arXiv subjects

Seth Ockerman

Publications and source records attributed to Seth Ockerman.

7 recordsLinked to original sources

arXiv2026

When More Cores Hurts: The Vector Database Scaling Paradox in HPC

Vector databases have been designed and optimized for cloud environments; however, emerging scientific AI workloads (e.g., molecular search, meteorological trajectory detection, and literature-driven hypothesis generation) demand efficient, scalable execution on HPC systems. We present a large-scale evaluation of three state-of-the-art vector databases -- Qdrant, Milvus, and Weaviate -- on two production supercomputers, scaling to 256 distributed workers across 64 compute nodes. We evaluate representative workload patterns -- mixed read/write and write-then-read -- using popular benchmarks, multimodal embeddings, and a novel real-world scientific dataset. Our results reveal that workload characteristics can limit latency reduction, additional cores can reduce query throughput by up to 30.67%, and scaling from 16 to 256 workers (16x) only yields a 5.46x improvement. This scaling paradox exposes the fundamental mismatch between cloud-oriented designs and HPC systems, highlighting the need for new, HPC-aware vector database designs.

cs.DC↗

arXiv2025

A Distributed Framework for Causal Modeling of Performance Variability in GPU Traces

Large-scale GPU traces play a critical role in identifying performance bottlenecks within heterogeneous High-Performance Computing (HPC) architectures. However, the sheer volume and complexity of a single trace of data make performance analysis both computationally expensive and time-consuming. To address this challenge, we present an end-to-end parallel performance analysis framework designed to handle multiple large-scale GPU traces efficiently. Our proposed framework partitions and processes trace data concurrently and employs causal graph methods and parallel coordinating chart to expose performance variability and dependencies across execution flows. Experimental results demonstrate a 67% improvement in terms of scalability, highlighting the effectiveness of our pipeline for analyzing multiple traces independently.

cs.DC↗

arXiv2025

Exploring Distributed Vector Databases Performance on HPC Platforms: A Study with Qdrant

Vector databases have rapidly grown in popularity, enabling efficient similarity search over data such as text, images, and video. They now play a central role in modern AI workflows, aiding large language models by grounding model outputs in external literature through retrieval-augmented generation. Despite their importance, little is known about the performance characteristics of vector databases in high-performance computing (HPC) systems that drive large-scale science. This work presents an empirical study of distributed vector database performance on the Polaris supercomputer in the Argonne Leadership Computing Facility. We construct a realistic biological-text workload from BV-BRC and generate embeddings from the peS2o corpus using Qwen3-Embedding-4B. We select Qdrant to evaluate insertion, index construction, and query latency with up to 32 workers. Informed by practical lessons from our experience, this work takes a first step toward characterizing vector database performance on HPC platforms to guide future research and optimization.

cs.DC↗

arXiv2025

PGT-I: Scaling Spatiotemporal GNNs with Memory-Efficient Distributed Training

Spatiotemporal graph neural networks (ST-GNNs) are powerful tools for modeling spatial and temporal data dependencies. However, their applications have been limited primarily to small-scale datasets because of memory constraints. While distributed training offers a solution, current frameworks lack support for spatiotemporal models and overlook the properties of spatiotemporal data. Informed by a scaling study on a large-scale workload, we present PyTorch Geometric Temporal Index (PGT-I), an extension to PyTorch Geometric Temporal that integrates distributed data parallel training and two novel strategies: index-batching and distributed-index-batching. Our index techniques exploit spatiotemporal structure to construct snapshots dynamically at runtime, significantly reducing memory overhead, while distributed-index-batching extends this approach by enabling scalable processing across multiple GPUs. Our techniques enable the first-ever training of an ST-GNN on the entire PeMS dataset without graph partitioning, reducing peak memory usage by up to 89% and achieving up to a 11.78x speedup over standard DDP with 128 GPUs.

cs.DC↗

arXiv2025

Scalable GPU Performance Variability Analysis framework

Analyzing large-scale performance logs from GPU profilers often requires terabytes of memory and hours of runtime, even for basic summaries. These constraints prevent timely insight and hinder the integration of performance analytics into automated workflows. Existing analysis tools typically process data sequentially, making them ill-suited for HPC workflows with growing trace complexity and volume. We introduce a distributed data analysis framework that scales with dataset size and compute availability. Rather than treating the dataset as a single entity, our system partitions it into independently analyzable shards and processes them concurrently across MPI ranks. This design reduces per-node memory pressure, avoids central bottlenecks, and enables low-latency exploration of high-dimensional trace data. We apply the framework to end-to-end Nsight Compute traces from real HPC and AI workloads, demonstrate its ability to diagnose performance variability, and uncover the impact of memory transfer latency on GPU kernel behavior.

cs.DC↗

arXiv2024

Accelerating Biological Spatial Cluster Analysis with the Parallel Integral Image Technique

Spatial cluster analysis (SCA) offers valuable insights into biological images; a common SCA technique is sliding window analysis (SWA). Unfortunately, SWA's computational cost hinders its application to larger images, limiting its use to small-scale images. With advancements in high-resolution microscopy, images now exceed the capabilities of previous SWA approaches, reaching sizes up to 70,000 by 85,000 pixels. To overcome these limitations, this paper introduces the parallel integral image approach to SWA, surpassing previous methods. We achieve a remarkable speedup of 131,806x on small-scale images and consistent speedups of over 10,000x on a variety of large-scale microscopy images. We analyze the computational complexity advantages of the parallel integral image approach and present experimental results that validate the superior performance of integral-image-based methods. Our approach is made available as an open-source Python PIP package available at https://github.com/OckermanSethGVSU/BioPII.

cs.CV↗

arXiv2022

A Case for Dataset Specific Profiling

Data-driven science is an emerging paradigm where scientific discoveries depend on the execution of computational AI models against rich, discipline-specific datasets. With modern machine learning frameworks, anyone can develop and execute computational models that reveal concepts hidden in the data that could enable scientific applications. For important and widely used datasets, computing the performance of every computational model that can run against a dataset is cost prohibitive in terms of cloud resources. Benchmarking approaches used in practice use representative datasets to infer performance without actually executing models. While practicable, these approaches limit extensive dataset profiling to a few datasets and introduce bias that favors models suited for representative datasets. As a result, each dataset's unique characteristics are left unexplored and subpar models are selected based on inference from generalized datasets. This necessitates a new paradigm that introduces dataset profiling into the model selection process. To demonstrate the need for dataset-specific profiling, we answer two questions:(1) Can scientific datasets significantly permute the rank order of computational models compared to widely used representative datasets? (2) If so, could lightweight model execution improve benchmarking accuracy? Taken together, the answers to these questions lay the foundation for a new dataset-aware benchmarking paradigm.

cs.LG↗