arXiv subjects

Ramses van Zon

Publications and source records attributed to Ramses van Zon.

At least 19 recordsLinked to original sources

arXiv2023

Parallelizing a 1-Dim Nagel-Schreckenberg Traffic Model

The Nagel-Schreckenberg model is a stochastic one-dimensional traffic model. In this assignment, we guide students through the process of implementing a shared-memory parallel and reproducible version of an existing serial code that implements this model, and to analyze its scaling behavior. One of the key elements in this traffic model is the presence of randomness, without which it would lack realistic phenomena such as traffic jams. Its implementation thus requires techniques associated with Monte Carlo simulations and pseudo-random number generation (PRNG). PRNGs are notoriously tricky to deal with in parallel when combined with the requirement of reproducibility. This assignment was created for the graduate course PHY1610 Scientific Computing for Physicists at the University of Toronto, which had its origin in the training program of the SciNet HPC Consortium, and is also very suitable for other scientific disciplines. Several variations of the assignment have been used over the years.

cs.DC↗

arXiv2023

Cybersecurity Training for Users of Remote Computing

End users of remote computing systems are frequently not aware of basic ways in which they could enhance protection against cyber-threats and attacks. In this paper, we discuss specific techniques to help and train users to improve cybersecurity when using such systems. To explain the rationale behind these techniques, we go into some depth explaining possible threats in the context of using remote, shared computing resources. Although some of the details of these prescriptions and recommendations apply to specific use cases when connecting to remote servers, such as a supercomputer, cluster, or Linux workstation, the main concepts and ideas can be applied to a wider spectrum of cases.

cs.CR↗

arXiv2019

Deploying a Top-100 Supercomputer for Large Parallel Workloads: the Niagara Supercomputer

Niagara is currently the fastest supercomputer accessible to academics in Canada. It was deployed at the beginning of 2018 and has been serving the research community ever since. This homogeneous 60,000-core cluster, owned by the University of Toronto and operated by SciNet, was intended to enable large parallel jobs and has a measured performance of 3.02 petaflops, debuting at #53 in the June 2018 TOP500 list. It was designed to optimize throughput of a range of scientific codes running at scale, energy efficiency, and network and storage performance and capacity. It replaced two systems that SciNet operated for over 8 years, the Tightly Coupled System (TCS) and the General Purpose Cluster (GPC). In this paper we describe the transition process from these two systems, the procurement and deployment processes, as well as the unique features that make Niagara a one-of-a-kind machine in Canada.

cs.DC↗

arXiv2019

Software-Enhanced Teaching and Visualization Capabilities of an Ultra-High-Resolution Video Wall

This paper presents a modular approach to enhance the capabilities and features of a visualization and teaching room using software. This approach was applied to a room with a large, high resolution (7680$\times$4320 pixels), tiled screen of 13 $\times$ 7.5 feet as its main display, and with a variety of audio and video inputs, connected over a network. Many of the techniques described are possible because of a software-enhanced setup, utilizing existing hardware and a collection of mostly open-source tools, allowing to perform collaborative, high-resolution visualizations as well as broadcasting and recording workshops and lectures. The software approach is flexible and allows one to add functionality without changing the hardware.

cs.GR↗

arXiv2019

Bridging the Educational Gap between Emerging and Established Scientific Computing Disciplines

In this paper we describe our experience in developing curriculum courses aimed at graduate students in emerging computational fields, including biology and medical science. We focus primarily on computational data analysis and statistical analysis, while at the same time teaching students best practices in coding and software development. Our approach combines a theoretical background and practical applications of concepts. The outcomes and feedback we have obtained so far have revealed several issues: students in these particular areas lack instruction like this although they would tremendously benefit from it; we have detected several weaknesses in the formation of students, in particular in the statistical foundations but also in analytical thinking skills. We present here the tools, techniques and methodology we employ while teaching and developing this type of courses. We also show several outcomes from this initiative, including potential pathways for fruitful multi-disciplinary collaborations.

cs.CY↗

arXiv2019

Trends in Demand, Growth, and Breadth in Scientific Computing Training Delivered by a High-Performance Computing Center

