diff --git a/SYNOP/STATS/fortran-programs/plots_for_one_station b/SYNOP/STATS/fortran-programs/plots_for_one_station
new file mode 100755
index 0000000000000000000000000000000000000000..ed3054838289d9c49461f9cd550f6b8849089333
Binary files /dev/null and b/SYNOP/STATS/fortran-programs/plots_for_one_station differ
diff --git a/SYNOP/STATS/fortran-programs/plots_for_one_station.f95 b/SYNOP/STATS/fortran-programs/plots_for_one_station.f95
index b74cb22e5ba26d8a8466fe831b7f9dda84a6cc8d..b8212593ec65829b2dea2bb99a57aac33cecb85f 100644
--- a/SYNOP/STATS/fortran-programs/plots_for_one_station.f95
+++ b/SYNOP/STATS/fortran-programs/plots_for_one_station.f95
@@ -167,6 +167,7 @@ program plots_for_one_station
   character*160 :: txt_data_time_series ! see above
   character*160 :: txt_data_quantiles ! see above
   character*160 :: txt_data_rank_histogram ! see above
+  character*160 :: out_dir
   integer :: year1,year2 ! first and last year of simulation
   integer :: month1,month2 ! first and last month of simulation 
   integer :: nyear ! number of years = year2-year1+1
@@ -227,7 +228,7 @@ program plots_for_one_station
        grads_data_time_series,grads_data_rank_histogram,&
        year1,year2,month1,month2,&
        txt_data_time_series,txt_data_rank_histogram,txt_data_quantiles,&
-       include_rank_histograms,l_code_in_char,l_round_6h,miss
+       include_rank_histograms,l_code_in_char,l_round_6h,out_dir,miss
   
   data color/9,14,4,11,5,13,3,10,7,12,8,2,6/
 !
@@ -345,7 +346,7 @@ program plots_for_one_station
 !
 ! Write the commands to the auxiliary script files for Grads   
 !
-   open(unit=1,form='formatted',file='vrange_commands')
+   open(unit=1,form='formatted',file=trim(out_dir)//'vrange_commands')
    write(1,'(A11,2F10.3)')'set vrange ',fmin_down(1),fmax_up(1)
    write(1,'(A11,2F10.3)')'set vrange ',fmin_down(2),fmax_up(2)
    write(1,'(A11,2F10.3)')'set vrange ',fmin_down(3),fmax_up(3)
@@ -357,7 +358,7 @@ program plots_for_one_station
    write(1,'(A13,F7.3)')'set vrange 0 ',1.1*(nquant+1)*freqmax(5) ! conversion to relative frequencies      
    close(1)
 
-   open(unit=1,form='formatted',file='time_series_commands')
+   open(unit=1,form='formatted',file=trim(out_dir)//'time_series_commands')
    do i=1,nyear
       write(1,'(A12)')'set cthick 4'
       write(1,'(A12)')'set cstyle 0'
@@ -376,37 +377,37 @@ program plots_for_one_station
    enddo   
    close(1)
 
-   open(unit=1,form='formatted',file='coordinates')
+   open(unit=1,form='formatted',file=trim(out_dir)//'coordinates')
    write(1,'(F8.3)')lon
    write(1,'(F8.3)')lat
    close(1)
    
    if(include_rank_histograms)then
-   open(unit=1,form='formatted',file='msd_and_p-value_00')
+   open(unit=1,form='formatted',file=trim(out_dir)//'msd_and_p-value_00')
       write(1,'(A15)')'set strsiz 0.17'
       write(1,'(A18)')'set string 1 l 4 0'
       write(1,'(A25,F5.3)')'draw string 1.3 &0 MSD=',msd(1)
       write(1,'(A29,F5.3)')'draw string 3.0 &0 p-value=',p_value(1)      
       close(1)
-   open(unit=1,form='formatted',file='msd_and_p-value_06')
+   open(unit=1,form='formatted',file=trim(out_dir)//'msd_and_p-value_06')
       write(1,'(A15)')'set strsiz 0.17'
       write(1,'(A18)')'set string 1 l 4 0'
       write(1,'(A25,F5.3)')'draw string 1.3 &0 MSD=',msd(2)
       write(1,'(A29,F5.3)')'draw string 3.0 &0 p-value=',p_value(2)      
       close(1)
-   open(unit=1,form='formatted',file='msd_and_p-value_12')
+   open(unit=1,form='formatted',file=trim(out_dir)//'msd_and_p-value_12')
       write(1,'(A15)')'set strsiz 0.17'
       write(1,'(A18)')'set string 1 l 4 0'
       write(1,'(A25,F5.3)')'draw string 1.3 &0 MSD=',msd(3)
       write(1,'(A29,F5.3)')'draw string 3.0 &0 p-value=',p_value(3)      
       close(1)
-   open(unit=1,form='formatted',file='msd_and_p-value_18')
+   open(unit=1,form='formatted',file=trim(out_dir)//'msd_and_p-value_18')
       write(1,'(A15)')'set strsiz 0.17'
       write(1,'(A18)')'set string 1 l 4 0'
       write(1,'(A25,F5.3)')'draw string 1.3 &0 MSD=',msd(4)
       write(1,'(A29,F5.3)')'draw string 3.0 &0 p-value=',p_value(4)      
       close(1)
-   open(unit=1,form='formatted',file='msd_and_p-value')
+   open(unit=1,form='formatted',file=trim(out_dir)//'msd_and_p-value')
       write(1,'(A15)')'set strsiz 0.17'
       write(1,'(A18)')'set string 1 l 4 0'
       write(1,'(A25,F5.3)')'draw string 1.3 &0 MSD=',msd(5)
diff --git a/SYNOP/STATS/fortran-programs/rank_histogram_summary_statistics b/SYNOP/STATS/fortran-programs/rank_histogram_summary_statistics
new file mode 100755
index 0000000000000000000000000000000000000000..8e727b3be9456b0ccd97e6a2a6822c2669e91214
Binary files /dev/null and b/SYNOP/STATS/fortran-programs/rank_histogram_summary_statistics differ
diff --git a/SYNOP/STATS/fortran-programs/rank_histograms_one_station b/SYNOP/STATS/fortran-programs/rank_histograms_one_station
new file mode 100755
index 0000000000000000000000000000000000000000..671c1c429f02e3e0ddbc96c7ab2ad3b081332169
Binary files /dev/null and b/SYNOP/STATS/fortran-programs/rank_histograms_one_station differ
diff --git a/SYNOP/STATS/produce_rank_histograms_all_stations.sh b/SYNOP/STATS/produce_rank_histograms_all_stations.sh
index f82de60f57c934924d47fc9c400d0f6256e5b488..24032a9d8e14775b531e2f25cdb88d0d90ffa94d 100755
--- a/SYNOP/STATS/produce_rank_histograms_all_stations.sh
+++ b/SYNOP/STATS/produce_rank_histograms_all_stations.sh
@@ -124,27 +124,30 @@ fi
 #
 # 1) Raw data from model simulation (this far, mimicked by observations)
 echo "   Raw data from model simulation (this far, mimicked by observations) ..."
-sim_dir="/scratch/project_465000454/ama/open_data_ODB"
-sim_file=${sim_dir}/FMI_open_data_2010-2021.odb
+sim_dir=$rootdir/SYNOP/output/ODB_data/$experiment #="/scratch/project_465000454/ama/open_data_ODB"
+sim_file=${sim_dir}/simulated_synop_data.odb
 echo "      $sim_file"
 
 # 2) Pre-computed quantiles
 echo "   Directory with pre-computed quantiles ..."
 #quant_dir=quantiles
-quant_dir=/scratch/project_465000454/ama/STATDATASYNOP/quantiles
+#quant_dir=/scratch/project_465000454/ama/STATDATASYNOP/quantiles
+quant_dir=$rootdir/SYNOP/input/STATDATASYNOP/quantiles
 echo "     $quant_dir"
 quant_file=${quant_dir}/quant_all_stations_${variable}_4.odb
 
