Biophysics VI Lecture

Link to the Biophysics VI lecture in WS2010/2011 http://www.kis.uni-kl.de/.

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Physics Software

As this is scientific research software it is under heavy development and probably unuseable for others. Drop me a mail if you are interested in this code.

  • Contributions to LAMMPS – Large-scale Atomic/Molecular Massively Parallel Simulator The LAMMPS is a massively parallel molecular dynamic simulation tool.
      • Damped long-ranged coulombic potentials
      • HDF file format extensions

    If you like to use my really experimental stuff, drop me a mail.

  • Angular Distribution based local structure analysis. Included in the main branch.
  • lammps-vim // Vim syntax highlighting for LAMMPS scripts Included in the main branch.
    git://repo.or.cz/lammps-vim.git
  • Local temperature/pressure detector On demand. Drop me a mail.
  • Strain rate detector On demand. Drop me a mail.
  • ClusterDetector // Cluster DetectorDetection of particle clusters. Written in C and including a Python interface.
    git://repo.or.cz/ClusterDetector.git
  • lm-algorithm // Levenberg-Marquardt-AlgorithmPY/HNC & OZ Equation Solver in Two Dimensions. The algorithm is described in this report.
    @Sourceforgeor git://repo.or.cz/lm.git
  • OpenGL / Povray MD Visualizer with gamepad support

High Performance Computing Workshop in Bandung…

At the end of the year 2009, the Computational Material Science Group, TU Kaiserslautern, organized a workshop on High-Performance Computing (HPC). The workshop was held from 7th to 9th December, 2009, at the Universitas Padjadjaran, Bandung Indonesia. Two group members, Dr. Yudi Rosandi and Dr. Gerolf Ziegenhain, were the main speakers of the workshop. The local organizer was Dr. Irwan Ary Dharmawan, from Dept. Physics, Universitas Padjadjaran.

Universitas Padjadjaran is one of large state universities in Indonesia, located in West Java. This university has 2 main campuses. The first is located downtown in the capital city, Bandung, and the second is about 27 km from the center of the city, in a suburb called Jatinangor. In the first campus the main administration offices are situated, while most of the faculties are located in the second campus. The workshop took place in the Physics Department, faculty of Mathematics and Natural Sciences, Jatinangor, in the shadow of Manglayang Mountain.

The aim of this workshop was to transfer knowledge on HPC from the computer design to the applications, as well as to give an introduction into the research environment which becomes available when using a cluster computer. The workshop was targeted to the university’s education staff members, researchers, and students. By holding the workshop, we meant to help the universities in Indonesia to improve its research quality by using the relatively low cost HPC facility.

Participants came from universities all around the island of Java and from research institutes, such as the Indonesian Research Foundation (LIPI) and the National Nuclear Power Research Center (BATAN). The participants were very enthusiastic in building a low-cost cluster computer to support their research. To accommodate the participant’s eagerness, some alternatives in HPC design were introduced, and the knowledge necessary to operating and working in a many-processor cluster were taught. In total, 22 participants attended; all of them stayed throughout the lectures until the end of the workshop.

Three lectures starts the daily schedule of the workshop, and ended by an after lunch two hours laboratory work. The course of lectures was design as following:

Day 1, “Introduction”

  • A glance to High Performance Computing (opening talk)
  • Introduction to High-performance Computing
  • HPC: planing, usage, and applications

Day 2, “The core flesh, Howto roll your own cluster, Running software”

  • Technological overview of HPC
  • Basic HPC installation
  • Strategies in Cluster-design

Day 3, “HPC Usage and Application”

  • Parallel Programming
  • Introduction to parallel molecular dynamics
  • High-performance Computing: A review of the past and an outlook to the future

Every break between lectures was filled with fruitful discussions. The speakers and participants shared their ideas among a very broad research fields. Most of the participants were very active in asking questions, concerning their different research needs. It seems that this workshop has become a communication medium which helped in sharing ideas between various institutions in Indonesia.

This workshop was sponsered by two companies. The first company was Supermicro, a computer company specializing in servers and high-end computing nodes. The computers used for cluster demonstration were provided by this company. The second was Telkomsel, the largest cellular communication company in Indonesia, which gave prizes for the outstanding participants.

From the final evaluation taken at the end of the event, we received many requests from the participants for continuing the workshop. Many showed their interest to take part in a similar or a continuation workshop in the following years. The workshop not only gave an introduction to HPC but also informed the participants about research possibilities in this field. The high research costs, which has become the main obstacle for performing high quality research in the developing counties like Indonesia, can be overcome by concentrating on theory and simulation-based research.

Participant’s Institution List

  • Universitas Padjadjaran
  • Universitas Jember
  • Universitas Brawijaya
  • Universitas Sriwijaya
  • Universitas Atma Jaya
  • Universitas Gajah Mada
  • Institut Teknologi Bandung
  • Institut Teknologi Telkom
  • PPIN-BATAN
  • PPI-LIPI

Impressions

Participants
Coffee Break Discussions
Coffee Break Discussions
Lectures
Lectures

Freies Buch: Theoretische Physik

Im Rahmen der Vorbereitungen auf die Physik Diplomprüfungen habe ich mit einigen Kommilitonen ein Buch über theoretische Physik verfasst: Theoretische Physik: Thermodynamik und statistische Mechanik.