WRF detailed setup procedure

apps/spack/build_spack.sh

@@ -2,7 +2,7 @@
 set -e
 APPS_SPACK_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
 APP_NAME=spack
-APP_VERSION=0.16.0
+APP_VERSION=0.16.3
 SHARED_APP=${SHARED_APP:-/apps}
 INTEL_MPI_VERSION=${INTEL_MPI_VERSION:-2018.4.274} # This should be retrieved dynamically
 

apps/spack/compilers.yaml

@@ -4,7 +4,7 @@ compilers:
     extra_rpaths: []
     flags: {}
     modules: []
-    operating_system: centos7
+    operating_system: almalinux8
     paths:
       cc: /usr/bin/gcc
       cxx: /usr/bin/g++
@@ -17,7 +17,7 @@ compilers:
     extra_rpaths: []
     flags: {}
     modules: [gcc-9.2.0]
-    operating_system: centos7
+    operating_system: almalinux8
     paths:
       cc: /opt/gcc-9.2.0/bin/gcc
       cxx: /opt/gcc-9.2.0/bin/g++

apps/spack/packages.yaml

@@ -2,7 +2,7 @@
 packages:
   openmpi:
     externals:
-    - spec: openmpi@4.0.5%[email protected]
+    - spec: openmpi@5.0.2%[email protected]
       modules:
       - mpi/openmpi
     buildable: False

apps/wrf/automation/build-folder-structure.sh

@@ -0,0 +1,50 @@
+#!/bin/bash
+
+WRFDAT="/data/wrfdata"
+
+echo "creating ${WRFDAT}/wpsdir/"
+mkdir -p ${WRFDAT}/wpsdir/
+
+echo "creating ${WRFDAT}/wrfdir/"
+mkdir -p ${WRFDAT}/wrfdir/
+
+echo "creating ${WRFDAT}/tables/wps/"
+mkdir -p ${WRFDAT}/tables/wps/
+
+echo "creating ${WRFDAT}/tables/wrf/"
+mkdir -p ${WRFDAT}/tables/wrf/
+
+echo "creating ${WRFDAT}/tables/namelist/"
+mkdir -p ${WRFDAT}/tables/namelist/
+
+echo "creating ${WRFDAT}/gfs_data/"
+mkdir -p ${WRFDAT}/gfs_data/
+
+echo "creating ${WRFDAT}/geog/"
+mkdir -p ${WRFDAT}/geog/
+
+echo "creating /apps/scripts/"
+mkdir -p /apps/scripts/
+
+echo "copying namelist*.wps"
+cp -f /data/azurehpc/apps/wrf/automation/namelist*.wps ${WRFDAT}/tables/namelist/
+
+echo "copying namelist*.input"
+cp -f /data/azurehpc/apps/wrf/automation/namelist*.input ${WRFDAT}/tables/namelist/
+
+echo "creating link to scripts"
+#cd /data/azurehpc/apps/wrf/automation/
+#cp /data/azurehpc/apps/wrf/automation/fwddatan.awk /apps/scripts/
+#cp /data/azurehpc/apps/wrf/automation/get_gfs_data.py /apps/scripts/
+#cp run_*.slurm run_*.pbs submit*.sh /apps/scripts/
+ln -s /data/azurehpc/apps/wrf/automation/* /apps/scripts/
+
+echo "creating links to WPF files"
+ln -s /apps/hbv3/wps-openmpi/WPS-4.1/* /data/wrfdata/tables/wps/
+
+echo "creating links to WRF files"
+ln -s /apps/hbv3/wrf-openmpi/WRF-4.1.5/run/* /data/wrfdata/tables/wrf/
+
+echo "Moving geog files"
+#mv albedo_modis albedo_modis.tar.bz2 greenfrac_fpar_modis greenfrac_fpar_modis.tar.bz2 lai_modis_10m lai_modis_10m.tar.bz2 maxsnowalb_modis maxsnowalb_modis.tar.bz2 modis_landuse_20class_30s_with_lakes modis_landuse_20class_30s_with_lakes.tar.bz2 orogwd_10m orogwd_10m.tar.bz2 soiltemp_1deg soiltemp_1deg.tar.bz2 soiltype_bot_30s soiltype_bot_30s.tar.bz2 soiltype_top_30s soiltype_top_30s.tar.bz2 topo_10m topo_10m.tar.bz2 topo_2m topo_2m.tar.bz2 topo_30s topo_30s.tar.bz2 topo_gmted2010_30s topo_gmted2010_30s.tar.bz2 geog 
+

