Creating a highly parallel and flexible discrete element software requires an interdisciplinary approach, where expertise from different disciplines is combined. On the one hand domain specialists provide interaction models between particles. On the other hand high-performance computing specialists optimize the code to achieve good performance on different hardware architectures. In particular, the software must be carefully crafted to achieve good scaling on massively parallel supercomputers. Combining all this in a flexible and extensible, widely usable software is a challenging task. In this article we outline the design decisions and concepts of a newly developed particle dynamics code MESA-PD that is implemented as part of the waLBerla multi-physics framework. Extensibility, flexibility, but also performance and scalability are primary design goals for the new software framework. In particular, the new modular architecture is designed such that physical models can be modified and extended by domain scientists without understanding all details of the parallel computing functionality and the underlying distributed data structures that are needed to achieve good performance on current supercomputer architectures. This goal is achieved by combining the high performance simulation framework waLBerla with code generation techniques. All code and the code generator are released as open source under GPLv3 within the publicly available waLBerla framework (this http URL).
Another approach to let the user extend the software framework is shown by some molecular dynamics packages. They use high level languages like Python or their own embedded domain specific language (DSL) to describe the simulation. In order to achieve good performance on various hardware architectures they use just-in-time compilation to generate user specific executables for various architectures. However, to support MPI or CUDA additional wrapper libraries like pyMPI and PyCUDA are needed. Many packages using this technique claim that this can be done with almost no loss in performance compared to native C++ code. Packages that provide such capabilities with a varying degree of just-in-time compilation are for example @cite_12 , @cite_13 , @cite_6 and @cite_4 .
@cite_4 @cite_13 @cite_6 @cite_12
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Developers of Molecular Dynamics (MD) codes face significant challenges when adapting existing simulation packages to new hardware. In a continuously diversifying hardware landscape it becomes increasingly difficult for scientists to be experts both in their own domain (physics chemistry biology) and specialists in the low level parallelisation and optimisation of their codes. To address this challenge, we describe a “Separation of Concerns” approach for the development of parallel and optimised MD codes: the science specialist writes code at a high abstraction level in a domain specific language (DSL), which is then translated into efficient computer code by a scientific programmer. In a related context, an abstraction for the solution of partial differential equations with grid based methods has recently been implemented in the (Py)OP2 library. Inspired by this approach, we develop a Python code generation system for molecular dynamics simulations on different parallel architectures, including massively parallel distributed memory systems and GPUs. We demonstrate the efficiency of the auto-generated code by studying its performance and scalability on different hardware and compare it to other state-of-the-art simulation packages. With growing data volumes the extraction of physically meaningful information from the simulation becomes increasingly challenging and requires equally efficient implementations. A particular advantage of our approach is the easy expression of such analysis algorithms. We consider two popular methods for deducing the crystalline structure of a material from the local environment of each atom, show how they can be expressed in our abstraction and implement them in the code generation framework. Dynamic, interpreted languages, like Python, are attractive for domain-experts and scientists experimenting with new ideas. However, the performance of the interpreter is often a barrier when scaling to larger data sets. This paper presents a just-in-time compiler for Python that focuses in scientific and array-oriented computing. Starting with the simple syntax of Python, Numba compiles a subset of the language into efficient machine code that is comparable in performance to a traditional compiled language. In addition, we share our experience in building a JIT compiler using LLVM[1]. Emerging many-core platforms are very difficult to program in a performance portable manner whilst achieving high efficiency on a diverse range of architectures. We present work in progress on PyOP2, a high-level embedded domain-specific language for mesh-based simulation codes that executes numerical kernels in parallel over unstructured meshes. Just-in-time kernel compilation and parallel scheduling are delayed until runtime, when problem-specific parameters are available. Using generative metaprogramming, performance portability is achieved, while details of the parallel implementation are abstracted from the programmer. PyOP2 kernels for finite element computations can be generated automatically from equations given in the domain-specific Unified Form Language. Interfacing to the multi-phase CFD code Fluidity through a very thin layer on top of PyOP2 yields a general purpose finite element solver with an input notation very close to mathematical formulae. Preliminary performance figures show speedups of up to 3.4× compared to Fluidity's built-in solvers