arXiv subjects

Jon A. Linker

Publications and source records attributed to Jon A. Linker.

At least 19 recordsLinked to original sources

arXiv2026

Portability of Fortran's 'do concurrent' on GPUs II

There continues to be growing interest in using standard language constructs for parallel and accelerated HPC computing, avoiding the need for (sometimes vendor-specific) external APIs. For Fortran applications, language features such as 'do concurrent' loops open the door for compilers to implement multi-threaded, GPU-accelerated, and even distributed multi-node code with only the standard language. Here, we explore the current status of using 'do concurrent' for GPU-accelerated Fortran applications across three major GPU vendors (NVIDIA, AMD, and Intel). Using a production application, we test their current capabilities, showing where the standard language alone can be used, and where augmenting the code with a directive-based API (e.g., OpenMP) is still desirable or required. Multi-GPU tests are performed with GPU-aware MPI libraries. We find that the three GPU vendors can now GPU-accelerate pure Fortran (zero directives), but that manual data movement directives can help with performance and compatibility. The results show that there is rapid advancement towards making GPU-accelerated scientific HPC code performance portable using the Fortran standard language.

cs.PL↗

arXiv2026

Tracking Magnetic Topological Change in a Time-Dependent Coronal Model

We apply the slip-back mapping method of Titov et al. 2009 and Lionello et al. 2020 to a thermodynamic MHD simulation to track topological changes in the magnetic field at a range of temporal cadences. The method constitutes the logical successor to a simple open-field map for a steady-state model, as it tracks changes in the open and closed fields for a time-dependent model by tracking individual magnetic elements as they advect across the map, rather than simply tracing field line connectivity from each cell. Through careful categorization of the slip-back mapping values and analysis of the flux changes, we not only effectively track the open flux but can recover the flux processed through interchange reconnection as well. The field lines involved in these processes are shown to follow lines of high squashing factor, as proposed by interchange reconnection-driven slow solar wind theory. The time-dependent model, which is scaled to solar minimum-like activity, projects that a median value of 3.5% of the total open flux in any given 24-hour interval has been processed through interchange reconnection. This corresponds to a relatively high proportion of the total open flux changes over time in the heliosphere. Our results show that not only is this method a useful tool for accurately tracking topological change in time-dependent simulations, but that its inherent complexity can be visually reduced into an intuitive 2D plot that simply and effectively communicates temporal changes.

astro-ph.SR↗

arXiv2026

Magnetic Connectivity in the Time-Dependent Corona and Heliosphere

Magnetic flux fills the heliosphere, expands outward from the solar corona, and is fundamentally related to the structure and dynamics of the solar corona and solar wind. Open magnetic flux and the fast wind are thought to originate from open magnetic field lines in coronal holes. Less understood processes in the streamer belt and the boundaries of coronal holes, associated with the more variable slow wind, may be formed by interchange reconnection between open and closed magnetic flux. Interchange reconnection is thought to give rise to field lines that are "folded," i.e. that turn back on themselves. The properties of strahl electrons measured in the solar wind give clues to the heliospheric magnetic connectivity. Unidirectionally outward strahl indicates open field lines, while bidirectional strahl is associated with closed magnetic flux and CMEs. Inward directed, unidirectional strahl is believed to indicate folded flux. We use two time-dependent, flux-evolutionary MHD models of the combined corona and heliosphere, one for a solar-minimum configuration, one for the 2024 total solar eclipse, to investigate the magnetic connectivity of the corona/heliosphere system. We examine how magnetic connectivity varies with distance from the Sun in the two configurations. We evaluate the evolutionary effects by contrasting time-dependent results with the corresponding steady-state calculations, and compare the model connectivities with statistical studies of strahl. The connectivities in the time-evolving simulations are roughly consistent with observed strahl occurrence rates, while those from the steady-state models are not. Our results suggest that complex magnetic connectivities are ubiquitous in the heliosphere.

