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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Genome evolution and transcriptome plasticity is associated with adaptation to monocot and dicot plants in Colletotrichum fungi

Colletotrichum fungi infect a wide diversity of monocot and dicot hosts, causing diseases on almost all economically important plants worldwide. Colletotrichum is also a suitable model for studying gene family evolution on a fine scale to uncover events in the genome associated with biological changes. Here we present the genome sequences of 30 Colletotrichum species covering the diversity within the genus. Evolutionary analyses revealed that the Colletotrichum ancestor diverged in the late Cretaceous in parallel with the diversification of flowering plants. We provide evidence of independent host jumps from dicots to monocots during the evolution of Colletotrichum, coinciding with a progressive shrinking of the plant cell wall degradative arsenal and expansions in lineage-specific gene families. Comparative transcriptomics of 4 species adapted to different hosts revealed similarity in gene content but high diversity in the modulation of their transcription profiles on different plant substrates. Combining genomics and transcriptomics, we identified a set of core genes such as specific transcription factors, putatively involved in plant cell wall degradation. These results indicate that the ancestral Colletotrichum were associated with dicot plants and certain branches progressively adapted to different monocot hosts, reshaping the gene content and its regulation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

An Algorithmic and Software Pipeline for Very Large Scale Scientific Data Compression with Error Guarantees

Efficient data compression is becoming increasingly critical for storing scientific data because many scientific applications produce vast amounts of data. This paper presents an end-to-end algorithmic and software pipeline for data compression that guarantees both error bounds on primary data (PD) and derived data, known as Quantities of Interest (QoI).We demonstrate the effectiveness of the pipeline by compressing fusion data generated by a large-scale fusion code, XGC, which produces tens of petabytes of data in a single day. We demonstrate that the compression is conducted by setting aside computational resources known as staging nodes, and does not impact the simulation performance. For efficient parallel I/O, the pipeline uses ADIOS2, which many codes such as XGC already use for their parallel I/O. We show that our approach can compress the data by two orders of magnitude while guaranteeing high accuracy on both the PD and the QoIs. Further, the amount of resources required by compression is a few percent of the resources required by simulation while ensuring that the compression time for each stage is less than the corresponding simulation time.This pipeline consists of three main steps. The first step decomposes the data using domain decomposition into small subdomains. Each subdomain is then compressed independently to achieve a high level of parallelism. The second step uses existing techniques that guarantee error bounds on the primary data for each subdomain. The third step uses a post-processing optimization technique based on Lagrange multipliers to reduce the QoI errors for data corresponding to each subdomain. The Lagrange multipliers generated can be further quantized or truncated to increase the compression level. All of the above characteristics of our approach make it highly practical to apply on-the-fly compression while guaranteeing errors on QoIs that are critical to the scientists.

Banerjee, Tania↗
DOE OSTI2017

Extreme scale unstructured adaptive CFD for aerodynamic flow control

Understanding the flow of fluid, either liquid or gas, through and around solid bodies has challenged man since the dawn of scientific inquiry. Many of the great minds of science and mathematics have progressively built up a hierarchy of fluid models since fluid flow impacts our lives in so many fundamental ways - from the early days of flow of water in viaducts to cities, to today's flight of planes. This chapter is concerned with the computational modeling of turbulent flow around aerodynamic bodies such as planes and wind turbines. In this case, viscous effects near the solid bodies create very thin boundary layers that yield highly anisotropic (gradients normal to the surface may be 10 6 larger than gradients along the surface) solutions to the governing non-linear partial differential equations (PDE); the Navier-Stokes equations. Furthermore, turbulent flows develop extremely broad ranges of length and time scales motivating the use of discretization methods capable of employing adaptivity and implicit time integration. The combination of these features - non-linear, anisotropy, adaptivity, and implicit - dramatically raise the complexity of the discretization, posing large challenges to efficient scalable parallel implementation. However, through careful design, the more complex algorithms can provide great reductions in computational cost relative to simpler methods (e.g., Cartesian grids with explicit time integration) that are easier to mate efficiently to hardware. In this chapter, we not only describe our approach but we also address the fact that while complex algorithms may never be as efficient flop-for-flop as simple methods, in the important measure of science-per-core-hour, they can still win big by making complex features like adaptivity and implicit methods as efficient and scalable as possible.

