Fixed precision in thermal expansion coefficient calc.

Loss of accuracy was caused by different sampling
of volume and enthalpy and as a result alpha was
computed incorrectly. With the present "fix" the volume
and enthalpy are both downsampled to what is written
in the .edr file. The real fix would be to store the product
of H and V in the .edr file, but that falls outside the
4.6 branch policy.

Change-Id: I1be06d689002d7c9d6be92bf1e377912f0be1efd
clarified OpenMP-related things in mdrun help/man

Added note on OMP_NUM_THREADS/GMX_PME_NUM_THREADS env vars and
improved description on the use-cases when MPI+OpenMP improves
performance.

Change-Id: I904f00c8a4b6907a006b9d4367406d3fa3f3ce42
Unify logic for timing counts

Made all integrators use the same logic for starting timing
mechanisms.

Change-Id: Id8cb154f7b96d977efffcc9533d4a6dd9894afbd
Remove unused fplog

Keeps gcc 4.8 build happy

Change-Id: I392b02c0950ead04c414dffd6340b364b804b7aa
cmake: added FFTW_URL to allow easy offline build

Change-Id: I9904ce03e0ee1b377e4961c1f8481fc98c10cba4
Merge branch 'release-4-6'

Conflicts:
	src/contrib/fftw/CMakeLists.txt
Resolved by merging bump to 3.3.3 and increased variable indirection
from both branches

	src/gromacs/legacyheaders/nbnxn_cuda_data_mgmt.h
Resolved with master - both branches have now removed fplog parameter
from the free function

	src/gromacs/legacyheaders/sim_util.h
	src/gromacs/mdlib/minimize.c
	src/gromacs/mdlib/tpi.c
	src/programs/mdrun/md.c
These are text clashes between master branch runtime ->
walltime_accounting encapsulation transition, and the recently merged
release-4-6 consolidation of start-time printing. There's no code
clash, though. Resolved by using the code that works consistent with
both refactorings. The call to the print_start function has to follow
the call to the walltime_accounting_start function, of course.

Change-Id: I1559fbadfc15eb7b7e880b17e4519159ba9b534e
Merge "Merge branch 'release-4-6'"