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teemi: An open-source literate programming approach for iterative design-build-test-learn cycles in bioengineering

Synthetic biology dictates the data-driven engineering of biocatalysis, cellular functions, and organism behavior. Integral to synthetic biology is the aspiration to efficiently find, access, interoperate, and reuse high-quality data on genotype-phenotype relationships of native and engineered biosystems under FAIR principles, and from this facilitate forward-engineering strategies. However, biology is complex at the regulatory level, and noisy at the operational level, thus necessitating systematic and diligent data handling at all levels of the design, build, and test phases in order to maximize learning in the iterative design-build-test-learn engineering cycle. To enable user-friendly simulation, organization, and guidance for the engineering of biosystems, we have developed an open-source python-based computer-aided design and analysis platform operating under a literate programming user-interface hosted on Github. The platform is called teemi and is fully compliant with FAIR principles. In this study we apply teemi for i) designing and simulating bioengineering, ii) integrating and analyzing multivariate datasets, and iii) machine-learning for predictive engineering of metabolic pathway designs for production of a key precursor to medicinal alkaloids in yeast. The teemi platform is publicly available at PyPi and GitHub.

59 BASIC BIOLOGICAL SCIENCES↗

Integration of the Kromek D3S Detector and Spot Robot For Secondary Inspections

Inspecting vehicles and containers for the presence of nuclear material is a challenging task for border control and security. When performed manually by inspectors, this task also has an associated risk of exposing the inspectors to unknown radiation. With the advent of agile, easy-to-program, quadruped robots like the Boston Dynamics Spot, automation of secondary inspection can improve the efficiency of the inspection process and alleviates the radiation risks to inspectors. In this project, Brookhaven National Laboratory and the University of Massachussetts at Lowell explored how to automate a simple secondary inspection mission. The Spot robot comes with its own software development kit (SDK) that allows clients/users to write custom code in the Python programming language to control the robot. Spot also has a payload computer called Spot-CORE, which runs the Ubuntu Linux operating system and allows users to integrate external sensors, such as a radiation detector, with Spot. In this study, the Kromek D3S detector has been integrated with Spot via the Spot-CORE, allowing Spot to capture gamma spectra and neutron counts for a specified acquisition period. Two custom routines, search and confirmation, have been developed and executed in this specified order. The search routine directs Spot to go around the nearest obstacle, e.g., vehicle and container, in a preset distance and step to collect gamma and neutron gross counts with the D3S detector. The radiation data and the robot location corresponding to each step are stored and fed to the confirmation routine at the end of the search. The confirmation routine then navigates Spot to the locations of the highest gamma or neutron counts to perform a long, e.g., one minute, measurement, and gives the operators the signature gamma spectra and neutron counts at the hotspots. This paper presents a detailed description of this automated system along with results of the preliminary tests in identifying the location and signature of a 137Cs radiation source in a vehicle.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

Variational Quantum Chemistry Programs in JaqalPaq

We present example quantum chemistry programs written with JaqalPaq, a python meta-programming language used to code in Jaqal (Just Another Quantum Assembly Language). These JaqalPaq algorithms are intended to be run on the Quantum Scientific Computing Open User Testbed (QSCOUT) platform at Sandia National Laboratories. Our exemplars use the variational quantum eigensolver (VQE) quantum algorithm to compute the ground state energies of the H2, HeH+, and LiH molecules. Since the exemplars focus on how to program in JaqalPaq, the calculations of the second-quantized Hamiltonians are performed with the PySCF python package, and the mappings of the fermions to qubits are obtained from the OpenFermion python package. Using the emulator functionality of JaqalPaq, we emulate how these exemplars would be executed on an error-free QSCOUT platform and compare the emulated computation of the bond-dissociation curves for these molecules with their exact forms within the relevant basis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Cardinal: Seismic and Geoacoustic Array Processing

