New version of thread_mpi with many minor enhancements

- Fixed issues with collective calls with 1 thread
- Fixed deadlocks with copy buffer turned on
- Turned off copy buffers by default for Gromacs
- Fixed error handling on low-level calls
- Low-level errors are now propagated correctly through MPI
- Simplified the atomics
- Compiles for platforms for which atomics are not supported.
- Added Fujitsu Sparc64 support

Change-Id: I3553906d6630cea8b1efe59fca293fe3c066c8d9