42 ENGINEERING↗
DOE OSTI2019

Proactive Data Containers for Scientific Storage (Final Report)

Emerging HPC systems are expected to be deployed with an unprecedented level of complexity, due to a deep system memory/storage hierarchy and heterogeneity of the storage hardware. This hierarchy is expected to range from CPU cache through several levels of volatile memory to nonvolatile memory, traditional hard disks, and tape. Simple and efficient methods of data management and movement through this hierarchy is critical for scientific applications using exascale systems. Existing storage system and I/O (SSIO) technologies face severe challenges in dealing with these requirements. POSIX and MPI I/O standards that are the basis for existing I/O libraries and parallel file systems present fundamental challenges in the areas of scalable metadata operations, semantics-based data movement performance tuning, asynchronous operation, and support for scalable consistency of distributed operations. Moving toward new paradigms for SSIO in the extreme-scale era, we have proposed to investigate novel object-based data abstractions and storage mechanisms that take advantage of the deep storage hierarchy and enable proactive automated performance tuning. In order to achieve these overarching goals, we initiated an effort to develop a fundamental new data abstraction, called Proactive Data Containers (PDC). A PDC is a container within a locus of storage (memory, NVRAM, disk, etc.) that stores science data in an object-centric manner. Managing data as objects enables powerful optimization opportunities for data movement and transformations. The R&D focus of this project are: 1) formulation of object-oriented PDCs and their mapping in different levels of the exascale storage hierarchy; 2) efficient strategies for moving data in deep storage hierarchies using PDCs; 3) techniques for transforming and reorganizing data based on application requirements; and 4) novel analysis paradigms for enabling data transformations and user-defined analysis on data in PDCs. Toward achieving these overarching goals, we designed an object-centric application programing interface (API) for HPC, scalable metadata management for object-centric storage systems, and data movement optimizations such as Data Elevator for moving data between two levels of storage devices and TAPIOCA for efficient aggregation of data on compute nodes. We then implemented several components of the PDC system. They include metadata management, data placement services, remote procedure calls, data aggregation, etc. We have put them together into the overall PDC framework.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Photon Doppler Velocimetry to Spatially Resolve Plasma Density in a Power Flow Gap

The understanding of power flow plasmas is important as we look towards next generation pulsed power (NGPP) as current losses could prohibit the goals of that facility. Therefore, it is important to have accurate diagnostics of the plasma parameters on the current machines, which can be used to help inform and improve simulations. Having these plasma parameters will help validate models and simulations to provide confidence when they are expanded to conditions relevant to NGPP. One important plasma parameter that can be measured is the electron density, which can be measured by photonic Doppler velocimetry (PDV). A PDV system has several key advantages over other interferometers by measuring relatively low densities (> 1 × 10 15 cm -2 ) with both spatial and temporal resolution. Experiments were performed on the Mykonos pulsed power machine, which is a 1 MA sub scale machine in which recent platforms have been developed to explore current densities relevant to the inner magnetically insulated transmission line (MITL) on the Z machine. Experiments were performed on two different platforms, the thin foil platform and the Mykonos parallel plate platform (MP3). In addition, a combination of both single-point and multi-point measurements were used. The single-point measurements proved to be very promising, providing a clear increase in density at about 70 ns into the current rise on thin foil experiments up to about 5 × 10 17 cm -3 before the probe stopped providing signal. While we did also see returns from multi-point measurements on both platforms, the signals were not as easy to interpret due to strong background effects. However, they do show initial promise for this diagnostic to measure density at several points across a 1 mm gap. These measurements provide insights in how to improve the diagnostic so that it can provide useful information on power flow relevant experiments.

47 OTHER INSTRUMENTATION↗
DOE OSTI2018

A distributed-memory approximation algorithm for maximum weight perfect bipartite matching

We design and implement an efficient parallel approximation algorithm for the problem of maximum weight perfect matching in bipartite graphs, i.e. the problem of finding a set of non-adjacent edges that covers all vertices and has maximum weight. This problem differs from the maximum weight matching problem, for which scalable approximation algorithms are known. It is primarily motivated by finding good pivots in scalable sparse direct solvers before factorization where sequential implementations of maximum weight perfect matching algorithms, such as those available in MC64, are widely used due to the lack of scalable alternatives. To overcome this limitation, we propose a fully parallel distributed memory algorithm that first generates a perfect matching and then searches for weightaugmenting cycles of length four in parallel and iteratively augments the matching with a vertex disjoint set of such cycles. For most practical problems the weights of the perfect matchings generated by our algorithm are very close to the optimum. An efficient implementation of the algorithm scales up to 256 nodes (17,408 cores) on a Cray XC40 supercomputer and can solve instances that are too large to be handled by a single node using the sequential algorithm.