 # 3) Pre-computed bootstrap MSD statistics
 echo "   Directory with pre-computed bootstrap MSD statistics ..." 
 #bootstrap_dir=bootstrap_statistics/${variable}_${period}
-bootstrap_dir=/scratch/project_465000454/ama/STATDATASYNOP/bootstrap_statistics/${variable}_${period}
+#bootstrap_dir=/scratch/project_465000454/ama/STATDATASYNOP/bootstrap_statistics/${variable}_${period}
+bootstrap_dir=$rootdir/SYNOP/input/STATDATASYNOP/bootstrap_statistics/${variable}_${period}
 echo "     $bootstrap_dir"
 msd_bootstrap_file=${bootstrap_dir}/MSD_bootstrap_${variable}_${period}_all_stations.odb
 
 # 4) Directory for results
 echo "   Directory for results ..."
-outdir=rank_histograms/${variable}_${year1}${month1}-${year2}${month2}
+#outdir=rank_histograms/${variable}_${year1}${month1}-${year2}${month2}
+outdir=$rootdir/SYNOP/output/scratch/$experiment/rank_histograms/${variable}_${year1}${month1}-${year2}${month2}
 echo "     $outdir"
 if test -d "$outdir"; then
   echo $outdir exists
@@ -175,7 +178,7 @@ echo "   List of synop stations (with geographical coordinates): $station_list"
 echo "   Compiling fortran-program to calculate rank histograms ..."
 echo "      fortran-programs/rank_histograms_one_station.f95"
 
-gfortran fortran-programs/rank_histograms_one_station.f95 -o rank_histograms_one_station
+#gfortran fortran-programs/rank_histograms_one_station.f95 -o rank_histograms_one_station
 
 #################################################################
 #
@@ -191,8 +194,8 @@ line_number=2
 #
 while [ ${line_number} -le `expr $n_lines` ]
 do
-  head -`expr ${line_number}` ${station_list} | tail -1 > input.txt
-  read station longitude latitude < input.txt
+  head -`expr ${line_number}` ${station_list} | tail -1 > $rootdir/SYNOP/output/scratch/$experiment/input.txt
+  read station longitude latitude < $rootdir/SYNOP/output/scratch/$experiment/input.txt
 echo "   **********"
 echo "   Synop station ID, longitude, latitude: ${station} ${longitude} ${latitude}"
 
@@ -205,7 +208,7 @@ echo "   Synop station ID, longitude, latitude: ${station} ${longitude} ${latitu
 # When simulation data are available, a means to retrieve the correct data points from it must be designed
 echo "   Selecting the simulation data (mimicked this far by observations) for synop station: ${station}"
 #
-odb_command="odb sql 'select year,month,day,hour,value where station=${station} and (year>=${year1} and year<=${year2}) and (hour=0 or hour=6 or hour=12 or hour=18) and variable=${variable}' -i ${sim_file} -o sim_data"
+odb_command="odb sql 'select year,month,day,hour,value where station=${station} and (year>=${year1} and year<=${year2}) and (hour=0 or hour=6 or hour=12 or hour=18) and variable=${variable}' -i ${sim_file} -o $rootdir/SYNOP/output/scratch/$experiment/sim_data"
 eval ${odb_command}
 #
 ###############################################################
@@ -214,12 +217,12 @@ echo "   Selecting the quantiles for synop station: ${station}"
 # 00, 06, 12 and 18 UTC are picked separately, since
 # select \* does not allow for parentheses (very strange)
 #
-rm quantile_selection_*
-odb sql select \* where hour=0 and station=${station} -i ${quant_file} -o quantile_selection_00
-odb sql select \* where hour=6 and station=${station} -i ${quant_file} -o quantile_selection_06
-odb sql select \* where hour=12 and station=${station} -i ${quant_file} -o quantile_selection_12
-odb sql select \* where hour=18 and station=${station} -i ${quant_file} -o quantile_selection_18
-cat quantile_selection_* > quantile_selection
+#rm quantile_selection_*
+odb sql select \* where hour=0 and station=${station} -i ${quant_file} -o $rootdir/SYNOP/output/scratch/$experiment/quantile_selection_00
+odb sql select \* where hour=6 and station=${station} -i ${quant_file} -o $rootdir/SYNOP/output/scratch/$experiment/quantile_selection_06
+odb sql select \* where hour=12 and station=${station} -i ${quant_file} -o $rootdir/SYNOP/output/scratch/$experiment/quantile_selection_12
+odb sql select \* where hour=18 and station=${station} -i ${quant_file} -o $rootdir/SYNOP/output/scratch/$experiment/quantile_selection_18
+cat $rootdir/SYNOP/output/scratch/$experiment/quantile_selection_* > $rootdir/SYNOP/output/scratch/$experiment/quantile_selection
 #
 ################################################################
 #
@@ -228,7 +231,7 @@ cat quantile_selection_* > quantile_selection
 # of the time period (included in the name of msd_bootstrap_file)
 # and (to a smaller extent) the selected station.
 #
-odb sql select \* where station=${station} -i ${msd_bootstrap_file} -o msd_bootstrap_selection
+odb sql select \* where station=${station} -i ${msd_bootstrap_file} -o $rootdir/SYNOP/output/scratch/$experiment/msd_bootstrap_selection
 #
 ###############################################################
 # Produce the rank histogram for one station.
@@ -251,16 +254,16 @@ fi
 
 
 #
-./rank_histograms_one_station <<EOF
+$SRC_OBSALL_DIR/SYNOP/STATS/fortran-programs/rank_histograms_one_station <<EOF
  &PARAM
-  infile='sim_data'
-  quantile_file='quantile_selection'
-  msd_bootstrap_file='msd_bootstrap_selection'  
+  infile='$rootdir/SYNOP/output/scratch/$experiment/sim_data'
+  quantile_file='$rootdir/SYNOP/output/scratch/$experiment/quantile_selection'
+  msd_bootstrap_file='$rootdir/SYNOP/output/scratch/$experiment/msd_bootstrap_selection'  
   outfile='${outdir}/rank_histograms_${variable}_${station}_${year1}${month1}-${year2}${month2}'
   hour1=0,hour2=18,hour_step=6
   year1=${year1},year2=${year2},month1=${month1},month2=${month2}
   grads_out=.false.
-  outfile_grads='rank_histograms_${variable}_${station}_${year1}${month1}-${year2}${month2}.grads'
+  outfile_grads='${outdir}/rank_histograms_${variable}_${station}_${year1}${month1}-${year2}${month2}.grads'
   l_code_in_char=.false.,l_round_hour=.false.
   &END
 EOF
@@ -273,10 +276,10 @@ odb import -d ' ' ${outdir}/rank_histograms_${variable}_${station}_${year1}${mon
 #
 # Remove unnecessary files
 #
-rm input.txt
-rm msd_bootstrap_selection
-rm quantile_selection*
-rm sim_data
+#rm input.txt
+#rm msd_bootstrap_selection
+#rm quantile_selection*
+#rm sim_data
 #
 ((line_number++))
 done
@@ -288,4 +291,4 @@ cat ${outdir}/rank_histograms_${variable}_*_${year1}${month1}-${year2}${month2}.
 #
 # Delete the fortran executable
 #
-rm rank_histograms_one_station
+#rm rank_histograms_one_station
diff --git a/SYNOP/STATS/produce_standard_plots_all_stations.sh b/SYNOP/STATS/produce_standard_plots_all_stations.sh
index 9b27914a1e89228212a570162b1648f3cb8fff87..33c0160c9a6a89fd8b270c6e3fe8ad52406df37e 100755
--- a/SYNOP/STATS/produce_standard_plots_all_stations.sh
+++ b/SYNOP/STATS/produce_standard_plots_all_stations.sh
@@ -132,26 +132,30 @@ fi
 #
 # 1) Raw data from model simulation (this far, mimicked by observations)
 echo "   Raw data from model simulation (this far, mimicked by observations) ..."
-sim_dir="/scratch/project_465000454/ama/open_data_ODB"
-sim_file=${sim_dir}/FMI_open_data_2010-2021.odb
+#sim_dir="/scratch/project_465000454/ama/open_data_ODB"
+sim_dir=$rootdir/SYNOP/output/ODB_data/$experiment
+sim_file=${sim_dir}/simulated_synop_data.odb
 echo "      $sim_file"
 
