Enhancing R with Advanced Compilation Tools and Methods

I describe an approach to compiling common idioms in R code directly to native machine code and illustrate it with several examples. Not only can this yield significant performance gains, but it allows us to use new approaches to computing in R. Importantly, the compilation requires no changes to R itself, but is done entirely via R packages. This allows others to experiment with different compilation strategies and even to define new domain-specific languages within R. We use the Low-Level Virtual Machine (LLVM) compiler toolkit to create the native code and perform sophisticated optimizations on the code. By adopting this widely used software within R, we leverage its ability to generate code for different platforms such as CPUs and GPUs, and will continue to benefit from its ongoing development. This approach potentially allows us to develop high-level R code that is also fast, that can be compiled to work with different data representations and sources, and that could even be run outside of R. The approach aims to both provide a compiler for a limited subset of the R language and also to enable R programmers to write other compilers. This is another approach to help us write high-level descriptions of what we want to compute, not how.Comment: Published in at http://dx.doi.org/10.1214/13-STS462 the Statistical Science (http://www.imstat.org/sts/) by the Institute of Mathematical Statistics (http://www.imstat.org

Programming agent-based demographic models with cross-state and message-exchange dependencies: A study with speculative PDES and automatic load-sharing

Agent-based modeling and simulation is a versatile and promising methodology to capture complex interactions among entities and their surrounding environment. A great advantage is its ability to model phenomena at a macro scale by exploiting simpler descriptions at a micro level. It has been proven effective in many fields, and it is rapidly becoming a de-facto standard in the study of population dynamics. In this article we study programmability and performance aspects of the last-generation ROOT-Sim speculative PDES environment for multi/many-core shared-memory architectures. ROOT-Sim transparently offers a programming model where interactions can be based on both explicit message passing and in-place state accesses. We introduce programming guidelines for systematic exploitation of these facilities in agent-based simulations, and we study the effects on performance of an innovative load-sharing policy targeting these types of dependencies. An experimental assessment with synthetic and real-world applications is provided, to assess the validity of our proposal

Peachy Parallel Assignments (EduHPC 2018)

Peachy Parallel Assignments are a resource for instructors teaching parallel and distributed programming. These are high-quality assignments, previously tested in class, that are readily adoptable. This collection of assignments includes implementing a subset of OpenMP using pthreads, creating an animated fractal, image processing using histogram equalization, simulating a storm of high-energy particles, and solving the wave equation in a variety of settings. All of these come with sample assignment sheets and the necessary starter code.Departamento de Informática (Arquitectura y Tecnología de Computadores, Ciencias de la Computación e Inteligencia Artificial, Lenguajes y Sistemas Informáticos)Facilitar la inclusión de ejercicios prácticos de programación paralela en cursos de Computación Paralela o de alto rendimiento (HPC)Comunicación en congreso: Descripción de ejercicios prácticos con acceso a material ya desarrollado y probado

Data Structures and Algorithms for Scalable NDN Forwarding

Named Data Networking (NDN) is a recently proposed general-purpose network architecture that aims to address the limitations of the Internet Protocol (IP), while maintaining its strengths. NDN takes an information-centric approach, focusing on named data rather than computer addresses. In NDN, the content is identified by its name, and each NDN packet has a name that specifies the content it is fetching or delivering. Since there are no source and destination addresses in an NDN packet, it is forwarded based on a lookup of its name in the forwarding plane, which consists of the Forwarding Information Base (FIB), Pending Interest Table (PIT), and Content Store (CS). In addition, as an in-network caching element, a scalable Repository (Repo) design is needed to provide large-scale long-term content storage in NDN networks. Scalable NDN forwarding is a challenge. Compared to the well-understood approaches to IP forwarding, NDN forwarding performs lookups on packet names, which have variable and unbounded lengths, increasing the lookup complexity. The lookup tables are larger than in IP, requiring more memory space. Moreover, NDN forwarding has a read-write data plane, requiring per-packet updates at line rates. Designing and evaluating a scalable NDN forwarding node architecture is a major effort within the overall NDN research agenda. The goal of this dissertation is to demonstrate that scalable NDN forwarding is feasible with the proposed data structures and algorithms. First, we propose a FIB lookup design based on the binary search of hash tables that provides a reliable longest name prefix lookup performance baseline for future NDN research. We have demonstrated 10 Gbps forwarding throughput with 256-byte packets and one billion synthetic forwarding rules, each containing up to seven name components. Second, we explore data structures and algorithms to optimize the FIB design based on the specific characteristics of real-world forwarding datasets. Third, we propose a fingerprint-only PIT design that reduces the memory requirements in the core routers. Lastly, we discuss the Content Store design issues and demonstrate that the NDN Repo implementation can leverage many of the existing databases and storage systems to improve performance

Approaching simulation to modelers: a user interface for large-scale demographic simulation

Extended version / Versió extesaAgent-based modeling is one of the promising modeling tools that can be used in the study of population dynamics. Two of the main obstacles hindering the use of agent-based simulation in practice are its scalability when the analysis requires large-scale models such as policy studies, and its ease-of-use especially for users with no programming experience. While there has been a significant work on the scalability issue, ease-of-use aspect has not been addressed in the same intensity. This paper presents a graphical user interface designed for a simulation tool which allows modelers with no programming background to specify agent-based demographic models and run them on parallel environments. The interface eases the definition of models to describe individual and group dynamics processes with both qualitative and quantitative data. The main advantage is to allow users to transparently run the models on high performance computing infrastructures.Postprint (author's final draft

IR2Vec: LLVM IR based Scalable Program Embeddings

We propose IR2Vec, a Concise and Scalable encoding infrastructure to represent programs as a distributed embedding in continuous space. This distributed embedding is obtained by combining representation learning methods with flow information to capture the syntax as well as the semantics of the input programs. As our infrastructure is based on the Intermediate Representation (IR) of the source code, obtained embeddings are both language and machine independent. The entities of the IR are modeled as relationships, and their representations are learned to form a seed embedding vocabulary. Using this infrastructure, we propose two incremental encodings:Symbolic and Flow-Aware. Symbolic encodings are obtained from the seed embedding vocabulary, and Flow-Aware encodings are obtained by augmenting the Symbolic encodings with the flow information. We show the effectiveness of our methodology on two optimization tasks (Heterogeneous device mapping and Thread coarsening). Our way of representing the programs enables us to use non-sequential models resulting in orders of magnitude of faster training time. Both the encodings generated by IR2Vec outperform the existing methods in both the tasks, even while using simple machine learning models. In particular, our results improve or match the state-of-the-art speedup in 11/14 benchmark-suites in the device mapping task across two platforms and 53/68 benchmarks in the Thread coarsening task across four different platforms. When compared to the other methods, our embeddings are more scalable, is non-data-hungry, and has betterOut-Of-Vocabulary (OOV) characteristics.Comment: Accepted in ACM TAC