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The Office of Science (SC) in the Department of Energy (DOE) invites interested parties to provide input relevant to the stewardship of the software ecosystem for scientific and high-performance computing.
Particle physics has an ambitious and broad global experimental programme for the coming decades. Large investments in building new facilities are already underway or under consideration. Scaling the present processing power and data storage needs by the foreseen increase in data rates in the next decade for HL-LHC is not sustainable within the current budgets. As a result, a more efficient usage of computing resources is required in order to realise the physics potential of future experiments. Software and computing are an integral part of experimental design, trigger and data acquisition, simulation, reconstruction, and analysis, as well as related theoretical predictions. A significant investment in computing and software is therefore critical. Advances in software and computing, including artificial intelligence (AI) and machine learning (ML), will be key for solving these challenges. Making better use of new processing hardware such as graphical processing units (GPUs) or ARM chips is a growing trend. This forms part of a computing solution that makes efficient use of facilities and contributes to the reduction of the environmental footprint of HEP computing. The HEP community already provided a roadmap for software and computing for the last EPPSU, and this paper updates that, with a focus on the most resource critical parts of our data processing chain.
Here, a review of current trends in scientific computing reveals a broad shift to open-source and higher-level programming languages such as Python and growing career opportunities over the next decade. Open-source modeling tools accelerate innovation in equation-based and data-driven applications. Significant resources have been deployed to develop data-driven tools (PyTorch, TensorFlow, Scikit-learn) from tech companies that rely on machine learning services to meet business needs while keeping the foundational tools open. Open-source equation-based tools such as Pyomo, CasADi, Gekko, and JuMP are also gaining momentum according to user community and development pace metrics. Integration of data-driven and principles-based tools is emerging. New compute hardware, productivity software, and training resources have the potential to radically accelerate progress. However, long-term support mechanisms are still necessary to sustain the momentum and maintenance of critical foundational packages.
The software allows for queueing and dispatch of tasks of small, varied, or uncertain runtimes across multiple HPC jobs, resources, and other computing systems. The software was designed to allow scientists to enqueue, run, and accumulate results from computational experiments in an efficient, manageable manner. For example, the software can be used to enqueue many small computational experiments and run them using several long-running multi-node HPC jobs that may or may not run simultaneously.
Here, we provide an overview of the software engineering efforts and their impact in QMCPACK, a production-level ab-initio Quantum Monte Carlo open-source code targeting high-performance computing (HPC) systems. Aspects included are: (i) strategic expansion of continuous integration (CI) targeting CPUs, using GitHub Actions own runners, and NVIDIA and AMD GPUs used in pre-exascale systems, (ii) incremental reduction of memory leaks using sanitizers, (iii) incorporation of Docker containers for CI and reproducibility, and (iv) refactoring efforts to improve maintainability, testing coverage, and memory lifetime management. We quantify the value of these improvements by providing metrics to illustrate the shift towards a predictive, rather than reactive, maintenance approach. Our goal, in documenting the impact of these efforts on QMCPACK, is to contribute to the body of knowledge on the importance of research software engineering (RSE) for the stewardship and advancement of community HPC codes to enable scientific discovery at scale.
The Erosion-Dilation continuous Phase-Size Distribution, ED-cPSD, is an application for calculating continuous pore and particle-size distribution from digital reconstructions and/or image-based structural data. It is based on the erosion-dilation continuous phase-size distribution method. A continuous size distribution is a measure of the probability density of finding a particle or pore of a certain size. These distributions are of interest in any field of study involving porous media, including but not limited to electrochemistry, petroleum engineering, geology, and food science. The algorithm behind the software provides a computationally efficient way to calculate phase-size distributions for large domains. For a 3D battery electrode reconstruction with 1.3 x 10 8 voxels, the particle size distribution is derived in under 2 min on a desktop, while also retaining flexibility and computational efficiency for HPC-scale multi-threading. The software can handle structures with over 10 9 voxels. The algorithm is roughly 280 times faster than a previous version on the same task.
