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3. The State of Fortran.

Author

Laurence J. Kedward, Bálint Aradi, Ondrej Certík, Milan Curcic, Sebastian Ehlert, Philipp Engel, Rohit Goswami, Michael Hirsch 0004, Asdrubal Lozada-Blanco, Vincent Magnin, Arjen Markus, Emanuele Pagone, Ivan Pribec, Brad Richardson, Harris Snyder, John Urban, and Jérémie Vandenplas more...

Published
2022
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6. Unified Software Design Patterns for Simulated Annealing

Author

Rohit, Goswami, Ruhila, S, Amrita, Goswami, Sonaly, Goswami, and Debabrata, Goswami

Abstract

Any optimization algorithm programming interface can be seen as a black-box function with additional free parameters. In this spirit, simulated annealing (SA) can be implemented in pseudo-code within the dimensions of a single slide with free parameters relating to the annealing schedule. Such an implementation, however, necessarily neglects much of the structure necessary to take advantage of advances in computing resources and algorithmic breakthroughs. Simulated annealing is often introduced in myriad disciplines, from discrete examples like the Traveling Salesman Problem (TSP) to molecular cluster potential energy exploration or even explorations of a protein’s configurational space. Theoretical guarantees also demand a stricter structure in terms of statistical quantities, which cannot simply be left to the user. We will introduce several standard paradigms and demonstrate how these can be “lifted” into a unified framework using object-oriented programming in Python. We demonstrate how clean, interoperable, reproducible programming libraries can be used to access and rapidly iterate on variants of Simulated Annealing in a manner which can be extended to serve as a best practices blueprint or design pattern for a data-driven optimization library. more...

Published
2023

9. Maintaining Fortran in Python in Perpetuity

Author

Rohit Goswami, Melissa Mendonca, Ralf Gommers, Thirumalai Shaktivel, and Pearu Peterson

Subjects
numpy, f2py, fortran
Abstract

This talk covers recent advances to the f2py project, including preliminary derived type support, better documentation, and restructured design to enhance new contributor experiences. Additionally, we will discuss the structure and role of interoperability libraries and how modern Fortran intends to harmoniously and symbiotically evolve within the Python ecosystem in the context of Fortran-Lang, the np.distutils deprecation, newer compute devices and the ever changing landscape of high performance programming. More details at: https://rgoswami.me/posts/scipycon-2022-meta, Fortran forms the computational bedrock of the scientific community. Despite the prevalence of the pack libraries (LAPACK, PROPACK etc.) within scipy and the fact that f2py has been an integral part of the numpy ecosystem for decades now, it is seldom brought up. In particular, newer, younger programming languages and projects are consistently brought up as possible contenders to the crown of numerical computing within the Scientific Python ecosystem. Being such a foundational project has a unique set of maintainability challenges as well. Hyrum's law rings especially true for f2py, scientific projects, both public and private, depend heavily on every aspect of the exposed API. A boon for scientific programming from the very beginning, f2py has enabled high performance computing without in-depth understanding of either the python-C API or the Fortran language itself. Even as f2py reinvents itself for modern Fortran constructs however, backwards compatibility requirements remain (e.g. scipy lags by two versions). From a brief historical overview of the scientific python ecosystem and interoperability issues we will move through the sustainability efforts through the years. We will cover changes in f2py, both planned and implemented, including the migration towards the Python-C Limited API, the newer argparse front-end, moving away from np.distutils, restructuring and reducing reliance on features implemented by the NumPy-C API, and supporting newer Fortran standards (with derived types being the poster child of missing Modern Fortran features). The talk will also briefly cover the code-generation and fortranobject constructs. The focus is not meant to be the internals so much as a 50-foot view of each constituent part of f2py and its long term viability. Part of the discussion will revolve around synergies with existing projects, both within the scientific Python ecosystem (scipy), and Fortran-Lang (LFortran), and by planning to involve younger developers via GSoC. Lastly, we will discuss how the FOSS community stepped up to support f2py and how we intend to continue to carry modern Fortran as a corner stone of the scientific python ecosystem for many years to come in no small part by providing a common set of interoperability standards in the form of NEPs (NumPy Enhancement Proposals). more...

