An official website of the United States government
Constructing k-nearest neighbor (kNN) graphs is a fundamental component in many machine learning and scientific computing applications. Despite its prevalence, efficiently building all-nearest-neighbor graphs at scale on distributed heterogeneous HPC systems remains challenging, especially for large sparse non-integer datasets. We introduce optimizations for algorithms based on forests of random projection trees. Our novel GPU kernels for batched, within leaf, exact searches achieve 1.18× speedup over sparse reference kernels with less peak memory, and up to 19× speedup over CPU for memory-intensive problems. Our library,PyRKNN, implements distributed randomized projection forests for approximate kNN search. Optimizations to reduce and hide communication overhead allow us to achieve 5× speedup, in per iteration performance, relative to GOFMM (another projection tree, MPI-based kNN library), for a 64M 128d dataset on 1,024 processes. On a single-node we achieve speedup over FAISS-GPU for dense datasets and up to 10× speedup over CPU-only libraries.PyRKNNuniquely supports distributed memory kNN graph construction for both dense and sparse coordinates on CPU and GPU accelerators.
more »
« less
ADAPT: An Event-Based Adaptive Collective Communication Framework
The increase in scale and heterogeneity of high-performance computing (HPC) systems predispose the performance of Message Passing Interface (MPI) collective communications to be susceptible to noise, and to adapt to a complex mix of hardware capabilities. The designs of state of the art MPI collectives heavily rely on synchronizations; these designs magnify noise across the participating processes, resulting in significant performance slowdown. Therefore, such design philosophy must be reconsidered to efficiently and robustly run on the large-scale heterogeneous platforms. In this paper, we present ADAPT, a new collective communication framework in Open MPI, using event-driven techniques to morph collective algorithms to heterogeneous environments. The core concept of ADAPT is to relax synchronizations, while mamtaining the minimal data dependencies of MPI collectives. To fully exploit the different bandwidths of data movement lanes in heterogeneous systems, we extend the ADAPT collective framework with a topology-aware communication tree. This removes the boundaries of different hardware topologies while maximizing the speed of data movements. We evaluate our framework with two popular collective operations: broadcast and reduce on both CPU and GPU clusters. Our results demonstrate drastic performance improvements and a strong resistance against noise compared to other state of the art MPI libraries. In particular, we demonstrate at least 1.3X and 1.5X speedup for CPU data and 2X and 10X speedup for GPU data using ADAPT event-based broadcast and reduce operations.
more »
« less
- Award ID(s):
- 1664142
- PAR ID:
- 10062120
- Date Published:
- Journal Name:
- The 27th International Symposium on High-Performance Parallel and Distributed Computing
- Page Range / eLocation ID:
- 118 to 130
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Geographic information systems deal with spatial data and its analysis. Spatial data contains many attributes with location information. Spatial autocorrelation is a fundamental concept in spatial analysis. It suggests that similar objects tend to cluster in geographic space. Hotspots, an example of autocorrelation, are statistically significant clusters of spatial data. Other autocorrelation measures like Moran’s I are used to quantify spatial dependence. Large scale spatial autocorrelation methods are compute- intensive. Fast methods for hotspots detection and analysis are crucial in recent times of COVID-19 pandemic. Therefore, we have developed parallelization methods on heterogeneous CPU and GPU environments. To the best of our knowledge, this is the first GPU and SIMD-based design and implementation of autocorrelation kernels. Earlier methods in literature introduced cluster-based and MapReduce-based parallelization. We have used Intrinsics to exploit SIMD parallelism on x86 CPU architecture. We have used MPI Graph Topology to minimize inter-process communication. Our benchmarks for CPU/GPU optimizations gain up to 750X relative speedup with a 8 GPU setup when compared to baseline sequential implementation. Compared to the best implementation using OpenMP + R-tree data structure on a single compute node, our accelerated hotspots benchmark gains a 25X speedup. For real world US counties and COVID data evolution calculated over 500 days, we gain up to 110X speedup reducing time from 33 minutes to 0.3 minutes.more » « less