This software combines nonlinear-manifold reduced order models (NM-ROMs) with domain decomposition (DD) techniques. NM-ROMs, which utilize a shallow, sparse autoencoder trained with full order model (FOM) snapshot data, approximate the FOM state on a nonlinear manifold. These models offer advantages over linear-subspace ROMs (LS-ROMs) particularly in scenarios with slowly decaying Kolmogorov n-width. However, the training of NM-ROMs involves a number of parameters that scale with the size of the FOM, and storing high-dimensional FOM snapshots can significantly increase the cost of ROM training for extreme-scale problems. To mitigate these costs, the software employs DD to partition the FOM into smaller subdomains, computes NM-ROMs for each, and then integrates these to form a global NM-ROM. This strategy offers multiple benefits: it enables parallel training of subdomain NM-ROMs, reduces the number of parameters needed, decreases the dimensional requirements of subdomain FOM training data, and allows for customization to the unique characteristics of each FOM subdomain. The use of a shallow, sparse autoencoder architecture in each subdomain NM-ROM facilitates the application of hyper-reduction (HR), simplifying the nonlinear complexities and enhancing computational speed. This software marks the inaugural application of NM-ROM combined with HR to a DD problem. It features an algebraic DD reformulation of the FOM, training of NM-ROMs with HR for each subdomain, and employs a sequential quadratic programming (SQP) solver for the evaluation of the coupled global NMROM. The effectiveness of the DD NM-ROM with HR is numerically demonstrated on the 2D steady-state Burgers' equation, showing an order of magnitude improvement in accuracy over the DD LS-ROM with HR.
LocOO3D is a software tool that computes geographical locations for seismic events at regional to global scales. This software has a rich set of features, including the ability to use custom 3D velocity models, correlated observations and master event locations. The LocOO3D software is especially useful for research related to seismic monitoring applications, since it allows users to easily explore a variety of location methods and scenarios and is compatible with the CSS3.0 data format used in monitoring applications. The LocOO3D software, User's Manual, and Examples are available on the web at: https://github.com/sandialabs/LocOO3D For additional information on GeoTess, SALSA3D, RSTT, and other related software, please see: https://github.com/sandialabs/GeoTessJava, www.sandia.gov/geotess, www.sandia.gov/salsa3d, and www.sandia.gov/rstt
The Joint Laboratory for Extreme-Scale Computing (JLESC) focuses on software challenges in high-performance computing systems to meet the needs of today’s science campaigns, which often require large resources, consist of multiple tasks, and generate vast amounts of data. In this context, extreme-scale workflows have been the key factor in enabling scientific discoveries by helping scientists automate the dependencies and data exchanges between workflow tasks, instead of managing those manually. Here, in this paper, we present representative extreme-scale workflows and feature workflow systems developed by JLESC participating institutions. We present lessons learned while developing these tools, alongside with the open challenges and future research directions in the field of extreme-scale workflows.
Bigger is often said to be better, and the newest extreme-scale computers certainly are bigger, with millions of processing units. Moreover, the breadth of science performed on the U.S. Department of Energy (DOE) computing facilities is expanding, with new technology such as artificial intelligence emerging. These advances are exciting, creating new opportunities for scientific discovery; however, they also raise new questions for scientists who want to exploit these advances for tackling more complex problems. Will my simulation code be able to utilize the accelerators in extreme-scale computing systems? Can I take advantage of the deepening memory hierarchy in heterogeneous processors? Is there a way around bottlenecks caused by the widening ratio of peak floating-point operations per second to I/0 bandwidth? How can I manage my huge amounts of data effectively? Can I analyze data in situ, or must I transfer it to offline storage for later analysis? To address such questions, DOE announced that it is providing $57.5 million over the next five years for two multidisciplinary teams — FASTMath and RAPIDS2 — to develop new tools and techniques to harness supercomputers for scientific discovery. The teams, called SciDAC Institutes, are part of the Scientific Discovery through Advanced Computing program.
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Common and community software packages, such as ROOT, Geant4 and event generators have been a key part of the LHC's success so far and continued development and optimisation will be critical in the future. The challenges are driven by an ambitious physics programme, notably the LHC accelerator upgrade to high-luminosity, HL-LHC, and the corresponding detector upgrades of ATLAS and CMS. In this document we address the issues for software that is used in multiple experiments (usually even more widely than ATLAS and CMS) and maintained by teams of developers who are either not linked to a particular experiment or who contribute to common software within the context of their experiment activity. We also give space to general considerations for future software and projects that tackle upcoming challenges, no matter who writes it, which is an area where community convergence on best practice is extremely useful.