Published
2022
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11. Centering inclusivity in the design of online conferences - An OHBM - Open Science perspective

Author

Elizabeth Levitis, Cassandra Doris Gould van Praag, Remi Gau, Stephan Heunis, Elizabeth DuPre, Greg Kiar, Katherine L Bottenhorn, Tristan Glatard, Aki Nikolaidis, Kirstie Jane Whitaker, Matteo Mancini, Guiomar Niso, Soroosh Afyouni, Eva Alonso Ortiz, Stefan Appelhoff, Aurina Arnatkeviciute, Melvin Selim ATAY, Tibor Auer, Giulia Baracchini, Johanna Margarete Marianne Bayer, Michael J. S. Beauvais, Janine Diane Bijsterbosch, Isil Poyraz Bilgin, Saskia Bollmann, Steffen Bollmann, Rotem Botvinik-Nezer, Molly G Bright, Vince D Calhoun, Xiao Chen, Sidhant Chopra, Hu Chuan-Peng, Thomas Close, Savannah Cookson, Cameron Craddock, Alejandro De La Vega, Benjamin De Leener, Damion Demeter, Paola Di Maio, Erin W Dickie, Simon B Eickhoff, Oscar Esteban, Karolina Finc, Matteo Frigo, Saampras Ganesan, Melanie Ganz, Kelly Garner, Eduardo A. Garza-Villarreal, Gabriel Gonzalez-Escamilla, Rohit Goswami, John David Griffiths, Tijl Grootswagers, Samuel Guay, Olivia Guest, Daniel A. Handwerker, Peer Herholz, Katja Heuer, Dorien Huijser, Vittorio Iacovella, Michael Joseph, Agah Karakuzu, David Keator, Xenia Kobeleva, Manoj Kumar, Angie Laird, Linda J. Larson-Prior, Alexandra Lautarescu, Alberto Lazari, Jon Haitz Legarreta Gorroño, Jeff jeffers, Jinglei Lv, Sina Mansour L., David Meunier, Dustin Moraczewski, Tulika Nandi, Samuel A. Nastase, Matthias Nau, Stephanie Noble, Martin Norgaard, Johnes Obungoloch, Robert Oostenveld, Edwina R Orchard, Ana Luísa Pinho, Russell Poldrack, Anqi Qiu, Pradeep Reddy Raamana, Ariel Rokem, Saige Rutherford, Malvika Sharan, Thomas Shaw, Warda T Syeda, Meghan M. Testerman, Roberto Toro, Sofie L. Valk, Sofie Van Den Bossche, Gael P. Varoquaux, Frantisek Vasa, Michele Veldsman, Jakub Vohryzek, Adina Svenja Wagner, Reubs J Walsh, Tonya White, null zuxfoucault, Xihe Xie, Chao-Gan Yan, Yu-Fang Yang, Yohan Yee, Gaston E Zanitti, Ana Van Gulick, Eugene Duff, Camille MAUMET, National Institute of Mental Health (NIMH), University College of London [London] (UCL), University of Oxford, Université Catholique de Louvain = Catholic University of Louvain (UCL), Eindhoven University of Technology [Eindhoven] (TU/e), McGill University = Université McGill [Montréal, Canada], Florida International University [Miami] (FIU), Concordia University [Montreal], Child Mind Institute, The Alan Turing Institute, University of Sussex, Cardiff University, École Polytechnique de Montréal (EPM), Indiana University [Bloomington], Indiana University System, Universidad Politécnica de Madrid (UPM), Max Planck Institute for Human Development, Max-Planck-Gesellschaft, Monash University [Melbourne], Middle East Technical University [Ankara] (METU), University of Surrey (UNIS), Montreal Neurological Institute and Hospital, University of Melbourne, Orygen Youth Health Research Centre [Melbourne], Washington University School of Medicine in St. Louis, Washington University in Saint Louis (WUSTL), University of Reading (UOR), University of Queensland [Brisbane], Dartmouth College [Hanover], Northwestern University [Evanston], Georgia State University, University System of Georgia (USG), Institute of Psychology [Beijing], Chinese Academy of Sciences [Changchun Branch] (CAS), University of Chinese Academy of Sciences [Beijing] (UCAS), Nanjing Normal University (NNU), The University of Sydney, University of California (UC), University of Texas at Austin [Austin], CHU Sainte Justine [Montréal], Institute for Globally Distributed Open Research and Education (IGDORE ), Centre for Addiction and Mental Health [Toronto] (CAMH), University of Toronto, Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf], Jülich Research Centre, Université de Lausanne = University of Lausanne (UNIL), Nicolaus Copernicus University [Toruń], Université Côte d'Azur (UCA), Computational Imaging of the Central Nervous System (ATHENA), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Rigshospitalet [Copenhagen], Copenhagen University Hospital, University of Copenhagen = Københavns Universitet (UCPH), University of Birmingham [Birmingham], Universidad Nacional Autónoma de México = National Autonomous University of Mexico (UNAM), Johannes Gutenberg - Universität Mainz = Johannes Gutenberg University (JGU), University of Iceland [Reykjavik], Indian Institute of Technology Kanpur (IIT Kanpur), Western Sydney University, Université de Montréal (UdeM), Radboud University [Nijmegen], Centre de Recherche Interdisciplinaire / Center for Research and Interdisciplinarity [Paris, France] (CRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Max Planck Institute for Human Cognitive and Brain Sciences [Leipzig] (IMPNSC), Erasmus University Rotterdam, Universiteit Leiden, University of Trento [Trento], Université du Québec à Montréal = University of Québec in Montréal (UQAM), University Hospital Bonn, German Research Center for Neurodegenerative Diseases - Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Princeton University, University of Arkansas for Medical Sciences (UAMS), Arkansas Children's Research Institute, King‘s College London, Université de Sherbrooke (UdeS), Aarhus University [Aarhus], Institut de Neurosciences de la Timone (INT), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Yale University [New Haven], Stanford University, Mbarara University of Science and Technology [Mbarara] (MUST), Karolinska Institutet [Stockholm], Université Paris-Saclay, National University of Singapore (NUS), Johns Hopkins University (JHU), University of Pittsburgh (PITT), Pennsylvania Commonwealth System of Higher Education (PCSHE), University of Washington [Seattle], Radboud University Medical Center [Nijmegen], University of Michigan [Ann Arbor], University of Michigan System, Institut Pasteur [Paris] (IP), Universiteit Gent = Ghent University (UGENT), Vrije Universiteit Amsterdam [Amsterdam] (VU), Department of Public Health, Erasmus University Medical Centre, Rotterdam, Erasmus University Medical Centre, Rotterdam, Academia Sinica, Weill Medical College of Cornell University [New York], Chinese Academy of Sciences [Beijing] (CAS), University of Würzburg, The Hospital for sick children [Toronto] (SickKids), Carnegie Mellon University [Pittsburgh] (CMU), Neuroimagerie: méthodes et applications (Empenn), Institut National de la Santé et de la Recherche Médicale (INSERM)-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-SIGNAUX ET IMAGES NUMÉRIQUES, ROBOTIQUE (IRISA-D5), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), R25-DA051675, National Institutes of Health, 1631325, National Science Foundation, 5R21MH118556-02, National Institute of Mental Health, BB/S008314/1, Biotechnology and Biological Sciences Research Council, G036716N, Fonds Wetenschappelijk Onderzoek, University of Oxford [Oxford], University of California, University of Lausanne (UNIL), University of Copenhagen = Københavns Universitet (KU), Universidad Nacional Autónoma de México (UNAM), Johannes Gutenberg - Universität Mainz (JGU), Radboud university [Nijmegen], Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), Leiden University, Institut Pasteur [Paris], Universiteit Gent = Ghent University [Belgium] (UGENT), Empenn, Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), and Maumet, Camille more...

