check_commit_mesonh.sh

#!/bin/bash

#set -x
set -e

# Repertoire où Mesonh MNH-V5-5-0 officiel est installe
#REFDIR=$HOME
# Repertoire où MNH-V5-5-0_PHYEX.tar.gz modifie pour accueillir PHYEX se trouve
#TARGZDIR=$HOME

availTests="007_16janvier/008_run2"
defaultTest="007_16janvier/008_run2"
separator='_' #- be carrefull, gmkpack (at least on belenos) has multiple allergies (':', '.', '@')
              #- seprator must be in sync with prep_code.sh separator

PHYEXTOOLSDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
function usage {
  echo "Usage: $0 [-h] [-c] [-r] [-C] [-s] [--expand] commit reference"
  echo "commit          commit hash (or a directory)"
  echo "reference       commit hash or a directory or nothing for ref"
  echo "-s              suppress compilation pack"
  echo "-c              performs compilation"
  echo "-r              runs the tests"
  echo "-C              checks the result against the reference"
  echo "--expand        use mnh_expand (code will use do loops)"
  echo ""
  echo "If nothing is asked (compilation, running, check) everything is done"
  echo
  echo "The directory (for commit only, not ref) can take the form server:directory"
  echo
  echo "If using a directory (for commit or reference) it must contain at least one '/'"
}

compilation=0
run=0
check=0
commit=""
reference=""
tests=""
suppress=0
useexpand=0

while [ -n "$1" ]; do
  case "$1" in
    '-h') usage;;
    '-s') suppress=1;;
    '-c') compilation=1;;
    '-r') run=$(($run+1));;
    '-C') check=1;;
    '--expand') useexpand=1;;
    #-b) param="$2"; shift ;;
    #--) shift; break ;;
     *) if [ -z "${commit-}" ]; then
          commit=$1
        else
          if [ -z "${reference-}" ]; then
            reference=$1
          else
            echo "Only two commit hash allowed on command line"
            exit 1
          fi
        fi;;
  esac
  shift
done

[ "$reference" == 'REF' ] && reference="" #Compatibility with check_commit_arome.sh

MNHPACK=${MNHPACK:=$HOME/MesoNH/PHYEX}
REFDIR=${REFDIR:=$PHYEXTOOLSDIR/pack/}
TARGZDIR=${TARGZDIR:=$PHYEXTOOLSDIR/pack/}
if [ -z "${tests-}" ]; then
  tests=$defaultTest
elif [ $tests == 'ALL' ]; then
  tests=$availTests
fi

if [ $compilation -eq 0 -a \
     $run -eq 0 -a \
     $check -eq 0 ]; then
  compilation=1
  run=1
  check=1
fi

if [ -z "${commit-}" ]; then
  echo "At least one commit hash must be provided on command line"
  exit 2
fi

#Two possibilities are supported for the simulations
# - they can be done in the the pack we are currently checking
# - they can be done in the reference pack
#They are done in the current pack except if the reference pack
#already contains a tested simulation
run_in_ref=$(ls -d $REFDIR/MNH-V5-5-0/MY_RUN/KTEST/007_16janvier/008_run2_* 2> /dev/null | tail -1 |wc -l)

#Name and directory for compiling and executing user pack
fromdir=''
if echo $commit | grep '/' > /dev/null; then
  fromdir=$commit
  tag=$(echo $commit | sed 's/\//'${separator}'/g' | sed 's/:/'${separator}'/g' | sed 's/\./'${separator}'/g')
else
  tag=$commit
fi
name=MNH-V5-5-0-$tag
[ $suppress -eq 1 -a -d $MNHPACK/$name ] && rm -rf $MNHPACK/$name
if [ $run_in_ref -eq 1 ]; then
  path_user_beg=$REFDIR/MNH-V5-5-0 #pack directory containing the simulation
  path_user_end=_$tag #to be appended to the 'run' simulation directory
else
  path_user_beg=$MNHPACK/$name #pack directory containing the simulation
  path_user_end= #to be appended to the 'run' simulation directory
fi