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Ion trajectory simulation in mass spectrometry systems from injection to detection is technically challenging but very important for better understanding the ion dynamics in instrument development. Here, in this work, we present SimELIT (Simulator of Eulerian and Lagrangian Ion Trajectories), a novel ion trajectory simulation platform. SimELIT is built upon a suite of multiphysics solvers compiled into OpenFOAM (an open-source numerical solver library particularly used for computational mechanics), with a simple web-based graphical user interface (GUI) allowing users to define the details of OpenFOAM cases and run simulations. SimELIT is a modular program and can provide extensions of physics (e.g., gas flows, electrodynamic fields) and thus enable ion trajectory simulations from the ion source to detector. The current version (SimELIT) provides two numerical solvers for ion trajectory simulations–(1) a Lagrangian particle tracker in vacuum and (2) a Eulerian ion density solver in background gas in the presence of electric fields. Here, we describe the architecture of SimELIT, including its use of Docker and the React Framework, and demonstrate the computation of ion trajectories of multiple m/z values in a static/linear voltage drop in vacuum (across a 1 m long flight tube). Further, the drift motion of ions under 1 Torr pressure conditions in a static background (N 2 ) gas through a 20 V/cm static electric field is shown. The results produced from SimELIT were compared with SIMION and theoretical estimates. In addition, we report the computation of ion trajectories in electrodynamic fields within a planar FAIMS device operating at atmospheric pressure.
SAND2023-05132O Videoshare is an application that allows users to communicate in a variety of ways, including voice, video, and text, over a local network without having to use a central server or an internet connection. The software features: • Screen-sharing and connecting to external IP cameras. • Ability to hold group calls on computers running the same software and network. • Ability to connect to other computers running the same software. • Curating potential connections and manually adding IP addresses to available connections. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.
Automatic differentiation (AD) is a well-known technique for evaluating analytic derivatives of calculations implemented on a computer, with numerous software tools available for incorporating AD technology into complex applications. However, a growing challenge for AD is the efficient differentiation of parallel computations implemented on emerging manycore computing architectures such as multicore CPUs, GPUs, and accelerators as these devices become more pervasive. In this work, we explore forward mode, operator overloading-based differentiation of C++ codes on these architectures using the widely available Sacado AD software package. In particular, we leverage Kokkos, a C++ tool providing APIs for implementing parallel computations that is portable to a wide variety of emerging architectures. Here we describe the challenges that arise when differentiating code for these architectures using Kokkos, and two approaches for overcoming them that ensure optimal memory access patterns as well as expose additional dimensions of fine-grained parallelism in the derivative calculation. We describe the results of several computational experiments that demonstrate the performance of the approach on a few contemporary CPU and GPU architectures. We then conclude with applications of these techniques to the simulation of discretized systems of partial differential equations.
The Molecular Sciences Software Institute's (MolSSI) Quantum Chemistry Archive (QCArchive) project is an umbrella name that covers both a central server hosted by MolSSI for community data and the Python-based software infrastructure that powers automated computation and storage of quantum chemistry (QC) results. The MolSSI-hosted central server provides the computational molecular sciences community a location to freely access tens of millions of QC computations for machine learning, methodology assessment, force-field fitting, and more through a Python interface. Facile, user-friendly mining of the centrally archived quantum chemical data also can be achieved through web applications found at the website. The software infrastructure can be used as a standalone platform to compute, structure, and distribute hundreds of millions of QC computations for individuals or groups of researchers at any scale. The QCArchiveInfrastructure is open-source (BSD-3C), code repositories can be found at github, and releases can be downloaded via PyPI and Conda. This article is categorized under: Electronic Structure Theory > Ab Initio Electronic Structure Methods Software > Quantum Chemistry Data Science > Computer Algorithms and Programming
The research work at University of California Santa Barbara (UCSB) resulted in several new developments in the areas of scientific machine learning, numerical analysis, and practical methods for data-driven modeling, prediction, reductions, and simulation. Many of the projects were carried out in collaboration with members of the national laboratories at Sandia National Laboratories (SNL), Pacific Northwestern National Laboratories (PNNL), and other institutions. Results included developing new scientific machine learning methods, related theory and mathematical frameworks for analysis and training, data-driven numerical solvers, and related tools and software for scientific computation. During the support period, over 16+ papers were submitted for publication, and 4 open-source software packages were developed and released (available at http://atzberger.org/). In addition, 7+ students and 2 post-docs were mentored in collaboration with the laboratory staff for future careers in academia, government labs, and industry.