arXiv subjects

Marlon Pierce

Publications and source records attributed to Marlon Pierce.

12 recordsLinked to original sources

arXiv2022

The Science Gateway Community Institute's Consulting Services Program: Lessons for Research Software Engineering Organizations

The Science Gateways Community Institute (SGCI) is an NSF Software Infrastructure for Sustained Innovation (S2I2) funded project that leads and supports the science gateway community. Major activities for SGCI include a) sustainability training, including the Focus Week week-long course designed to help science gateway operators develop sustainability plans, and the Jumpstart virtual short-course; b) usability and user experience consulting; c) a community catalog of science gateways and science gateway software; d) workforce development activities, including a coding institute for students, internship opportunities, and hackathons; e) an annual conference; and f) in-depth technical support for client gateway projects. The goals of SGCI's Embedded Technical Support component are to help the institute's clients to create new science gateways or to significantly enhance existing science gateways. Examples of the latter include helping to implement major new capabilities and to implement significant usability improvements suggested by SGCI's usability consultants. The Embedded Technical Support component was managed by Indiana University and involved research software engineers at San Diego Supercomputer Center, Texas Advanced Computing Center, Indiana University, and Purdue University (through 2019). Since 2016, the component has involved 20 research software engineers as consultants and has conducted 59 client consultations. This short paper provides a summary of lessons learned from the Embedded Technical Support program that may be useful for the research software engineering community.

cs.SE↗

arXiv2022

A Framework to capture and reproduce the Absolute State of Jupyter Notebooks

Jupyter Notebooks are an enormously popular tool for creating and narrating computational research projects. They also have enormous potential for creating reproducible scientific research artifacts. Capturing the complete state of a notebook has additional benefits; for instance, the notebook execution may be split between local and remote resources, where the latter may have more powerful processing capabilities or store large or access-limited data. There are several challenges for making notebooks fully reproducible when examined in detail. The notebook code must be replicated entirely, and the underlying Python runtime environments must be identical. More subtle problems arise in replicating referenced data, external library dependencies, and runtime variable states. This paper presents solutions to these problems using Juptyer's standard extension mechanisms to create an archivable system state for a running notebook. We show that the overhead for these additional mechanisms, which involve interacting with the underlying Linux kernel, does not introduce substantial execution time overheads, demonstrating the approach's feasibility.

cs.DC↗

arXiv2022

Experiences with managing data parallel computational workflows for High-throughput Fragment Molecular Orbital (FMO) Calculations

Fragment Molecular Orbital (FMO) calculations provide a framework to speed up quantum mechanical calculations and so can be used to explore structure-energy relationships in large and complex biomolecular systems. These calculations are still onerous, especially when applied to large sets of molecules. Therefore, cyberinfrastructure that provides mechanisms and user interfaces that manage job submissions, failed job resubmissions, data retrieval, and data storage for these calculations are needed. Motivated by the need to rapidly identify drugs that are likely to bind to targets implicated in SARS-CoV-2, the virus that causes COVID-19, we developed a static parameter sweeping framework with Apache Airavata middleware to apply to complexes formed between SARS-CoV-2 M-pro (the main protease in SARS-CoV-2) and 2820 small-molecules in a drug-repurposing library. Here we describe the implementation of our framework for managing the executions of the high-throughput FMO calculations. The approach is general and so should find utility in large-scale FMO calculations on biomolecular systems.

physics.chem-ph↗

arXiv2021

Experiences with Integrating Custos SecurityServices

Science gateways are user-facing cyberinfrastruc-ture that provide researchers and educators with Web-basedaccess to scientific software, computing, and data resources.Managing user identities, accounts, and permissions are essentialtasks for science gateways, and gateways likewise must man-age secure connections between their middleware and remoteresources. The Custos project is an effort to build open sourcesoftware that can be operated as a multi-tenanted service thatprovides reliable implementations of common science gatewaycybersecurity needs, including federated authentication, iden-tity management, group and authorization management, andresource credential management. Custos aims further to provideintegrated solutions through these capabilities, delivering end-to-end support for several science gateway usage scenarios. Thispaper examines four deployment scenarios using Custos andassociated extensions beyond previously described work. Thefirst capability illustrated by these scenarios is the need forCustos to provide hierarchical tenant management that allowsmultiple gateway deployments to be federated together andalso to support consolidated, hosted science gateway platformservices. The second capability illustrated by these scenarios is theneed to support service accounts that can support non-browserapplications and agent applications that can act on behalf ofusers on edge resources. We illustrate how the latter can be builtusing Web security standards combined with Custos permissionmanagement mechanisms.

cs.DC↗

arXiv2021

A Multi-Protocol, Secure, and Dynamic Data Storage Integration Frameworkfor Multi-tenanted Science Gateway Middleware

Science gateways are user-centric, end-to-end cyberinfrastructure for managing scientific data and executions of computational software on distributed resources. In order to simplify the creation and management of science gateways, we have pursued a multi-tenanted, platform-as-a-service approach that allows multiple gateway front-ends (portals) to be integrated with a consolidated middleware that manages the movement of data and the execution of workflows on multiple back-end scientific computing resources. An important challenge for this approach is to provide an end-to-end data movement and management solution that allows gateway users to integrate their own data stores with the gateway platform. These user-provided data stores may include commercial cloud-based object store systems, third-party data stores accessed through APIs such as REST endpoints, and users' own local storage resources. In this paper, we present a solution design and implementation based on the integration of a managed file transfer (MFT) service (Airavata MFT) into the platform.