apps/wrf/automation/fwddatan.awk

@@ -0,0 +1,88 @@
+{ data = $1;
+  hplus = $2;
+  len = length(data);
+  res = len - 6;
+  dias_mes = "31,28,31,30,31,30,31,31,30,31,30,31"
+  ano = substr(data,1,4);
+  mes = substr(data,5,2);
+  dia = substr(data,7,2);
+  resto = substr(data,9,res);
+  fs=","
+  a=split(dias_mes,dias,fs);
+#  an1 = (1900+ano)/4.0;
+  an1 = ano/4.0;
+  bix = substr(an1,1,3);
+
+  if (bix == an1){
+     dias_mes = "31,29,31,30,31,30,31,31,30,31,30,31";
+     split(dias_mes,dias,fs);}
+
+  diao = dia
+  if(diao<10) { diao= substr(data,8,1) + 1 - 1};
+
+  hres = resto + hplus;
+  ndia = hres/24.0;
+  diai = int (ndia)
+
+  if(diai >= 1)
+  {
+   hres = hres - (diai*24)
+   diao = dia + diai;
+  };
+
+    if(mes<10) {mes = substr(data,6,1) + 1 - 1};
+
+    if(diao > dias[mes])
+    {
+      diao = diao - dias[mes];
+      mes=mes+1;
+      if(mes > 12)
+      {
+        mes=1;
+        anoteste=ano;
+        ano = ano +1;
+        if(ano==100)
+        {
+          ano="0";
+        };
+
+      };
+    };
+
+
+  if(hres < 0)
+  {
+   diai = diai - 1
+   hres = hres - (diai*24)
+   if(hres == 24)
+   {
+     hres=0;
+     diai = diai + 1;
+   };
+   diao = dia + diai;
+  };
+
+    if(diao<1)
+    {
+      mes=mes-1;
+
+      if(mes<1)
+      {
+        mes=12;
+        ano = ano -1;
+        if(ano<0)
+        {
+          ano=99;
+        };
+      };
+      diao = dias[mes] + diao ;
+    }
+
+
+  if(diao<10) {diao="0"diao};
+  if(ano<10) {ano="0"ano};
+  if(mes<10) {mes="0"mes};
+  if(hres<10) {hres="0"hres};
+
+  print ano mes diao hres;
+}

apps/wrf/automation/get_gfs_data.py

@@ -0,0 +1,73 @@
+#from wget import download
+import wget
+import datetime as dt
+import os, subprocess
+import sys
+from time import time as timer
+from multiprocessing.pool import ThreadPool
+#import requests
+year = int(sys.argv[1])
+month = int(sys.argv[2])
+day = int(sys.argv[3])
+
+##dia = dt.date.today()
+#dia = dt.datetime(dia.year,dia.month,dia.day,12)
+dia = dt.datetime(year,month,day,12)
+print(dia)
+inicio = 00
+##fim = 28         ## Dados para 1 dia
+fim = 135      ## Dados para 5 dias
+
+data_sys = dia.strftime("%Y%m%d%H")
+data_gfs = dia.strftime("%Y%m%d")
+
+##path_home = "/data/wrfdata/itv-data/"
+path_home = "/data/wrfdata/gfs_data/"
+
+
+#### CASO O DIRETORIO PARA O DOWNLOAD NAO EXISTE, ELE SERA CRIADO ####
+
+if not os.path.isdir(path_home + "/" + data_sys ):
+        os.system("mkdir -p " + path_home + data_sys )
+
+#### URL (http://nomads.ncep.noaa.gov/pub/data/nccf/com/gfs/prod)
+#### Alteracao realizada em 10 / set / 2020
+#### URL (ftp://ftpprd.ncep.noaa.gov/pub/data/nccf/com/gfs/prod)
+
+#### DOWNLOAD DOS ARQUIVOS #####
+args_inputs = []
+j=0
+for i in range(inicio,fim,3):
+        k = str(i)
+        if i < 10 :
+                k = ('00' + k)
+        if i >= 10 and i < 100 :
+                k = ('0' + k)
+
+        gfs = "gfs.t12z.pgrb2.0p25.f" + k
+        print(gfs)
+
+        if not os.path.isfile(path_home + "/" + data_sys + "/" + gfs):
+                f_out = path_home + "/" + data_sys + '/' + gfs
+
+####            url = ('http://nomads.ncep.noaa.gov/pub/data/nccf/com/gfs/prod/gfs.' + data_gfs + '/12/' + gfs)
+####            url = ('ftp://ftpprd.ncep.noaa.gov/pub/data/nccf/com/gfs/prod/gfs.' + data_gfs + '/12/' + gfs)
+####            url = ('ftp://ftpprd.ncep.noaa.gov/pub/data/nccf/com/gfs/prod/gfs.' + data_gfs + '/12/atmos/' + gfs)
+                url = ('https://nomads.ncep.noaa.gov/pub/data/nccf/com/gfs/prod/gfs.' + data_gfs + '/12/atmos/' + gfs)
+
+                args_inputs.append ((f_out, url))
+                j=j+1
+
+def fetch_url(entry):
+        path, uri = entry
+        print ("Downloading...", path)
+        filename = wget.download(uri,path_home + data_sys)
+        return path
+
+start=timer()
+results = ThreadPool(6).imap_unordered(fetch_url, args_inputs)
+
+for path in results:
+        print(path)
+
+print("Elapsed Time: ", timer() - start)

