An algorithmic matching pipelined compiler and a reusable algorithmic pipelined core comprise a high throughput processor system. The reusable algorithmic pipelined core is a reconfigurable processing core with a pipelined structure comprising a processor with a setup interface for programming any of a plurality of operations as determined by setup data, a logic decision processor for programming a look up table, a loop counter and a constant register, and a block of memory. This can be used to perform functions. A reconfigurable, programmable circuit routes data and results from one core to another core and/or IO controller and/or interrupt generator, as required to complete an algorithm without further intervention from a central or peripheral processor during processing of an algorithm.