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This source code includes tutorials targeting a general audience that will help users to use high performance computing environments and systems at Livermore Computing and beyond. Examples of HPC tools covered include mpi and posix. Tutorials may include source code demonstrating usage.
The Multiphysics Object-Oriented Simulation Environment (MOOSE) serves as a common library of classes between applications developed for advanced reactor analysis, fusion device engineering, spent fuel cask analysis, geochemistry studies, among other fields. These applications drive the development of the framework to meet their needs. Systems in MOOSE group capabilities that share a common purpose and generally common code. They can be leveraged by all downstream applications, providing extensive code re-use and shared maintenance. They facilitate the discovery by new users of the classes meeting at least partially their needs, and offer the same opportunities for customization as other systems. The addition of a new system to MOOSE opens new ways of solving or discretizing nonlinear problems, of performing distributed postprocessing, and a plethora of other needs. While new systems can be introduced in downstream applications rather than at the framework level, the framework team monitors common needs across the community and often triggers their addition. Documentation, training material, development needs can be centralized, limiting duplicated work across the community. The last three years have seen a large expansion in the capabilities of MOOSE. The supporting role of the framework in the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program has created numerous feature requests to support neutronics, thermal hydraulics, computational fluid dynamics and thermo-mechanics simulations in the Griffin, SAM, Pronghorn and Bison applications respectively. Similarly, laboratory-directed research and development (LDRD) projects in additive manufacturing, high-Reynolds flow simulations, structure optimization also necessitate an expansion of the framework capabilities. This summary reports on the new systems created in MOOSE, their design, their capabilities and some of the relevant interfaces.
High-energy physics (HEP) experiments have developed millions of lines of code over decades that are optimized to run on traditional x86 CPU systems. However, we are seeing a rapidly increasing fraction of floating point computing power in leadership-class computing facilities and traditional data centers coming from new accelerator architectures, such as GPUs. HEP experiments are now faced with the untenable prospect of rewriting millions of lines of x86 CPU code, for the increasingly dominant architectures found in these computational accelerators. This task is made more challenging by the architecture-specific languages and APIs promoted by manufacturers such as NVIDIA, Intel and AMD. Producing multiple, architecture-specific implementations is not a viable scenario, given the available person power and code maintenance issues. The Portable Parallelization Strategies team of the HEP Center for Computational Excellence is investigating the use of Kokkos, SYCL, OpenMP, std::execution::parallel and alpaka as potential portability solutions that promise to execute on multiple architectures from the same source code, using representative use cases from major HEP experiments, including the DUNE experiment of the Long Baseline Neutrino Facility, and the ATLAS and CMS experiments of the Large Hadron Collider. This cross-cutting evaluation of portability solutions using real applications will help inform and guide the HEP community when choosing their software and hardware suites for the next generation of experimental frameworks. We present the outcomes of our studies, including performance metrics, porting challenges, API evaluations, and build system integration.
GENE solves the five-dimensional gyrokinetic equations to simulate the development and evolution of plasma microturbulence in magnetic fusion devices. The plasma model used is close to first principles and computationally very expensive to solve in the relevant physical regimes. In order to use the emerging computational capabilities to gain new physics insights, several new numerical and computational developments are required. Here, we focus on the fact that it is crucial to efficiently utilize GPUs (graphics processing units) that provide the vast majority of the computational power on such systems. In this paper, we describe the various porting approaches considered and given the constraints of the GENE code and its development model, justify the decisions made, and describe the path taken in porting GENE to GPUs. We introduce a novel library called gtensor that was developed along the way to support the process. Performance results are presented for the ported code, which in a single node of the Summit supercomputer achieves a speed-up of almost 15× compared to running on central processing unit (CPU) only. Typical GPU kernels are memory-bound, achieving about 90% of peak. Our analysis shows that there is still room for improvement if we can refactor/fuse kernels to achieve higher arithmetic intensity. We also performed a weak parallel scalability study, which shows that the code runs well on a massively parallel system, but communication costs start becoming a significant bottleneck.
