RRTMG cloud overlap method update (#184)

- updates `.gitmodules` and the submodule pointer for fv3atm for code review and testing of the following changes in fv3atm and ccpp-physics:
    - add two new cloud overlap methods for RRTMG to ccpp-physics - see detailed description in NCAR/ccpp-physics#477.
    - add necessary variables to `GFS_typedefs.{F90,meta} and fix a few metadata entries - see NOAA-EMC/fv3atm#157
- contains changes from @DusanJovic-NOAA from branch https://github.com/DusanJovic-NOAA/ufs-weather-model/commits/update_compile_script that removes the old gnumake `compile.sh` script and replaces it with the new cmake `compile_cmake.sh` script (which is renamed to `compile.sh`)
- contains follow-up work in the regression test scripts to use `NEMS_COMPILER` throughout instead of a mixture of `NEMS_COMPILER` and `COMPILER` (note: `NEMS_COMPILER` should be renamed to something like `UFS_COMPILER` or `RT_COMPILER` in the future, along with corresponding changes for `NEMS_MACHINE` etc.)
- fixes the `readlink` command in the top-level `build.sh` and in `tests/compile.sh` for macOS (similar to what was done for branch release/public-v1
- remove lines `cp ${PATHRT}/../FV3/ccpp/suites/suite_${CCPP_SUITE}.xml suite_${CCPP_SUITE}.xml` from `tests/fv3_conf/ccpp*.IN`, i.e. no longer copy suite definition files to regression test run directories
- replace GSL drag suite with CIRES UGWP/GFS GWD in `tests/tests/fv3_ccpp_rrfs_v1beta` and `tests/tests/fv3_ccpp_rrfs_v1beta_debug` (cherry-picked from PR #205 for branch release/public-v2)

build.sh

@@ -1,7 +1,11 @@
 #!/bin/bash
 set -eu
 
-MYDIR=$(cd "$(dirname "$(readlink -f -n "${BASH_SOURCE[0]}" )" )" && pwd -P)
+if [[ $(uname -s) == Darwin ]]; then
+  readonly MYDIR=$(cd "$(dirname "$(greadlink -f -n "${BASH_SOURCE[0]}" )" )" && pwd -P)
+else
+  readonly MYDIR=$(cd "$(dirname "$(readlink -f -n "${BASH_SOURCE[0]}" )" )" && pwd -P)
+fi
 
 export CMAKE_C_COMPILER=${CMAKE_C_COMPILER:-mpicc}
 export CMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER:-mpicxx}

tests/RegressionTests_cheyenne.gnu.log

@@ -1,9 +1,9 @@
-Sat Sep 12 20:37:13 MDT 2020
+Wed Sep 23 16:39:24 MDT 2020
 Start Regression test
 
 
-baseline dir = /glade/p/ral/jntp/GMTB/ufs-weather-model/RT/NEMSfv3gfs/develop-20200914/GNU/fv3_gfdlmp_ccpp
-working dir  = /glade/scratch/heinzell/FV3_RT/rt_12235/fv3_ccpp_gfdlmp_prod
+baseline dir = /glade/p/ral/jntp/GMTB/ufs-weather-model/RT/NEMSfv3gfs/develop-20200923/GNU/fv3_gfdlmp_ccpp
+working dir  = /glade/scratch/heinzell/FV3_RT/rt_68881/fv3_ccpp_gfdlmp_prod
 Checking test 001 fv3_ccpp_gfdlmp results ....
  Comparing atmos_4xdaily.tile1.nc .........OK
  Comparing atmos_4xdaily.tile2.nc .........OK
@@ -50,8 +50,8 @@ Checking test 001 fv3_ccpp_gfdlmp results ....
 Test 001 fv3_ccpp_gfdlmp PASS
 
 
-baseline dir = /glade/p/ral/jntp/GMTB/ufs-weather-model/RT/NEMSfv3gfs/develop-20200914/GNU/fv3_gfs_v15p2_ccpp
-working dir  = /glade/scratch/heinzell/FV3_RT/rt_12235/fv3_ccpp_gfs_v15p2_prod
+baseline dir = /glade/p/ral/jntp/GMTB/ufs-weather-model/RT/NEMSfv3gfs/develop-20200923/GNU/fv3_gfs_v15p2_ccpp
+working dir  = /glade/scratch/heinzell/FV3_RT/rt_68881/fv3_ccpp_gfs_v15p2_prod
 Checking test 002 fv3_ccpp_gfs_v15p2 results ....
  Comparing atmos_4xdaily.tile1.nc .........OK
  Comparing atmos_4xdaily.tile2.nc .........OK
@@ -118,8 +118,8 @@ Checking test 002 fv3_ccpp_gfs_v15p2 results ....
 Test 002 fv3_ccpp_gfs_v15p2 PASS
 
