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Name: Michael Banck
Member since: 2004-01-06 11:43:31
Last Login: 2013-11-21 14:00:28

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PostgreSQL talk at Linux-Stammtisch

Next Wednesday (November 27th), the Munich Linux-Stammtisch is happening again. This time the topic will be Open-Source databases. Mathias Brandstetter will present MySQL and I will give a talk about PostgreSQL.

So if you are from or around Munich and using/interested in PostgreSQL in particular or databases in general, come around! The Stammtisch is in the Maximiliansstüberl at Hofbräukeller, starting from 19:00. As a Brotzeit is sponsored for attendees, you need to sign up either at the Xing page or here.

Debian 7.0 "wheezy" has been released this weekend!

Quite a few new Debichem packages are now available in a stable Debian release for the first time:


  • Ab-Initio Quantum Chemistry Packages:

    • ACES III
      ACESIII is an electronic structure calculation program with a focus on correlated methods. It is the parallel successor to ACESII, employing the Super Instruction Assembly Language (SIAL) as parallelization framework.
    • CP2K
      CP2K is a program to perform simulations of solid state, liquid, molecular and biological systems. It is especially aimed at massively parallel and linear scaling electronic structure methods and state-of-the-art ab-inito molecular dynamics (AIMD) simulations.
    • NWChem
      NWCHem is a computational chemistry program package. It provides methods which are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters.
    • Quantum ESPRESSO
      Quantum ESPRESSO (formerly known as PWscf) is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving, ultrasoft, and PAW).

  • Cheminformatics Toolkits:

    • Cinfony
      Cinfoy provides a common Python interface to various cheminformatics toolkits. This makes it possible to use the complementary features of cheminformatics toolktis using a common interface. If functionality is provided by more than one toolkit, the Cinfony user can choose the implementation they prefer.
    • Indigo
      Indigo is a C++ based organic chemistry and cheminformatics software environment.
    • RDKit
      RDKit is a Python/C++ based cheminformatics and machine-learning software environment.

  • Other Cheminformatics packages:

    • chemfp
      Chem-fingerprints is a set of formats and related tools for the storage, exchange, and search of cheminformatics fingerprint data sets.
    • fmcs
      Fcms finds the maximum common substructure (MCS) of a group (or cluster) of chemical structures and report the result as a SMARTS string.
    • Opsin
      OPSIN (Open Parser for Systematic IUPAC Nomenclature) converts IUPAC compound names to semantic chemical information and outputs a structure either as as CML (Chemical Markup Language), SMILES, or InChI.

  • Visualization Packages:

    • Jmol
      Jmol is a Java molecular viewer for three-dimensional chemical structures. Features include reading a variety of file types and output from quantum chemistry programs, and animation of multi-frame files and computed normal modes from quantum programs. It includes with features for chemicals, crystals, materials and biomolecules. Jmol might be useful for students, educators, and researchers in chemistry and biochemistry.
    • Qutemol
      QuteMol is an interactive, high quality molecular visualization system. It exploits the current GPU capabilities through OpenGL shaders to offer an array of innovative visual effects. QuteMol visualization techniques are aimed at improving clarity and an easier understanding of the 3D shape and structure of large molecules or complex proteins.
    • ShelXle
      ShelXle combines an editor with syntax highlighting for the SHELXL-associated .ins (input) and .res (output) files with an interactive graphical display for visualization of a three-dimensional structure including the electron density (Fo) and difference density (Fo-Fc) maps.
    • XCrySDen
      XCrySDen is a crystalline and molecular structure visualisation program, which aims at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated. It can run on most UNIX platforms, without any special hardware requirements.

  • Data Parsing Packages:

    • cclib
      cclib is a Python library that provides parsers for computational chemistry log files. It also provides a platform to implement algorithms in a package-independent manner.
    • JGromacs
      JGromacs is a Java library designed to facilitate the development of cross-platform analysis applications for Molecular Dynamics (MD) simulations. The package contains parsers for file formats applied by GROMACS (GROningen MAchine for Chemical Simulations), one of the most widely used MD simulation packages.

