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++.”
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.
“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.”
“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 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.”