-
SLATE (Software for Linear Algebra Targeting Exascale) is a distributed, dense linear algebra library targeting both CPU-only and GPU-accelerated systems, developed over the course of the Exascale Computing Project (ECP). While it began with several documents setting out its initial design, significant design changes occurred throughout its development. In some cases, these were anticipated: an early version used a simple consistency flag that was later replaced with a full-featured consistency protocol. In other cases, performance limitations and software and hardware changes prompted a redesign. Sequential communication tasks were parallelized; host-to-host MPI calls were replaced with GPU device-to-device MPI calls; more advanced algorithms such as Communication Avoiding LU and the Random Butterfly Transform (RBT) were introduced. Early choices that turned out to be cumbersome, error prone, or inflexible have been replaced with simpler, more intuitive, or more flexible designs. Applications have been a driving force, prompting a lighter weight queue class, nonuniform tile sizes, and more flexible MPI process grids. Of paramount importance has been building a portable library that works across several different GPU architectures – AMD, Intel, and NVIDIA – while keeping a clean and maintainable codebase. Here we explore the evolving design choices and their effects, both in terms of performance and software sustainability.more » « less
-
Accurate simulation of earthquake scenarios is essential for advancing seismic hazard analysis and risk mitigation strategies. At the San Diego Supercomputer Center (SDSC), our research focuses on optimizing the performance and reliability of large-scale earthquake simulations using the AWP-ODC software. By implementing GPU-aware MPI calls, we enable direct data processing within GPU memory, eliminating the need for explicit data transfers between CPU and GPU. This GPU-aware MPI achieves nearly ideal parallel efficiency at full scale across both Nvidia and AMD GPUs, leveraging the MVAPICH-PLUS support on Frontier at Oak Ridge National Laboratory and Vista at the Texas Advanced Computing Center. We utilized the MVAPICH-Plus 4.0 compiler to enable ZFP compression, which significantly enhances inter-node communication efficiency – a critical improvement given the communication bottleneck inherent in large-scale simulations. Our GPU-aware AWP-ODC versions include linear forward, topography and nonlinear Iwan-type solvers with discontinuous mesh support. On the Frontier system with MVAPICH 4.0, Hip-aware MPI calls on MI250X GPUs deliver nearly ideal weak-scaling speedup up to 8,192 nodes for both linear and topography versions. On TACC’s Vista system, CUDA-aware MPI calls on GH200 GPUs substantially outperform their non-GPU-aware counterparts across all three solver versions. This poster will present a detailed evaluation of GPU-aware AWP-ODC using MVAPICH, including the impact of ZFP message compression compared to the native versions. Our results highlight the importance of Mvapich support for GPU-ware MPI and on-the-fly compression techniques for accelerating and scaling earthquake simulations.more » « less
-
Multi-Agent Reinforcement Learning (MARL) is a key technology in artificial intelligence applications such as robotics, surveillance, energy systems, etc. Multi-Agent Deep Deterministic Policy Gradient (MADDPG) is a state-of-the-art MARL algorithm that has been widely adopted and considered a popular baseline for novel MARL algorithms. However, existing implementations of MADDPG on CPU and CPU-GPU platforms do not exploit fine-grained parallelism between cooperative agents and handle inter-agent communication sequentially, leading to sub-optimal throughput performance in MADDPG training. In this work, we develop the first high-throughput MADDPG accelerator on a CPU-FPGA heterogeneous platform. Specifically, we develop dedicated hardware modules that enable parallel training of each agent's internal Deep Neural Networks (DNNs) and support low-latency inter-agent communication using an on-chip agent interconnection network. Our experimental results show that the speed performance of agent neural network training improves by a factor of 3.6×−24.3× and 1.5×−29.5× compared with state-of-the-art CPU and CPU-GPU implementations. Our design achieves up to a 1.99× and 1.93× improvement in overall system throughput compared with CPU and CPU-GPU implementations, respectively.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Conference Paper:
- https://doi.org/10.1145/3208040.3208054
