Make JRA55 default forcing dataset (#533)

* Update test suite, add complete set of jra55 tests.

jra55 tests for different grids
  gx3 uses jra55_gx3
  gx1 uses jra55_gx1
  tx1 is already using jra55 by default (no changes to tests required)
  gbox* uses internal forcing, no jra55 data (no changes to tests required)

remove ocn_data_dir='default' and bgc_data_dir='default' in set_nml.jra55*
files because it causes the bgc tests to fail.  the bgc tests work with WOA bgc
forcing data with jra55 physics forcing data.

iobinary tests must use the old gx3 binary forcing, the jra55_gx3 netcdf data
causes an abort because iobinary is tested with netcdf turned off.  the old
gx3 data is NCAR_bulk in binary format.

alt01 with jra55 uses the alt01a setting.  the difference is that
use_leap_years is set to false in alt01a.  It's set to true by default
in the jra55 datasets.

* add wget of JRA55_gx3 forcing to travis yml

* add set_nml.alt01a

* Update options and tests to make JRA55 the default

set_nml.gx3 and set_nml.gx1 are now JRA55 by default
get rid of set_nml.jra55* files
add set_nml.gx3ncarbulk and set_nml.gx1coreii which invokes prior forcing datasets
modify the test suites to do identical tests but with new options, compare
  to prior implementation by creating a renamed regression baseline via
  a script and links to generate the new names.  Use zz* for the new set_nml
  options temporarily just to make it easy to generate the new links
  (the zz ensures the new options are last in the list by alphabet)
chmod -x all set_* files for consistency

* rename zz test options

this is done as a clean separate step so new baselines can be established to
continue to evolve the test cases and allow regression testing

* remove most old forcing test cases

* rename alt01a to alt01 in test options and suite

.travis.yml

@@ -25,7 +25,11 @@ install:
 
   # Fetch forcing data
   - "wget https://zenodo.org/record/3728362/files/CICE_data_gx3_forcing_NCAR_bulk-20200320.tar.gz &&
-    tar xvfz CICE_data_gx3_forcing_NCAR_bulk-20200320.tar.gz -C ~"
+    tar xvfz CICE_data_gx3_forcing_NCAR_bulk-20200320.tar.gz -C ~" 
+
+  # Fetch jra55_gx3 forcing data
+  - "wget https://zenodo.org/record/3728364/files/CICE_data_gx3_forcing_JRA55-20200320.tar.gz &&
+    tar xvfz CICE_data_gx3_forcing_JRA55-20200320.tar.gz -C ~" 
 
   # Mirror entire data folder
   #- "lftp ftp://anonymous:travis@travis-ci.org@ftp.cgd.ucar.edu 

configuration/scripts/options/set_nml.alt01

@@ -1,4 +1,5 @@
 nilyr = 1
+use_leap_years = .false.
 ice_ic = 'default'
 restart = .false.
 distribution_type = 'roundrobin'

configuration/scripts/options/set_nml.gx1

@@ -1,5 +1,8 @@
 dt = 3600.0
 runtype = 'initial'
+year_init      = 2005
+use_leap_years = .true.
+use_restart_time = .false.
 ice_ic  = 'ICE_MACHINE_INPUTDATA/CICE_data/ic/gx1/iced_gx1_v5.nc'
 grid_format = 'bin'
 grid_type   = 'displaced_pole'
@@ -10,11 +13,9 @@ maskhalo_dyn   = .true.
 maskhalo_remap = .true.
 maskhalo_bound = .true.
 fyear_init      = 2005
-ycycle          = 1
-atm_data_format = 'bin'
-atm_data_type   = 'LYq'
-atm_data_dir    = 'ICE_MACHINE_INPUTDATA/CICE_data/forcing/gx1/COREII'
-precip_units    = 'mm_per_sec'
+atm_data_format = 'nc'
+atm_data_type   = 'JRA55_gx1'
+atm_data_dir    = 'ICE_MACHINE_INPUTDATA/CICE_data/forcing/gx1/JRA55'
+precip_units    = 'mks'
 ocn_data_dir    = 'ICE_MACHINE_INPUTDATA/CICE_data/forcing/gx1/COREII'
 bgc_data_dir    = 'ICE_MACHINE_INPUTDATA/CICE_data/forcing/gx1/WOA/MONTHLY'
-

configuration/scripts/options/set_nml.gx1coreii

@@ -0,0 +1,9 @@
+year_init      = 1997
+use_leap_years = .false.
+use_restart_time = .true.
+fyear_init      = 2005
+ycycle          = 1
+atm_data_format = 'bin'
+atm_data_type   = 'LYq'
+atm_data_dir    = 'ICE_MACHINE_INPUTDATA/CICE_data/forcing/gx1/COREII'
+precip_units    = 'mm_per_sec'

