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14 records

All sources NASA NTRS DOE OSTI

DOE OSTI2018

Dynamic Data Repartitioning for Load-Balanced Parallel Particle Tracing

We present a novel dynamic load-balancing algorithm based on data repartitioning for parallel particle tracing in flow visualization. Instead of static data assignment, we dynamically repartition the data into blocks and reassign the blocks to processes to balance the workload distribution among the processes. Block repartitioning is performed based on a dynamic workload estimation method that predicts the workload in the flow field on the fly as the input. In our approach, we allow data duplication in the repartitioning, enabling the same data blocks to be assigned to multiple processes. Load balance is achieved by regularly exchanging the blocks (together with the particles in the blocks) among processes according to the output of the data repartitioning. Compared with other load-balancing algorithms, our approach does not need any preprocessing on the raw data and does not require any dedicated process for work scheduling, while it has the capability to balance uneven workload efficiently. Results show improved load balance and high efficiency of our method on tracing particles in both steady and unsteady flow.

data repartitioning↗

DOE OSTI2021

Multichannel Analysis of Surface Waves Accelerated (MASWAccelerated): Software for efficient surface wave inversion using MPI and GPUs

Multichannel Analysis of Surface Waves (MASW) is a technique frequently used in geotechnical engineering and engineering geophysics to infer 1D layered models of seismic shear wave velocities in the top tens to hundreds of meters of the subsurface. We aim to accelerate MASW calculations by capitalizing on modern computer hardware available in the workstations of most engineers: multiple cores and graphics processing units (GPUs). We propose new parallel and GPU accelerated algorithms for computing 1D MASW inversion, and provide software implementations in C using Message Passing Interface (MPI) and CUDA. These algorithms take advantage of sparsity that arises in the problem, and the work balance between processes considers typical data trends. We compare our methods to an existing open source Matlab MASW tool. Our serial C implementation achieves a 2x speedup over the Matlab software, and we continue to see improvements by parallelizing the problem with MPI. Here we see nearly perfect strong and weak scaling for uniform data, and improve strong scaling for realistic data by repartitioning the problem to process mapping. By utilizing GPUs available on most modern workstations, we observe an additional 1.3x speedup over the serial C implementation on the first use of the method. We typically repeatedly evaluate theoretical dispersion curves as part of an optimization procedure, and on the GPU the kernel can be cached for faster reuse on later runs. We observe a 3.2x speedup on the cached GPU runs compared to the serial C runs. This work is the first open-source parallel or GPU-accelerated software tool for MASW imaging, and should enable geotechnical engineers to fully utilize all computer hardware at their disposal.

58 GEOSCIENCES↗

DOE OSTI2014

TU-A-12A-08: Computing Longitudinal Material Changes in Bone Metastases Using Dual Energy Computed Tomography

Purpose: This study demonstrates a methodology for tracking changes in metastatic bone disease using trajectories in material basis space in serial dual energy computed tomography (DECT) studies. Methods: This study includes patients with bone metastases from breast cancer that had clinical surveillance CT scans using a General Electric CT750HD in dual energy mode. A radiologist defined regions-of-interested (ROI) for bone metastasis, normal bone, and marrow across the serial DECT scans. Our approach employs a Radon transform to forward-projection the basis images, namely, water and iodine, into sinogram space. This data is then repartitioned into fat/bone and effective density/Z image pairs using assumed energy spectrums for the x-ray energies. This approach both helps remove negative material densities and avoids adding spectrum-hardening artifacts. These new basis data sets were then reconstructed via filtered back-projection to create new material basis pair images. The trajectories of these pairs were then plotted in the new basis space providing a means to both visualize and quantitatively measure changes in the material properties of the tumors. Results: ROI containing radiologist defined metastatic bone disease showed well-defined trajectories in both fat/bone and effective density/Z space. ROI that contained radiologist defined normal bone and marrow did not exhibit any discernible trajectories and were stable from scan to scan. Conclusions: The preliminary results show that changes in material composition and effective density/Z image pairs were seen primarily in metastasis and not in normal tissue. This study indicates that by using routine clinical DECT it may be possible to monitor therapy response of bone metastases because healing or worsening bone metastases change material composition of bone. Additional studies are needed to further validate these results and to test for their correlation with outcome.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2017