The Advanced Test Reactor (ATR) Complex at Idaho National Laboratory (INL) relies on Battery Backed Power (BBP) systems and Uninterruptible Power Supplies (UPS) to ensure continuous power supply to critical components. This project aims to enhance the reliability and functionality of the battery monitoring and control systems by updating the State-of-Charge (SOC) system, Programmable Logic Controller (PLC), and Human-Machine Interface (HMI) for the nuclear safety-related battery banks. The current system, while functional, has areas for improvement, particularly in recharging calculations and alarm functions. The project objectives include developing flow charts, programming the new PLC and HMI, conducting bench tests, and updating design documentation. Additionally, the project ensures compliance with safety standards, develops training materials, creates comprehensive documentation, and integrates seamlessly with existing ATR infrastructure. The new SOC system is designed to be scalable for future upgrades, improve efficiency, enhance data accuracy, implement redundancy features, and achieve project goals within budget constraints while considering environmental impact. The methodology involved familiarizing with BBP and UPS systems, collecting current readings, rescaling signals, learning ladder logic, and updating the HMI. The transition from SLC 5/03 PLC using RS Logix 500 to CompactLogix 5380 using Studio 5000 was a key step. Despite challenges in transferring outdated PLC ladder logic and HMI code, starting from scratch led to a more accurate and efficient monitoring system, contributing to improved safety and operational efficiency. The project is currently awaiting approval of the Engineering Calculation and Analysis Report (ECAR) before implementation.
To evaluate the re-design and reconfiguration of a dual-fluidized bed (DFB) gasification system into a recirculating pyrolysis reactor, Computation Fluid Dynamic (CFD) simulations of the system were conducted. The Barracuda Virtual Reactor® computational particle fluid dynamic code was used to perform simulations of the pyrolysis process. Modeling of the chemical reaction kinetics for both gas phase and solid particle phase were included. The recirculating pyrolysis reactor shown in Fig. 1a is based on a bubbling-bed biomass pyrolyzer and a riser combustor to convert the remaining char. The operational differences in the re-configuration of the DFB gasification system into a recirculating pyrolysis system for the production of bio-oil are (1) replacement of a low-surface area inert bed material with a high-surface-area bed material that has acidic properties to provide catalytic activity for the production of bio-oil with reduced oxygen content, (2) lower temperature and residence time for bio-oil production from pyrolysis, (3) replacement of the fluidization gas in the bubbling bed pyrolyzer from steam to nitrogen, and (4) the reduction of pyrolyzer freeboard volume. The bed material used for catalytic pyrolysis is Sasol 300 (300-micron dia., bulk density 0.94 kg/l, and surface area 130 m2/g) and is a theta-alumina with mild acidity. This is in comparison with previous standard bed material Carbo HSP (430-micron dia., bulk density 2.01 kg/l, and surface area 0.03 m2/g) used for gasification. For bio-oil production, pyrolysis in the bubbling bed requires temperatures in the range of 550 C in comparison with gasification temperatures near 850 C. To attain this lower temperature requires management of the energy mass balances, with control of the bed material recirculation rate between bubbling bed pyrolyzer and riser combustor, the introduction of a nitrogen purge in the pyrolyzer, and adjusting the pressure balance between the two vessels. To extract bio-oil from the pyrolysis reactor with a snorkel, two different freeboard configurations were evaluated. In Fig. 1 b the existing high freeboard configuration is shown and in Fig. 1 c the reduced freeboard design is presented. The introduction of a nitrogen purge for the high free board configuration provided the highest bio-oil production from the CFD simulations. To decrease the bed-material circulation rate, primary and secondary air on the combustor side were reduced, and the pressure on the combustor was slightly increased. A portion of the biomass and bio-oil was observed to be transported to the combustor, leading to a smaller pyrolysis yield. The control of the pyrolyzer temperature is performed by controlling the circulation rate. Good fluidization of the bubbling bed and cascade PID control are required to keep the temperature from oscillating due to large time delay experienced when changing primary and secondary air. (a) (b) (c) Figure 1. (a) Dual Fluidized Bed pyrolysis system configuration, (b) mole fraction of nonpolar biooil in high freeboard configuration, and (c) mole fraction of nonpolar bio-oil in low freeboard configuration with nitrogen purge introduced in both configurations.
