Advogato blog for mbanck

5 May 2013

Sun, 5 May 2013 14:10:24 GMT

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).

18 Jan 2013

Fri, 18 Jan 2013 10:26:19 GMT

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

Wed, 4 Jul 2012 14:41:52 GMT

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.

24 Nov 2011

Thu, 24 Nov 2011 08:58:08 GMT

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.

6 Nov 2011

Sun, 6 Nov 2011 11:24:09 GMT

I am currently sitting in the train to Goslar, where the German Conference on Cheminformatics will take place. As part of the Free Software Session, I will give a session on DebiChem. This is the first I attend this conference and I am looking forward to meet Noel O'Boyle and hopefully others from the community.

In light of this, I have packaged and uploaded RDKit and Cinfony over the last weeks and also updated the Debichem task pages, introducing a Cheminformatics Task at the same time. I feel we still need at least tasks for Chemical Education (to expose e.g. Kalzium more prominently), and possibly Protein Docking and Crystallography. So if you have experience/opinions in these fields (or want to propose other fields), drop me a mail or contact us at debichem-devel@lists.alioth.debian.org.

4 Oct 2011

Tue, 4 Oct 2011 21:04:01 GMT

Woodchuck and FrOSCon

At the end of August, I attended FrOSCon in Bonn again, after skipping it last year. The evening before FrOSCon however, I visited Neal Walfield, his wife Isabel and their little son Noam in Düsseldorf. Besides having a great time and a lovely dinner, I was most impressed by their collection of Maemo devices (they had at least two N770s, an N900 and, to my jealousy, an N950) which Neal is doing research on these days. He works on woodchuck, which is a project investigating how to improve data availability on mobile devices and our conversation prompted him to implement ATP Woodchuck, which makes smarter decisions when to run APT upgrade on your Maemo device then the standard updater. As part of the research, they also run a user behaviour study which I joined, where one installs a client which records various data off your N900 and sends them anonymized (he seems to be doing a good job at that) to figure out how people use their mobile devices and hopefully enhance the experience. So if you have a N900, you should consider joining the study so they get better data.

The next day, I picked up Martin Michlmayr nearby and we headed for FrOSCon. I was quite impressed by the Makerbot at the Tarent booth, but I still don't know what they are really doing and why they had it on display... In the afternoon, I attended a couple of talks in the PostgreSQL developer room and a talk about a big OpenVPN deployment, before ending the day with the excellent as always social event barbeque. On Sunday, I went to quite a few talks, but I thought that two of them were particularly interesting:

Michael "Monty" Widenius of MySQL gave a talk titled "Why going open source will improve your product" about starting businesses on an open source project, or how business can/should open-source their product. Besides a detailed discussion about the various forms of Open Source licenses and the Open-Core model, he proposed the idea of "Business Source" (see slide 20 of his presentation), where a startup would distribute the source code under a non-commercial (but otherwise open-source) license with the explicit guarantee that the license would be changed to a true FLOSS license at some defined point in the future, giving the company a head start to develop and nurture their project. I asked whether this has been already implemented in practise and how the community could be sure that e.g. lawyers after a hostile takeover would not just remove that part of the copyright notice, as long as a true distribution under a FLOSS license has not happened yet. Monty wasn't aware of any real-word cases, and he did not seem to be concerned about this and said the original intent would be clear in a possible court case. This was the first time I heard about this approach, I wonder how other people think about it, whether it would work in practise and be a useful thing to have?

Second, I attended a talk by Gregor Geiermann, a Ph.D. student in linguistics on "Perceptions of rudeness in Free Software communities". He conducted an online survey about the perceived rudeness of several forum thread posts on Ubuntu Forums. Survey participants were first asked a couple of generic questions about their gender, nationality etc. and were then presented with a series of posts. For each post, they were asked to rate how rude they thought it was on a scale of 1 to 5 and they also had the possibility to highlight the parts of the post they considered rude as well as add comments. He presented a neat web application for analyzing the results, which makes it possible to select different groups (he did male vs. female and Americans vs. Germans in the talk) and have their overall rudeness ratings as well as the highlighted texts visualized as different shades of blue. Comments can be easily accessed. There were quite a few interesting differences e.g. in how Germans perceived rudeness compared to Americans (RTFM comments were considered less rude by Germans for example, IIRC). In response to my question, he said he intended to release the web application as open source and this might be an interesting tool for FLOSS projects to analyze how their public communication channels are perceived by various groups. Unfortunately, I cannot find any other resources about this on the web as of today, so I should try to contact him about it at some point.

31 Jan 2011

Mon, 31 Jan 2011 20:22:17 GMT

Debian Med Bioinformatics Sprint

Last weekend, I was at the Debian Med Meeting in Travemünde near Lübeck, thanks to an invitation by Steffen Möller and Andreas Tille.

It was a great opportunity to finally meet Steffen and some of the other bioinformatics people in Debian like Manuel Prinz face-to-face for the first time. Also, lots of upstream and related bioinformatics packagers from e.g. Biolinux were present as well, many of them from the UK.

I discussed with and helped some people about Debian packaging. There is a big push to get Debian packages done and integrated in Debian and Ubuntu, but often enough people are not exactly sure what the requirements are and what needs to be done. Hopefully, the sprint was successful to clear things up and move forward.

