dtc/develop: merge gsd/develop, allow environment variable NEMS_MACHINE to overwrite (or set) MACHINE_ID

.gitmodules

@@ -12,8 +12,8 @@
 	branch = GFS-FMS
 [submodule "WW3"]
 	path = WW3
-	url = https://github.com/NCAR/gmtb-ww3
-	branch = dtc/develop
+	url = https://github.com/NOAA-EMC/WW3
+	branch = develop
 [submodule "stochastic_physics"]
 	path = stochastic_physics
 	url = https://github.com/noaa-psd/stochastic_physics

parm/ccpp_gsd_sar-model_configure.IN

@@ -0,0 +1,48 @@
+total_member:            1
+PE_MEMBER01:             840
+start_year:              2019
+start_month:             07
+start_day:               12
+start_hour:              12
+start_minute:            0
+start_second:            0
+nhours_fcst:             3
+RUN_CONTINUE:            .false.
+ENS_SPS:                 .false.
+dt_atmos:                50
+cpl:                     .false.
+calendar:                'julian'
+memuse_verbose:          .false.
+atmos_nthreads:          2
+use_hyper_thread:        .false.
+ncores_per_node:         24
+debug_affinity:          .true.
+restart_interval:        0
+output_1st_tstep_rst:    .false.
+quilting:                .true.
+print_esmf:              .false.
+
+write_groups:            1
+write_tasks_per_group:   24
+num_files:               2
+filename_base:           'dyn''phy'
+output_file:             'netcdf'
+write_nemsioflip:        .false.
+write_fsyncflag:         .false.
+
+output_grid:             'lambert_conformal'
+cen_lon:                 -97.5
+cen_lat:                 38.5
+stdlat1:                 38.5
+stdlat2:                 38.5
+nx:                      1738
+ny:                      974
+lon1:                    -122.21414225
+lat1:                    22.41403305
+dx:                      3000.0
+dy:                      3000.0
+
+nfhout:                  1
+nfhmax_hf:               60
+nfhout_hf:               1
+nsout:                   -1