configuration/scripts/options/set_nml.gx3

@@ -1,15 +1,18 @@
 dt = 3600.0
 runtype = 'initial'
+year_init      = 2005
+use_leap_years = .true.
+use_restart_time = .false.
 ice_ic  = 'ICE_MACHINE_INPUTDATA/CICE_data/ic/gx3/iced_gx3_v5.nc'
 grid_format = 'bin'
 grid_type   = 'displaced_pole'
 grid_file   = 'ICE_MACHINE_INPUTDATA/CICE_data/grid/gx3/grid_gx3.bin'
 kmt_file    = 'ICE_MACHINE_INPUTDATA/CICE_data/grid/gx3/kmt_gx3.bin'
 bathymetry_file = 'ICE_MACHINE_INPUTDATA/CICE_data/grid/gx3/global_gx3.bathy.nc'
-fyear_init      = 1997
-atm_data_format = 'bin'
-atm_data_type   = 'ncar'
-atm_data_dir    = 'ICE_MACHINE_INPUTDATA/CICE_data/forcing/gx3/NCAR_bulk'
+fyear_init      = 2005
+atm_data_format = 'nc'
+atm_data_type   = 'JRA55_gx3'
+atm_data_dir    = 'ICE_MACHINE_INPUTDATA/CICE_data/forcing/gx3/JRA55'
+precip_units    = 'mks'
 ocn_data_format = 'bin'
 ocn_data_dir    = 'ICE_MACHINE_INPUTDATA/CICE_data/forcing/gx3/'
-

configuration/scripts/options/set_nml.gx3ncarbulk

@@ -0,0 +1,9 @@
+year_init      = 1997
+use_leap_years = .false.
+use_restart_time = .true.
+fyear_init      = 1997
+atm_data_format = 'bin'
+atm_data_type   = 'ncar'
+atm_data_dir    = 'ICE_MACHINE_INPUTDATA/CICE_data/forcing/gx3/NCAR_bulk'
+precip_units    = 'mm_per_month'
+

configuration/scripts/options/set_nml.yi2008

@@ -0,0 +1,3 @@
+year_init      = 2008
+fyear_init      = 2008
+

configuration/scripts/tests/base_suite.ts

@@ -5,9 +5,9 @@ smoke          gx3     1x4        debug,diag1,run2day
 smoke          gx3     4x1        debug,diag1,run5day
 restart        gx3     8x2        debug
 smoke          gx3     8x2        diag24,run1year,medium
-decomp         gx3     4x2x25x29x5
-smoke          gx3     4x2        diag1,run5day          smoke_gx3_8x2_diag1_run5day
-smoke          gx3     4x1        diag1,run5day,thread   smoke_gx3_8x2_diag1_run5day
+decomp         gx3     4x2x25x29x5  none
+smoke          gx3     4x2        diag1,run5day             smoke_gx3_8x2_diag1_run5day
+smoke          gx3     4x1        diag1,run5day,thread      smoke_gx3_8x2_diag1_run5day
 restart        gx1    40x4        droundrobin,medium
 restart        tx1    40x4        dsectrobin,medium
 restart        gx3     4x4        none
@@ -33,21 +33,25 @@ smoke          gbox80  1x1        boxslotcyl
 smoke          gx3     8x2        bgcz
 smoke          gx3     8x2        bgcz,debug
 smoke          gx3     8x1        bgcskl,debug
-#smoke          gx3     4x1        bgcz,thread        smoke_gx3_8x2_bgcz
+#smoke          gx3     4x1       bgcz,thread        smoke_gx3_8x2_bgcz
 restart        gx1     4x2        bgcsklclim,medium
 restart        gx1     8x1        bgczclim,medium
-smoke          gx1    24x1        jra55_gx1_2008,medium,run90day
-smoke          gx3     8x1        jra55_gx3_2008,medium,run90day
-restart        gx1    24x1        jra55_gx1,short
-restart        gx3     8x1        jra55_gx3,short
+smoke          gx1    24x1        medium,run90day,yi2008
+smoke          gx3     8x1        medium,run90day,yi2008
+restart        gx1    24x1        short
+restart        gx3     8x1        short
 smoke          gx3     4x2        fsd1,diag24,run5day,debug
 smoke          gx3     8x2        fsd12,diag24,run5day,short
 restart        gx3     4x2        fsd12,debug,short
 smoke          gx3     8x2        fsd12ww3,diag24,run1day,medium
 smoke          gx3     4x1        isotope,debug
 restart        gx3     8x2        isotope
-restart        gx3     4x4        iobinary
+restart        gx3     4x4        gx3ncarbulk,iobinary
 restart        gx3     4x4        histall,precision8,cdf64
 smoke          gx3    30x1        bgcz,histall
 smoke          gx3    14x2        fsd12,histall
 smoke          gx3     4x1        dynpicard,medium
+
+restart        gx3     8x2        gx3ncarbulk,debug
+restart        gx3     4x4        gx3ncarbulk,diag1
+restart        gx1    24x1        gx1coreii,short