Azad, Ariful↗
DOE OSTI2022

Mesoflow: An Open-Source Reacting Flow Solver for Catalysis at Mesoscale

We present the capabilities and software performance metrics of our open-source continuum solver for catalysis, Mesoflow, developed specifically for modeling transport and chemistry at the mesoscale. Our solver utilizes Cartesian block-structured adaptive mesh refinement to resolve complex catalyst surface morphologies directly obtained from X-ray tomography data. An immersed boundary based formulation enables rapid representation of complex geometries prevalent in most mesoporous catalyst interfaces. The solver is developed on top of open-source performance portable library, AMReX, providing parallel execution capabilities on current and upcoming high-performance-computing (HPC) architectures. Our flexible software framework enables integration of complex chemical mechanisms at heterogenous interfaces and time-split algorithms for circumventing highly disparate reaction and flow time-scales. Our current studies indicate a ten-fold performance gain by using graphics-processing-units (GPUs) compared to a single processor for representative problem sizes (2 million cell mesh). We will also present a brief introduction on how to build and use this software for application problems pertaining to catalytic upgrading and gas transport within porous catalyst particles.

adaptive meshing↗
DOE OSTI2024

Decomposition and Algorithmic Approaches for Solving Large-Scale Process Family Design Problems

Our most recent work expands the water desalination case study from 76 variants to 10,897 variants using the equation-oriented model built in Pyomo as part of the PARETO project. Using the discretization formulation presented in Stinchfield (2024a), rather than solving for all 10,897 variants simultaneously, we decompose the formulation into subproblems containing subsets of variants from the process family. We solve the overall problem with Progressive Hedging (PH) deployed in parallel on a distributed HPC cluster using the open-source Python package mpi-sppy (Knueven et al., 2023). This approach allowed us to solve this process family design problem to ~1.5% relative optimality gap in about 5 hours; in comparison, Gurobi reached ~50% relative optimality gap in about 6 hours (Stinchfield et al., 2024b). However, this approach still requires discretization of the common unit module design ranges; additionally, PH acts as a heuristic for MILP’s with gap-closing capabilities. Ideally, we would not have to use ML surrogates or discretization to solve this problem, instead solving the process family design problem with the equation-oriented model directly to achieve the most accurate results. However, recall that we did not consider solving the MINLP directly due to complexity and size. In this work, we aim to decompose and solve this large-scale MINLP using a Structured Nonlinear Global Optimization algorithm presented by Cao and Zavala (2019).

Stinchfield, Georgia↗
DOE OSTI2023

Near-Cloud Atmospheric Ingredients for Deep Convection Initiation

A lack of routine environmental observations located near deepening cumulus congestus clouds limits verification of important theorized and simulated updraft–environment interaction processes occurring during deep convection initiation (CI). We analyze radiosonde profiles collected during several hundred CI events near a mountain range in central Argentina during the CACTI field campaign. Statistical analyses illustrate environmental conditions supporting radar-observed CI outcomes that span a spectrum of convective cell depths, widths, and durations, as well as events lacking precipitating convection. Tested environmental factors include a large variety of sounding-derived measurements of CAPE, CIN, moisture, terrain-relative winds, vertical shear, and lifted parcel properties, with supplemental model reanalysis of background larger-scale vertical motion. CAPE and CIN metrics do not consistently differentiate CI success from failure. Only a few environmental factors contain consistent monotonic relationships among the spectrum of cloud depths achieved during CI: (i) the depth and strength of background ascent, and (ii) the component of low-level flow oriented parallel to the ridgeline. These metrics suggest that the ability of the surrounding flow to lift parcels to their LFC and terrain-modified flow are consistently relevant processes for CI. Low- to midlevel relative humidity strongly discriminated between CI and non-CI events, likely reflecting entrainment-driven dilution processes. However, we could not confidently conclude that relative humidity similarly discriminated robust from marginal CI events. Circumstantial evidence was found linking cell width, an important cloud property governing the probability of CI, to LCL height, boundary layer depth, depth and magnitude of the CIN layer, and ambient wind shear.

