source: BOL/script_install/install_lmdz.sh @ 4208

#!/bin/bash

#set -vx

###########################################################################
# Author : Laurent Fairhead et Frédéric Hourdin
# Usage  : install_lmdz.sh -help
#
# bash installation script of the LMDZ model on different computer types :
# Linux PC, "mesocentre" (IPSL-UPMC, IPSL-X), super-computer (IDRIS)
#
# The model is downloaded in the following directory tree
# $MODEL/modipsl/modeles/...
# using the "modipsl" infrastructure created by the "IPSL"
# for coupled (atmosphere/ocean/vegetation/chemistry) climate modeling
# activities.
# Here we only download atmospheric (LMDZ) and vegetation (ORCHIDEE)
# components.
#
# The sources of the models can be found in the "modeles" directory.
# In the present case, LMDZ, ORCHIDEE, and IOIPSL or XIOS (handling of input-outputs
# using the NetCDF library).
#
# The script downloads various source files (including a version of NetCDF)
# and utilities, compiles the model, and runs a test simulation in a
# minimal configuration.
#
# Prerequisites : pgf90/gfortran, bash or ksh, wget , gunzip, tar, ...
#
# Modif 18/11/2011
#    changes for option real 8.
#      We compile with -r8 (or equivalent) and -DNC_DOUBLE for the GCM
#      but with -r4 for netcdf. Variable real must be set to
#      r4 or r8 at the beginning of the script below.
#
###########################################################################

echo install_lmdz.sh DEBUT `date`
set -e

################################################################
# Choice of installation options
################################################################

################################################################
# A function to fetch files either locally or on the internet
################################################################
function myget { #1st and only argument should be file name
  # Path on local computer where to look for the datafile
  if [ -f /u/lmdz/WWW/LMDZ/pub/$1 ] ; then
    \cp -f -p /u/lmdz/WWW/LMDZ/pub/$1 .
  elif [ -f ~/LMDZ/pub/$1 ] ; then
    \cp -f -p ~/LMDZ/pub/$1 .
  else
    wget --no-check-certificate -nv http://lmdz.lmd.jussieu.fr/pub/$1
    save_pub_locally=0
    if [ $save_pub_locally = 1 ] ; then # saving wget files on ~/LMDZ/pub
       dir=~/LMDZ/pub/`dirname $1` ; mkdir -p $dir ; cp -r `basename $1` $dir
    fi
  fi
}

# 04_2021 : tester si r4 marche encore !
#real=r4
real=r8


#########################################################################
# Valeur par défaut des parametres
#########################################################################
svn=""
#version=trunk
version=20220131.trunk

getlmdzor=1
netcdf=1   #  1 for automatic installation
           #  0 for no installation
           #  /.../../netcdf-4.0.1 if wanting to link with an already
           #  compiled netcdf library (implies to check option compatibility)
check_linux=1
ioipsl=1
bench=1
pclinux=1
pcmac=0 # default: not on a Mac
compiler=gfortran
SCM=0
# surface/vegetation scheme treatment
# controlled by the single variable veget which can have the following values
# - NONE: bucket scheme (default)
# - CMIP6: orchidee version used in CMIP exercise, rev 5661
# - number: orchidee version number
veget=NONE
# choose the resolution for the bench runs
# grid_resolution= 32x24x11 or 48x36x19 for tests (test without ORCHIDEE)
#                  96x71x19  standard configuration
grid_resolution=144x142x79
grid_resolution=96x95x39
grid_resolution=48x36x19
grid_resolution=32x32x39
# choose the physiq version you want to test
#physiq=NPv6.0.14splith
physiq=

## parallel can take the values none/mpi/omp/mpi_omp
parallel=mpi_omp
parallel=none
idris_acct=lmd
OPT_GPROF=""
OPT_MAKELMDZ=""
MODEL=""

## also compile XIOS? (and more recent NetCDF/HDF5 libraries) Default=no
with_xios="n"
opt_makelmdz_xios=""

## compile with oldrad/rrtm/ecrad radiatif code (Default=rrtm)
rad=rrtm

## compile_with_fcm=1 : use makelmdz_fcm (1) or makelmdz (0)
compile_with_fcm=1

#Compilation with Cosp (cosp=NONE/v1/v2 ; default=NONE)
cosp=NONE
opt_cosp=""

# Check if on a Mac
if [ `uname` = "Darwin" ]
then
    pcmac=1
    export MAKE=make
fi
#echo "pcmac="$pcmac

env_file=""

#########################################################################
#  Options interactives
#########################################################################
while (($# > 0))
   do
   case $1 in
     "-h") cat <<........fin
    $0 [ -v version ] [ -r svn_release ]
           [ -parallel PARA ] [ -d GRID_RESOLUTION ] [ -bench 0/1 ]
           [-name LOCAL_MODEL_NAME] [-gprof] [-opt_makelmdz] [-rad RADIATIF]

    -v       "version" like 20150828.trunk
             see http://www.lmd.jussieu.fr/~lmdz/Distrib/LISMOI.trunk

    -r       "svn_release" : either the svn release number or "last"

    -compiler gfortran|ifort|pgf90 (default: gfortran)

    -parallel PARA : can be mpi_omp (mpi with openMP) or none (for sequential)

    -d        GRID_RESOLUTION should be among the available benchs if -bench 1
              among which : 48x36x19, 48x36x39
              if wanting to run a bench simulation in addition to compilation
              default : 48x36x19

    -bench     activating the bench or not (0/1). Default 1

    -name      LOCAL_MODEL_NAME : default = LMDZversion.release

    -netcdf    PATH : full path to an existing installed NetCDF library
               (without -netcdf: also download and install the NetCDF library)

    -xios      also download and compile the XIOS library
               (requires the NetCDF4-HDF5 library, also installed by default)
               (requires to also have -parallel mpi_omp)

    -gprof     to compile with -pg to enable profiling with gprof

    -cosp      to run without our with cospv1 or cospv2 [none/v1/v2]

    -rad RADIATIF can be oldrad, rrtm or ecrad radiatif code

    -nofcm     to compile without fcm

    -SCM        install 1D version automatically

    -debug      compile everything in debug mode

    -opt_makelmdz     to call makelmdz or makelmdz_fcm with additional options

    -physiq    to choose which physics package to use

    -env_file  specify an arch.env file to overwrite the existing one

    -veget surface model to run [NONE/CMIP6/xxxx]