The fusion code XGC: Enabling kinetic study of multi-scale edge turbulent transport in ITER

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2017

The fusion code XGC: Enabling kinetic study of multi-scale edge turbulent transport in ITER [Book Chapter]

The XGC fusion gyrokinetic code combines state-of-the-art, portable computational and algorithmic technologies to enable complicated multiscale simulations of turbulence and transport dynamics in ITER edge plasma on the largest US open-science computer, the CRAY XK7 Titan, at its maximal heterogeneous capability, which have not been possible before due to a factor of over 10 shortage in the time-to-solution for less than 5 days of wall-clock time for one physics case. Frontier techniques such as nested OpenMP parallelism, adaptive parallel I/O, staging I/O and data reduction using dynamic and asynchronous applications interactions, dynamic repartitioning for balancing computational work in pushing particles and in grid related work, scalable and accurate discretization algorithms for non-linear Coulomb collisions, and communication-avoiding subcycling technology for pushing particles on both CPUs and GPUs are also utilized to dramatically improve the scalability and time-to-solution, hence enabling the difficult kinetic ITER edge simulation on a present-day leadership class computer.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2016

Field-gradient partitioning for fracture and frictional contact in the material point method: Field-gradient partitioning for fracture and frictional contact in the material point method [Fracture and frictional contact in material point method using damage-field gradients for velocity-field partitioning]

Contact and fracture in the material point method require grid-scale enrichment or partitioning of material into distinct velocity fields to allow for displacement or velocity discontinuities at a material interface. We present a new method which a kernel-based damage field is constructed from the particle data. The gradient of this field is used to dynamically repartition the material into contact pairs at each node. Our approach avoids the need to construct and evolve explicit cracks or contact surfaces and is therefore well suited to problems involving complex 3-D fracture with crack branching and coalescence. A straightforward extension of this approach permits frictional ‘self-contact’ between surfaces that are initially part of a single velocity field, enabling more accurate simulation of granular flow, porous compaction, fragmentation, and comminution of brittle materials. Finally, numerical simulations of self contact and dynamic crack propagation are presented to demonstrate the accuracy of the approach.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Spotlight: efficient automated global optimization in rietveld analysis of diffraction data

Performing reliable Rietveld analysis on tens or hundreds of powder diffraction datasets from parametric or time-resolved experiments often poses a bottleneck in extracting meaningful results from the data. While automated analysis of data has recently been demonstrated, high temperature annealing studies, during which phase transformations occur and lattice parameters may change due to repartitioning of elements, are prime examples where automation by a simple phase identification from a database of room temperature structures or automation by sequential refinements is likely to fail. To enable reliable, efficient, automated Rietveld analysis, we present a Python package named Spotlight , building on established Rietveld packages such as MAUD, GSAS , or GSAS-II , which extends the refinement of best fit parameters to a global optimization using an ensemble of optimizers leveraging hierarchical parallel execution on high-performance computing clusters. Spotlight further enables the efficient design of refinement plans through the iterative automated machine-learning of a surrogate for the refinement on which the global optimizations are performed until results from the surrogate converge to the response surface data. We demonstrate Spotlight with the analysis of uranium molybdenum and Ti–6Al–4V datasets, as well as in two open-source tutorials analyzing aluminium oxide and lead sulphate.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Energy Flux Densities near the Electron Dissipation Region in Asymmetric Magnetopause Reconnection

Magnetic reconnection is of fundamental importance to plasmas because of its role in releasing and repartitioning stored magnetic energy. Previous results suggest that this energy is predominantly released as ion enthalpy flux along the reconnection outflow. Using Magnetospheric Multiscale data we find the existence of very significant electron energy flux densities in the vicinity of the magnetopause electron dissipation region, orthogonal to the ion energy outflow. Finally, these may significantly impact models of electron transport, wave generation, and particle acceleration.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2016

Tunable allosteric library of caspase-3 identifies coupling between conserved water molecules and conformational selection