 # 2) Pre-computed quantiles
 echo "   Directory for pre-computed quantiles ..."
 #quant_dir=quantiles
-quant_dir=/scratch/project_465000454/ama/STATDATASYNOP/quantiles
+#quant_dir=/scratch/project_465000454/ama/STATDATASYNOP/quantiles
+quant_dir=$rootdir/SYNOP/input/STATDATASYNOP/quantiles
 echo "     $quant_dir"
 quant_file=${quant_dir}/quant_all_stations_${variable}_4.odb
 
 # 3) Pre-computed rank histogram data
 echo "   Directory for pre-computed rank histogram data ..."
-rh_dir=rank_histograms/${variable}_${year1}${month1}-${year2}${month2}
+#rh_dir=rank_histograms/${variable}_${year1}${month1}-${year2}${month2}
+rh_dir=$rootdir/SYNOP/output/scratch/$experiment/rank_histograms/${variable}_${year1}${month1}-${year2}${month2}
 echo "     $rh_dir"
 rh_file=${rh_dir}/rank_histograms_${variable}_${year1}${month1}-${year2}${month2}_all_stations.odb 
 
 # 4) Directory for figures
 echo "   Directory for figures ..."
-figure_dir=figures/standard_plots_${variable}_${year1}${month1}-${year2}${month2}
+#figure_dir=figures/standard_plots_${variable}_${year1}${month1}-${year2}${month2}
+figure_dir=$rootdir/SYNOP/output/figures/$experiment
 echo "     $figure_dir"
 if test -d "$figure_dir"; then
   echo $figure_dir exists
@@ -181,7 +185,7 @@ echo "   List of synop stations (with geographical coordinates): $station_list"
 echo "   Compiling the Fortran program needed for creating the figures ..."
 echo "      fortran-programs/plots_for_one_station.f95"
 
-gfortran fortran-programs/plots_for_one_station.f95 -o plots_for_one_station
+#gfortran fortran-programs/plots_for_one_station.f95 -o plots_for_one_station
 
 #################################################################
 #
@@ -197,8 +201,8 @@ line_number=2
 #
 while [ ${line_number} -le `expr $n_lines` ]
 do
-  head -`expr ${line_number}` ${station_list} | tail -1 > input.txt
-  read station longitude latitude < input.txt
+  head -`expr ${line_number}` ${station_list} | tail -1 > $rootdir/SYNOP/output/scratch/$experiment/input.txt
+  read station longitude latitude < $rootdir/SYNOP/output/scratch/$experiment/input.txt
 echo "   **********"
 echo "   Synop station ID, longitude, latitude: ${station} ${longitude} ${latitude}"
 #
@@ -207,14 +211,14 @@ echo "   Synop station ID, longitude, latitude: ${station} ${longitude} ${latitu
 # When simulation data are available, a means to retrieve the correct data points from it must be designed.
 echo "   Selecting the simulation data (mimicked this far by observations) for synop station: ${station}"
 #
-odb_command="odb sql 'select year,month,day,hour,value where station=${station} and (year>=${year1} and year<=${year2}) and (hour=0 or hour=6 or hour=12 or hour=18) and variable=${variable}' -i ${sim_file} -o sim_data"
+odb_command="odb sql 'select year,month,day,hour,value where station=${station} and (year>=${year1} and year<=${year2}) and (hour=0 or hour=6 or hour=12 or hour=18) and variable=${variable}' -i ${sim_file} -o $rootdir/SYNOP/output/scratch/$experiment/sim_data"
 eval ${odb_command}
 
 ################################################################
 # Select the rank histogram data for the station
 echo "   Selecting rank histogram data for synop station: ${station}"
 #
-odb sql select \* where station=${station} -i ${rh_file} -o rank_histograms_${variable}_${station}_${year1}${month1}-${year2}${month2}
+odb sql select \* where station=${station} -i ${rh_file} -o $rootdir/SYNOP/output/scratch/$experiment/rank_histograms_${variable}_${station}_${year1}${month1}-${year2}${month2}
 #
 ###############################################################
 # Select the quantiles for the station
@@ -223,12 +227,12 @@ echo "   Selecting the quantiles for synop station: ${station}"
 # 00, 06, 12 and 18 UTC are picked separately, since
 # select \* does not allow for parentheses (very strange)
 #
-rm quantile_selection_*
-odb sql select \* where hour=0 and station=${station} -i ${quant_file} -o quantile_selection_00
-odb sql select \* where hour=6 and station=${station} -i ${quant_file} -o quantile_selection_06
-odb sql select \* where hour=12 and station=${station} -i ${quant_file} -o quantile_selection_12
-odb sql select \* where hour=18 and station=${station} -i ${quant_file} -o quantile_selection_18
-cat quantile_selection_* > quantile_selection
+#rm quantile_selection_*
+odb sql select \* where hour=0 and station=${station} -i ${quant_file} -o $rootdir/SYNOP/output/scratch/$experiment/quantile_selection_00
+odb sql select \* where hour=6 and station=${station} -i ${quant_file} -o $rootdir/SYNOP/output/scratch/$experiment/quantile_selection_06
+odb sql select \* where hour=12 and station=${station} -i ${quant_file} -o $rootdir/SYNOP/output/scratch/$experiment/quantile_selection_12
+odb sql select \* where hour=18 and station=${station} -i ${quant_file} -o $rootdir/SYNOP/output/scratch/$experiment/quantile_selection_18
+cat quantile_selection_* > $rootdir/SYNOP/output/scratch/$experiment/quantile_selection
 #
 ##############################################################
 #
@@ -240,11 +244,13 @@ cat quantile_selection_* > quantile_selection
 #      in GrADS, but plotting in GrADS is omitted in this script.
 #
 ###############################################################
-./plots_for_one_station <<EOF
+# ?????????
+if [ 0 -eq 1 ]; then
+ ./plots_for_one_station <<EOF
  &PARAM
   sim_file='sim_data'
   year1=${year1},year2=${year2},month1=${month1},month2=${month2}
-  quantile_file='quantile_selection'
+  quantile_file='$rootdir/SYNOP/output/scratch/$experiment/quantile_selection'
   rank_histogram_file='rank_histograms_${variable}_${station}_${year1}${month1}-${year2}${month2}'
   grads_data_time_series='time_series_${variable}_${station}_${year1}${month1}-${year2}${month2}.grads'
   grads_data_rank_histogram='rank_histogram_${variable}_${station}_${year1}${month1}-${year2}${month2}.grads'
@@ -254,11 +260,28 @@ cat quantile_selection_* > quantile_selection
   l_code_in_char=.false.,l_round_6h=.false.
  &END
 EOF
-
+fi
+if [ 1 -eq 1 ]; then
+ $SRC_OBSALL_DIR/SYNOP/STATS/fortran-programs/plots_for_one_station <<EOF
+ &PARAM
+  sim_file='$rootdir/SYNOP/output/scratch/$experiment/sim_data'
+  year1=${year1},year2=${year2},month1=${month1},month2=${month2}
+  quantile_file='$rootdir/SYNOP/output/scratch/$experiment/quantile_selection'
+  rank_histogram_file='$rootdir/SYNOP/output/scratch/$experiment/rank_histograms_${variable}_${station}_${year1}${month1}-${year2}${month2}'
+  grads_data_time_series='$rootdir/SYNOP/output/scratch/$experiment/time_series_${variable}_${station}_${year1}${month1}-${year2}${month2}.grads'
+  grads_data_rank_histogram='$rootdir/SYNOP/output/scratch/$experiment/rank_histogram_${variable}_${station}_${year1}${month1}-${year2}${month2}.grads'
+  txt_data_time_series='$rootdir/SYNOP/output/scratch/$experiment/time_series_${variable}_${station}_${year1}${month1}-${year2}${month2}.txt'
+  txt_data_rank_histogram='$rootdir/SYNOP/output/scratch/$experiment/rank_histogram_${variable}_${station}_${year1}${month1}-${year2}${month2}.txt'
+  txt_data_quantiles='$rootdir/SYNOP/output/scratch/$experiment/quantiles_${variable}_${station}.txt'
+  l_code_in_char=.false.,l_round_6h=.false.
+  out_dir='$rootdir/SYNOP/output/scratch/$experiment/'
+ &END
+EOF
+fi
 ################################################################
 # Produce the figure in Python
 #
-cat <<EOF > standard_plot.cfg
+cat <<EOF > $rootdir/SYNOP/output/scratch/$experiment/standard_plot.cfg
 [data]
 variable=${variable}
 station_id=${station}
@@ -270,9 +293,9 @@ month_beg=${month1}
 month_end=${month2}
 