........fin
     exit ;;
     "-v") version=$2 ; shift ; shift ;;
     "-r") svn=$2 ; shift ; shift ;;
     "-compiler") compiler=$2
                  case $compiler in
                    "gfortran"|"ifort"|"pgf90") compiler=$2 ; shift ; shift ;;
                    *) echo "Only gfortran , ifort or pgf90 for the compiler option" ; exit
                  esac ;;
     "-d") grid_resolution=$2 ; shift ; shift ;;
     "-gprof") OPT_GPROF="-pg" ; shift ;;
     "-cosp") cosp=$2
              case $cosp in
                  "none"|"v1"|"v2") cosp=$2 ; shift ; shift ;;
                  *) echo Only none v1 v2 for cosp option ; exit
              esac ;;
     "-nofcm") compile_with_fcm=0 ; shift ;;
     "-SCM") SCM=1 ; shift ;;
     "-opt_makelmdz") OPT_MAKELMDZ="$2" ; shift ; shift ;;
     "-rrtm") rrtm="$2" ; if [ "$2" = "false" ] ; then rad="oldrad" ; else rad="rrtm" ; fi ; shift ; shift ;;
     "-rad") rad=$2
             case $rad in
                "oldrad"|"rrtm"|"ecrad") rad=$2 ; shift ; shift ;;
                *) echo Only oldrad rrtm ecrad for rad option ; exit
             esac ;;
     "-parallel") parallel=$2
                  case $parallel in
                    "none"|"mpi"|"omp"|"mpi_omp") parallel=$2 ; shift ; shift ;;
                    *) echo Only none mpi omp mpi_omp for the parallel option ; exit
                  esac ;;
     "-bench") bench=$2 ; shift ; shift ;;
     "-debug") optim=-debug ; shift ;;
     "-name") MODEL=$2 ; shift ; shift ;;
     "-netcdf") netcdf=$2 ; shift ; shift ;;
     "-physiq") physiq=$2 ; shift ; shift ;;
     "-xios") with_xios="y" ; shift ;;
     "-env_file") env_file=$2 ; shift ; shift ;;
     "-veget") veget=$2 ; shift ; shift ;;
     *) ./install_lmdz.sh -h ; exit
   esac
done

# Option de compilation du rayonnement : depend de $mysvn ><= r4185, sera donc definie plus bas
#opt_rad=""
#case $rad in
#   rrtm) opt_rad="-rad rrtm" ;;
#   ecrad) opt_rad="-rad ecrad" ;;
#esac


# Option de compilation pour Cosp
opt_cosp=""
case cosp in
   v1) opt_cosp="-cosp true" ;;
   v2) opt_cosp="-cospv2 true" ;;
esac

# Check on veget version
#if [ "$veget" != 'NONE'  -a "$veget" != "CMIP6" -a "$veget" != +([0-9]) ] ; then
if [ $veget != 'NONE'   -a $veget != "CMIP6" ] ; then
    re='^[0-9]+$'
    if ! [[ $veget =~ $re ]] ; then
        echo 'Valeur de l option veget non valable'
        exit
    fi
fi

#Define veget-related suffix for gcm name
if [ "$veget" = 'NONE' ] ; then
    suff_orc=''
    #For use with tutorial, orchidee_rev is also defined (will be written in surface_env at the end of the script)
    orchidee_rev=''
else
    suff_orc='_orch'
fi


if [ $parallel = none ] ; then sequential=1; suff_exe='_seq' ; else sequential=0; suff_exe='_para_mem' ; fi

#Chemin pour placer le modele
if [ "$MODEL" = "" ] ; then MODEL=./LMDZ$version$svn$optim ; fi


arch=local


if [ $compiler = g95 ] ; then echo g95 is not supported anymore ; exit ; fi

################################################################
# Specificite des machines
################################################################

hostname=`hostname`
if [ "$pclinux" = 1 ] ; then o_ins_make="-t g95" ; else o_ins_make="" ; fi

case ${hostname:0:5} in

   jean-)   compiler="mpiifort" ;
            par_comp="mpiifort" ;
            o_ins_make="-t jeanzay" ;
            make=gmake ;
            module purge
            module load intel-compilers/19.0.4 ;
            #module load intel-mpi/19.0.4 ;
            #module load intel-mkl/19.0.4 ;
            module load hdf5/1.10.5-mpi ;
            module load netcdf/4.7.2-mpi ;
            module load netcdf-fortran/4.5.2-mpi ;
            module load subversion/1.9.7 ;
            export NETCDF_LIBDIR=./
            export NETCDFFORTRAN_INCDIR=./
            export NETCDFFORTRAN_LIBDIR=./
            arch=X64_JEANZAY ;;

   cicla|camel)   compiler="gfortran" ;
            if [ $parallel != none ] ; then
              module load openmpi/1.6.5-gfortran ;
              root_mpi=$MPI_HOME ;
              path_mpi=$root_mpi/bin ;
              par_comp=${path_mpi}/mpif90 ;
              mpirun=${path_mpi}/mpirun ;
            fi ;
            arch=local  ;
            make=make ;
            o_ins_make="-t g95" ;;

   *)       if [ $parallel = none -o -f /usr/bin/mpif90 ] ; then
                path_mpi=`which mpif90 | sed -e s:/mpif90::` ;
                if [ -d /usr/lib64/openmpi ] ; then
                  root_mpi="/usr/lib64/openmpi"
                else
                  root_mpi="/usr"
                fi
            else
               echo "Cannot find mpif90" ;
               if [ $parallel = none ] ; then exit ; fi ;
            fi ;
            if [ $parallel != none ] ; then
              root_mpi=$(which mpif90 | sed -e s:/bin/mpif90::)
              path_mpi=$(which mpif90 | sed -e s:/mpif90::)
              export LD_LIBRARY_PATH=${root_mpi}/lib:$LD_LIBRARY_PATH
            fi
            par_comp=${path_mpi}/mpif90 ;
            mpirun=${path_mpi}/mpirun ;
            arch=local  ;
            make=make ;
            o_ins_make="-t g95"
esac

# Flags for parallelism:
if [ $parallel != none ] ; then
  # MPI_LD are the flags needed for linking with MPI
  MPI_LD="-L${root_mpi}/lib -lmpi"
  if [ "$compiler" = "gfortran" ] ; then
    # MPI_FLAGS are the flags needed for compilation with MPI
    MPI_FLAGS="-fcray-pointer"
    # OMP_FLAGS are the flags needed for compilation with OpenMP
    OMP_FLAGS="-fopenmp -fcray-pointer"
    # OMP_LD are the flags needed for linking with OpenMP
    OMP_LD="-fopenmp"
  elif [ "$compiler" = "ifort" ] ; then
    MPI_FLAGS=""
    OMP_FLAGS="-openmp"
    OMP_LD="-openmp"
  else # pgf90
    MPI_FLAGS=""
    OMP_FLAGS="-mp"
    OMP_LD="-mp"
  fi
fi

#####################################################################
# Test for old gfortran compilers
# If the compiler is too old (older than 4.3.x) we test if the
# temporary gfortran44 patch is available on the computer in which
# case the compiler is changed from gfortran to gfortran44
# Must be aware than parallelism can not be activated in this case
#####################################################################

if [ "$compiler" = "gfortran" ] ; then
   gfortran=gfortran
   gfortranv=`gfortran --version | \
   head -1 | awk ' { print $NF } ' | awk -F. ' { print $1 * 10 + $2 } '`
   if [ $gfortranv -le 43 ] ; then
       echo ERROR : Your gfortran compiler is too old
       echo 'Please choose a new one (ifort) and change the line'
       echo compiler=xxx
       echo in the install_lmdz.sh script and rerun it
       if [ `which gfortran44 | wc -w` -ne 0 ] ; then
          gfortran=gfortran44
       else
          echo gfotran trop vieux ; exit
       fi
   fi
   compiler=$gfortran
fi
#####################################################################

