SIML: A Fast SIMD Algorithm for Calculating LINGO Chemical Similarities on GPUs and CPUs

SIML: A Fast SIMD Algorithm for Calculating LINGO Chemical Similarities on GPUs and CPUs

LINGOs are a holographic measure of chemical similarity based on text comparison of SMILES strings. We present a new algorithm for calculating LINGO similarities amenable to parallelization on SIMD architectures (such as GPUs and vector units of modern CPUs). We show that it is nearly 3x as fast as existing algorithms on a CPU, and over 80x faster than existing methods when run on a GPU.

Fast Sort on CPUs, GPUs and Intel MIC Architectures

Image Processing on Modern CPUs and GPUs

Magnus integrators on multicore CPUs and GPUs

In the present paper we consider numerical methods to solve the Schr\"odinger equation with a time dependent Hamiltonian. We will consider both short-range interactions, which lead to evolution equations involving sparse matrices, and long-range interactions, which lead to dense matrices. Both of these settings show very different computational characteristics. We use Magnus integrators for tim...

BROCCOLI: Software for fast fMRI analysis on many-core CPUs and GPUs

Analysis of functional magnetic resonance imaging (fMRI) data is becoming ever more computationally demanding as temporal and spatial resolutions improve, and large, publicly available data sets proliferate. Moreover, methodological improvements in the neuroimaging pipeline, such as non-linear spatial normalization, non-parametric permutation tests and Bayesian Markov Chain Monte Carlo approach...