 [input]
-sim_data=time_series_${variable}_${station}_${year1}${month1}-${year2}${month2}.txt
-quantile_sel=quantiles_${variable}_${station}.txt
-rank_hists=rank_histogram_${variable}_${station}_${year1}${month1}-${year2}${month2}.txt
+sim_data=$rootdir/SYNOP/output/scratch/$experiment/time_series_${variable}_${station}_${year1}${month1}-${year2}${month2}.txt
+quantile_sel=$rootdir/SYNOP/output/scratch/$experiment/quantiles_${variable}_${station}.txt
+rank_hists=$rootdir/SYNOP/output/scratch/$experiment/rank_histogram_${variable}_${station}_${year1}${month1}-${year2}${month2}.txt
 
 [output]
 fig_name=${figure_dir}/standard_plot_${variable}_${station}_${year1}${month1}-${year2}${month2}_python.png
@@ -281,27 +304,27 @@ EOF
 ################################################################
 #
 echo "   Calling python to plot quantiles rank histogram for synop station: ${station}" 
-python3 python/plot_quantiles_rankhist_synop.py standard_plot.cfg
+python3 python/plot_quantiles_rankhist_synop.py $rootdir/SYNOP/output/scratch/$experiment/standard_plot.cfg
 
 ################################################################
 # Remove unnecessary files
 echo "   Removing unnecessary temporary files ..."
 
-rm input.txt
-rm vrange_*
-rm msd_and_p-value
-rm quantile_selection
-rm rank_histograms_${variable}_${station}_${year1}${month1}-${year2}${month2}
-rm sim_data
+#rm input.txt
+#rm vrange_*
+#rm msd_and_p-value
+#rm quantile_selection
+#rm rank_histograms_${variable}_${station}_${year1}${month1}-${year2}${month2}
+#rm sim_data
 ###rm msd_bootstrap_selection
 ###rm standard_plot_one_station
-rm time_series_commands
-rm time_series_${variable}_${station}_${year1}${month1}-${year2}${month2}.grads
-rm rank_histogram_${variable}_${station}_${year1}${month1}-${year2}${month2}.grads
-rm standard_plot.cfg
-rm time_series_${variable}_${station}_${year1}${month1}-${year2}${month2}.txt
-rm quantiles_${variable}_${station}.txt
-rm rank_histogram_${variable}_${station}_${year1}${month1}-${year2}${month2}.txt
+#rm time_series_commands
+#rm time_series_${variable}_${station}_${year1}${month1}-${year2}${month2}.grads
+#rm rank_histogram_${variable}_${station}_${year1}${month1}-${year2}${month2}.grads
+#rm standard_plot.cfg
+#rm time_series_${variable}_${station}_${year1}${month1}-${year2}${month2}.txt
+#rm quantiles_${variable}_${station}.txt
+#rm rank_histogram_${variable}_${station}_${year1}${month1}-${year2}${month2}.txt
 #
 ((line_number++))
 done
@@ -309,7 +332,7 @@ done
 ################################################################
 # The Fortran executable is not needed any more:
 #
-rm plots_for_one_station
-rm quantile_selection_*
-rm msd_and_p-value_*
-rm coordinates
+#rm plots_for_one_station
+#rm quantile_selection_*
+#rm msd_and_p-value_*
+#rm coordinates
diff --git a/SYNOP/STATS/python/plot_p_values_map_synop.py b/SYNOP/STATS/python/plot_p_values_map_synop.py
index 4c17da7b5b1e6d0e9ad8e494230425161e861f2d..bc243153490de92db3b5a0366505f46f203bcd1d 100644
--- a/SYNOP/STATS/python/plot_p_values_map_synop.py
+++ b/SYNOP/STATS/python/plot_p_values_map_synop.py
@@ -34,7 +34,7 @@ def read_data(p_values_file):
     return p_values_data
 
 
-def plot_p_values(p_values):
+def plot_p_values(p_values,figname):
     '''
     Description: plot p values on a map restricted to an area limited by lons (19, 32) and lats (59, 71)
     Input: numpy array  
@@ -122,21 +122,24 @@ def plot_p_values(p_values):
     fig.suptitle('SYNOP stations: p-values for ' + variable_shortnames[variable] +'\nquantiles in ' + timestring, fontsize=fs1)
 
     # save figure
-    plt.savefig('p_values.png', dpi=300)
+    #plt.savefig('p_values.png', dpi=300)
+    plt.savefig(figname, dpi=300)
     
 
-def main(p_values_file):
+def main(p_values_file,figurename):
     '''
     Main file: (1) reads in p values from file, (2) plot p values on a map
     '''
     
     p_values_data = read_data(p_values_file)
 
-    plot_p_values(p_values_data)
+    plot_p_values(p_values_data,figurename)
     
 
 if __name__=='__main__':
     p_values_file = sys.argv[1]
-    timestring = sys.argv[2]
+    timestring = sys.argv[2] # Not used?????????
+    figurename = sys.argv[3]
     
-    main(p_values_file)
+    #main(p_values_file) # original
+    main(p_values_file,figurename)
diff --git a/SYNOP/STATS/python/plot_rankhist_sum_all_stations_synop.py b/SYNOP/STATS/python/plot_rankhist_sum_all_stations_synop.py
index 83d945b539259d42bde2c47455225c811f69b2d0..4fbcc46a983e0deb38218391f91180a3f703556b 100644
--- a/SYNOP/STATS/python/plot_rankhist_sum_all_stations_synop.py
+++ b/SYNOP/STATS/python/plot_rankhist_sum_all_stations_synop.py
@@ -17,7 +17,7 @@ import matplotlib.pyplot as plt
 from matplotlib.ticker import (MultipleLocator, AutoMinorLocator)
 import sys
 
-def plot_rank_hist(p_freq, q_freq, number_of_stations, p01, p1, p5, max_freq_p, max_freq_q):
+def plot_rank_hist(p_freq, q_freq, number_of_stations, p01, p1, p5, max_freq_p, max_freq_q,figname):
     '''
     Input: p_freq, q_freq, number of stations, p01, p1, p5, max freq p, max freq q
     Description: Plots p and q frequencies and saves the figure with figname
@@ -103,7 +103,7 @@ def plot_rank_hist(p_freq, q_freq, number_of_stations, p01, p1, p5, max_freq_p,
     fig.suptitle(title, fontsize=fs1)
     
