High-throughput sequencing has revolutionized the way we understand biology. With state-of-the-art technologies one can nowadays re-sequence a human genome for less than 1,000$. However, key technical problems are still present. First, with current technologies one cannot sequence a long DNA molecule as a whole, but rather only read it out as many relatively short chunks; as a result, data analysis becomes complicated.
Elmer is an open source finite element software suite particularly well suited for the study of multiphysical problems. In Elmer each physical model is a dynamically linked solver and there is no upper limit to the number of different solvers. Elmer includes at least basic models for many branches of computational engineering, e.g. fluid mechanics, solid mechanics, heat transfer, electromagnetics, acoustics. Elmer has been parallized with MPI and has demonstrated good scalability up to thousands of cores.
The 5th IMACS Conference on Mathematical Modelling and Computational Methods in Applied Sciences and Engineering, in honour of Professor Owe Axelsson's 80th birthday.
Applications need to be effectively parallelised, using techniques such as MPI message-passing and OpenMP multithreading, to fully exploit the capabilities of modern systems for high-performance computing.The course introduces the open-source community-developed Score-P instrumentation and measurement infrastructure, and the Scalasca and Vampir tools using it, to provide a practical basis for portable performance analysis of parallel applications.
The availability of Intel Xeon Phi Coprocessor opens opportunities in the HPC domain for highly parallel algorithms/applications by providing a large amount of processing cores, each with 512 bit large SIMD vectors. While the programming models of the coprocessor are not much different to the ones known from Intel Xeon systems, there are still some specific characteristics.
OpenMP® is the de facto standard for writing parallel applications for shared memory computers. With multi-core processors in everything from tablets to high-end servers, the need for multithreaded applications is growing and OpenMP is one of the most straightforward ways to write such programs.