RAxML-OMP: An Efficient Program for Phylogenetic Inference on SMPs
Inference of phylogenetic trees comprising hundreds or even thousands of organisms based on the Maximum Likelihood (ML) method is computationally extremely intensive. In order to accelerate computations we implemented RAxML-OMP, an efficient OpenMP-parallelization for Symmetric Multi-Processing machines (SMPs) based on the sequential program RAxML-V (Randomized Axelerated Maximum Likelihood). RAxML-V is a program for inference of evolutionary trees based upon the ML method and incorporates several advanced search algorithms like fast hill-climbing and simulated annealing. We assess performance of RAxML-OMP on the widely used Intel Xeon, Intel Itanium, and AMD Opteron architectures. RAxML-OMP scales particularly well on the AMD Opteron architecture and achieves even super-linear speedups for large datasets (with a length ≥ 5.000 base pairs) due to improved cache-efficiency and data locality. RAxML-OMP is freely available as open source code.

title: Developing Applications for Multicomputer Systems on Workstation Clusters
abstract: Much computational power on state-of-the-art multicomputers like the Paragon is wasted with porting applications. Using networks of workstations is an attempt to withdraw this workload from multicomputer systems. Therefore an environment is needed which provides the programming interface of multicomputers on coupled workstations. The paper describes the design and implementation of the NXLib environment which allows to use Ethernet coupled workstations as a development platform for applications targeted for Intel Paragon systems.

title: NXLib - A Parallel Programming Environment for Workstation Clusters
abstract: Workstations provide an attractive platform to develop software. This paper describes the NXLib environment which enables users to use this platform to develop parallel applications. The source code compatibility of NXLib applications with Intel's Paragon multicomputer system easily allows to migrate these applications to a supercomputer. The performance which can be achieved with either platform is compared using two applications. In addition performance results of NXLib communication calls and comparisons with other widespread messagepassing libraries for workstation clusters are presented.

title: Tracing the MPI-IO Calls' Disk Accesses
abstract: With parallel file I/O we are faced with the situation that we do not have appropriate tools to get an insight into the I/O server behavior depending on the I/O calls in the corresponding parallel MPI program. We present an approach that allows us to also get event traces from the I/O server environment and to merge them with the client trace. Corresponding events will be matched and visualized. We integrate this functionality into the parallel file system PVFS2 and the MPICH2 tool Jumpshot.

title: Performance Assessment of Parallel Spectral Analysis: Towards a Practical Performance Model for Parallel Medical Applications
abstract: To determine the need for a parallel computer on campus a committee of the Graduate Program in Computer Science surveyed selected Dartmouth College faculty and students in December and January We hope that the information in this report can be used by many groups on campus including the Computer Science graduate program and DAGS summer institute Kiewit s NH Supercomputer Initiative and by numerous researchers hoping to collaborate with people in other disciplines We found signi cant interest in parallel supercomputing on campus An on campus par allel supercomputing facility would not only support numerous courses and research projects but would provide a locus for intellectual activity in parallel computing encouraging interdisci plinary collaboration We believe that this report is a rst step in that direction All of the committee members can be reached by email at fullname Dartmouth edu where dots replace spaces in the name e g David Kotz Dartmouth edu Dartmouth Parallel Computer Needs January

title: A Universal Infrastructure for the Run-Time Monitoring of Parallel and Distributed Applications
abstract: On-line tools for parallel and distributed programs require a facility to observe and possibly manipulate the programs’ run-time behavior, a so called monitoring system. Currently, most tools use proprietary monitoring techniques that are incompatible to each other and usually apply only to specific target platforms. The On-line Monitoring Interface Specification (OMIS) is the first specification of a universal interface between different tools and a monitoring system, thus enabling interoperable, portable and uniform tool environments. The paper gives an introduction into the basic concepts of OMIS and presents the design and implementation of an OMIS compliant monitoring system (OCM).

title: Editorial for the ISC’10 Scientific Sessions Proceedings
abstract: The International Supercomputing Conference started in 1986 as the “Supercomputer Seminar” organized by Prof. Hans Meuer, then director of the computer center and professor for computer science at the Universitat Mannheim (Germany). Since these early days the annual conference became a major international event in the HPC community. As the conference grew bigger, it moved from Mannheim over Heidelberg and Dresden to Hamburg. In 2010 the conference will celebrate its 25th birthday! About 2,000 attendees and more than 140 exhibitors from over 45 countries are expected to attend, turning ISC’10 into a powerful and memorable event. Over the years we decided to strengthen the scientific part of the conference and present selected talks on relevant research results in the field of HPC. These scientific sessions started in 2007 as a separate day preceding the conference. Slides and accompanying papers were made available via the conference web site. Now, the scientific sessions evolved into an integral part of the conference, being scheduled in the afternoon of the first day. The call for participation was issued in winter 2009 inviting researchers and developers to submit latest results of their work as full research papers to the program committee of the scientific sessions. Altogether we received 25 submissions from authors all over the world. In a peer-reviewing process with an international committee we selected the best 13 papers for publication in this journal and for presentation during the scientific sessions of the conference.

title: Analyzing Metadata Performance in Distributed File Systems
abstract: The performance of metadata processing in large distributed file systems currently presents larger challenges than scaling of data throughput. The paper presents a novel, distributed benchmark called DMetabench for measuring the performance of metadata operations (e.g. file creation). DMetabench runs in environments with potentially thousands of nodes and allows an assessment of the scalability of metadata operations. Additionally, precise run-time performance data is preserved which allows for a better understanding of performance artifacts. Validation results from production file systems at the Leibniz Supercomputing Centre (LRZ) are provided and discussed. Possible applications of knowledge about metadata performance scaling include the choice of an optimal parallelization strategy for metadata-itensive workload in a specific runtime environment.

title: A flat, timing-driven design system for a high-performance CMOS processor chipset
abstract: We describe the methodology used for the design of the CMOS processor chipset used in the IBM S/390 Parallel Enterprise Server-Generation 3. The majority of the logic is implemented by standard cell elements placed and routed flat, using timing-driven techniques. The result is a globally optimized solution without artificial floorplan boundaries. We show that the density in terms of transistors per mm/sup 2/ is comparable to the most advanced custom designs and that the impact of interconnect delay on the cycle time is very small. Compared to custom design, this approach offers excellent turn-around-time and considerably reduces overall effort.