Fix script to run examples locally

checks/run-validation.sh

@@ -1,31 +1,19 @@
 #!/bin/bash
 # Testscript running validation tests according to GitHub Actions but without comparison to master
 #
-# Copyright (c) 2023 Simon Homes
+# Copyright (c) 2023      Simon Homes
+# Copyright (c) 2024      Christoph Niethammer <[email protected]>
 #
 
 repoPath="$PWD/.."  # Path to root directory
 
 export OMP_NUM_THREADS=2
 
+inputlist="${repoPath}/examples/example-list.txt"
 logfileName="${repoPath}/examples/run-validation.log"
 rm -f ${logfileName}
 
-IFS=$'\n'
-for i in $(cat "${repoPath}/examples/example-list.txt" )
-do
-	# skip if comment or empty line
-	if [[ $i == \#* || -z "$i" ]]
-	then
-		continue
-	fi
-	cd ${repoPath}/examples/$(dirname $i)
+cd ${repoPath}/examples
+./run-examples.sh -v --inputlist "${inputlist}" --logfile "${logfileName}"
 
-	# run the examples
-	printf "Running example: ${i} ... " | tee -a ${logfileName}
-	EXE=${repoPath}/build/src/MarDyn
-
-	mpirun --oversubscribe -np 4 ${EXE} $(basename $i) --steps=20 | tee -a ${logfileName}
-	printf "done\n"
-done
 

examples/run-examples.sh

@@ -1,36 +1,149 @@
 #!/bin/bash
 # Testscript running all examples from example-list.txt
 #
-# Copyright (c) 2017      Christoph Niethammer <[email protected]>
+# Copyright (c) 2017-2024 Christoph Niethammer <[email protected]>
 #
 
-MARDYN_EXE="mpirun -np 1 $PWD/../src/MarDyn"
-MARDYN_OPTIONS="--steps 10 -v"
+# Some default values
+MARDYN_EXE="$PWD/../src/MarDyn"
+MARDYN_ARGS="--steps 20 -v"
+MPIRUN_EXE="mpirun"
+# Oversubscribe is specific to OpenMPI. If you use something different this flag needs to be removed / replaced.
+MPIRUN_ARGS="-n 4 --oversubscribe"
 EXAMPLE_LIST_FILE=${EXAMPLE_LIST_FILE:=example-list.txt}
 LOGFILE=${LOGFILE:=$PWD/run-examples.log}
 
-#mapfile -t all_examples < $EXAMPLE_LIST_FILE # requires bash4 ...
-declare -a all_examples
-while IFS= read -r; do all_examples+=("$REPLY"); done < $EXAMPLE_LIST_FILE
+TEMP=$(getopt -o vh --long "help,inputlist:,logfile:,mardyn_args:,mardyn_exe:,mpirun_args:,mpirun_exe:,verbose" -- $@)
 
+if [ $? -ne 0 ]; then
+  echo "Error parsing commandline"
+  exit 1
+fi
+
+eval set -- "$TEMP"
+unset TEMP
+
+function print_help() {
+cat <<EOF
+$(basename $0) is a script to execute MarDyn examples from a inputfile list file
+
+A inputlist file contains one path per line to a configuration file to be passed to MarDyn.
+MarDyn is executed with one configuration file at a time.
+In the inputlist file empty lines and lines starting with '#' are ignored.
+
+Usage:
+   $0 [OPTIONS ...]
+   $0 [-h|--help]
+
+Options:
+ -i,--inputlist   <FILE>    path to an inputfile list
+    --logfile     <FILE>    path for the logfile
+    --mpirun_exe  <mpirun>  mpirun command or path to mpirun executable
+    --mpirun_args <ARGS>    arguments to be passed to the mpirun command
+    --mardyn_exe  <MarDyn>  path to a MarDyn executable
+    --mardyn_args <ARGS>    arguments to be passed to MarDyn for each input file
+ -v,--verbose               verbose output
+ -h,--help                  show this help
+
+EOF
+}
+
+while true; do
+  case "$1" in
+    '--logfile')
+      LOGFILE="$2"
+      shift 2
+      continue
+      ;;
+    '--mardyn_exe')
+       MARDYN_EXE="$2"
+       shift 2
+       continue
+       ;;
+    '--mardyn_args')
+       MARDYN_ARGS="$2"
+       shift 2
+       continue
+       ;;
+    '--mpirun_exe')
+       MPIRUN_EXE="$2"
+       shift 2
+       continue
+       ;;
+    '--mpirun_args')
+       MPIRUN_ARGS="$2"
+       shift 2
+       continue
+       ;;
+    '--inputlist')
+       EXAMPLE_LIST_FILE="$2"
+       shift 2
+       continue
+       ;;
+    '-v'|'--verbose')
+       VERBOSE=true
+       shift
+       continue
+       ;;
+    '-h'|'--help')
+       PRINT_HELP_AND_EXIT=true
+       shift
+       break
+       ;;
+   '--')
+       shift
+       break
+       ;;
+    * )
+       echo "ERROR Unknown Option $1"
+       exit 1
+       ;;
+  esac
+done
+
+if [ $PRINT_HELP_AND_EXIT ]; then
+    print_help
+    exit 0
+fi
+
+
+all_examples=()
 failed_examples=()
 
-# definitions for esear color output to display
-Color_Off='\e[0m'       # Text Reset
-IGreen='\e[0;92m'       # Intense Green
-IRed='\e[0;91m'         # Intense Red
-IMagenta='\e[0;95m'     # magenta
+while IFS= read -r line ; do
+  # Skip comment lines, starting with `#`.
+  [[ "$line" =~ ^#.*$ ]] && continue
+  # Skip empty lines
+  [[ "$line" =~ ^$ ]] && continue
+
+  example="$line"
+  if [ $VERBOSE ]; then
+    echo "Going to run example file $example"
+  fi
+  all_examples+=("$example")
+done < "$EXAMPLE_LIST_FILE"
+
+if [ $VERBOSE ]; then
+   echo "Writing test outputs to $LOGFILE"
+fi
+
+# definitions for easy color output if we are running in a terminal
+if [ -t 0 -a -t 1 -a -t 2 ]; then
+  Color_Off='\e[0m'       # Text Reset
+  IGreen='\e[0;92m'       # Intense Green
+  IRed='\e[0;91m'         # Intense Red
+  IMagenta='\e[0;95m'     # magenta
+fi
 
 logfile=$LOGFILE
 date > $logfile
-for example in ${all_examples[@]}
-do
+for example in ${all_examples[@]} ; do
   example_dir=$(dirname $example)
   example_inp_file=$(basename $example)
-  echo -e -n "Running example ${IMagenta}$example_inp_file${Color_Off} in $example_dir ... "
+  echo -e -n "Running example ${IMagenta}$example_inp_file${Color_Off} in ${IMagenta}$example_dir${Color_Off} ... "
   echo "Running example $example_inp_file in $example_dir" >> $logfile
   pushd "$example_dir" >/dev/null
-  cmd="$MARDYN_EXE $MARDYN_OPTIONS $example_inp_file"
+  cmd="$MPIRUN_EXE $MPIRUN_ARGS $MARDYN_EXE $MARDYN_ARGS $example_inp_file"
   echo $cmd >>$logfile
   { $cmd ; } >>$logfile 2>&1
   ret=$?
@@ -43,6 +156,7 @@ do
     echo "Running example $example_inp_file in $example_dir ... Result: failed" >> $logfile
   fi
   popd >/dev/null
+  sleep 1 # sleep for 1 second to make cancelation with CTR-C easier
 done
 
 echo "----------------------------------------"