when running in parallel. Producing high-performance implementations from simple, portable computation specifications is a challenge that compilers have tried to address for several decades. More recently, a relatively stable architectural landscape has evolved into a set of increasingly diverging and rapidly changing CPU and accelerator designs, with the main common factor being dramatic increases in the levels of parallelism available. The growth of architectural heterogeneity and parallelism, combined with the very slow development cycles of traditional compilers, has motivated the development of autotuning tools that can quickly respond to changes in architectures and programming models, and enable very specialized optimizations that are not possible or likely to be provided by mainstream compilers. In this paper we describe the new OpenCL code generator and autotuner OrCL and the introduction of detailed performance measurement into the autotuning process. OrCL is implemented within the Orio autotuning framework, which enables the rapid development of experimental languages and code optimization strategies aimed at achieving good performance on new platforms without rewriting or hand-optimizing critical kernels. The combination of the new OpenCL autotuning and TAU measurement capabilities enables users to consistently evaluate autotuning effectiveness across a range of architectures, including several NVIDIA and AMD accelerators and Intel Xeon Phi processors, and to compare the OpenCL and CUDA code generation capabilities. We present results of autotuning several numerical kernels that typically dominate the execution time of iterative sparse linear system solution and key computations from a 3-D parallel simulation of solid fuel ignition. Languages, compilers, and computer-aided design tools will be essential for scalable quantum computing, which promises an exponential leap in our ability to execute complex tasks. LIQUi|> is a modular software architecture designed to control quantum hardware. It enables easy programming, compilation, and simulation of quantum algorithms and circuits, and is independent of a specific quantum architecture. LIQUi|> contains an embedded, domain-specific language designed for programming quantum algorithms, with F# as the host language. It also allows the extraction of a circuit data structure that can be used for optimization, rendering, or translation. The circuit can also be exported to external hardware and software environments. Two different simulation environments are available to the user which allow a trade-off between number of qubits and class of operations. LIQUi|> has been implemented on a wide range of runtimes as back-ends with a single user front-end. We describe the significant components of the design architecture and how to express any given quantum algorithm. Theano is a compiler for mathematical expressions in Python that combines the convenience of NumPy's syntax with the speed of optimized native machine language. The user composes mathematical expressions in a high-level description that mimics NumPy's syntax and semantics, while being statically typed and functional (as opposed to imperative). These expressions allow Theano to provide symbolic differentiation. Before performing computation, Theano optimizes the choice of expressions, translates them into C++ (or CUDA for GPU), compiles them into dynamically loaded Python modules, all automatically. Common machine learn- ing algorithms implemented with Theano are from 1:6 to 7:5 faster than competitive alternatives (including those implemented with C C++, NumPy SciPy and MATLAB) when compiled for the CPU and between 6:5 and 44 faster when compiled for the GPU. This paper illustrates how to use Theano, outlines the scope of the compiler, provides benchmarks on both CPU and GPU processors, and explains its overall design. Just-in-time (JIT) compilation of running programs provides more optimization opportunities than offline compilation. Modern JIT compilers, such as those in virtual machines like Oracle's HotSpot for Java or Google's V8 for JavaScript, rely on dynamic profiling as their key mechanism to guide optimizations. While these JIT compilers offer good average performance, their behavior is a black box and the achieved performance is highly unpredictable. In this paper, we propose to turn JIT compilation into a precision tool by adding two essential and generic metaprogramming facilities: First, allow programs to invoke JIT compilation explicitly. This enables controlled specialization of arbitrary code at run-time, in the style of partial evaluation. It also enables the JIT compiler to report warnings and errors to the program when it is unable to compile a code path in the demanded way. Second, allow the JIT compiler to call back into the program to perform compile-time computation. This lets the program itself define the translation strategy for certain constructs on the fly and gives rise to a powerful JIT macro facility that enables "smart" libraries to supply domain-specific compiler optimizations or safety checks. We present Lancet, a JIT compiler framework for Java bytecode that enables such a tight, two-way integration with the running program. Lancet itself was derived from a high-level Java bytecode interpreter: staging the interpreter using LMS (Lightweight Modular Staging) produced a simple bytecode compiler. Adding abstract interpretation turned the simple compiler into an optimizing compiler. This fact provides compelling evidence for the scalability of the staged-interpreter approach to compiler construction. In the case of Lancet, JIT macros also provide a natural interface to existing LMS-based toolchains such as the Delite