Data collected via seismic and infrasound array deployments are leveraged in the geosciences to detect and characterize a myriad of natural and anthropogenic sources. These deployments consist of numerous sensors placed in a predetermined configuration to amplify signal strength and improve the efficacy of array processing techniques used to measure signal directionality and waveform coherence. High‐fidelity feature extraction is often predicated on interstation distance as well as the frequency content and wavelength of an incident signal. Numerous array processing softwares analyze data in sequential frequency bands to obtain a more detailed characterization of a signal. However, current algorithms are limited in their ability to determine optimal array configuration for each band. We introduce an open‐source Python code, called Cardinal, to process seismic and infrasound array data in discretized time–frequency space with the option of applying an adaptive array design to determine optimal subarray configuration for each frequency band. To reduce computational time, the array processing step can be run in parallel using multithreading. Furthermore, the software has the capability to aggregate array processing results from different time–frequency pixels to produce separate sets of detections, or families, with added utility via the application of an adaptive semblance threshold, which aids in isolating signals‐of‐interest from coherent background noise. Upon appropriate configuration, Cardinal exhibits the potential to combine distinct seismic and infrasound phases into separate families.

Adaptive Array↗

S4PST: Sustainability for Programming Systems and Tools: May Workshop Report

The US Department of Energy (DOE) Exascale Computing Project (ECP) has fostered and strengthened the use of modern software engineering practices for developing applications and libraries, and this effort has resulted in the coordinated and interoperable E4S1 and xSDK2 ecosystems. Although this approach is cost-effective, it relies on robust programming systems and tools (PST) as the underlying foundation for our HPC software. At present, our primary PST stack consists of traditional high-performance computing (HPC) languages, namely Fortran, C, C++, and the popular Python language for data analysis and AI workflows. These languages support various programming frameworks and run-time abstractions that enable parallelism and concurrency across multiple node architectures and thousands of nodes through a variety of interconnect systems. However, to accommodate users’ diverse needs, certain aspects of the HPC ecosystem are delegated to vendor-specific or third-party implementations that extend beyond a particular scientific domain. This broader scope results in a multitude of specifications and variations, which leads to a complex orchestration of many-ecosystems. Unfortunately, this complexity in the ecosystem imposes additional overhead costs on consumers during the latter stages of the development cycle. In addition to the software ecosystem challenge, the upcoming conclusion of the ECP by December 2023 has raised significant concerns within the HPC programming systems community, from both the economic and social perspectives. The ECP has implemented a management structure for software development and funding decisions across all ECP participants by following a conventional hierarchical and centralized approach. However, this structure has prompted certain considerations within the community, particularly in anticipation of the Software Sustainability initiative by the DOE’s Advanced Scientific Computing Research Program (ASCR). For the success of this new initiative, it is of utmost importance to secure consistent funding and foster close engagement with researchers and core developers of existing programming-system products. This collaboration is vital to maintaining the critical capabilities of the current software during the transition phase while proactively adapting to future technology and workforce trends. The community recognizes the significance of adapting to emerging trends and is aware of the inherent fragility of the HPC software ecosystem, particularly in relation to programming systems that cater to all users. The ability to adapt and evolve is essential to staying relevant and effectively addressing these technical, economic, and social challenges. The S4PST team, which represents one of the six ASCR Software Sustainability seedling projects, is dedicated to tackling these challenges through community-based approaches that go beyond the scope of the DOE. This involves collaboration between national laboratories with academia, non-DOE institutions, hardware and system vendors, and international partners. By fostering these partnerships, we aim to create a robust and sustainable HPC software ecosystem that can effectively meet the needs of the community. This new community effort, driven by the eight DOE labs, will take on the responsibility of guiding funding decisions for programming-systems development and maintenance with transparency and consistency across all decisions. Additionally, the team will offer common technical services to the programming systems community, irrespective of their funding situations, and facilitate community-wide incubation to proactively nurture the software ecosystem. By actively engaging with stakeholders and employing a collaborative approach, we can collectively shape the future of programming systems and ensure a robust and thriving HPC software landscape. On May 11–12, 2023, the S4PST team conducted its inaugural kick-off workshop at the Innovative Computing Laboratory (ICL) in the University of Tennessee, Knoxville, hosted by Hartwig Anzt. The workshop encompassed various sessions dedicated to presentations and discussions, with the aim of comprehending the team members’ perspectives on the vision of software sustainability. Additionally, the workshop aimed to identify the technical, economic, and social requirements for sustaining the programming-systems community in the field of HPC. This report provides a summary of the S4PST effort by highlighting five major thrust areas discussed during the workshop: (i) community, (ii) technical support, (iii) training and diversity, (iv) verification, validation and correctness, and (v) emerging technologies. It also encompasses an overview of the presentations and discussions held throughout the event, our views and potential synergies with other seedling efforts, along with the outcomes and key takeaways from our initial discussions.