The native ensemble of caspases is described globally by a complex energy landscape where the binding of substrate selects for the active conformation, whereas targeting an allosteric site in the dimer interface selects an inactive conformation that contains disordered active-site loops. Mutations and posttranslational modifications stabilize high-energy inactive conformations, with mostly formed, but distorted, active sites. To examine the interconversion of active and inactive states in the ensemble, we used detection of related solvent positions to analyze 4,995 waters in 15 high-resolution (<2.0 Å) structures of wild-type caspase-3, resulting in 450 clusters with the most highly conserved set containing 145 water molecules. The data show that regions of the protein that contact the conserved waters also correspond to sites of posttranslational modifications, suggesting that the conserved waters are an integral part of allosteric mechanisms. To test this hypothesis, we created a library of 19 caspase-3 variants through saturation mutagenesis in a single position of the allosteric site of the dimer interface, and we show that the enzyme activity varies by more than four orders of magnitude. Altogether, our database consists of 37 high-resolution structures of caspase-3 variants, and we demonstrate that the decrease in activity correlates with a loss of conserved water molecules. Furthermore, the data show that the activity of caspase-3 can be fine-tuned through globally desolvating the active conformation within the native ensemble, providing a mechanism for cells to repartition the ensemble and thus fine-tune activity through conformational selection.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2015

Parallel adaptive wavelet collocation method for PDEs

A parallel adaptive wavelet collocation method for solving a large class of Partial Differential Equations is presented. The parallelization is achieved by developing an asynchronous parallel wavelet transform, which allows one to perform parallel wavelet transform and derivative calculations with only one data synchronization at the highest level of resolution. The data are stored using tree-like structure with tree roots starting at a priori defined level of resolution. Both static and dynamic domain partitioning approaches are developed. For the dynamic domain partitioning, trees are considered to be the minimum quanta of data to be migrated between the processes. This allows fully automated and efficient handling of non-simply connected partitioning of a computational domain. Dynamic load balancing is achieved via domain repartitioning during the grid adaptation step and reassigning trees to the appropriate processes to ensure approximately the same number of grid points on each process. The parallel efficiency of the approach is discussed based on parallel adaptive wavelet-based Coherent Vortex Simulations of homogeneous turbulence with linear forcing at effective non-adaptive resolutions up to 2048{sup 3} using as many as 2048 CPU cores.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2017

Phase equilibria in the NaF-CdO-NaPO{sub 3} system at 873 K and crystal structure and physico-chemical characterizations of the new Na{sub 2}CdPO{sub 4}F fluorophosphate

Isothermal sections of the diagram representing phase relationships in the NaF-CdO-NaPO{sub 3} system have been investigated by solid state reactions and powder X-ray diffraction. This phase diagram investigation confirms the polymorphism of the NaCdPO{sub 4} side component and the structure of the ß high temperature polymorph (orthorhombic, space group Pnma and unit cell parameters a=9.3118(2), b=7.0459(1), c=5.1849(1) Å has been refined. A new fluorophosphate, Na{sub 2}CdPO{sub 4}F, has been discovered and its crystal structure determined and refined from powder X-ray diffraction data. It exhibits a new 3D structure with orthorhombic symmetry, space group Pnma and unit cell parameters a=5.3731(1), b=6.8530(1), c=12.2691(2) Å. The structure is closely related to those of the high temperature polymorph of the nacaphite Na{sub 2}CaPO{sub 4}F and the fluorosilicate Ca{sub 2}NaSiO{sub 4}F but differs essentially in the cationic repartition since the structure is fully ordered with one Na site (8d) and one Cd site (4c). Relationships with other Na{sub 2}M{sup II}PO{sub 4}F (M{sup II}=Mg, Ca, Mn, Fe, Co, Ni) have been examined and the crystal-chemical and topographical analysis of these fluorophosphates is briefly reviewed. IR, Raman, optical and {sup 19}F, {sup 23}Na, {sup 31}P MAS NMR characterizations of Na{sub 2}CdPO{sub 4}F have been investigated. - Graphical abstract: The structure of the compound Na{sub 2}CdPO{sub 4}F, discovered during the study of the phase relationships in the NaF-CdO-NaPO{sub 3} system, has been determined and compared with other Na{sub 2}M{sup II}PO{sub 4}F fluorophosphates. - Highlights: • XRD analysis of the isothermal section of the NaF-CdO-NaPO{sub 3} system at 923 K. • Rietveld refinement of the high temperature polymorph β-NaCdPO{sub 4}. • Crystal structure of the new Na{sub 2}CdPO{sub 4}F fluorophosphate determined from powder XRD. • Crystal structure - composition relationships of Na{sub 2}M{sup II}PO{sub 4}F compounds are reviewed. • IR, Raman, optical and {sup 19}F, {sup 23}Na, {sup 31}P MAS NMR characterizations of Na{sub 2}CdPO{sub 4}F.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