astro-ph.SR↗

arXiv2025

Energetic Particles from Quasi-Separatrix Layers and Current Sheets at the Sun

Quasi-separatrix layers (QSLs) at the Sun are created from regions where channels of open magnetic flux have footpoints near regions of large-scale closed magnetic flux. These regions are particularly prone to magnetic reconnection at the Sun. In recent simulations of coronal mass ejections (CMEs) with the Magnetohydrodynamic Algorithm outside a Sphere (MAS) model coupled to the Energetic Particle Radiation Environment Module (EPREM) model, common sources of energetic particles were discovered over broad longitudinal distributions in the background solar wind, far from the sites of particle acceleration driven by compressions and shocks in front of CMEs. Further investigation revealed these to be accelerated energetic particles from the QSLs and current sheets. The energy released from magnetic reconnection near the QSL drives reconnection exhausts and field-aligned flows, which in turn accelerate energetic particles. The reconnection process also releases material previously contained within closed magnetic field structures, which are often rich in heavy ions and $^3$He ions, as corroborated by recent PSP observations. Therefore, the seed populations produced by QSLs are expected to be rich in $^3$He and heavy ions. Thus, we present the first global model of energetic particles accelerated from QSLs and above current sheets from the Sun. Our results provide a plausible source for seed populations near the Sun, which likely have $^3$He and heavy ion enhancements. These results aid in the development of predictive solar energetic particle models.

astro-ph.SR↗

arXiv2025

Open-source Flux Transport (OFT). I. HipFT -- High-performance Flux Transport

Global solar photospheric magnetic maps play a critical role in solar and heliospheric physics research. Routine magnetograph measurements of the field occur only along the Sun-Earth line, leaving the far-side of the Sun unobserved. Surface Flux Transport (SFT) models attempt to mitigate this by modeling the surface evolution of the field. While such models have long been established in the community (with several releasing public full-Sun maps), none are open source. The Open Source Flux Transport (OFT) model seeks to fill this gap by providing an open and user-extensible SFT model that also builds on the knowledge of previous models with updated numerical and data acquisition/assimilation methods along with additional user-defined features. In this first of a series of papers on OFT, we introduce its computational core: the High-performance Flux Transport (HipFT) code (github.com/predsci/hipft). HipFT implements advection, diffusion, and data assimilation in a modular design that supports a variety of flow models and options. It can compute multiple realizations in a single run across model parameters to create ensembles of maps for uncertainty quantification and is high-performance through the use of multi-CPU and multi-GPU parallelism. HipFT is designed to enable users to easily write extensions, enhancing its flexibility and adaptability. We describe HipFT's model features, validations of its numerical methods, performance of its parallel and GPU-accelerated code implementation, analysis/post-processing options, and example use cases.

astro-ph.SR↗

arXiv2024

Portability of Fortran's `do concurrent' on GPUs

There is a continuing interest in using standard language constructs for accelerated computing in order to avoid (sometimes vendor-specific) external APIs. For Fortran codes, the {\tt do concurrent} (DC) loop has been successfully demonstrated on the NVIDIA platform. However, support for DC on other platforms has taken longer to implement. Recently, Intel has added DC GPU offload support to its compiler, as has HPE for AMD GPUs. In this paper, we explore the current portability of using DC across GPU vendors using the in-production solar surface flux evolution code, HipFT. We discuss implementation and compilation details, including when/where using directive APIs for data movement is needed/desired compared to using a unified memory system. The performance achieved on both data center and consumer platforms is shown.

cs.PL↗

arXiv2024

Advancing parabolic operators in thermodynamic MHD models II: Evaluating a Practical Time Step Limit for Unconditionally Stable Methods

Unconditionally stable time stepping schemes are useful and often practically necessary for advancing parabolic operators in multi-scale systems. However, serious accuracy problems may emerge when taking time steps that far exceed the explicit stability limits. In our previous work, we compared the accuracy and performance of advancing parabolic operators in a thermodynamic MHD model using an implicit method and an explicit super time-stepping (STS) method. We found that while the STS method outperformed the implicit one with overall good results, it was not able to damp oscillatory behavior in the solution efficiently, hindering its practical use. In this follow-up work, we evaluate an easy-to-implement method for selecting a practical time step limit (PTL) for unconditionally stable schemes. This time step is used to `cycle' the operator-split thermal conduction and viscosity parabolic operators. We test the new time step with both an implicit and STS scheme for accuracy, performance, and scaling. We find that, for our test cases here, the PTL dramatically improves the STS solution, matching or improving the solution of the original implicit scheme, while retaining most of its performance and scaling advantages. The PTL shows promise to allow more accurate use of unconditionally stable schemes for parabolic operators and reliable use of STS methods.

cs.CE↗

arXiv2024

On the Origin of the sudden Heliospheric Open Magnetic Flux Enhancement during the 2014 Pole Reversal

