Merge branch 'agsalin/update-to-cime5.3' (PR #1413)

Update CIME to cime5.3

Update ACME to use CIME 5.3.x up to ESMCI hash 6156e0a from Thursday 4/13.

scripts_regression_tests and acme_developer tests pass on penn workstation.

This CIME change involves a large cosmetic change in CIME. Several directories have been renamed.

    The main interface to CIME, the scripts dir remains unchanged.
    cime/cime_config is renamed to cime/config
    The Fortran source code has been consolidated in src directory: externals, components, share, and drivers
    The driver_cpl directory has been moved to src/drivers/mct to prepare for multiple coupler options
    The share/csm_share/share directory has been renamed src/share/util.
    The cime script infrastructure source, utils/python/CIME, has moved to scripts/lib/CIME.

@singhbalwinder : please make sure PNNL cluster merge look correct
@mfdeakin-sandia : please look at cprnc/CMakeLists.txt and also confirm no run_acme changes.

Fixes #1311
Fixes #1380
Fixes #1382
Fixes #1383
Fixes #1396
Fixes #1402
Fixes #1416

[BFB]

* agsalin/update-to-cime5.3: (5649 commits)
  Fix titan problem
  Reset invalid pio_numiotasks
  Fix merge mistake
  Re-add eca testmod, was somehow lost in big merge
  Restore ACME version of shr_orb_cosz
  Fixed whitespace errors in Makefile killing COSP
  HOMME test typo fix
  Fixes to get tests to pass.
  Update ACME for new CIME directory structure
  More renaming.
  Rename ACME/cime directories in prep for CIME merge
  HOMME Improvement
  More edits to README
  Suggest a more portable usage of mktemp
  Tweak a comment
  Add comment on acme side
  Fix case for new unit_testing attribute to get_mpirun
  Allow run_tests.py to auto-determine the machine name
  fix an error
  make user-compset a seperate test
  ...

CMakeLists.txt

@@ -6,7 +6,7 @@ project(cime_tests Fortran C)
 
 # We rely on pio for cmake utilities like findnetcdf.cmake, so that we don't
 # need to duplicate this cmake code
-list(APPEND CMAKE_MODULE_PATH "${CIME_ROOT}/externals/pio2/cmake")
+list(APPEND CMAKE_MODULE_PATH "${CIME_ROOT}/src/externals/pio2/cmake")
 
 list(APPEND CMAKE_MODULE_PATH ${CIME_CMAKE_MODULE_DIRECTORY})
 include(CIME_utils)
@@ -19,7 +19,7 @@ include_directories(${NetCDF_C_INCLUDE_DIRS} ${NetCDF_Fortran_INCLUDE_DIRS})
 # ------------------------------------------------------------------------
 # Build mct
 # ------------------------------------------------------------------------
-set(MCT_ROOT "${CIME_ROOT}/externals/mct")
+set(MCT_ROOT "${CIME_ROOT}/src/externals/mct")
 
 ExternalProject_add(mct_project
   PREFIX ${CMAKE_CURRENT_BINARY_DIR}
@@ -58,14 +58,14 @@ link_directories(${CMAKE_CURRENT_BINARY_DIR}/mct/mpeu)
 
 # csm_share (we don't build it here because it seems to be built differently
 # by different tests?)
-set(SHARE_ROOT "${CIME_ROOT}/share/csm_share")
-add_subdirectory(${SHARE_ROOT}/shr csm_share)
+set(SHARE_ROOT "${CIME_ROOT}/src/share")
+add_subdirectory(${SHARE_ROOT}/util csm_share)
 include_directories(${SHARE_ROOT}/include)
 
 # esmf_wrf_timemgr not built here because it depends on csm_share.
-add_subdirectory(${CIME_ROOT}/share/esmf_wrf_timemgr esmf_wrf_timemgr)
-include_directories(${CIME_ROOT}/share/esmf_wrf_timemgr)
+add_subdirectory(${SHARE_ROOT}/esmf_wrf_timemgr esmf_wrf_timemgr)
+include_directories(${SHARE_ROOT}/esmf_wrf_timemgr)
 
 # Now the actual test directories.
-add_subdirectory(driver_cpl/unit_test)
-add_subdirectory(share/csm_share/test/unit)
+add_subdirectory(${CIME_ROOT}/src/drivers/mct/unit_test)
+add_subdirectory(${SHARE_ROOT}/test/unit)