Updates to build system for use in CI on Parallelworks

[laurenchilutti]

These updates allow for more flexibility in the SHiELD build system. These changes are required for CI. A summary of the changes:

• The permissions on the scripts in RTS/CI are changed to be executable
• Added an optional argument to the RTS/CI scripts. This argument is a container command e.g. --mpi=pmi2 singularity exec -B <file directory> <container>
• Some files needed to have bash headers as opposed to sh
• Kept any use of modules to the site environment files
• Updated the way LIBS and INCLUDE are set in intel.mk for netcdf. This adds support for environments where netcdf-fortran and netcdf-c are not installed into the same directory.

[laurenchilutti]

Im working on testing the changes you suggested now - for the default case you say "construct INCLUDE via NETCDF_ROOT and libs with extended lib-list" I interpret this as: INCLUDE = -I$(NETCDF_ROOT)/include LIBS += -lnetcdff -lnetcdf -lhdf5_hl -lhdf5 -lz Can you confirm this is what we should do by default?

Thanks!

[laurenchilutti]

I just pushed some changes - I have tested the intel build on parallelworks, gaea, and our AMD box.