Coupling fracture facies with in-situ permeability measurements to generate stochastic simulations of tight carbonate aquifer properties: Example from the Lower Cretaceous aquifer, Northern Provence, SE France

The relationships between fracture facies and permeability distribution have been explored using a well-constrained 3D implicit structural model of hemipelagic low porosity/low permeability carbonate from the Northern Provence region, SE France. Fracture and permeability facies were determined using an extensive dataset of 99 hydrogeological wells. Data processing was undertaken using a step-by-step approach, involving: (i) identification of the fracture facies based on well logs detailing structure and stratigraphy; (ii) determination of permeability facies from the a priori correlation between the dimension of the hydraulic radius of influence (deduced from slug test analyses) and the type of reservoir heterogeneity (fissure, fracture, fault zone, etc.); (iii) three dimensional plot of fracture and permeability facies in the geological model using a variographic analysis of data. Thirty-three sequential indicator simulations (SIS) based on geostatistic analyses were realised on both fracture and permeability facies. Finally, a connectivity algorithm was developed to compute the probability of connection between selected infiltration areas and the major aquifer springs via moderate- to high-permeability geological bodies. Key results are: (i) fault zones have a greater role in controlling permeability facies distribution than on fracture facies repartition; (ii) there is little correlation between permeability and fracture facies distributions; (iii) connectivity results highlight the compartmentalisation of aquifers in the Cadarache area, the extensions of permeable geological bodies being limited by the N130 faults.

58 GEOSCIENCES↗

DOE OSTI2026

torch-einshard v1.0

torch-einshard is a Python library for describing local and distributed PyTorch tensor computations with compact, einsum-like notation. Its expressions name logical axes, specify how they are sharded across a PyTorch DeviceMesh, and represent partial reductions. The library automatically performs contractions, permutations, reshaping, splitting, gathering, reduction, reduce-scatter, and repartitioning while preserving autograd. Additional features include sharding-aware FFTs, tensor rolls, halo exchange, sliding windows, 1D–3D convolutions, uneven-shard handling, parameter initialization and gradient management, and cost-based execution planning. It is designed for scientific machine learning and large-model workloads, including tensor-, sequence-, and spatial-parallel MLPs, attention, convolutions, and spectral operations. Compared with manually combining torch.einsum and distributed collectives, torch-einshard expresses both the mathematical operation and data placement in one readable formula. This reduces boilerplate and synchronization errors, keeps forward and backward communication consistent, and allows the library to select optimized collective strategies without changing model code.

Morozov, Dmitriy [Lawrence Berkeley National Labor↗

DOE OSTI2024

Dataset for manuscript "Consequences of the failure of equipartition for the p-V behavior of liquid water and the hydration free energy components of a small protein"

Previously, we showed that in the molecular dynamics simulation of a rigid model of water it is necessary to use an integration time-step dt that is less than or equal to 0.5 fs to ensure equipartition between translational and rotational modes. We extended that study in the NVT ensemble to NpT conditions and to an aqueous protein. We study neat liquid water with the rigid, SPC/E model and the protein BBA (PDB ID: 1FME) solvated in the rigid, TIP3P model. We examined integration time-steps ranging from 0.5 fs to 4.0 fs for various thermostat plus barostat combinations. We find that a small time-step, dt, is necessary to ensure consistent prediction of the simulation volume. Hydrogen mass repartitioning alleviates the problem somewhat, but is ineffective for the typical time-step used with this approach. The compressibility, a measure of volume fluctuations, is seen to be sensitive to dt. Using the mean volume estimated from the NpT simulation, we examined the electrostatic and van der Waals contribution to the hydration free energy of the protein in the NVT ensemble. These contributions are also sensitive to dt. In going from a time-step of 2 fs to a time-step of 0.5 fs, the change in the net electrostatic plus van der Waals contribution to the hydration of BBA is already in excess of the folding free energy reported for this protein. The data-set contains the simulation metadata and log files that support the claims noted above.

59 BASIC BIOLOGICAL SCIENCES↗