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

Asymmetric Berry-Phase Interference Patterns in a Single-Molecule Magnet

A Mn4 single-molecule magnet displays asymmetric Berry-phase interference patterns in the transverse-field (HT) dependence of the magnetization tunneling probability when a longitudinal field (HL) is present, contrary to symmetric patterns observed for HL=0. Reversal of HL results in a reflection of the transverse-field asymmetry about HT=0, as expected on the basis of the time-reversal invariance of the spin-orbit Hamiltonian which is responsible for the tunneling oscillations. A fascinating motion of Berry-phase minima within the transverse-field magnitude-direction phase space results from a competition between noncollinear magnetoanisotropy tensors at the two distinct Mn sites.Comment: 4 double-column page

Non-parabolicity of the conduction band of wurtzite GaN

Using cyclotron resonance, we measure the effective mass, $m$*, of electrons in AlGaN/GaN heterostructures with densities, $n_{2D}\sim 1-6\times10^{12}$cm$^{-2}$. From our extensive data, we extrapolate a band edge mass of $(0.208\pm0.002) m_e$. By comparing our $m$* data with the results of a multi-band \textbf{k.p} calculation we infer that the effect of remote bands is essential in explaining the observed conduction band non-parabolicity (NP). Our calculation of polaron mass corrections -- including finite width and screening - suggests those to be negligible. It implies that the behavior of $m*(n_{2D})$ can be understood solely in terms of NP. Finally, using our NP and polaron corrections, we are able to reduce the large scatter in the published band edge mass values

Parallel programming of industrial applications

In the introductory material, we overview the typical MPP environment for real application computing and the special tools available such as parallel debuggers and performance analyzers. Next, we draw from a series of real applications codes and discuss the specific challenges and problems that are encountered in parallelizing these individual applications. The application areas drawn from include biomedical sciences, materials processing and design, plasma and fluid dynamics, and others. We show how it was possible to get a particular application to run efficiently and what steps were necessary. Finally we end with a summary of the lessons learned from these applications and predictions for the future of industrial parallel computing. This tutorial is based on material from a forthcoming book entitled: �Industrial Strength Parallel Computing� to be published by Morgan Kaufmann Publishers (ISBN l-55860-54)

Far-UV Emissions of the Sun in Time: Probing Solar Magnetic Activity and Effects on Evolution of Paleo-Planetary Atmospheres

We present and analyze FUSE observations of six solar analogs. These are single, main-sequence G0-5 strs selected as proxies for the Sun at several stages of its main-sequence lifetime. The emission features in the FUSE 920-1180 A wavelength range allow for a critical probe of the hot plasma over three decades in temperature. Using the flux ratio CIII 1176/977 as diagnostics, we investigate the dependence of the electron pressure of the transition region as a function of the rotation period, age and magnetic activity. The results from these solar proxies indicate that the electron pressure of the stellar ~10^5-K plasma decreases by a factor of about 70 between the young, fast-rotating magnetically active star and the old, slow-rotating inactive star. Also, the observations indicate that the average surface fluxes of emission features strongly decrease with increasing stellar age and longer rotation period. The emission flux evolution with age or rotation period is well fitted by power laws, which become steeper from cooler chromospheric (10^4 K) to hotter coronal (10^7 K) plasma. The relationship for the integrated (920-1180 A) FUSE flux indicates that the solar far-ultraviolet emissions were about twice the present value 2.5 Gyr ago and about 4 times the present value 3.5 Gyr ago. Note also that the FUSE/FUV flux of the Zero-Age Main Sequence Sun could have been higher by as much as 50 times. Our analysis suggests that the strong FUV emissions of the young Sun may have played a crucial role in the developing planetary system, in particular through the photoionization, photochemical evolution and possible erosion of the planetary atmospheres. (abridged)Comment: 15 pages, 8 figures, accepted for publication in Ap

Trilinos users guide.

The Trilinos Project is an effort to facilitate the design, development, integration and ongoing support of mathematical software libraries. A new software capability is introduced into Trilinos as a package. A Trilinos package is an integral unit usually developed by a small team of experts in a particular algorithms area such as algebraic preconditioners, nonlinear solvers, etc. The Trilinos Users Guide is a resource for new and existing Trilinos users. Topics covered include how to configure and build Trilinos, what is required to integrate an existing package into Trilinos and examples of how those requirements can be met, as well as what tools and services are available to Trilinos packages. Also discussed are some common practices that are followed by many Trilinos package developers. Finally, a snapshot of current Trilinos packages and their interoperability status is provided, along with a list of supported computer platforms

Transcutaneous spinal cord stimulation combined with locomotor training to improve walking ability in people with chronic spinal cord injury: study protocol for an international multi-centred double-blinded randomised sham-controlled trial (eWALK)

