OSG Newsletter, Febuary, 2009

 

Please remember to register for the OSG All Hands by February 20th, 2009

http://indico.fnal.gov/conferenceDisplay.py?confId=2012

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SBGrid Using the OSG

SBGrid, a consortium of 100 structural biology labs across the country, has a central team, based at Harvard Medical School provides an integrated computing environment with hundreds of specialty software packages available for a range of platforms (Linux, OS X, and SGI). Over the past year, SBGrid has become increasingly involved with OSG, both through the provision of two compute clusters, available to all VOs, and in the development of novel workflows for computationally intensive protein structure determination.

A critical field at the boundary of biology, physics, and chemistry, structural biology studies the bio-mechanics of cellular processes mediated by proteins at an atomic level resolution. Because current techniques to determine the physical geometry of protein structures is time consuming, possibly taking many person-months to complete, SBGrid is developing techniques that will automate the process and will include information from the existing database of 50,000 macromolecular structures. This has relied on replication of the corpus of 150,000 known macromolecular domains, requiring 40 GB of persisted storage space, to all OSG sites used by the workflow. Collating and presenting the resulting data is a challenge, because a single study consists of tens of thousands of files and approximately 3 GB of data. Web-based data visualization has been developed to facilitate this step.

Since the start of the year SBGrid has utilized over 10,000 hours of compute time on remote OSG compute resources, running more than 5,000 jobs.

~ Ian Stokes-Rees

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Introducing Xrootd

Recently, the OSG Software stack was expanded to include a new way to set up a Storage Element with BeStMan and Xrootd. Although BeStMan has been in the VDT for a long time, it was recently updated to work well with Xrootd, and we added Xrootd as a supported component in our software stack. BeStMan is a relatively lightweight Storage Resource Management system that is easy to set up with a single disk on a single computer. However, it is now relatively easy to expand its capabilities by using Xrootd as a high-performance storage backend. This was requested by the ATLAS experiment, but it may be of interest to a wider audience. If you are interested in learning more, you can see more details on the VDT's web site:

http://vdt.cs.wisc.edu/components/bestman.html

~ Alain Roy
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