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

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

@@ -1,22 +1,77 @@
 # Test         Grid    PEs        Sets    BFB-compare
+smoke          gx3     8x2        zzgx3ncarbulk,diag1,run5day
+smoke          gx3     1x1        zzgx3ncarbulk,debug,diag1,run2day
+smoke          gx3     1x4        zzgx3ncarbulk,debug,diag1,run2day
+smoke          gx3     4x1        zzgx3ncarbulk,debug,diag1,run5day
+restart        gx3     8x2        zzgx3ncarbulk,debug
+smoke          gx3     8x2        zzgx3ncarbulk,diag24,run1year,medium
+decomp         gx3     4x2x25x29x5  zzgx3ncarbulk
+smoke          gx3     4x2        zzgx3ncarbulk,diag1,run5day          smoke_gx3_8x2_diag1_run5day_zzgx3ncarbulk
+smoke          gx3     4x1        zzgx3ncarbulk,diag1,run5day,thread   smoke_gx3_8x2_diag1_run5day_zzgx3ncarbulk
+restart        gx1    40x4        zzgx1coreii,droundrobin,medium
+restart        tx1    40x4        dsectrobin,medium
+restart        gx3     4x4        zzgx3ncarbulk,none
+restart        gx3     6x2        zzgx3ncarbulk,alt01
+restart        gx3     8x2        zzgx3ncarbulk,alt02
+restart        gx3     4x2        zzgx3ncarbulk,alt03
+restart        gx3     4x4        zzgx3ncarbulk,alt04
+restart        gx3     4x4        zzgx3ncarbulk,alt05
+restart        gx3     6x2        zzgx3ncarbulk,alt01,debug,short
+restart        gx3     8x2        zzgx3ncarbulk,alt02,debug,short
+restart        gx3     4x2        zzgx3ncarbulk,alt03,debug,short
+smoke          gx3     4x4        zzgx3ncarbulk,alt04,debug,short
+smoke          gx3     4x4        zzgx3ncarbulk,alt05,debug,short
+restart        gbox128 4x2        short
+restart        gbox128 4x2        boxdyn,short
+restart        gbox128 4x2        boxdyn,short,debug
+restart        gbox128 2x2        boxadv,short
+smoke          gbox128 2x2        boxadv,short,debug
+restart        gbox128 4x4        boxrestore,short
+smoke          gbox128 4x4        boxrestore,short,debug
+restart        gbox80  1x1        box2001
+smoke          gbox80  1x1        boxslotcyl
+smoke          gx3     8x2        zzgx3ncarbulk,bgcz
+smoke          gx3     8x2        zzgx3ncarbulk,bgcz,debug
+smoke          gx3     8x1        zzgx3ncarbulk,bgcskl,debug
+#smoke          gx3     4x1        zzgx3ncarbulk,bgcz,thread        smoke_gx3_8x2_bgcz_zzgx3ncarbulk
+restart        gx1     4x2        zzgx1coreii,bgcsklclim,medium
+restart        gx1     8x1        zzgx1coreii,bgczclim,medium
+smoke          gx1    24x1        zzgx1coreii,medium,run90day
+smoke          gx3     8x1        zzgx3ncarbulk,medium,run90day
+restart        gx1    24x1        zzgx1coreii,short
+restart        gx3     8x1        zzgx3ncarbulk,short
+smoke          gx3     4x2        zzgx3ncarbulk,fsd1,diag24,run5day,debug
+smoke          gx3     8x2        zzgx3ncarbulk,fsd12,diag24,run5day,short
+restart        gx3     4x2        zzgx3ncarbulk,fsd12,debug,short
+smoke          gx3     8x2        zzgx3ncarbulk,fsd12ww3,diag24,run1day,medium
+smoke          gx3     4x1        zzgx3ncarbulk,isotope,debug
+restart        gx3     8x2        zzgx3ncarbulk,isotope
+restart        gx3     4x4        zzgx3ncarbulk,iobinary
+restart        gx3     4x4        zzgx3ncarbulk,histall,precision8,cdf64
+smoke          gx3    30x1        zzgx3ncarbulk,bgcz,histall
+smoke          gx3    14x2        zzgx3ncarbulk,fsd12,histall
+smoke          gx3     4x1        zzgx3ncarbulk,dynpicard,medium
+
+# jra55
+# Test         Grid    PEs        Sets    BFB-compare
 smoke          gx3     8x2        diag1,run5day
 smoke          gx3     1x1        debug,diag1,run2day
 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
-restart        gx3     6x2        alt01
+restart        gx3     6x2        alt01a
 restart        gx3     8x2        alt02
