fixed bug with sd integrator and OpenMP threading

This could cause small error in the integration or a segv.
This bug was introduced with d120c370
Fixes #1138

Change-Id: I4ae2c0c857cb68e796d01c5b2e0ea42beaf13d4a
Fix CUDA_HOST_COMPILER flag name

Fixes #1143

Change-Id: If34f27aa8fa73420ac85d4ec6997e8ebe78261d4
Added extra check in for setaffinity support.

The Linux version of tMPI_Thread_setaffinity_support() did not check
whether pthread_setaffinity_np() would actually work on the system
it's running on. It now checks by running pthread_getaffinity_np()
and checking its return value.

This is relevant for, for example, Bluegene systems which don't
support explicit affinity setting.

Change-Id: I4833e7384067f897013d6fa4d0b35963ae740fcf