Code improvements for massive submission

src/SH12A_ddd/postprocess.sh

@@ -15,22 +15,17 @@ echo "-----------">> README.md
 echo "(add your description here)" >> README.md
 echo "" >> README.md
 
-#switch to wdir and build all
+#switch to wdir and convert all bdo files to ddd files
 cd $pwdir/$wdir
 for shdir in $(find . -mindepth 3 -maxdepth 3 -type d )
 do
     echo
     echo "Processing directory: "$wdir/$shdir
 
-	cd $shdir
-	echo convertmc tripddd --many "*.bdo"
+	  cd $shdir
+	  convertmc tripddd --many "*.bdo"
     cd $pwdir
-
-    # strip energy directory from dir current dir name
-    tdir=`dirname $shdir`
-
-    # build energy specific target directory and copy ddd file to it
-    targetdir=$ddir/$tdir
-    mkdir -p $targetdir
-    echo cp -v $shdir/*.ddd $targetdir/.
 done
+
+cd $pwdir
+find $wdir -name "*.ddd"  | xargs -i sh -c 'echo {}; echo {} | mkdir -p $ddir/`cut -d/ -f3-4`/; cp -v {} $ddir/`cut -d/ -f3-4`/'

src/SH12A_ddd/prepare.py

@@ -68,16 +68,16 @@ def fwhm_to_sigma(fwhm):
         """
         return fwhm / (2.0 * np.sqrt(2.0 * np.log(2.0)))
 
-    def read(self, dir):
+    def read(self, dir_path):
         """
         Reads the template files, and stores them in self object.
         """
-        fname_beam = os.path.join(dir, "beam.dat")
-        fname_geo = os.path.join(dir, "geo.dat")
-        fname_mat = os.path.join(dir, "mat.dat")
-        fname_det = os.path.join(dir, "detect.dat")
+        fname_beam = os.path.join(dir_path, "beam.dat")
+        fname_geo = os.path.join(dir_path, "geo.dat")
+        fname_mat = os.path.join(dir_path, "mat.dat")
+        fname_det = os.path.join(dir_path, "detect.dat")
 
-        self.template_dir = dir
+        self.template_dir = dir_path
 
         with open(fname_beam) as file:
             self.tbeam = file.readlines()
@@ -88,7 +88,7 @@ def read(self, dir):
         with open(fname_det) as file:
             self.tdet = file.readlines()
 
-    def write(self, ion):
+    def write(self):
         """
         Write the SH12A output files to self.path for given ion.
         Stopping power files are symlinked to the files found in template/
@@ -205,9 +205,9 @@ def main(args):
         logger.info(ion.name)
         for energy in np.arange(ion.emin, ion.emax, ion.estep):
             t.generate_dats(ion, energy, nstat, nsave, rifi=True)
-            t.write(ion)
+            t.write()
             t.generate_dats(ion, energy, nstat, nsave, rifi=False)
-            t.write(ion)
+            t.write()
 
 
 if __name__ == '__main__':

src/SH12A_ddd/rsshield.sh

@@ -9,12 +9,16 @@
 #SBATCH --output=shieldhitJob.%j.out     # standard output file name
 #SBATCH --error=shieldhitJob.%j.err      # standard error output file name
 #SBATCH --ntasks=1
-#SBATCH --contiguous
+#SBATCH --ntasks-per-node=1
+#SBATCH -p plgrid
+#SBATCH --time=0:59:00
+
 
 #echo Node ID       $SLURM_NODEID
 #echo NTasks        $SLURM_NTASKS
 #echo NNodes        $SLURM_NNODES
 #echo LocalID       $SLURM_LOCALID
 #echo Array task ID $SLURM_ARRAY_TASK_ID
 
-shieldhit -N${SLURM_ARRAY_TASK_ID}
+# overwrite number of histories and set upper limit on execution time
+shieldhit -N${SLURM_ARRAY_TASK_ID} -n 10000000 --time="00:58:00"

src/SH12A_ddd/submit.sh

@@ -7,7 +7,6 @@ for shdir in $(find . -mindepth 3 -maxdepth 3 -type d )
 do
 	cd $shdir
 	echo $shdir
-	# echo sbatch --array 0-16 rsshield.sh
-	echo sbatch --array 0 ../../../../rsshield.sh
+	sbatch --array 0 ../../../../rsshield.sh
 	cd ${wdir}/wdir
 done

src/SH12A_ddd/template/geo.dat

@@ -1,5 +1,5 @@
 *---><---><--------><------------------------------------------------>
-    0    0           Water target for DDD generation.
+    1    0           Water target for DDD generation.
 *---><---><--------><--------><--------><--------><--------><-------->
 * phantom / target
   RPP    1     -30.0      30.0     -30.0      30.0       0.0      60.0