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Conference Paper

Making campus bridging work for researchers: a case study with mlRho


Haubold,  Bernhard
Research Group Bioinformatics, Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society;

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Thota, A., Haubold, B., Michael, S., Doak, T., Xu, S., & Henschel, R. (2013). Making campus bridging work for researchers: a case study with mlRho. In N. Wilkins-Diehr (Ed.), Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery. XSEDE '13. New York, NY, USA: Association for Computing Machinery.

Cite as:
An increasing number of biologists' computational demands have outgrown the capacity of desktop workstations and they are turning to supercomputers to run their simulations and calculations. Many of today's computational problems, however, require larger resource commitments than even individual universities can provide. XSEDE is one of the rst places researchers turn to when they outgrow their campus resources. XSEDE machines are far larger (by at least an order of magnitude) than what most universities oer. Transitioning from a campus resource to an XSEDE resource is seldom a trivial task. XSEDE has taken many steps to make this easier, including the Campus Bridging initiative, the Campus Champions program, the Extended Collaborative Support Service (ECSS) [1] program, and through education and outreach. In this paper, our team of biologists and application support analysts (including a Campus Champion) dissect a computationally intensive biology project and share the insights we gain to help strengthen the programs mentioned above. We worked on a project to calculate population mutation and recombination rates of tens of genome proles using ml- Rho [2], a serial, open-source, genome analysis code. For the initial investigation, we estimated that we would need 6.3 million service units (SUs) on the Ranger system. Three of the most important places where the biologists needed help in transitioning to XSEDE were (i) preparing the proposal for 6.3 million SUs on XSEDE, (ii) scaling up the existing work ow to hundreds of cores and (iii) performance optimization. The Campus Bridging initiative makes all of these tasks easier by providing tools and a consistent software stack across centers. Ideally, Campus Champions are able to provide support on (i), (ii) and (iii), while ECSS sta can assist with (ii) and (iii). But (i), (ii) and (iii) are often not part of a Campus Champion's regular job description. To someone writing an XSEDE proposal for the rst time, a link to the guidelines and a few pointers may not always be enough for a successful application. In this paper we describe a new role for a campus bridging expert to play in closing the gaps between existing programs and present mlRho as a case study.