cs.DC↗

arXiv2021

Toward Interoperable Cyberinfrastructure: Common Descriptions for Computational Resources and Applications

The user-facing components of the Cyberinfrastructure (CI) ecosystem, science gateways and scientific workflow systems, share a common need of interfacing with physical resources (storage systems and execution environments) to manage data and execute codes (applications). However, there is no uniform, platform-independent way to describe either the resources or the applications. To address this, we propose uniform semantics for describing resources and applications that will be relevant to a diverse set of stakeholders. We sketch a solution to the problem of a common description and catalog of resources: we describe an approach to implementing a resource registry for use by the community and discuss potential approaches to some long-term challenges. We conclude by looking ahead to the application description language.

cs.DC↗

arXiv2020

MultiCloud Resource Management using Apache Mesos for Planned Integration with Apache Airavata

We discuss initial results and our planned approach for incorporating Apache Mesos based resource management that will enable design and development of scheduling strategies for Apache Airavata jobs so that they can be launched on multiple clouds, wherein several VMs do not have Public IP addresses. We present initial work and next steps on the design of a meta-scheduler using Apache Mesos. Apache Mesos presents a unified view of resources available across several clouds and clusters. Our meta-scheduler can potentially examine and identify the cases where multiple small jobs have been submitted by the same scientists and then redirect job from the same community account or user to different clusters. Our approach uses a NAT firewall to make nodes/VMs, without a Public IP, visible to Mesos for the unified view.

cs.PF↗

arXiv2018

Community Organizations: Changing the Culture in Which Research Software Is Developed and Sustained

Software is the key crosscutting technology that enables advances in mathematics, computer science, and domain-specific science and engineering to achieve robust simulations and analysis for science, engineering, and other research fields. However, software itself has not traditionally received focused attention from research communities; rather, software has evolved organically and inconsistently, with its development largely as by-products of other initiatives. Moreover, challenges in scientific software are expanding due to disruptive changes in computer hardware, increasing scale and complexity of data, and demands for more complex simulations involving multiphysics, multiscale modeling and outer-loop analysis. In recent years, community members have established a range of grass-roots organizations and projects to address these growing technical and social challenges in software productivity, quality, reproducibility, and sustainability. This article provides an overview of such groups and discusses opportunities to leverage their synergistic activities while nurturing work toward emerging software ecosystems.

cs.CY↗

arXiv2012

A High Throughput Workflow Environment for Cosmological Simulations

The next generation of wide-area sky surveys offer the power to place extremely precise constraints on cosmological parameters and to test the source of cosmic acceleration. These observational programs will employ multiple techniques based on a variety of statistical signatures of galaxies and large-scale structure. These techniques have sources of systematic error that need to be understood at the percent-level in order to fully leverage the power of next-generation catalogs. Simulations of large-scale structure provide the means to characterize these uncertainties. We are using XSEDE resources to produce multiple synthetic sky surveys of galaxies and large-scale structure in support of science analysis for the Dark Energy Survey. In order to scale up our production to the level of fifty 10^10-particle simulations, we are working to embed production control within the Apache Airavata workflow environment. We explain our methods and report how the workflow has reduced production time by 40% compared to manual management.

astro-ph.CO↗

arXiv2000

Quantum Films Adsorbed on Graphite: Third and Fourth Helium Layers

Using a path-integral Monte Carlo method for simulating superfluid quantum films, we investigate helium layers adsorbed on a substrate consisting of graphite plus two solid helium layers. Our results for the promotion densities and the dependence of the superfluid density on coverage are in agreement with experiment. We can also explain certain features of the measured heat capacity as a function of temperature and coverage.

cond-mat.stat-mech↗

arXiv1998

Path integral Monte Carlo simulation of the second layer of helium-4 adsorbed on graphite

We have developed a path integral Monte Carlo method for simulating helium films and apply it to the second layer of helium adsorbed on graphite. We use helium-helium and helium-graphite interactions that are found from potentials which realistically describe the interatomic interactions. The Monte Carlo sampling is over both particle positions and permutations of particle labels. From the particle configurations and static structure factor calculations, we find that this layer possesses, in order of increasing density, a superfluid liquid phase, a sqrt(7) x sqrt(7) commensurate solid phase that is registered with respect to the first layer, and an incommensurate solid phases. By applying the Maxwell construction to the dependence of the low-temperature total energy on the coverage, we are able to identify coexistence regions between the phases. From these, we deduce an effectively zero-temperature phase diagram. Our phase boundaries are in agreement with heat capacity and torsional oscillator measurements, and demonstrate that the experimentally observed disruption of the superfluid phase is caused by the growth of the commensurate phase. We further observe that the superfluid phase has a transition temperature consistent with the two-dimensional value. Promotion to the third layer occurs for densities above 0.212 atom/A^2, in good agreement with experiment. Finally, we calculate the specific heat for each phase and obtain peaks at temperatures in general agreement with experiment.

cond-mat↗

arXiv1998

Phase diagram of second layer of helium adsorbed on graphite

Using realistic helium-helium and helium-graphite interactions and the path integral Monte Carlo method, we are able to identify the gas, superfluid liquid, commensurate-solid, and incommensurate-solid phases, and the coexistence regions between them, for the second layer of helium on graphite. The phase boundaries and the specific heat that we determine are in good agreement with experiment. The appearance and disappearance of superfluidity with increasing coverage can be explained by the growth of coexistence phases, as was observed by torsional oscillator experiments.

cond-mat↗