[AlPhaPha] Adding cpu cores automatic detection

Projects/AlPhaPha/2024/ChainSnake.sh

-for run in {245..252}; do
+for run in {201..259}; do
     ./convert_snakemake_generic.sh "$run"
     wait
 done

Projects/AlPhaPha/2024/Snakefile

@@ -3,7 +3,7 @@ import subprocess
 
 # Lire le répertoire d'entrée depuis les arguments de configuration
 #input_directory = config["folder"]
-input_directory = os.getcwd() + "/../DataMacro/output/run_252"
+input_directory = os.getcwd() + "/../DataMacro/output/run_247"
 origin = [] 
 # Iterate over files in input_directory
 for filename in os.listdir(input_directory):
@@ -12,14 +12,14 @@ for filename in os.listdir(input_directory):
     origin.append(filename)
 
 # Définir le répertoire de sortie pour les fichiers convertis
-phy_directory = os.getcwd() + "/../DataMacro/output/analysis/run_252"
+phy_directory = os.getcwd() + "/../DataMacro/output/analysis/run_247"
 #phy_directory = "./"
 
 # define target files directory
 analysedfile = []
 for inputfile in origin:
   #analysedfile.append("/home/morfouacep/Physics/NPTool/nptool/Projects/ana_e850/root/analysis/"+inputfile.replace("_raw_","_"))
-  analysedfile.append( os.getcwd() + "/../DataMacro/output/analysis/run_252/"+inputfile)
+  analysedfile.append( os.getcwd() + "/../DataMacro/output/analysis/run_247/"+inputfile)
 
 ## batch rules
 rule all:

Projects/AlPhaPha/2024/convert_snakemake_generic.sh

@@ -3,6 +3,7 @@
 #Declare run number
 #RUN_NUMBER="246"
 RUN_NUMBER="$1"
+num_cores=$(( $(nproc) - 4 ))
 
 # Check if Snakefile exists
 if [[ ! -f "Snakefile" ]]; then
@@ -15,13 +16,17 @@ sed -i "s/run_[a-zA-Z0-9]\{3\}/run_${RUN_NUMBER}/g" Snakefile
 echo "All occurrences of 'run_*' have been replaced with 'run_${RUN_NUMBER}' in Snakefile."
 
 echo "- executing snakemake file for npanalysis..."
-snakemake --cores 30 --forceall --keep-incomplete --keep-going --rerun-incomplete --restart-times 3
+snakemake --cores ${num_cores} --forceall --keep-incomplete --keep-going --rerun-incomplete --restart-times 3
 
 echo "- snakemake executed successfully!"
 echo "- Merging file..."
 
-OName="\"Run${RUN_NUMBER}AoQ\""
+OName="\"Run${RUN_NUMBER}\""
 OPATH="\"root/analysis\""
 Path="\"../DataMacro/output/analysis/run_${RUN_NUMBER}/run_raw_${RUN_NUMBER}_\""
 
 root -l -q "../DataMacro/Merger.C(30,${OPATH},${OName},${Path})"
+
+wait 
+
+rm ../DataMacro/output/analysis/run_${RUN_NUMBER}/run_raw_*.root

Projects/AlPhaPha/DataMacro/Secator.sh

@@ -16,7 +16,7 @@ for ((i=0; i<MAX_JOBS; i++)); do
 done
 
 
-for run in {220..262}; do
+for run in {201..262}; do
     read -u 3  # Wait for an available slot
     {
         root -l -q "./Secator.C(\"/home/efremovt/Data/2to_SSD/2024/np_raw/run_raw_"$run".root\",\"output/run_"$run"/\", 30)"