arXiv subjects

Gheorghe-Teodor Bercea

Publications and source records attributed to Gheorghe-Teodor Bercea.

9 recordsLinked to original sources

arXiv2024

Porting HPC Applications to AMD Instinct$^\text{TM}$ MI300A Using Unified Memory and OpenMP

AMD Instinct$^\text{TM}$ MI300A is the world's first data center accelerated processing unit (APU) with memory shared between the AMD "Zen 4" EPYC$^\text{TM}$ cores and third generation CDNA$^\text{TM}$ compute units. A single memory space offers several advantages: i) it eliminates the need for data replication and costly data transfers, ii) it substantially simplifies application development and allows an incremental acceleration of applications, iii) is easy to maintain, and iv) its potential can be well realized via the abstractions in the OpenMP 5.2 standard, where the host and the device data environments can be unified in a more performant way. In this article, we provide a blueprint of the APU programming model leveraging unified memory and highlight key distinctions compared to the conventional approach with discrete GPUs. OpenFOAM, an open-source C++ library for computational fluid dynamics, is presented as a case study to emphasize the flexibility and ease of offloading a full-scale production-ready application on MI300 APUs using directive-based OpenMP programming.

cs.DC↗

arXiv2023

"Sliced" Subwindow Search: a Sublinear-complexity Solution to the Maximum Rectangle Problem

Considering a 2D matrix of positive and negative numbers, how might one draw a rectangle within it whose contents sum higher than all other rectangles'? This fundamental problem, commonly known the maximum rectangle problem or subwindow search, spans many computational domains. Yet, the problem has not been solved without demanding computational resources at least linearly proportional to the size of the matrix. In this work, we present a new approach to the problem which achieves sublinear time and memory complexities by interpolating between a small amount of equidistant sections of the matrix. Applied to natural images, our solution outperforms the state-of-the-art by achieving an 11x increase in speed and memory efficiency at 99% comparative accuracy. In general, our solution outperforms existing solutions when matrices are sufficiently large and a marginal decrease in accuracy is acceptable, such as in many problems involving natural images. As such, it is well-suited for real-time application and in a variety of computationally hard instances of the maximum rectangle problem.

cs.DS↗

arXiv2022

Reliable Actors with Retry Orchestration

Cloud developers have to build applications that are resilient to failures and interruptions. We advocate for a fault-tolerant programming model for the cloud based on actors, retry orchestration, and tail calls. This model builds upon persistent data stores and messages queues readily available on the cloud. Retry orchestration not only guarantees that (1) failed actor invocations will be retried but also that (2) completed invocations are never repeated and (3) it preserves a strict happen-before relationship across failures within call stacks. Tail calls can break complex tasks into simple steps to minimize re-execution during recovery. We review key application patterns and failure scenarios. We formalize a process calculus to precisely capture the mechanisms of fault tolerance in this model. We briefly describe our implementation. Using an application inspired by a typical enterprise scenario, we validate the functional correctness of our implementation and assess the impact of fault preparedness and recovery on performance.

cs.DC↗

arXiv2020

Compiling ONNX Neural Network Models Using MLIR

Deep neural network models are becoming increasingly popular and have been used in various tasks such as computer vision, speech recognition, and natural language processing. Machine learning models are commonly trained in a resource-rich environment and then deployed in a distinct environment such as high availability machines or edge devices. To assist the portability of models, the open-source community has proposed the Open Neural Network Exchange (ONNX) standard. In this paper, we present a high-level, preliminary report on our onnx-mlir compiler, which generates code for the inference of deep neural network models described in the ONNX format. Onnx-mlir is an open-source compiler implemented using the Multi-Level Intermediate Representation (MLIR) infrastructure recently integrated in the LLVM project. Onnx-mlir relies on the MLIR concept of dialects to implement its functionality. We propose here two new dialects: (1) an ONNX specific dialect that encodes the ONNX standard semantics, and (2) a loop-based dialect to provide for a common lowering point for all ONNX dialect operations. Each intermediate representation facilitates its own characteristic set of graph-level and loop-based optimizations respectively. We illustrate our approach by following several models through the proposed representations and we include some early optimization work and performance results.

