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
Keep clang Address Sanitizer happy

Allocating 15 bytes with the 8-byte aligned memory at offset 8 of
15, would overflow the buffer, which would be fairly likely to
have no effect. But ASan notices this if you run it on AVX hardware,
unlike the Jenkins build which runs on SSE4.1. The good news is
that this fix is enough to make all the existing tests pass under
ASan on AVX.

Change-Id: I61ff11687709e096c70a162d3514227cb243561d
cmake eats slashes

Change-Id: I5ea157c4a5e9df2212643b49ba9b270ffd9a6978
Issue fatal errors rather than use broken shell code

Refs #1429

Change-Id: I18a17f1e232a86a13f4e3b591bd992702af3017b
Added safety check for fitting group in anaeig.

Previously, g_anaeig would not check the number of atoms in the selected
fit group against the number of atoms in the reference structure if this
was read from the eigenvector file (g_covar adds the reference structure
to the eigenvector file if fit and analysis group are identitcal). As a
result, anaeig would run out of bounds when selecting the atoms for
fitting, reading random values from memory.

This simple check should prevent this behaviour by terminating anaeig
with a fatal error similar to the one that is invoked if the group
selected for analysis has an incorrect number of atoms.

Change-Id: I63a1e1629144e539808d95d867e0ad0673480fdf
Merge remote-tracking branch 'gromacs/release-4-6' into release-4-6-TPI_modifications