apps/wrf/automation/namelist-new.input

@@ -0,0 +1,140 @@
+&time_control
+ run_days                 = 0,
+ run_hours                = 132,
+ run_minutes              = 0,
+ run_seconds              = 0,
+ start_year               = aai,     aai,
+ start_month              = mmi,     mmi,
+ start_day                = ddi,     ddi,
+ start_hour               = hhi,     hhi,
+ end_year                 = aaf,     aaf,
+ end_month                = mmf,     mmf,
+ end_day                  = ddf,     ddf,
+ end_hour                 = hhf,     hhf,
+ interval_seconds         = 10800,
+ input_from_file          = .true.,.true.,
+ history_interval         = 60,  60,
+ frames_per_outfile       = 1, 1,
+ restart                  = .false.,
+ restart_interval         = 7200,
+ io_form_history          = 2,
+ io_form_restart          = 2,
+ io_form_input            = 2,
+ io_form_boundary         = 2,
+ debug_level              = 0,
+
+ /
+
+ &domains
+!time_step                = 100,
+ time_step                = 80,
+ time_step_fract_num      = 0,
+ time_step_fract_den      = 1,
+ max_dom                  = 2,
+ s_we                     = 1,        1,
+ e_we                     = 420,      982,
+ s_sn                     = 1,        1,
+ e_sn                     = 300,      646,
+ p_top_requested          = 7200,
+ num_metgrid_levels       = 34,
+ num_metgrid_soil_levels  = 4,
+ use_surface              = .true.,
+ sfcp_to_sfcp             = .true.,
+ dx                       = 9000.,    3000.,
+ dy                       = 9000.,    3000.,
+ grid_id                  = 1,        2,
+ parent_id                = 1,        1,
+ i_parent_start           = 1,       46,
+ j_parent_start           = 1,       39,
+ parent_grid_ratio        = 1,        3,
+ parent_time_step_ratio   = 1,        3,
+ feedback                 = 1,
+ smooth_option            = 0,
+ /
+
+ &physics
+ mp_physics               = 95,       95,
+ ra_lw_physics            = 4,        4,
+ ra_sw_physics            = 4,        4,
+ slope_rad                = 1,        1,
+ topo_shading             = 0,        1,
+ radt                     = 30,       30,
+ sf_urban_physics         = 1,        1,
+ sf_sfclay_physics        = 1,        1,
+ sf_surface_physics       = 2,        2,
+ bl_pbl_physics           = 1,        1,
+ bldt                     = 0,        0,
+ cu_physics               = 3,        3,
+ cudt                     = 5,        5,
+ cugd_avedx               = 3,
+ sst_update               = 0,
+ isfflx                   = 1,
+ ifsnow                   = 0,
+ icloud                   = 1,
+ surface_input_source     = 1,
+ num_soil_layers          = 4,
+ maxiens                  = 1,
+ maxens                   = 3,
+ maxens2                  = 3,
+ maxens3                  = 16,
+ ensdim                   = 144,
+
+ /
+
+ &fdda
+ /
+
+ &dynamics
+ dyn_opt                  = 2,
+ rk_ord                   = 3,
+ w_damping                = 1,
+ diff_opt                 = 1,   1,
+ km_opt                   = 4,   4,
+ damp_opt                 = 3,
+ base_temp                = 290.,
+ zdamp                    = 5000.,    5000.,
+ dampcoef                 = 0.2,     0.2,
+ khdif                    = 0,        0,
+ kvdif                    = 0,        0,
+ smdiv                    = 0.1,      0.1,
+ emdiv                    = 0.01,     0.01,
+ epssm                    = 0.1,      0.1,
+ non_hydrostatic          = .true.,   .true.,
+ time_step_sound          = 0,        0,
+ h_mom_adv_order          = 5,        5,
+ v_mom_adv_order          = 3,        3,
+ h_sca_adv_order          = 3,        5,
+ v_sca_adv_order          = 2,        3,
+ moist_adv_opt            = 1,        1,
+ scalar_adv_opt           = 1,        1,
+ chem_adv_opt             = 1,        1,
+ tke_adv_opt              = 1,        1,
+ diff_6th_opt             = 1,        1,
+ diff_6th_factor          = 0.12,     0.12,
+ /
+
+ &bdy_control
+ spec_bdy_width           = 5,
+ spec_zone                = 1,
+ relax_zone               = 4,
+ specified                = .true.,   .false.,
+ periodic_x               = .false.,  .false.,
+ symmetric_xs             = .false.,  .false.,
+ symmetric_xe             = .false.,  .false.,
+ open_xs                  = .false.,  .false.,
+ open_xe                  = .false.,  .false.,
+ periodic_y               = .false.,  .false.,
+ symmetric_ys             = .false.,  .false.,
+ symmetric_ye             = .false.,  .false.,
+ open_ys                  = .false.,  .false.,
+ open_ye                  = .false.,  .false.,
+ nested                   = .false.,  .true.,
+ /
+
+ &grib2
+ /
+
+ &namelist_quilt
+ nio_tasks_per_group = 0,
+ nio_groups = 1,
+ /