Computing plays an indispensable role in scientific research. Presently, researchers in science have different problems, needs, and beliefs about computation than professional programmers. In order to accelerate the progress of science, computer scientists must understand these problems, needs, and beliefs. To this end, this paper presents a survey of scientists from diverse disciplines, practicing computational science at a doctoral-granting university with very high research activity. The survey covers many things, among them, prevalent programming practices within this scientific community, the importance of computational power in different fields, use of tools to enhance performance and software productivity, computational resources leveraged, and prevalence of parallel computation. The results reveal several patterns that suggest interesting avenues to bridge the gap between scientific researchers and programming tools developers.

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Automatic parallelization for clusters is a promising alternative to time-consuming, error-prone manual parallelization. However, automatic parallelization is frequently limited by the imprecision of static analysis. Moreover, due to the inherent fragility of static analysis, small changes to the source code can significantly undermine performance. By replacing static analysis with speculation and profiling, automatic parallelization becomes more robust and applicable. A naïve automatic speculative parallelization does not scale for distributed memory clusters, due to the high bandwidth required to validate speculation. This work is the first automatic speculative DOALL (Spec-DOALL) parallelization system for clusters. We have implemented a prototype automatic parallelization system, called Cluster Spec-DOALL, which consists of a Spec-DOALL parallelizing compiler and a speculative runtime for clusters. Since the compiler optimizes communication patterns, and the runtime is optimized for the cases in which speculation succeeds, Cluster Spec-DOALL minimizes the communication and validation overheads of the speculative runtime. Across 8 benchmarks, Cluster Spec-DOALL achieves a geomean speedup of 43.8× on a 120-core cluster, whereas DOALL without speculation achieves only 4.5× speedup. This demonstrates that speculation makes scalable fully-automatic parallelization for clusters possible.

With the right techniques, multicore architectures may be able to continue the exponential performance trend that elevated the performance of applications of all types for decades. While many scientific programs can be parallelized without speculative techniques, speculative parallelism appears to be the key to continuing this trend for general-purpose applications. Recently-proposed code parallelization techniques, such as those by Bridges et al. and by Thies et al., demonstrate scalable performance on multiple cores by using speculation to divide code into atomic units (transactions) that span multiple threads in order to expose data parallelism. Unfortunately, most software and hardware Thread-Level Speculation (TLS) memory systems and transactional memories are not sufficient because they only support single-threaded atomic units. Multi-threaded Transactions (MTXs) address this problem, but they require expensive hardware support as currently proposed in the literature. This paper proposes a Software MTX (SMTX) system that captures the applicability and performance of hardware MTX, but on existing multicore machines. The SMTX system yields a harmonic mean speedup of 13.36x on native hardware with four 6-core processors (24 cores in total) running speculatively parallelized applications.