More Like this

1. Issues in the Reproducibility of Deep Learning Results

   https://doi.org/10.1109/SPMB47826.2019.9037840  

   Jean-Paul, S. ; Elseify, T. ; Obeid, I. ; Picone, J. ( December 2019 , IEEE Signal Processing in Medicine and Biology Symposium (SPMB))

   Obeid, I. ; Selesnik, I. ; Picone, J. (Ed.)

   The Neuronix high-performance computing cluster allows us to conduct extensive machine learning experiments on big data [1]. This heterogeneous cluster uses innovative scheduling technology, Slurm [2], that manages a network of CPUs and graphics processing units (GPUs). The GPU farm consists of a variety of processors ranging from low-end consumer grade devices such as the Nvidia GTX 970 to higher-end devices such as the GeForce RTX 2080. These GPUs are essential to our research since they allow extremely compute-intensive deep learning tasks to be executed on massive data resources such as the TUH EEG Corpus [2]. We use TensorFlow [3] as the core machine learning library for our deep learning systems, and routinely employ multiple GPUs to accelerate the training process. Reproducible results are essential to machine learning research. Reproducibility in this context means the ability to replicate an existing experiment – performance metrics such as error rates should be identical and floating-point calculations should match closely. Three examples of ways we typically expect an experiment to be replicable are: (1) The same job run on the same processor should produce the same results each time it is run. (2) A job run on a CPU and GPU should producemore »identical results. (3) A job should produce comparable results if the data is presented in a different order. System optimization requires an ability to directly compare error rates for algorithms evaluated under comparable operating conditions. However, it is a difficult task to exactly reproduce the results for large, complex deep learning systems that often require more than a trillion calculations per experiment [5]. This is a fairly well-known issue and one we will explore in this poster. Researchers must be able to replicate results on a specific data set to establish the integrity of an implementation. They can then use that implementation as a baseline for comparison purposes. A lack of reproducibility makes it very difficult to debug algorithms and validate changes to the system. Equally important, since many results in deep learning research are dependent on the order in which the system is exposed to the data, the specific processors used, and even the order in which those processors are accessed, it becomes a challenging problem to compare two algorithms since each system must be individually optimized for a specific data set or processor. This is extremely time-consuming for algorithm research in which a single run often taxes a computing environment to its limits. Well-known techniques such as cross-validation [5,6] can be used to mitigate these effects, but this is also computationally expensive. These issues are further compounded by the fact that most deep learning algorithms are susceptible to the way computational noise propagates through the system. GPUs are particularly notorious for this because, in a clustered environment, it becomes more difficult to control which processors are used at various points in time. Another equally frustrating issue is that upgrades to the deep learning package, such as the transition from TensorFlow v1.9 to v1.13, can also result in large fluctuations in error rates when re-running the same experiment. Since TensorFlow is constantly updating functions to support GPU use, maintaining an historical archive of experimental results that can be used to calibrate algorithm research is quite a challenge. This makes it very difficult to optimize the system or select the best configurations. The overall impact of all of these issues described above is significant as error rates can fluctuate by as much as 25% due to these types of computational issues. Cross-validation is one technique used to mitigate this, but that is expensive since you need to do multiple runs over the data, which further taxes a computing infrastructure already running at max capacity. GPUs are preferred when training a large network since these systems train at least two orders of magnitude faster than CPUs [7]. Large-scale experiments are simply not feasible without using GPUs. However, there is a tradeoff to gain this performance. Since all our GPUs use the NVIDIA CUDA® Deep Neural Network library (cuDNN) [8], a GPU-accelerated library of primitives for deep neural networks, it adds an element of randomness into the experiment. When a GPU is used to train a network in TensorFlow, it automatically searches for a cuDNN implementation. NVIDIA’s cuDNN implementation provides algorithms that increase the performance and help the model train quicker, but they are non-deterministic algorithms [9,10]. Since our networks have many complex layers, there is no easy way to avoid this randomness. Instead of comparing each epoch, we compare the average performance of the experiment because it gives us a hint of how our model is performing per experiment, and if the changes we make are efficient. In this poster, we will discuss a variety of issues related to reproducibility and introduce ways we mitigate these effects. For example, TensorFlow uses a random number generator (RNG) which is not seeded by default. TensorFlow determines the initialization point and how certain functions execute using the RNG. The solution for this is seeding all the necessary components before training the model. This forces TensorFlow to use the same initialization point and sets how certain layers work (e.g., dropout layers). However, seeding all the RNGs will not guarantee a controlled experiment. Other variables can affect the outcome of the experiment such as training using GPUs, allowing multi-threading on CPUs, using certain layers, etc. To mitigate our problems with reproducibility, we first make sure that the data is processed in the same order during training. Therefore, we save the data from the last experiment and to make sure the newer experiment follows the same order. If we allow the data to be shuffled, it can affect the performance due to how the model was exposed to the data. We also specify the float data type to be 32-bit since Python defaults to 64-bit. We try to avoid using 64-bit precision because the numbers produced by a GPU can vary significantly depending on the GPU architecture [11-13]. Controlling precision somewhat reduces differences due to computational noise even though technically it increases the amount of computational noise. We are currently developing more advanced techniques for preserving the efficiency of our training process while also maintaining the ability to reproduce models. In our poster presentation we will demonstrate these issues using some novel visualization tools, present several examples of the extent to which these issues influence research results on electroencephalography (EEG) and digital pathology experiments and introduce new ways to manage such computational issues.« less
2. FPGA-Based Acceleration of Time Series Similarity Prediction: From Cloud to Edge

