© 2010 Pittsburgh Supercomputing Center Pittsburgh Supercomputing Center RP Update July 1, 2010 Bob Stock Associate Director

© 2010 Pittsburgh Supercomputing Center Topics for Today Anton –Special-purpose machine for molecular dynamics simulation available for use this fall Bioinformatics Training Update

© 2010 Pittsburgh Supercomputing Center Anton and DESRES Anton is a special purpose machine developed by D. E. Shaw Research –For molecular dynamics simulation –“Orders of magnitude faster than was previously possible” D. E. Shaw Research (DESRES) “is an independent research laboratory that conducts basic scientific research in the field of computational biochemistry” Chief Scientist is David E. Shaw

© 2010 Pittsburgh Supercomputing Center Anton Funding Anton machine provided to NRBSC at PSC for one full year by DESRES without cost for non-commercial research use by not-for- profit institutions Operations funded by two-year $2.7 million grant from National Institute of General Medical Sciences (NIGMS), part of NIH NRBSC is PSC’s National Resource for Biomedical Supercomputing:

© 2010 Pittsburgh Supercomputing Center Anton Machine at NRBSC Production machine –4 cabinets, each with 128 special purpose nodes –Arrival expected September 1 –Production expected October 1 Test machine –64 nodes –Onsite and operational References for technical details on later slide

© 2010 Pittsburgh Supercomputing Center Access to Anton NRBSC solicited proposals for computer time on Anton Expected number of awards –10-15 awards of 100,000 node hours –20-30 awards of 50,000 node hours Received more requests than can be accommodated

© 2010 Pittsburgh Supercomputing Center Anton Allocation Decisions Proposals initially assessed for technical feasibility by NRBSC and PSC staff Final peer review by committee to be convened by the National Research Council Allocation decisions are expected in late August 2010 User groups will have access to the machine in phases

© 2010 Pittsburgh Supercomputing Center Anton Usage Simulations on Anton use Maestro format for input –Maestro format is also used by DESRES’s high performance MD code DESMOND –Anton does not “run” Desmond but prior knowledge of Desmond will be useful to users Each job uses all 512 nodes Training workshop may be held for users in late August or early September

© 2010 Pittsburgh Supercomputing Center Anton Technical Information For details of technical information and scientific results see – –In particular, David E. Shaw, et al., "Anton: A Special-Purpose Machine for Molecular Dynamics Simulation," Proceedings of the 34th Annual International Symposium on Computer Architecture (ISCA '07), San Diego, California, June 9–13, 2007

© 2010 Pittsburgh Supercomputing Center Bioinformatics Training Update Previous PSC RP updates covered MARC and BEST programs –MARC aims to increase minority participation in biomedical research through a broadly-based program assisting minority serving institutions with the development of Bioinformatics programs –BEST exposes high school teachers to modern molecular biology concepts and evaluates inclusion of computational biology and bioinformatics into high school curricula New: High School Research Internships

© 2010 Pittsburgh Supercomputing Center High School Research Internship Starting Summer 2010, June 14 to July 23 Four unpaid research interns, from two of the three high schools that piloted BEST –Two young women and two young men

© 2010 Pittsburgh Supercomputing Center High School Research Internship Perspective: apply the skills of computer science to biological sequence data Two weeks of instruction in Python Collaborate with PSC senior scientists on a specific problem in biological sequencing Opportunity for publications