ISMB 2005 Tutorial Proposal

Title Of Tu torialATT A CKING PERFORMAN CE B OTTLENECKSMotivationWith CPU chip speeds peaking, simply upgrading the processor no longer offers theperformance benefit that it did, leaving many of us facing a brick wall. This performancetutorial will teach you how to overcome this barrier and get more out of your applicationsusing your existing system(s ). Basically, there are two approaches to address aperformance bottleneck: 1) software – modify the code itself to parallelize and optimizeit; 2 ) hardware – increase the efficiency of utilization through scheduled resourceallocation. Both approaches will be covered in this tutorial through detailed case studiespresented jointly by Sun and Delaware Biotechnology Institute (D BI). Researchers fromDBI will present several problems they (a nd their users) typically encounter and eachproblem will be solved based on software parallelization achieved through the OpenMPprogramming model or distributed resource management approaches. Solutioninstructions will be provided so those with similar problems can then use theseapproaches to a ddress th eir own I T is sues. In recent years, clusters of relatively inexpensive servers have become the most popularsolution to cope with a growing requirement for computational resources, althoughinternal competition for storage space in the data center as well as access to thoseresources is becoming especially acute. Without an appropriate resource managementpolicy, ...