   https://doi.org/10.1145/3555810  

   Kalantar, Amin ; Zimmerman, Zachary ; Brisk, Philip ( July 2022 , ACM Transactions on Reconfigurable Technology and Systems)

   With the proliferation of low-cost sensors and the Internet of Things, the rate of producing data far exceeds the compute and storage capabilities of today’s infrastructure. Much of this data takes the form of time series, and in response, there has been increasing interest in the creation of time series archives in the last decade, along with the development and deployment of novel analysis methods to process the data. The general strategy has been to apply a plurality of similarity search mechanisms to various subsets and subsequences of time series data in order to identify repeated patterns and anomalies; however, the computational demands of these approaches renders them incompatible with today’s power-constrained embedded CPUs. To address this challenge, we present FA-LAMP, an FPGA-accelerated implementation of the Learned Approximate Matrix Profile (LAMP) algorithm, which predicts the correlation between streaming data sampled in real-time and a representative time series dataset used for training. FA-LAMP lends itself as a real-time solution for time series analysis problems such as classification. We present the implementation of FA-LAMP on both edge- and cloud-based prototypes. On the edge devices, FA-LAMP integrates accelerated computation as close as possible to IoT sensors, thereby eliminating the need to transmit andmore »store data in the cloud for posterior analysis. On the cloud-based accelerators, FA-LAMP can execute multiple LAMP models on the same board, allowing simultaneous processing of incoming data from multiple data sources across a network. LAMP employs a Convolutional Neural Network (CNN) for prediction. This work investigates the challenges and limitations of deploying CNNs on FPGAs using the Xilinx Deep Learning Processor Unit (DPU) and the Vitis AI development environment. We expose several technical limitations of the DPU, while providing a mechanism to overcome them by attaching custom IP block accelerators to the architecture. We evaluate FA-LAMP using a low-cost Xilinx Ultra96-V2 FPGA as well as a cloud-based Xilinx Alveo U280 accelerator card and measure their performance against a prototypical LAMP deployment running on a Raspberry Pi 3, an Edge TPU, a GPU, a desktop CPU, and a server-class CPU. In the edge scenario, the Ultra96-V2 FPGA improved performance and energy consumption compared to the Raspberry Pi; in the cloud scenario, the server CPU and GPU outperformed the Alveo U280 accelerator card, while the desktop CPU achieved comparable performance; however, the Alveo card offered an order of magnitude lower energy consumption compared to the other four platforms. Our implementation is publicly available at https://github.com/aminiok1/lamp-alveo.« less
3. Profiling NVIDIA Jetson Embedded GPU Devices for Autonomous Machines

   https://doi.org/10.5121/csit.2020.101811  

   Li, Yazhou ; Zheng, Yahong Rosa ( December 2020 , International Conference on Signal, Image Processing and Embedded Systems)