configuration/scripts/tests/decomp_suite.ts

@@ -1,6 +1,6 @@
 # Test         Grid    PEs        Sets    BFB-compare
 restart        gx3     4x2x25x29x4   dslenderX2
-decomp         gx3     4x2x25x29x5
+decomp         gx3     4x2x25x29x5   none
 sleep 30
 restart        gx3     1x1x50x58x4   droundrobin,thread restart_gx3_4x2x25x29x4_dslenderX2
 restart        gx3     4x1x25x116x1  dslenderX1,thread  restart_gx3_4x2x25x29x4_dslenderX2

configuration/scripts/tests/first_suite.ts

@@ -1,5 +1,5 @@
-# Test         Grid    PEs        Sets    BFB-compare
-smoke          gx3     8x2        diag1,run5day
+# Test         Grid    PEs           Sets       BFB-compare
+smoke          gx3     8x2           diag1,run5day
 restart        gx3     4x2x25x29x4   dslenderX2
 logbfb         gx3     4x2x25x29x4   dslenderX2,diag1,reprosum
-smoke          gx3     1x2        run2day
+smoke          gx3     1x2           run2day

configuration/scripts/tests/io_suite.ts

@@ -1,15 +1,16 @@
 # Test         Grid    PEs        Sets    BFB-compare
 # some iobinary configurations fail due to bathymetry netcdf file requirement, remove them
-restart        gx3     8x4        debug,histall,iobinary,precision8
-#restart        gx3    12x2        alt01,histall,iobinary
-restart        gx3    16x2        alt02,histall,iobinary,precision8
-#restart        gx3     4x2        alt03,histall,iobinary
-restart        gx3     8x4        alt04,histall,iobinary,precision8
-restart        gx3     4x4        alt05,histall,iobinary
-restart        gx3    32x1        bgcz,histall,iobinary,precision8
-restart        gx3    16x2        bgcskl,histall,iobinary
-restart        gx3    14x2        isotope,histall,iobinary,precision8
-restart        gx3    16x2        fsd12,histall,iobinary
+# iobinary cannot work with JRA55 because netcdf is turned off
+restart        gx3     8x4        gx3ncarbulk,debug,histall,iobinary,precision8
+#restart        gx3    12x2        gx3ncarbulk,alt01,histall,iobinary
+restart        gx3    16x2        gx3ncarbulk,alt02,histall,iobinary,precision8
+#restart        gx3     4x2        gx3ncarbulk,alt03,histall,iobinary
+restart        gx3     8x4        gx3ncarbulk,alt04,histall,iobinary,precision8
+restart        gx3     4x4        gx3ncarbulk,alt05,histall,iobinary
+restart        gx3    32x1        gx3ncarbulk,bgcz,histall,iobinary,precision8
+restart        gx3    16x2        gx3ncarbulk,bgcskl,histall,iobinary
+restart        gx3    14x2        gx3ncarbulk,isotope,histall,iobinary,precision8
+restart        gx3    16x2        gx3ncarbulk,fsd12,histall,iobinary
 
 restart        gx3    32x1        debug,histall,ionetcdf
 restart        gx3    15x2        alt01,histall,ionetcdf,precision8,cdf64

configuration/scripts/tests/nothread_quicksuite.ts

@@ -1,5 +1,4 @@
 # Test         Grid    PEs        Sets    BFB-compare
-
 restart        gx3     16x1       diag1
 smoke          gx3     1x1        debug,diag1,run2day
 smoke          gx3     4x1        debug,diag1,run2day,thread

configuration/scripts/tests/nothread_suite.ts

@@ -14,7 +14,7 @@ smoke          gx3     16x1       diag24,run1year,medium
 #restart        tx1     160x1      dsectrobin,medium
 
 restart        gx3     16x1       none
-restart        gx3     16x1       iobinary
+restart        gx3     16x1       gx3ncarbulk,iobinary
 
 restart        gx3     12x1       alt01
 restart        gx3     16x1       alt02
@@ -43,11 +43,11 @@ smoke          gbox128 24x1       boxrestore,short,debug
 restart        gbox80  1x1        box2001
 smoke          gbox80  1x1        boxslotcyl
 
