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Accelerated Drug Discovery with Intel Xeon Phi

drug discovery

Drug discovery has accelerated with the advent of high performance computing and new algorithms. “A structural bioinformatics algorithm, eFindSuite, can be used to demonstrate how moving the code to a highly parallel implementation can speed up the computation, by using both the Intel Xeon processor and the Intel Xeon Phi coprocessor. eFindSuite is implemented in both Fortran 77 and C++.”

Pairwise DNA Optimization using Intel Xeon Phi


The Smith-Waterman algorithm is widely used for pairwise DNA sequence alignment. The computation, consisting of looking for pattern in very long strings of the DNA alphabet, is very demanding. Using the Intel Xeon Phi, tremendous performance gains can be obtained, as long as the algorithms have been modified to take advantage of parallelism.

PGI Accelerator Compilers Add OpenACC Support for x86


“Our goal is to enable HPC developers to easily port applications across all major CPU and accelerator platforms with uniformly high performance using a common source code base,” said Douglas Miles, director of PGI Compilers & Tools at NVIDIA. “This capability will be particularly important in the race towards exascale computing in which there will be a variety of system architectures requiring a more flexible application programming approach.”

WRF Microphysics Optimization


“Microphysics provides atmospheric heat and moisture tendencies. This module has been optimized to take advantage of the Intel Xeon Phi coprocessor. However, some manual optimization can lead to even greater performance gains. By using manual optimizations, the overall speedup on a host CPU (Intel Xeon E5-2670) was 2.8 X, while the performance of running on the Intel Xeon Phi coprocessor was 3.5 X.”

Bill Gropp Presents: MPI and Hybrid Programming Models

Bill Gropp

Bill Gropp presented this talk at the Argonne Training Program on Extreme-Scale Computing. “Where it is used as an alternative to MPI, OpenMP often has difficulty achieving the performance of MPI (MPI’s much-criticized requirement that the user directly manage data motion ensures that the programmer does in fact manage that memory motion, leading to improved performance). This suggests that other programming models can be productively combined with MPI as long as they complement, rather than replace, MPI.”

Preview of Fall 2015 HPC Events


After spending a lovely six straight weeks at home, I find myself marveling at how many conferences are in the queue this Fall leading up to SC15 in Austin. Starting this week at the HPC User Forum, insideHPC will be on the road, bringing you the very latest in high performance computing.

Titan Supercomputer Powers the Future of Forecasting


Knowing how the weather will behave in the near future is indispensable for countless human endeavors. Now, researchers at ECMWF are leveraging the computational power of the Titan supercomputer at Oak Ridge to improve weather forecasting.

Training the Next Generation of Code Developers for HPC

Rob Farber

This is the first article in a two-part series by Rob Farber about the challenges facing the HPC community in training people to write code and develop algorithms for current and future, massively-parallel, massive-scale HPC systems.

OpenMPCon Lists Abstracts and Tutorials


Today the OpenMPCon Developer Conference published their abstracts of papers and tutorials.

Speaker Lineup Announced for OpenMPCon Developer Conference


Today the OpenMP Architecture Review Board (ARB) announced the full line-up of world-class keynote speakers, technical presentations, tutorials and panel sessions to be hosted at the inaugural OpenMPCon Developer Conference, which will take place Sept. 28-30 in Aachen, Germany.