Code cleanup (using namespace std)

.github/workflows/ls1_staticCodeAnalysis.yml

@@ -0,0 +1,21 @@
+name: Static-Code-Analysis
+
+on:
+  push:
+    # pushes to master
+    branches: [ master ]
+  pull_request:
+    # PRs to master
+    branches: [ master ]
+
+jobs:
+  static_analysis:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Setup
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y cpplint
+      - name: Run static code analysis script
+        run: ./checks/run-staticAnalysis.sh $PWD

.gitignore

@@ -7,11 +7,10 @@ src/MarDyn
 src/MarDyn.*
 !src/MarDyn.cpp
 src/MarDyn_*.*
-!src/MarDyn_version.h*
 .project
 .settings
 *.so.1.0
 *.a
 *.so
 doxygen_doc/
-__pycache__/
+__pycache__/

checks/check-buildOptions.sh

@@ -0,0 +1,52 @@
+#!/bin/bash
+# Script to test the building process by altering through different build options
+# It uses the default settings and sets the specified options one by one
+
+numJobs=20
+
+checkFolder=$PWD
+buildFolder=$PWD/../build_test_$(date '+%Y-%m-%d')
+
+declare -A optionsList
+
+optionsList[ENABLE_MPI]=ON
+optionsList[VECTOR_INSTRUCTIONS]=SSE
+optionsList[VECTOR_INSTRUCTIONS]=AVX2
+optionsList[CMAKE_BUILD_TYPE]=Debug
+optionsList[OPENMP]=ON
+optionsList[ENABLE_AUTOPAS]=ON
+optionsList[ENABLE_UNIT_TESTS]=ON
+optionsList[QUICKSCHED]=ON
+optionsList[FMM_FFT]=ON
+optionsList[WITH_PAPI]=ON
+optionsList[ENABLE_ALLLBL]=ON
+optionsList[ENABLE_VTK]=ON
+optionsList[REDUCED_MEMORY_MODE]=ON
+
+
+# CMAKE
+mkdir -p $buildFolder
+cd $buildFolder
+
+echo "Running CMAKE in folder: $buildFolder"
+
+for option in "${!optionsList[@]}"
+do
+	echo "   Running option: ${option}=${optionsList[${option}]}"
+	rm $buildFolder/* -rf
+	( CC=mpicc CXX=mpicxx cmake -D${option}=${optionsList[${option}]} .. && make -j${numJobs} ; echo "$?" ) &> $checkFolder/build_test_cmake_${option}.log
+done
+
+
+# MAKE
+cd $checkFolder/../src
+
+echo "Running make in src"
+
+for option in "${!optionsList[@]}"
+do
+	echo "   Running option: ${option}=${optionsList[${option}]}"
+	make clean &> /dev/null
+	( make -j${numJobs} -f Makefile ${option}=${optionsList[${option}]} ; echo "$?" ) &> $checkFolder/build_test_make_${option}.log
+done
+