We analyze the changes in the training and educational efforts of the SciNet HPC Consortium, a Canadian academic High Performance Computing center, in the areas of Scientific Computing and High-Performance Computing, over the last six years. Initially, SciNet offered isolated training events on how to use HPC systems and write parallel code, but the training program now consists of a broad range of workshops and courses that users can take toward certificates in scientific computing, data science, or high-performance computing. Using data on enrollment, attendence, and certificate numbers from SciNet's education website, used by almost 1800 users so far, we extract trends on the growth, demand, and breadth of SciNet's training program. Among the results are a steady overall growth, a sharp and steady increase in the demand for data science training, and a wider participation of 'non-traditional' computing disciplines, which has motivated an increasingly broad spectrum of training offerings. Of interest is also that many of the training initiatives have evolved into courses that can be taken as part of the graduate curriculum at the University of Toronto.

cs.CY↗

arXiv2016

Scientific Computing, High-Performance Computing and Data Science in Higher Education

We present an overview of current academic curricula for Scientific Computing, High-Performance Computing and Data Science. After a survey of current academic and non-academic programs across the globe, we focus on Canadian programs and specifically on the education program of the SciNet HPC Consortium, using its detailed enrollment and course statistics for the past four to five years. Not only do these data display a steady and rapid increase in the demand for research-computing instruction, they also show a clear shift from traditional (high performance) computing to data-oriented methods. It is argued that this growing demand warrants specialized research computing degrees. The possible curricula of such degrees are described next, taking existing programs as an example, and adding SciNet's experiences of student desires as well as trends in advanced research computing.

cs.CY↗

arXiv2012

Free Energy Landscape of Protein-like Chains with Discontinuous Potentials

In this article the configurational space of two simple protein models consisting of polymers composed of a periodic sequence of four different kinds of monomers is studied as a function of temperature. In the protein models, hydrogen bond interactions, electrostatic repulsion, and covalent bond vibrations are modeled by discontinuous step, shoulder and square-well potentials, respectively. The protein-like chains exhibit a secondary alpha helix structure in their folded states at low temperatures, and allow a natural definition of a configuration by considering which beads are bonded. Free energies and entropies of configurations are computed using the parallel tempering method in combination with hybrid Monte Carlo sampling of the canonical ensemble of the discontinuous potential system. The probability of observing the most common configuration is used to analyze the nature of the free energy landscape, and it is found that the model with the least number of possible bonds exhibits a funnel-like free energy landscape at low enough temperature for chains with fewer than 30 beads. For longer proteins, the landscape consists of several minima, where the configuration with the lowest free energy changes significantly by lowering the temperature and the probability of observing the most common configuration never approaches one due to the degeneracy of the lowest accessible potential energy.

cond-mat.soft↗

arXiv2012

Mapping quantum-classical Liouville equation: projectors and trajectories

The evolution of a mixed quantum-classical system is expressed in the mapping formalism where discrete quantum states are mapped onto oscillator states, resulting in a phase space description of the quantum degrees of freedom. By defining projection operators onto the mapping states corresponding to the physical quantum states, it is shown that the mapping quantum-classical Liouville operator commutes with the projection operator so that the dynamics is confined to the physical space. It is also shown that a trajectory-based solution of this equation can be constructed that requires the simulation of an ensemble of entangled trajectories. An approximation to this evolution equation which retains only the Poisson bracket contribution to the evolution operator does admit a solution in an ensemble of independent trajectories but it is shown that this operator does not commute with the projection operators and the dynamics may take the system outside the physical space. The dynamical instabilities, utility and domain of validity of this approximate dynamics are discussed. The effects are illustrated by simulations on several quantum systems.

physics.chem-ph↗

arXiv2011

Free Energy Landscape of a Protein-Like Chain in a Fluid with Discontinuous Potentials

