Added generation of glint_io.F90 and glint_mbal_io.F90.


git-svn-id: https://svn-cism-model.cgd.ucar.edu/glimmer-cism2/branches/seacism@1637 2cfc7cc4-626f-0410-8325-f6cb4dace9bf

Former-commit-id: d3c9297042325a30fa91c6df080d41da9716ba42
Cmake file used to guild glint_example program.


git-svn-id: https://svn-cism-model.cgd.ucar.edu/glimmer-cism2/branches/seacism@1638 2cfc7cc4-626f-0410-8325-f6cb4dace9bf

Former-commit-id: 6cb44ae5943768859b0c23676983b3366b1d62c9
Added CISM_COUPLED variable, to set options for a CISM build to be linked with CESM.
Removed some extraneous definition lines.


git-svn-id: https://svn-cism-model.cgd.ucar.edu/glimmer-cism2/branches/seacism@1639 2cfc7cc4-626f-0410-8325-f6cb4dace9bf

Former-commit-id: b34824ed47053924c6537eda59e43ae0131350be
Added CISM_COUPLED, which sets CISM build options for linking with CESM. Added
glint_example program build.  Fixed some link and include calls. 


git-svn-id: https://svn-cism-model.cgd.ucar.edu/glimmer-cism2/branches/seacism@1640 2cfc7cc4-626f-0410-8325-f6cb4dace9bf

Former-commit-id: a3f5ef9bcd0ecfe1a327d7ade686802eb9455b35
Modified to accommodate the CESM-coupled build. If CISM COUPLED is ON, the
new autogenerate-script-no-io-srcs will be called. Added some input variable
error checking. 


git-svn-id: https://svn-cism-model.cgd.ucar.edu/glimmer-cism2/branches/seacism@1641 2cfc7cc4-626f-0410-8325-f6cb4dace9bf

Former-commit-id: 45547f63dd1e1e4ba05e300c810ca6c66f2d2d88
In autogenerate-script, separated straight file copy commands for *io.F90 generation commands.
The script autogenerate-script-no-io-srcs only does the 2 straight copy commands.


git-svn-id: https://svn-cism-model.cgd.ucar.edu/glimmer-cism2/branches/seacism@1642 2cfc7cc4-626f-0410-8325-f6cb4dace9bf

Former-commit-id: cb8c1abd4aee22c684451a247de1fead9c999a2b
Removed unneeded call to autogenerate-script.


git-svn-id: https://svn-cism-model.cgd.ucar.edu/glimmer-cism2/branches/seacism@1643 2cfc7cc4-626f-0410-8325-f6cb4dace9bf

Former-commit-id: 7542bb55a67ecd1154b2560d3b5c48eedb79c8d5
In autogenerate scripts, using 'cp -p' rather than just 'cp'. This
preserves the file's modification time, which prevents files from
needing to be rebuilt if you haven't changed anything, thus speeding
up the rebuild time.


git-svn-id: https://svn-cism-model.cgd.ucar.edu/glimmer-cism2/branches/seacism@1646 2cfc7cc4-626f-0410-8325-f6cb4dace9bf

Former-commit-id: 61aa6a8379e0f970d846f9c7718969c70b757a24
fix use of GLIMMER_SOURCEMOD_DIR (used for cesm builds)

git-svn-id: https://svn-cism-model.cgd.ucar.edu/glimmer-cism2/branches/seacism@1647 2cfc7cc4-626f-0410-8325-f6cb4dace9bf

Former-commit-id: 0dc5d1df3780f9e5bfe934431a868b459f52eb72
Generates the *io.F90 files in the build dir, under fortran_autogen_srcs, instead
of in-place in the dirrerent source dirs.  This needed for the CESM-coupled version
of the CISM build.


git-svn-id: https://svn-cism-model.cgd.ucar.edu/glimmer-cism2/branches/seacism@1648 2cfc7cc4-626f-0410-8325-f6cb4dace9bf

Former-commit-id: a80a5e8816554f512d5a2454e8c9fb72c7f33d85
Added call to autogenerate-in-biuld-dir, when CISM_COUPLED is set. This
creates the *io.F90 files in the build dir, under fortran_autogen_srcs.
These are added to the list of files to compile, and the corresponding files
from the source dirs, e.g. glide_io.F90, are removed from the compilation list.


git-svn-id: https://svn-cism-model.cgd.ucar.edu/glimmer-cism2/branches/seacism@1649 2cfc7cc4-626f-0410-8325-f6cb4dace9bf

Former-commit-id: 8634ef488115fd96527f36fbe0cdaaf13e587468
a small but important change to the master build script on hopper

git-svn-id: https://svn-cism-model.cgd.ucar.edu/glimmer-cism2/branches/seacism@1650 2cfc7cc4-626f-0410-8325-f6cb4dace9bf

