arXiv subjects

Edoardo Di Napoli

Publications and source records attributed to Edoardo Di Napoli.

At least 19 recordsLinked to original sources

arXiv2026

RSE of a Quantum Transport Code and its Effects

This paper presents our research software engineering (RSE) experiences over two years with libNEGF, a quantum transport code. We describe practical approaches to code quality assurance--including continuous integration, automated testing, and compiler warning correction--and performance engineering through continuous benchmarking. Our systematic application of these practices revealed critical defects: uninitialized memory reads, out-of-bounds writes, and notably, a misunderstood mathematical model in our boundary condition handling. We also document how continuous benchmarking exposed performance regressions caused by HPC system configuration changes. Our findings provide data points suggesting that a dangerous class of defects--equivalent to undefined behavior in C/C++ and processor-dependent behavior in Fortran--is as prevalent in Fortran scientific codes as elsewhere. While libNEGF is implemented in Fortran, most recommendations are applicable to scientific software regardless of implementation language, and they can be implemented selectively or in their entirety for both new and existing projects.

cs.SE↗

arXiv2026

Data-Driven Spectral Prediction for Accelerating Large-Scale Electronic Structure Calculations

Simulating large molecular systems comprising thousands of atoms requires highly scalable methodologies. While modern Density Functional Theory (DFT) codes exhibit linear scaling, solving the associated large, sparse generalized eigenproblems remains a critical computational bottleneck on exascale architectures. In the context of the LimitX project, we propose a data-driven framework to accelerate these calculations. By shifting the machine learning target from discrete eigenvalues to the coefficients of an interpolating Chebyshev polynomial, and by comparing both all-atom and fragment-based structural representations, we successfully overcome the dimensionality constraints of large-scale spectral prediction. We investigate three machine learning models (Kernel Ridge Regression, Graph Neural Networks, and Random Forests) trained on a novel 2 TB dataset of protein dimers. The predicted spectra provide initial guesses that effectively bypass early Self-Consistent Field (SCF) iterations in BigDFT. Ultimately, these spectral predictors will be deployed to dynamically optimize upcoming rational filter-based eigensolvers, such as FrASE, which is currently in initial development.

physics.comp-ph↗

arXiv2026

Revisiting recursive methods for Dyson and Keldysh in NEGF: Part I

The simulation of quantum transport in nanodevices requires the solution of the Dyson and Keldysh equations, a task dominated by the inversion of massive, block-tridiagonal matrices. While the Recursive Green's Function (RGF) method has long been the standard $O(N)$ solver for quasi-1D systems, its formulation has typically been restricted to sequential execution and nearest-neighbor interactions. In this work, we carefully reformulate RGF through the lens of Domain Decomposition and Schur Complement theory. This allows us to extend the recursive formalism to block $n$-diagonal systems (handling higher-order stencils) and to derive a parallel algorithm, Domain-Decomposition based RGF (DDRGF), which stitches macroscopic domains via reduced interface systems. We explore data dependencies in DDRGF in detail, by means of block-sparse structures and tracing back to the desired output as a block tridiagonal approximation, giving a clear, reproducible and extensible formulation. We validate these algorithms using \texttt{LibNEGF.jl}, a Julia-based implementation, demonstrating that the structural insights of domain decomposition provide a robust pathway for high-performance quantum transport simulations on modern multi-core clusters. The theory presented here lays down the base for tackling the Keldysh problem, to be similarly handled in future stages of our work. Although the target here is the acceleration of kernels in the non-equilibrium Green's function method, the algorithms and the implementations presented can be immediately used in any application involving block $n$-diagonal systems.

