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Parallel Runtime Interface for Fortran (PRIF) Specification (Rev. 0.4)

This document specifies an interface to support the parallel features of Fortran, named the Parallel Runtime Interface for Fortran (PRIF). PRIF is a proposed solution in which the runtime library is responsible for coarray allocation, deallocation and accesses, image synchronization, atomic operations, events, and teams. In this interface, the compiler is responsible for transforming the invocation of Fortran-level parallel features into procedure calls to the necessary PRIF procedures. The interface is designed for portability across shared- and distributed-memory machines, different operating systems, and multiple architectures. Implementations of this interface are intended as an augmentation for the compiler's own runtime library. With an implementation-agnostic interface, alternative parallel runtime libraries may be developed that support the same interface. One benefit of this approach is the ability to vary the communication substrate. A central aim of this document is to define a parallel runtime interface in standard Fortran syntax, which enables us to leverage Fortran to succinctly express various properties of the procedure interfaces, including argument attributes.

97 MATHEMATICS AND COMPUTING↗

Next-generation sequencing dataset of genome-scale CRISPRi in Synechococcus sp. PCC 7002 across seven conditions

A 33,298-member sgRNA library developed for Synechococus sp. PCC 7002 was screened with two replicates across seven growth conditions and sequenced with Illumina NextSeq (paired end, 2x150 bp) for a total of ~700M reads. The original plasmid library and the library after transformation into a dCas9-containing and dCas9-absent strain were also sequenced as a reference for initial sgRNA abundance.

genome- wide screens environmental acclimation spe↗

A goldilocks computational protocol for inhibitor discovery targeting DNA damage responses including replication-repair functions

While many researchers can design knockdown and knockout methodologies to remove a gene product, this is mainly untrue for new chemical inhibitor designs that empower multifunctional DNA Damage Response (DDR) networks. Here, we present a robust Goldilocks (GL) computational discovery protocol to efficiently innovate inhibitor tools and preclinical drug candidates for cellular and structural biologists without requiring extensive virtual screen (VS) and chemical synthesis expertise. By computationally targeting DDR replication and repair proteins, we exemplify the identification of DDR target sites and compounds to probe cancer biology. Our GL pipeline integrates experimental and predicted structures to efficiently discover leads, allowing early-structure and early-testing (ESET) experiments by many laboratories. By employing an efficient VS protocol to examine protein-protein interfaces (PPIs) and allosteric interactions, we identify ligand binding sites beyond active sites, leveraging in silico advances for molecular docking and modeling to screen PPIs and multiple targets. A diverse 3,174 compound ESET library combines Diamond Light Source DSI-poised, Protein Data Bank fragments, and FDA-approved drugs to span relevant chemotypes and facilitate downstream hit evaluation efficiency for academic laboratories. Two VS per library and multiple ranked ligand binding poses enable target testing for several DDR targets. This GL library and protocol can thus strategically probe multiple DDR network targets and identify readily available compounds for early structural and activity testing to overcome bottlenecks that can limit timely breakthrough drug discoveries. By testing accessible compounds to dissect multi-functional DDRs and suggesting inhibitor mechanisms from initial docking, the GL approach may enable more groups to help accelerate discovery, suggest new sites and compounds for challenging targets including emerging biothreats and advance cancer biology for future precision medicine clinical trials.

59 BASIC BIOLOGICAL SCIENCES↗

On a Simplified Approach to Achieve Parallel Performance and Portability Across CPU and GPU Architectures

This paper presents software advances to easily exploit computer architectures consisting of a multi-core CPU and CPU+GPU to accelerate diverse types of high-performance computing (HPC) applications using a single code implementation. The paper describes and demonstrates the performance of the open-source C++ matrix and array (MATAR) library that uniquely offers: (1) a straightforward syntax for programming productivity, (2) usable data structures for data-oriented programming (DOP) for performance, and (3) a simple interface to the open-source C++ Kokkos library for portability and memory management across CPUs and GPUs. The portability across architectures with a single code implementation is achieved by automatically switching between diverse fine-grained parallelism backends (e.g., CUDA, HIP, OpenMP, pthreads, etc.) at compile time. The MATAR library solves many longstanding challenges associated with easily writing software that can run in parallel on any computer architecture. This work benefits projects seeking to write new C++ codes while also addressing the challenges of quickly making existing Fortran codes performant and portable over modern computer architectures with minimal syntactical changes from Fortran to C++. We demonstrate the feasibility of readily writing new C++ codes and modernizing existing codes with MATAR to be performant, parallel, and portable across diverse computer architectures.