     # save figure
-    figname='rank_hist_sumstats.png'
+    #figname='rank_hist_sumstats.png'
     plt.savefig(figname, dpi=300)
 
 def read_data(rh_summary_file):
@@ -131,7 +131,8 @@ if __name__=='__main__':
     p5 = sys.argv[5]
     max_freq_p = float(sys.argv[6])
     max_freq_q = float(sys.argv[7])
+    figname = sys.argv[8]
 
     p_freq, q_freq = read_data(rh_summary_file)
-    plot_rank_hist(p_freq, q_freq, number_of_stations, p01, p1, p5, max_freq_p, max_freq_q)
+    plot_rank_hist(p_freq, q_freq, number_of_stations, p01, p1, p5, max_freq_p, max_freq_q,figname)
 
diff --git a/SYNOP/STATS/summary_rank_histograms_all_stations.sh b/SYNOP/STATS/summary_rank_histograms_all_stations.sh
index e5b7e385f01ab31be2a96949fdda6b6c067a5c95..267b0e217dc0abfaf890598502873e5187ddf0cb 100755
--- a/SYNOP/STATS/summary_rank_histograms_all_stations.sh
+++ b/SYNOP/STATS/summary_rank_histograms_all_stations.sh
@@ -103,7 +103,7 @@ fi
 echo "   Compiling the Fortran program that produces the rank histogram summary statistics ..."
 echo "      fortran-programs/rank_histogram_summary_statistics.f95"
 
-gfortran fortran-programs/rank_histogram_summary_statistics.f95 -o rank_histogram_summary_statistics
+#gfortran fortran-programs/rank_histogram_summary_statistics.f95 -o rank_histogram_summary_statistics
 
 ##################################################################
 #
@@ -111,7 +111,8 @@ gfortran fortran-programs/rank_histogram_summary_statistics.f95 -o rank_histogra
 #
 # 1) Rank histogram directory and input name file name without extension
 echo "   Directory for rank histogram ..."
-rh_dir=rank_histograms/${variable}_${year1}${month1}-${year2}${month2}
+#rh_dir=rank_histograms/${variable}_${year1}${month1}-${year2}${month2}
+rh_dir=$rootdir/SYNOP/output/scratch/$experiment/rank_histograms/${variable}_${year1}${month1}-${year2}${month2}
 echo "     $rh_dir"
 rh_file=${rh_dir}/rank_histograms_${variable}_${year1}${month1}-${year2}${month2}_all_stations
 rh_summary_file=${rh_dir}/rank_histograms_${variable}_${year1}${month1}-${year2}${month2}_summary
@@ -121,7 +122,8 @@ out_file=${rh_dir}/rh_summary_${variable}_${year1}${month1}-${year2}${month2}
 
 # 3) Directory for figures
 echo "   Directory for figures ..."
-figure_dir=figures
+#figure_dir=figures
+figure_dir=$rootdir/SYNOP/output/figures/$experiment
 echo "     $figure_dir"
 
 ##################################################################
@@ -135,7 +137,7 @@ odb sql select \* -i ${rh_file}.odb -o ${rh_file}.txt
 #
 echo "   Calculating the rank histogram summary statistics ..."
 #
-./rank_histogram_summary_statistics <<EOF
+$SRC_OBSALL_DIR/SYNOP/STATS/fortran-programs/rank_histogram_summary_statistics <<EOF
  &PARAM
   infile='${rh_file}.txt'
   outfile_p_freq='${rh_summary_file}_p-freq.txt'
@@ -148,7 +150,7 @@ echo "   Calculating the rank histogram summary statistics ..."
   grads_out=.true.
  &END
 EOF
-rm rank_histogram_summary_statistics
+#rm rank_histogram_summary_statistics
 
 ##############################################################
 #
@@ -191,9 +193,10 @@ echo "   (1) Plotting - P-Values Summary on 2D map ..."
 
 python_script=python/plot_p_values_map_synop.py
 
-python3 ${python_script} ${rh_summary_file}_p-values.txt ${year1}${month1}-${year2}${month2}
+#python3 ${python_script} ${rh_summary_file}_p-values.txt ${year1}${month1}-${year2}${month2}
+python3 ${python_script} ${rh_summary_file}_p-values.txt ${year1}${month1}-${year2}${month2} ${figure_dir}/p-value_map_${variable}_${year1}${month1}-${year2}${month2}.png
 
-mv p_values.png ${figure_dir}/p-value_map_${variable}_${year1}${month1}-${year2}${month2}.png
+#mv p_values.png ${figure_dir}/p-value_map_${variable}_${year1}${month1}-${year2}${month2}.png
 echo "        Output file: ${figure_dir}/p-value_map_${variable}_${year1}${month1}-${year2}${month2}.png"
 
 #####################################################################
@@ -204,9 +207,10 @@ echo "   (2) Plotting - Rank Histogram Summary Statistics ..."
 
 python_script=python/plot_rankhist_sum_all_stations_synop.py
 
-python3 ${python_script} ${rh_summary_file} ${number_of_stations} ${p01} ${p1} ${p5} ${max_freq_p} ${max_freq_q} ${figname}
+#python3 ${python_script} ${rh_summary_file} ${number_of_stations} ${p01} ${p1} ${p5} ${max_freq_p} ${max_freq_q} ${figname}
+python3 ${python_script} ${rh_summary_file} ${number_of_stations} ${p01} ${p1} ${p5} ${max_freq_p} ${max_freq_q} ${figure_dir}/rank-hist-sumstats_${variable}_${year1}${month1}-${year2}${month2}.png
 
-mv rank_hist_sumstats.png ${figure_dir}/rank-hist-sumstats_${variable}_${year1}${month1}-${year2}${month2}.png
+#mv rank_hist_sumstats.png ${figure_dir}/rank-hist-sumstats_${variable}_${year1}${month1}-${year2}${month2}.png
 echo "        Output file: ${figure_dir}/rank-hist-sumstats_${variable}_${year1}${month1}-${year2}${month2}.png"
 
 ######################################################################
diff --git a/SYNOP/graph_mod_obs.py b/SYNOP/graph_mod_obs.py
index e5c48406c58598245d4dbf958f65f530f8f85866..d48cf07e0901fdef6d6147e55f485556a1d081a5 100644
--- a/SYNOP/graph_mod_obs.py
+++ b/SYNOP/graph_mod_obs.py
@@ -145,7 +145,10 @@ def readmod(type_mod, path_tmp_mod, tmpfilename):
 #############################################################################
 # Passing parameters to program
 try:
-    fnamedate = sys.argv[1]; met_param = sys.argv[2]
+    path_tmp_obs=sys.argv[1]
+    path_tmp_mod=sys.argv[2]
+    outpath=sys.argv[3]
+    fnamedate = sys.argv[4]; met_param = sys.argv[5]
     print (fnamedate)
     print (met_param)
     print ('Command line: py-script-name YYYYMMDDHH met_param-acronym')
@@ -163,8 +166,8 @@ except:
 # ----- on Lumi
 #path_tmp_obs='/projappl/project_465000454/ama/DEOBS/SYNOP/DATAOBS/'
 #path_tmp_mod='/projappl/project_465000454/ama/DEOBS/SYNOP/DATAMOD/'
-path_tmp_obs='DATAOBS/'
-path_tmp_mod='DATAMOD/'
+#path_tmp_obs='DATAOBS/'
+#path_tmp_mod='DATAMOD/'
 
 print ('Path to dir with extacted OBS data: ', path_tmp_obs)
 print ('Path to dir with extacted MOD data: ', path_tmp_mod)
@@ -336,7 +339,7 @@ plt.text(mod_max,obs_max-3.0, rec_nr_obs)
 ##plt.show()
 
 # Saving figure to png-format-file
-fnamesave=type_obs+'_'+fnamedate+'_'+met_param+'.png'
+fnamesave=outpath+type_obs+'_'+fnamedate+'_'+met_param+'.png'
 plt.savefig(fnamesave, dpi = 300, bbox_inches="tight")
 
 print('Output graphical file is: ', fnamesave)
diff --git a/SYNOP/gsv_mod_data.sh b/SYNOP/gsv_mod_data.sh
index e711b932d646f3eb993818ad1c627e7d46ffba97..28d341e3ee70a70b77e42c0d32f5aed1242b491b 100755
--- a/SYNOP/gsv_mod_data.sh
+++ b/SYNOP/gsv_mod_data.sh
@@ -14,7 +14,7 @@ gsv_extr_filename="2t_r360x180.nc"
 
