add flac compression batch script

dc1/noise_sim/compress_hdf5.slurm

@@ -0,0 +1,68 @@
+#!/bin/bash
+#SBATCH --qos=regular
+#SBATCH --time=05:00:00
+#SBATCH --nodes=1
+#SBATCH --job-name=CMBS4_todcompress
+#SBATCH --licenses=SCRATCH
+#SBATCH --constraint=cpu
+#SBATCH --account=mp107
+
+# set parent directory corresponding to one frequency band
+PARENT_DIRECTORY="/global/cfs/cdirs/cmbs4/dc/dc0/staging/noise_sim/outputs_rk/LAT0_CHLAT/f090"
+
+# set range of observations to compress by this script (inclusive)
+START_INDEX=1
+END_INDEX=30
+
+echo "Listing all observations in $PARENT_DIRECTORY"
+
+# list all observations in parent directory and save to a variable
+SUBDIR_LIST=$(find "$PARENT_DIRECTORY" -mindepth 1 -maxdepth 1 -type d | sort)
+# extract observations names for printing to console
+SUBDIR_NAMES=$(echo "$SUBDIR_LIST" | xargs -I{} basename {})
+echo "Observations found: "
+echo "$SUBDIR_NAMES"
+
+echo "Proceeding to compress observations indexed in range: $START_INDEX-$END_INDEX"
+# select subset of observations (subdirectories) based on range and save to a variable
+SELECTED_SUBDIRS=$(echo "$SUBDIR_LIST" | sed -n "${START_INDEX},${END_INDEX}p")
+# extract selected observations names for printing to console
+SELECTED_SUBDIR_NAMES=$(echo "$SELECTED_SUBDIRS" | xargs -I{} basename {})
+echo "Selected observations: "
+echo "$SELECTED_SUBDIR_NAMES"
+
+# loop through selected subdirectories and process each one
+for subdir in $SELECTED_SUBDIRS; do
+  echo "Processing observation: $(basename $subdir)"
+  # search for files with the expected starting keywords : 'RISING' or 'SETTING'
+  FILE_LIST=$(find "$subdir" -type f \( -name "RISING*" -o -name "SETTING*" \) -printf "%p ")
+  # extract file names for printing to console
+  echo "Files to compress: "
+  for filename in $FILE_LIST; do
+    echo $(basename $filename)
+  done
+
+  # call compression script on the list of files
+  date
+  echo "Calling flac compression script ..."
+  srun -n 128 python compress_hdf5.py --verify --obs $FILE_LIST > "log_$(basename $subdir).txt" 2>&1
+
+  # if python script runs without error, delete backup files
+  if [ $? -eq 0 ]; then
+    echo "FLAC compression script ran successfully. Deleting backup files..."
+    if find "$subdir" -type f -name "*uncompressed.h5" -delete; then
+      echo "Backup files deleted successfully."
+      date
+    else
+      # If backup files deletion fails for some reason we stop the everything to avoid any risk of running out of disk memory.
+      echo "Error deleting backup files. Exiting loop over observations."
+      date
+      break
+    fi
+  else
+    echo "FLAC compression script encountered an error. Not deleting any files."
+    date
+  fi
+done
+
+echo "Observation batch $START_INDEX-$END_INDEX processing in $(basename $PARENT_DIRECTORY) band done. Please verify log files."