97 MATHEMATICS AND COMPUTING↗

Enabling Parallel Performance and Portability of Solid Mechanics Simulations Across CPU and GPU Architectures

Efficiently simulating solid mechanics is vital across various engineering applications. As constitutive models grow more complex and simulations scale up in size, harnessing the capabilities of modern computer architectures has become essential for achieving timely results. This paper presents advancements in running parallel simulations of solid mechanics on multi-core CPUs and GPUs using a single-code implementation. This portability is made possible by the C++ matrix and array (MATAR) library, which interfaces with the C++ Kokkos library, enabling the selection of fine-grained parallelism backends (e.g., CUDA, HIP, OpenMP, pthreads, etc.) at compile time. MATAR simplifies the transition from Fortran to C++ and Kokkos, making it easier to modernize legacy solid mechanics codes. We applied this approach to modernize a suite of constitutive models and to demonstrate substantial performance improvements across different computer architectures. This paper includes comparative performance studies using multi-core CPUs along with AMD and NVIDIA GPUs. Results are presented using a hypoelastic–plastic model, a crystal plasticity model, and the viscoplastic self-consistent generalized material model (VPSC-GMM). The results underscore the potential of using the MATAR library and modern computer architectures to accelerate solid mechanics simulations.

Morgan, Nathaniel (ORCID:0000000276118449)↗

Challenges and Solutions for Leave-One-Out Biosensor Design in the Context of a Rugged Fitness Landscape

The leave-one-out (LOO) green fluorescent protein (GFP) approach to biosensor design combines computational protein design with split protein reconstitution. LOO-GFPs reversibly fold and gain fluorescence upon encountering the target peptide, which can be redefined by computational design of the LOO site. Such an approach can be used to create reusable biosensors for the early detection of emerging biological threats. Enlightening biophysical inferences for nine LOO-GFP biosensor libraries are presented, with target sequences from dengue, influenza, or HIV, replacing beta strands 7, 8, or 11. An initially low hit rate was traced to components of the energy function, manifesting in the over-rewarding of over-tight side chain packing. Also, screening by colony picking required a low library complexity, but designing a biosensor against a peptide of at least 12 residues requires a high-complexity library. This double-bind was solved using a “piecemeal” iterative design strategy. Also, designed LOO-GFPs fluoresced in the unbound state due to unwanted dimerization, but this was solved by fusing a fully functional prototype LOO-GFP to a fiber-forming protein, Drosophila ultrabithorax, creating a biosensor fiber. One influenza hemagglutinin biosensor is characterized here in detail, showing a shifted excitation/emission spectrum, a micromolar affinity for the target peptide, and an unexpected photo-switching ability.

Chemistry↗

Replication Package for "Union-Find and Usability: A Case Study and Analysis of Rust Formal Verifier

This replication package is a case study on automated deductive verification for Rust for practical programs. It is a companion artifact to a corresponding usability study on verification titled "Union-Find and Usability: A Case Study and Analysis of Rust Formal Verifiers". It seeks to answer the question "Can Rust developers today use Rust verifiers to verify their code?". To answer this question, the study contrasts the verification experience of two mature Rust verifiers, Creusot and Prusti, by using the tools to develop a verified implementation of union-find in Rust. The union-find implementation is based on real-world code as used in the popular egg E-graph library. The artifact consists of two different verified libraries, one using Creusot and one using Prusti. The libraries have similar Rust interfaces and high-level proofs but differ in their details: Creusot and Prusti have different annotation languages and support different proof styles. Each implementation can be verified with its respective tool and compiles as a traditional Rust development.

Sarracino, John↗

Electromagnetic Transient Modeling of Data Centers

This report serves as a user manual for the accompanying EMT model library developed by the National Laboratory of the Rockies (NLR) for various equipment in large data centers. The EMT model library enables detailed modeling of large data center loads for conducting grid stability studies. The EMT model library for data centers include detailed models of a 5.5 kW power supply unit (PSU), a 2.5 uninterruptible power supply (UPS), a 260 MW gas turbine-generator, a 500 kW motor load, and a 33 kW IT rack. These components represent all major equipment in data centers that need to be modeled for performing grid stability studies for data centers.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Aerospace medicine and biology. an annotated bibliography, 1954 literature, volume iii

