add doc dir

convertGSIhofx2ioda/modifyOMB.py

@@ -130,12 +130,6 @@ def process_file(self, infile, outfile, varlist=[]):
 
     n = 0
     for grp in ncin.groups:
-      if(grp.find('hofxm0_') >=0):
-        continue
-
-      if(grp.find('hofx_y_mean_xb0') >=0):
-        continue
-
       n += 1
       if (self.debug):
         print('\tgroup No. %d: %s' %(n, grp))

doc/gen.sh

@@ -0,0 +1,89 @@
+#!/bin/bash
+
+#set -x
+
+ taskspernode=40
+ NUMMEM=80
+ MYLAYOUT=1,20
+
+#cpu_list=(   6    12    18    24    30    36     72     78)
+#nodelist=(   1     1     1     1     1     1      2      2)
+#lay_list=("1,1" "1,2" "1,3" "1,4" "1,5" "1,6" "1,12" "1,13")
+
+#cpu_list=(  36)
+#nodelist=(   1)
+#lay_list=("2,3")
+
+#cpu_list=(  78)
+#nodelist=(   2)
+#lay_list=(1,13)
+
+#cpu_list=( 156)
+#nodelist=(   4)
+#lay_list=(2,13)
+
+#cpu_list=( 312)
+#nodelist=(   8)
+#lay_list=(4,13)
+
+ cpu_list=( 36   78  156  312)
+ nodelist=(  1    2    4    8)
+ lay_list=(3,2 1,13 2,13 4,13)
+
+ templatedir=/work2/noaa/gsienkf/weihuang/jedi/case_study/templates
+ topdir=/work2/noaa/gsienkf/weihuang/jedi/case_study
+#caselist=(aircraft amsua iasi satwind scatwind sfcship sondes surf vadwind windprof)
+ caselist=(amsua iasi)
+
+#------------------------------------------------------------------------------
+ n=0
+ for j in ${!caselist[@]}
+ do
+   case=${caselist[$j]}
+   echo "Case: $case"
+   casedir=${topdir}/${case}
+
+   cd ${casedir}
+   ln -sf ../Data .
+   ln -sf ../ioda_v2_data .
+
+   for i in ${!cpu_list[@]}
+   do
+     echo "element $i is ${myArray[$i]}"
+     totalcpus=${cpu_list[$i]}
+     nodes=${nodelist[$i]}
+     MYLAYOUT=${lay_list[$i]}
+
+     workdir=${casedir}/run_${NUMMEM}.${taskspernode}t${nodes}n_${totalcpus}p
+     mkdir -p ${workdir}
+     cd ${workdir}
+
+     sed -e "s?TASKSPERNODE?${taskspernode}?g" \
+         -e "s?TOTALNODES?${nodes}?g" \
+         -e "s?TOTALCPUS?${totalcpus}?g" \
+         -e "s?WORKDIR?${workdir}?g" \
+         -e "s?NUMMEM?${NUMMEM}?g" \
+         -e "s?MYLAYOUT?${MYLAYOUT}?g" \
+         ${templatedir}/slurm.template > run.slurm
+
+     sed -e "s?LAYOUT?${MYLAYOUT}?" \
+         -e "s?NUMBEROFMEMBERS?${NUMMEM}?" \
+         ${templatedir}/getkf.yaml.template > getkf.yaml
+
+     cat ${templatedir}/${case}.obs.yaml.template >> getkf.yaml
+
+    #if [ $n -lt 1 ]
+    #then
+      #DEPEND=$(sbatch --parsable run.slurm)
+      #echo "job_id: ${DEPEND}"
+      #sbatch run.slurm
+    #else
+      #DEPEND=$(sbatch --dependency=afterany:${DEPEND} --parsable run.slurm)
+       sbatch run.slurm
+    #fi
+
+     n=$((n+1))
+     cd ${casedir}
+   done
+ done
+