parm/ccpp_gsd_sar.nml.IN

@@ -0,0 +1,296 @@
+&amip_interp_nml
+       interp_oi_sst = .true.
+       use_ncep_sst = .true.
+       use_ncep_ice = .false.
+       no_anom_sst = .false.
+       data_set = 'reynolds_oi',
+       date_out_of_range = 'climo',
+/
+
+&atmos_model_nml
+       blocksize = 32
+       chksum_debug = .false.
+       dycore_only = .false.
+       fdiag = 3
+       ccpp_suite = 'FV3_GSD_SAR'
+/
+
+&diag_manager_nml
+       prepend_date = .F.
+/
+
+&fms_io_nml
+       checksum_required   = .false.
+       max_files_r = 100,
+       max_files_w = 100,
+/
+
+&fms_nml
+       clock_grain = 'ROUTINE',
+       domains_stack_size = 2000200,
+       print_memory_usage = .false.
+/
+
+&fv_grid_nml
+       grid_file = 'INPUT/grid_spec.nc'
+/
+
+ &fv_core_nml
+       layout   = 34,24
+       io_layout = 1,1
+       npx      = 1735
+       npy      = 1009
+       ntiles   = 1,
+       npz    = 64
+       !grid_type = -1
+       make_nh = .T.
+       fv_debug = .T.
+       range_warn = .T.
+       reset_eta = .F.
+       n_sponge = 24
+       nudge_qv = .F.
+       tau = 5.
+       rf_cutoff = 20.e2
+       d2_bg_k1 = 0.20
+       d2_bg_k2 = 0.04
+       kord_tm = -11
+       kord_mt =  11
+       kord_wz =  11
+       kord_tr =  11
+       hydrostatic = .F.
+       phys_hydrostatic = .F.
+       use_hydro_pressure = .F.
+       beta = 0.
+       a_imp = 1.
+       p_fac = 0.1
+       k_split  = 4
+       n_split  = 5
+       nwat = 6
+       na_init = 1
+       d_ext = 0.0
+       dnats = 0
+       fv_sg_adj = 300
+       d2_bg = 0.
+       nord =  2
+       dddmp = 0.1
+       d4_bg = 0.12
+       vtdm4 = 0.02
+       ke_bg = 0.
+       do_vort_damp = .true.
+       external_ic = .T.
+       external_eta = .T.
+       gfs_phil = .false.
+       nggps_ic = .T.
+       mountain = .F.
+       ncep_ic = .F.
+       d_con = 1.0
+       delt_max = 0.002
+       hord_mt = 6
+       hord_vt = 6
+       hord_tm = 6
+       hord_dp = -6
+       hord_tr = 8
+       adjust_dry_mass = .F.
+       consv_te = 0.
+       do_sat_adj = .F.
+       consv_am = .F.
+       fill = .T.
+       dwind_2d = .F.
+       print_freq = 6
+       warm_start = .F.
+       no_dycore = .false.
+       z_tracer = .T.
+       read_increment = .F.
+       res_latlon_dynamics = "fv3_increment.nc"
+
+       do_schmidt = .true.
+       target_lat = 38.5
+       target_lon = -97.5
+       stretch_fac = 0.999
+!!     nord_zs_filter = 4
+       n_zs_filter = 0
+       regional = .true.
+       bc_update_interval = 3
+
+       full_zs_filter = .F. !unreleased feature
+
+       nord_zs_filter = 4
+       n_zs_filter = 0 ! safety
+/
+
+&surf_map_nml
+    zero_ocean = .F.
+    cd4 = 0.12
+    cd2 = -1
+    n_del2_strong = 0
+    n_del2_weak = 2
+    n_del4 = 1
+    max_slope = 0.4
+    peak_fac = 1.
+/
+
+&external_ic_nml
+       filtered_terrain = .true.
+       levp = 65
+       gfs_dwinds = .true.
+       checker_tr = .F.
+       nt_checker = 0
+/
+
+&gfs_physics_nml
+       fhzero         = 6.
+       h2o_phys       = .true.
+       ldiag3d        = .false.
+       fhcyc          = 0
+       nst_anl        = .true.
+       use_ufo        = .true.
+       pre_rad        = .false.
+       ncld           = 5
+       imp_physics    = 8
+       ttendlim       = 0.005
+       ltaerosol      = .T.
+       lradar         = .T.
+       pdfcld         = .false.
+       fhswr          = 3600.
+       fhlwr          = 3600.
+       ialb           = 1
+       iems           = 1
+       iaer           = 111
+       ico2           = 2
+       isubc_sw       = 2
+       isubc_lw       = 2
+       isol           = 2
+       lwhtr          = .true.
+       swhtr          = .true.
+       cnvgwd         = .false.
+       shal_cnv       = .false.
+       cal_pre        = .false.
+       redrag         = .true.
+       dspheat        = .true.
+       hybedmf        = .F.
+       satmedmf       = .false.