 
-baseline dir = /glade/p/ral/jntp/GMTB/ufs-weather-model/RT/NEMSfv3gfs/develop-20200914/GNU/fv3_gfs_v16beta_ccpp
-working dir  = /glade/scratch/heinzell/FV3_RT/rt_12235/fv3_ccpp_gfs_v16beta_prod
+baseline dir = /glade/p/ral/jntp/GMTB/ufs-weather-model/RT/NEMSfv3gfs/develop-20200923/GNU/fv3_gfs_v16beta_ccpp
+working dir  = /glade/scratch/heinzell/FV3_RT/rt_68881/fv3_ccpp_gfs_v16beta_prod
 Checking test 003 fv3_ccpp_gfs_v16beta results ....
  Comparing atmos_4xdaily.tile1.nc .........OK
  Comparing atmos_4xdaily.tile2.nc .........OK
@@ -186,8 +186,8 @@ Checking test 003 fv3_ccpp_gfs_v16beta results ....
 Test 003 fv3_ccpp_gfs_v16beta PASS
 
 
-baseline dir = /glade/p/ral/jntp/GMTB/ufs-weather-model/RT/NEMSfv3gfs/develop-20200914/GNU/fv3_gfs_v16beta_flake_ccpp
-working dir  = /glade/scratch/heinzell/FV3_RT/rt_12235/fv3_ccpp_gfs_v16beta_flake_prod
+baseline dir = /glade/p/ral/jntp/GMTB/ufs-weather-model/RT/NEMSfv3gfs/develop-20200923/GNU/fv3_gfs_v16beta_flake_ccpp
+working dir  = /glade/scratch/heinzell/FV3_RT/rt_68881/fv3_ccpp_gfs_v16beta_flake_prod
 Checking test 004 fv3_ccpp_gfs_v16beta_flake results ....
  Comparing atmos_4xdaily.tile1.nc .........OK
  Comparing atmos_4xdaily.tile2.nc .........OK
@@ -254,8 +254,8 @@ Checking test 004 fv3_ccpp_gfs_v16beta_flake results ....
 Test 004 fv3_ccpp_gfs_v16beta_flake PASS
 
 
-baseline dir = /glade/p/ral/jntp/GMTB/ufs-weather-model/RT/NEMSfv3gfs/develop-20200914/GNU/fv3_gsd_ccpp
-working dir  = /glade/scratch/heinzell/FV3_RT/rt_12235/fv3_ccpp_gsd_prod
+baseline dir = /glade/p/ral/jntp/GMTB/ufs-weather-model/RT/NEMSfv3gfs/develop-20200923/GNU/fv3_gsd_ccpp
+working dir  = /glade/scratch/heinzell/FV3_RT/rt_68881/fv3_ccpp_gsd_prod
 Checking test 005 fv3_ccpp_gsd results ....
  Comparing atmos_4xdaily.tile1.nc .........OK
  Comparing atmos_4xdaily.tile2.nc .........OK
@@ -346,8 +346,8 @@ Checking test 005 fv3_ccpp_gsd results ....
 Test 005 fv3_ccpp_gsd PASS
 
 
-baseline dir = /glade/p/ral/jntp/GMTB/ufs-weather-model/RT/NEMSfv3gfs/develop-20200914/GNU/fv3_thompson_ccpp
-working dir  = /glade/scratch/heinzell/FV3_RT/rt_12235/fv3_ccpp_thompson_prod
+baseline dir = /glade/p/ral/jntp/GMTB/ufs-weather-model/RT/NEMSfv3gfs/develop-20200923/GNU/fv3_thompson_ccpp
+working dir  = /glade/scratch/heinzell/FV3_RT/rt_68881/fv3_ccpp_thompson_prod
 Checking test 006 fv3_ccpp_thompson results ....
  Comparing atmos_4xdaily.tile1.nc .........OK
  Comparing atmos_4xdaily.tile2.nc .........OK
@@ -414,8 +414,8 @@ Checking test 006 fv3_ccpp_thompson results ....
 Test 006 fv3_ccpp_thompson PASS
 
 
-baseline dir = /glade/p/ral/jntp/GMTB/ufs-weather-model/RT/NEMSfv3gfs/develop-20200914/GNU/fv3_thompson_no_aero_ccpp
-working dir  = /glade/scratch/heinzell/FV3_RT/rt_12235/fv3_ccpp_thompson_no_aero_prod
+baseline dir = /glade/p/ral/jntp/GMTB/ufs-weather-model/RT/NEMSfv3gfs/develop-20200923/GNU/fv3_thompson_no_aero_ccpp
+working dir  = /glade/scratch/heinzell/FV3_RT/rt_68881/fv3_ccpp_thompson_no_aero_prod
 Checking test 007 fv3_ccpp_thompson_no_aero results ....
  Comparing atmos_4xdaily.tile1.nc .........OK
  Comparing atmos_4xdaily.tile2.nc .........OK
@@ -482,8 +482,8 @@ Checking test 007 fv3_ccpp_thompson_no_aero results ....
 Test 007 fv3_ccpp_thompson_no_aero PASS
 
