Posts Tagged 'grid computing'

ADEM on github

For my first Ruby project, I reimplemented ADEM from scratch. ADEM is tool for automatically installing applications on the Open Science Grid via pacman. Here is a glimpse of the interface.

ADEM is a tool for deploying and managing software on the Open Science Grid.

    adem command [options]

    adem config --display
    adem sites --update
    adem app --avail

  Further help:
    adem config -h/--help        Configure ADEM
    adem sites -h/--help         Manipulate the site list
    adem app -h/--help           Application installation
    adem help                    This help message

The original subversion repository is found in A Github repository is also mirrored in git://

Happy grid computing!


SwiftScript Vim syntax file

One weekend I was reading an article howto made a Vim syntax file. In application I decided to make one for the Swift workflow system. Most of the script contains simple word matches for some Swift keywords. Then I copied the matching rules for comments from the C syntax files in the standard Vim distribution. For a preview, checkout the screenshot below which uses the desert256.vim colorscheme in a gnome-terminal:

oops_swift by yecartes, on Flickr

Fig. a Swift workflow syntax highlighted

The syntax file can be downloaded from my graduate student code-shanty page.

Why do research in the Philippines?

Because installing grid computing middleware can get you to this:

7th PANDA Grid Workshop, Bohol, Philippines, May 4 – 8, 2009
organised by
Ateneo de Manila University
Sponsored also by EPSRC, IoP, PPARC and the Royal Society of Edinburgh
The aim of the workshop is to bring together grid administrators and software developers in an informal setting, involving open discussions. The focus will include grid maintenance and monitoring and data production with PandaRoot.

Organising committee:

    Rafael P. Saldana (Ateneo)
    Kilian Schwarz (GSI)
    Dan Protopopescu (Glasgow)

Contact person:


    Holy Name University,
    Lesage and Gallares Streets,
    6300 Tagbilaran City,
    Bohol, Philippines

Let’s look at the itinerary:

Tagbilaran City (May 3, 4, 5)

Metro Centre Hotel and Convention Center
Pres. Carlos P. Garcia Avenue
Tagbilaran City, Bohol
Philippines, 6300

Panglao Island (May 6, 7, 8, 9, 10)

Bohol Beach Club
Bo. Bolod, Panglao Island, Bohol 6340

Shet, gusto kong umuwi!!!

On science productivity

Grid computing infrastructures were made to support execution of science applications at larger scales. One challenge today in running your science in these behemoth systems the requirement of “griddification” or “supercomputerification”. You need to know how to make the best of your hardware or grid sites in order to orchestrate beautiful workflows and process your science. So a lot of research has been done to create languages such as Swift to make life easier for these domain scientists.

I was debugging a science application for the last several months to run on petascale (100×10^3++ processors) systems. The main goal of the domain scientist was to process hundres of thousands data sequences. I got too much carried away in the debugging to make the application work and have only looked at 3000 of the set In other words, not much *real* work has been done.

Now I should always remember when debugging, remember the scientists who took pain in measuring this data or who can’t get data. (Much like an analogy of “finish your food because there are millions of children hungry in developing countries”).

Midwest Grid School 2008 @UChicago

Yey! Malapit na malapit lang 🙂 More information about the program and registration information is found in its OSG Page. Workshop dates from Sept 17-19.

The Open Science Grid (OSG), the TeraGrid and the Computation Institute of The University of Chicago present a three day intensive course in grid computing and its application to scientific discovery.

The course introduces the techniques of grid and distributed computing for science and engineering fields, with hands-on training in the use of national grid computing resources. The workshop introduces essential skills that will be needed by researchers in the natural and applied sciences, engineering, and computer science to conduct and support large-scale computation and data analysis in emerging grid and distributed computing environments.

School participants will work with grid computing experts during the 3-day training. The workshop will focus on enabling the use of the national cyberinfrastructure –The Open Science Grid and TeraGrid– to perform large-scale computations and data-intensive processing in the your field of research. Participants will learn to use grids of thousands of processors and will be able to continue to use these resources for their research after the class. We encourage you to bring your research project to us for suggestions and help in porting your application to the grid. We would like to offer you support in transitioning your application to this platform.

The future of public health: grid gains traction

From iSGTW Feature – The future of public health: grid gains traction.

Feature – The future of public health: The grid gains traction

Dr. Ida A. Bengston (1881-1952) was one of the first women employed on the scientific staff of the Hygienic Laboratory of the Public Health Service, the predecessor to the National Institutes of Health. Bengston was particularly noted for her studies of bacterial toxins.

What are the infrastructure challenges of public health informatics that requires leveraging the grid?  Of course Doc Eloy Marcelo has his CHITS and also there is the OpenMRS project.  Perhaps this is an *integration* of existing systems? It would be interesting to see a web service interfacing CHITS and OpenMRS.

GRID Computing Now! – Competition 2008

From GRID Computing Now! – Competition 2008. Too bad it’s only open for UK residents 😦

Enter the Grid Computing Now! Competition 2008

Grid Computing Now! is pleased to announce its second competition for applying innovative grid computing solutions to an environmental problem. The competition is supported by the British Computer Society, The 451 Group, Intellect, Memset, Microsoft, National e-Science Centre, Oxford e-Research Centre, the Technology Strategy Board and WWF.

Of course supercomputing systems have are already widely used to analyze weather patterns like MM5 and other NWP suites. So what solutions kinds of solutions can show one’s creativity? The middleware component is very interesting for us system integrators but we build the system so that the end-user (the average scientist) can make their data exploration much faster and draw deeper insight into a situation. Computational scientists, meterologists and disaster rescue operatives coordinate their workflows together to support relief efforts in a natural disaster. It is indeed true that today’s grand challenges in science is also the concern of everyone in the society and not just a single discipline.

Other links that might be of interest is the press release of the previous winners. But I can’t find the links to the project deployments of the winning projects. Anyone know their URLs?