Notebook-as-a-VRE (NaaVRE): From private notebooks to a collaborative cloud virtual research environment

Virtual Research Environments (VREs) provide user-centric support in the lifecycle of research activities, e.g., discovering and accessing research assets, or composing and executing application workflows. A typical VRE is often implemented as an integrated environment, which includes a catalog of research assets, a workflow management system, a data management framework, and tools for enabling collaboration among users. Notebook environments, such as Jupyter, allow researchers to rapidly prototype scientific code and share their experiments as online accessible notebooks. Jupyter can support several popular languages that are used by data scientists, such as Python, R, and Julia. However, such notebook environments do not have seamless support for running heavy computations on remote infrastructure or finding and accessing software code inside notebooks. This paper investigates the gap between a notebook environment and a VRE and proposes an embedded VRE solution for the Jupyter environment called Notebook-as-a-VRE (NaaVRE). The NaaVRE solution provides functional components via a component marketplace and allows users to create a customized VRE on top of the Jupyter environment. From the VRE, a user can search research assets (data, software, and algorithms), compose workflows, manage the lifecycle of an experiment, and share the results among users in the community. We demonstrate how such a solution can enhance a legacy workflow that uses Light Detection and Ranging (LiDAR) data from country-wide airborne laser scanning surveys for deriving geospatial data products of ecosystem structure at high resolution over broad spatial extents. This enables users to scale out the processing of multi-terabyte LiDAR point clouds for ecological applications to more data sources in a distributed cloud environment.Comment: A revised version has been published in the journal software practice and experienc

Document Automation Architectures: Updated Survey in Light of Large Language Models

This paper surveys the current state of the art in document automation (DA). The objective of DA is to reduce the manual effort during the generation of documents by automatically creating and integrating input from different sources and assembling documents conforming to defined templates. There have been reviews of commercial solutions of DA, particularly in the legal domain, but to date there has been no comprehensive review of the academic research on DA architectures and technologies. The current survey of DA reviews the academic literature and provides a clearer definition and characterization of DA and its features, identifies state-of-the-art DA architectures and technologies in academic research, and provides ideas that can lead to new research opportunities within the DA field in light of recent advances in generative AI and large language models.Comment: The current paper is the updated version of an earlier survey on document automation [Ahmadi Achachlouei et al. 2021]. Updates in the current paper are as follows: We shortened almost all sections to reduce the size of the main paper (without references) from 28 pages to 10 pages, added a review of selected papers on large language models, removed certain sections and most of diagrams. arXiv admin note: substantial text overlap with arXiv:2109.1160

Contribution à la convergence d'infrastructure entre le calcul haute performance et le traitement de données à large échelle