I also managed to finalize the initial Jmol packaging and uploaded it to Debian towards the end of the sprint. I plan to update the other bioinformatics related packages in debichem like pymol and openbabel as soon as squeeze is released.

Overall, it was a great weekend, many thanks to NERC and Debian for making it possible, and to Steffen Möller for organizing it!

11 Dec 2010

Sat, 11 Dec 2010 22:56:42 GMT

On Cancun's Success and Wikileaks

The success of the international climate conference in Cancun appears to be a great (and desperately needed) leap forward in the struggle to preserve our climate. At least news sources in Germany marvel at the very much unexpected and bigger-than-hoped outcome of the final declaration.

However, I keep wondering whether this could also be the first big success of Wikileak's power: what if Cablegate's timely leakage of the US and China's double-game at the Kopenhagen summit has scared their delegations so much they did not dare to repeat the backstabbing of the climate conference a second (or thrice?) time - in fear of their actions being defaced another time next year?

If this was the case, one could either call this Diplomacy by Fear or Diplomacy by Transparency - I choose to pick the latter. And if it indeed turns out Wikileaks had been the prime source behind a success for our planet, nominating the organization for the Nobel Peace prize does not look so absurd to me as it did last week.

8 Aug 2010

Sun, 8 Aug 2010 16:36:12 GMT

So, DebConf is over and it was a blast. I wanted to blog about my talks for a couple of days, but the conference was so great that I did not get around to it until now.

The unique thing about this year's conference were the outstanding contributions by non-Debian FLOSS people from the east coast. I am really glad the organizers decided to reach out to the communi ty and take this opportunity when a lot of great minds were just a couple of hours away. Also, discussing and hanging out with the local team people was so much fun and interesting that it was wor th the visit alone.

The venue was just perfect, the dorms were on campus, the cafeteria had an all-you-can-eat buffet, everything was in short walking distance and the Columbia campus is beautiful. I would have liked to go to a couple more places in the evenings, but hanging out in the Carman basement lounge with awesome people was just as good. A big thanks to Richard Darst, Biella, Micah and the rest of the crew.

The Debian GNU/Hurd talk went quite well, I was pleasantly surprised so many people made it to the Davis auditorium. I wanted to do the presentation on Debian GNU/Hurd (and I had it working before the talk), but as my notebook has a different resolution than the projector, I decided to play it safe and just show a d-i run in qemu. Nevertheless, Jeremie's wo rk on debian-installer is impressive, I got it installed on my ThinkPad without a problem (using qemu) and it automatically installed and setup grub2. Unfortunately, grub2 seems to be having issues when booting my notebook natively, but I got it to work with grub-legacy, including X and evince.

There were quite a few comments and I had interesting conversations afterwards with a couple of people. It is a shame Emilio Pozuelo Monfort (pochu) could not make it to DebConf to give the talk himself, he did lots of great work on porting packages and fixing the Hurd and glibc for various testsuites over the last couple of months.

My other talk about GOsa and FAI was a bit rougher, I scrambled to get FAI integration in GOsa to work based on Mark Pavlichuk'sinstallation scripts which I fixed up over the last couple of weeks to the point where one can install a client using the FAI simple demo classes (which I ported to GOsa's FAI LDAP). There were some problems with the demonstration during the talk and I guess it was a tough audience for a web-based admin tool but I hopefully got my point across that we should salvage this work done for the city of Munich. Indeed, I had great discussions with Andreas Mundt from debian-edu afterwards who posted a summary and call for discussion to the debian-edu mailing list.

4 Aug 2010

Wed, 4 Aug 2010 16:55:10 GMT

Science and Math Track at DebConf10

This year's DebConf10 (which is great, by the way) at Columbia University, New York will feature Tracks for the first time. We had a Community Outreach track on Debian Day (to be continued by more awesome talks over the rest of the week), a Java track on Monday and an Enterprise track yesterday.

Tomorrow, Thursday afternoon, the S cience and Math track (which I am organizing) will take place in the Interschool lab on level 7 of Schapiro Center.

The Track will start at 14:00 with a short welcome from me, followed by presentations of debian-science by Sylvestre Ledru and debian-math by David Bremner.

At 15:00, Michael Hanke and Yaroslav Halchenko will present their talk on "Debian as the ultimate platform for neuroimaging research".

This will be followed at 16:00 by three mini-talks on "New developments in Science Packaging". Adam C. Powell, IV will talk about MPI, Sylvestre Ledru will present linear algebra implementations in Debian and finally Michael Hanke and Yaroslav Halchenko will discuss the citation/reference infrastructure.

At the end of track, the annual debian-science round-table will happen at 17:00, where David Bremner (mathematics), Michael Hanke (neuro-debian), Sylvestre Ledru (debian- science/pkg-scicomp), Adam C. Powell, IV (debian- science/pkg-scicomp) and myself (debichem) will discuss matters about cross-field debian-science and math related topics.

If afterwards there are still outstanding matters to be discussed, we can schedule ad-hoc sessions for science or math matters on Friday or Saturday.

See you at the science track tomorrow!