Engineering topics

Fox, Armando

Publications and source records attributed to Fox, Armando.

4 records

DOE OSTI2018

Indigo: A Domain-Specific Language for Fast, Portable Image Reconstruction

© 2018 IEEE. Linear operators used in iterative methods like conjugate gradient have typically been implemented either as ''matrix-driven'' subroutines backed by explicit sparse or dense matrices, or as ''matrix-free'' subroutines that implement specific linear operations directly (e.g. FFTs). The matrix-driven approach is generally more portable because it can target widely-Available BLAS libraries, but it can be inefficient in terms of time and space complexity. In contrast, the matrix-free approach is more performant because it leverages structure in operations, but it requires each operator be re-implemented on each new platform. To increase performance and portability, we propose a hybrid approach that represents linear operators as expression trees. Leaf nodes in the tree are either matrix-free or matrix-driven operators, and interior nodes represent mathematical compositions (sums, products, transposes) or structural compositions (stacks, block diagonals, etc.) of the leaf operators. This representation enables expert-guided reordering and fusion transformations that can improve performance or reduce memory pressure. We implement our approach in a domain-specific language called Indigo. We assess Indigo on image reconstruction problems arising in four application areas: magnetic resonance imaging, ptychography, magnetic particle imaging, and fluorescent microscopy. We give performance results from vendor BLAS libraries, and we introduce specializations to Sparse BLAS routines that achieve near-Roofline performance on multi-core, many-core, and GPU systems.

Driscoll, Michael↗

DOE OSTI2017

Snowflake: A Lightweight Portable Stencil DSL

Stencil computations are not well optimized by general-purpose production compilers and the increased use of multicore, manycore, and accelerator-based systems makes the optimization problem even more challenging. In this paper we present Snowflake, a Domain Specific Language (DSL) for stencils that uses a 'micro-compiler' approach, i.e., small, focused, domain-specific code generators. The approach is similar to that used in image processing stencils, but Snowflake handles the much more complex stencils that arise in scientific computing, including complex boundary conditions, higher-order operators (larger stencils), higher dimensions, variable coefficients, non-unit-stride iteration spaces, and multiple input or output meshes. Snowflake is embedded in the Python language, allowing it to interoperate with popular scientific tools like SciPy and iPython; it also takes advantage of built-in Python libraries for powerful dependence analysis as part of a just-in-time compiler. We demonstrate the power of the Snowflake language and the micro-compiler approach with a complex scientific benchmark, HPGMG, that exercises the generality of stencil support in Snowflake. By generating OpenMP comparable to, and OpenCL within a factor of 2x of hand-optimized HPGMG, Snowflake demonstrates that a micro-compiler can support diverse processor architectures and is performance-competitive whilst preserving a high-level Python implementation.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2014

Parallel processing of filtered queries in attributed semantic graphs

Execution of complex analytic queries on massive semantic graphs is a challenging problem in big-data analytics that requires high-performance parallel computing. In a semantic graph, vertices and edges carry attributes of various types and the analytic queries typically depend on the values of these attributes. Thus, the computation must view the graph through a filter that passes only those individual vertices and edges of interest. Previous investigations have developed Knowledge Discovery Toolbox (KDT), a sophisticated Python library for parallel graph computations. In KDT, the user can write custom graph algorithms by specifying operations between edges and vertices ( semiring operations ). The user can also customize existing graph algorithms by writing filters. While the high-level language for this customization enables domain scientists to productively express their graph analytics requirements, the customized queries perform poorly due to the overhead of having to call into the Python virtual machine for each vertex and edge. In this work, we use the Selective Embedded Just-In-Time Specialization (SEJITS) approach to automatically translate semiring operations and filters defined by programmers into a lower-level efficiency language, bypassing the upcall into Python. We evaluate our approach by comparing it with the high-performance Combinatorial BLAS engine and show that our approach combines the benefits of programming in a high-level language with executing in a low-level parallel environment. We increase the system's flexibility by developing techniques that provide users with the ability to define new vertex and edge types from Python. We also present a new Roofline model for graph traversals and show that we achieve performance that is significantly closer to the bounds suggested by the Roofline. Finally, to further understand the complex interaction with the underlying architecture, we present an analysis using performance counters that quantifies the improvement in hardware behavior in the context our SEJITS methodology. Comprehensively, we demonstrate the first known solution to the problem of obtaining high performance from a productivity language when applying graph algorithms selectively on semantic graphs with hundreds of millions of edges and scaling to thousands of processors for graphs.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2012

High-performance analysis of filtered semantic graphs

High performance is a crucial consideration when executing a complex analytic query on a massive semantic graph. In a semantic graph, vertices and edges carry "attributes" of various types. Analytic queries on semantic graphs typically depend on the values of these attributes; thus, the computation must either view the graph through a filter that passes only those individual vertices and edges of interest, or else must first materialize a subgraph or subgraphs consisting of only the vertices and edges of interest. The filtered approach is superior due to its generality, ease of use, and memory efficiency, but may carry a performance cost. In the Knowledge Discovery Toolbox (KDT), a Python library for parallel graph computations, the user writes filters in a high-level language, but those filters result in relatively low performance due to the bottleneck of having to call into the Python interpreter for each edge. In this work, we use the Selective Embedded JIT Specialization (SEJITS) approach to automatically translate filters defined by programmers into a lower-level efficiency language, bypassing the upcall into Python. We evaluate our approach by comparing it with the high-performance C++ /MPI Combinatorial BLAS engine, and show that the productivity gained by using a high-level filtering language comes without sacrificing performance.

97 MATHEMATICS AND COMPUTING↗