97 MATHEMATICS AND COMPUTING↗

pyTCR: A tropical cyclone rainfall model for python

pyTCR is a climatology software package developed in the Python programming language. It integrates the capabilities of several legacy physical models and increases computational efficiency to allow rapid estimation of tropical cyclone (TC) rainfall consistent with the large-scale environment. Specifically, pyTCR implements a horizontally distributed and vertically integrated model [Zhu et al., 2013] for simulating rainfall driven by TCs. Along storm tracks, rainfall is estimated by computing the cross-boundary-layer, upward water vapor transport caused by different mechanisms including frictional convergence, vortex stretching, large-scale baroclinic effect (i.e., wind shear), topographic forcing, and radiative cooling [Lu et al., 2018]. The package provides essential functionalities for modeling and interpreting spatio-temporal TC rainfall data. pyTCR requires a limited number of model input parameters, making it a convenient and useful tool for analyzing rainfall mechanisms driven by TCs. To sample rare (most intense) rainfall events that are often of great societal interest, pyTCR adapts and leverages outputs from a statistical-dynamical TC downscaling model [Lin et al., 2023] capable of rapidly generating a large number of synthetic TCs given a certain climate. As a result, pyTCR significantly reduces computational effort and improves the efficiency in capturing extreme TC rainfall events at the tail of the distributions from limited datasets. Furthermore, the TC downscaling model is forced entirely by large-scale environmental conditions from reanalysis data or coupled General Circulation Models (GCMs), simplifying the projection of TC-induced rainfall and wind speed under future climate using pyTCR. Finally, pyTCR can be coupled with hydrological and wind models to assess risks associated with independent and compound events (e.g., storm surges and freshwater flooding).

54 ENVIRONMENTAL SCIENCES↗

PyGDH: Python Grid Discretization Helper

Mathematical models expressed in the form of discretized equations play an important role inmany scientific disciplines. In our experience, few domain scientists have sufficient backgroundin numerical computing (or the time required to acquire such a background) to use manyflexible and powerful but complex open source packages, such as FEniCS (Alnæs et al., 2015)and OpenFOAM (The OpenFOAM Foundation Ltd, n.d.). Many user-friendly open sourcepackages, such as FiPy (J. E. Guyer & Warren, 2009), and many commercial packages, suchas COMSOL Multiphysics (COMSOL AB, n.d.) and Simcenter STAR-CCM+ (Siemens DigitalIndustries Software, n.d.), provide limited flexibility in the equations that users can express.Additionally, the use of commercial packages, which by nature do not perform calculationstransparently, can hinder reproducibility, which is vital to the scientific process. PyGDH(“pigged”) is a Python 2 / Python 3 (Python Software Foundation, 1991–2020) package thatis meant to be accessible to scientists who might not be specialists in scientific computing,while approaching the level of flexibility associated with writing dedicated programs tailoredto solving specific problems. The PyGDH User’s Guide provides detailed instructions forcreating numerical models, including a brief introduction to necessary command line andPython (Python Software Foundation, 1991–2020) skills, and discussions of discretization andvalidation. Note that PyGDH emphasizes flexibility and simplicity over performance, and wasnot designed for high-performance applications or models describing complex spatial domains.