Former-commit-id: 1b1ed5f1d918f7c755c015d67961c028197af843
removed suffix logic from simple_glide timers, as per MJH's request, and updated a few timer names

git-svn-id: https://svn-cism-model.cgd.ucar.edu/glimmer-cism2/branches/seacism@1651 2cfc7cc4-626f-0410-8325-f6cb4dace9bf

Former-commit-id: 01ee2ad41ae1d5b319330dc2f2079be6c3b5b52e
Allow user to specify CMAKE_Fortran_MODULE_DIRECTORY in cmake call (helps with CESM build)

git-svn-id: https://svn-cism-model.cgd.ucar.edu/glimmer-cism2/branches/seacism@1652 2cfc7cc4-626f-0410-8325-f6cb4dace9bf

Former-commit-id: 706ddfc09986277ad1b581e1893d3447ac40e82e
fix cmake syntax

git-svn-id: https://svn-cism-model.cgd.ucar.edu/glimmer-cism2/branches/seacism@1653 2cfc7cc4-626f-0410-8325-f6cb4dace9bf

Former-commit-id: 60aabf9262aaabcbfbd8e359e4ecbbafd5771992
updating performance timers in Picard nonlinear solver code

git-svn-id: https://svn-cism-model.cgd.ucar.edu/glimmer-cism2/branches/seacism@1654 2cfc7cc4-626f-0410-8325-f6cb4dace9bf

Former-commit-id: 0d3825f4e6488471b45c18721ed75740bf88d2a7
Changing install path for Trilinos' jaguar cmake script to be "install" subdirectory.


git-svn-id: https://svn-cism-model.cgd.ucar.edu/glimmer-cism2/branches/seacism@1655 2cfc7cc4-626f-0410-8325-f6cb4dace9bf

Former-commit-id: af332d9ccff486d820d3f46b7a645067cfb71749
Added or modified scripts to support CESM-coupled build.  This includes keeping all changed files out
of the source tree, instead putting them in the build directory.
  
1) autogenerate-in-build-dir -- now only makes *_.F90 files in <build_dir>/fortran_autogen_srcs.

2) autocopy-to-build-dir copies config.inc to <build_dir>/fortran_autocopy_includes,
   and copies libglimmer/glimmer_vers.F90.cmake.in to <build_dir>/fortran_autogen_srcs/glimmer_vers.F90.

3) autogen-extras-in-build-dir  makes *_.F90 files for the 'extra' executables, currently eis_glide, and
   puts them in in <build_dir>/fortran_autogen_srcs  


git-svn-id: https://svn-cism-model.cgd.ucar.edu/glimmer-cism2/branches/seacism@1656 2cfc7cc4-626f-0410-8325-f6cb4dace9bf

Former-commit-id: f21be4821459e176a57e7647cf1ff8464c982dbf
Modified to better accommodate the CESM-coupled build, including putting all
modified files in the build directory, instead of writing them to the source tree.
This is done with the cmake-scripts/auto* just committed.  There is still a
small issue with correctly handling creation and use of glint_io.F90 and
glint_mbal_io.F90, that I need to resolve.  This shouldn't cause anyone
problems.  Let me know if you do have any problems with this version of
CMakeLists.txt.


git-svn-id: https://svn-cism-model.cgd.ucar.edu/glimmer-cism2/branches/seacism@1657 2cfc7cc4-626f-0410-8325-f6cb4dace9bf

Former-commit-id: c3f8ad8eefacc7ceaf102399a4c761d84554cc66
Add ability to use default i/o files rather than running python
script, needed for CESM build. I have added some default i/o files by
copying the files that were autogenerated by the python script in a
recent build.

Also, reworked how the FORTRAN_AUTOGEN_SOURCES are added to the
FORTRANSOURCES list in the cmake build, in a way that allows these to
be overridden by CESM SourceMods. The new method involves explicitly
specifying all of the sources that could possibly end up in
FORTRAN_AUTOGEN_SOURCES. While this is not very maintainable, we
should be able to remove it once people are no longer using
directories in which they have done autotools-based builds or older
cmake-based builds. (It would be possible to change this logic so that
it is more dynamic, similar to how SOURCEMODs are handled, but that
would involve adding some ugly logic for something that is only meant
as a short-term workaround.)

Tested 4 builds on hopper (all cmake builds):
- gnu from a clean checkout
- pgi from a clean checkout
- gnu from a directory that had old autogenerated files in-source
- pgi from a directory that had old autogenerated files in-source


git-svn-id: https://svn-cism-model.cgd.ucar.edu/glimmer-cism2/branches/seacism@1658 2cfc7cc4-626f-0410-8325-f6cb4dace9bf

Former-commit-id: c3fd5d59bf1f3cd1c32a4fdf5cceecf6a0c697b6