-smoke          gx3     16x1        jra55_gx3_2008,medium,run90day
-restart        gx3     12x1        jra55_gx3,short
+smoke          gx3     16x1        medium,run90day,yi2008
+restart        gx3     12x1        short
 #tcraig, hangs nodes intermittently on izumi
-#smoke          gx1     24x1       jra55_gx1_2008,medium,run90day
-#restart        gx1     24x1       jra55_gx1,short
+#smoke          gx1     24x1       medium,run90day,yi2008
+#restart        gx1     24x1       short
 
 smoke          gx3     16x1       bgcz
 smoke          gx3     16x1       bgcz,debug
@@ -56,7 +56,7 @@ smoke          gx3     24x1       bgcskl,debug
 #restart        gx1     128x1      bgcsklclim,medium
 #restart        gx1     256x1      bgczclim,medium
 
-decomp         gx3     8x1x5x29x20
+decomp         gx3     8x1x5x29x20   none
 restart        gx3     1x1x50x58x4   droundrobin        restart_gx3_8x1x25x29x2_dslenderX2
 restart        gx3     4x1x25x116x1  dslenderX1         restart_gx3_8x1x25x29x2_dslenderX2
 restart        gx3     12x1x4x29x9   dspacecurve        restart_gx3_8x1x25x29x2_dslenderX2

configuration/scripts/tests/quick_suite.ts

@@ -1,6 +1,6 @@
 # Test         Grid    PEs        Sets    BFB-compare
-smoke          gx3     8x2        diag1,run5day       
-smoke          gx3     1x1        diag1,run1day       
+smoke          gx3     8x2        diag1,run5day
+smoke          gx3     1x1        diag1,run1day
 restart        gbox128 8x1        diag1
 restart        gx3     4x2        debug,diag1,run5day
 smoke          gx3     4x1        diag1,run5day,thread   smoke_gx3_8x2_diag1_run5day

configuration/scripts/tests/reprosum_suite.ts

@@ -4,8 +4,8 @@ logbfb        gx3     4x2x25x29x4   dslenderX2,diag1,reprosum
 sleep 60
 logbfb        gx3     1x1x50x58x4   droundrobin,diag1,thread,maskhalo,reprosum logbfb_gx3_4x2x25x29x4_diag1_dslenderX2_reprosum
 logbfb        gx3     4x1x25x116x1  dslenderX1,diag1,thread,maskhalo,reprosum  logbfb_gx3_4x2x25x29x4_diag1_dslenderX2_reprosum
-logbfb        gx3     1x20x5x29x80  dsectrobin,diag1,short,reprosum   logbfb_gx3_4x2x25x29x4_diag1_dslenderX2_reprosum
-logbfb        gx3     8x2x8x10x20   droundrobin,diag1,reprosum        logbfb_gx3_4x2x25x29x4_diag1_dslenderX2_reprosum
-logbfb        gx3     6x2x50x58x1   droundrobin,diag1,reprosum        logbfb_gx3_4x2x25x29x4_diag1_dslenderX2_reprosum
+logbfb        gx3     1x20x5x29x80  dsectrobin,diag1,short,reprosum            logbfb_gx3_4x2x25x29x4_diag1_dslenderX2_reprosum
+logbfb        gx3     8x2x8x10x20   droundrobin,diag1,reprosum                 logbfb_gx3_4x2x25x29x4_diag1_dslenderX2_reprosum
+logbfb        gx3     6x2x50x58x1   droundrobin,diag1,reprosum                 logbfb_gx3_4x2x25x29x4_diag1_dslenderX2_reprosum
 logbfb        gx3     6x2x4x29x18   dspacecurve,diag1,maskhalo,reprosum        logbfb_gx3_4x2x25x29x4_diag1_dslenderX2_reprosum
-#logbfb        gx3     8x2x8x10x20   droundrobin,diag1                 logbfb_gx3_4x2x25x29x4_diag1_dslenderX2
+#logbfb        gx3     8x2x8x10x20   droundrobin,diag1                          logbfb_gx3_4x2x25x29x4_diag1_dslenderX2

configuration/scripts/tests/travis_suite.ts

@@ -3,5 +3,5 @@ smoke          gx3     1x2        run2day
 smoke          gx3     1x1        debug,run1day
 smoke          gx3     2x2        debug,run1day
 smoke          gx3     2x1        run2day,thread  smoke_gx3_1x2_run2day
-restart        gx3     2x1
-restart        gx3     1x2
+restart        gx3     2x1        
+restart        gx3     1x2