97 MATHEMATICS AND COMPUTING↗

Equation-based and data-driven modeling: Open-source software current state and future directions

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.

97 MATHEMATICS AND COMPUTING↗

PythonFOAM: In-situ data analyses with OpenFOAM and Python

Here, we outline the development of a general-purpose Python-based data analysis tool for OpenFOAM. Our implementation relies on the construction of OpenFOAM applications that have bindings to data analysis libraries in Python. Double precision data in OpenFOAM is cast to a NumPy array using the NumPy C-API and Python modules may then be used for arbitrary data analysis and manipulation on flow-field information. We highlight how the proposed wrapper may be used for an in-situ online singular value decomposition (SVD) implemented in Python and accessed from the OpenFOAM solver PimpleFOAM. Here, 'in-situ' refers to a programming paradigm that allows for a concurrent computation of the data analysis on the same computational resources utilized for the partial differential equation solver. In addition, to demonstrate parallel deployments, we deploy a distributed SVD, which collects snapshot data across the ranks of a distributed simulation to compute the global left singular vectors. Crucially, both OpenFOAM and Python share the same message passing interface (MPI) communicator for this deployment which allows Python objects and functions to exchange NumPy arrays across ranks. Subsequently, we provide scaling assessments of this distributed SVD on multiple nodes of Intel Broadwell and KNL architectures for canonical test cases such as the large eddy simulations of a backward facing step and a channel flow at friction Reynolds number of 395. Finally, we demonstrate the deployment of a deep neural network for compressing the flow-field information using an autoencoder to demonstrate an ability to use state-of-the-art machine learning tools in the Python ecosystem.

97 MATHEMATICS AND COMPUTING↗

Improved Verification and Validation Testing and Tools [Slides]

All MCNP team supported V&V test suites are now developed in a separate repository from the MCNP source code within a Python-based framework. This entire framework will be distributed with the upcoming MCNP6.3 release. Most V&V test suites distributed with MCNP6.2 will be distributed in new framework. New V&V test suites are done or being worked on for the MCNP6.3 release.

97 MATHEMATICS AND COMPUTING↗

Generating Models of the Flattop Critical Assembly for Benchmark Experiments with Python

Los Alamos National Laboratory has been performing nuclear criticality experiments since 1946 at the Pajarito site, starting the Los Alamos Critical Experiments Facility in 1948. A transition period occurred between 2004 and 2011 as operations moved to the National Criticality Experiments Research Center (NCERC), where criticality experiments are now performed. Criticality experiments are essential for determination and verification of nuclear data used in calculations and modeling—such as radiation transport codes—throughout the industry, enhancing nuclear criticality safety. In addition to nuclear data validation and benchmarking, the remotely operated critical assemblies at NCERC are used for a variety of experiments and training classes supporting criticality safety.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Library for Evolutionary Algorithms in Python (LEAP)

There are generally three types of scientific software users: users that solve problems using existing science software tools, researchers that explore new approaches by extending existing code, and educators that teach students scientific concepts. Python is a general-purpose programming language that is accessible to beginners, such as students, but also as a language that has a rich scientific programming ecosystem that facilitates writing research software. Additionally, as high-performance computing (HPC) resources become more readily available, software support for parallel processing becomes more relevant to scientific software.There currently are no Python-based evolutionary computation frameworks that support all three types of scientific software users. Moreover, some support synchronous concurrent fitness evaluation that do not efficiently use HPC resources. We pose here a new Python-based EC framework that uses an established generalized unified approach to EA concepts to provide an easy to use toolkit for users wishing to use an EA to solve a problem, for researchers to implement novel approaches, and for providing a low-bar to entry to EA concepts for students. Additionally, this toolkit provides a scalable asynchronous fitness evaluation implementation friendly to HPC that has been vetted on hardware ranging from laptops to the world’s fastest supercomputer, Summit.

