fix/3d-boundary-layers

Recent merge of feature/mesh_spacing broke a number of parts of the mesh generation, mostly do with orientation.

The CAD orientation routines have now been rewritten in this branch and the relevant code updated.

3 more regression tests, which didnt work prior to this fix, have been added

A small amount of wall time optimisation has been done to the OCC cad interface and the reduction of some L0 asserts to L1.

See merge request !744

tidy/warnings

This gets rid of all the compile warnings for the buildbot "full" equivalent on ubuntu 16.04, mac and the compute nodes.

See merge request !743

Fix/PetSc_mkl

this fixes blas/lapack detection of the PetSc configuration for systems which have no native blas/lapack installed

When native blas/lapack is enabled, we use this for PetSc (just like before, now we just do it explicitly and not by accident) , when MKL is enabled we use MKL and for all other cases, PetSc will download its own blas/lapack and compile it itself. This might be extended to ACML and other blas/lapack providers in the future but i can only test native and MKL on my systems.

See merge request !740

feature/thirdpartylibs

Add thirdparty installs to fortran compiled libraries.

Done:
blas/lapack

See merge request !732

Fix/fc interpolator

Provide a fix for the interpolator in FieldUtils which currently using the wrong offset to place interpolated points back into the new field. This is mainly a problem when quad elements are listed before tri elements since this automatically leads to the incorrect offset. This would have not been a problem if tris went before quads. This MR also therefore adds in a regression test for this case.

See merge request !746

Cell model translator for cardiac solver.

This adds a python utility for generating cell model code from CellML models.

See merge request !723

Fix/test fail dump output

This MR fixes the issue of the tester not producing output when a test executable segfaults or other system error occurs.

It also adds an option to generate a hostfile which explicitly specifies the maximum number of required slots when running MPI executables, since newer versions of OpenMPI now stop jobs requesting more than the number of available CPU cores by default (which causes our buildbot to fail).

See merge request !745

Add fix for PETSc detection on Debian 9/Ubuntu 16.04

This MR fixes a problem with detecting PETSc with later Debian/PETSc packages, which is currently preventing the Debian 9 buildbot from compiling properly.

See merge request !735