The amount of produced data, either in the scientific community or the commercialworld, is constantly growing. The field of Big Data has emerged to handle largeamounts of data on distributed computing infrastructures. High-Performance Computing (HPC) infrastructures are traditionally used for the execution of computeintensive workloads. However, the HPC community is also facing an increasingneed to process large amounts of data derived from high definition sensors andlarge physics apparati. The convergence of the two fields -HPC and Big Data- iscurrently taking place. In fact, the HPC community already uses Big Data tools,which are not always integrated correctly, especially at the level of the file systemand the Resource and Job Management System (RJMS).In order to understand how we can leverage HPC clusters for Big Data usage, andwhat are the challenges for the HPC infrastructures, we have studied multipleaspects of the convergence: We initially provide a survey on the software provisioning methods, with a focus on data-intensive applications. We contribute a newRJMS collaboration technique called BeBiDa which is based on 50 lines of codewhereas similar solutions use at least 1000 times more. We evaluate this mechanism on real conditions and in simulated environment with our simulator Batsim.Furthermore, we provide extensions to Batsim to support I/O, and showcase thedevelopments of a generic file system model along with a Big Data applicationmodel. This allows us to complement BeBiDa real conditions experiments withsimulations while enabling us to study file system dimensioning and trade-offs.All the experiments and analysis of this work have been done with reproducibilityin mind. Based on this experience, we propose to integrate the developmentworkflow and data analysis in the reproducibility mindset, and give feedback onour experiences with a list of best practices.RésuméLa quantité de données produites, que ce soit dans la communauté scientifiqueou commerciale, est en croissance constante. Le domaine du Big Data a émergéface au traitement de grandes quantités de données sur les infrastructures informatiques distribuées. Les infrastructures de calcul haute performance (HPC) sont traditionnellement utilisées pour l’exécution de charges de travail intensives en calcul. Cependant, la communauté HPC fait également face à un nombre croissant debesoin de traitement de grandes quantités de données dérivées de capteurs hautedéfinition et de grands appareils physique. La convergence des deux domaines-HPC et Big Data- est en cours. En fait, la communauté HPC utilise déjà des outilsBig Data, qui ne sont pas toujours correctement intégrés, en particulier au niveaudu système de fichiers ainsi que du système de gestion des ressources (RJMS).Afin de comprendre comment nous pouvons tirer parti des clusters HPC pourl’utilisation du Big Data, et quels sont les défis pour les infrastructures HPC, nousavons étudié plusieurs aspects de la convergence: nous avons d’abord proposé uneétude sur les méthodes de provisionnement logiciel, en mettant l’accent sur lesapplications utilisant beaucoup de données. Nous contribuons a l’état de l’art avecune nouvelle technique de collaboration entre RJMS appelée BeBiDa basée sur 50lignes de code alors que des solutions similaires en utilisent au moins 1000 fois plus.Nous évaluons ce mécanisme en conditions réelles et en environnement simuléavec notre simulateur Batsim. En outre, nous fournissons des extensions à Batsimpour prendre en charge les entrées/sorties et présentons le développements d’unmodèle de système de fichiers générique accompagné d’un modèle d’applicationBig Data. Cela nous permet de compléter les expériences en conditions réellesde BeBiDa en simulation tout en étudiant le dimensionnement et les différentscompromis autours des systèmes de fichiers.Toutes les expériences et analyses de ce travail ont été effectuées avec la reproductibilité à l’esprit. Sur la base de cette expérience, nous proposons d’intégrerle flux de travail du développement et de l’analyse des données dans l’esprit dela reproductibilité, et de donner un retour sur nos expériences avec une liste debonnes pratiques

The Future of High Energy Physics Software and Computing

Software and Computing (S&C) are essential to all High Energy Physics (HEP) experiments and many theoretical studies. The size and complexity of S&C are now commensurate with that of experimental instruments, playing a critical role in experimental design, data acquisition/instrumental control, reconstruction, and analysis. Furthermore, S&C often plays a leading role in driving the precision of theoretical calculations and simulations. Within this central role in HEP, S&C has been immensely successful over the last decade. This report looks forward to the next decade and beyond, in the context of the 2021 Particle Physics Community Planning Exercise ("Snowmass") organized by the Division of Particles and Fields (DPF) of the American Physical Society.Comment: Computational Frontier Report Contribution to Snowmass 2021; 41 pages, 1 figure. v2: missing ref and added missing topical group conveners. v3: fixed typo

Comparing the Performance of Julia on CPUs versus GPUs and Julia-MPI versus Fortran-MPI: a case study with MPAS-Ocean (Version 7.1)