Storm environments↗
DOE OSTI2022

Enhancing scalability of a matrix-free eigensolver for studying many-body localization

We propose several techniques to enhance the parallel scalability of a matrix-free eigensolver designed for studying many-body localization (MBL) of quantum spin chain models with nearest-neighbor interactions and on-site disorder. This type of problem is computationally challenging because the dimension of the associated Hamiltonian matrix grows exponentially with respect to the number of spins L, and we need to average over different realizations of the random disorder to obtain relevant statistical behavior. For each disorder realization, we need to compute eigenvalues from different regions of the spectrum and their corresponding eigenvectors. In previous work, the interior eigenstates for a single eigenvalue problem are computed via the shift-and-invert Lanczos algorithm. Due to the extremely high memory footprint of the LU factorizations, this technique is not well suited for large L’s. For example, we need thousands of compute nodes on modern high performance computing infrastructures to go beyond L = 24. The matrix-free approach does not suffer from this memory bottleneck, however, its scalability is limited by a computation and communication load imbalance. To reduce this imbalance and to significantly enhance the scalability of the matrix-free eigensolver, we reorder the matrix and leverage the consistent space runtime, CSPACER. We also show its efficiency in managing irregular communication patterns at scale compared to optimized MPI non-blocking two-sided and one-sided RMA implementation variants. This effort enables us to study MBL for spin chains with a larger number of spins. The efficiency and effectiveness of the proposed algorithm is demonstrated by computing eigenstates on a massively parallel many-core high performance computer.

METIS↗
DOE OSTI2022

Neuromorphic scaling advantages for energy-efficient random walk computations

Neuromorphic computing, which aims to replicate the computational structure and architecture of the brain in synthetic hardware, has typically focused on artificial intelligence applications. What is less explored is whether such brain-inspired hardware can provide value beyond cognitive tasks. Here we show that the high degree of parallelism and configurability of spiking neuromorphic architectures makes them well suited to implement random walks via discrete-time Markov chains. Overall, these random walks are useful in Monte Carlo methods, which represent a fundamental computational tool for solving a wide range of numerical computing tasks. Using IBM’s TrueNorth and Intel’s Loihi neuromorphic computing platforms, we show that our neuromorphic computing algorithm for generating random walk approximations of diffusion offers advantages in energy-efficient computation compared with conventional approaches. We also show that our neuromorphic computing algorithm can be extended to more sophisticated jump-diffusion processes that are useful in a range of applications, including financial economics, particle physics and machine learning.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Small tensor product distributed active space (STP-DAS) framework for relativistic and non-relativistic multiconfiguration calculations: Scaling from 10 9 on a laptop to 10 12 determinants on a supercomputer

Despite the power and flexibility of configuration interaction (CI) based methods in computational chemistry, their broader application is limited by an exponential increase in both computational and storage requirements, particularly due to the substantial memory needed for excitation lists that are crucial for scalable parallel computing. Here, the objective of this work is to develop a new CI framework, namely, the small tensor product distributed active space (STP-DAS) framework, aimed at drastically reducing memory demands for extensive CI calculations on individual workstations or laptops, while simultaneously enhancing scalability for extensive parallel computing. Moreover, the STP-DAS framework can support various CI-based techniques, such as complete active space (CAS), restricted active space, generalized active space, multireference CI, and multireference perturbation theory, applicable to both relativistic (two- and four-component) and non-relativistic theories, thus extending the utility of CI methods in computational research. We conducted benchmark studies on a supercomputer to evaluate the storage needs, parallel scalability, and communication downtime using a realistic exact-two-component CASCI (X2C-CASCI) approach, covering a range of determinants from 10 9 to 10 12 . Additionally, we performed large X2C-CASCI calculations on a single laptop and examined how the STP-DAS partitioning affects performance.

