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

Grid generation for time dependent problems: Criteria and methods

The problem of generating local mesh refinements when solving time dependent partial differential equations was examined. The problem of creating an appropriate grid, given a mesh function h defined over the spatial domain is discussed. A data structure which permits efficient use of the resulting grid is described. A good choice for h is an estimate of the local truncation error, and several ways to estimate it are discussed. The efficiency and implementation problems of these error estimates were compared

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

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

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

Random Access in Nondelimited Variable-length Record Collections for Parallel Reading with Hadoop

The industry standard Packet CAPture (PCAP) format for storing network packet traces is normally only readable in serial due to its lack of delimiters, indexing, or blocking. This presents a challenge for parallel analysis of large networks, where packet traces can be many gigabytes in size. In this work we present RAPCAP, a novel method for random access into variable-length record collections like PCAP by identifying a record boundary within a small number of bytes of the access point. Unlike related heuristic methods that can limit scalability with a nonzero probability of error, the new method offers a correctness guarantee with a well formed file and does not rely on prior knowledge of the contents. We include a practical implementation of the algorithm with an extension to the Hadoop framework, and a performance comparison to serial ingestion. Finally, we present a number of similar storage types that could utilize a modified version of RAPCAP for random access