parallelism and DSL framework, which can now serve as accelerator macros for arbitrary JVM bytecode. The Java Virtual Machine (JVM) has become an execution platform targeted by many programming languages. However, unlike with Java, a statically-typed language, the performance of the JVM and its Just-In-Time (JIT) compiler with dynamically-typed languages lags behind purpose-built language-specific JIT compilers. In this paper, we aim to contribute to the understanding of the workloads imposed on the JVM by dynamic languages. We use various metrics to characterize the dynamic behavior of a variety of programs written in three dynamic languages (Clojure, Python, and Ruby) executing on the JVM. We identify the differences with respect to Java, and briefly discuss their implications. C has been used as a portable target language for implementing languages like Standard ML and Scheme. Previous efforts at compiling these languages to C have produced efficient code, but have compromised on portability and proper tail recursion. We show how to compile Standard ML to C wihout making such compromises. The compilation technique is based on converting Standard ML to a continuation-passing style λ-calculus intermediate language and then compiling this language to C. The code generated by this compiler achieves an execution speed that is about a factor of two slower than that generated by a native code compiler. The compiler generates highly portable code, yet still supports advanced features like garbage collection and first-class continuations. We analyze the performance and determine the aspects of the compilation method that lead to the observed slowdown. We also suggest changes to C compilers that would better support such compilation methods. Hypervisors use software switches to steer packets to and from virtual machines (VMs). These switches frequently need upgrading and customization—to support new protocol headers or encapsulations for tunneling and overlays, to improve measurement and debugging features, and even to add middlebox-like functions. Software switches are typically based on a large body of code, including kernel code, and changing the switch is a formidable undertaking requiring domain mastery of network protocol design and developing, testing, and maintaining a large, complex codebase. Changing how a software switch forwards packets should not require intimate knowledge of its implementation. Instead, it should be possible to specify how packets are processed and forwarded in a high-level domain-specific language (DSL) such as P4, and compiled to run on a software switch. We present PISCES, a software switch derived from Open vSwitch (OVS), a hard-wired hypervisor switch, whose behavior is customized using P4. PISCES is not hard-wired to specific protocols; this independence makes it easy to add new features. We also show how the compiler can analyze the high-level specification to optimize forwarding performance. Our evaluation shows that PISCES performs comparably to OVS and that PISCES programs are about 40 times shorter than equivalent changes to OVS source code. Performance is of utmost importance for linear algebra libraries since they usually are the core of numerical and simulation packages and use most of the available compute time and resources. However, especially in large scale simulation frameworks the readability and ease of use of mathematical expressions is essential for a continuous maintenance, modification, and extension of the software framework. Based on these requirements, in the last decade C++ Expression Templates have gained a reputation as a suitable means to combine an elegant, domain-specific, and intuitive user interface with “HPC-grade” performance. Unfortunately, many of the available ET-based frameworks fall short of the expectation to deliver high performance, adding to the general mistrust towards C++ math libraries. In this paper we present performance results for Smart Expression Template libraries, demonstrating that by proper combination of high-level C++ code and low-level compute kernels both requirements, an elegant interface and high performance, can be achieved. Compile-time optimization is often limited by a lack of target machine and input data set knowledge. Without this information, compilers may be forced to make conservative assumptions to preserve correctness and to avoid performance degradation. In order to cope with this lack of information at compile-time, adaptive and dynamic systems can be used to perform optimization at runtime when complete knowledge of input and machine parameters is available. This paper presents a compiler-supported high-level adaptive optimization system. Users describe, in a domain specific language, optimizations performed by stand-alone optimization tools and backend compiler flags, as well as heuristics for applying these optimizations dynamically at runtime. The ADAPT compiler reads these descriptions and generates application-specific runtime systems to apply the heuristics. To facilitate the usage of existing tools and compilers, overheads are minimized by decoupling optimization from execution. Our system, ADAPT, supports a range of paradigms proposed recently, including dynamic compilation, parameterization and runtime sampling. We demonstrate our system by applying several optimization techniques to a suite of benchmarks on two target machines. ADAPT is shown to consistently outperform statically generated executables, improving performance by as much as 70 . This paper presents the design and implementation of PolyMage, a domain-specific language and compiler for image processing pipelines. An image processing pipeline can be viewed as a graph of interconnected stages