math.NA↗

arXiv2026

Chebyshev Accelerated Subspace Eigensolver for Pseudo-hermitian Hamiltonians

Studying the optoelectronic structure of materials can require the computation of several thousands of the smallest positive eigenpairs of a pseudo-hermitian Hamiltonian. Iterative eigensolvers may be preferred over direct methods for this task since their complexity is a function of the desired fraction of the spectrum. In addition, they generally rely on highly optimized and scalable kernels such as matrix-vector multiplications that leverage the massive parallelism and the computational power of modern exascale systems. The Chebyshev Accelerated Subspace iteration Eigensolver (ChASE) is able to compute several thousands of the most extreme eigenpairs of dense hermitian matrices with proven scalability over massive parallel accelerated clusters. This work presents an extension of ChASE to solve for a portion of the smallest positive eigenpairs of pseudo-hermitian Hamiltonians as they appear in the treatment of excitonic materials. By exploiting the numerical structure and spectral properties of the Hamiltonian matrix, we preserve the characteristic positive-negative symmetry in the treatment of the eigenvectors and propose an oblique variant of Rayleigh-Ritz projection that features quadratic convergence of the Ritz values with no explicit construction of the dual basis. Additionally, we introduce a parallel implementation of the recursive matrix-product operation appearing in the Chebyshev filter with limited amount of global communications. Our development is supported by a full numerical analysis and experimental tests.

math.NA↗

arXiv2026

Estimating the condition number of Chebyshev filtered vectors with application to the ChASE library

Chebyshev filtered subspace iteration is a well-known algorithm for the solution of (symmetric/Hermitian) algebraic eigenproblems which has been implemented in several application codes~\cite{Kronik:2006ff, abinit:2020} or in stand alone libraries~\cite{ChASE}. An essential part of the algorithm is the QR-factorization of the array of vectors spanning the active subspace that have been filtered by the Chebyshev filter. Typically such an array has an a-priori unknown high condition number that directly influences the choice of QR-factorization algorithm. In this work we show how such condition number can be bound from above with precise and inexpensive estimates. We then proceed to use these estimates to implement a mechanism for the choice of QR-factorization in the ChASE library. We show how such mechanism enhance the performance of the library without compromising on its accuracy.

math.NA↗

arXiv2023

Advancing the distributed Multi-GPU ChASE library through algorithm optimization and NCCL library

As supercomputers become larger with powerful Graphics Processing Unit (GPU), traditional direct eigensolvers struggle to keep up with the hardware evolution and scale efficiently due to communication and synchronization demands. Conversely, subspace eigensolvers, like the Chebyshev Accelerated Subspace Eigensolver (ChASE), have a simpler structure and can overcome communication and synchronization bottlenecks. ChASE is a modern subspace eigensolver that uses Chebyshev polynomials to accelerate the computation of extremal eigenpairs of dense Hermitian eigenproblems. In this work we show how we have modified ChASE by rethinking its memory layout, introducing a novel parallelization scheme, switching to a more performing communication-avoiding algorithm for one of its inner modules, and substituting the MPI library by the vendor-optimized NCCL library. The resulting library can tackle dense problems with size up to $N=\mathcal{O}(10^6)$, and scales effortlessly up to the full 900 nodes -- each one powered by 4$\times$A100 NVIDIA GPUs -- of the JUWELS Booster hosted at the Jülich Supercomputing Centre.

cs.DC↗

arXiv2023

Computing formation enthalpies through an explainable machine learning method: the case of Lanthanide Orthophosphates solid solutions

In the last decade, the use of Machine and Deep Learning (MDL) methods in Condensed Matter physics has seen a steep increase in the number of problems tackled and methods employed. A number of distinct MDL approaches have been employed in many different topics; from prediction of materials properties to computation of Density Functional Theory potentials and inter-atomic force fields. In many cases the result is a surrogate model which returns promising predictions but is opaque on the inner mechanisms of its success. On the other hand, the typical practitioner looks for answers that are explainable and provide a clear insight on the mechanisms governing a physical phenomena. In this work, we describe a proposal to use a sophisticated combination of traditional Machine Learning methods to obtain an explainable model that outputs an explicit functional formulation for the material property of interest. We demonstrate the effectiveness of our methodology in deriving a new highly accurate expression for the enthalpy of formation of solid solutions of lanthanides orthophosphates.

