Making campus bridging work for researchers: A case study with mlRho. Thota, A., Michael, S., Xu, S., Haubold, B., Doak, T., & Henschel, R. In Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery (XSEDE '13), pages 8, 2013.
Making campus bridging work for researchers: A case study with mlRho [link]Website  doi  abstract   bibtex   
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 first 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 offer. 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 profiles using mlRho [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 workow 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 staff 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 first 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. © 2013 by the Association for Computing Machinery, Inc.
@inproceedings{
 title = {Making campus bridging work for researchers: A case study with mlRho},
 type = {inproceedings},
 year = {2013},
 keywords = {Application programs,Bigjob,Employment,Genes,Genetics,High-throughput,Job analysis,MlRho,Optimization,Performa,Re},
 pages = {8},
 websites = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84882383550&doi=10.1145%2F2484762.2484803&partnerID=40&md5=67cc69a3e36848a9909f0d5b80ef338c},
 city = {San Diego, CA},
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 created = {2018-02-27T18:07:33.065Z},
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 last_modified = {2019-08-26T19:07:38.566Z},
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 starred = {false},
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 citation_key = {Thota2013},
 source_type = {conference},
 notes = {cited By 0; Conference of Conference on Extreme Science and Engineering Discovery Environment, XSEDE 2013 ; Conference Date: 22 July 2013 Through 25 July 2013; Conference Code:98539},
 private_publication = {false},
 abstract = {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 first 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 offer. 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 profiles using mlRho [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 workow 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 staff 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 first 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. © 2013 by the Association for Computing Machinery, Inc.},
 bibtype = {inproceedings},
 author = {Thota, A and Michael, S and Xu, S and Haubold, B and Doak, T and Henschel, R},
 doi = {10.1145/2484762.2484803},
 booktitle = {Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery (XSEDE '13)}
}
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