TGQR 2010Q2 Report.pdf - Teragridforum.org

USGS National Map infrastructure and TeraGrid. They will also study the integration of a land
use model.
RENCI Science Portal.
The RENCI team wrote numerous web service clients which help the learning curve involved in
writing/using web service clients that call into the RENCI Science Portal (RSP) infrastructure.
Clients include Autodock (NCBR), UrQMD (Duke), BLAST+ (WUSTL), KlustaKwik (Duke),
MEME/MAST (UNC), MAQ (Duke) and ProteinEffects (Duke). Several new applications have
been installed: ProteinEffects, SamTools (pileup) and KlustaKwik.
The team has continued working with various researchers to create large BLAST runs using the
BLASTMaster Desktop and RSP web service infrastructure. The Genome Center at WUSTL
continues to make use of the RSP system via web services. Web service clients have been honed
to work cohesively with Jython based scripts at WUSTL. This enables bridging different
programming expertise (Java at RENCI and Python at WUSTL). The RSP has been used as a
proxy for launching jobs using the RSP web service infrastructure (business logic on third-party
web site calls into RSP web services).
Next quarter work concludes for this team. They will continue to work with researchers to utilize
TeraGrid and maintain account credentials across all configured clusters (TeraGrid, OSG, and
local RENCI clusters). They will refactor the backend software used to submit glidein jobs out to
remote resources using the next generation Portal Glidein Factory. This will be plugin-based
(OSGi). Granularity of pre-staging data and binary building will be improved.
UltraScan.
UltraScan (PI Prof. Borries Demeler, U Texas Health Science Center at San Antonio) is a
gateway supporting the computationally intense analysis of data collected on macromolecules by
an analytical ultracentrifuge. The gateway is used by researchers throughout the world and also
makes use of computational resources throughout the world. While some end users have their
own centrifuges and use the analysis capabilities of the gateway, others send samples to use both
the centrifuge and the analysis software. The IU gateways team completed initial integration of
Open Grid Computing Environment tools (application management, registration, and monitoring
services) with Ultrascan portal to submit jobs on Queenbee and Ranger. The team implemented
job monitoring for job status, job cancel method based on requests from the UltraScan
development team. Future work includes the addition of checkpointing for long-running jobs, the
use of a community account on TeraGrid resources. Resource discovery methods developed
through TeraGrid’s advanced support work with the GridChem project were applied in this
project as well. Final production integration of OGCE tools with UltraScan's production
environment depends on final GRAM5 stability validation on Ranger.
Gateways built with many different technologies have been able to make effective use of OGCE.
The LEAD gateway is portlet-based. GridChem is a Java swing client side application and
Ultrascan is php and perl-based. All have been able to effectively use OGCE. In addition, a large
MPI application that forks off many independent runs will be a focus for improvement through
TeraGrid’s ASTA program.
Finally, the Ultrascan gateway infrastructure has been replicated on IU’s Quarry hosting service
so that improvements can be made without impacting the production environment.
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