cs.CE↗

arXiv2022

ChASE -- A Distributed Hybrid CPU-GPU Eigensolver for Large-scale Hermitian Eigenvalue Problems

As modern massively parallel clusters are getting larger with beefier compute nodes, traditional parallel eigensolvers, such as direct solvers, struggle keeping the pace with the hardware evolution and being able to scale efficiently due to additional layers of communication and synchronization. This difficulty is especially important when porting traditional libraries to heterogeneous computing architectures equipped with accelerators, such as Graphics Processing Unit (GPU). Recently, there have been significant scientific contributions to the development of filter-based subspace eigensolver to compute partial eigenspectrum. The simpler structure of these type of algorithms makes for them easier to avoid the communication and synchronization bottlenecks typical of direct solvers. The Chebyshev Accelerated Subspace Eigensolver (ChASE) is a modern subspace eigensolver to compute partial extremal eigenpairs of large-scale Hermitian eigenproblems with the acceleration of a filter based on Chebyshev polynomials. In this work, we extend our previous work on ChASE by adding support for distributed hybrid CPU-multi-GPU computing architectures. Our tests show that ChASE achieves very good scaling performance up to 144 nodes with 526 NVIDIA A100 GPUs in total on dense eigenproblems of size up to $360$k.

cs.DC↗

arXiv2020

The LAPW method with eigendecomposition based on the Hari--Zimmermann generalized hyperbolic SVD

In this paper we propose an accurate, highly parallel algorithm for the generalized eigendecomposition of a matrix pair $(H, S)$, given in a factored form $(F^{\ast} J F, G^{\ast} G)$. Matrices $H$ and $S$ are generally complex and Hermitian, and $S$ is positive definite. This type of matrices emerges from the representation of the Hamiltonian of a quantum mechanical system in terms of an overcomplete set of basis functions. This expansion is part of a class of models within the broad field of Density Functional Theory, which is considered the golden standard in condensed matter physics. The overall algorithm consists of four phases, the second and the fourth being optional, where the two last phases are computation of the generalized hyperbolic SVD of a complex matrix pair $(F,G)$, according to a given matrix $J$ defining the hyperbolic scalar product. If $J = I$, then these two phases compute the GSVD in parallel very accurately and efficiently.

math.NA↗

arXiv2020

Solving the Bethe-Salpeter equation on massively parallel architectures

The last ten years have witnessed fast spreading of massively parallel computing clusters, from leading supercomputing facilities down to the average university computing center. Many companies in the private sector have undergone a similar evolution. In this scenario, the seamless integration of software and middleware libraries is a key ingredient to ensure portability of scientific codes and guarantees them an extended lifetime. In this work, we describe the integration of the ChASE library, a modern parallel eigensolver, into an existing legacy code for the first-principles computation of optical properties of materials via solution of the Bethe-Salpeter equation for the optical polarization function. Our numerical tests show that, as a result of integrating ChASE and parallelizing the reading routine, the code experiences a remarkable speedup and greatly improved scaling behavior on both multi- and many-core architectures. We demonstrate that such a modernized BSE code will, by fully exploiting parallel computing architectures and file systems, enable domain scientists to accurately study complex material systems that were not accessible before.