Study design: An international multi-centred, double-blinded, randomised sham-controlled trial (eWALK). Objective: To determine the effect of 12 weeks of transcutaneous spinal stimulation (TSS) combined with locomotor training on walking ability in people with spinal cord injury (SCI). Setting: Dedicated SCI research centres in Australia, Spain, USA and Scotland. Methods: Fifty community-dwelling individuals with chronic SCI will be recruited. Participants will be eligible if they have bilateral motor levels between T1 and T11, a reproducible lower limb muscle contraction in at least one muscle group, and a Walking Index for SCI II (WISCI II) between 1 and 6. Eligible participants will be randomised to one of two groups, either the active stimulation group or the sham stimulation group. Participants allocated to the stimulation group will receive TSS combined with locomotor training for three 30-min sessions a week for 12 weeks. The locomotor sessions will include walking on a treadmill and overground. Participants allocated to the sham stimulation group will receive the same locomotor training combined with sham stimulation. The primary outcome will be walking ability with stimulation using the WISCI II. Secondary outcomes will record sensation, strength, spasticity, bowel function and quality of life. Trial registration: ANZCTR.org.au identifier ACTRN1262000124192

Abstract: Analysis of acute skin rejection in non-human primate models of face and hand allotransplantation

Introduction: The incidence of acute rejection (AR) of the skin within the first year after hand or face transplantation is approximately 85% and up to 56% of patients experience multiple episodes1. Significant immunosuppression is required to prevent allograft loss, and recent studies suggest that repeated AR episodes can lead to VCA dysfunction and loss2. The mechanisms underlying variability in AR presentation remain poorly defined however. Materials and Methods: 8 cynomolgus monkeys received either an orthotopic hand (n=2) or heterotopic face VCA (n=6) from MHC-mismatched donors following induction with anti-thymocyte globulin. Post-operatively, triple immunosuppression – tacrolimus, mycophenolate mofetil, methylprednisolone – was maintained for up to 120 days before bone marrow transplantation (BMT) was performed. Protocol biopsies of VCA skin were performed at 30-day intervals for histopathology and flow cytometric analysis of resident skin leukocyte populations; VCA-resident cells were differentiated by H38 status (mouse antihuman HLA class I monoclonal antibody that cross reacts with cynomolgus monkeys) for donor or recipient derivation. Clinical AR was treated with steroids and further biopsies were taken for histologic confirmation; corresponding anti-donor responses were evaluated by mixed lymphocyte reaction (MLR) and allo-antibody formation. Results: Up to three episodes of AR (from POD 14, Banff I to II) developed while recipient animals were maintained on triple immunosuppression. Corresponding flow cytometric analyses demonstrate > 80% of skin-resident T lymphocytes (CD4+, CD8+) within VCA dermis were of recipient origin, suggesting rapid immigration of various lineages into the VCA. These observations coincided with the first episode of AR in fully mismatched recipients but haplomatched animals remained rejection-free. All but one episode of AR were successfully treated. No allo-antibodies were detected and anti-donor responses by MLR were comparable to that against third-party. Following BMT, mixed chimerism was detected and enabled immunosuppression withdrawal. However, this was transient and once lost, clinical AR developed and nearly 100% of both dermal and epidermal lymphocytes were recipient-derived. Conclusion: We report a clinically-relevant model for studying AR in VCA. Our results suggest that further understanding of the relative importance of MHC differences in transplant pairs may lead to differences in outcomes for VCA recipients maintained under standard immunosuppression. Immunosuppression-free tolerance of non-hematopoietic antigens in composite tissues can be achieved, but require additional strategies to achieve stable, rather than transient mixed chimerism following BMT

Quality Output Checklist and Content Assessment (QuOCCA): a new tool for assessing research quality and reproducibility

Research must be well designed, properly conducted and clearly and transparently reported. Our independent medical research institute wanted a simple, generic tool to assess the quality of the research conducted by its researchers, with the goal of identifying areas that could be improved through targeted educational activities. Unfortunately, none was available, thus we devised our own. Here, we report development of the Quality Output Checklist and Content Assessment (QuOCCA), and its application to publications from our institute's scientists. Following consensus meetings and external review by statistical and methodological experts, 11 items were selected for the final version of the QuOCCA: research transparency (items 1-3), research design and analysis (items 4-6) and research reporting practices (items 7-11). Five pairs of raters assessed all 231 articles published in 2017 and 221 in 2018 by researchers at our institute. Overall, the results were similar between years and revealed limited engagement with several recommended practices highlighted in the QuOCCA. These results will be useful to guide educational initiatives and their effectiveness. The QuOCCA is brief and focuses on broadly applicable and relevant concepts to open, high-quality, reproducible and well-reported science. Thus, the QuOCCA could be used by other biomedical institutions and individual researchers to evaluate research publications, assess changes in research practice over time and guide the discussion about high-quality, open science. Given its generic nature, the QuOCCA may also be useful in other research disciplines