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A low-diameter, fast interconnection network is going to be a prerequisite for building exascale machines. A two-level direct network has been proposed by several groups as a scalable design for future machines. IBM's PERCS topology and the dragonfly network discussed in the DARPA exascale hardware study are examples of this design. The presence of multiple(More)
Due to next-generation sequence technologies, sequencing of bacterial genomes is no longer one of the main bottlenecks in bacterial research and the number of new genomes deposited in public databases continues to increase at an accelerating rate. Among these new genomes, several belong to the same species and were generated for pan-genomic studies. A(More)
The advent of petascale computing has introduced new challenges (e.g. heterogeneity, system failure) for programming scalable parallel applications. Increased complexity and dynamism in science and engineering applications of today have further exacerbated the situation. Addressing these challenges requires more emphasis on concepts that were previously of(More)
As machines increase in scale, many researchers have predicted that failure rates will correspondingly increase. Soft errors do not inhibit execution, but may silently generate incorrect results. Recent trends have shown that soft error rates are increasing, and hence they must be detected and handled to maintain correctness. We present a holistic(More)
Collectives are an important and frequently used component of MPI. Bucket algorithms, also known as "large vector" algorithms, were introduced in the early 90's and have since evolved as a well known paradigm for large MPI collectives. Many modern day supercomputers such as the IBM Blue Gene and Cray XT are based on torus interconnects that offer a highly(More)
Despite the identification of many factors that facilitate ribosome assembly, the molecular mechanisms by which they drive ribosome biogenesis are poorly understood. Here, we analyze the late stages of assembly of the 50S subunit using Bacillus subtilis cells depleted of RbgA, a highly conserved GTPase. We found that RbgA-depleted cells accumulate late(More)
—Performance of applications executed on large parallel systems suffer due to load imbalance. Load balancing is required to scale such applications to large systems. However, performing load balancing incurs a cost which may not be known a priori. In addition, application characteristics may change due to its dynamic nature and the parallel system used for(More)
—Hardware and software co-design is becoming increasingly important due to complexities in supercomputing architectures. Simulating applications before there is access to the real hardware can assist machine architects in making better design decisions that can optimize application performance. At the same time, the application and runtime can be optimized(More)