The free energy landscape of a protein-like chain in a fluid was studied by combining discontinuous molecular dynamics and parallel tempering. The model protein is a repeating sequence of four different beads, with interactions mimicking those in real proteins. Neighbor distances and angles are restricted to physical ranges and one out of the four kinds of beads can form hydrogen bonds with each other, except if they are too close in the chain. In contrast to earlier studies of this model, an explicit square-well solvent is included. Beads that can form intra-chain hydrogen bonds, can also form (weaker) hydrogen bonds with solvent molecules, while other beads are insoluble. By categorizing the protein configurations according to their intra-chain bonds, one can distinguish unfolded, helical, and collapsed helical structures. Simulations for chains of 15, 20 and 25 beads show that at low temperatures, the most likely structures are helical or collapsed helical, despite the low entropy of these structures. The temperature at which helical structures become dominant is higher than in the absence of a solvent. The cooperative effect of the solvent is attributed to the presence of hydrophobic beads. A phase transition of the solvent prevented the simulations of the 20-bead and 25-bead chains of reaching low enough temperatures to confirm whether the free energy landscape is funnel-shaped, although the results do not contradict that possibility.

cond-mat.soft↗

arXiv2010

Constructing smooth potentials of mean force, radial, distribution functions and probability densities from sampled data

In this paper a method of obtaining smooth analytical estimates of probability densities, radial distribution functions and potentials of mean force from sampled data in a statistically controlled fashion is presented. The approach is general and can be applied to any density of a single random variable. The method outlined here avoids the use of histograms, which require the specification of a physical parameter (bin size) and tend to give noisy results. The technique is an extension of the Berg-Harris method [B.A. Berg and R.C. Harris, Comp. Phys. Comm. 179, 443 (2008)], which is typically inaccurate for radial distribution functions and potentials of mean force due to a non-uniform Jacobian factor. In addition, the standard method often requires a large number of Fourier modes to represent radial distribution functions, which tends to lead to oscillatory fits. It is shown that the issues of poor sampling due to a Jacobian factor can be resolved using a biased resampling scheme, while the requirement of a large number of Fourier modes is mitigated through an automated piecewise construction approach. The method is demonstrated by analyzing the radial distribution functions in an energy-discretized water model. In addition, the fitting procedure is illustrated on three more applications for which the original Berg-Harris method is not suitable, namely, a random variable with a discontinuous probability density, a density with long tails, and the distribution of the first arrival times of a diffusing particle to a sphere, which has both long tails and short-time structure. In all cases, the resampled, piecewise analytical fit outperforms the histogram and the original Berg-Harris method.

cond-mat.stat-mech↗

arXiv2008

Effective pair potentials for spherical nanoparticles

An effective description for spherical nanoparticles in a fluid of point particles is presented. The points inside the nanoparticles and the point particles are assumed to interact via spherically symmetric additive pair potentials, while the distribution of points inside the nanoparticles is taken to be spherically symmetric and smooth. The resulting effective pair interactions between a nanoparticle and a point particle, as well as between two nanoparticles, are then given by spherically symmetric potentials. If overlap between particles is allowed, the effective potential generally has non-analytic points, but for each effective potential the expressions for different overlapping cases can be written in terms of one analytic auxiliary potential. Effective potentials for hollow nanoparticles (appropriate e.g. for buckyballs) are also considered, and shown to be related to those for solid nanoparticles. Finally, explicit expressions are given for the effective potentials derived from basic pair potentials of power law and exponential form, as well as from the commonly used London-Van der Waals, Morse, Buckingham, and Lennard-Jones potential. The applicability of the latter is demonstrated by comparison with an atomic description of nanoparticles with an internal face centered cubic structure.

cond-mat.stat-mech↗

arXiv2008

Quantum free energy differences from non-equilibrium path integrals: I. Methods and numerical application

The imaginary-time path integral representation of the canonical partition function of a quantum system and non-equilibrium work fluctuation relations are combined to yield methods for computing free energy differences in quantum systems using non-equilibrium processes. The path integral representation is isomorphic to the configurational partition function of a classical field theory, to which a natural but fictitious Hamiltonian dynamics is associated. It is shown that if this system is prepared in an equilibrium state, after which a control parameter in the fictitious Hamiltonian is changed in a finite time, then formally the Jarzynski non-equilibrium work relation and the Crooks fluctuation relation are shown to hold, where work is defined as the change in the energy as given by the fictitious Hamiltonian. Since the energy diverges for the classical field theory in canonical equilibrium, two regularization methods are introduced which limit the number of degrees of freedom to be finite. The numerical applicability of the methods is demonstrated for a quartic double-well potential with varying asymmetry. A general parameter-free smoothing procedure for the work distribution functions is useful in this context.