cs.CE↗

arXiv2020

A Long-Range Ising Model of a Barabási-Albert Network

Networks that have power-law connectivity, commonly referred to as the scale-free networks, are an important class of complex networks. A heterogeneous mean-field approximation has been previously proposed for the Ising model of the Barabási-Albert model of scale-free networks with classical spins on the nodes wherein it was shown that the critical temperature for such a system scales logarithmically with network size. For finite sizes, there is no criticality for such a system and hence no true phase transition in terms of singular behavior. Further, in the thermodynamic limit, the mean-field prediction of an infinite critical temperature for the system may exclude any true phase transition even then. Nevertheless, with an eye on potential applications of the model on biological systems that are generally finite, one may still try to find approximations that describe the relevant observables quantitatively. Here we present an alternative, approximate formulation for the description of the Ising model of a Barabási-Albert Network. Using the classical definition of magnetization, we show that Ising models on a network can be well-approximated by a long-range interacting homogeneous Ising model wherein each node of the network couples to all other spins with a strength determined by the mean degree of the Barabási-Albert Network. In such an effective long-range Ising model of a Barabási-Albert Network, the critical temperature is directly proportional to the number of preferentially attached links added to grow the network. The proposed model describes the magnetization of the majority of the sites with average or smaller than average degree better compared to the heterogeneous mean-field approximation. The long-range Ising model is the only homogeneous description of Barabási-Albert networks that we know of.

cond-mat.dis-nn↗

arXiv2020

Solution to the modified Helmholtz equation for arbitrary periodic charge densities

We present a general method for solving the modified Helmholtz equation without shape approximation for an arbitrary periodic charge distribution, whose solution is known as the Yukawa potential or the screened Coulomb potential. The method is an extension of Weinert's pseudo-charge method [M. Weinert, J. Math. Phys. 22, 2433 (1981)] for solving the Poisson equation for the same class of charge density distributions. The inherent differences between the Poisson and the modified Helmholtz equation are in their respective radial solutions. These are polynomial functions, for the Poisson equation, and modified spherical Bessel functions, for the modified Helmholtz equation. This leads to a definition of a modified pseudo-charge density and modified multipole moments. We have shown that Weinert's convergence analysis of an absolutely and uniformly convergent Fourier series of the pseudo-charge density is transferred to the modified pseudo-charge density. We conclude by illustrating the algorithmic changes necessary to turn an available implementation of the Poisson solver into a solver for the modified Helmholtz equation.

physics.comp-ph↗

arXiv2020

Rational spectral filters with optimal convergence rate

In recent years, contour-based eigensolvers have emerged as a standard approach for the solution of large and sparse eigenvalue problems. Building upon recent performance improvements through non-linear least square optimization of so-called rational filters, we introduce a systematic method to design these filters by minimizing the worst-case convergence ratio and eliminate the parametric dependence on weight functions. Further, we provide an efficient way to deal with the box-constraints which play a central role for the use of iterative linear solvers in contour-based eigensolvers. Indeed, these parameter-free filters consistently minimize the number of iterations and the number of FLOPs to reach convergence in the eigensolver. As a byproduct, our rational filters allow for a simple solution to load balancing when the solution of an interior eigenproblem is approached by the slicing of the sought after spectral interval.

math.NA↗

arXiv2019

A Modified Ising Model of Barabási-Albert Network with Gene-type Spins

The central question of systems biology is to understand how individual components of a biological system such as genes or proteins cooperate in emerging phenotypes resulting in the evolution of diseases. As living cells are open systems in quasi-steady state type equilibrium in continuous exchange with their environment, computational techniques that have been successfully applied in statistical thermodynamics to describe phase transitions may provide new insights to emerging behavior of biological systems. Here we will systematically evaluate the translation of computational techniques from solid-state physics to network models that closely resemble biological networks and develop specific translational rules to tackle problems unique to living systems. Hence we will focus on logic models exhibiting only two states in each network node. Motivated by the apparent asymmetry between biological states where an entity exhibits boolean states i.e. is active or inactive, we present an adaptation of symmetric Ising model towards an asymmetric one fitting to living systems here referred to as the modified Ising model with gene-type spins. We analyze phase transitions by Monte Carlo simulations and propose mean-field solution of modified Ising model of a network type that closely resembles real-world network, the Barabási-Albert model of scale-free networks. We show that asymmetric Ising models show similarities to symmetric Ising models with external field and undergoes a discontinuous phase transition of the first-order and exhibits hysteresis. The simulation setup presented here can be directly used for any biological network connectivity dataset and is also applicable for other networks that exhibit similar states of activity. This is a general statistical method to deal with non-linear large scale models arising in the context of biological systems and is scalable to any network size.