 
-baseline dir = /glade/p/ral/jntp/GMTB/ufs-weather-model/RT/NEMSfv3gfs/develop-20200914/GNU/fv3_rrfs_v1beta_ccpp
-working dir  = /glade/scratch/heinzell/FV3_RT/rt_12235/fv3_ccpp_rrfs_v1beta_prod
+baseline dir = /glade/p/ral/jntp/GMTB/ufs-weather-model/RT/NEMSfv3gfs/develop-20200923/GNU/fv3_rrfs_v1beta_ccpp
+working dir  = /glade/scratch/heinzell/FV3_RT/rt_68881/fv3_ccpp_rrfs_v1beta_prod
 Checking test 008 fv3_ccpp_rrfs_v1beta results ....
  Comparing atmos_4xdaily.tile1.nc .........OK
  Comparing atmos_4xdaily.tile2.nc .........OK
@@ -574,14 +574,14 @@ Checking test 008 fv3_ccpp_rrfs_v1beta results ....
 Test 008 fv3_ccpp_rrfs_v1beta PASS
 
 
-baseline dir = /glade/p/ral/jntp/GMTB/ufs-weather-model/RT/NEMSfv3gfs/develop-20200914/GNU/fv3_control_ccpp
-working dir  = /glade/scratch/heinzell/FV3_RT/rt_12235/fv3_ccpp_control_debug_prod
+baseline dir = /glade/p/ral/jntp/GMTB/ufs-weather-model/RT/NEMSfv3gfs/develop-20200923/GNU/fv3_control_ccpp
+working dir  = /glade/scratch/heinzell/FV3_RT/rt_68881/fv3_ccpp_control_debug_prod
 Checking test 009 fv3_ccpp_control_debug results ....
 Test 009 fv3_ccpp_control_debug PASS
 
 
-baseline dir = /glade/p/ral/jntp/GMTB/ufs-weather-model/RT/NEMSfv3gfs/develop-20200914/GNU/fv3_gfs_v15p2_debug_ccpp
-working dir  = /glade/scratch/heinzell/FV3_RT/rt_12235/fv3_ccpp_gfs_v15p2_debug_prod
+baseline dir = /glade/p/ral/jntp/GMTB/ufs-weather-model/RT/NEMSfv3gfs/develop-20200923/GNU/fv3_gfs_v15p2_debug_ccpp
+working dir  = /glade/scratch/heinzell/FV3_RT/rt_68881/fv3_ccpp_gfs_v15p2_debug_prod
 Checking test 010 fv3_ccpp_gfs_v15p2_debug results ....
  Comparing atmos_4xdaily.tile1.nc .........OK
  Comparing atmos_4xdaily.tile2.nc .........OK
@@ -648,8 +648,8 @@ Checking test 010 fv3_ccpp_gfs_v15p2_debug results ....
 Test 010 fv3_ccpp_gfs_v15p2_debug PASS
 
 
-baseline dir = /glade/p/ral/jntp/GMTB/ufs-weather-model/RT/NEMSfv3gfs/develop-20200914/GNU/fv3_gfs_v16beta_debug_ccpp
-working dir  = /glade/scratch/heinzell/FV3_RT/rt_12235/fv3_ccpp_gfs_v16beta_debug_prod
+baseline dir = /glade/p/ral/jntp/GMTB/ufs-weather-model/RT/NEMSfv3gfs/develop-20200923/GNU/fv3_gfs_v16beta_debug_ccpp
+working dir  = /glade/scratch/heinzell/FV3_RT/rt_68881/fv3_ccpp_gfs_v16beta_debug_prod
 Checking test 011 fv3_ccpp_gfs_v16beta_debug results ....
  Comparing atmos_4xdaily.tile1.nc .........OK
  Comparing atmos_4xdaily.tile2.nc .........OK
@@ -716,8 +716,8 @@ Checking test 011 fv3_ccpp_gfs_v16beta_debug results ....
 Test 011 fv3_ccpp_gfs_v16beta_debug PASS
 
 
-baseline dir = /glade/p/ral/jntp/GMTB/ufs-weather-model/RT/NEMSfv3gfs/develop-20200914/GNU/fv3_multigases_ccpp
-working dir  = /glade/scratch/heinzell/FV3_RT/rt_12235/fv3_ccpp_multigases_prod
+baseline dir = /glade/p/ral/jntp/GMTB/ufs-weather-model/RT/NEMSfv3gfs/develop-20200923/GNU/fv3_multigases_ccpp
+working dir  = /glade/scratch/heinzell/FV3_RT/rt_68881/fv3_ccpp_multigases_prod
 Checking test 012 fv3_ccpp_multigases results ....
  Comparing atmos_4xdaily.tile1.nc .........OK
  Comparing atmos_4xdaily.tile2.nc .........OK
@@ -791,5 +791,5 @@ Test 012 fv3_ccpp_multigases PASS
 
 
 REGRESSION TEST WAS SUCCESSFUL
-Sat Sep 12 20:53:15 MDT 2020
-Elapsed time: 00h:16m:03s. Have a nice day!
+Wed Sep 23 17:03:55 MDT 2020
+Elapsed time: 00h:24m:32s. Have a nice day!