#Name and directory for the reference
reffromdir=''
if echo $reference | grep '/' > /dev/null; then
  reffromdir=$reference
  reftag=$(echo $reference | sed 's/\//'${separator}'/g' | sed 's/:/'${separator}'/g' | sed 's/\./'${separator}'/g')
else
  reftag=$reference
fi
refname=MNH-V5-5-0-$reftag
if [ $run_in_ref -eq 1 ]; then
  path_ref_beg=$REFDIR/MNH-V5-5-0
  if [ "$reference" == "" ]; then
    path_ref_end=
  else
    path_ref_end=_$reftag
  fi
else
  path_ref_end=
  if [ "$reference" == "" ]; then
    path_ref_beg=$REFDIR/MNH-V5-5-0
  else
    path_ref_beg=$MNHPACK/MNH-V5-5-0-$reftag
  fi
fi

if [ $compilation -eq 1 ]; then
  echo "### Compilation of commit $commit"

  if [ -d $MNHPACK/$name ]; then
    echo "Pack already exists ($MNHPACK/$name), suppress it to be able to compile it again (or use the -s option to automatically suppress it)"
    exit 5
  fi

  # Prepare the pack
  cd $MNHPACK
  cp $TARGZDIR/MNH-V5-5-0_PHYEX.tar.gz .
  tar xfz MNH-V5-5-0_PHYEX.tar.gz 
  rm MNH-V5-5-0_PHYEX.tar.gz
  mv MNH-V5-5-0 $name
  cd $name/src
  rm -rf PHYEX

  MNH_EXPAND_DIR=$PHYEXTOOLSDIR/mnh_expand
  export PATH=$MNH_EXPAND_DIR/filepp:$MNH_EXPAND_DIR/MNH_Expand_Array:$PATH

  if [ $useexpand == 1 ]; then
    expand_options="-D MNH_EXPAND -D MNH_EXPAND_LOOP"
  else
    expand_options=""
  fi
  subs="-s turb -s micro -s aux -s ext -s conv"
  prep_code=$PHYEXTOOLSDIR/prep_code.sh
  if [ "$fromdir" == '' ]; then
    echo "Clone repository, and checkout commit $commit (using prep_code.sh)"
    if [[ $commit == mesonh${separator}* ]]; then
      $prep_code --renameFf -c $commit PHYEX #This commit is ready for inclusion
    else
      $prep_code --renameFf -c $commit $expand_options $subs -m mesonh PHYEX
    fi
  else
    echo "Copy $fromdir"
    scp -q -r $fromdir PHYEX
    $prep_code --renameFf $expand_options $subs -m mesonh PHYEX
  fi
  rm -rf PHYEX/.git
  find PHYEX -type f -exec touch {} \; #to be sure a recompilation occurs

  # Move manually ext/ files in src/MNH
  mv -f PHYEX/ext/* MNH/
  rmdir PHYEX/ext

  cd $MNHPACK/$name/src/PHYEX/turb
  # Delete files of MNH-V5-5-0/src/MNH and MNH/src/LIB/SURCOUCHE/src with same name
  for rep in turb micro conv aux ; do
    cd ../$rep
    for f in *.f90; do
      echo $f
      rm -f ../../MNH/$f
      rm -f ../../LIB/SURCOUCHE/src/$f
    done
  done
  cd ..
  