 restart        gx3     4x2        alt03
 restart        gx3     4x4        alt04
 restart        gx3     4x4        alt05
-restart        gx3     6x2        alt01,debug,short
+restart        gx3     6x2        alt01a,debug,short
 restart        gx3     8x2        alt02,debug,short
 restart        gx3     4x2        alt03,debug,short
 smoke          gx3     4x4        alt04,debug,short
@@ -33,76 +88,21 @@ 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,zzyi2008
+smoke          gx3     8x1        medium,run90day,zzyi2008
+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        zzgx3ncarbulk,iobinary
 restart        gx3     4x4        histall,precision8,cdf64
 smoke          gx3    30x1        bgcz,histall
 smoke          gx3    14x2        fsd12,histall
 smoke          gx3     4x1        dynpicard,medium
-
-# jra55
-# Test         Grid    PEs        Sets    BFB-compare
-smoke          gx3     8x2        jra55_gx3,diag1,run5day
-smoke          gx3     1x1        jra55_gx3,debug,diag1,run2day
-smoke          gx3     1x4        jra55_gx3,debug,diag1,run2day
-smoke          gx3     4x1        jra55_gx3,debug,diag1,run5day
-restart        gx3     8x2        jra55_gx3,debug
-smoke          gx3     8x2        jra55_gx3,diag24,run1year,medium
-decomp         gx3     4x2x25x29x5  jra55_gx3
-smoke          gx3     4x2        jra55_gx3,diag1,run5day   smoke_gx3_8x2_diag1_jra55_gx3_run5day
-smoke          gx3     4x1        jra55_gx3,diag1,run5day,thread      smoke_gx3_8x2_diag1_jra55_gx3_run5day
-restart        gx1    40x4        jra55_gx1,droundrobin,medium
-restart        tx1    40x4        dsectrobin,medium
-restart        gx3     4x4        jra55_gx3,none
-restart        gx3     6x2        jra55_gx3,alt01a
-restart        gx3     8x2        jra55_gx3,alt02
-restart        gx3     4x2        jra55_gx3,alt03
-restart        gx3     4x4        jra55_gx3,alt04
-restart        gx3     4x4        jra55_gx3,alt05
-restart        gx3     6x2        jra55_gx3,alt01a,debug,short
-restart        gx3     8x2        jra55_gx3,alt02,debug,short
-restart        gx3     4x2        jra55_gx3,alt03,debug,short
-smoke          gx3     4x4        jra55_gx3,alt04,debug,short
-smoke          gx3     4x4        jra55_gx3,alt05,debug,short
-restart        gbox128 4x2        short
-restart        gbox128 4x2        boxdyn,short
-restart        gbox128 4x2        boxdyn,short,debug
-restart        gbox128 2x2        boxadv,short
-smoke          gbox128 2x2        boxadv,short,debug
-restart        gbox128 4x4        boxrestore,short
-smoke          gbox128 4x4        boxrestore,short,debug
-restart        gbox80  1x1        box2001
-smoke          gbox80  1x1        boxslotcyl
-smoke          gx3     8x2        jra55_gx3,bgcz
-smoke          gx3     8x2        jra55_gx3,bgcz,debug
-smoke          gx3     8x1        jra55_gx3,bgcskl,debug
-#smoke          gx3     4x1       jra55_gx3,bgcz,thread        smoke_gx3_8x2_bgcz
-restart        gx1     4x2        jra55_gx1,bgcsklclim,medium
-restart        gx1     8x1        jra55_gx1,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          gx3     4x2        jra55_gx3,fsd1,diag24,run5day,debug
-smoke          gx3     8x2        jra55_gx3,fsd12,diag24,run5day,short
-restart        gx3     4x2        jra55_gx3,fsd12,debug,short
-smoke          gx3     8x2        jra55_gx3,fsd12ww3,diag24,run1day,medium
-smoke          gx3     4x1        jra55_gx3,isotope,debug
-restart        gx3     8x2        jra55_gx3,isotope
-restart        gx3     4x4        iobinary
-restart        gx3     4x4        jra55_gx3,histall,precision8,cdf64
-smoke          gx3    30x1        jra55_gx3,bgcz,histall
-smoke          gx3    14x2        jra55_gx3,fsd12,histall
-smoke          gx3     4x1        jra55_gx3,dynpicard,medium