checks/run-staticAnalysis.sh

@@ -0,0 +1,120 @@
+#!/bin/bash
+# Script to run static code analysis
+
+#set strict pipefail option
+#set -eo pipefail
+
+# A path to the root folder of ls1 mardyn can be set via an argument; if not, the parent folder of "checks" is used
+if [ $# -eq 1 ]
+then
+  rootFolder=$1
+else
+  rootFolder=$PWD/..
+fi
+
+echo "Running in $rootFolder"
+
+warnings=""
+
+codeFiles=$( find $rootFolder/src -name "*.h" -or -name "*.cpp" -printf "%p " )
+
+# Similar to check_format of MegaMol repo
+for file in $codeFiles; do
+
+  # Check if using namespace std is used
+  if grep -q "using namespace std;" "$file"; then
+    echo "\"using namespace std;\" was used in $file"
+    warnings+="Do not use \"using namespace std;\"\n"
+  fi
+
+  # Check if using Log::global_log is used
+  if grep -q "using namespace std;" "$file"; then
+    echo "\"using Log::global_log;\" was used in $file"
+    warnings+="Do not use \"using Log::global_log;\"\n"
+  fi
+
+  # Check if file is UTF-8 (or ASCII)
+  encoding=$(file -b --mime-encoding "$file")
+  if [[ $encoding != "us-ascii" && $encoding != "utf-8" ]]; then
+    # Fix
+    #tmp_file=$(mktemp)
+    #iconv -f "$encoding" -t utf-8 -o "$tmp_file" "$file"
+    #mv -f "$tmp_file" "$file"
+    echo "The following file is not ASCII/UTF-8 encoded: $file"
+    warnings+="At least one file is not ASCII/UTF-8 encoded\n"
+  fi
+
+  # Check if file contains CRLF line endings
+  fileinfo=$(file -k "$file")
+  if [[ $fileinfo == *"CRLF"* ]]; then
+    # Fix
+    #sed -i 's/\r$//' "$file"
+    echo "The following file contains CRLF line endings: $file"
+    warnings+="At least one file contains CRLF line endings\n"
+  fi
+
+  # Check if file starts with BOM
+  if [[ $fileinfo == *"BOM"* ]]; then
+    # Fix
+    #sed -i '1s/^\xEF\xBB\xBF//' "$file"
+    echo "The following file starts with BOM: $file"
+    warnings+="At least one file starts with BOM\n"
+  fi
+
+  # Check if file ends with newline
+  if [[ -n "$(tail -c 1 "$file")" ]]; then
+    # Fix
+    #sed -i -e '$a\' "$file"
+    echo "The following file does not end with newline: $file"
+    warnings+="At least one file does not end with newline\n"
+  fi
+
+done
+
+# Only print warnings once
+warnings=$(printf "$warnings" | sort | uniq)
+warnings="# Warnings\n"$warnings"\n\n"
+
+# Run cpplint
+
+# Lines starting with one minus sign are filters which exclude certain rules
+
+#-runtime/int,\
+#-readability/alt_tokens,\
+#-whitespace/blank_line,\
+#-whitespace/braces,\
+#-whitespace/comma,\
+#-whitespace/comments,\
+#-whitespace/indent,\
+#-whitespace/operators,\
+#-whitespace/parens,\
+
+currentVersion=$(git rev-parse --abbrev-ref HEAD)
+
+for VERSION in "new" "master"
+do
+  echo "Checking ${VERSION} version"
+
+  if [[ "${VERSION}" == "master" ]]
+  then
+    git fetch &> /dev/null
+    git switch master &> /dev/null
+  else
+    git switch ${currentVersion} &> /dev/null
+  fi
+
+  cpplint --filter=-whitespace/tab --linelength=200 --counting=detailed ${codeFiles} &> $rootFolder/staticAnalysis_${VERSION}.log
+
+  grep "Category\|Total errors found" $rootFolder/staticAnalysis_${VERSION}.log > $rootFolder/staticAnalysis_${VERSION}_summary.log
+
+done
+
+git switch ${currentVersion} &> /dev/null
+
+warnings+="\n# cpplint\n   New or fixed warnings/errors (master <-> new commit):\n\`\`\`master $(printf '%54s' " ") | new\n"
+
+# Delete "--suppress-common-lines" to see all errors/warnings
+warnings+=$(diff -y --suppress-common-lines $rootFolder/staticAnalysis_master_summary.log $rootFolder/staticAnalysis_new_summary.log)
+
+printf "\n\n$warnings\n"
+printf "$warnings\`\`\`\n" >> $GITHUB_STEP_SUMMARY

checks/run-validation.sh

@@ -0,0 +1,31 @@
+#!/bin/bash
+# Testscript running validation tests according to GitHub Actions but without comparison to master
+#
+# Copyright (c) 2023 Simon Homes
+#
+
+repoPath="$PWD/.."  # Path to root directory
+
+export OMP_NUM_THREADS=2
+
+logfileName="${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)
+
+	# 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
+

src/Common.cpp

@@ -45,10 +45,10 @@ void calculateDistances( float * __restrict__ valuesA[3], float* __restrict__ co
 		float ** __restrict__ distances, float *** __restrict__ distanceVectors ) {
 
 /*	for (int i = 0; i < numValuesA; i++) {
-		std::cout << "A Points: " << valuesA[0][i] << "," << valuesA[1][i] << "," << valuesA[2][i] << endl;
+		std::cout << "A Points: " << valuesA[0][i] << "," << valuesA[1][i] << "," << valuesA[2][i] << std::endl;
 	}
 	for (int i = 0; i < numValuesB; i++) {
-			std::cout << "B Points: " << valuesB[0][i] << "," << valuesB[1][i] << "," << valuesB[2][i] << endl;
+			std::cout << "B Points: " << valuesB[0][i] << "," << valuesB[1][i] << "," << valuesB[2][i] << std::endl;
 	}
 */