1. A reconfigurable computing system for enabling high performance computing, comprising: a host platform running an operating system (OS); a reconfigurable processing kernel module; a plurality of drivers interacting with the OS; one or more reconfigurable hardware modules; a software stack interacting with the OS and providing access to the reconfigurable hardware, wherein the reconfigurable processing kernel module manages reconfigurable processes and coordinates data transfer to and from host, and wherein the reconfigurable processing kernel modifies the OS to utilize the software stack, enabling the use of reconfigurable hardware modules through the use of hardware specific driver instructions; and an application compiler that segments source code of an application into first code for the host platform and second code for the one or more reconfigurable hardware modules, compiles the first code for the host platform into a binary file, compiles the second code for the one or more reconfigurable hardware modules into a bitstream file, and links the binary file and the bitstream file into an executable file for the application.