## if also compiling XIOS, parallel must be mpi_omp
if [ "$with_xios" = "y" -a "$parallel" != "mpi_omp" ] ; then
  echo "Error, you must set -parallel mpi_omp if you want XIOS"
  exit
fi

if [ "$with_xios" = "y" ] ; then
  opt_makelmdz_xios="-io xios"
fi

if [ "$cosp" = "v2" -a "$with_xios" = "n" ] ; then
  echo "Error, Cospv2 cannot run without Xios"
  exit
fi

echo '################################################################'
echo  Choix des options de compilation
echo '################################################################'

export FC=$compiler
export F90=$compiler
export F77=$compiler
export CPPFLAGS=
OPTIMNC=$OPTIM
BASE_LD="$OPT_GPROF"
OPTPREC="$OPT_GPROF"
ARFLAGS="rs" ; if [ -f /etc/issue ] ; then if [ "`grep -i ubuntu /etc/issue`" != "" ] ; then if [ "`grep -i ubuntu /etc/issue | awk ' { print $2 } ' | cut -d. -f1`" -ge 16 ] ; then ARFLAGS="rU" ; fi ; fi ; fi



if [ "$compiler" = "$gfortran" ] ; then
   OPTIM='-O3'
   OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all -fbacktrace -finit-real=snan"
   OPTDEV="-Wall -fbounds-check"
   fmod='I '
   OPTPREC="$OPTPREC -cpp -ffree-line-length-0"
   if [ $real = r8 ] ; then OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE" ; fi
   export F90FLAGS=" -ffree-form $OPTIMNC"
   export FFLAGS=" $OPTIMNC"
   export CC=gcc
   export CXX=g++
   export fpp_flags="-P -C -traditional -ffreestanding"

elif [ $compiler = mpif90 ] ; then
   OPTIM='-O3'
   OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all"
   OPTDEV="-Wall -fbounds-check"
   BASE_LD="$BASE_LD -lblas"
   fmod='I '
   if [ $real = r8 ] ; then OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE -fcray-pointer" ; fi
   export F90FLAGS=" -ffree-form $OPTIMNC"
   export FFLAGS=" $OPTIMNC"
   export CC=gcc
   export CXX=g++

elif [ $compiler = pgf90 ] ; then
   OPTIM='-O2 -Mipa -Munroll -Mnoframe -Mautoinline -Mcache_align'
   OPTDEB='-g -Mdclchk -Mbounds -Mchkfpstk -Mchkptr -Minform=inform -Mstandard -Ktrap=fp -traceback'
   OPTDEV='-g -Mbounds -Ktrap=fp -traceback'
   fmod='module '
   if [ $real = r8 ] ; then OPTPREC="$OPTPREC -r8 -DNC_DOUBLE" ; fi
   export CPPFLAGS="-DpgiFortran"
   export CC=pgcc
   export CFLAGS="-O2 -Msignextend"
   export CXX=pgCC
   export CXXFLAGS="-O2 -Msignextend"
   export FFLAGS="-O2 $OPTIMNC"
   export F90FLAGS="-O2 $OPTIMNC"
   compile_with_fcm=1

elif [ $compiler = ifort ] ; then
   OPTIM="-O2 -fp-model strict -ip -align all "
   OPTDEV="-p -g -O2 -traceback -fp-stack-check -ftrapuv -check"
   OPTDEB="-g -no-ftz -traceback -ftrapuv -fp-stack-check -check"
   fmod='module '
   if [ $real = r8 ] ; then OPTPREC="$OPTPREC -real-size 64 -DNC_DOUBLE" ; fi
   export CPP="icc -E"
   export FFLAGS="-O2 -ip -fpic -mcmodel=large"
   export FCFLAGS="-O2 -ip -fpic -mcmodel=large"
   export CC=icc
   export CFLAGS="-O2 -ip -fpic -mcmodel=large"
   export CXX=icpc
   export CXXFLAGS="-O2 -ip -fpic -mcmodel=large"
   export fpp_flags="-P -traditional"
   # Pourquoi forcer la compilation fcm. Marche mieux sans
   #compile_with_fcm=1

elif [ $compiler = mpiifort ] ; then
   echo on ne fait rien la
   # Pourquoi forcer la compilation fcm. Marche mieux sans
   #compile_with_fcm=1

else
   echo unexpected compiler $compiler ; exit
fi

OPTIMGCM="$OPTIM $OPTPREC"

hostname=`hostname`

##########################################################################
# If installing on known machines such as Jean-Zay at IDRIS,
# don't check for available software and don't install netcdf
if [ ${hostname:0:5} = jean- ] ; then
  netcdf=0 # no need to recompile netcdf, alreday available
  check_linux=0
  pclinux=0
  ioipsl=0 # no need to recompile ioipsl, already available
  #netcdf="/smplocal/pub/NetCDF/4.1.3"
  compiler="mpiifort"
  fmod='module '
  if [ $real = r8 ] ; then OPTPREC="$OPTPREC -i4 -r8 -DNC_DOUBLE" ; fi
  OPTIM="-auto -align all -O2 -fp-model strict -xHost "
  OPTIMGCM="$OPTIM $OPTPREC"
fi
##########################################################################


mkdir -p $MODEL
echo $MODEL
MODEL=`( cd $MODEL ; pwd )` # to get absolute path, if necessary


echo '################################################################'
if [ "$check_linux" = 1 ] ; then
echo   Check if required software is available
echo '################################################################'

#### Ehouarn: test if the required shell is available
#### Maj FH-LF-AS 2021-04 : default=bash ; if bash missing, use ksh
use_shell="bash" # default
if [ "`which bash`" = "" ] ; then
  echo "no bash ; we will use ksh"
  use_shell="ksh"
  if [ "`which ksh`" = "" ] ; then
    echo "bash (or ksh) needed!! Install it!"
    exit
  fi
fi

for logiciel in wget tar gzip make $compiler gcc ; do
if [ "`which $logiciel`" = "" ] ; then
echo You must first install $logiciel on your system
exit
fi
done

if [ $pclinux = 1 ] ; then
cd $MODEL
cat <<eod > tt.f90
print*,'coucou'
end
eod
$compiler tt.f90 -o a.out
./a.out >| tt
if [ "`cat tt | sed -e 's/ //g' `" != "coucou" ] ; then
echo problem installing with compiler $compiler ; exit ; fi
\rm tt a.out tt.f90
fi
fi

###########################################################################
if [ $getlmdzor = 1 -a ! -d $MODEL/modipsl ] ; then
###########################################################################
   echo '##########################################################'
   echo  Download a slightly modified version of  LMDZ
   echo '##########################################################'
   cd $MODEL
   myget src/modipsl.$version.tar.gz
   echo install_lmdz.sh wget_OK `date`
   gunzip modipsl.$version.tar.gz
   tar xf modipsl.$version.tar
   \rm modipsl.$version.tar
fi

