Research Software Science: Expanding the Impact of Research Software Engineering

Software plays a central role in scientific discovery. Improving how we develop and use software for research can have both broad and deep impacts on a spectrum of challenges and opportunities society faces today. The emergence of the research software engineer (RSE) role correlates with the growing complexity of scientific challenges and the diversity of software team skills. In this article, research software science (RSS), an idea related to RSE and particularly suited to research software teams, is described. RSS promotes the use of scientific methodologies to explore and establish broadly applicable knowledge. Using RSS, we can pursue sustainable, repeatable, and reproducible software improvements that positively impact research software toward improved scientific discovery

Scalable Delivery of Scalable Libraries and Tools: How ECP Delivered a Software Ecosystem for Exascale and Beyond

The Exascale Computing Project (ECP) was one of the largest open-source scientific software development projects ever. It supported approximately 1,000 staff from US Department of Energy laboratories, and university and industry partners. About 250 staff contributed to 70 scientific libraries and tools to support applications on multiple exascale computing systems that were also under development. Funded as a construction project, ECP adopted an earned-value management system, based on milestones. and a key performance parameter system based, in part, on integrations. With accelerated delivery schedules and significant project risk, we also emphasized software quality using community policies, automated testing, and continuous integration. Software Development Kit teams provided cross-team collaboration. Products were delivered via E4S, a curated portfolio of libraries and tools. In this paper, we discuss the organizational and management elements that enabled the efficient and effective delivery of ECP libraries and tools, lessons learned and next steps.Comment: 9 pages, 5 figures, submitted to IEEE Computing in Science and Engineerin

Supporting 64-bit global indices in Epetra and other Trilinos packages -- Techniques used and lessons learned

The Trilinos Project is an effort to facilitate the design, development, integration and ongoing support of mathematical software libraries within an object-oriented framework. It is intended for large-scale, complex multiphysics engineering and scientific applications. Epetra is one of its basic packages. It provides serial and parallel linear algebra capabilities. Before Trilinos version 11.0, released in 2012, Epetra used the C++ int data-type for storing global and local indices for degrees of freedom (DOFs). Since int is typically 32-bit, this limited the largest problem size to be smaller than approximately two billion DOFs. This was true even if a distributed memory machine could handle larger problems. We have added optional support for C++ long long data-type, which is at least 64-bit wide, for global indices. To save memory, maintain the speed of memory-bound operations, and reduce further changes to the code, the local indices are still 32-bit. We document the changes required to achieve this feature and how the new functionality can be used. We also report on the lessons learned in modifying a mature and popular package from various perspectives -- design goals, backward compatibility, engineering decisions, C++ language features, effects on existing users and other packages, and build integration

Verified lifting of stencil computations

This paper demonstrates a novel combination of program synthesis and verification to lift stencil computations from low-level Fortran code to a high-level summary expressed using a predicate language. The technique is sound and mostly automated, and leverages counter-example guided inductive synthesis (CEGIS) to find provably correct translations. Lifting existing code to a high-performance description language has a number of benefits, including maintainability and performance portability. For example, our experiments show that the lifted summaries can enable domain specific compilers to do a better job of parallelization as compared to an off-the-shelf compiler working on the original code, and can even support fully automatic migration to hardware accelerators such as GPUs. We have implemented verified lifting in a system called STNG and have evaluated it using microbenchmarks, mini-apps, and real-world applications. We demonstrate the benefits of verified lifting by first automatically summarizing Fortran source code into a high-level predicate language, and subsequently translating the lifted summaries into Halide, with the translated code achieving median performance speedups of 4.1X and up to 24X for non-trivial stencils as compared to the original implementation.United States. Department of Energy. Office of Science (Award DE-SC0008923)United States. Department of Energy. Office of Science (Award DE-SC0005288

Triosephosphate isomerase I170V alters catalytic site, enhances stability and induces pathology in a Drosophila model of TPI deficiency ☆

Triosephosphate isomerase (TPI) is a glycolytic enzyme which homodimerizes for full catalytic activity. Mutations of the TPI gene elicit a disease known as TPI Deficiency, a glycolytic enzymopathy noted for its unique severity of neurological symptoms. Evidence suggests that TPI Deficiency pathogenesis may be due to conformational changes of the protein, likely affecting dimerization and protein stability. In this report, we genetically and physically characterize a human disease-associated TPI mutation caused by an I170V substitution. Human TPI I170V elicits behavioral abnormalities in Drosophila. An examination of hTPI I170V enzyme kinetics revealed this substitution reduced catalytic turnover, while assessments of thermal stability demonstrated an increase in enzyme stability. The crystal structure of the homodimeric I170V mutant reveals changes in the geometry of critical residues within the catalytic pocket. Collectively these data reveal new observations of the structural and kinetic determinants of TPI Deficiency pathology, providing new insights into disease pathogenesis

Structure of a highly conserved domain of rock1 required for shroom-mediated regulation of cell morphology

Rho-associated coiled coil containing protein kinase (Rho-kinase or Rock) is a well-defined determinant of actin organization and dynamics in most animal cells characterized to date. One of the primary effectors of Rock is non-muscle myosin II. Activation of Rock results in increased contractility of myosin II and subsequent changes in actin architecture and cell morphology. The regulation of Rock is thought to occur via autoinhibition of the kinase domain via intramolecular interactions between the N-terminus and the C-terminus of the kinase. This autoinhibited state can be relieved via proteolytic cleavage, binding of lipids to a Pleckstrin Homology domain near the C-terminus, or binding of GTP-bound RhoA to the central coiled-coil region of Rock. Recent work has identified the Shroom family of proteins as an additional regulator of Rock either at the level of cellular distribution or catalytic activity or both. The Shroom-Rock complex is conserved in most animals and is essential for the formation of the neural tube, eye, and gut in vertebrates. To address the mechanism by which Shroom and Rock interact, we have solved the structure of the coiled-coil region of Rock that binds to Shroom proteins. Consistent with other observations, the Shroom binding domain is a parallel coiled-coil dimer. Using biochemical approaches, we have identified a large patch of residues that contribute to Shrm binding. Their orientation suggests that there may be two independent Shrm binding sites on opposing faces of the coiled-coil region of Rock. Finally, we show that the binding surface is essential for Rock colocalization with Shroom and for Shroom-mediated changes in cell morphology. © 2013 Mohan et al