In order to accurately model implosion hydrodynamics in a radiation-hydrodynamics code, it is essential to include accurate accounting for energy deposition physics. In inertial confinement fusion (ICF), where capsules are driven by lasers or laser-driven x-rays, energy deposition profiles and energy transport have a strong impact on the development and evolution of capsule dynamics and hydrodynamic instabilities. Nevertheless, accurately modeling laser beam propagation in radiation-hydrodynamics codes presents unique challenges associated with disparate resolution requirements, the potential to seed spurious noise in highly unstable systems, and computational expense. We discuss a new method for coupling laser ray-tracing physics to a radiation hydrodynamics code, developed in the process of implementing the Mazinisin laser ray-trace into the xRAGE radiation hydrodynamics code. In contrast to previous approaches, in which laser ray-tracing is performed on the radiation-hydrodynamics mesh, our method involves a mesh generation and evolution strategy that addresses the unique requirements of the laser ray-trace in a separate mesh, enabling performance enhancements and strategies to reduce noise seeded by the discretization of beams into computational rays. In addition, we have employed several methods to ensure that spurious mesh imprinting is minimized. These involved optimizing the laser and radiation-hydrodynamics meshes as well as interpolation between them and requires the use of an exact initialization method for the radiation-hydrodynamics mesh. Furthermore, these techniques have enabled efficient computation of laser-driven implosions and other experiments with minimal introduction of spurious noise.
Despite the importance of phages for the dynamics and functions of microbial communities, it remains largely unexplored how symbiotic phages adapt in activated sludge systems and influence microbial aggregate stability, which is critical for clarification and reliable performance. Here, based on 12,127 phage contigs recovered from 12 activated sludge microbiomes, the symbiotic phages exhibited broad host ranges and infected dominant prokaryotes in activated sludge. Moreover, these phage communities exhibited high lysogenicity (49% to 66% lysogenic phages) and harbored diverse auxiliary metabolic genes (AMGs) that could enhance microbial aggregate stability, such as genes coding for lipopolysaccharide, peptidoglycan, and extracellular polysaccharide biosynthesis. Additionally, prokaryotic antiviral systems were widely distributed in dominant prokaryotes, particularly the Restriction-Modification (RM) and CRISPR-Cas systems, which could mitigate potential harmful phage infections. Overall, this study reveals the contemporary beneficial relationship between phages and prokaryotic hosts in activated sludge microbiomes and the potential benefits of symbiotic phages on floc stability.
This report documents work performed under a Strategic Partnership Project between Argonne National Laboratory (ANL) and the United Kingdom Atomic Energy Authority (UKAEA). The overall goal of this project is to extend OpenMC [1], a community-developed Monte Carlo particle transport code, to be able to perform fixed-source transmutation calculations. In fission and fusion reactors, the high flux of energetic neutrons causes materials within the reactor to “transmute,” or undergo a nuclear reaction that results in the addition/removal of neutrons and protons from the nucleus of an atom. If subjected to these reactions for long enough, the overall composition and physical properties of the material itself begin to change as a result of transmutation. Such a feature is vital for predicting the decrease in tritium production rate within a breeder blanket during the lifetime of a fusion reactor. OpenMC is capable of simulating neutron transport in fission/fusion systems, thereby allowing it to estimate the flux that causes transmutation. It is also capable of solving the transmutation equations, which determine how the composition of a material changes over time due to neutron irradiation and radioactive decay. However, solving the transmutation equations was previously only possible when the source of neutrons came from a fission system. In a fusion system, the source of neutrons is typically determined by a separate code and then given as an input to the particle transport simulation. This is known as a fixed source calculation. Through this project, we have extended OpenMC to solve the transmutation equations for a fixed source calculation. Evaluating the change in material compositions due to transmutation and its effect on physical properties is of key importance to a range of engineering analyses for fission and fusion systems. For example, in a fusion reactor, estimating the dose rate at different physical locations resulting from irradiated materials in the reactor allows designers to ensure that workers are not exposed to doses beyond applicable regulations. In order to properly dispose of irradiated materials, designers also need to estimate the radiotoxicity, which again relies on knowledge of the material composition at some future time. The specific tasks for this project that were agreed to between ANL and UKAEA were as follows: 1. Make changes and additions in the openmc.deplete and related modules in OpenMC to support transmutation calculations following a fixed source transport simulation. 2. Make necessary changes to OpenMC to model transmutation due to an arbitrary set of reactions needed for fusion applications. Use this new capability to generate a depletion chain file based on the TENDL nuclear data library. 3. Improve the openmc.deplete module in OpenMC to keep track of gases produced as a by-product of nuclear reactions during transmutation calculations. 4. Validate the new capabilities by carrying out fixed-source transmutation calculations on a suitable benchmark problem using OpenMC and a comparable Monte Carlo neutron transport code.