###########################################################################
if [ $netcdf = 1 -a ! -d $MODEL/netcdf ] ; then
###########################################################################
   cd $MODEL
   netcdflog=`pwd`/netcdf.log
   echo '##########################################################'
   echo Compiling the Netcdf library
   echo '##########################################################'
   echo log file : $netcdflog
   if [ "$with_xios" = "n" ] ; then
      # keep it simple
      #wget http://www.lmd.jussieu.fr/~lmdz/Distrib/netcdf-4.0.1.tar.gz
      myget import/netcdf-4.0.1.tar.gz
      gunzip netcdf-4.0.1.tar.gz
      tar xvf netcdf-4.0.1.tar
      \rm -f netcdf-4.0.1.tar
    
      cd netcdf-4.0.1
    
      localdir=`pwd -P`
      ./configure --prefix=$localdir --enable-shared --disable-cxx
      #sed -e 's/gfortran/'$gfortran'/g' Makefile >| tmp ; mv -f tmp Makefile
      $make check > $netcdflog 2>&1
      $make install >> $netcdflog 2>&1
    #LF rajout d'une verrue, pour une raison non encore expliquee, la librairie est parfois rangée dans lib64
    #   et non dans lib par certains compilateurs
      if [ ! -e lib -a -d lib64 ] ; then ln -s lib64 lib; fi
   else
      # download and compile hdf5 and netcdf, etc. using the install_netcdf4_hdf5.bash script
      #wget http://www.lmd.jussieu.fr/~lmdz/Distrib/install_netcdf4_hdf5.bash
      myget import/install_netcdf4_hdf5.bash
      chmod u=rwx install_netcdf4_hdf5.bash
      if [ "$compiler" = "gfortran" ] ; then
      ./install_netcdf4_hdf5.bash -prefix $MODEL/netcdf4_hdf5 -CC gcc -FC gfortran -CXX g++ -MPI $root_mpi  > $netcdflog 2>&1
      elif [ "$compiler" = "ifort" ] ; then
      ./install_netcdf4_hdf5.bash -prefix $MODEL/netcdf4_hdf5 -CC icc -FC ifort -CXX icpc -MPI $root_mpi  > $netcdflog 2>&1
      elif [ "$compiler" = "pgf90" ] ; then
      ./install_netcdf4_hdf5.bash -prefix $MODEL/netcdf4_hdf5 -CC pgcc -FC pgf90 -CXX pgCC -MPI $root_mpi  > $netcdflog 2>&1
      else
        echo "unexpected compiler $compiler" ; exit
      fi
   fi  # of if [ "$with_xios" = "n" ]
   echo install_lmdz.sh netcdf_OK `date`
fi # of if [ $netcdf = 1 ]

# ncdfdir contains the directory where netcdf is installed
if [ $netcdf = 0 -o $netcdf = 1 ] ; then
   if [ "$with_xios" = "y" ] ; then
      ncdfdir=$MODEL/netcdf4_hdf5
   else
      ncdfdir=$MODEL/netcdf-4.0.1
   fi
else
   ncdfdir=$netcdf
fi

#=========================================================================
if [[ ! -f $MODEL/modipsl/lib/libioipsl.a ]]
then
if [ $ioipsl = 1 ] ; then
#=========================================================================
   echo OK ioipsl=$ioipsl
   echo '##########################################################'
   echo 'Installing MODIPSL, the installation package manager for the '
   echo 'IPSL models and tools'
   echo '##########################################################'
   echo `date`

   cd $MODEL/modipsl
   \rm -rf lib/*
   cd util
   cp AA_make.gdef AA_make.orig
   F_C="$compiler -c " ; if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then F_C="$compiler -c -cpp " ; fi
   if [ "$compiler" = "pgf90" ] ; then F_C="$compiler -c -Mpreprocess" ; fi
   sed -e 's/^\#.*.g95.*.\#.*.$/\#/' AA_make.gdef > tmp
   sed -e "s:F_L = g95:F_L = $compiler:" -e "s:F_C = g95 -c -cpp:F_C = $F_C": \
   -e 's/g95.*.w_w.*.(F_D)/g95      w_w = '"$OPTIMGCM"'/' \
   -e 's:g95.*.NCDF_INC.*.$:g95      NCDF_INC= '"$ncdfdir"'/include:' \
   -e 's:g95.*.NCDF_LIB.*.$:g95      NCDF_LIB= -L'"$ncdfdir"'/lib -lnetcdff -lnetcdf:' \
   -e 's:g95      L_O =:g95      L_O = -Wl,-rpath='"$ncdfdir"'/lib:' \
   -e "s:-fmod=:-$fmod:" -e 's/-fno-second-underscore//' \
   -e 's:#-Q- g95      M_K = gmake:#-Q- g95      M_K = make:' \
   tmp >| AA_make.gdef

   if [ $pcmac == 1 ]
   then
       cp AA_make.gdef tmp
       sed -e 's/rpath=/rpath,/g' tmp > AA_make.gdef
   fi


 # We use lines for g95 even for the other compilers to run ins_make
   if [ "$use_shell" = "ksh" ] ; then
     ./ins_make $o_ins_make
   else # bash
     sed -e s:/bin/ksh:/bin/bash:g ins_make > ins_make.bash
     if [ "`grep jeanzay AA_make.gdef`" = "" ] ; then # Bidouille pour compiler sur ada des vieux modipsl.tar
         echo 'Warning jean-zay not in AA_make.gdef'
         echo 'Think about updating'
         exit 1
     fi

     chmod u=rwx ins_make.bash
     ./ins_make.bash $o_ins_make
   fi # of if [ "$use_shell" = "ksh" ]

   echo install_lmdz.sh MODIPSL_OK `date`

   cd $MODEL/modipsl/modeles/IOIPSL/src
   ioipsllog=`pwd`/ioipsl.log
   echo '##########################################################'
   echo 'Compiling IOIPSL, the interface library with Netcdf'
   echo '##########################################################'
   echo `date`
   echo log file : $ioipsllog

   if [ "$use_shell" = "bash" ] ; then
     cp Makefile Makefile.ksh
     sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile
   fi
 # if [ "$pclinux" = 1 ] ; then
     # Build IOIPSL modules and library
     $make clean
     $make > $ioipsllog 2>&1
     if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then # copy module files to lib
       cp -f *.mod ../../../lib
     fi
     # Build IOIPSL tools (ie: "rebuild", if present)
     if [ -f $MODEL/modipsl/modeles/IOIPSL/tools/rebuild ] ; then
       cd $MODEL/modipsl/modeles/IOIPSL/tools
       # adapt Makefile & rebuild script if in bash
       if [ "$use_shell" = "bash" ] ; then
         cp Makefile Makefile.ksh
         sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile
         cp rebuild rebuild.ksh
         sed -e 's:/bin/ksh:/bin/bash:g' \
             -e 's:print -u2:echo:g' \
             -e 's:print:echo:g' rebuild.ksh > rebuild
       fi
       $make clean
       $make > $ioipsllog 2>&1
     fi
# fi # of if [ "$pclinux" = 1 ]

else # of if [ $ioipsl = 1 ]
   if [ ${hostname:0:5} = jean- ] ; then
      cd $MODEL/modipsl
      cd util
        if [ "`grep jeanzay AA_make.gdef`" = "" ] ; then
         echo 'Warning jean-zay not in AA_make.gdef'
         echo 'Think about updating'
         exit 1
        fi
        ./ins_make $o_ins_make
# Compile IOIPSL on jean-zay
        cd $MODEL/modipsl/modeles/IOIPSL/src
        gmake > ioipsl.log
        cd $MODEL/modipsl/modeles/IOIPSL/tools
        gmake > ioipsl.log

   fi
   echo install_lmdz.sh ioipsl_OK `date`
fi # of if [ $ioipsl = 1 ]
fi
# Saving ioipsl lib for possible parallel compile
  cd $MODEL/modipsl
  tar cf ioipsl.tar lib/ bin/

