Fix Gslib verbose output

This MR updates the version of gsmpi to fix the suppression of autotuning timings output unless the `--verbose` flag is set. There are then some modifications throughout the code to enable the use of the verbose flag.

See merge request !652

Performance fix for ExtractDataToCoeffs

This MR fixes a significant performance issue in `ExpList::v_ExtractDataToCoeffs` when post-processing large simulations. This function is called once for each field definition that is present in the input file.  Presently, this function constructs a `std::map` from geometry IDs to their location inside `m_exp`. When post-processing large simulations, where there is generally one field definition per processor in the input file, this function therefore consumes a huge amount of extraneous CPU time.

This has been fixed by adding a new member variable to hold a `boost::unordered_map` which is significantly faster in lookup and population speeds. This is populated on the first call of `v_ExtractDataToCoeffs`. Runtime of the FieldConvert InputFld module for a 700k tet mesh reduced from ~520s to ~6s.

See merge request !672

fix insert surface

Extremely minor fix to a merge from last week

See merge request !673

Feature/write-surface-stl

This output module for nekmesh takes the linear surface mesh and outputs it as a standard .stl surface triangulation format.
The stl is formatted in such a way that star-ccm can read the surface as an input and obey it when generating the 3d mesh.
This will form part of the NekMesh+star-ccm mesh generation pipeline

See merge request !668

Improve Homogeneous1D dealiasing efficiency

This MR optimizes the homogeneous dealiasing, mostly by eliminating many redundant Fourier transformations (42 regular and 12 padded per time step, if I am not mistaken...).

This also implements the case with both homogeneous and spectral/hp dealiasing.

See merge request !622

Feature/merge-surface-mesh

This merge fixes some ccmio code and adds a new module which can take the high-order information from a surface mesh and insert it into the current working mesh. This only works if the two linear surfaces match. They dont have to be the same Ids because ANN is used to find corresponding nodes.
This will be part of the MeshGen with starccm pipeline

See merge request !669

APE: Fix basefield handling

This MR introduces a continuous expansion for the APESolvers basefields. 

This fixes a bug where interpolated fields  cause the solver to diverge because currently, only discontinuities of the perturbation fields are handled in the rieman solvers.  Forcing the basefield to be continuous evades this problem, enables smoothing (in a future MR) and increases the overall stability.

This also means we have to go back to the constant c formulation which should not cause any issues since the old implementation was quite unstable anyway.

This also adds the ability to compute the CFL number to the APESolver and  adds the sourceterm to the fields written to fld files.

See merge request !664

fix/cmake-dependencies

With the creation of FieldUtils the dependencies of the libraries and utilities on each other and a little off. This fixes that.

The only major change is, because none of the utilities depend on solverutils anymore it has been made a function of NEKTAR_USE_SOLVERS. This is so that, for people like me, who don't compile the solvers, time isn't wasted compiling unnecessary libraries.

See merge request !671

Feature/boundary layer generation upgrade

This branch brings the first update to the Nekmesh mesh generation system.

The primary new feature is a complete overhaul of the boundary layer generation capability meaning boundary layers can be generated on much more complicated CAD than the convex only requirements of the old system.

It also adds new documentation to Nektar describing how to operate the mesh generator.

There is a modification to the nodal triangles in the reference elements to make the orderings consistent with what people believed nektar used. This will break some peoples meshes if they use NodalTriFekete or NodalTriElec curve face tags.

Regression tests have been added for the mesh generation.

Completed:
+ Boundary layer upgrade
+ Nodal triangle edit
+ Regression tests
+ Finish docs

See merge request !576