Coletti, Mark↗

Using Parameter Sweep in WaterTAP to Analyze New Water Treatment Technologies

We describe a powerful and generalized parameter sweep tool in this report that was originally developed to analyze the performance of existing and novel water treatment models being developed in WaterTAP. Since WaterTAP is built upon IDAES and Pyomo, the parameter sweep tool can be used to systematically explore and debug the behavior of most Pyomo and IDAES numerical models. In order to enable meaningful analyses, the parameter sweep tool has been designed with the following features: 1) Model flexibility: The parameter sweep tool does not enforce any restrictions on the types of models that can be used with it. As long as a Pyomo model can be solved and the parameter is active and mutable, the tool only needs functions that describe how to run the model, the sweep parameters, and the output quantities of interest. 2) Flexible sampling: The parameter sweep tool has inbuilt functions to generate samples from a random distribution or a multidimensional Euclidean space. Furthermore, the users have to ability to supply samples generated from a tool of their choice. 3) Multiple sweep types: A user can choose from one of 3 types of parameter sweeps depending on their needs. 4) Detailed outputs: Outputs generated by the parameter sweep tool can be stored in detailed H5 file or user-friendly CSV files for post processing. 5) Parallel computing: The parameter sweep supports shared and distributed memory parallel computing to enable the use of high performance computers (HPC) for large-scale analyses. 6) Modular: The parameter sweep tool is self-contained and can easily be integrated within an outer-loop analysis or as desired by the user. 7) Ease of use: The tool is well documented and a simple sweep can be easily executed by following the online documentation in a few lines of code. We demonstrate the use of the parameter sweep tool on a simple water treatment system from the WaterTAP repository and show its parallel scaling performance on an Apple laptop and NREL's Eagle HPC. The parameter sweep tool is actively being used with models currently being developed within WaterTAP and we expect its use to grow beyond it to other IDAES and Pyomo models.

97 MATHEMATICS AND COMPUTING↗

VENTSAR V3.0: A Python GUI for Estimating Contaminant Concentrations on or Near Buildings Due to Building Effects and Plume Rise and For Calculating Inhalation and Plume Shine Doses

VENTSAR: Originated as VENTAX (Smith and Weber 1983) on the IBM Mainframe at the Savannah River Site (SRS) as a Fortran program. Updated to VENTSAR XL V1.0 (Simpkins 1997) as a spreadsheet version using macros created in Microsoft Excel. Later updated to VENTSAR XL V2.0 (Dixon 2018) as a spreadsheet executing a modified version of the original VENTAX Fortran code. Estimates contaminant concentrations on or near a building from a release at a nearby location. Calculates concentrations for a given meteorological exceedance probability or for a given stability and wind speed combination. Can model a single building with or without a penthouse on top or a ground location from either a stack or ground release. Plume rise can be considered. Contaminant releases can be chemical or radioactive with downwind concentrations determined at user-specified distances. Wind passing over and around buildings creates a complicated dispersion pattern. Air-intake vents may be located on building roofs or near the ground downwind of a release source. An estimation of pollutant concentrations on or near a structure is important in determining expected pollutant levels. Meteorological data are selected based on a specific area of the site. Fortran-based VENTAX able to make fast, complex mathematical calculations. Not user-friendly VENTSAR XL V1.0 no longer supported due to obsolete Excel macros. VENTSAR XL V2.0 an interim solution using an Excel spreadsheet to interface with the modified VENTAX Fortran code. Requires user to have Microsoft Excel. Not an intuitive interface for someone unfamiliar with VENTSAR. Does not perform dose calculations. VENTSAR V3.0 goal to combine the strengths of previous versions of VENTSAR into a single, powerful yet user-friendly program with a Graphical User Interface (GUI). Not dependent upon a specific program or plug-ins. Self-contained package to be used on any computer running Microsoft Windows. User-friendly, intuitive GUI created in Python for parameter input. Executes same modified VENTAX Fortran code as VENTSAR XL V2.0. Outputs formatted text file of completed calculations for easy review and dissemination. Performs inhalation and plume shine dose calculations for up to 11 user-selected nuclides from a nuclide dose factor library of almost 500 nuclides. 12 test cases were created for verification of V1.0 and V2.0. Same test cases run in V3.0 to verify correct performance. V3.0 produced similar results to V1.0. Confirmed GUI did not alter calculations in any way. Comparisons of the test case results confirm the V3.0 GUI does not influence the VENTSAR calculations. Simply passes same input parameters to VENTAX Fortran code for execution. Provides end user an easy-to-use, intuitive tool to quickly make building effect and plume rise calculations, as well as, inhalation and plume shine dose calculations. No experience with or working knowledge of Fortran, Excel, command line, or macros required. Self-contained package allows VENTSAR be deployed to any Windows computer without the need for specific programs or plug-ins.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

