HPF to OpenMP on the Origin2000: a case study

The geophysics group at CRS4 has long developed echo reconstruction codes in HPF on distributed-memory machines. Now, however, with the arrival of shared-memory machines and their native OpenMP compilers, the transfer to OpenMP would seem to present the logical next step in our code development strategy. Recent experience with porting one of our important HPF codes to OpenMP does not bear this out—at least not on the Origin2000. The OpenMP code suffers from the immaturity of the standard, and the operating system's handling of UNIX threads seems to severely penalize OpenMP performance. On the other hand, the HPF code on the Origin2000 is fast, scalable and not disproportionately sensitive to load on the machine.1147–1154Pubblicat

N‐terminus of hMLH1 confers interaction of hMutLα and hMutLβ with hMutSα

Mismatch repair is a highly conserved system that ensures replication fidelity by repairing mispairs after DNA synthesis. In humans, the two protein heterodimers hMutSα (hMSH2‐hMSH6) and hMutLα (hMLH1‐hPMS2) constitute the centre of the repair reaction. After recognising a DNA replication error, hMutSα recruits hMutLα, which then is thought to transduce the repair signal to the excision machinery. We have expressed an ATPase mutant of hMutLα as well as its individual subunits hMLH1 and hPMS2 and fragments of hMLH1, followed by examination of their interaction properties with hMutSα using a novel interaction assay. We show that, although the interaction requires ATP, hMutLα does not need to hydrolyse this nucleotide to join hMutSα on DNA, suggesting that ATP hydrolysis by hMutLα happens downstream of complex formation. The analysis of the individual subunits of hMutLα demonstrated that the hMutSα–hMutLα interaction is predominantly conferred by hMLH1. Further experiments revealed that only the N‐terminus of hMLH1 confers this interaction. In contrast, only the C‐terminus stabilised and co‐immunoprecipitated hPMS2 when both proteins were co‐expressed in 293T cells, indicating that dimerisation and stabilisation are mediated by the C‐terminal part of hMLH1. We also examined another human homologue of bacterial MutL, hMutLβ (hMLH1–hPMS1). We show that hMutLβ interacts as efficiently with hMutSα as hMutLα, and that it predominantly binds to hMutSα via hMLH1 as well

Development of a ROT22 - DATAMAP interface

This report (Contract NAS2-10331- Mod 10), outlines the development and validation of an interface between the three-dimensional transonic analysis program ROT22 and the Data from Aeromechanics Test and Analytics-Management and Analysis Package (DATAMAP). After development of the interface, the validation is carried out as follows. First, the DATAMAP program is used to analyze a portion of the Tip Aerodynamics and Acoustics Test (TAAT) data. Specifically, records 2872 and 2873 are analyzed at an azimuth of 90 deg, and record 2806 is analyzed at 60 deg. Trim conditions for these flight conditions are then calculated using the Bell performance prediction program ARAM45. Equivalent shaft, pitch, and twist angles are calculated from ARAM45 results and used as input to the ROT22 program. The interface uses the ROT22 results and creates DATAMAP information files from which the surface pressure contours and sectional pressure coefficients are plotted. Twist angles input to ROT22 program are then iteratively modified in the tip region until the computed pressure coefficients closely match the measurements. In all cases studied, the location of the shock is well predicted. However, the negative pressure coefficients were underpredicted. This could be accounted for by blade vortex interaction effects

Compressive gate set tomography

Flexible characterization techniques that identify and quantify experimental imperfections under realistic assumptions are crucial for the development of quantum computers. Gate set tomography is a characterization approach that simultaneously and self-consistently extracts a tomographic description of the implementation of an entire set of quantum gates, as well as the initial state and measurement, from experimental data. Obtaining such a detailed picture of the experimental implementation is associated with high requirements on the number of sequences and their design, making gate set tomography a challenging task even for only two qubits. In this work, we show that low-rank approximations of gate sets can be obtained from significantly fewer gate sequences and that it is sufficient to draw them randomly. Such tomographic information is needed for the crucial task of dealing with coherent noise. To this end, we formulate the data processing problem of gate set tomography as a rank-constrained tensor completion problem. We provide an algorithm to solve this problem while respecting the usual positivity and normalization constraints of quantum mechanics by using second-order geometrical optimization methods on the complex Stiefel manifold. Besides the reduction in sequences, we demonstrate numerically that the algorithm does not rely on structured gate sets or an elaborate circuit design to robustly perform gate set tomography and is therefore more broadly applicable than traditional approaches.Comment: 14+12 pages, several figures and diagram

Uniform Substitution for Dynamic Logic with Communicating Hybrid Programs

This paper introduces a uniform substitution calculus for $\mathsf{dL}_\text{CHP}$, the dynamic logic of communicating hybrid programs. Uniform substitution enables parsimonious prover kernels by using axioms instead of axiom schemata. Instantiations can be recovered from a single proof rule responsible for soundness-critical instantiation checks rather than being spread across axiom schemata in side conditions. Even though communication and parallelism reasoning are notorious for necessitating subtle soundness-critical side conditions, uniform substitution when generalized to $\mathsf{dL}_\text{CHP}$ manages to limit and isolate their conceptual overhead. Since uniform substitution has proven to simplify the implementation of hybrid systems provers substantially, uniform substitution for $\mathsf{dL}_\text{CHP}$ paves the way for a parsimonious implementation of theorem provers for hybrid systems with communication and parallelism.Comment: CADE 202