 # (2) path to dir where such file is placed
 #path_gsv_mod_data="/projappl/project_465000454/ama/DEOBS/SYNOP/GSVMODDATA/"
-path_gsv_mod_data="GSVMODDATA/"
+path_gsv_mod_data=$rootdir/SYNOP/output/scratch/$experiment/GSVMODDATA
 
 cd $path_gsv_mod_data; pwd
 
@@ -25,6 +25,7 @@ until [ -f $gsv_extr_filename ]
 do
      echo "   File is not available in dir: $path_gsv_mod_data"
      sleep 10
+     cp ${SRC_OBSALL_DIR}/SYNOP/GSVMODDATA/2t_r360x180.nc $path_gsv_mod_data/
 done
 echo "   File found: $gsv_extr_filename"
 
diff --git a/SYNOP/main_synop.sh b/SYNOP/main_synop.sh
index 008f1846a8b2ea85b4db975eae5c143d36a6b053..188339b1b82fd0d726d67d19563725e510a9847b 100755
--- a/SYNOP/main_synop.sh
+++ b/SYNOP/main_synop.sh
@@ -47,18 +47,19 @@ echo "    STEP #0 : PRE-CHEKING EXISTANCE OF NECESSARY DIRECTORIES ..."
 echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
 pwd
 echo "   Directory for pre-processing mod data extracted with gsv ..."
-inp_dir_gsvmoddata="GSVMODDATA"
+inp_dir_gsvmoddata=$rootdir/SYNOP/output/scratch/$experiment/GSVMODDATA #"GSVMODDATA"
 echo "$inp_dir_gsvmoddata"
 if test -d "$inp_dir_gsvmoddata"; then
   echo $inp_dir_gsvmoddata exists
 else
   echo $inp_dir_gsvmoddata does not exist
   echo "   Creating directory: $inp_dir_gsvmoddata"
-  mkdir $inp_dir_gsvmoddata
+  mkdir -p $inp_dir_gsvmoddata
+  cp SYNOP/GSVMODDATA/*.nc $inp_dir_gsvmoddata # for testing
 fi
 
 echo "   Directory for processing observation data ..."
-inp_dir_dataobs="DATAOBS"
+inp_dir_dataobs=$rootdir/SYNOP/output/scratch/$experiment/DATAOBS #"DATAOBS"
 echo "$inp_dir_dataobs"
 if test -d "$inp_dir_dataobs"; then
   echo $inp_dir_dataobs exists
@@ -69,7 +70,7 @@ else
 fi
 
 echo "   Directory for processing modeled data ..."
-inp_dir_datamod="DATAMOD"
+inp_dir_datamod=$rootdir/SYNOP/output/scratch/$experiment/DATAMOD #"DATAMOD"
 echo "$inp_dir_datamod"
 if test -d "$inp_dir_datamod"; then
   echo $inp_dir_datamod exists
@@ -79,15 +80,26 @@ else
   mkdir $inp_dir_datamod
 fi
 
+echo "   Directory for saving ODB data ..."
+inp_dir_data_ODB=$rootdir/SYNOP/output/ODB_data/$experiment
+echo $inp_dir_data_ODB
+if test -d "$inp_dir_data_ODB"; then
+  echo $inp_dir_data_ODB exists
+else
+  echo $inp_dir_data_ODB does not exist
+  echo "   Creating directory: $inp_dir_data_ODB"
+  mkdir $inp_dir_data_ODB
+fi
+
 echo "   Directory for saving graphical output ..."
-inp_dir_graphs="GRAPHS"
+inp_dir_graphs=$rootdir/SYNOP/output/figures/$experiment #"GRAPHS"
 echo "$inp_dir_graphs"
 if test -d "$inp_dir_graphs"; then
   echo $inp_dir_graphs exists
 else
   echo $inp_dir_graphs does not exist
   echo "   Creating directory: $inp_dir_graphs"
-  mkdir $inp_dir_graphs
+  mkdir -p $inp_dir_graphs
 fi
 
 echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
@@ -113,7 +125,7 @@ echo "===================================================================="
 # List all available splitted files (by time-slices) in dir GSVMODDATA/
 # Define YYYY MM DD HH to start calculations for time-slices
 
-tmp_file_tstamps="file_with_tstamps.txt"
+tmp_file_tstamps=$rootdir/SYNOP/output/scratch/$experiment/file_with_tstamps.txt #"file_with_tstamps.txt"
 #ls GSVMODDATA/ > $tmp_file_tstamps
 ls $inp_dir_gsvmoddata > $tmp_file_tstamps
 tail -n 1 "$tmp_file_tstamps" | tee >(wc -c | xargs -I {} truncate "$tmp_file_tstamps" -s -{})
@@ -142,6 +154,7 @@ echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
 #./synop_obs.sh 2020 01 20 15 00 00 $varMETnum $lon_val_min $lon_val_max $lat_val_min $lat_val_max
 b_min="00"
 b_sec="00"
+pwd
 ./synop_obs.sh $b_yy $b_mm $b_dd $b_hh $b_min $b_sec $varMETnum $lon_val_min $lon_val_max $lat_val_min $lat_val_max
 
 echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
@@ -173,9 +186,9 @@ echo " SCRIPT --- graph_mod_obs.py"
 echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
 #python graph_mod_obs.py 2020012000 2t
 #python graph_mod_obs.py 2020012015 $varMETstr
-python graph_mod_obs.py $b_yyyymmddhh $varMETstr
+python graph_mod_obs.py $inp_dir_dataobs/ $inp_dir_datamod/ $inp_dir_graphs/ $b_yyyymmddhh $varMETstr
 
-mv *.png GRAPHS/
+#mv *.png $inp_dir_graphs # GRAPHS/
 
 echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
 echo "               ..... STEP 4 - COMPLETED ....."
diff --git a/SYNOP/synop_mod.sh b/SYNOP/synop_mod.sh
index f5a0cd903186bf02572959a2704a0ef55c40ee06..c1bd15d8906027f5e32267d852e09b7923e64bdc 100755
--- a/SYNOP/synop_mod.sh
+++ b/SYNOP/synop_mod.sh
@@ -29,17 +29,17 @@ echo "Bash version ${BASH_VERSION}..."
 
 echo "   Input path to location of files with extracted (using gsv_interface) modelled data:"
 #inp_path_mod="/projappl/project_465000454/ama/DEOBS/SYNOP/GSVMODDATA/"
-inp_path_mod="GSVMODDATA/"
+inp_path_mod=$rootdir/SYNOP/output/scratch/$experiment/GSVMODDATA/ #"GSVMODDATA/"
 echo "      $inp_path_mod"
 
 echo "   Input path to location of files with extracted (using sql) observed data:"
 #inp_path_obs="/projappl/project_465000454/ama/DEOBS/SYNOP/DATAOBS/"
-inp_path_obs="DATAOBS/"
+inp_path_obs=$rootdir/SYNOP/output/scratch/$experiment/DATAOBS/ #"DATAOBS/"
 echo "      $inp_path_obs"
 
 echo "   Output path to location of modelled data interpolated to coordinates of synop stations:"
 #out_path_mod="/projappl/project_465000454/ama/DEOBS/SYNOP/DATAMOD/"
-out_path_mod="DATAMOD/"
+out_path_mod=$rootdir/SYNOP/output/scratch/$experiment/DATAMOD/ #"DATAMOD/"
 echo "      $out_path_mod"
 
 # Input name of nc-file with modelled data extracted with gsv_interface
@@ -60,7 +60,7 @@ infile=$inp_path_obs$infile
 
 # Name of output file with interpolated modelled data to positions of synop stations
 vardef="_"
-outfile="mod_synop$vardef$timefilename$vardef$varMETstr.dat"
+outfile=$rootdir/SYNOP/output/scratch/$experiment/mod_synop$vardef$timefilename$vardef$varMETstr.dat #"mod_synop$vardef$timefilename$vardef$varMETstr.dat"
 
 echo "   Name of output file for interpolated mod data: $outfile"
 
@@ -87,7 +87,7 @@ echo "   Number of records (numrec) in obs data file: $numrec"
 
 echo "   Creating unstructured grid for 2D geographical locations of synop stations ..."
 
