Inefficient parallel I/O is known to be a major bottleneck among scientific applications employed on supercomputers as the number of processor cores grows into the thousands. Our prior experience indicated that parallel I/O libraries such as HDF5 that rely on MPI-IO do not scale well beyond 10K processor cores, especially on parallel file systems (like Lustre) with single point of resource contention. Our previous optimization efforts for a massively parallel multi-phase and multi-component subsurface simulator (PFLOTRAN) led to a two-phase I/O approach at the application level where a set of designated processes participate in the I/O process by splitting the I/O operation into a communication phase and a disk I/O phase. The designated I/O processes are created by splitting the MPI global communicator into multiple sub-communicators. The root process in each sub-communicator is responsible for performing the I/O operations for the entire group and then distributing the data to rest of the group. This approach resulted in over 25X speedup in HDF I/O read performance and 3X speedup in write performance for PFLOTRAN at over 100K processor cores on the ORNL Jaguar supercomputer. This research describes the design and development of a general purpose parallel I/O library called Scorpio that incorporates our optimized two-phase I/O approach. The library provides a simplified higher level abstraction to the user, sitting atop existing parallel I/O libraries (such as HDF5) and implements optimized I/O access patterns that can scale on larger number of processors. Performance results with standard benchmark problems and PFLOTRAN indicate that our library is able to maintain the same speedups as before with the added flexibility of being applicable to a wider range of I/O intensive applications.

In recent years the power of Grid computing has grown exponentially through the development of advanced middleware systems. While usage has increased, the penetration of Grid computing in the scientific community has been less than expected by some. This is due to a steep learning curve and high entry barrier that limit the use of Grid computing and advanced cyberinfrastructure. In order for the scientists to focus on actual scientific tasks, specialized tools and services need to be developed to ease the integration of complex middleware. Our solution is Cyberaide Shell, an advanced but simple to use systemshell which provides access to the powerful cyberinfrastructure available today. Cyberaide Shell provides a dynamic interface that allows access to complex cyberinfrastructure in an easy and intuitive fashion on an ad-hoc basis. This is accomplished by abstracting the complexities of resource, task, and application management through a scriptable command line interface. Through a service integration mechanism, the shellpsilas functionality is exposed to a wide variety of frameworks and programming languages. Cyberaide Shell includes specialized experiment management and workflow commands that, with the scriptable nature of a shell, provide a set of services which where previously unavailable. The usability of Cyberaide Shell is demonstrated using a Water Threat Management application deployed on the TeraGrid.

The authors present a metacomputing application of multivariate, nonhierarchical statistical clustering to geographic environmental data from the 48 conterminous United States in order to produce maps of regions of ecological similarity, called ecoregions. These maps represent finer scale regionalizations than do those generated by the traditional technique: an expert with a marker pen. Several variables (e.g., temperature, organic matter, rainfall etc.) thought to affect the growth of vegetation are clustered at resolutions as fine as one square kilometer (1 km 2). These data can represent over 7.8 million map cells in an n–dimensional (n = 9 to 25) data space. A parallel version of the iterative statistical clustering algorithm is developed by the authors using the MPI (Message Passing Interface) message passing routines. The parallel algorithm uses a classical, self–scheduling, single–program, multiple data (SPMD) organization; performs dynamic load balancing for reasonable performance in heterogeneous metacomputing environments; and provides fault tolerance by saving intermediate results for easy restarts in case of hardware failure. The parallel algorithm was tested on various geographically distributed heterogeneous metacomputing configurations involving an IBM