While this third volume of the bibliography was in preparation, a number of changes and new developments took place which, it is hoped, will be instrumental in furthering the bibliography's main objective: to provide as rapidly as possible comprehensive coverage of the aerospace-medical and bio-astronautical literature. To begin with, it will be noted that the title of the compilation has been changed from Aviation Medicine to Aerospace Medicine and Biology. This will bring into relief the fact that the general subject scope of the bibliography has been expanded to include new areas of interest in space-medical and space-biological research. Thus, to the subject fields heretofore covered by the bibliography (a full listing of which may be found in the Preface to Volume 2) new ones have been added, such as Biological Rhythms, Biological Orientation, Closed Ecological Systems, Physiological and Psychological Effects of Heat, Cold, Isolation, Restraint, and many others. Another important change was administrative in nature. Sponsorship of the bibliography for the fiscal year 1959/60 was taken over by the U. S. Advanced Research Project Agency (ARPA), the U. S. Aeronautics and Space Administration (NASA), and the Defense Research Board of Canada. Under a substantially increased budget, the Library of Congress was enabled to produce two volumes during the fiscal year. The Library also agreed to prepare selected abstracts from the current aerospace and bio-astronautic literature, which are published monthly in Aerospace Medicine, the official organ of the Aerospace Medical Association.*) If the present rate of production can be maintained, it will be possible to bring the bibliography up to date within about three years. In format, style, and arrangement, this volume follows closely the preceding ones. References are arranged alphabetically by author; abstracts are informative; and full bibliographic information is provided, including foreign and translated titles, volume and issue numbers, place of publication (if foreign), inclusive paging, full dates, and library call numbers or other location symbols. While the bulk of the publication is devoted to journal articles, reports, and monographs published during the year 1954, items published in 1952 or 1953 not included in the preceding volumes have been incorporated in this volume. For quick identification, the publication years of these off-year references have been printed next to the first author's name. As before, cumulated corporate and secondary author and subject indexes are included, the latter being revised and enlarged considerably, in keeping with the over-all expansion of subject scope.

Aerospace medicine↗

Ballistocardiography, a Bibliography <1877 - 1964<

The publication of this bibliography on Ballistocardiography, NASA SP-7021 (FAA AM 65-15) fulfills a long-standing requirement for a comprehensive and retrospective collection of references on a subject that is of particular interest to medical investigators and cardiovascular physiologists engaged in aerospace studies. Ballistocardiography is a technique for producing a graphical representation of repetitive motions of the human body arising from the sudden ejection of blood into the great vessels with each heart beat. Standard ballistocardiographic techniques are emphasized in the references included in the bibliography, but attention is also given to several related methods that are used to record these phenomena and to the equipment and instrumentation employed in such investigations. The format of the citations in NASA SP-7021 (FAA AM 65-15) was chosen to resemble, as closely as possible, the format that is now being used in the Index Medicwl published by the National Library of Medicine, except that English titles of foreign language articles appear in parentheses instead of in brackets as they do in Index Medicus. In each case, an attempt was made to identify the language of the article, or the place of publication of the foreign language journal. Since the citations were gathered over a period of years and occasionally from sources which do not appear in standard indexes, complete information was not always available. Citations are arranged alphabetically by personal author. In a large measure, the comprehensivenes of this collection of references is due to information obtained from card files compiled and maintained by Dr. William R. Scarborough of the Georgetown Clinical Research Institute, Office of Aviation Medicine, FAA, supplemented by the private collections of Drs. Isaac Starr, Abraham Noordergraaf, and John L. Nickerson. Selection and preparation of individual references and general editing of the material was done by Dr. Scarborough, who received valuable assistance from Mrs. Claire Tedesco of the Medical Library Branch of the FAA Library. Final compilation and printing were completed under the supervision of NASA.

AEROSPACE MEDICINE↗

The X-ray system of crystallographic programs for any computer having a PIDGIN FORTRAN compiler

A manual is presented for the use of a library of crystallographic programs. This library, called the X-ray system, is designed to carry out the calculations required to solve the structure of crystals by diffraction techniques. It has been implemented at the University of Maryland on the Univac 1108. It has, however, been developed and run on a variety of machines under various operating systems. It is considered to be an essentially machine independent library of applications programs. The report includes definition of crystallographic computing terms, program descriptions, with some text to show their application to specific crystal problems, detailed card input descriptions, mass storage file structure and some example run streams.

Stewart, J. M.↗

Generalized EC&LSS computer program configuration control

The generalized environmental control and life support system (ECLSS) computer program (G189A) simulation of the shuttle orbiter ECLSS was upgraded. The G189A component model configuration was changed to represent the current PV102 and subsequent vehicle ECLSS configurations as defined by baseline ARS and ATCS schematics. The diagrammatic output schematics of the gas, water, and freon loops were also revised to agree with the new ECLSS configuration. The accuracy of the transient analysis was enhanced by incorporating the thermal mass effects of the equipment, structure, and fluid in the ARS gas and water loops and in the ATCS freon loops. The sources of the data used to upgrade the simulation are: (1) ATCS freon loop line sizes and lengths; (2) ARS water loop line sizes and lengths; (3) ARS water loop and ATCS freon loop component and equipment weights; and (4) ARS cabin and avionics bay thermal capacitance and conductance values. A single G189A combination master program library tape was generated which contains all of the master program library versions which were previously maintained on separate tapes. A new component subroutine, PIPETL, was developed and incorporated into the G189A master program library.