#=========================================================================
if [ "$with_xios" = "y" ] ; then
  echo '##########################################################'
  echo 'Compiling XIOS'
  echo '##########################################################'
  cd $MODEL/modipsl/modeles
  xioslog=`pwd`/xios.log
  #wget http://www.lmd.jussieu.fr/~lmdz/Distrib/install_xios.bash
  myget import/install_xios.bash
  chmod u=rwx install_xios.bash
  if [ ${hostname:0:5} = jean- ] ; then
     svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5 XIOS
     cd XIOS/arch
     svn update
     cd ..
     echo "Compiling XIOS, start" `date` "(it takes about 20 min on Jean-Zay)"
     echo "log file: $xioslog"
     ./make_xios --prod --arch $arch --job 4 > xios.log 2>&1
  else
     ./install_xios.bash -prefix $MODEL/modipsl/modeles \
                      -netcdf ${ncdfdir} -hdf5 ${ncdfdir} \
                      -MPI $root_mpi -arch $arch > xios.log 2>&1
  fi # of case Jean-Zay
  if [ -f XIOS/lib/libxios.a ] ; then
     echo "XIOS library successfully generated"
     echo install_lmdz.sh XIOS_OK `date`
  fi
fi

#============================================================================
veget_version=false
if [ "$veget" != 'NONE' ] ; then
  cd $MODEL/modipsl/modeles/ORCHIDEE
  set +e ; svn upgrade ; set -e
  if [ "$veget" = "CMIP6" ] ; then
    veget_version=orchidee2.0
    orchidee_rev=6592
  else # specific orchidee revision newer than CMIP6, on 2_1 or 2_2 branches
    veget_version=orchidee2.1
    orchidee_rev=$veget
     if [ $veget -lt 4465 ] ; then
             echo 'Stopping, ORCHIDEE version too old, script needs work on the CPP flags to pass to makelmdz'
             exit 1
     fi
     set +e
     # which branch is my version on?
     orcbranch=`svn log -v -q svn://forge.ipsl.jussieu.fr/orchidee/ -r $veget |grep ORCHIDEE |head -1| sed -e 's:ORCHIDEE/.*$:ORCHIDEE:' | awk '{print $2}'`
     # switch to that branch
     echo IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at orchidee-help@listes.ipsl.fr
     svn switch -r $veget --accept theirs-full svn://forge.ipsl.jussieu.fr/orchidee/$orcbranch
     svn log -r $veget | grep  $veget
     if [  $? -gt 0 ] ; then
          echo 'Cannot update ORCHIDEE as not on the right branch for ORCHIDEE'
          exit
      fi
      set -e
      set +e ; svn update -r $veget ; set -e
  fi
  # Correctif suite debug Jean-Zay
  sed -i -e 's/9010  FORMAT(A52,F17.14)/9010  FORMAT(A52,F20.14)/' src_stomate/stomate.f90
  opt_orc="-prod" ; if [ "$optim" = "-debug" ] ; then opt_orc="-debug" ; fi

  orchideelog=`pwd`/orchidee.log
  echo '########################################################'
  echo 'Compiling ORCHIDEE, the continental surface model '
  echo '########################################################'
  echo Start of the first compilation of orchidee, in sequential mode: `date`
  echo log file : $orchideelog

  export ORCHPATH=`pwd`
  xios_orchid="-noxios"
  if [ "$with_xios" = "y" ] ; then
    xios_orchid="-xios"
  fi
  if [ -d tools ] ; then
###################################################################
# Pour les experts qui voudraient changer de version d'orchidee.
# Attention : necessite d'avoir le password pour orchidee

      # Correctif suite debug Jean-Zay
      if [ -f src_global/time.f90 ] ; then sed -i -e 's/CALL tlen2itau/\!CALL tlen2itau/' src_global/time.f90 ; fi
###################################################################
     if [ "$veget_version" == "false" ] ; then veget_version=orchidee2.0 ; fi
      cd arch
      sed -e s:"%COMPILER        .*.$":"%COMPILER            $compiler":1 \
     -e s:"%LINK            .*.$":"%LINK                $compiler":1 \
     -e s:"%FPP_FLAGS       .*.$":"%FPP_FLAGS           $fpp_flags":1 \
     -e s:"%PROD_FFLAGS     .*.$":"%PROD_FFLAGS         $OPTIM":1 \
     -e s:"%DEV_FFLAGS      .*.$":"%DEV_FFLAGS          $OPTDEV":1 \
     -e s:"%DEBUG_FFLAGS    .*.$":"%DEBUG_FFLAGS        $OPTDEB":1 \
     -e s:"%BASE_FFLAGS     .*.$":"%BASE_FFLAGS         $OPTPREC":1 \
     -e s:"%BASE_LD         .*.$":"%BASE_LD             $BASE_LD":1 \
     -e s:"%ARFLAGS         .*.$":"%ARFLAGS             $ARFLAGS":1 \
     arch-gfortran.fcm > arch-local.fcm
     echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib -lnetcdff -lnetcdf\"" > arch-local.path
     echo "NETCDF_INCDIR=${ncdfdir}/include" >> arch-local.path
     echo "IOIPSL_INCDIR=$ORCHPATH/../../lib" >> arch-local.path
     echo "IOIPSL_LIBDIR=$ORCHPATH/../../lib" >> arch-local.path
     echo 'XIOS_INCDIR=${ORCHDIR}/../XIOS/inc' >> arch-local.path
     echo 'XIOS_LIBDIR="${ORCHDIR}/../XIOS/lib -lxios"' >> arch-local.path
     cd ../

     echo ./makeorchidee_fcm -j $xios_orchid $opt_orc -parallel none -arch $arch
     ./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel none -arch $arch > $orchideelog 2>&1
     pwd
  else # of "if [ -d tools ]"
     if [ -d src_parallel ] ; then
       liste_src="parallel parameters global stomate sechiba driver"
       if [ "$veget_version" == "false" ] ; then veget_version=orchidee2.0 ; fi
     fi
     for d in $liste_src ; do src_d=src_$d
        echo src_d $src_d
        echo ls ; ls
        if [ ! -d $src_d ] ; then echo Problem orchidee : no $src_d ; exit ; fi
        cd $src_d ; \rm -f *.mod make ; $make clean
        $make > $orchideelog 2>&1 ; if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then cp -f *.mod ../../../lib ; fi
        cd ..
     done
  fi # of "if [ -d tools ]"
  echo install_lmdz.sh orchidee_compil_seq_OK `date`
fi # of if [ "$veget" != 'NONE' ]


#============================================================================
# Ehouarn: the directory name LMDZ* depends on version/tar file...
if [ -d $MODEL/modipsl/modeles/LMD* ] ; then
  echo '###############################################################'
  echo 'Preparing LMDZ compilation : arch file, svn switch if needed...'
  echo '###############################################################'
  cd $MODEL/modipsl/modeles/LMD*
  LMDZPATH=`pwd`
else
  echo "ERROR: No LMD* directory !!!"
  exit
fi