  # Delete old files of MNH-V5-5-0/src/MNH that is now called by mode_... NO /aux NEEDED!
  find turb micro conv -name 'mode_*' > remove_non_mode.sh
  sed -i 's/turb\/mode_/rm -f MNH\//g' remove_non_mode.sh
  sed -i 's/micro\/mode_/rm -f MNH\//g' remove_non_mode.sh
  sed -i 's/conv\/mode_/rm -f MNH\//g' remove_non_mode.sh
  chmod +x remove_non_mode.sh
  mv remove_non_mode.sh ../.
  cd ../
  ./remove_non_mode.sh
  # nettoyage, routine non appellee : 
  rm -f MNH/mf_turb_greyzone.f90
  rm -f MNH/compute_frac_ice.f90

  #Configure and compilation
  ./configure
  set +e #file ends with a test that can return false
  . ../conf/profile_mesonh-*
  set -e
  make -j 8 | tee ../Output_compilation
  make installmaster | tee -a ../Output_compilation
fi

if [ $run -ge 1 ]; then
  echo "### Running of commit $commit"

  if [ ! -f $MNHPACK/$name/exe/MESONH* ]; then
    echo "Pack does not exist ($MNHPACK/$name) or compilation has failed, please check"
    exit 6
  fi

  for t in $(echo $tests | sed 's/,/ /g'); do
    case=$(echo $t | cut -d / -f 1)
    exedir=$(echo $t | cut -d / -f 2)
    if [ $run_in_ref -eq 1 ]; then
      cd $REFDIR/MNH-V5-5-0/MY_RUN/KTEST/$case/
      [ ! -d ${exedir}_$commit ] && cp -R ${exedir} ${exedir}_$commit
      cd $REFDIR/MNH-V5-5-0/MY_RUN/KTEST/$case/${exedir}_$commit
    else
      cd $MNHPACK/$name/MY_RUN/KTEST/$case/
      for rep in ???_*; do
        if [ $rep != ${exedir} ]; then
          rm -rf $rep
          ln -s $REFDIR/MNH-V5-5-0/MY_RUN/KTEST/$case/$rep .
        fi
      done
      [ -d ${exedir} ] && rm -rf ${exedir}
      cp -R $REFDIR/MNH-V5-5-0/MY_RUN/KTEST/$case/${exedir} .
      cd ${exedir}
    fi
  
    set +e #file ends with a test that can return false
    [ $compilation -eq 0 ] && . $MNHPACK/$name/conf/profile_mesonh-*
    set -e
    ./clean_mesonh_xyz
    ./run_mesonh_xyz | tee Output_run
  done
fi

if [ $check -eq 1 ]; then
  echo "### Check commit $commit against commit $reference"

  allt=0
  for t in $(echo $tests | sed 's/,/ /g'); do
    case=$(echo $t | cut -d / -f 1)
    exedir=$(echo $t | cut -d / -f 2)

    path_user=$path_user_beg/MY_RUN/KTEST/007_16janvier/008_run2$path_user_end
    path_ref=$path_ref_beg/MY_RUN/KTEST/007_16janvier/008_run2$path_ref_end
    if [ ! -d $path_user ]; then
      echo "$path_user is missing, please run the simulation"
      exit 7
    fi
    if [ ! -d $path_ref ]; then
      echo "$path_ref is missing, please run the reference simulation"
      exit 8
    fi

    if [ $case == 007_16janvier ]; then
      echo "Compare with python..."
      # Compare variable of both Synchronous and Diachronic files with printing difference
      set +e
      $PHYEXTOOLSDIR/compare.py $path_user $path_ref
      t=$?
      set -e
      allt=$(($allt+$t))
      
      #Check bit-repro before date of creation of Synchronous file from ncdump of all values (pb with direct .nc file checks)
      file1=$path_user/16JAN.1.12B18.001.nc 
      file2=$path_ref/16JAN.1.12B18.001.nc
      echo "Compare with ncdump..."
      set +e
      diff <(ncdump $file1 | head -c 62889) <(ncdump $file2 | head -c 62889)
      t=$?
      set -e
      allt=$(($allt+$t))
    fi
  done

  if [ $allt -eq 0 ]; then
    status="OK"
  else
    status="Files are different"
  fi
  echo "...comparison done: $status"
fi