+       lheatstrg      = .F.
+       do_mynnedmf    = .T.
+       do_mynnsfclay  = .false.
+       random_clds    = .false.
+       trans_trac     = .true.
+       cnvcld         = .false.
+       imfshalcnv     = 0
+       imfdeepcnv     = 0
+       cdmbgwd        = 3.5,0.25
+       prslrd0        = 0.
+       ivegsrc        = 1
+       isot           = 1
+       debug          = .false.
+       oz_phys        = .false.
+       oz_phys_2015   = .true.
+       nstf_name      = 2,1,1,0,5
+       cplflx         = .F.
+       iau_delthrs    = 6
+       iaufhrs        = 30
+       iau_inc_files  = ''
+       do_sppt        = .F.
+       do_shum        = .F.
+       do_skeb        = .F.
+       do_sfcperts    = .F.
+       lsm            = 3
+       lsoil          = 4
+       lsoil_lsm      = 9
+       iopt_dveg      = 2
+       iopt_crs       = 1
+       iopt_btr       = 1
+       iopt_run       = 1
+       iopt_sfc       = 1
+       iopt_frz       = 1
+       iopt_inf       = 1
+       iopt_rad       = 1
+       iopt_alb       = 2
+       iopt_snf       = 4
+       iopt_tbot      = 2
+       iopt_stc       = 1
+       icloud_bl         = 1
+       bl_mynn_tkeadvect = .true.
+       bl_mynn_edmf      = 1
+       bl_mynn_edmf_mom  = 1
+/
+
+&interpolator_nml
+       interp_method = 'conserve_great_circle'
+/
+
+&namsfc
+       FNGLAC   = "global_glacier.2x2.grb",
+       FNMXIC   = "global_maxice.2x2.grb",
+       FNTSFC   = "RTGSST.1982.2012.monthly.clim.grb",
+       FNSNOC   = "global_snoclim.1.875.grb",
+       FNZORC   = "igbp",
+       FNALBC   = "global_snowfree_albedo.bosu.t126.384.190.rg.grb",
+       FNALBC2  = "global_albedo4.1x1.grb",
+       FNAISC   = "CFSR.SEAICE.1982.2012.monthly.clim.grb",
+       FNTG3C   = "global_tg3clim.2.6x1.5.grb",
+       FNVEGC   = "global_vegfrac.0.144.decpercent.grb",
+       FNVETC   = "global_vegtype.igbp.t126.384.190.rg.grb",
+       FNSOTC   = "global_soiltype.statsgo.t126.384.190.rg.grb",
+       FNSMCC   = "global_soilmgldas.t126.384.190.grb",
+       FNMSKH   = "seaice_newland.grb",
+       FNTSFA   = "",
+       FNACNA   = "",
+       FNSNOA   = "",
+       FNVMNC   = "global_shdmin.0.144x0.144.grb",
+       FNVMXC   = "global_shdmax.0.144x0.144.grb",
+       FNSLPC   = "global_slope.1x1.grb",
+       FNABSC   = "global_mxsnoalb.uariz.t126.384.190.rg.grb",
+       LDEBUG   =.false.,
+       FSMCL(2) = 99999
+       FSMCL(3) = 99999
+       FSMCL(4) = 99999
+       FTSFS    = 90
+       FAISS    = 99999
+       FSNOL    = 99999
+       FSICL    = 99999
+       FTSFL    = 99999,
+       FAISL    = 99999,
+       FVETL    = 99999,
+       FSOTL    = 99999,
+       FvmnL    = 99999,
+       FvmxL    = 99999,
+       FSLPL    = 99999,
+       FABSL    = 99999,
+       FSNOS    = 99999,
+       FSICS    = 99999,
+/
+&nam_stochy
+  lon_s=768,
+  lat_s=384, 
+  ntrunc=382,
+  SKEBNORM=1,
+  SKEB_NPASS=30,
+  SKEB_VDOF=5,
+  SKEB=@[SKEB],
+  SKEB_TAU=2.16E4,
+  SKEB_LSCALE=1000.E3,
+  SHUM=@[SHUM],
+  SHUM_TAU=21600,
+  SHUM_LSCALE=500000,
+  SPPT=@[SPPT],
+  SPPT_TAU=21600,
+  SPPT_LSCALE=500000,
+  SPPT_LOGIT=.TRUE.,
+  SPPT_SFCLIMIT=.TRUE.,
+  ISEED_SHUM=1,
+  ISEED_SKEB=2,
+  ISEED_SPPT=3,
+/
+&nam_sfcperts
+  NSFCPERT=6,
+  PERTZ0=-999.,
+  PERTSHC=-999.,
+  PERTZT=-999.,
+  PERTLAI=-999.,
+  PERTVEGF=-999.,
+  PERTALB=-999.,
+  SFC_TAU=21600,
+  SFC_LSCALE=500000,
+  ISEED_SFC=0,
+  SPPT_LAND=.FALSE.,
+/

tests/detect_machine.sh

@@ -122,6 +122,9 @@ case $(hostname -f) in
   login4.stampede2.tacc.utexas.edu) MACHINE_ID=stampede ;; ### stampede4
 esac
 
+# Overwrite auto-detect with NEMS_MACHINE if set
+MACHINE_ID=${NEMS_MACHINE:-${MACHINE_ID}}
+
 # For Theia and Cheyenne, append compiler
 if [ $MACHINE_ID = theia ] || [ $MACHINE_ID = hera ] || [ $MACHINE_ID = cheyenne ] || [ $MACHINE_ID = jet ] || [ $MACHINE_ID = gaea ] || [ $MACHINE_ID = stampede ] ; then
     MACHINE_ID=${MACHINE_ID}.${COMPILER}