-unstr_grid_file="grid_unstructured_synop.txt"
+unstr_grid_file=$rootdir/SYNOP/output/scratch/$experiment/grid_unstructured_synop.txt #"grid_unstructured_synop.txt"
 echo "   Name of file with unstructured grid: $unstr_grid_file"
 
 echo "gridtype = unstructured" > $unstr_grid_file  # adding grid type
@@ -108,8 +108,8 @@ done < $infile
 
 echo "   CDO calculating weights for unstructured grid ... "
 #cdo genbil,$unstr_grid_file -selname,2t $ncinfile weights_synop.nc
-cdo genbil,$unstr_grid_file -selname,$varMETstr $ncinfile weights_synop.nc
-cdo remap,$unstr_grid_file,weights_synop.nc $ncinfile tmpfile_synop_new.nc
+cdo genbil,$unstr_grid_file -selname,$varMETstr $ncinfile $rootdir/SYNOP/output/scratch/$experiment/weights_synop.nc
+cdo remap,$unstr_grid_file,$rootdir/SYNOP/output/scratch/$experiment/weights_synop.nc $ncinfile $rootdir/SYNOP/output/scratch/$experiment/tmpfile_synop_new.nc
 
 while IFS=' ' read -r f1 f2 f3 f4 f5 f6 f7 f8 f9 f10 f11
 do
@@ -135,12 +135,12 @@ do
    # without weights - original ...
    #cdo -s -outputtab,date,time,lon,lat,value -remapnn,"lon=${longitude}_lat=${latitude}" -selvar,${varMETstr} $ncinfile > tmpout_${station}_${variable}.txt
    # with weight - modified
-   cdo -s -outputtab,date,time,lon,lat,value -remapnn,"lon=${longitude}_lat=${latitude}" -selvar,${varMETstr} tmpfile_synop_new.nc > tmpout_${station}_${variable}.txt
-   cat tmpout_${station}_${variable}.txt | sed '1,1d' > tmpoutrev_${station}_${variable}.txt # deliting header line
-   sed -i s/$/" "${variable}/ tmpoutrev_${station}_${variable}.txt  # adding variable ID
-   sed -i s/$/" "${station}/ tmpoutrev_${station}_${variable}.txt   # adding station ID
-   cat tmpoutrev_${station}_${variable}.txt >> $outfile             # adding record to summary file
-   rm -rf tmpout_*.txt tmpoutrev_*.txt                              # cleaning tmp-files
+   cdo -s -outputtab,date,time,lon,lat,value -remapnn,"lon=${longitude}_lat=${latitude}" -selvar,${varMETstr} $rootdir/SYNOP/output/scratch/$experiment/tmpfile_synop_new.nc > $rootdir/SYNOP/output/scratch/$experiment/tmpout_${station}_${variable}.txt
+   cat $rootdir/SYNOP/output/scratch/$experiment/tmpout_${station}_${variable}.txt | sed '1,1d' > $rootdir/SYNOP/output/scratch/$experiment/tmpoutrev_${station}_${variable}.txt # deliting header line
+   sed -i s/$/" "${variable}/ $rootdir/SYNOP/output/scratch/$experiment/tmpoutrev_${station}_${variable}.txt  # adding variable ID
+   sed -i s/$/" "${station}/ $rootdir/SYNOP/output/scratch/$experiment/tmpoutrev_${station}_${variable}.txt   # adding station ID
+   cat $rootdir/SYNOP/output/scratch/$experiment/tmpoutrev_${station}_${variable}.txt >> $outfile             # adding record to summary file
+   rm -f $rootdir/SYNOP/output/scratch/$experiment/tmpout_*.txt #$rootdir/SYNOP/output/scratch/$experiment/tmpoutrev_*.txt                              # cleaning tmp-files
 
 done < $infile
 
@@ -151,8 +151,8 @@ sed -i 's/:/  /' $outfile
 sed -i 's/:/  /' $outfile
 
 # Removing extra temporary files ...
-rm -rf tmpfile_synop_new.nc weights_synop.nc
-rm -rf grid_unstructured_synop.txt 
+rm -r $rootdir/SYNOP/output/scratch/$experiment/tmpfile_synop_new.nc $rootdir/SYNOP/output/scratch/$experiment/weights_synop.nc
+rm -r $rootdir/SYNOP/output/scratch/$experiment/grid_unstructured_synop.txt 
 
 
 ###############################################################################
@@ -175,14 +175,15 @@ header_mod_synop_data="year@descr:integer month@descr:integer day@descr:integer
 sed  -i "1i ${header_mod_synop_data}" $outfile
 
 # Adding data to odb file ...
-mod_synop_odb="/scratch/project_465000454/ama/open_data_ODB/synop_mod_data_2010-2021.odb"   # Opt1 - new
+#mod_synop_odb="/scratch/project_465000454/ama/open_data_ODB/synop_mod_data_2010-2021.odb"   # Opt1 - new
 ##mod_synop_odb="/scratch/project_465000454/ama/open_data_ODB/synop_open_data_2010-2021.odb"  # Opt2 - original
+mod_synop_odb=$rootdir/SYNOP/output/ODB_data/$experiment/simulated_synop_data.odb #synop_open_data_2010-2021.odb
 echo "   Path and Name of odb-file with saved records:"
 echo "      $mod_synop_odb"
 
-odb import -d ' ' $outfile tmp_mod_synop_odb.odb
-cat tmp_mod_synop_odb.odb >> $mod_synop_odb
-rm -rf tmp_mod_synop_odb.odb
+odb import -d ' ' $outfile $rootdir/SYNOP/output/scratch/$experiment/tmp_mod_synop_odb.odb
+cat $rootdir/SYNOP/output/scratch/$experiment/tmp_mod_synop_odb.odb >> $mod_synop_odb
+rm -f $rootdir/SYNOP/output/scratch/$experiment/tmp_mod_synop_odb.odb
 
 # Deleting header line as 1st line in mod_synop_YYYYMMDDHH.dat file ... 
 sed -i -e "1d" $outfile
diff --git a/SYNOP/synop_obs.sh b/SYNOP/synop_obs.sh
index d0c9fdfff384c3130b371468d0b148f86173d275..b3b0037b195a837535fff3291dc31821167bcadc 100755
--- a/SYNOP/synop_obs.sh
+++ b/SYNOP/synop_obs.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
-echo "Bash version ${BASH_VERSION}..."
+#echo "Bash version ${BASH_VERSION}..."
 #module list
-pwd
+
 ########################################################################
 # DestinE Climate DT Project
 #
@@ -93,7 +93,8 @@ fi
 # On Lumi (ODB as a single file)
 
 echo "   Path to dir where ODB file is placed:"
-in_dir=/scratch/project_465000454/ama/open_data_ODB
+#in_dir=/scratch/project_465000454/ama/open_data_ODB
+in_dir=$rootdir/SYNOP/input/ODB_data
 echo "      $in_dir"
 
 echo "   Name of ODB file containing all synop obs data:"
@@ -101,7 +102,8 @@ in_file=synop_open_data_2010-2021.odb
 echo "      $in_file"
 
 echo "   Name of file for extracted synop obs data at geographical coordinates of stations:"
-out_file=obs_synop_${yyyymmdd}${hour}
+#out_file=obs_synop_${yyyymmdd}${hour}
+out_file=$rootdir/SYNOP/output/scratch/$experiment/DATAOBS/obs_synop_${yyyymmdd}${hour}
 echo "      $out_file"
 rm -f ${out_file}
 