###########################################################
# For those who want to use fcm to compile via :
#  makelmdz_fcm -arch local .....
############################################################

if [ "$pclinux" = "1" ] ; then

# create local 'arch' files (if on Linux PC):
cd arch
# arch-local.path file
echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib -lnetcdff -lnetcdf\"" > arch-local.path
echo "NETCDF_INCDIR=-I${ncdfdir}/include" >> arch-local.path
echo 'IOIPSL_INCDIR=$LMDGCM/../../lib' >> arch-local.path
echo 'IOIPSL_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
echo 'XIOS_INCDIR=$LMDGCM/../XIOS/inc' >> arch-local.path
echo 'XIOS_LIBDIR=$LMDGCM/../XIOS/lib' >> arch-local.path
echo 'ORCH_INCDIR=$LMDGCM/../../lib' >> arch-local.path
echo 'ORCH_LIBDIR=$LMDGCM/../../lib' >> arch-local.path

if [ $pcmac == 1 ] ; then
    BASE_LD="$BASE_LD -Wl,-rpath,${ncdfdir}/lib"
else
    BASE_LD="$BASE_LD -Wl,-rpath=${ncdfdir}/lib"
fi
# Arch-local.fcm file (adapted from arch-linux-32bit.fcm)

if [ $real = r8 ] ; then FPP_DEF=NC_DOUBLE ; else FPP_DEF="" ; fi
sed -e s:"%COMPILER        .*.$":"%COMPILER            $compiler":1 \
    -e s:"%LINK            .*.$":"%LINK                $compiler":1 \
    -e s:"%PROD_FFLAGS     .*.$":"%PROD_FFLAGS         $OPTIM":1 \
    -e s:"%DEV_FFLAGS      .*.$":"%DEV_FFLAGS          $OPTDEV":1 \
    -e s:"%DEBUG_FFLAGS    .*.$":"%DEBUG_FFLAGS        $OPTDEB":1 \
    -e s:"%BASE_FFLAGS     .*.$":"%BASE_FFLAGS         $OPTPREC":1 \
    -e s:"%FPP_DEF         .*.$":"%FPP_DEF             $FPP_DEF":1 \
    -e s:"%BASE_LD         .*.$":"%BASE_LD             $BASE_LD":1 \
    -e s:"%ARFLAGS         .*.$":"%ARFLAGS             $ARFLAGS":1 \
    arch-linux-32bit.fcm > arch-local.fcm

cd ..
### Adapt "bld.cfg" (add the shell):
#whereisthatshell=$(which ${use_shell})
#echo "bld::tool::SHELL   $whereisthatshell" >> bld.cfg

fi # of if [ "$pclinux" = 1 ]


cd $MODEL/modipsl/modeles/LMDZ*
lmdzlog=`pwd`/lmdz.log

##################################################################
# Possibly update LMDZ if a specific svn release is requested
##################################################################

set +e ; svn upgrade ; set -e

if [ "$svn" = "last" ] ; then svnopt="" ; else svnopt="-r $svn" ; fi
if [ "$svn" != "" ] ; then
    set +e ; svn info | grep -q 'http:'
    if [ $? = 0 ] ; then
        svn switch --relocate http://svn.lmd.jussieu.fr/LMDZ https://svn.lmd.jussieu.fr/LMDZ
    fi
    svn update $svnopt
fi
set -e

##################################################################
# Retrieve the final svn release number, and adjust compilation options accordingly
mysvn=`svnversion . | egrep -o "[0-9]+"`

# Option de compilation du rayonnement : depend de $mysvn ><= r4185
opt_rad=""

case $rad in
    oldrad) iflag_rrtm=0 ; NSW=2 ; opt_rad="" ;;
    rrtm)   iflag_rrtm=1 ; NSW=6 ; if [ $mysvn -le 4185 ] ; then opt_rad="-rrtm true" ; else opt_rad="-rad rrtm" ; fi ;;
    ecrad)  iflag_rrtm=2 ; NSW=6 ; opt_rad="-rad ecrad" ;;
    *) echo Only oldrad rrtm ecrad for rad option ; exit
esac

if [ $mysvn -le 4185 -a $rad = "ecrad" ] ; then echo "ecrad only available for LMDZ rev starting with 4186 " ; exit ; fi

##################################################################

echo '##################################################################'
echo "Preparing script compile.sh for LMDZ compilation"
echo "It will only be run automatically if bench=1/tuto"
echo Here bench=$bench
echo '##################################################################'

if [ "$env_file" != "" ] ; then mv arch/arch-${arch}.env arch/arch-${arch}.orig ; \cp -f $env_file arch/arch-${arch}.env ; fi

if [ $compile_with_fcm = 1 ] ; then makelmdz="makelmdz_fcm $optim -arch $arch -j 8 " ; else makelmdz="makelmdz $optim -arch $arch" ; fi

# sequential compilation
if [ "$sequential" = 1 ] ; then
  echo Sequential compilation command, saved in compile.sh:
  echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp -d ${grid_resolution} -v $veget_version gcm "
  echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp -d ${grid_resolution} -v $veget_version gcm " >> compile.sh
  chmod +x ./compile.sh
  if [ $bench = 1 ] ; then
    echo install_lmdz.sh start_lmdz_seq_compilation `date`
    echo log file: $lmdzlog
    ./compile.sh > $lmdzlog 2>&1
    echo install_lmdz.sh end_lmdz_seq_compilation `date`
  fi
fi # fin sequential

# compiling in parallel mode
if [ $parallel != "none" ] ; then
  echo '##########################################################'
  echo ' Parallel compile '
  echo '##########################################################'
  echo "(after saving the sequential libs and binaries)"
  cd $MODEL/modipsl
  tar cf sequential.tar bin/ lib/
  \rm -rf bin/ lib/
  tar xf ioipsl.tar
  #
  # Orchidee
  #
  cd $ORCHPATH
  if [ -d src_parallel -a $veget != 'NONE' ] ; then
     cd arch
     sed  \
     -e s:"%COMPILER.*.$":"%COMPILER            $par_comp":1 \
     -e s:"%LINK.*.$":"%LINK                $par_comp":1 \
     -e s:"%MPI_FFLAG.*.$":"%MPI_FFLAGS          $MPI_FLAGS":1 \
     -e s:"%OMP_FFLAG.*.$":"%OMP_FFLAGS          $OMP_FLAGS":1 \
     -e s:"%MPI_LD.*.$":"%MPI_LD              $MPI_LD":1 \
     -e s:"%OMP_LD.*.$":"%OMP_LD              $OMP_LD":1 \
     arch-local.fcm > tmp.fcm

     mv tmp.fcm arch-local.fcm
     cd ../
     echo Compiling ORCHIDEE in parallel mode `date`
     echo logfile $orchideelog
     echo "NOTE : to recompile it when necessary, use ./compile_orc.sh in modipsl/modeles/ORCHIDEE"
     echo ./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc -parallel $parallel -arch $arch > compile_orc.sh
     echo ./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel $parallel -arch $arch >> compile_orc.sh
     echo echo Now you must also recompile LMDZ, by running ./compile.sh in modeles/LMDZ >> compile_orc.sh
     chmod u+x compile_orc.sh
     ./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc -parallel $parallel -arch $arch > $orchideelog 2>&1
     ./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel $parallel -arch $arch >> $orchideelog 2>&1
     echo End of ORCHIDEE compilation in parallel mode `date`
  elif [ $veget != 'NONE' ] ; then
    echo '##########################################################'
    echo ' Orchidee version too old                                 '
    echo ' Please update to new version                             '
    echo '##########################################################'
    exit
  fi # of [ -d src_parallel -a $veget != 'NONE' ]