Some programming languages are easy to develop at the cost of slow execution, while others are fast at runtime but much more difficult to write. Julia is a programming language that aims to be the best of both worlds – a development and production language at the same time. To test Julia's utility in scientific high-performance computing (HPC), we built an unstructured-mesh shallow water model in Julia and compared it against an established Fortran-MPI ocean model, the Model for Prediction Across Scales–Ocean (MPAS-Ocean), as well as a Python shallow water code. Three versions of the Julia shallow water code were created: for single-core CPU, graphics processing unit (GPU), and Message Passing Interface (MPI) CPU clusters. Comparing identical simulations revealed that our first version of the Julia model was 13 times faster than Python using NumPy, where both used an unthreaded single-core CPU. Further Julia optimizations, including static typing and removing implicit memory allocations, provided an additional 10–20× speed-up of the single-core CPU Julia model. The GPU-accelerated Julia code was almost identical in terms of performance to the MPI parallelized code on 64 processes, an unexpected result for such different architectures. Parallelized Julia-MPI performance was identical to Fortran-MPI MPAS-Ocean for low processor counts and ranges from 2× faster to 2× slower for higher processor counts. Our experience is that Julia development is fast and convenient for prototyping but that Julia requires further investment and expertise to be competitive with compiled codes. We provide advice on Julia code optimization for HPC systems.</p

On benchmarking of deep learning systems: software engineering issues and reproducibility challenges

Since AlexNet won the ImageNet Large Scale Visual Recognition Challenge (ILSVRC) in 2012, Deep Learning (and Machine Learning/AI in general) gained an exponential interest. Nowadays, their adoption spreads over numerous sectors, like automotive, robotics, healthcare and finance. The ML advancement goes in pair with the quality improvement delivered by those solutions. However, those ameliorations are not for free: ML algorithms always require an increasing computational power, which pushes computer engineers to develop new devices capable of coping with this demand for performance. To foster the evolution of DSAs, and thus ML research, it is key to make it easy to experiment and compare them. This may be challenging since, even if the software built around these devices simplifies their usage, obtaining the best performance is not always straightforward. The situation gets even worse when the experiments are not conducted in a reproducible way. Even though the importance of reproducibility for the research is evident, it does not directly translate into reproducible experiments. In fact, as already shown by previous studies regarding other research fields, also ML is facing a reproducibility crisis. Our work addresses the topic of reproducibility of ML applications. Reproducibility in this context has two aspects: results reproducibility and performance reproducibility. While the reproducibility of the results is mandatory, performance reproducibility cannot be neglected because high-performance device usage causes cost. To understand how the ML situation is regarding reproducibility of performance, we reproduce results published for the MLPerf suite, which seems to be the most used machine learning benchmark. Because of the wide range of devices and frameworks used in different benchmark submissions, we focus on a subset of accuracy and performance results submitted to the MLPerf Inference benchmark, presenting a detailed analysis of the difficulties a scientist may find when trying to reproduce such a benchmark and a possible solution using our workflow tool for experiment reproducibility: PROVA!. We designed PROVA! to support the reproducibility in traditional HPC experiments, but we will show how we extended it to be used as a 'driver' for MLPerf benchmark applications. The PROVA! driver mode allows us to experiment with different versions of the MLPerf Inference benchmark switching among different hardware and software combinations and compare them in a reproducible way. In the last part, we will present the results of our reproducibility study, demonstrating the importance of having a support tool to reproduce and extend original experiments getting deeper knowledge about performance behaviours

Optimizing Computations and Allocations on High Performance and Cloud Computing Systems

Over the last decade, many research and development projects have focused on Cloud Computing systems. After forming around the early research papers and the first commercial cloud offerings in 2006-2008, the field has seen a tremendous progress and has provided the primary infrastructure and technology for applications at small, medium, and large scales. Cloud Computing systems have provided diverse on-demand resources to individual researchers and developers, groups and entire institutions, as well as commercial companies and government organizations. Clouds have also found their niche in scientific computing applications, offering attractive alternatives to High Performance Computing models and systems. While cloud economics and technologies have significantly matured recently, there is much active research revolving around topics such as optimality, usability, manageability, and reproducibility in the latest studies. This dissertation presents our findings and relevant developments at the intersection of Cloud Computing and such “flavors” of computing as High Performance Computing and High Throughput Computing. We primarily focus on optimality issues in this area and propose solutions that address the needs of individual researchers and research groups with limited computational and financial resources