which process images successively. Each stage typically performs one of point-wise, stencil, reduction or data-dependent operations on image pixels. Individual stages in a pipeline typically exhibit abundant data parallelism that can be exploited with relative ease. However, the stages also require high memory bandwidth preventing effective utilization of parallelism available on modern architectures. For applications that demand high performance, the traditional options are to use optimized libraries like OpenCV or to optimize manually. While using libraries precludes optimization across library routines, manual optimization accounting for both parallelism and locality is very tedious. The focus of our system, PolyMage, is on automatically generating high-performance implementations of image processing pipelines expressed in a high-level declarative language. Our optimization approach primarily relies on the transformation and code generation capabilities of the polyhedral compiler framework. To the best of our knowledge, this is the first model-driven compiler for image processing pipelines that performs complex fusion, tiling, and storage optimization automatically. Experimental results on a modern multicore system show that the performance achieved by our automatic approach is up to 1.81x better than that achieved through manual tuning in Halide, a state-of-the-art language and compiler for image processing pipelines. For a camera raw image processing pipeline, our performance is comparable to that of a hand-tuned implementation. In this paper we advocate that it is time for a radical rethinking of database systems design. Developers should be able to leverage high-level programming languages without having to pay a price in efficiency. To realize our vision of abstraction without regret, we present LegoBase, a query engine written in the high-level programming language Scala. The key technique to regain efficiency is to apply generative programming: the Scala code that constitutes the query engine, despite its high-level appearance, is actually a program generator that emits specialized, low-level C code. We show how the combination of high-level and generative programming allows to easily implement a wide spectrum of optimizations that are difficult to achieve with existing low-level query compilers, and how it can continuously optimize the query engine. We evaluate our approach with the TPC-H benchmark and show that: (a) with all optimizations enabled, our architecture significantly outperforms a commercial in-memory database system as well as an existing query compiler, (b) these performance improvements require programming just a few hundred lines of high-level code instead of complicated low-level code that is required by existing query compilers and, finally, that (c) the compilation overhead is low compared to the overall execution time, thus making our approach usable in practice for efficiently compiling query engines. The complexity of modern scientific simulations combined with the complexity of the high-performance computer hardware on which they run places an ever-increasing burden on scientific software developers, with clear impacts on both productivity and performance. We argue that raising the level of abstraction of the programming model environment is a key element of addressing this situation. We present examples of two distinctly different approaches to raising the level of abstraction of the programming model while maintaining or increasing performance: the Tensor Contraction engine, a narrowly-focused domain specific language together with an optimizing compiler; and Extended Global Arrays, a programming framework that integrates programming models dealing with different layers of the memory storage hierarchy using compiler analysis and code transformation techniques. Scholars are increasingly citing electronic “web references” which are not preserved in libraries or full text archives. WebCite is a new standard for citing web references. To “webcite” a document involves archiving the cited Web page through www.webcitation.org and citing the WebCite permalink instead of (or in addition to) the unstable live Web page. This journal has amended its “instructions for authors” accordingly, asking authors to archive cited Web pages before submitting a manuscript. Almost 200 other journals are already using the system. We discuss the rationale for WebCite, its technology, and how scholars, editors, and publishers can benefit from the service. Citing scholars initiate an archiving process of all cited Web references, ideally before they submit a manuscript. Authors of online documents and websites which are expected to be cited by others can ensure that their work is permanently available by creating an archived copy using WebCite and providing the citation information including the WebCite link on their Web document(s). Editors should ask their authors to cache all cited Web addresses (Uniform Resource Locators, or URLs) “prospectively” before submitting their manuscripts to their journal. Editors and publishers should also instruct their copyeditors to cache cited Web material if the author has not done so already. Finally, WebCite can process publisher submitted “citing articles” (submitted for example as eXtensible Markup Language [XML] documents) to automatically archive all cited Web pages shortly before or on publication. Finally, WebCite can act as a focussed crawler, caching retrospectively references of already published articles. Copyright issues are addressed by honouring respective Internet standards (robot exclusion files, no-cache and no-archive tags). Long-term preservation is ensured by agreements with libraries and digital preservation organizations. The resulting WebCite Index may also have applications for research assessment exercises, being able to measure the impact of Web services and published Web documents through access and Web citation metrics. @PARASPLIT [J Med Internet Res 2005;7(5):e60] In this paper, we compose six di erent Python and Prolog VMs into 4 pairwise compositions: one using C interpreters; one running on the JVM; one using meta-tracing interpreters; and one using a C interpreter and a meta-tracing interpreter. We show that programs that cross the language barrier frequently execute faster in a meta-tracing composition, and that meta-tracing imposes a significantly lower overhead on composed programs relative to mono-language programs. 