  # LMDZ
  cd $LMDZPATH
  if [ $arch = local ] ; then
    cd arch
    sed -e s:"%COMPILER.*.$":"%COMPILER            $par_comp":1 \
    -e s:"%LINK.*.$":"%LINK                $par_comp":1 \
    -e s:"%MPI_FFLAG.*.$":"%MPI_FFLAGS          $MPI_FLAGS":1 \
    -e s:"%OMP_FFLAG.*.$":"%OMP_FFLAGS          $OMP_FLAGS":1 \
    -e s:"%ARFLAGS.*.$":"%ARFLAGS          $ARFLAGS":1 \
    -e s@"%BASE_LD.*.$"@"%BASE_LD             -Wl,-rpath=${root_mpi}/lib:${ncdfdir}/lib"@1 \
    -e s:"%MPI_LD.*.$":"%MPI_LD              $MPI_LD":1 \
    -e s:"%OMP_LD.*.$":"%OMP_LD              $OMP_LD":1 \
    arch-local.fcm > tmp.fcm
    mv tmp.fcm arch-local.fcm
    cd ../
  fi
  rm -f compile.sh
  echo resol=${grid_resolution} >> compile.sh
  if [ ${hostname:0:5} = jean- -a "$cosp" = "v2" ] ; then

  echo LMDZ compilation command in parallel mode, saved in compile.sh, is :
  echo "(ATTENTION le probleme de cospv2 sur jean-zay en mode prod n est pas corrige ! )"
# ATTENTION le probleme de cospv2 sur jean-zay en mode prod n est pas corrige
     echo ./$makelmdz -dev $optim $OPT_MAKELMDZ $opt_rad $opt_cosp $opt_makelmdz_xios -d \$resol -v $veget_version -mem -parallel $parallel gcm >> compile.sh
     echo ./$makelmdz -dev $optim $OPT_MAKELMDZ $opt_rad $opt_cosp $opt_makelmdz_xios -d \$resol -v $veget_version -mem -parallel $parallel gcm
  else
    echo ./$makelmdz $optim $OPT_MAKELMDZ $opt_rad $opt_cosp $opt_makelmdz_xios -d \$resol -v $veget_version -mem -parallel $parallel gcm >> compile.sh
    echo ./$makelmdz $optim $OPT_MAKELMDZ $opt_rad $opt_cosp $opt_makelmdz_xios -d \$resol -v $veget_version -mem -parallel $parallel gcm
  fi
  chmod +x ./compile.sh

  if [ $bench = 1 ] ; then
     echo Compiling LMDZ in parallel mode `date`,  LMDZ log file: $lmdzlog ; ./compile.sh > $lmdzlog 2>&1
  fi

fi # of if [ $parallel != "none" ]


##################################################################
# Verification du succes de la compilation
##################################################################

# Recherche de l'executable dont le nom a change au fil du temps ...
# suffix contains radiative option starting with revision 4186
if [ $mysvn -ge 4186 ] ; then suff_exe=_${rad}${suff_exe} ; fi
gcm=""
#for exe in gcm.e bin/gcm_${grid_resolution}_phylmd_seq_orch.e bin/gcm_${grid_resolution}_phylmd_seq.e bin/gcm_${grid_resolution}_phylmd_para_mem_orch.e bin/gcm_${grid_resolution}_phylmd_para_mem.e  ; do
for exe in gcm.e bin/gcm_${grid_resolution}_phylmd${suff_exe}${suff_orc}.e ; do   if [ -f $exe ] ; then gcm=$exe ; fi
done

if [ "$gcm" = "" ] ; then
  if [ $bench = 1 ] ; then
    echo 'Compilation failed !! Cannot run the benchmark;'
    exit
  else
    echo 'Compilation not done (only done when bench=1)'
  fi
else
   echo '##########################################################'
   echo 'Compilation successfull !! ' `date`
   echo '##########################################################'
   echo The executable is $gcm
fi

##################################################################
# Below, we run a benchmark if bench=1 or tuto
##################################################################

if [ $bench = tuto ] ; then
   myget Training/tutorial.tar ; tar xvf tutorial.tar ; cd TUTORIAL ; ./init.sh

elif [[ $bench = 1 && ! -d BENCH${grid_resolution} ]] ; then
   # TOUTE CETTE SECTION DEVRAIT DISPARAITRE POUR UNE COMMANDE
   # OU DES BENCHS PAR MOTS CLES COMME tuto

   echo '##########################################################'
   echo ' Running a test run '
   echo '##########################################################'

   \rm -rf BENCH${grid_resolution}
   bench=bench_lmdz_${grid_resolution}
   echo install_lmdz.sh before bench download  `date`
   #wget http://www.lmd.jussieu.fr/~lmdz/Distrib/$bench.tar.gz
   myget 3DBenchs/$bench.tar.gz
   echo install_lmdz.sh after bench download  `date`
   tar xvf $bench.tar.gz

   if [ "$cosp" = "v1" -o "$cosp" = "v2" ] ; then
     cd BENCH${grid_resolution}
   # copier les fichiers namelist input et output our COSP
     cp ../DefLists/cosp*_input_nl.txt .
     cp ../DefLists/cosp*_output_nl.txt .
   # Activer la cles ok_cosp pour tourner avec COSP
     sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp
      \mv -f tmp config.def
     cd ..
   fi

   if [ -n "$physiq" ]; then
     cd BENCH${grid_resolution}
     if [ -f physiq.def_${physiq} ]; then
       cp physiq.def_${physiq} physiq.def
       echo using physiq.def_${physiq}
     else
       echo using standard physiq.def
     fi
     cd ..
   else
     echo using standard physiq.def
   fi

   if [ "$with_xios" = "y" ] ; then
     cd BENCH${grid_resolution}
     cp ../DefLists/iodef.xml .
     cp ../DefLists/context_lmdz.xml .
     cp ../DefLists/field_def_lmdz.xml .
   # A raffiner par la suite
     echo A FAIRE : Copier les *xml en fonction de l option cosp
     cp ../DefLists/field_def_cosp*.xml .
     cp ../DefLists/file_def_hist*xml .
     # adapt iodef.xml to use attached mode
     sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' iodef.xml > tmp
     \mv -f tmp iodef.xml

     # and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
     # except for histday
     for histfile in file_def_hist*xml
     do
       if [ "$histfile" = "file_def_histday_lmdz.xml" ] ; then
       sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' $histfile > tmp ; \mv -f tmp $histfile
       sed -e 's@output_level="_AUTO_"@output_level="5"@' $histfile > tmp ; \mv -f tmp $histfile
       sed -e 's@compression_level="2"@compression_level="0"@' $histfile > tmp ; \mv -f tmp $histfile
       else
       sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' $histfile > tmp ; \mv -f tmp $histfile
       fi
     done
     # and add option "ok_all_xml=y" in config.def
     echo "### XIOS outputs" >> config.def
     echo 'ok_all_xml=.true.' >> config.def

     #activer les sorties pour Cosp
     if [ "$cosp" = "v1" ] ; then
      histfile=file_def_histdayCOSP_lmdz.xml
      sed -e 's@enabled=".FALSE."@enabled=".TRUE."@' $histfile > tmp ; \mv -f tmp $histfile
      sed -e 's@output_level="_AUTO_"@output_level="5"@' $histfile > tmp ; \mv -f tmp $histfile
      sed -e 's@compression_level="2"@compression_level="0"@' $histfile > tmp ; \mv -f tmp $histfile
     fi
     if [ "$cosp" = "v2" ] ; then
      histfile=file_def_histdayCOSPv2_lmdz.xml
      sed -e 's@compression_level="2"@compression_level="0"@' $histfile > tmp ; \mv -f tmp $histfile
      contextfile=context_lmdz.xml
      sed -e 's@src="./file_def_histdayCOSP_lmdz.xml"@src="./file_def_histdayCOSPv2_lmdz.xml"@' $contextfile > tmp ; \mv -f tmp $contextfile
      sed -e 's@src="./file_def_histmthCOSP_lmdz.xml"@src="./file_def_histmthCOSPv2_lmdz.xml"@' $contextfile > tmp ; \mv -f tmp $contextfile
      sed -e 's@src="./file_def_histhfCOSP_lmdz.xml"@src="./file_def_histhfCOSPv2_lmdz.xml"@' $contextfile > tmp ; \mv -f tmp $contextfile
      fieldfile=field_def_lmdz.xml
      sed -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' $fieldfile > tmp ; \mv -f tmp $fieldfile
     fi

     cd ..
   fi

   # Cas Bensh avec ecrad
   if [ "$rad" = "ecrad" ] ; then
     cd BENCH${grid_resolution}
     cp  ../DefLists/namelist_ecrad .
     cp -r ../libf/phylmd/ecrad/data .
     cd ..
   fi