doc/genlinks.sh

@@ -0,0 +1,26 @@
+#!/bin/bash
+
+ set -x
+
+ src_dir=/work2/noaa/gsienkf/weihuang/C96_psonly_delp/2020011006
+
+ number_members=80
+ n=1
+ while [ $n -le $number_members ]
+ do
+   if [ $n -lt 10 ]
+   then
+     member_str=mem00${n}
+   elif [ $n -lt 100 ]
+   then
+     member_str=mem0${n}
+   else
+     member_str=mem${n}
+   fi
+
+  #ln -sf ${src_dir}/${member_str}/INPUT ${member_str}
+   cp coupler.res ${member_str}/.
+
+   n=$(( $n + 1 ))
+ done
+

doc/how2run.jedi-sondes

@@ -0,0 +1,67 @@
+How to run JEDI with radiosondes
+
+Wei Huang
+
+This is for runs on orion.
+
+1. convert GSI daignose observation file to IODA2
+   a. working directory: /work2/noaa/gsienkf/weihuang/jedi/case_study/diag2iodav2
+   b. prepare observation files to "obs" directory, like:
+      diag_conv_t_ges.2020011006_ensmean2.nc4
+      diag_conv_q_ges.2020011006_ensmean2.nc4
+      diag_conv_uv_ges.2020011006_ensmean2.nc4
+   c. run script diag2ioda.sh
+   d. after run this script, generate ioda2 observation files in directory "out", like:
+      aircraft_q_obs_2020011006.nc4
+      aircraft_tsen_obs_2020011006.nc4
+      aircraft_uv_obs_2020011006.nc4
+      satwind_obs_2020011006.nc4
+      scatwind_obs_2020011006.nc4
+      sfc_ps_obs_2020011006.nc4
+      sfcship_ps_obs_2020011006.nc4
+      sfcship_q_obs_2020011006.nc4
+      sfcship_tsen_obs_2020011006.nc4
+      sfcship_tv_obs_2020011006.nc4
+      sfcship_uv_obs_2020011006.nc4
+      sondes_ps_obs_2020011006.nc4
+      sondes_q_obs_2020011006.nc4
+      sondes_tsen_obs_2020011006.nc4
+      sondes_tv_obs_2020011006.nc4
+      sondes_uv_obs_2020011006.nc4
+      vadwind_obs_2020011006.nc4
+      windprof_obs_2020011006.nc4
+
+2. rename above directory to JEDI top directory as directory: ioda_v2_data
+   For run with sondes only, files:
+      sondes_q_obs_2020011006.nc4
+      sondes_tsen_obs_2020011006.nc4
+      sondes_tv_obs_2020011006.nc4
+   are used.
+
+   NOTE: use sondes_ps_obs_2020011006.nc4 as surface pressure data will be more convient,
+	 as it is close to surface observations.
+
+3. run JEDI sondes data
+   a. prepare ensemble Data, as in: /work2/noaa/gsienkf/weihuang/jedi/Data/ens
+   b. working directory: /work2/noaa/gsienkf/weihuang/jedi/case_study/sondes
+   c. edit script gen.sh:
+	i) setup task used per node
+	ii) Number of ensembles members
+	iii) IO layout
+	iv) number of node used
+	v) casename
+	vi) datetime
+	vii) obsin(s)
+	viii) obsout(s)
+	ix) link Data and obs directory
+	x) process two templates: slurm.template for a run script: run.slurm;
+                                  getkf.yaml.template to produce getkf.yaml file.
+	xi) run as batch job: "sbatch run.slurm".
+
+4. in getkf.yaml.template, there are kinds of output options.
+   a. the current option is output to FV3 tiles.
+      in directory: /work2/noaa/gsienkf/weihuang/jedi/case_study/vis/regrid
+      one can use interp.sh to interpolate FV3 cube data to regular lat-lon grid.
+   b. commented out one is latlon (actually Gaussian) grid.
+      be aware that this Gaussian grid may not exactly the same as GSI Gaussian grid.
+