MILK : a Python scripting interface to MAUD for automation of Rietveld analysis

Modern diffraction experiments ( e.g. in situ parametric studies) present scientists with many diffraction patterns to analyze. Interactive analyses via graphical user interfaces tend to slow down obtaining quantitative results such as lattice parameters and phase fractions. Furthermore, Rietveld refinement strategies ( i.e. the parameter turn-on-off sequences) tend to be instrument specific or even specific to a given dataset, such that selection of strategies can become a bottleneck for efficient data analysis. Managing multi-histogram datasets such as from multi-bank neutron diffractometers or caked 2D synchrotron data presents additional challenges due to the large number of histogram-specific parameters. To overcome these challenges in the Rietveld software Material Analysis Using Diffraction ( MAUD ), the MAUD Interface Language Kit ( MILK ) is developed along with an updated text batch interface for MAUD . The open-source software MILK is computer-platform independent and is packaged as a Python library that interfaces with MAUD . Using MILK , model selection ( e.g. various texture or peak-broadening models), Rietveld parameter manipulation and distributed parallel batch computing can be performed through a high-level Python interface. A high-level interface enables analysis workflows to be easily programmed, shared and applied to large datasets, and external tools to be integrated with MAUD . Through modification to the MAUD batch interface, plot and data exports have been improved. The resulting hierarchical folders from Rietveld refinements with MILK are compatible with Cinema: Debye–Scherrer , a tool for visualizing and inspecting the results of multi-parameter analyses of large quantities of diffraction data. In this manuscript, the combined Python scripting and visualization capability of MILK is demonstrated with a quantitative texture and phase analysis of data collected at the HIPPO neutron diffractometer.

97 MATHEMATICS AND COMPUTING↗

Equilipy: a python package for calculating phase equilibria

The CALPHAD (CALculation of PHAse Diagram) approach (Nigel Saunders & Miodownik, 1998) provides predictions for thermodynamically stable phases in multicomponent-multiphase materials across a wide range of temperatures. Consequently, the CALPHAD calculations became an essential tool in materials and process design (Luo, 2015). Such design tasks frequently require navigating a high-dimensional space due to multiple components involved in the system. This increasing complexity demands high-throughput CALPHAD calculations, especially in the rapidly evolving field of alloy design. In response to the need, we developed Equilipy an open-source Python package designed for calculating phase equilibria of multicomponent-multiphase systems. Equilipy is specifically tailored for high-throughput CALPHAD calculations, offering parallel computations across multiple processors and nodes with the given NPT input conditions namely elemental compositions (N), pressure (P), and temperature (T). Equilipy utilizes the program structure and Gibbs energy functions from the Fortran-based program, Thermochimica (Piro et al., 2013), with incorporating a new Gibbs energy minimization algorithm. This algorithm, originally developed by Capitani and Brown in 1987 (Capitani & Brown, 1987), has been revised and implemented to enhance the stability and performance of calculations. The Fortran codes are precompiled and interfaced with Python via F2PY, ensuring high computation speed. Benchmark tests shown in Figure 1 demonstrate that Equilipy’s computation speed is comparable to those of established commercial software, TC-Python and PanPython. This result highlights its efficiency and potential applications in various scientific and industrial fields.

97 MATHEMATICS AND COMPUTING↗