Despite revolutionizing fungal genetic engineering, conventional CRISPR/Cas9-mediated knockouts rely on DNA double-strand breaks (DSBs), which can cause unwanted insertions and deletions, chromosomal abnormalities, and cytotoxicity. Base editors such as adenine base editors (ABEs), which convert A‧T to G‧C, and cytosine base editors (CBEs), which convert C‧G to T‧A, offer a safer alternative by enabling predictable, target-specific single-nucleotide changes without introducing DSBs. To overcome the limitations of traditional genome editing in filamentous fungi, we developed efficient base-editing systems in Aspergillus niger . For the first time, we constructed an ABE in A. niger , achieving up to 80% editing efficiency and inducing predictable A-to-G mutations at the intended intron sites, disrupting gene function through mRNA mis-splicing. We also developed a highly efficient CBE system, capable of introducing premature stop codons with 50–100% efficiency. To broaden the editing scope, we implemented a Cas9-NG variant recognizing a relaxed PAM sequence requiring only a single guanine (G), enabling editing at start codons and splice sites. Leveraging this expanded scope, we established gene disruption approaches by targeting start codons via ABE-mediated A-to-G conversions (ATG-to-GTG and ATG-to-ACG) and CBE-mediated C-to-T conversion (ATG-to-ATA). Additionally, our base-editing systems enable multiplex gRNA delivery and marker-free editing of multiple genes. Collectively, the scope-expanding strategies increase the number of genes targetable for disruption by base-editing in A. niger by 26.3% and enable near-complete coverage of 96% of the coding genes. Overall, this work demonstrates the potential of ABE and CBE systems as versatile, efficient, and safer alternatives to DSBs-based gene disruption in filamentous fungi.
For both coolant and fueled variants of molten salt reactors (MSRs), the corrosion of structural materials is a significant challenge. The corrosion stems from chemical and electrochemical reactions initiated by fissile material, fission products, and impurities in the salt. Lower-fidelity models rely on empirical correlations for mass transfer, simplified lumped temperature profiles, and similar assumptions. They do not capture detailed spatial variations in complex geometries, creating the need for high-fidelity modeling to bridge this gap.As we approach the demonstration and possible deployment of MSRs in this decade, the development of a high-fidelity, high-performance simulator becomes imperative. To simulate the complex electrochemical environment and corrosion within molten salt systems, we have developed the Molten Salt Chemistry And TranspOrt (MOSCATO) code. This endeavor is comprised of three essential components. First, mass transfer equations are coupled with the Navier-Stokes equations in order to account for the transport of species in the salt. Second, the diffusion of alloy constituents, such as Cr, Fe, Ni, etc. is simulated within the structural metals. Third, the alloy and salt domains are coupled to account for the heterogeneous chemical and electrochemical reactions that occur at the salt-alloy interface.MOSCATO manages all three components within the framework of the highly scalable, open-source spectral element method computational fluid dynamics code Nek5000/NekRS. This integration enables MOSCATO to harness the immense computational power of modern high-performance computing resources, ensuring both high fidelity and computational speed.In addition to code development, we have initiated a comprehensive verification and validation campaign, utilizing data from diverse sources. First, MOSCATO's electrochemical solver was verified with reference numerical data. Then validation occurred against experiments: one of a thermal galvanic cell and the other for corrosion in flowing molten salt of FLiNaK (LiF-NaF-KF). This campaign verified and validated MOSCATO as a reliable tool for simulating electrochemical environments and corrosion in molten salt systems.