Coronal holes are recognized as the primary sources of heliospheric open magnetic flux (OMF). However, a noticeable gap exists between in-situ measured OMF and that derived from remote sensing observations of the Sun. In this study, we investigate the OMF evolution and its connection to solar structures throughout 2014, with special emphasis on the period from September to October, where a sudden and significant OMF increase was reported. By deriving the OMF evolution at 1au, modeling it at the source surface, and analyzing solar photospheric data, we provide a comprehensive analysis of the observed phenomenon. First, we establish a strong correlation between the OMF increase and the solar magnetic field derived from a Potential Field Source Surface (PFSS) model ($cc_{\mathrm{Pearson}}=0.94$). Moreover, we find a good correlation between the OMF and the open flux derived from solar coronal holes ($cc_{\mathrm{Pearson}}=0.88$), although the coronal holes only contain $14-32\%$ of the Sun's total open flux. However, we note that while the OMF evolution correlates with coronal hole open flux, there is no correlation with the coronal hole area evolution ($cc_{\mathrm{Pearson}}=0.0$). The temporal increase in OMF correlates with the vanishing remnant magnetic field at the southern pole, caused by poleward flux circulations from the decay of numerous active regions months earlier. Additionally, our analysis suggests a potential link between the OMF enhancement and the concurrent emergence of the largest active region in solar cycle 24. In conclusion, our study provides insights into the strong increase in OMF observed during September to October 2014.

astro-ph.SR↗

arXiv2023

Coronal Models and Detection of Open Magnetic Field

A plethora of coronal models, from empirical to more complex magnetohydrodynamic (MHD) ones, are being used for reconstructing the coronal magnetic field topology and estimating the open magnetic flux. However, no individual solution fully agrees with coronal hole observations and in situ measurements of open flux at 1~AU, as there is a strong deficit between model and observations contributing to the known problem of the missing open flux. In this paper we investigate the possible origin of the discrepancy between modeled and observed magnetic field topology by assessing the effect on the simulation output by the choice of the input boundary conditions and the simulation set up, including the choice of numerical schemes and the parameter initialization. In the frame of this work, we considered four potential field source surface based models and one fully MHD model, different types of global magnetic field maps and model initiation parameters. After assessing the model outputs using a variety of metrics, we conclude that they are highly comparable regardless of the differences set at initiation. When comparing all models to coronal hole boundaries extracted by extreme ultraviolet (EUV) filtergrams we find that they do not compare well. This miss-match between observed and modeled regions of open field is a candidate contributing to the open flux problem.

astro-ph.SR↗

arXiv2023

Global MHD Simulations of the Time-Dependent Corona

We describe, test, and apply a technique to incorporate full-sun, surface flux evolution into an MHD model of the global solar corona. Requiring only maps of the evolving surface flux, our method is similar to that of Lionello et al. (2013), but we introduce two ways to correct the electric field at the lower boundary to mitigate spurious currents. We verify the accuracy of our procedures by comparing to a reference simulation, driven with known flows and electric fields. We then present a thermodynamic MHD calculation lasting one solar rotation driven by maps from the magnetic flux evolution model of Schrijver & DeRosa (2003). The dynamic, time-dependent nature of the model corona is illustrated by examining the evolution of the open flux boundaries and forward modeled EUV emission, which evolve in response to surface flows and the emergence and cancellation flux. Although our main goal is to present the method, we briefly investigate the relevance of this evolution to properties of the slow solar wind, examining the mapping of dipped field lines to the topological signatures of the "S-Web" and comparing charge state ratios computed in the time-dependently driven run to a steady state equivalent. Interestingly, we find that driving on its own does not significantly improve the charge states ratios, at least in this modest resolution run that injects minimal helicity. Still, many aspects of the time-dependently driven model cannot be captured with traditional steady-state methods, and such a technique may be particularly relevant for the next generation of solar wind and CME models.

astro-ph.SR↗

arXiv2023

Time-Dependent Dynamics of the Corona

We present in this Letter the first global comparison between traditional line-tied steady state magnetohydrodynamic models and a new, fully time-dependent thermodynamic magnetohydrodynamic simulation of the global corona. The maps are scaled to the approximate field distributions and magnitudes around solar minimum using the Lockheed Evolving Surface-Flux Assimilation Model to incorporate flux emergence and surface flows over a full solar rotation, and include differential rotation and meridional flows. Each time step evolves the previous state of the plasma with a new magnetic field input boundary condition. We find that this method is a significant improvement over steady-state models, as it closely mimics the constant photospheric driving on the Sun. The magnetic energy levels are higher in the time-dependent model, and coronal holes evolve more along the following edge than they do in steady-state models. Coronal changes, as illustrated with forward-modeled emission maps, evolve on longer timescales with time-dependent driving. We discuss implications for active and quiet Sun scenarios, solar wind formation, and widely-used steady state assumptions like potential field source surface calculations.

