arXiv subjects

Brandon Cook

Publications and source records attributed to Brandon Cook.

6 recordsLinked to original sources

arXiv2023

ARcode: HPC Application Recognition Through Image-encoded Monitoring Data

Knowing HPC applications of jobs and analyzing their performance behavior play important roles in system management and optimizations. The existing approaches detect and identify HPC applications through machine learning models. However, these approaches rely heavily on the manually extracted features from resource utilization data to achieve high prediction accuracy. In this study, we propose an innovative application recognition method, ARcode, which encodes job monitoring data into images and leverages the automatic feature learning capability of convolutional neural networks to detect and identify applications. Our extensive evaluations based on the dataset collected from a large-scale production HPC system show that ARcode outperforms the state-of-the-art methodology by up to 18.87% in terms of accuracy at high confidence thresholds. For some specific applications (BerkeleyGW and e3sm), ARcode outperforms by over 20% at a confidence threshold of 0.8.

cs.DC↗

arXiv2023

Analyzing Resource Utilization in an HPC System: A Case Study of NERSC Perlmutter

Resource demands of HPC applications vary significantly. However, it is common for HPC systems to primarily assign resources on a per-node basis to prevent interference from co-located workloads. This gap between the coarse-grained resource allocation and the varying resource demands can lead to HPC resources being not fully utilized. In this study, we analyze the resource usage and application behavior of NERSC's Perlmutter, a state-of-the-art open-science HPC system with both CPU-only and GPU-accelerated nodes. Our one-month usage analysis reveals that CPUs are commonly not fully utilized, especially for GPU-enabled jobs. Also, around 64% of both CPU and GPU-enabled jobs used 50% or less of the available host memory capacity. Additionally, about 50% of GPU-enabled jobs used up to 25% of the GPU memory, and the memory capacity was not fully utilized in some ways for all jobs. While our study comes early in Perlmutter's lifetime thus policies and application workload may change, it provides valuable insights on performance characterization, application behavior, and motivates systems with more fine-grain resource allocation.

cs.DC↗

arXiv2023

Efficient Intra-Rack Resource Disaggregation for HPC Using Co-Packaged DWDM Photonics

The diversity of workload requirements and increasing hardware heterogeneity in emerging high performance computing (HPC) systems motivate resource disaggregation. Resource disaggregation allows compute and memory resources to be allocated individually as required to each workload. However, it is unclear how to efficiently realize this capability and cost-effectively meet the stringent bandwidth and latency requirements of HPC applications. To that end, we describe how modern photonics can be co-designed with modern HPC racks to implement flexible intra-rack resource disaggregation and fully meet the bit error rate (BER) and high escape bandwidth of all chip types in modern HPC racks. Our photonic-based disaggregated rack provides an average application speedup of 11% (46% maximum) for 25 CPU and 61% for 24 GPU benchmarks compared to a similar system that instead uses modern electronic switches for disaggregation. Using observed resource usage from a production system, we estimate that an iso-performance intra-rack disaggregated HPC system using photonics would require 4x fewer memory modules and 2x fewer NICs than a non-disaggregated baseline.

cs.DC↗

arXiv2021

Accelerating quantum many-body configuration interaction with directives

Many-Fermion Dynamics-nuclear, or MFDn, is a configuration interaction (CI) code for nuclear structure calculations. It is a platform-independent Fortran 90 code using a hybrid MPI+X programming model. For CPU platforms the application has a robust and optimized OpenMP implementation for shared memory parallelism. As part of the NESAP application readiness program for NERSC's latest Perlmutter system, MFDn has been updated to take advantage of accelerators. The current mainline GPU port is based on OpenACC. In this work we describe some of the key challenges of creating an efficient GPU implementation. Additionally, we compare the support of OpenMP and OpenACC on AMD and NVIDIA GPUs.

cs.DC↗

arXiv2021

Accelerating an Iterative Eigensolver for Nuclear Structure Configuration Interaction Calculations on GPUs using OpenACC

To accelerate the solution of large eigenvalue problems arising from many-body calculations in nuclear physics on distributed-memory parallel systems equipped with general-purpose Graphic Processing Units (GPUs), we modified a previously developed hybrid MPI/OpenMP implementation of an eigensolver written in FORTRAN 90 by using an OpenACC directives based programming model. Such an approach requires making minimal changes to the original code and enables a smooth migration of large-scale nuclear structure simulations from a distributed-memory many-core CPU system to a distributed GPU system. However, in order to make the OpenACC based eigensolver run efficiently on GPUs, we need to take into account the architectural differences between a many-core CPU and a GPU device. Consequently, the optimal way to insert OpenACC directives may be different from the original way of inserting OpenMP directives. We point out these differences in the implementation of sparse matrix-matrix multiplications (SpMM), which constitutes the main cost of the eigensolver, as well as other differences in the preconditioning step and dense linear algebra operations. We compare the performance of the OpenACC based implementation executed on multiple GPUs with the performance on distributed-memory many-core CPUs, and demonstrate significant speedup achieved on GPUs compared to the on-node performance of a many-core CPU. We also show that the overall performance improvement of the eigensolver on multiple GPUs is more modest due to the communication overhead among different MPI ranks.

cs.DC↗

arXiv2018

Optimizing the Union of Intersections LASSO ($UoI_{LASSO}$) and Vector Autoregressive ($UoI_{VAR}$) Algorithms for Improved Statistical Estimation at Scale

The analysis of scientific data of increasing size and complexity requires statistical machine learning methods that are both interpretable and predictive. Union of Intersections (UoI), a recently developed framework, is a two-step approach that separates model selection and model estimation. A linear regression algorithm based on UoI, $UoI_{LASSO}$, simultaneously achieves low false positives and low false negative feature selection as well as low bias and low variance estimates. Together, these qualities make the results both predictive and interpretable. In this paper, we optimize the $UoI_{LASSO}$ algorithm for single-node execution on NERSC's Cori Knights Landing, a Xeon Phi based supercomputer. We then scale $UoI_{LASSO}$ to execute on cores ranging from 68-278,528 cores on a range of dataset sizes demonstrating the weak and strong scaling of the implementation. We also implement a variant of $UoI_{LASSO}$, $UoI_{VAR}$ for vector autoregressive models, to analyze high dimensional time-series data. We perform single node optimization and multi-node scaling experiments for $UoI_{VAR}$ to demonstrate the effectiveness of the algorithm for weak and strong scaling. Our implementations enable to use estimate the largest VAR model (1000 nodes) we are aware of, and apply it to large neurophysiology data 192 nodes).

cs.LG↗