Scalable Unix Commands for Parallel Processors: A High-Performance Implementation

We describe a family of MPI applications we call the Parallel Unix Commands. These commands are natural parallel versions of common Unix user commands such as ls, ps, and find, together with a few similar commands particular to the parallel environment. We describe the design and implementation of these programs and present some performance results on a 256-node Linux cluster. The Parallel Unix Commands are open source and freely available.Comment: 9 pages, 2 figure

A Multilevel Approach to Topology-Aware Collective Operations in Computational Grids

The efficient implementation of collective communiction operations has received much attention. Initial efforts produced "optimal" trees based on network communication models that assumed equal point-to-point latencies between any two processes. This assumption is violated in most practical settings, however, particularly in heterogeneous systems such as clusters of SMPs and wide-area "computational Grids," with the result that collective operations perform suboptimally. In response, more recent work has focused on creating topology-aware trees for collective operations that minimize communication across slower channels (e.g., a wide-area network). While these efforts have significant communication benefits, they all limit their view of the network to only two layers. We present a strategy based upon a multilayer view of the network. By creating multilevel topology-aware trees we take advantage of communication cost differences at every level in the network. We used this strategy to implement topology-aware versions of several MPI collective operations in MPICH-G2, the Globus Toolkit[tm]-enabled version of the popular MPICH implementation of the MPI standard. Using information about topology provided by MPICH-G2, we construct these multilevel topology-aware trees automatically during execution. We present results demonstrating the advantages of our multilevel approach by comparing it to the default (topology-unaware) implementation provided by MPICH and a topology-aware two-layer implementation.Comment: 16 pages, 8 figure

Therapie bei Progression und Rezidiv des Ovarialkarzinoms

Secondary surgery after failure of primary treatment is a promising and reasonable option only for patients with a relapse-free interval of at least 6-12 months who should have ideally achieved a tumor-free status after primary therapy. As after primary surgery, size of residual tumor is the most significant predictor of survival after secondary surgery. Even in the case of multiple tumor sites, complete removal of the tumor can be achieved in nearly 30% of the patients. Treatment results are much better in specialized oncology centers with optimal interdisciplinary cooperation compared with smaller institutions. Chemotherapy can be used both for consolidation after successful secondary surgery and for palliation in patients with inoperable recurrent disease. Since paclitaxel has been integrated into first-line chemotherapy, there is no defined standard for second-line chemotherapy. Several cytotoxic agents have shown moderate activity in this setting, including treosulfan, epirubicin, and newer agents such as topotecan, gemcitabine, vinorelbine, and PEG(polyethylene glycol)-liposomal doxorubicin. Thus, the German Arbeitsgemeinschaft Gynakologische Onkologie (AGO) has initiated several randomized studies in patients with recurrent ovarian cancer in order to define new standards for second-line chemotherapy

Learning from the Success of MPI

The Message Passing Interface (MPI) has been extremely successful as a portable way to program high-performance parallel computers. This success has occurred in spite of the view of many that message passing is difficult and that other approaches, including automatic parallelization and directive-based parallelism, are easier to use. This paper argues that MPI has succeeded because it addresses all of the important issues in providing a parallel programming model.Comment: 12 pages, 1 figur

An agent-based approach to immune modelling

This study focuses on trying to understand why the range of experience with respect to HIV infection is so diverse, especially as regards to the latency period. The challenge is to determine what assumptions can be made about the nature of the experience of antigenic invasion and diversity that can be modelled, tested and argued plausibly. To investigate this, an agent-based approach is used to extract high-level behaviour which cannot be described analytically from the set of interaction rules at the cellular level. A prototype model encompasses local variation in baseline properties contributing to the individual disease experience and is included in a network which mimics the chain of lymphatic nodes. Dealing with massively multi-agent systems requires major computational efforts. However, parallelisation methods are a natural consequence and advantage of the multi-agent approach. These are implemented using the MPI library

Passage time distributions in large Markov chains

Accepted versio

Quantum Monte Carlo Study of Strongly Correlated Electrons: Cellular Dynamical Mean-Field Theory

We study the Hubbard model using the Cellular Dynamical Mean-Field Theory (CDMFT) with quantum Monte Carlo (QMC) simulations. We present the algorithmic details of CDMFT with the Hirsch-Fye QMC method for the solution of the self-consistently embedded quantum cluster problem. We use the one- and two-dimensional half-filled Hubbard model to gauge the performance of CDMFT+QMC particularly for small clusters by comparing with the exact results and also with other quantum cluster methods. We calculate single-particle Green's functions and self-energies on small clusters to study their size dependence in one- and two-dimensions.Comment: 14 pages, 18 figure

Breakup of the aligned H2_2 molecule by xuv laser pulses: A time-dependent treatment in prolate spheroidal coordinates

We have carried out calculations of the triple-differential cross section for one-photon double ionization of molecular hydrogen for a central photon energy of $75$~eV, using a fully {\it ab initio}, nonperturbative approach to solve the time-dependent \Schro equation in prolate spheroidal coordinates. The spatial coordinates $\xi$ and $\eta$ are discretized in a finite-element discrete-variable representation. The wave packet of the laser-driven two-electron system is propagated in time through an effective short iterative Lanczos method to simulate the double ionization of the hydrogen molecule. For both symmetric and asymmetric energy sharing, the present results agree to a satisfactory level with most earlier predictions for the absolute magnitude and the shape of the angular distributions. A notable exception, however, concerns the predictions of the recent time-independent calculations based on the exterior complex scaling method in prolate spheroidal coordinates [Phys.~Rev.~A~{\bf 82}, 023423 (2010)]. Extensive tests of the numerical implementation were performed, including the effect of truncating the Neumann expansion for the dielectronic interaction on the description of the initial bound state and the predicted cross sections. We observe that the dominant escape mode of the two photoelectrons dramatically depends upon the energy sharing. In the parallel geometry, when the ejected electrons are collected along the direction of the laser polarization axis, back-to-back escape is the dominant channel for strongly asymmetric energy sharing, while it is completely forbidden if the two electrons share the excess energy equally.Comment: 17 pages, 9 figure

Beyond XSPEC: Towards Highly Configurable Analysis

We present a quantitative comparison between software features of the defacto standard X-ray spectral analysis tool, XSPEC, and ISIS, the Interactive Spectral Interpretation System. Our emphasis is on customized analysis, with ISIS offered as a strong example of configurable software. While noting that XSPEC has been of immense value to astronomers, and that its scientific core is moderately extensible--most commonly via the inclusion of user contributed "local models"--we identify a series of limitations with its use beyond conventional spectral modeling. We argue that from the viewpoint of the astronomical user, the XSPEC internal structure presents a Black Box Problem, with many of its important features hidden from the top-level interface, thus discouraging user customization. Drawing from examples in custom modeling, numerical analysis, parallel computation, visualization, data management, and automated code generation, we show how a numerically scriptable, modular, and extensible analysis platform such as ISIS facilitates many forms of advanced astrophysical inquiry.Comment: Accepted by PASP, for July 2008 (15 pages