astro-ph.SR↗

arXiv2023

Acceleration of a production Solar MHD code with Fortran standard parallelism: From OpenACC to `do concurrent'

There is growing interest in using standard language constructs for accelerated computing, avoiding the need for (often vendor-specific) external APIs. These constructs hold the potential to be more portable and much more `future-proof'. For Fortran codes, the current focus is on the {\tt do concurrent} (DC) loop. While there have been some successful examples of GPU-acceleration using DC for benchmark and/or small codes, its widespread adoption will require demonstrations of its use in full-size applications. Here, we look at the current capabilities and performance of using DC in a production application called Magnetohydrodynamic Algorithm outside a Sphere (MAS). MAS is a state-of-the-art model for studying coronal and heliospheric dynamics, is over 70,000 lines long, and has previously been ported to GPUs using MPI+OpenACC. We attempt to eliminate as many of its OpenACC directives as possible in favor of DC. We show that using the NVIDIA {\tt nvfortran} compiler's Fortran 202X preview implementation, unified managed memory, and modified MPI launch methods, we can achieve GPU acceleration across multiple GPUs without using a single OpenACC directive. However, doing so results in a slowdown between 1.25x and 3x. We discuss what future improvements are needed to avoid this loss, and show how we can still retain close

cs.MS↗

arXiv2022

A Magnetogram-matching Method for Energizing Magnetic Flux Ropes Toward Eruption

We propose a new ``helicity-pumping'' method for energizing coronal equilibria that contain a magnetic flux rope (MFR) toward an eruption. We achieve this in a sequence of magnetohydrodynamics relaxations of small line-tied pulses of magnetic helicity, each of which is simulated by a suitable rescaling of the current-carrying part of the field. The whole procedure is ``magnetogram-matching'' because it involves no changes to the normal component of the field at the photospheric boundary. The method is illustrated by applying it to an observed force-free configuration whose MFR is modeled with our regularized Biot--Savart law method. We find that, in spite of the bipolar character of the external field, the MFR eruption is sustained by two reconnection processes. The first, which we refer to as breakthrough reconnection, is analogous to breakout reconnection in quadrupolar configurations. It occurs at a quasi-separator inside a current layer that wraps around the erupting MFR and is caused by the photospheric line-tying effect. The second process is the classical flare reconnection, which develops at the second quasi-separator inside a vertical current layer that is formed below the erupting MFR. Both reconnection processes work in tandem with the magnetic forces of the unstable MFR to propel it through the overlying ambient field, and their interplay may also be relevant for the thermal processes occurring in the plasma of solar flares. The considered example suggests that our method will be beneficial for both the modeling of observed eruptive events and theoretical studies of eruptions in idealized magnetic configurations.

astro-ph.SR↗

arXiv2021

Can Fortran's 'do concurrent' replace directives for accelerated computing?

Recently, there has been growing interest in using standard language constructs (e.g. C++'s Parallel Algorithms and Fortran's do concurrent) for accelerated computing as an alternative to directive-based APIs (e.g. OpenMP and OpenACC). These constructs have the potential to be more portable, and some compilers already (or have plans to) support such standards. Here, we look at the current capabilities, portability, and performance of replacing directives with Fortran's do concurrent using a mini-app that currently implements OpenACC for GPU-acceleration and OpenMP for multi-core CPU parallelism. We replace as many directives as possible with do concurrent, testing various configurations and compiler options within three major compilers: GNU's gfortran, NVIDIA's nvfortran, and Intel's ifort. We find that with the right compiler versions and flags, many directives can be replaced without loss of performance or portability, and, in the case of nvfortran, they can all be replaced. We discuss limitations that may apply to more complicated codes and future language additions that may mitigate them. The software and Singularity containers are publicly provided to allow the results to be reproduced.