Subjects
SDG 16 - Peace, collaborative events, [SCCO.NEUR]Cognitive science/Neuroscience, [SCCO.NEUR] Cognitive science/Neuroscience, SDG 16 - Peace, Justice and Strong Institutions, Review, Justice and Strong Institutions, online conferences, diversity, World Wide Web, inclusivity, open science, ddc:610, Sociology
Abstract

As the global health crisis unfolded throughout the world, many academic conferences moved online in 2020. This move has been hailed as a positive step towards inclusivity in its attenuation of economic, physical and legal barriers and effectively enabled many individuals who have traditionally been underrepresented to join and participate. A number of studies have outlined how moving online made it possible to gather a more global community and has increased opportunities for individuals with various constraints, e.g. caregiving responsibilities. Yet, the mere existence of online conferences is unfortunately no guarantee that everyone can attend and participate meaningfully. In fact, many elements of an online conference are still significant barriers to truly diverse participation: the tools used can be inaccessible for some individuals; the scheduling choices can favour some geographical locations; the setup of the conference can provide more visibility to well-established researchers and reduce opportunities for early career researchers. While acknowledging the benefits of an online setting, especially for individuals who have traditionally been underrepresented or excluded, we recognize that fostering social justice requires inclusivity to actively be centered in every aspect of online conference design.Here, we draw from the literature and from our own experiences to identify practices that purposefully encourage a diverse community to: attend, participate in, and lead online conferences. Reflecting on how to design more inclusive online events is especially important as multiple scientific organizations have announced that they will continue offering an online version of their event when in-person conferences can resume. more...

Published
2021
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12. Semi-Supervised Approaches to Ultrafast Pulse Shaping

Author

Debabrata Goswami, Rohit Goswami, and Amrita Goswami

Subjects
Pulsed laser, Computer science, Control aspects, Electronic engineering, Schematic, Optimal control, Pulse shaping, Ultrashort pulse, Domain (software engineering), Pulse (physics)
Abstract

Spatiotemporal control aspects of pulsed laser experiments rely on the ability to modulate the shape of the generated pulses efficiently. Drawing from current state-of-the-art theoretical aspects of computational simulations to reduce the sim-to-real bottlenecks, we devise a novel schematic for the generation of on-the-fly calibrated pulse trains with more accountability than existing techniques under the domain of optimal control theory. The techniques presented further diminish the divide between experiment and theory. more...

Published
2021
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13. Translational and rotational dynamics of a self-propelled Janus probe in crowded environments

Author

Subhasish Chaki, Rohit Goswami, Ligesh Theeyancheri, Raghunath Chelakkot, Nairhita Samanta, and Rajarshi Chakrabarti

Subjects
Physics, Area fraction, Quantitative Biology::Biomolecules, Drop (liquid), Dynamics (mechanics), FOS: Physical sciences, Janus particles, 02 engineering and technology, General Chemistry, Decoupling (cosmology), Condensed Matter - Soft Condensed Matter, 021001 nanoscience & nanotechnology, Condensed Matter Physics, 01 natural sciences, Viscoelasticity, Condensed Matter::Soft Condensed Matter, Chemical physics, 0103 physical sciences, Soft Condensed Matter (cond-mat.soft), Janus, 010306 general physics, 0210 nano-technology, Rotational dynamics
Abstract

