Taking advantage of hybrid systems for sparse direct solvers via task-based runtimes

The ongoing hardware evolution exhibits an escalation in the number, as well as in the heterogeneity, of computing resources. The pressure to maintain reasonable levels of performance and portability forces application developers to leave the traditional programming paradigms and explore alternative solutions. PaStiX is a parallel sparse direct solver, based on a dynamic scheduler for modern hierarchical manycore architectures. In this paper, we study the benefits and limits of replacing the highly specialized internal scheduler of the PaStiX solver with two generic runtime systems: PaRSEC and StarPU. The tasks graph of the factorization step is made available to the two runtimes, providing them the opportunity to process and optimize its traversal in order to maximize the algorithm efficiency for the targeted hardware platform. A comparative study of the performance of the PaStiX solver on top of its native internal scheduler, PaRSEC, and StarPU frameworks, on different execution environments, is performed. The analysis highlights that these generic task-based runtimes achieve comparable results to the application-optimized embedded scheduler on homogeneous platforms. Furthermore, they are able to significantly speed up the solver on heterogeneous environments by taking advantage of the accelerators while hiding the complexity of their efficient manipulation from the programmer.Comment: Heterogeneity in Computing Workshop (2014

GHOST: Building blocks for high performance sparse linear algebra on heterogeneous systems

While many of the architectural details of future exascale-class high performance computer systems are still a matter of intense research, there appears to be a general consensus that they will be strongly heterogeneous, featuring "standard" as well as "accelerated" resources. Today, such resources are available as multicore processors, graphics processing units (GPUs), and other accelerators such as the Intel Xeon Phi. Any software infrastructure that claims usefulness for such environments must be able to meet their inherent challenges: massive multi-level parallelism, topology, asynchronicity, and abstraction. The "General, Hybrid, and Optimized Sparse Toolkit" (GHOST) is a collection of building blocks that targets algorithms dealing with sparse matrix representations on current and future large-scale systems. It implements the "MPI+X" paradigm, has a pure C interface, and provides hybrid-parallel numerical kernels, intelligent resource management, and truly heterogeneous parallelism for multicore CPUs, Nvidia GPUs, and the Intel Xeon Phi. We describe the details of its design with respect to the challenges posed by modern heterogeneous supercomputers and recent algorithmic developments. Implementation details which are indispensable for achieving high efficiency are pointed out and their necessity is justified by performance measurements or predictions based on performance models. The library code and several applications are available as open source. We also provide instructions on how to make use of GHOST in existing software packages, together with a case study which demonstrates the applicability and performance of GHOST as a component within a larger software stack.Comment: 32 pages, 11 figure

Hardware acceleration of reaction-diffusion systems:a guide to optimisation of pattern formation algorithms using OpenACC

Reaction Diffusion Systems (RDS) have widespread applications in computational ecology, biology, computer graphics and the visual arts. For the former applications a major barrier to the development of effective simulation models is their computational complexity - it takes a great deal of processing power to simulate enough replicates such that reliable conclusions can be drawn. Optimizing the computation is thus highly desirable in order to obtain more results with less resources. Existing optimizations of RDS tend to be low-level and GPGPU based. Here we apply the higher-level OpenACC framework to two case studies: a simple RDS to learn the ‘workings’ of OpenACC and a more realistic and complex example. Our results show that simple parallelization directives and minimal data transfer can produce a useful performance improvement. The relative simplicity of porting OpenACC code between heterogeneous hardware is a key benefit to the scientific computing community in terms of speed-up and portability

Domain-Specific Acceleration and Auto-Parallelization of Legacy Scientific Code in FORTRAN 77 using Source-to-Source Compilation

Massively parallel accelerators such as GPGPUs, manycores and FPGAs represent a powerful and affordable tool for scientists who look to speed up simulations of complex systems. However, porting code to such devices requires a detailed understanding of heterogeneous programming tools and effective strategies for parallelization. In this paper we present a source to source compilation approach with whole-program analysis to automatically transform single-threaded FORTRAN 77 legacy code into OpenCL-accelerated programs with parallelized kernels. The main contributions of our work are: (1) whole-source refactoring to allow any subroutine in the code to be offloaded to an accelerator. (2) Minimization of the data transfer between the host and the accelerator by eliminating redundant transfers. (3) Pragmatic auto-parallelization of the code to be offloaded to the accelerator by identification of parallelizable maps and reductions. We have validated the code transformation performance of the compiler on the NIST FORTRAN 78 test suite and several real-world codes: the Large Eddy Simulator for Urban Flows, a high-resolution turbulent flow model; the shallow water component of the ocean model Gmodel; the Linear Baroclinic Model, an atmospheric climate model and Flexpart-WRF, a particle dispersion simulator. The automatic parallelization component has been tested on as 2-D Shallow Water model (2DSW) and on the Large Eddy Simulator for Urban Flows (UFLES) and produces a complete OpenCL-enabled code base. The fully OpenCL-accelerated versions of the 2DSW and the UFLES are resp. 9x and 20x faster on GPU than the original code on CPU, in both cases this is the same performance as manually ported code.Comment: 12 pages, 5 figures, submitted to "Computers and Fluids" as full paper from ParCFD conference entr