cs.MS↗

arXiv2021

Variations in Finite Difference Potential Fields

The potential field (PF) solution of the solar corona is a vital modeling tool for a wide range of applications, including minimum energy estimates, coronal magnetic field modeling, and empirical solar wind solutions. Given its popularity, it is important to understand how choices made in computing a PF may influence key properties of the solution. Here we study PF solutions for the global coronal magnetic field on 2012 June 13, computed with our high-performance finite difference code POT3D. Solutions are analyzed for their global properties and locally around NOAA AR 11504, using the net open flux, open field boundaries, total magnetic energy, and magnetic structure as metrics. We explore how PF solutions depend on 1) the data source, type, and processing of the inner boundary conditions, 2) the choice of the outer boundary condition height and type, and 3) the numerical resolution and spatial scale of information at the lower boundary. We discuss the various qualitative and quantitative differences that naturally arise by using different maps as input, and illustrate how coronal morphology and open flux depend most strongly on the outer boundary condition. We also show how large-scale morphologies and the open magnetic flux are remarkably insensitive to model resolution, while the surface mapping and embedded magnetic complexity vary considerably. This establishes important context for past, current, and future applications of the PF for coronal and solar wind modeling.

astro-ph.SR↗

arXiv2021

Using Parker Solar Probe observations during the first four perihelia to constrain global magnetohydrodynamic models

Parker Solar Probe (PSP) is providing an unprecedented view of the Sun's corona as it progressively dips closer into the solar atmosphere with each solar encounter. Each set of observations provides a unique opportunity to test and constrain global models of the solar corona and inner heliosphere and, in turn, use the model results to provide a global context for interpreting such observations. In this study, we develop a set of global magnetohydrodynamic (MHD) model solutions of varying degrees of sophistication for PSP's first four encounters and compare the results with in situ measurements from PSP, Stereo-A, and Earth-based spacecraft, with the objective of assessing which models perform better or worse. All models were primarily driven by the observed photospheric magnetic field using data from Solar Dynamics Observatory's Helioseismic and Magnetic Imager (HMI) instrument. Overall, we find that there are substantial differences between the model results, both in terms of the large-scale structure of the inner heliosphere during these time periods, as well as in the inferred time-series at various spacecraft. The "thermodynamic" model, which represents the "middle ground", in terms of model complexity, appears to reproduce the observations most closely for all four encounters. Our results also contradict an earlier study that had hinted that the open flux problem may disappear nearer the Sun. Instead, our results suggest that this "missing" solar flux is still missing even at 26.9 Rs, and thus it cannot be explained by interplanetary processes. Finally, the model results were also used to provide a global context for interpreting the localized in situ measurements.

physics.space-ph↗

arXiv2019

Predicting the Structure of the Solar Corona and Inner Heliosphere during Parker Solar Probe's First Perihelion Pass

NASA's Parker Solar Probe (Parker) spacecraft reached its first perihelion of 35.7 solar radii on November 5th, 2018. To aid in mission planning, and in anticipation of the unprecedented measurements to be returned, in late October, we developed a three-dimensional magnetohydrodynamic (MHD) solution for the solar corona and inner heliosphere, driven by the then available observations of the Sun's photospheric magnetic field. Our model incorporates a wave-turbulence-driven (WTD) model to heat the corona. Here, we present our predictions for the structure of the solar corona and the likely {\it in situ} measurements that Parker will be returning over the next few months. We infer that, in the days prior to 1st Encounter, Parker was immersed in wind emanating from a positive-polarity equatorial coronal hole. During the encounter, however, field lines from the spacecraft mapped to another, negative-polarity equatorial coronal hole. Following the encounter, Parker was magnetically connected to the large, positive-polarity northern polar coronal hole. When the Parker data become available, these model results can be used to assist in their calibration and interpretation, and, additionally, provide a global context for interpreting the localized {\it in situ} measurements. In particular, we can identify what types of solar wind Parker encountered, what the underlying magnetic structure was, and how complexities in the orbital trajectory can be interpreted within a global, inertial frame. Ultimately, the measurements returned by Parker can be used to constrain current theories for heating the solar corona and accelerating the solar wind.

physics.space-ph↗

arXiv2019

Coupled MHD-Focused Transport Simulations for Modeling Solar Particle Events

We describe the initial version of the Solar Particle Event (SPE) Threat Assessment Tool or STAT. STAT relies on elements of Corona-Heliosphere (CORHEL) and the Earth-Moon-Mars Radiation Environment Module (EMMREM), and allows users to investigate coronal mass ejection (CME) driven SPEs using coupled magnetohydrodynamic (MHD) and focused transport solutions. At the present time STAT focuses on modeling solar energetic particle (SEP) acceleration in and transport from the low corona, where the highest energy SEP events are generated. We illustrate STAT's capabilities with a model of the July 14, 2000 "Bastille Day" event, including innovative diagnostics for understanding the three-dimensional distribution of particle fluxes and their relation to the structure of the underlying CME driver. A preliminary comparison with NOAA GOES measurements is shown.

astro-ph.SR↗