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Bicer, Tekin

Publications and source records attributed to Bicer, Tekin.

12 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Diaspora: Resilience-Enabling Services for Real-Time Distributed Workflows

The need for real-time processing to enable automated decision making and experimental steering has driven a shift from high-performance computing workflows on a centralized system to a distributed approach that integrates remote data sources, edge devices, and diverse compute facilities. Under this paradigm, data can be processed close to the source where it is generated, thus reducing latency and bandwidth usage. System resilience is thus a key challenge, requiring distributed workflows to survive component failures and to meet stringent quality-of-service requirements, which results in the need to mitigate anomalies such as congestion and low availability of resources. To address these challenges, we propose Diaspora, a unified resilience framework that is inspired by event-driven communication patterns used in public clouds. Specifically, we propose an event fabric that extends across sites, facilities, and computations to provide timely, reliable, and accurate information about data, application, and resource status. On top of the event fabric, we build resilience-enabling services that combine QoS-aware data streaming, resilient data views, resilient compute and data resources, and anomaly detection and prediction, all of which collectively enhance workflow resilience for these scientific cases.

Rao, Nageswara↗
DOE OSTI2024

Efficient distributed continual learning for steering experiments in real-time

Deep learning has emerged as a powerful method for extracting valuable information from large volumes of data. However, when new training data arrives continuously (i.e., is not fully available from the beginning), incremental training suffers from catastrophic forgetting (i.e., new patterns are reinforced at the expense of previously acquired knowledge). Training from scratch each time new training data becomes available would result in extremely long training times and massive data accumulation. Rehearsal-based continual learning has shown promise for addressing the catastrophic forgetting challenge, but research to date has not addressed performance and scalability. To fill this gap, we propose an approach based on a distributed rehearsal buffer that efficiently complements data-parallel training on multiple GPUs to achieve high accuracy, short runtime, and scalability. It leverages a set of buffers (local to each GPU) and uses several asynchronous techniques for updating these local buffers in an embarrassingly parallel fashion, all while handling the communication overheads necessary to augment input minibatches using unbiased, global sampling. We further propose a generalization of rehearsal buffers to support both classification and generative learning tasks, as well as more advanced rehearsal strategies (notably Dark Experience Replay, leveraging knowledge distillation). We illustrate this approach with a real-life HPC streaming application from the domain of ptychographic image reconstruction. Furthermore, we run extensive experiments on up to 128 GPUs of the ThetaGPU supercomputer to compare our approach with baselines representative of training-from-scratch (the upper bound in terms of accuracy) and incremental training (the lower bound). Results show that rehearsal-based continual learning achieves a top-5 validation accuracy close to the upper bound, while simultaneously exhibiting a runtime close to the lower bound.

Asynchronous data management↗
DOE OSTI2024

CommBench: Micro-Benchmarking Hierarchical Networks with Multi-GPU, Multi-NIC Nodes

Modern high-performance computing systems have multiple GPUs and network interface cards (NICs) per node. The resulting network architectures have multilevel hierarchies of subnetworks with different interconnect and software technologies. These systems offer multiple vendor-provided communication capabilities and library implementations (IPC, MPI, NCCL, RCCL, OneCCL) with APIs providing varying levels of performance across the different levels. Understanding this performance is currently difficult because of the wide range of architectures and programming models (CUDA, HIP, OneAPI). We present CommBench, a library with cross-system portability and a high-level API that enables developers to easily build microbenchmarks relevant to their use cases and gain insight into the performance (bandwidth & latency) of multiple implementation libraries on different networks. We demonstrate CommBench with three sets of microbenchmarks that profile the performance of six systems. Our experimental results reveal the effect of multiple NICs on optimizing the bandwidth across nodes and also present the performance characteristics of four available communication libraries within and across nodes of NVIDIA, AMD, and Intel GPU networks.