cond-mat.stat-mech↗

arXiv2008

Quantum free energy differences from non-equilibrium path integrals: II. Convergence properties for the harmonic oscillator

Non-equilibrium path integral methods for computing quantum free energy differences are applied to a quantum particle trapped in a harmonic well of uniformly changing strength with the purpose of establishing the convergence properties of the work distribution and free energy as the number of degrees of freedom M in the regularized path integrals goes to infinity. The work distribution is found to converge when M tends to infinity regardless of the switching speed, leading to finite results for the free energy difference when the Jarzynski non-equilibrium work relation or the Crooks fluctuation relation are used. The nature of the convergence depends on the regularization method. For the Fourier method, the convergence of the free energy difference and work distribution go as 1/M, while both quantities converge as 1/M^2 when the bead regularization procedure is used. The implications of these results to more general systems are discussed.

cond-mat.stat-mech↗

arXiv2008

Efficient algorithms for rigid body integration using optimized splitting methods and exact free rotational motion

Hamiltonian splitting methods are an established technique to derive stable and accurate integration schemes in molecular dynamics, in which additional accuracy can be gained using force gradients. For rigid bodies, a tradition exists in the literature to further split up the kinetic part of the Hamiltonian, which lowers the accuracy. The goal of this note is to comment on the best combination of optimized splitting and gradient methods that avoids splitting the kinetic energy. These schemes are generally applicable, but the optimal scheme depends on the desired level of accuracy. For simulations of liquid water it is found that the velocity Verlet scheme is only optimal for crude simulations with accuracies larger than 1.5%, while surprisingly a modified Verlet scheme (HOA) is optimal up to accuracies of 0.4% and a fourth order gradient scheme (GIER4) is optimal for even higher accuracies.

cond-mat.stat-mech↗

arXiv2007

Event-Driven Dynamics of Rigid Bodies Interacting via Discretized Potentials

A framework for performing event-driven, adaptive time step simulations of systems of rigid bodies interacting under stepped or terraced potentials in which the potential energy is only allowed to have discrete values is outlined. The scheme is based on a discretization of an underlying continuous potential that effectively determines the times at which interaction energies change. As in most event-driven approaches, the method consists of specifying a means of computing the free motion, evaluating the times at which interactions occur, and determining the consequences of interactions on subsequent motion for the terraced-potential. The latter two aspects are shown to be simply expressible in terms of the underlying smooth potential. Within this context, algorithms for computing the times of interaction events and carrying out efficient event-driven simulations are discussed. The method is illustrated on system composed of rigid rods in which the constituents interact via a terraced potential that depends on the relative orientations of the rods.

cond-mat.soft↗

arXiv2007

Symplectic algorithms for simulations of rigid body systems using the exact solution of free motion

Elegant integration schemes of second and fourth order for simulations of rigid body systems are presented which treat translational and rotational motion on the same footing. This is made possible by a recent implementation of the exact solution of free rigid body motion. The two schemes are time-reversible, symplectic, and exactly respect conservation principles for both the total linear and angular momentum vectors. Simulations of simple test systems show that the second order scheme is stable and conserves all constants of the motion to high precision. Furthermore, the schemes are demonstrated to be more accurate and efficient than existing methods, except for high densities, in which case the second order scheme performs at least as well, showing their general applicability. Finally, it is demonstrated that the fourth order scheme is more efficient than the second order scheme provided the time step is smaller than a system-dependent threshold value.

cond-mat.soft↗

arXiv2007

Stationary State Fluctuation Theorems for Driven Langevin Systems

Recent results on the stationary state Fluctuation Theorems for work and heat fluctuations of Langevin systems are presented. The relevance of finite time corrections in understanding experimental and simulation results is explained in the context of an exactly solvable model, namely a Brownian particle in a harmonic potential, which is dragged through the surrounding fluid. In this model, work fluctuations obey the conventional form of the fluctuation theorem while heat fluctuations satisfy an extended form. The connection with other work in recent literature is pointed out, and further generalizations are suggested.

cond-mat.stat-mech↗