   This paper presents two methods, tegrastats GUI version jtop and Nsight Systems, to profile NVIDIA Jetson embedded GPU devices on a model race car which is a great platform for prototyping and field testing autonomous driving algorithms. The two profilers analyze the power consumption, CPU/GPU utilization, and the run time of CUDA C threads of Jetson TX2 in five different working modes. The performance differences among the five modes are demonstrated using three example programs: vector add in C and CUDA C, a simple ROS (Robot Operating System) package of the wall follow algorithm in Python, and a complex ROS package of the particle filter algorithm for SLAM (Simultaneous Localization and Mapping). The results show that the tools are effective means for selecting operating mode of the embedded GPU devices.
4. ADEPT: a domain independent sequence alignment strategy for gpu architectures

   https://doi.org/10.1186/s12859-020-03720-1  

   Awan, Muaaz G. ; Deslippe, Jack ; Buluc, Aydin ; Selvitopi, Oguz ; Hofmeyr, Steven ; Oliker, Leonid ; Yelick, Katherine ( December 2020 , BMC Bioinformatics)

   Abstract Background Bioinformatic workflows frequently make use of automated genome assembly and protein clustering tools. At the core of most of these tools, a significant portion of execution time is spent in determining optimal local alignment between two sequences. This task is performed with the Smith-Waterman algorithm, which is a dynamic programming based method. With the advent of modern sequencing technologies and increasing size of both genome and protein databases, a need for faster Smith-Waterman implementations has emerged. Multiple SIMD strategies for the Smith-Waterman algorithm are available for CPUs. However, with the move of HPC facilities towards accelerator based architectures, a need for an efficient GPU accelerated strategy has emerged. Existing GPU based strategies have either been optimized for a specific type of characters (Nucleotides or Amino Acids) or for only a handful of application use-cases. Results In this paper, we present ADEPT, a new sequence alignment strategy for GPU architectures that is domain independent, supporting alignment of sequences from both genomes and proteins. Our proposed strategy uses GPU specific optimizations that do not rely on the nature of sequence. We demonstrate the feasibility of this strategy by implementing the Smith-Waterman algorithm and comparing it to similar CPU strategies asmore »well as the fastest known GPU methods for each domain. ADEPT’s driver enables it to scale across multiple GPUs and allows easy integration into software pipelines which utilize large scale computational systems. We have shown that the ADEPT based Smith-Waterman algorithm demonstrates a peak performance of 360 GCUPS and 497 GCUPs for protein based and DNA based datasets respectively on a single GPU node (8 GPUs) of the Cori Supercomputer. Overall ADEPT shows 10x faster performance in a node-to-node comparison against a corresponding SIMD CPU implementation. Conclusions ADEPT demonstrates a performance that is either comparable or better than existing GPU strategies. We demonstrated the efficacy of ADEPT in supporting existing bionformatics software pipelines by integrating ADEPT in MetaHipMer a high-performance denovo metagenome assembler and PASTIS a high-performance protein similarity graph construction pipeline. Our results show 10% and 30% boost of performance in MetaHipMer and PASTIS respectively.« less
5. A sampling and learning framework to prove motion planning infeasibility

   https://doi.org/10.1177/02783649231154674  

   Li, Sihui ; Dantam, Neil T. ( February 2023 , The International Journal of Robotics Research)

   We present a learning-based approach to prove infeasibility of kinematic motion planning problems. Sampling-based motion planners are effective in high-dimensional spaces but are only probabilistically complete. Consequently, these planners cannot provide a definite answer if no plan exists, which is important for high-level scenarios, such as task-motion planning. We apply data generated during multi-directional sampling-based planning (such as PRM) to a machine learning approach to construct an infeasibility proof. An infeasibility proof is a closed manifold in the obstacle region of the configuration space that separates the start and goal into disconnected components of the free configuration space. We train the manifold using common machine learning techniques and then triangulate the manifold into a polytope to prove containment in the obstacle region. Under assumptions about the hyper-parameters and robustness of configuration space optimization, the output is either an infeasibility proof or a motion plan in the limit. We demonstrate proof construction for up to 4-DOF configuration spaces. A large part of the algorithm is parallelizable, which offers potential to address higher dimensional configuration spaces.