@@ -166,10 +168,17 @@ echo "      year, month, day, hour, minute, second : $year $month $day $hour $mi
 #         2020               1              20               0               0               0       24.956800       60.326698              39        3.500000          100968
 
 echo "   Cleaning and moving extracted from odb synop obs data into separate folder DATAOBS ..."
-cat ${out_file} | sed '1,1d' > ${out_file}.dat
-rm -rf ${out_file}
-pwd
-mv ${out_file}.dat DATAOBS/
+if [ $test_run == 'true' ]; then
+    echo "### Note: running synop_obs.sh in test mode ###"
+    echo "2020 1 20 0 0 0 23.576000 68.602997 39 1.100000 102019" > ${out_file}.dat
+    echo "2020 1 20 0 0 0 20.850901 69.042801 39 1.200000 102017" >> ${out_file}.dat
+    echo "2020 1 20 0 0 0 25.423300 64.142601 39 1.300000 101695" >> ${out_file}.dat
+else
+    cat ${out_file} | sed '1,1d' > ${out_file}.dat
+fi
+rm -f ${out_file}
+#pwd
+#mv ${out_file}.dat DATAOBS/
 
 #  Some more 'odb sql' examples:
 #
diff --git a/compile_programs.sh b/compile_programs.sh
new file mode 100644
index 0000000000000000000000000000000000000000..c2613347e489aea8f02c37af38bc586b2c2b3fb4
--- /dev/null
+++ b/compile_programs.sh
@@ -0,0 +1,24 @@
+#!/bin/bash
+
+# Use this to compile all Fortran programs before containerization if they are not compiled yet.
+# List of programs that are used during the run:
+
+# SYNOP:
+# SYNOP/STATS/fortran-programs/rank_histograms_one_station.f95
+# SYNOP/STATS/fortran-programs/plots_for_one_station.f95
+# SYNOP/STATS/fortran-programs/rank_histogram_summary_statistics.f95
+
+# TEMP:
+# RADSOUND/STATRS/fortran-programs/rank_histograms_one_station.f95
+# RADSOUND/STATRS/fortran-programs/plots_for_one_station.f95
+# RADSOUND/STATRS/fortran-programs/rank_histogram_summary_statistics.f95
+
+gfortran SYNOP/STATS/fortran-programs/rank_histograms_one_station.f95 -o SYNOP/STATS/fortran-programs/rank_histograms_one_station
+gfortran SYNOP/STATS/fortran-programs/plots_for_one_station.f95 -o SYNOP/STATS/fortran-programs/plots_for_one_station
+gfortran SYNOP/STATS/fortran-programs/rank_histogram_summary_statistics.f95 -o SYNOP/STATS/fortran-programs/rank_histogram_summary_statistics
+
+gfortran RADSOUND/STATRS/fortran-programs/rank_histograms_one_station.f95 -o RADSOUND/STATRS/fortran-programs/rank_histograms_one_station
+gfortran RADSOUND/STATRS/fortran-programs/plots_for_one_station.f95 -o RADSOUND/STATRS/fortran-programs/plots_for_one_station
+gfortran RADSOUND/STATRS/fortran-programs/rank_histogram_summary_statistics.f95 -o RADSOUND/STATRS/fortran-programs/rank_histogram_summary_statistics
+
+
diff --git a/load_modules.sh b/load_modules.sh
index 3f378da57384714c64409134603e0121233ddae6..7dad629c05c978fb20d09ad28db5d1558a4711a8 100755
--- a/load_modules.sh
+++ b/load_modules.sh
@@ -1,7 +1,9 @@
 #!/bin/bash
 
-# In the case of testing the software, export the following variable
+# In the case of testing the software, export the following variables
 export test_run=true
+export rootdir=/projappl/project_465000454/data/OBSALL
+export experiment='a001'
 
 echo "#######################################################"
 echo "###                  OBSALL Apps                    ###"
@@ -31,6 +33,6 @@ module load metkit/1.11.0-cpeCray-23.03.lua
 ## later upgrade OBSALL Apps for Polytope tool 
 ## (required for SATELLITE observations) in Phase-2
 
-module list
+#module list
 
 
diff --git a/quick_test_as_batchjob.bash b/quick_test_as_batchjob.bash
index 7a321e03c701b36593205e016fdc77c783e5a550..46a7c132d6ba1e8740bdf05b4fed2afb8c7d03af 100644
--- a/quick_test_as_batchjob.bash
+++ b/quick_test_as_batchjob.bash
@@ -1,7 +1,7 @@
 #!/bin/bash -l
 #SBATCH --job-name=test_obsall   # Job name
 #SBATCH --output=test_obsall.eo # Name of stdout output file
-#SBATCH --error=test_obsall_2.eo# Name of stderr error file
+#SBATCH --error=test_obsall.eo# Name of stderr error file
 #SBATCH --partition=small       # Partition (queue) name small, debug
 #SBATCH --ntasks=1              # One task (process)
 #SBATCH --cpus-per-task=1     # Number of cores (threads)
@@ -9,9 +9,12 @@
 #SBATCH --time=12:00:00         # Run time (hh:mm:ss)
 #SBATCH --account=project_465000454  # Project for billing
 
+module purge
 source load_modules.sh
 
 # In the case of testing the software, export the following variable
 export test_run=true
+export experiment='a002'
 
-python run_obsall.py
+#python run_obsall.py
+./run_obsall.sh
diff --git a/run_obsall.sh b/run_obsall.sh
index 9b7e6060866c581843da3e4c558c8ac110d90703..5954461246f278eeb414e6ec89a454d1ca075348 100755
--- a/run_obsall.sh
+++ b/run_obsall.sh
@@ -4,26 +4,32 @@ echo "Bash version ${BASH_VERSION}..."
 ## OBSALL Apps (3 parts: SYNOP, TEMP, AMSU-A observations)
 
 ## Loading necessary modules ...
-module use /project/project_465000454/devaraju/modules/LUMI/23.03/C
-module load LUMI/23.03
-module load partition/C
-module load PrgEnv-gnu
-module load ecCodes/2.32.0-cpeCray-23.03.lua
-module load odb_api/0.18.1-cpeCray-23.03.lua
-module load python-climatedt/3.11.3-cpeCray-23.03.lua
-module load pyfdb/0.0.2-cpeCray-23.03.lua
-module load cray-hdf5/1.12.2.3
-module load cray-netcdf/4.9.0.3
-module load rttov/13.2
-module load radsim/3.2
-module load fdb/5.11.94-cpeCray-23.03.lua
-module load eckit/1.25.0-cpeCray-23.03.lua
-module load metkit/1.11.0-cpeCray-23.03.lua
+#module use /project/project_465000454/devaraju/modules/LUMI/23.03/C
+#module load LUMI/23.03
+#module load partition/C
+#module load PrgEnv-gnu
+#module load ecCodes/2.32.0-cpeCray-23.03.lua
+#module load odb_api/0.18.1-cpeCray-23.03.lua
+#module load python-climatedt/3.11.3-cpeCray-23.03.lua
+#module load pyfdb/0.0.2-cpeCray-23.03.lua
+#module load cray-hdf5/1.12.2.3
+#module load cray-netcdf/4.9.0.3
+#module load rttov/13.2
+#module load radsim/3.2
+#module load fdb/5.11.94-cpeCray-23.03.lua
+#module load eckit/1.25.0-cpeCray-23.03.lua
+#module load metkit/1.11.0-cpeCray-23.03.lua
+
+#VVV for convenient testing in terminal VVV#
+#source load_modules.sh
+#AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA#
 
 ## Import required libraries
 ## import sys
 ## import subprocess
 
+export SRC_OBSALL_DIR=$(pwd)
+
 ## --- Processing ground-based observations (SYNOP)
 echo "**********************************************************"
 echo "DestinE Climate Digital Twin - OBSALL Apps"
@@ -37,6 +43,7 @@ cd SYNOP
 pwd
 ./main_synop.sh
 pwd
+exit # Only SYNOP prepared properly for containerization.
 
 ## --- Processing radiosounding observations (TEMP)
 echo "**********************************************************"