   # Adjusting bench physiq.def to radiative code chosen
   cd BENCH${grid_resolution}
   sed -e 's/iflag_rrtm=.*.$/iflag_rrtm='$iflag_rrtm'/' -e 's/NSW=.*.$/NSW='$NSW'/' physiq.def > tmpdef
   \mv tmpdef physiq.def
   cd ..

   cp $gcm BENCH${grid_resolution}/gcm.e

   cd BENCH${grid_resolution}
   # On cree le fichier bench.sh au besoin
   # Dans le cas 48x36x39 le bench.sh existe deja en parallele

   if [ "$grid_resolution" = "48x36x39" ] ; then
      echo On ne touche pas au bench.sh
      # But we have to adapt "run_local.sh" for $mpirun
      sed -e "s@mpirun@$mpirun@g" run_local.sh > tmp
      mv -f tmp run_local.sh
      chmod u=rwx run_local.sh
   elif [ "${parallel:0:3}" = "mpi" ] ; then
      # Lancement avec deux procs mpi et 2 openMP
      echo "export OMP_STACKSIZE=800M" > bench.sh
      if [ "${parallel:4:3}" = "omp" ] ; then
        echo "export OMP_NUM_THREADS=2" >> bench.sh
      fi
      if [ "$cosp" = "v1" -o "$cosp" = "v2" ] ; then
         if [ ${hostname:0:5} = jean- ] ; then
        chmod +x ../arch.env
           ../arch.env  
           echo "ulimit -s 2000000" >> bench.sh
         else
           echo "ulimit -s 200000" >> bench.sh
         fi     
      else
         echo "ulimit -s unlimited" >> bench.sh
      fi
      if [ ${hostname:0:5} = jean- ] ; then
        . ../arch/arch-${arch}.env
        echo "srun -n 2 -A $idris_acct@cpu gcm.e > listing  2>&1" >> bench.sh
      else
        echo "$mpirun -np 2 gcm.e > listing  2>&1" >> bench.sh
      fi
      # Add rebuild, using reb.sh if it is there
      echo 'if [ -f reb.sh ] ; then' >> bench.sh
      echo '  ./reb.sh histday ; ./reb.sh histmth ; ./reb.sh histhf ; ./reb.sh histins ; ./reb.sh stomate_history ; ./reb.sh sechiba_history ; ./reb.sh sechiba_out_2 ' >> bench.sh
      echo 'fi' >> bench.sh
   else
      echo "./gcm.e > listing  2>&1" > bench.sh
   fi
   # Getting orchidee stuff
   if [ $veget == 'CMIP6' ] ; then
       #echo 'myget 3DBenchs/BENCHorch11.tar.gz'
       #myget 3DBenchs/BENCHorch11.tar.gz
       #tar xvzf BENCHorch11.tar.gz
       echo 'myget 3DBenchs/BENCHCMIP6.tar.gz'
       myget 3DBenchs/BENCHCMIP6.tar.gz
       tar xvzf BENCHCMIP6.tar.gz
       sed -e "s:VEGET=n:VEGET=y:" config.def > tmp
       mv -f tmp config.def
       if [ "$with_xios" = "y" ] ; then
         cp ../../ORCHIDEE/src_xml/context_orchidee.xml .
         echo '<context id="orchidee" src="./context_orchidee.xml"/>' > add.tmp
         cp ../../ORCHIDEE/src_xml/field_def_orchidee.xml .
         cp ../../ORCHIDEE/src_xml/file_def_orchidee.xml .
         cp ../../ORCHIDEE/src_xml/file_def_input_orchidee.xml .
         if [ -f ../../ORCHIDEE/src_xml/context_input_orchidee.xml ] ; then
        cp ../../ORCHIDEE/src_xml/context_input_orchidee.xml .
        echo '<context id="orchidee" src="./context_input_orchidee.xml"/>' >> add.tmp
         fi
         sed -e '/id="LMDZ"/r add.tmp' iodef.xml > tmp
         mv tmp iodef.xml
         sed -e'{/sechiba1/ s/enabled="_AUTO_"/type="one_file" enabled=".TRUE."/}' file_def_orchidee.xml > tmp ; \mv -f tmp file_def_orchidee.xml
         sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' file_def_orchidee.xml > tmp ; \mv -f tmp file_def_orchidee.xml
         sed -e 's@output_level="_AUTO_"@output_level="1"@' file_def_orchidee.xml > tmp ; \mv -f tmp file_def_orchidee.xml
         sed -e 's@output_freq="_AUTO_"@output_freq="1d"@' file_def_orchidee.xml > tmp ; \mv -f tmp file_def_orchidee.xml
         sed -e 's@compression_level="4"@compression_level="0"@' file_def_orchidee.xml > tmp ; \mv -f tmp file_def_orchidee.xml
         sed -e 's@XIOS_ORCHIDEE_OK = n@XIOS_ORCHIDEE_OK = y@' orchidee.def > tmp ; \mv -f tmp orchidee.def
       fi
   fi
   echo EXECUTION DU BENCH
   set +e
   date ; ./bench.sh > out.bench 2>&1 ; date
   set -e
   tail listing


   echo '##########################################################'
   echo 'Simulation finished in' `pwd`
      echo 'You have compiled with:'
      cat ../compile.sh
   if [ $parallel = "none" ] ; then
     echo 'You may re-run it with : cd ' `pwd` ' ; gcm.e'
     echo 'or ./bench.sh'
   else
     echo 'You may re-run it with : '
     echo 'cd ' `pwd` '; ./bench.sh'
   #  echo 'ulimit -s unlimited'
   #  echo 'export OMP_NUM_THREADS=2'
   #  echo 'export OMP_STACKSIZE=800M'
   #  echo "$mpirun -np 2 gcm.e "
   fi
   echo '##########################################################'

fi # bench


#################################################################
# Installation eventuelle du 1D
#################################################################

if [ $SCM = 1 ] ; then
cd $MODEL
#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/1D.tar.gz
myget 1D/1D.tar.gz
tar xvf 1D.tar.gz
cd 1D
./run.sh -rad $rad
fi
#set -vx

#################################################################
# sauvegarde des options veget pour utilisation eventuelle tutorial_prod
#################################################################
cd $MODEL/modipsl/modeles
#echo surface_env file created in $MODEL
echo 'veget='$veget > surface_env
#opt_veget="-v $veget_version"
#echo 'opt_veget="'$opt_veget\" >> surface_env
echo 'opt_veget="'-v $veget_version\" >> surface_env
echo 'orchidee_rev='$orchidee_rev >> surface_env
echo 'suforch='$suff_orc >> surface_env