A numerical simulation-based study to investigate the stability properties of inherently three-dimensional plasma magnetic configurations is presented. These configurations, called stellarators and heliotrons, use external helical coils to provide the twisting magnetic field that is required to confine ionized plasma particles. In contrast to the tokamak configuration, which nominally has the property of axisymmetry, electrical current does not need to be induced in stellarator and heliotron plasma. Experiments have shown that these three-dimensional configurations are remarkably robust to macroscopic instability, even when driven to relatively high levels of plasma pressure. Our understanding of how the plasma is able to withstand macroscopic instability will be enhanced by the work proposed here. The effort will generalize existing numerical modeling capability, and it will apply the new capability to model macroscopic dynamics in these three-dimensional configurations. The development work has been applied to the NIMROD simulation code (https://nimrodteam.org) that was originally based on axisymmetric problem domains. It has been generalized to accommodate the three-dimensional shaping of the plasma volume in stellarators and heliotrons. Its use of equilibrium data has also been generalized, and the implementation allows different numerical representation of the magnetic field. Analysis has been performed to inform the selection of numerical methods, and a method to accelerate the iterative solution of the necessary algebraic systems has been developed and implemented. Verification of the new NIMSTELL code on benchmark problems has also been an important part of the effort.
This code is designed to predict and analyze the decay heat generated in molten salt reactors (MSRs) using a hybrid approach that combines machine learning and segmented polynomial fitting. The accurate prediction of decay heat is essential for reactor safety and the optimization of spent fuel storage. The code operates through several key components: 1) Data Architecture: It incorporates a modular data architecture that handles various MSR-specific operational parameters such as power density, humidity content, and air ingress. These parameters are sampled using Sobol sequences to ensure comprehensive coverage of operational uncertainties. 2) Machine Learning Framework: The code employs a diverse set of machine learning models, including polynomial regression, decision trees, random forests, gradient boosting, support vector regression, k-nearest neighbors, multi-layer perceptrons, and symbolic regression. These models are trained to predict decay heat over a wide temporal range, from immediate shutdown up to 10,000 years. 3) Region-Optimized Training: The temporal domain is divided into multiple regions, each modeled separately to capture distinct decay heat characteristics across different time scales. This approach significantly improves the accuracy and interpretability of predictions. 4) Segmented Polynomial Interpretation (SPI): The SPI method translates machine learning predictions into piecewise polynomial equations. These equations are physically interpretable and can be directly integrated into existing engineering workflows and safety analyses. 5) Front-End Interfaces: The code includes both a Jupyter notebook interface for research development and a Streamlit web application for operational deployment. These interfaces allow users to interactively explore decay heat predictions, adjust operational parameters, and visualize results in real-time. 6) Applications: The framework supports various applications, including safety system validation and spent fuel container optimization. It enables real-time evaluation of worst-case decay heat scenarios, informing the design of passive safety systems and optimizing container designs for long-term storage. Overall, this code provides a robust, accurate, and user-friendly tool for predicting decay heat in MSRs, enhancing reactor safety, and optimizing spent fuel management.
Abstract We present a new implementation of real‐time time‐dependent density functional theory (RT‐TDDFT) for calculating excited‐state dynamics of periodic systems in the open‐source Python‐based PySCF software package. Our implementation uses Gaussian basis functions in a velocity gauge formalism and can be applied to periodic surfaces, condensed‐phase, and molecular systems. As representative benchmark applications, we present optical absorption calculations of various molecular and bulk systems and a real‐time simulation of field‐induced dynamics of a (ZnO) 4 molecular cluster on a periodic graphene sheet. We present representative calculations on optical response of solids to infinitesimal external fields as well as real‐time charge‐transfer dynamics induced by strong pulsed laser fields. Due to the widespread use of the Python language, our RT‐TDDFT implementation can be easily modified and provides a new capability in the PySCF code for real‐time excited‐state calculations of chemical and material systems.