1. Overview Programming language composition aims to allow the mixing of programming languages in a fine-grained manner. This vision brings many challenging problems, from the interaction of language semantics to performance. In this paper, we investigate the runtime performance of composed programs in high-level languages. We start from the assumption that execution of such programs is most likely to be through composing language implementations that use interpreters and VMs, rather than traditional compilers. This raises the question: how do di erent styles of composition a ect performance? Clearly, such a question cannot have a single answer but, to the best of our knowledge, this issue has not been explored in the past. This paper's hypothesis is that meta-tracing - a relatively new technique used to produce JIT (Just-In-Time) compilers from interpreters (1) - will lead to faster interpreter composition than traditional approaches. To test this hypothesis, we present a Python and Prolog composition which allows Python programs to embed and call Prolog programs. We then implement the composition in four di erent ways, comparing the absolute times and the relative cross-language costs of each. In addition to the 'traditional' approaches to composing interpreters (in C and upon the JVM), we also investigate the application of meta-tracing to interpreter composition. The experiments we then carry out confirm our initial hypothesis. There is a long tradition of composing Prolog with other languages (with e.g. Icon (2), Lisp (3), and Smalltalk (4)) because one can express certain types of programs far easier in Prolog than in other languages. We have two additional reasons for choosing this pairing. First, these languages represent very di erent points in the language design space: Prolog's inherently Industry is increasingly turning to reconfigurable architectures like FPGAs and CGRAs for improved performance and energy efficiency. Unfortunately, adoption of these architectures has been limited by their programming models. HDLs lack abstractions for productivity and are difficult to target from higher level languages. HLS tools are more productive, but offer an ad-hoc mix of software and hardware abstractions which make performance optimizations difficult. In this work, we describe a new domain-specific language and compiler called Spatial for higher level descriptions of application accelerators. We describe Spatial's hardware-centric abstractions for both programmer productivity and design performance, and summarize the compiler passes required to support these abstractions, including pipeline scheduling, automatic memory banking, and automated design tuning driven by active machine learning. We demonstrate the language's ability to target FPGAs and CGRAs from common source code. We show that applications written in Spatial are, on average, 42 shorter and achieve a mean speedup of 2.9x over SDAccel HLS when targeting a Xilinx UltraScale+ VU9P FPGA on an Amazon EC2 F1 instance. In this paper, we introduce PFPSim, a host-compiled simulator for early validation and analysis of packet processing applications on programmable forwarding plane architectures. The simulation model is automatically generated from a high-level description of the hardware software architecture of the forwarding device and the behavioral description of the various modules in the architecture. Our high-level architectural description language is capable of defining many-core network processors as well as reconfigurable pipelines. The behavior of the fixed-function processing elements in the architecture is defined in C++. The code targeted for the processor cores, or reconfigurable pipeline stages, is compiled from P4, an emerging programming language for packet processing applications. Application developers can use PFPSim as a virtual prototype to simulate and debug their applications before hardware availability. Moreover, forwarding device architects can use PFPSim to evaluate the trade-offs between different hardware software design decisions. This paper introduces an annotation language and a compiler that together can customize a library implementation for specific application needs. Our approach is distinguished by its ability to exploit high level, domain-specific information in the customization process. In particular, the annotations provide semantic information that enables our compiler to analyze and optimize library operations as if they were primitives of a domain-specific language. Thus, our approach yields many of the performance benefits of domain-specific languages, without the effort of developing a new compiler for each domain. This paper presents the annotation language, describes its role in optimization, and illustrates the benefits of the overall approach. Using a partially implemented compiler, we show how our system can significantly improve the performance of two applications written using the PLAPACK parallel linear algebra library.