some changes

muri_realtime.sh

-doy0=$(date -d -2hours  +%j)
-doy1=$(date   +%j)
-hour0=$(date -d -2hours +%H)
-hour1=$(date  +%H)
+source /home/awalther/ALGO/ssec_scripts/load_modules
+doy0=$(date -d -2hours  +%-j)
+doy1=$(date   +%-j)
+hour0=$(date -d -2hours +%-H)
+hour1=$(date  +%-H)
 echo $hour0 $hour1
+cd /home/awalther/ALGO/ssec_scripts/
 if [ $doy0 -eq $doy1 ]
     then 	
-   ./run_clavrx_muri.sh $doy0 45 $hour0 $hour1 all 2022
+   /bin/bash /home/awalther/ALGO/ssec_scripts/run_clavrx_muri.sh $doy0 45 $hour0 $hour1 spitfire 2022
    echo "same doy"
    else
-   ./run_clavrx_muri.sh $doy0 45 $hour0 23 all 2022
-   ./run_clavrx_muri.sh $doy1 45 0 $doy1 all 2022
+   /bin/bash /home/awalther/ALGO/ssec_scripts/run_clavrx_muri.sh $doy0 45 $hour0 23 spitfire 2022
+   /bin/bash /home/awalther/ALGO/ssec_scripts/run_clavrx_muri.sh $doy1 45 0 $doy1 spitfire 2022
 fi	

run_clavrx.sh

@@ -17,27 +17,19 @@ qsub_node=${5:-all}
 options=${7:-clavrx_options}
 region=${8:-0}
 # general paths
-iris_files_path='/home/awalther/ALGO/clavrx-dev/clavrx_bin/'
-iris_files_path='/home/awalther/SOFTWARE/clavrx_abi_aerosol_algorithm/clavrx_bin/'
+iris_files_path='/home/awalther/ALGO/exe_clavrx/'
 clavrx_run_file="clavrxorb"
 clavrx_l2_var_list="level2_list"
 l2_path='./'
 
 
-
-
-
-
-
-
-
 work_dir="/apollo/cloud/personal/$user/patmosx_processing/scripts/"
 out_path_base="/apollo/cloud/scratch/Satellite_Output/andi/MURI/"
 #out_path_base="/apollo/cloud/scratch/Satellite_Output/andi/TEST/"
 
-. sensor_list.sh
-. grid_list.sh
-. time_tools.sh
+. ./sensor_list.sh
+. ./grid_list.sh
+. ./time_tools.sh
 
 
 yyyydoy_tools $year $doy
@@ -97,6 +89,8 @@ case $sen_num in
   33)
  l1b_path='/ships19/cloud/PROJECTS/CLIMCAPS/DATA/CLAVRX/L1B/J1/2021/JAN/'
  l2_path='/ships19/cloud/PROJECTS/CLIMCAPS/DATA/CLAVRX/L2/J1/2021/JAN/'
+ l1b_path='/apollo/cloud/scratch/Satellite_Input/VIIRS/global/2019/'
+ l2_path='/apollo/cloud/scratch/Satellite_Input/VIIRS/global/2019/'
    ;; 
 esac
 
@@ -110,14 +104,20 @@ echo $l2_path
 
 for (( hhh = $hour0; hhh <= $hour1; hhh ++ ))
 do
-  . sensor_list.sh
+  . ./sensor_list.sh
   path_search_info $sen_num $year $doy $hhh
   yyyydoy_tools $year $doy $hhh
   
   tmp_script=$work_dir$satname'_'$year'_'$doy_str'_'$hour_str'_'$region'_patmosx.sh'
   tmp_work_dir=$work_dir$satname'_'$year'_'$doy_str'_'$hour_str'_'$region'/'
   echo '==>'$tmp_script
-  write_batch.sh $tmp_script $logs_path$satname'_'$year'_'$doy_str'_'$hour_str'_'$region'_patmosx.log' $qsub_node
+  ./write_batch.sh $tmp_script $logs_path$satname'_'$year'_'$doy_str'_'$hour_str'_'$region'_patmosx.log' $qsub_node
+  echo "module purge" >> $tmp_script
+  echo "module load gcc" >> $tmp_script
+  echo "module load hdf/4.2.15-nocdf" >> $tmp_script
+  echo "module load hdf5" >> $tmp_script
+  echo "module load netcdf4" >> $tmp_script
+
   echo "[ ! -d $tmp_work_dir ] && mkdir -v -p $tmp_work_dir" >> $tmp_script
   
   echo "cp $iris_files_path/write_filelist.sh $tmp_work_dir" >> $tmp_script

run_clavrx_muri.sh

@@ -35,9 +35,9 @@ work_dir="/apollo/cloud/personal/$user/patmosx_processing/scripts/"
 out_path_base="/apollo/cloud/scratch/Satellite_Output/andi/MURI/"
 #out_path_base="/apollo/cloud/scratch/Satellite_Output/andi/TEST/"
 
-. sensor_list.sh
-. grid_list.sh
-. time_tools.sh
+. /home/awalther/ALGO/ssec_scripts/sensor_list.sh
+. /home/awalther/ALGO/ssec_scripts/grid_list.sh
+. /home/awalther/ALGO/ssec_scripts/time_tools.sh
 
 
 yyyydoy_tools $year $doy
@@ -110,14 +110,14 @@ echo $l2_path
 
 for (( hhh = $hour0; hhh <= $hour1; hhh ++ ))
 do
-  . sensor_list.sh
+  . /home/awalther/ALGO/ssec_scripts/sensor_list.sh
   path_search_info $sen_num $year $doy $hhh
   yyyydoy_tools $year $doy $hhh
   
   tmp_script=$work_dir$satname'_'$year'_'$doy_str'_'$hour_str'_'$region'_patmosx.sh'
   tmp_work_dir=$work_dir$satname'_'$year'_'$doy_str'_'$hour_str'_'$region'/'
   echo '==>'$tmp_script
-  write_batch.sh $tmp_script $logs_path$satname'_'$year'_'$doy_str'_'$hour_str'_'$region'_patmosx.log' $qsub_node
+  /home/awalther/ALGO/ssec_scripts/write_batch.sh $tmp_script $logs_path$satname'_'$year'_'$doy_str'_'$hour_str'_'$region'_patmosx.log' $qsub_node
   echo "[ ! -d $tmp_work_dir ] && mkdir -v -p $tmp_work_dir" >> $tmp_script
   
   echo "cp $iris_files_path/write_filelist.sh $tmp_work_dir" >> $tmp_script
@@ -128,7 +128,7 @@ do
 
   echo "cd $tmp_work_dir" >> $tmp_script
 
-  echo "./write_filelist.sh $l1b_path $l2_path $file_srch $file_srch2" >> $tmp_script
+  echo "/home/awalther/ALGO/ssec_scripts/write_filelist.sh $l1b_path $l2_path $file_srch $file_srch2" >> $tmp_script
  # echo "./$clavrx_run_file -default $options -lines_per_seg $n_lines_per_seg -level2_list $clavrx_l2_var_list" >> $tmp_script
  echo "./$clavrx_run_file" >> $tmp_script
 

sensor_list.sh

@@ -406,7 +406,7 @@ function sensor_info {
     doy=$3
     hour=$4
     
-    . time_tools.sh
+    . ./time_tools.sh
     yyyydoy_tools $year $doy $hour
     
     case $1 in