Hydrogeochemical processes associated with Aquifer Thermal Energy Storage (ATES) operations can often impact the system performance owing to mineral precipitation either at the wellbore or in the aquifer owing to changes in temperature and fluid disequilibria. Although failure of ATES systems due to mineral precipitation ("fouling") is common, predictive reactive-transport models have rarely been applied to plan their design and operation. Here, the objective of this study is to develop a reactive-transport model by coupling thermal, hydrological, and chemical (THC) processes to evaluate effects of introduced atmospheric oxygen on water chemistry, mineral precipitation/dissolution, porosity, and permeability changes associated with an ATES system at Stockton University (New Jersey, USA). The THC model builds on a Thermal-Hydrological-Mechanical (THM) model of the site that evaluated system failure owing to possible fracturing in the caprock or around the wellbore. The causes of the system failure are not known – potential causes include hydraulic fracturing owing to elevated pump pressures that took place, a flow pathway created by one of the boreholes, or a pre-existing natural hydrologic connection between the upper unconfined aquifer and the ATES aquifer, any of which could have led to oxygenated water entering the reservoir and causing the observed Fe-oxide fouling on well screens. The THC model is used to evaluate some of the hypotheses and observations regarding system failure owing to geochemical processes. The reactive-transport code TOUGHREACT V4 was used to model the THC processes during seasonal heating and cooling operations at the Stockton ATES site over 6 years of operation. In the THC simulations, the primary effects on geochemistry were observed when the injection water is saturated with atmospheric oxygen. Simulations show greater precipitation of goethite near the cold wells as compared to the warm wells. Although volume fractions of Fe-hydroxides were relatively small, the model was aimed at processes in the aquifer at the scale of meters and larger rather than at the scale of mm or cm (i.e., a well screen). Kaolinite is the dominant precipitating phase, also around the cold wells. Illite dissolves near the cold wells and precipitates near the warm wells. There is a net decrease in the porosity near the cold wells and increase near the warm wells, although a slight amount of thermal contraction near the cold wells and expansion near the warm wells is responsible for a significant proportion of the porosity change. Owing to the coarse discretization of the numerical grid near the wells (compared to the screen thickness) the magnitude of permeability changes at the wellbore are likely underestimated. The reactive transport model in this study can be used for characterization of aquifers, optimizing the operational parameters (temperature, pressure, pH etc.), and planning of mitigation strategies for ATES systems.
StochasticGW is a code for computing accurate quasi-particle (QP) energies of molecules and material systems in the GW approximation. StochasticGW utilizes the stochastic Resolution of the Identity (sROI) technique to enable a massively parallel implementation with computational costs that scale semilinearly with system size, allowing the method to access systems with tens of thousands of electrons. Here, we introduce a new implementation, StochasticGW-GPU, for which the main bottleneck steps have been ported to GPUs and give substantial performance improvements over previous versions of the code. We showcase the new code by computing band gaps of hydrogenated silicon clusters (Si x H y ) containing up to 10,001 atoms and 35,144 electrons, and we obtain individual QP energies with a statistical precision of better than ±0.03 eV with times-to-solution of less than 1 h.
Bacterial phosphosignaling has long been synonymous with the histidine kinases of the two component systems (TCSs), but many bacteria, including Mycobacterium tuberculosis (Mtb), also code for Ser/Thr protein kinases (STPKs). STPKs are the main phosphosignaling enzymes in eukaryotes, but the full extent of phosphorylation on protein Ser/Thr and Tyr (O-phosphorylation) in bacteria is unclear. Here, we explored the global signaling capacity of the STPKs in Mtb. We generated a panel of STPK loss- and gain-of-function strains and measured the resulting O-phosphorylation and transcriptional changes. This deep phosphoproteome shows that O-phosphorylation in Mtb is a vastly underexplored protein modification that affects >70% of the proteome. The substrate-kinase interactions of STPKs show an extensive interface with the transcriptional machinery, resulting in STPK regulation of gene expression of over 30% of Mtb genes. Finally, Mtb O-phosphorylation gives rise to an expansive, distributed, and cooperative network of a complexity that has previously only been associated with eukaryotic phosphosignaling networks.
STFNO (Sparsified Time-dependent PDEs FNO code) is an extension of the popular Fourier Neural Operator (FNO) architecture to the solution of coupled systems of time-dependent partial differential equations. STFNO leverages the sparsified dependencies on the field quantities based on the semi-discretiezed form of the PDEs, enabling significant reduction in the number of model parameters. STFNO has been extensively tested on two fusion simulation codes, NIMROD and GTC, and can be easily tailored to other systems of PDEs.