We computationally investigate the dynamics of a self-propelled Janus probe in crowded environments. The crowding is caused by the presence of viscoelastic polymers or non-viscoelastic disconnected monomers. Our simulations show that the translational, as well as rotational mean square displacements, have a distinctive three-step growth for fixed values of self-propulsion force, and steadily increase with self-propulsion, irrespective of the nature of the crowder. On the other hand, in the absence of crowders, the rotational dynamics of the Janus probe is independent of self-propulsion force. On replacing the repulsive polymers with sticky ones, translational and rotational mean square displacements of the Janus probe show a sharp drop. Since different faces of a Janus particle interact differently with the environment, we show that the direction of self-propulsion also affects its dynamics. The ratio of long-time translational and rotational diffusivities of the self-propelled probe with a fixed self-propulsion, when plotted against the area fraction of the crowders, passes through a minima and at higher area fraction merges to its value in the absence of the crowder. This points towards the decoupling of translational and rotational dynamics of the self-propelled probe at intermediate area fraction of the crowders. However, such translational-rotational decoupling is absent for passive probes., Comment: Simulation videos are available on request more...

Published
2020

15. Qubit Network Barriers to Deep Learning

Author

Rohit Goswami, Amrita Goswami, and Debabrata Goswami

Subjects
Artificial neural network, Computer science, business.industry, Distributed computing, Deep learning, Computer Science::Neural and Evolutionary Computation, Topology (electrical circuits), Bottleneck, Qubit, Convergence (routing), Quantum algorithm, Artificial intelligence, business, Quantum computer
Abstract

The popularity of artificial neural networks (ANNs) of great depth and Quantum computing have led to many speculations as to their convergence. We enumerate barriers to utilizing qubit networks for deep learning architectures. We also describe the criteria for an effective usage of qubit networks and then assert that the bottleneck in their implementation is a lack of quantum algorithms for utilizing the topology of a deep neural network. more...

Published
2019
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17. Study of ice nucleation on silver iodide surface with defects

Author

Rohit Goswami, Prerna, Atanu K. Metya, Jayant K. Singh, and S.V. Shevkunov

Subjects
Work (thermodynamics), Materials science, 010304 chemical physics, Biophysics, Silver iodide, Fraction (chemistry), 010402 general chemistry, Condensed Matter Physics, 01 natural sciences, 0104 chemical sciences, law.invention, Molecular dynamics, chemistry.chemical_compound, chemistry, law, Chemical physics, 0103 physical sciences, Ice nucleus, Physical and Theoretical Chemistry, Crystallization, Supercooling, Molecular Biology, Topology (chemistry)
Abstract

In this work, we have considered the crystallisation behaviour of supercooled water in the presence of surface defects of varying size (surface fraction, α from 1 to 0.5). Ice nucleation on Ag exposed β-AgI (0001 plane) surface is investigated by molecular dynamics simulation at a temperature of 240 K. For systems with α>0.67, the surface layers crystallise within 150 ns. In the system with defects, we observe two distinct stacking patterns in the layers near the surface and find that systems with AA stacking cause a monotonic decrease in the early nucleation dynamics with an increase in defect size. Where AB stacking (α=0.833) is observed, the effect of the defect is diminished and the dynamics are similar to the plain AgI surface. This is supported by the variation in the orientational dynamics, hydrogen bond network stability, and tetrahedrality with respect to the defects. We quantify results in terms of the network topology using double-diamond cages (DDCs) and hexagonal cages (HCs). The configurations of the initially formed layers of ice strongly affect the subsequent growth even at long timescales. We assert that the retarded ice growth due to defects can be explained by the relative increase in DDCs with respect to HCs. more...

Published
2019
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19. Quantum Distributed Computing with Shaped Laser Pulses

Author

Rohit Goswami and Debabrata Goswami

Subjects
Physics, Distributed feedback laser, Quantum decoherence, business.industry, TheoryofComputation_GENERAL, Laser, Adiabatic quantum computation, law.invention, Optics, law, ComputerSystemsOrganization_MISCELLANEOUS, Quantum information, business, Adiabatic process, Quantum, Hardware_LOGICDESIGN, Quantum computer
Abstract

Shaped laser pulses can control decoherence under quantum adiabatic method of logic operations to result in a possible scalable quantum computer by distributing the computing load on a set of optically adiabatic quantum computing nodes. more...

Published
2016
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