECIFIC LANGUAGES

A long-standing challenge in High-Performance Computing (HPC) is the simultaneous achievement of programmer productivity and hardware computational efficiency. The challenge has been exacerbated by the onset of multi- and many-core CPUs and accelerators. Only a few expert programmers have been able to hand-code domain-specific data transformations and vectorization schemes needed to extract the best possible performance on such architectures. In this research, we examined the possibility of automating these methods by developing a Domain-Specific Language (DSL) framework. Our DSL approach extends C++14 by embedding into it a high-level data-parallel array language, and by using a domain-specific compiler to compile to hybrid-parallel code. We also implemented an array index-space transformation algebra within this high-level array language to manipulate array data-layouts and data-distributions. The compiler introduces a novel method for SIMD auto-vectorization based on array data-layouts. Our new auto-vectorization technique is shown to outperform the default auto-vectorization strategy by up to 40% for stencil computations. The compiler also automates distributed data movement with overlapping of local compute with remote data movement using polyhedral integer set analysis. Along with these main innovations, we developed a new technique using C++ template metaprogramming for developing embedded DSLs using C++. We also proposed a domain-specific compiler intermediate representation that simplifies data flow analysis of abstract DSL constructs. We evaluated our framework by constructing a DSL for the HPC grand-challenge domain of lattice quantum chromodynamics. Our DSL yielded performance gains of up to twice the flop rate over existing production C code for selected kernels. This gain in performance was obtained while using less than one-tenth the lines of code. The performance of this DSL was also competitive with the best hand-optimized and hand-vectorized code, and is an order of magnitude better than existing production DSLs.Doctor of Philosoph