q-bio.QM↗

arXiv2018

ChASE: Chebyshev Accelerated Subspace iteration Eigensolver for sequences of Hermitian eigenvalue problems

Solving dense Hermitian eigenproblems arranged in a sequence with direct solvers fails to take advantage of those spectral properties which are pertinent to the entire sequence, and not just to the single problem. When such features take the form of correlations between the eigenvectors of consecutive problems, as is the case in many real-world applications, the potential benefit of exploiting them can be substantial. We present ChASE, a modern algorithm and library based on subspace iteration with polynomial acceleration. Novel to ChASE is the computation of the spectral estimates that enter in the filter and an optimization of the polynomial degree which further reduces the necessary FLOPs. ChASE is written in C++ using the modern software engineering concepts which favor a simple integration in application codes and a straightforward portability over heterogeneous platforms. When solving sequences of Hermitian eigenproblems for a portion of their extremal spectrum, ChASE greatly benefits from the sequence's spectral properties and outperforms direct solvers in many scenarios. The library ships with two distinct parallelization schemes, supports execution over distributed GPUs, and it is easily extensible to other parallel computing architectures.

cs.MS↗

arXiv2017

Perfect spike detection via time reversal

Spiking neuronal networks are usually simulated with three main simulation schemes: the classical time-driven and event-driven schemes, and the more recent hybrid scheme. All three schemes evolve the state of a neuron through a series of checkpoints: equally spaced in the first scheme and determined neuron-wise by spike events in the latter two. The time-driven and the hybrid scheme determine whether the membrane potential of a neuron crosses a threshold at the end of of the time interval between consecutive checkpoints. Threshold crossing can, however, occur within the interval even if this test is negative. Spikes can therefore be missed. The present work derives, implements, and benchmarks a method for perfect retrospective spike detection. This method can be applied to neuron models with affine or linear subthreshold dynamics. The idea behind the method is to propagate the threshold with a time-inverted dynamics, testing whether the threshold crosses the neuron state to be evolved, rather than vice versa. Algebraically this translates into a set of inequalities necessary and sufficient for threshold crossing. This test is slower than the imperfect one, but faster than an alternative perfect tests based on bisection or root-finding methods. Comparison confirms earlier results that the imperfect test rarely misses spikes (less than a fraction $1/10^8$ of missed spikes) in biologically relevant settings. This study offers an alternative geometric point of view on neuronal dynamics.

q-bio.NC↗

arXiv2017

Non-Linear Least-Squares Optimization of Rational Filters for the Solution of Interior Eigenvalue Problems

Rational filter functions can be used to improve convergence of contour-based eigensolvers, a popular family of algorithms for the solution of the interior eigenvalue problem. We present a framework for the optimization of rational filters based on a non-convex weighted Least-Squares scheme. When used in combination with the FEAST library, our filters out-perform existing ones on a large and representative set of benchmark problems. This work provides a detailed description of: (1) a set up of the optimization process that exploits symmetries of the filter function for Hermitian eigenproblems, (2) a formulation of the gradient descent and Levenberg-Marquardt algorithms that exploits the symmetries, (3) a method to select the starting position for the optimization algorithms that reliably produces effective filters, (4) a constrained optimization scheme that produces filter functions with specific properties that may be beneficial to the performance of the eigensolver that employs them.

cs.CE↗

arXiv2016

Parallel adaptive integration in high-performance functional Renormalization Group computations

The conceptual framework provided by the functional Renormalization Group (fRG) has become a formidable tool to study correlated electron systems on lattices which, in turn, provided great insights to our understanding of complex many-body phenomena, such as high- temperature superconductivity or topological states of matter. In this work we present one of the latest realizations of fRG which makes use of an adaptive numerical quadrature scheme specifically tailored to the described fRG scheme. The final result is an increase in performance thanks to improved parallelism and scalability.

cs.CE↗