cs.PL↗

arXiv2017

Implementing implicit OpenMP data sharing on GPUs

OpenMP is a shared memory programming model which supports the offloading of target regions to accelerators such as NVIDIA GPUs. The implementation in Clang/LLVM aims to deliver a generic GPU compilation toolchain that supports both the native CUDA C/C++ and the OpenMP device offloading models. There are situations where the semantics of OpenMP and those of CUDA diverge. One such example is the policy for implicitly handling local variables. In CUDA, local variables are implicitly mapped to thread local memory and thus become private to a CUDA thread. In OpenMP, due to semantics that allow the nesting of regions executed by different numbers of threads, variables need to be implicitly \emph{shared} among the threads of a contention group. In this paper we introduce a re-design of the OpenMP device data sharing infrastructure that is responsible for the implicit sharing of local variables in the Clang/LLVM toolchain. We introduce a new data sharing infrastructure that lowers implicitly shared variables to the shared memory of the GPU. We measure the amount of shared memory used by our scheme in cases that involve scalar variables and statically allocated arrays. The evaluation is carried out by offloading to K40 and P100 NVIDIA GPUs. For scalar variables the pressure on shared memory is relatively low, under 26\% of shared memory utilization for the K40, and does not negatively impact occupancy. The limiting occupancy factor in that case is register pressure. The data sharing scheme offers the users a simple memory model for controlling the implicit allocation of device shared memory.

cs.PL↗

arXiv2016

A structure-exploiting numbering algorithm for finite elements on extruded meshes, and its performance evaluation in Firedrake

We present a generic algorithm for numbering and then efficiently iterating over the data values attached to an extruded mesh. An extruded mesh is formed by replicating an existing mesh, assumed to be unstructured, to form layers of prismatic cells. Applications of extruded meshes include, but are not limited to, the representation of 3D high aspect ratio domains employed by geophysical finite element simulations. These meshes are structured in the extruded direction. The algorithm presented here exploits this structure to avoid the performance penalty traditionally associated with unstructured meshes. We evaluate the implementation of this algorithm in the Firedrake finite element system on a range of low compute intensity operations which constitute worst cases for data layout performance exploration. The experiments show that having structure along the extruded direction enables the cost of the indirect data accesses to be amortized after 10-20 layers as long as the underlying mesh is well-ordered. We characterise the resulting spatial and temporal reuse in a representative set of both continuous-Galerkin and discontinuous-Galerkin discretisations. On meshes with realistic numbers of layers the performance achieved is between 70% and 90% of a theoretical hardware-specific limit.

cs.MS↗

arXiv2016

Firedrake: automating the finite element method by composing abstractions

Firedrake is a new tool for automating the numerical solution of partial differential equations. Firedrake adopts the domain-specific language for the finite element method of the FEniCS project, but with a pure Python runtime-only implementation centred on the composition of several existing and new abstractions for particular aspects of scientific computing. The result is a more complete separation of concerns which eases the incorporation of separate contributions from computer scientists, numerical analysts and application specialists. These contributions may add functionality, or improve performance. Firedrake benefits from automatically applying new optimisations. This includes factorising mixed function spaces, transforming and vectorising inner loops, and intrinsically supporting block matrix operations. Importantly, Firedrake presents a simple public API for escaping the UFL abstraction. This allows users to implement common operations that fall outside pure variational formulations, such as flux-limiters.

cs.MS↗

arXiv2016

Automated generation and symbolic manipulation of tensor product finite elements

We describe and implement a symbolic algebra for scalar and vector-valued finite elements, enabling the computer generation of elements with tensor product structure on quadrilateral, hexahedral and triangular prismatic cells. The algebra is implemented as an extension to the domain-specific language UFL, the Unified Form Language. This allows users to construct many finite element spaces beyond those supported by existing software packages. We have made corresponding extensions to FIAT, the FInite element Automatic Tabulator, to enable numerical tabulation of such spaces. This tabulation is consequently used during the automatic generation of low-level code that carries out local assembly operations, within the wider context of solving finite element problems posed over such function spaces. We have done this work within the code-generation pipeline of the software package Firedrake; we make use of the full Firedrake package to present numerical examples.

math.NA↗

arXiv2014

COFFEE: an Optimizing Compiler for Finite Element Local Assembly

The numerical solution of partial differential equations using the finite element method is one of the key applications of high performance computing. Local assembly is its characteristic operation. This entails the execution of a problem-specific kernel to numerically evaluate an integral for each element in the discretized problem domain. Since the domain size can be huge, executing efficient kernels is fundamental. Their op- timization is, however, a challenging issue. Even though affine loop nests are generally present, the short trip counts and the complexity of mathematical expressions make it hard to determine a single or unique sequence of successful transformations. Therefore, we present the design and systematic evaluation of COF- FEE, a domain-specific compiler for local assembly kernels. COFFEE manipulates abstract syntax trees generated from a high-level domain-specific language for PDEs by introducing domain-aware composable optimizations aimed at improving instruction-level parallelism, especially SIMD vectorization, and register locality. It then generates C code including vector intrinsics. Experiments using a range of finite-element forms of increasing complexity show that significant performance improvement is achieved.

cs.MS↗