Complete-active space self-consistent field↗
DOE OSTI2018

Accurate, Fast and Scalable Kernel Ridge Regression on Parallel and Distributed Systems

Kernel Ridge Regression (KRR) is a fundamental method in machine learning. Given an n-by-d data matrix as input, a traditional implementation requires Θ(n2) memory to form an n-by-n kernel matrix and Θ(n3) flops to compute the final model. These time and storage costs prohibit KRR from scaling up to large datasets. For example, even on a relatively small dataset (a 520k-by-90 input requiring 357 MB), KRR requires 2 TB memory just to store the kernel matrix. Additionally, the reason is that n usually is much larger than d for real-world applications. On the other hand, weak scaling becomes a problem: if we keep d and n/p fixed as p grows (p is # machines), the memory needed grows as Θ(p) per processor and the flops as Θ(p2) per processor. In the perfect weak scaling situation, both the memory needed and the flops grow as Θ(1) per processor (i.e. memory and flops are constant). The traditional Distributed KRR implementation (DKRR) only achieved 0.32% weak scaling efficiency from 96 to 1536 processors. In this work, we propose two new methods to address these problems: the Balanced KRR (BKRR) and K-means KRR (KKRR). These methods consider alternative ways to partition the input dataset into p different parts, generating p different models, and then selecting the best model among them. Compared to a conventional implementation, KKRR2 (optimized version of KKRR) improves the weak scaling efficiency from 0.32% to 38% and achieves a 591x speedup for getting the same accuracy by using the same data and the same hardware (1536 processors). BKRR2 (optimized version of BKRR) achieves a higher accuracy than the current fastest method using less training time for a variety of datasets. For the applications requiring only approximate solutions, BKRR2 improves the weak scaling efficiency to 92% and achieves 3505x speedup (theoretical speedup: 4096x).

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

An overlapping domain decomposition method for large-scale problems

Discretization of dynamical models defined through partial differential equations leads to large-scale systems. Time-depending condition involves an iterative integration of such kind of systems. In this paper, a novel technique based on overlapped domain decomposition, without preconditioner and scalable, is presented. Due to the domain decomposition, subproblems are solved in parallel without communications, cutting off the computation time and optimizing the computational cost. This direct method describes an optimized parallel strategy to solve the initial problem, providing the exact solution, up to rounding errors. Moreover, it takes into account both physical nature of the problem and deriving numerical properties of the system. It is highly recommended in case of band matrices and a long time interval because of an increasing gain in terms of performance and computational cost with the number of integrations. A deep analysis of the computational cost concludes the paper.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Numerical modeling of fluid flow in a fault zone: a case of study from Majella Mountain (Italy)

We present the preliminary results of a numerical model of fluid flow in a fault zone, based on field data acquired at the Majella Mountain, (Italy). The fault damage zone is described as a discretely fractured medium, and the fault core as a porous medium. Our model utilizes dfnWorks, a parallelized computational suite, developed at Los Alamos National Laboratory to model the damage zone and characterizes its hydraulic parameters. We present results from the field investigations and the basic computational workflow, along with preliminary results of fluid flow simulations at the scale of the fault.

58 GEOSCIENCES↗
DOE OSTI2018

Self-optimized construction of transition rate matrices from accelerated atomistic simulations with Bayesian uncertainty quantification

Here, a massively parallel method to build large transition rate matrices from temperature-accelerated molecular dynamics trajectories is presented. Bayesian Markov model analysis is used to estimate the expected residence time in the known state space, providing crucial uncertainty quantification for higher-scale simulation schemes such as kinetic Monte Carlo or cluster dynamics. The estimators are additionally used to optimize where exploration is performed and the degree of temperature acceleration on the fly, giving an autonomous, optimal procedure to explore the state space of complex systems. The method is tested against exactly solvable models and used to explore the dynamics of C15 interstitial defects in iron. Our uncertainty quantification scheme allows for accurate modeling of the evolution of these defects over timescales of several seconds.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Domain-decomposition nonlinear manifold reduced order model

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.

Diaz, AlejandroN↗
DOE OSTI2023

LLNL/thicket

Thicket is a python-based toolkit for Exploratory Data Analysis (EDA) of parallel performance data that enables performance optimization and understanding of applications’ performance on supercomputers. It bridges the performance tool gap between being able to consider only a single instance of a simulation run (e.g., single platform, single measurement tool, or single scale) and finding actionable insights in multi-dimensional, multi-scale, multi-architecture, and multi-tool performance datasets.

Brink, Stephanie Labasan↗