configuration/scripts/tests/decomp_suite.ts

@@ -1,6 +1,22 @@
 # Test         Grid    PEs        Sets    BFB-compare
+restart        gx3     4x2x25x29x4   zzgx3ncarbulk,dslenderX2
+decomp         gx3     4x2x25x29x5   zzgx3ncarbulk
+sleep 30
+restart        gx3     1x1x50x58x4   zzgx3ncarbulk,droundrobin,thread restart_gx3_4x2x25x29x4_dslenderX2_zzgx3ncarbulk
+restart        gx3     4x1x25x116x1  zzgx3ncarbulk,dslenderX1,thread  restart_gx3_4x2x25x29x4_dslenderX2_zzgx3ncarbulk
+restart        gx3     6x2x4x29x18   zzgx3ncarbulk,dspacecurve        restart_gx3_4x2x25x29x4_dslenderX2_zzgx3ncarbulk
+restart        gx3     8x2x8x10x20   zzgx3ncarbulk,droundrobin        restart_gx3_4x2x25x29x4_dslenderX2_zzgx3ncarbulk
+restart        gx3     6x2x50x58x1   zzgx3ncarbulk,droundrobin        restart_gx3_4x2x25x29x4_dslenderX2_zzgx3ncarbulk
+restart        gx3     4x2x19x19x10  zzgx3ncarbulk,droundrobin        restart_gx3_4x2x25x29x4_dslenderX2_zzgx3ncarbulk
+restart        gx3     1x20x5x29x80  zzgx3ncarbulk,dsectrobin,short   restart_gx3_4x2x25x29x4_dslenderX2_zzgx3ncarbulk
+restart        gx3     16x2x5x10x20  zzgx3ncarbulk,drakeX2            restart_gx3_4x2x25x29x4_dslenderX2_zzgx3ncarbulk
+restart        gx3     8x2x8x10x20   zzgx3ncarbulk,droundrobin,maskhalo   restart_gx3_4x2x25x29x4_dslenderX2_zzgx3ncarbulk
+restart        gx3     1x4x25x29x16  zzgx3ncarbulk,droundrobin        restart_gx3_4x2x25x29x4_dslenderX2_zzgx3ncarbulk
+
+# jra55
+# 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
@@ -13,19 +29,3 @@ restart        gx3     16x2x5x10x20  drakeX2            restart_gx3_4x2x25x29x4_
 restart        gx3     8x2x8x10x20   droundrobin,maskhalo   restart_gx3_4x2x25x29x4_dslenderX2
 restart        gx3     1x4x25x29x16  droundrobin        restart_gx3_4x2x25x29x4_dslenderX2
 
-# jra55
-# Test         Grid    PEs        Sets    BFB-compare
-restart        gx3     4x2x25x29x4   jra55_gx3,dslenderX2
-decomp         gx3     4x2x25x29x5   jra55_gx3
-sleep 30
-restart        gx3     1x1x50x58x4   jra55_gx3,droundrobin,thread restart_gx3_4x2x25x29x4_dslenderX2_jra55_gx3
-restart        gx3     4x1x25x116x1  jra55_gx3,dslenderX1,thread  restart_gx3_4x2x25x29x4_dslenderX2_jra55_gx3
-restart        gx3     6x2x4x29x18   jra55_gx3,dspacecurve        restart_gx3_4x2x25x29x4_dslenderX2_jra55_gx3
-restart        gx3     8x2x8x10x20   jra55_gx3,droundrobin        restart_gx3_4x2x25x29x4_dslenderX2_jra55_gx3
-restart        gx3     6x2x50x58x1   jra55_gx3,droundrobin        restart_gx3_4x2x25x29x4_dslenderX2_jra55_gx3
-restart        gx3     4x2x19x19x10  jra55_gx3,droundrobin        restart_gx3_4x2x25x29x4_dslenderX2_jra55_gx3
-restart        gx3     1x20x5x29x80  jra55_gx3,dsectrobin,short   restart_gx3_4x2x25x29x4_dslenderX2_jra55_gx3
-restart        gx3     16x2x5x10x20  jra55_gx3,drakeX2            restart_gx3_4x2x25x29x4_dslenderX2_jra55_gx3
-restart        gx3     8x2x8x10x20   jra55_gx3,droundrobin,maskhalo   restart_gx3_4x2x25x29x4_dslenderX2_jra55_gx3
-restart        gx3     1x4x25x29x16  jra55_gx3,droundrobin        restart_gx3_4x2x25x29x4_dslenderX2_jra55_gx3
-