  • Development Libraries:

    • libint
      The libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory. The idea of the library is to let computer write optimized code for computing such integrals. There are two primary advantages to this: much less human effort is required to write code for computing new integrals, and code can be optimized specifically for a particular computer architecture (e.g., vector processor).
What I have been up to over the last couple of years

I have now worked at credativ for four years. A sizable part of that time I spent working with the Munich City Council's LiMux project. The focus of our work is helping them with their LDAP/web-based GOsa user and system installation(based on FAI)/configuration/management system. Personally, I mostly did project management and QA besides occasional coding, bug fixing and on-site consulting.

Contrary to a lot of our other customers, the Munich city council openly acknowledges the work by external companies and lets us talk about it as well. I wrote a lengthy blog post (now available in english) last month about our work. It explains how the LiMux project is using GOsa and FAI and work we did for them.

The project took a long time, but managed to pull off the mass migration over the last two years and reached their goal of 12000 migrated workstation last November. It is now widely regarded as a "success story" by german news sites, and I am glad to have had a small part in it. I really think this was (and still is) an important project, especially after several others backpedalled and Munich remained the last high-profile public sector migration in the german speaking countries.

Besides that, the LiMux project members are really nice people I get along with well both on working hours and during the Munich Debconf11 bid and organizing various BSPs at their office. It is a bit of a shame that not more of their work and customizations are available in Debian, but hopefully this well happen one day. At least our changes to GOsa are up on github.
4 Jul 2012 (updated 5 Jul 2012 at 09:56 UTC) »
Update on computational chemistry packages in Debian

For many years, me and the Debichem team maintained two computational chemistry packages, first MPQC and later PSI3. In recent years however, two respected quantum chemistry codes have been open sourced and are now available in Debian: ACESIII and NWChem. Make no mistake, those are not recently started codes or some Ph.D.'s pet-project but state-of-the-art projects targeted at massively parallel supercomputers and developed at the University of Florida's Quantum Chemistry Project (QTP) in the case of ACESIII and at Pacific Northwest National Laboratory (PNNL) for NWChem.

While ACESIII has a somewhat narrow focus on Coupled-Cluster (unfortunately, the current version does not yet implement analytic gradients for the "golden standard" CCSD(T) method) and Multi-Body Perturbation Theory methods, NWChem is a very versatile package supporting a variety of molecular quantum chemistry methods (including Density Functional Theory (DFT)), as well as periodic plane-wave electronic structure and (ab-initio and classical) molecular dynamics. At this point, NWChem probably covers 90% of all use cases for routine computational chemistry compared to the popular non-free codes Gaussian and GAMESS, while likely exhibiting superior parallel scaling at least compared to Gaussian.

Over the last year, I have packaged and integrated NWChem and ACESIII for Debian, and they are now both in testing. Furthermore, I have recently overhauled the packaging of MPQC and enabled parallel execution via MPI. Further, both MPQC and PSI will see updated versions (MPQC3 and PSI4) in the near future with significant increased functionality, including some unique (at least among open source codes) features like Symmetry-Adapted Perturbation Theory (SAPT) for PSI4 and general explicitly correlated corrections ([2]f12) for MPQC3. Unfortunately, they both did not get released in time for the wheezy freeze.

On the periodic/plane-wave front, I have also packaged and uploaded Quantum ESPRESSO (formerly PwSCF), a set of plane-wave programs, and I have been working with Ólafur Jens Sigurðsson to get the latest Abinit release packaged. The nanoscale-physics team is also targeting further periodic ab-initio packages like BigDFT and Octopus, but those as well did not land in time for the freeze.

Finally, I also packaged and uploaded CP2K, a well-engineered and versatile periodic plane-wave/pseudo-potential code which focuses on state-of-the-art ab-initio Molecular Dynamics (AIMD) using Density Functional Theory. Some of the authors have recently published a paper reporting linear scaling benchmark calculations on a system with a million atoms using almost 50,000 CPU cores.

All of the above mentioned packages are included either in the molecular ab-initio or the periodic ab-initio Debichem tasks.

Tomorrow (25th November) evening, I will be giving a short talk about PostgreSQL at the monthly Munich Open-Source-Treffen event.

The meetings start around 6PM and are always in Cafe Netzwerk in Luisenstr. 11, a nice and cosy hangout and hackerspace for young Munich students near Hauptbahnhof.

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