Task-based programming models have enabled the optimized execution of the computation workloads of applications. These programming models can take advantage of large-scale distributed infrastructures by allowing the parallel and distributed execution of applications in high-level work components calledtasks. Nevertheless, in the era of Big Data and Exascale, the amount of data produced by modern scientific applications has already surpassed terabytes and is rapidly increasing. Hence, I/O performance became the bottleneck to overcome in order to achieve more total performance improvement. New storage technologies offer higher bandwidth and faster solutions than traditional Parallel File Systems (PFS). Such storage devices are deployed in modern day infrastructures to boost I/O performance by offering a fast layer that absorbs the generated data. Therefore, it is necessary for any programming model targeting more performance to manage this heterogeneity and take advantage of it to improve the I/O performance of applications. Towards this goal, we propose in this article a set of programming model capabilities that we refer to asStorage-Heterogeneity Awareness. Such capabilities include: (i) abstracting the heterogeneity of storage systems, and (ii) optimizing I/O performance by supporting dedicated I/O schedulers and an automatic data flushing technique. The evaluation section of this article presents the performance results of different applications on the MareNostrum CTE-Power heterogeneous storage cluster. Our experiments demonstrate that a storage-heterogeneity aware programming model can achieve up to almost 5x I/O performance speedup and 48% total time improvement compared to the reference PFS-based usage of the execution infrastructure.

The increasing complexity of modern and future computing systems makes it challenging to develop applications that aim for maximum performance. Hybrid parallel programming models offer new ways to exploit the capabilities of the underlying infrastructure. However, the performance gain is sometimes accompanied by increased programming complexity. We introduce an extension to PyCOMPSs, a high-level task-based parallel programming model for Python applications, to support tasks that use MPI natively as part of the task model. Without compromising application's programmability, using Native MPI tasks in PyCOMPSs offers up to 3x improvement in total performance for compute intensive applications and up to 1.9x improvement in total performance for I/O intensive applications over sequential implementation of the tasks.

BACKGROUND: Next Generation Genome sequencing techniques became affordable for massive sequencing efforts devoted to clinical characterization of human diseases. However, the cost of providing cloud-based data analysis of the mounting datasets remains a concerning bottleneck for providing cost-effective clinical services. To address this computational problem, it is important to optimize the variant analysis workflow and the used analysis tools to reduce the overall computational processing time, and concomitantly reduce the processing cost. Furthermore, it is important to capitalize on the use of the recent development in the cloud computing market, which have witnessed more providers competing in terms of products and prices. RESULTS: In this paper, we present a new package called MC-GenomeKey (Multi-Cloud GenomeKey) that efficiently executes the variant analysis workflow for detecting and annotating mutations using cloud resources from different commercial cloud providers. Our package supports Amazon, Google, and Azure clouds, as well as, any other cloud platform based on OpenStack. Our package allows different scenarios of execution with different levels of sophistication, up to the one where a workflow can be executed using a cluster whose nodes come from different clouds. MC-GenomeKey also supports scenarios to exploit the spot instance model of Amazon in combination with the use of other cloud platforms to provide significant cost reduction. To the best of our knowledge, this is the first solution that optimizes the execution of the workflow using computational resources from different cloud providers. CONCLUSIONS: MC-GenomeKey provides an efficient multicloud based solution to detect and annotate mutations. The package can run in different commercial cloud platforms, which enables the user to seize the best offers. The package also provides a reliable means to make use of the low-cost spot instance model of Amazon, as it provides an efficient solution to the sudden termination of spot machines as a result of a sudden price increase. The package has a web-interface and it is available for free for academic use.