changed MPI_COMM_WORLD into MPI_COMM_CODES and made model-net-mpi-replay a function instead of a main

Fixed fat-tree model seg fault

See merge request !18

Need to cut down synthetic dragonfly network size, currently running out of memory on jenkins server (commenting the test for now)

Updating base fat tree synthetic .conf

See merge request !16

Cortex

Integration of Cortex in CODES. Cortex can be enabled with --with-cortex=... when configuring CODES. When Cortex is enabled, it will be used in place of DUMPI and automatically translate MPI collectives using algorithms as implemented in Mpich.

This merge request also adds support for MPI_Sendrecv in the MPI replayer, and corrects an issue with CODES expecting the size of a posted MPI_Recv to match with the corresponding MPI_Send's size, which is not a requirement in the MPI standard.

See merge request !14