Blakely, R. L.↗

A simulation model for wind energy storage systems. Volume 2: Operation manual

A comprehensive computer program (SIMWEST) developed for the modeling of wind energy/storage systems utilizing any combination of five types of storage (pumped hydro, battery, thermal, flywheel, and pneumatic) is described. Features of the program include: a precompiler which generates computer models (in FORTRAN) of complex wind source/storage/application systems, from user specifications using the respective library components; a program which provides the techno-economic system analysis with the respective I/O the integration of system dynamics, and the iteration for conveyance of variables; and capability to evaluate economic feasibility as well as general performance of wind energy systems. The SIMWEST operation manual is presented and the usage of the SIMWEST program and the design of the library components are described. A number of example simulations intended to familiarize the user with the program's operation is given along with a listing of each SIMWEST library subroutine.

Warren, A. W.↗

Quantitative comparison of combined gas chromatographic/mass spectrometric profiles of complex mixtures

The paper describes a method called HISLIB for automatic quantitative comparison of gas chromatographic/mass spectrometric (GC/MS) results obtained on complex mixtures of organic compounds. The method is based on comparing new mixtures to 'historical' libraries of previous results. Co-occurrence of components is determined by matching relative retention indices (RRIs) and mass spectra after background removal and resolution of overlapping GC components. Internal standards are used to quantify the relative concentrations of components. Applications of HISLIB include validation of analytical procedures to isolate complex mixtures; development of historical libraries which might include complete summaries of all past observations, compilations of controls, or any other selected subset of results; improvement of the quality of existing libraries of mass spectral data; and detection of differences in kind and/or amounts of individual components. Limitations of the method are mentioned along with causes of their occurrence.

Smith, D. H.↗

Linear-Algebra Programs

The Basic Linear Algebra Subprograms (BLAS) library is a collection of 38 FORTRAN-callable routines for performing basic operations of numerical linear algebra. BLAS library is portable and efficient source of basic operations for designers of programs involving linear algebriac computations. BLAS library is supplied in portable FORTRAN and Assembler code versions for IBM 370, UNIVAC 1100 and CDC 6000 series computers.

Lawson, C. L.↗

NALNET book system: Cost benefit study

The goals of the NASA's library network system, NALNET, the functions of the current book system, the products and services of a book system required by NASA Center libraries, and the characteristics of a system that would best supply those products and services were assessed. Emphasis was placed on determining the most cost effective means of meeting NASA's requirements for an automated book system. Various operating modes were examined including the current STIMS file, the PUBFILE, developing software improvements for products as appropriate to the Center needs, and obtaining cataloging and products from the bibliographic utilities including at least OCLC, RLIN, BNA, and STIF. It is recommended that NALNET operate under the STIMS file mode and obtain cataloging and products from the bibliographic utilities. The recommendations are based on the premise that given the current state of the art in library automation it is not cost effective for NASA to maintain a full range of cataloging services on its own system. The bibliographic utilities can support higher quality systems with a greater range of services at a lower total cost.

Dewath, N. V.↗

Processing MAGSAT data for comparison with geoid anomalies

A digital data library of MAGSAT data consisting of 1,615,636 measurements from the quiet data set, is geographically sorted, and allows rapid analysis and processing of all the quiet magnetic data about any selected location. Because this library of MAGSAT data is compatible with existing gravity and geoid data library processing and display system software, correlations between MAGSAT, surface gravity, GEOS-3 radar altimeter geoid and bathymetric data sets can be conveniently detected and analyzed. Polynomial trends from each half-orbit were removed as an effective way of estimating and removing ring current effects following estimation of the core field contribution. It was found that a third order polynomial is the lowest polynomial order that appears to provide the best consistency of residual anomalies between coincident orbits.

Bowin, C. O.↗

Use of laboratory spectra for determining vegetation assemblages in Landsat images

A spectral library is a diverse collection of reflectance spectra which are used, not as an image-matching data base, but rather as an interpretive link to the physical/chemical processes that cause absorption of light in plants, minerals, rocks, and soils. Techniques for using this library to interpret Landsat MSS data are described, including the process of normalization which largely eliminates brightness effects of both laboratory and image data. Three image-to-library programs are explained. These have been used successfully to descriminate very small (less than 10 percent) changes in plant species components, to detect the presence of vegetation in units where percent cover is only 5 percent, and to recognize unusual vegetation patterns that relate to substrate changes where the substrate is not directly resolvable.

Adams, J. D.↗