Hidayetoglu, Mert↗
DOE OSTI2024

Suppressing strain propagation in ultrahigh-Ni cathodes during fast charging via epitaxial entropy-assisted coating

Surface reconstruction and the associated severe strain propagation have long been reported as the major cause of cathode failure during fast charging and long-term cycling. Despite tremendous attempts, no known strategies can simultaneously address the electro-chemomechanical instability without sacrificing energy and power density. Here we report an epitaxial entropy-assisted coating strategy for ultrahigh-Ni LiNi x Co y Mn 1-x-y O 2 (x ≥ 0.9) cathodes via an oriented attachment-driven reaction between Wadsley-Roth phase-based oxides and the layered-oxide cathodes. Further, the high anti-cracking and anti-corrosion tolerances as well as the fast ionic transport of the entropy-assisted surface effectively improved the fast charging/discharging capability, wide temperature tolerance and thermal stability of the ultrahigh-Ni cathodes. Comprehensive analysis from the primary and secondary particle level to the electrode level using multi-scale in situ synchrotron X-ray probes reveals greatly reduced lattice dislocations, anisotropic lattice strain and oxygen release as well as improved bulk/local structural stability, even when charging beyond the threshold state of charge (75%) of layered cathodes. Layered Ni-rich oxide cathodes are susceptible to challenges with surface reconstruction and strain propagation, limiting their cyclability. The authors propose a solution involving oriented attachment-driven reactions, utilizing Wadsley-Roth nanocrystals and layered oxide to induce an epitaxial entropy-assisted coating, effectively addressing these issues.

25 ENERGY STORAGE↗
DOE OSTI2022

Large Scale Caching and Streaming of Training Data for Online Deep Learning

The training of deep neural network models on large data remains a difficult problem, despite progress towards scalable techniques. In particular, there is a mismatch between the random but predetermined order in which AI flows select training samples and the streaming I/O patterns for which traditional HPC data storage (e.g., parallel file systems) are designed. In addition, as more data are obtained, it is feasible neither simply to train learning models incrementally, due to catastrophic forgetting (i.e., bias towards new samples), nor to train frequently from scratch, due to prohibitive time and/or resource constraints. In this paper, we study data management techniques that combine caching and streaming with rehearsal support in order to enable efficient access to training samples in both offline training and continual learning. We revisit state-of-art streaming approaches based on data pipelines that transparently handle prefetching, caching, shuffling, and data augmentation, and discuss the challenges and opportunities that arise when combining these methods with data-parallel training techniques. We also report on preliminary experiments that evaluate the I/O overheads involved in accessing the training samples from a parallel file system (PFS) under several concurrency scenarios, highlighting the impact of the PFS on the design of the data pipelines.

data pipelines↗
DOE OSTI2021

MemXCT: Design, Optimization, Scaling, and Reproducibility of X-Ray Tomography Imaging

Here, this work extends our previous research entitled "MemXCT: Memory-centric X-ray CT Reconstruction with Massive Parallelization" that was originally published at SC19 conference (Hidayetoglu et al., 2019) with reproducibility of the computational imaging performance. X-ray computed tomography (XCT) is regularly used at synchrotron light sources to study the internal morphology of materials at high resolution. However, experimental constraints, such as radiation sensitivity, can result in noisy or undersampled measurements. Further, depending on the resolution, sample size and data acquisition rates, the resulting noisy dataset can be in the order of terabytes. Advanced iterative reconstruction techniques can produce high-quality images from noisy measurements, but their computational requirements have made their use an exception rather than the rule. We propose a novel memory-centric approach that avoids redundant computations at the expense of additional memory complexity. We develop a memory-centric iterative reconstruction system, MemXCT, that uses an optimized SpMV implementation with two-level pseudo-Hilbert ordering and multi-stage input buffering. We evaluate MemXCT on various supercomputer architectures involving KNL and GPU. MemXCT can reconstruct a large (11Kx11K) mouse brain tomogram in 10 seconds using 4096 KNL nodes (256K cores). The results presented in our original article at the SC19 were based on large-scale supercomputing resources. The MemXCT application was selected for the Student Cluster Competition (SCC) Reproducibility Challenge and evaluated on a variety of cloud computing resources by universities around the world in the SC20 conference. We summarize the results of the top-ranked SCC Reproducibility Challenge teams and identify the most pertinent measures for ensuring the reproducibility of our experiments in this article.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

