A Square Block Format for Symmetric Band Matrices

This contribution describes a Square Block, SB, format for storing a banded symmetric matrix. This is possible by rearranging “in place” LAPACK Band Layout to become a SB layout: store submatrices as a set of square blocks. The new format reduces storage space, provides higher locality of memory accesses, results in regular access patterns, and exposes parallelism

Accelerating Sparse Arithmetic in the Context of Newton's Method for Small Molecules with Bond Constraints

Molecular dynamics is used to study the time evolution of systems of atoms. It is common to constrain bond lengths in order to increase the time step of the simulation. Here we accelerate Newton's method for solving the constraint equations for a system consisting of many identical small molecules. Starting with a modular and generic base code using a sequential data layout, we apply three different optimization techniques. The compiled code approach is used to generate subroutines equivalent to a single step of Newton's method for a user specified molecule. Differing from the generic subroutines, these specific routines contain no loops and no indirect addressing. Interleaving the data describing different molecules generates vectorizable loops. Finally, we apply task fusion. The simultaneous application of all three techniques increases the speed of the base code by a factor of 15 for single precision calculations

The asymptotic behavior of the joint linear complexity profile of multisequences

10.1007/s00605-005-0392-2Monatshefte fur Mathematik1502141-15