Fix non-critical typo in #ifdef GMX_OMPEN_MP

Added #include to make it work.

Change-Id: Icea244c4fb63aee6ae67a29370d08177a66129a8
Fixed compilation issue due to gcc4.8

by turning off warnings.

Change-Id: Ice3dd8dec8cb9dc590fb293c1face3ed603f7abb
Fixed essential dynamics (ED) continuation from .cpt for reference=average

ED runs where the reference and average structure indices are the same can
crash when continued from checkpoint. For these cases (where reference =
average atom indices) obviously the set of atomic positions for the reference
and average structures is always identical. Therefore, only one of the two
structures is stored (which is the average structure edi->sav). When reading
the old values of these structures from the checkpoint file, edi->sav.x_old
therefore needs to be copied both to xstart and xfit in init_edsam().

Change-Id: Ieb1f029f4a927999dfb4579ee7c3bebe15071dc8
Essential dynamics: move bNeedDoEdsam evaluation to separate function

The bool variable edi->bNeedDoEdsam is used to signal whether any essential
dynamics constraints have to be evaluated for the ED group. This variable
was evaluated at the beginning of an ED simulation in write_edo_legend().
The latter is however not called if continuing from checkpoint. To
get rid of having to remember whether edi->bNeedDoEdsam was already
initialized, there is now a function bNeedDoEdsam(edi) that is evaluated
every time when called.
Also corrected a few typos.

Change-Id: Iab899a677a85ee8270354859c98cc9e5a9db34b7
Pass on default value of radstep in make_edi

This is a bugfix for make_edi when -radfix is chosen. Problem was:
if the user did not specify -radstep, then the default value of 0
was not written to the sam.edi output file. Now it is. Also
renamed "radfix" variable to "radstep" because that better reflects
what it is.

Change-Id: I0cc6ee84d42b18ee0ea6b045cdfb0c1d55d51b9f
cmake: make GMX_BUILD_OWN_FFTW work without fortran compiler

Fixes #1412

Change-Id: I4739c112630ad7e264ce314d2da0b29932ea3041
Patch for Native Client builds.

This patch contains the source changes necessary to compile Gromacs
for Native Client.  Patch is based on original work by Ivan Krasin,
additional changes from Joseph Coffland.
Also included are a few compiler warning fixes and a minor FAHCORE
tweak.

Change-Id: I085c52ff1d8e45ec8ffb8c56f5877313d6225bb2
Checkpointing fix for Native Client

Native Client doesn't allow file renames.  We can over-write output
files, however.  For checkpoints, live dangerously and skip backups.
The alternate would be to use an in-memory file system, but then we're
still screwed if the program gets killed partway through writing the
on-disk version.  Other alternates:  keep all checkpoints.

Change-Id: I952ee6436e69f015633a150f94fca65c7271c6bb
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
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
avoid mdrun crash when rdtscp is not supported

When using rdtscp, mdrun now detects at runtime whether the CPU supports
this instruction and if this is not the case, it issues a fatal error
and instructs the user to recompile mdrun for the compute host. Note
that this will happen rarely, only when cross-compiling from a newer
host for a rather old one.

Additionally, when the user manually picks AVX, we also turn on RDTSCP
as all AVX-capable CPUs support it.

Also made CMake advanced cache option for GMX_USE_RDTSCP. This replaces
the previously hidden GMX_DISTRIBUTABLE_BUILD option.

Fixes #1428

Change-Id: I8bc884ef9ea8ea4661626b60490182ae2b302648
Fix aligned store to unaligned memory

Also fixes that unaligned store was used when not necessary.

Change-Id: I44bb222a07ec0af65198667787b8673b3c6cd2e7
added gmx_is_{single,double}_precision

* allows easy detection of the precision for cmake, autotools
  without parsing the output of gmx_print_version_info (no
  cross-compile support) or the output of strings command (unix
  only)
* linking against libgmx with/out -DGMX_DOUBLE will lead to
  unpredictable segfaults

Change-Id: I472f10ae374a1f42c94c55e156b53f8905bdf098