Joint ptycho-tomography with deep generative priors

Abstract Joint ptycho-tomography is a powerful computational imaging framework to recover the refractive properties of a 3D object while relaxing the requirements for probe overlap that is common in conventional phase retrieval. We use an augmented Lagrangian scheme for formulating the constrained optimization problem and employ an alternating direction method of multipliers (ADMM) for the joint solution. ADMM allows the problem to be split into smaller and computationally more efficient subproblems: ptychographic phase retrieval, tomographic reconstruction, and regularization of the solution. We extend our ADMM framework with plug-and-play (PnP) denoisers by replacing the regularization subproblem with a general denoising operator based on machine learning. While the PnP framework enables integrating such learned priors as denoising operators, tuning of the denoiser prior remains challenging. To overcome this challenge, we propose a denoiser parameter to control the effect of the denoiser and to accelerate the solution. In our simulations, we demonstrate that our proposed framework with parameter tuning and learned priors generates high-quality reconstructions under limited and noisy measurement data.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Predicting Execution Times for Disk-based and In-Situ Parallel Data Analytics (Final Technical Report)

In recent years, there has been a significant amount of interests in in-situ analytics on simulation programs. For a variety of reasons, it is desirable to be able to predict the execution time of an analytics program. At the same time, frameworks such as MapReduce have become popular for scientific data analytics. This paper focuses on developing performance models for predicting execution time of parallel data analytics, with a special emphasis on in-situ analytics. We take two distinct approach towards performance prediction. We first expand SKOPE (a SKeleton framewOrk for Performance Exploration) with performance models for disk data read, cache performance, and page fault penalty. Second, an analytical performance model is also developed. We have evaluated our performance prediction framework as well as the analytical model on three hardware setups with well-known data mining algorithms implemented in three programming paradigms, MapReduce, MATE (a MapReduce-like parallel system with an alternate API for multi-core environments) and Smart (a MapReduce-like framework for in-situ analytics). Results show that our performance prediction framework along with the incorporated performance models are capable of accurately predicting execution times for parallel scientific analytics on different hardware setups.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

TomoGAN: low-dose synchrotron x-ray tomography with generative adversarial networks: discussion

Synchrotron-based x-ray tomography is a noninvasive imaging technique that allows for reconstructing the internal structure of materials at high spatial resolutions from tens of micrometers to a few nanometers. In order to resolve sample features at smaller length scales, however, a higher radiation dose is required. Therefore, the limitation on the achievable resolution is set primarily by noise at these length scales. We present TomoGAN, a denoising technique based on generative adversarial networks, for improving the quality of reconstructed images for low-dose imaging conditions. We evaluate our approach in two photon-budget-limited experimental conditions: (1) sufficient number of low-dose projections (based on Nyquist sampling), and (2) insufficient or limited number of high-dose projections. In both cases, the angular sampling is assumed to be isotropic, and the photon budget throughout the experiment is fixed based on the maximum allowable radiation dose on the sample. Evaluation with both simulated and experimental datasets shows that our approach can significantly reduce noise in reconstructed images, improving the structural similarity score of simulation and experimental data from 0.18 to 0.9 and from 0.18 to 0.41, respectively. Furthermore, the quality of the reconstructed images with filtered back projection followed by our denoising approach exceeds that of reconstructions with the simultaneous iterative reconstruction technique, showing the computational superiority of our approach.

42 ENGINEERING↗
DOE OSTI2020

GPU-Based Static Data-Flow Analysis for Fast and Scalable Android App Vetting

Many popular vetting tools for Android applications use static code analysis techniques. In particular, Interprocedural Data-Flow Graph (IDFG) construction is the computation at the core of Android static data-flow analysis and consumes most of the analysis time. Many analysis tools use a worklist algorithm, an iterative fixed-point approach, to construct the IDFG. In this paper, we observe that a straightforward GPU parallelization of the worklist algorithm leads to significant underutilization of the GPU resources. We identify four performance bottlenecks, namely, frequent dynamic memory allocations, high branch divergence, workload imbalance, and irregular memory access patterns. Accordingly, we propose GDroid, a GPU-based worklist algorithm implementation with multiple fine-grained optimizations tailored to common characteristics of Android applications. The optimizations considered are: matrix-based data structure, memory access-based node grouping, and worklist merging. Our experimental evaluation, performed on 1000 Android applications, shows that the proposed optimizations are beneficial to performance, and GDroid can achieve up to 128X speedups against a plain GPU implementation.

Android security↗