Distributed computing as a virtual supercomputer: Tools to run and manage large-scale BOINC simulations

Distributed computing (DC) projects tackle large computational problems by exploiting the donated processing power of thousands of volunteered computers, connected through the Internet. To efficiently employ the computational resources of one of world's largest DC efforts, GPUGRID, the project scientists require tools that handle hundreds of thousands of tasks which run asynchronously and generate gigabytes of data every day. We describe RBoinc, an interface that allows computational scientists to embed the DC methodology into the daily work-flow of high-throughput experiments. By extending the Berkeley Open Infrastructure for Network Computing (BOINC), the leading open-source middleware for current DC projects, with mechanisms to submit and manage large-scale distributed computations from individual workstations, RBoinc turns distributed grids into cost-effective virtual resources that can be employed by researchers in work-flows similar to conventional supercomputers. The GPUGRID project is currently using RBoinc for all of its in silico experiments based on molecular dynamics methods, including the determination of binding free energies and free energy profiles in all-atom models of biomolecules.