Changeset 5361 for BOL/script_install


Ignore:
Timestamp:
Dec 2, 2024, 5:21:37 PM (2 weeks ago)
Author:
Laurent Fairhead
Message:

Switching to modular install_lmdz.sh and new testing version (r5244)

File:
1 edited

Legend:

Unmodified
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  • BOL/script_install/install_lmdz.sh

    r5021 r5361  
    11#!/bin/bash
    2 
    3 #set -vx
     2set -eu  # error on command failure, and on unset variables
     3export LC_ALL=C  # standardize awk format
    44
    55###########################################################################
    … …  
    2626# minimal configuration.
    2727#
    28 # Prerequisites : pgf90/gfortran, bash or ksh, wget , gunzip, tar, ...
     28# Prerequisites : gfortran, bash or ksh, wget, gunzip, tar, ...
    2929#
    3030# Modif 18/11/2011
    … …  
    3636###########################################################################
    3737
    38 echo install_lmdz.sh DEBUT `date`
    39 set -e
    40 
    41 ################################################################
    42 # Choice of installation options
    43 ################################################################
    44 
    45 ################################################################
    46 # A function to fetch files either locally or on the internet
    47 ################################################################
    48 function myget { #1st and only argument should be file name
    49     # Path on local computer where to look for the datafile
    50     if [ -f /u/lmdz/WWW/LMDZ/pub/$1 ] ; then
    51         \cp -f -p /u/lmdz/WWW/LMDZ/pub/$1 .
    52     elif [ -f ~/LMDZ/pub/$1 ] ; then
    53         \cp -f -p ~/LMDZ/pub/$1 .
     38### Functions
     39
     40function myget {
     41  # Get a file from LMDZ repository, make it executable if .(ba)sh
     42  local url=$1
     43
     44  local filename
     45  filename=$(basename "$url")
     46
     47  wget --no-check-certificate -nv "http://lmdz.lmd.jussieu.fr/pub/$url"
     48  if [[ $filename =~ .*\.(ba)?sh ]]; then chmod +x "$filename"; fi
     49}
     50
     51function do_compile_sh {
     52  local component=$1
     53  local command=$2
     54  local log
     55
     56  log="$(pwd)/$component.log"
     57  echo "$command" > compile.sh
     58  echo "Compiling $component using $(\cat compile.sh) (log: $log) $(date)"
     59    chmod +x ./compile.sh
     60    if ! ./compile.sh &> "$log"; then
     61        echo "STOP: $component compilation failed, exiting"; exit 1
     62    fi
     63    echo "Finished $component compilation $(date)"
     64}
     65
     66function get_svn_branch {
     67  local url=$1
     68  local rev=$2
     69  local res
     70
     71  res=$(svn log -v -q "$url" -r "$rev" -l 1 | cut -d "/" -f -4)
     72  if echo "$res" | grep -q "/trunk/"; then
     73    res=$(echo "$res" | grep "/trunk/" | head -1 | cut -d "/" -f 2-3)
     74  elif echo "$res" | grep -q "/branches/"; then
     75    res=$(echo "$res" | grep "/branches/" | head -1 | cut -d "/" -f 2-4)
     76  else
     77    echo "Could not determine svn branch for $url, r=$rev"
     78  fi
     79  echo "$res"
     80}
     81
     82function set_default_params {
     83    # Valeur par défaut des parametres
     84    svn_lmdz=""
     85    version="20241018.trunk"
     86
     87    netcdf=1
     88    bench=1
     89    SCM=0
     90    veget="none"
     91    grid_resolution="32x32x39"
     92    benchphysiq=""
     93    compphysiq="lmd"
     94    is_1D="n"
     95    fortran_file="gcm"
     96
     97    parallel="none"
     98    trusting="testing"
     99    MODEL=""
     100
     101    with_xios=0
     102    opt_makelmdz_xios=""
     103
     104    icolmdz=0
     105    dynamico_commit="11001689"
     106
     107    rad="rrtm"
     108
     109    compile_with_fcm=1
     110
     111    cosp="none"
     112    aerosols=0
     113    strataer=0
     114    inlandsis=0
     115
     116    make_j=8
     117    clean_install=1
     118    local="$(pwd)"
     119
     120    # Check if on a Mac /!\ Probably doesn't work anymore, to fix one day...
     121    if [[ $(uname) = "Darwin" ]]; then
     122        export MAKE="make"
     123    fi
     124
     125    optim_flag="-prod"
     126    arch="local"
     127
     128    arch="local-gfortran"
     129    arch_dir=""
     130
     131    jobcmd=""
     132}
     133
     134function read_cmdline_args {
     135    while (($# > 0)); do
     136        case $1 in
     137            "-h") cat <<........fin
     138        $0 [ -v version ] [ -r svn_release ]
     139               [ -parallel PARA ] [ -d GRID_RESOLUTION ] [ -bench 0/1 ]
     140               [-name LOCAL_MODEL_NAME] [-rad RADIATIF]
     141
     142        -v       "version" like 20150828.trunk, see http://www.lmd.jussieu.fr/~lmdz/Distrib/LISMOI.trunk (default <$version>)
     143
     144        -r       "svn_release" : either the svn release number or "last" (default <$svn_lmdz>)
     145
     146        -parallel parallel support: mpi, omp, mpi_omp (mpi with openMP) or none (default: <$parallel>)
     147
     148        -d        "grid resolution": should be among the available benchs if -bench 1 (valid values: 48x36x19, 48x36x39) (default : <$grid_resolution>)
     149
     150        -bench     activating the bench or not (0/1) (default: <$bench>)
     151
     152        -unstable  use unstable tar instead of testing
     153
     154        -name      name of the folder to install to (default <$MODEL>)
     155
     156        -netcdf    0, 1 or PATH. 0: do not download NetCDF, look for it in standard locations (/usr);  1: download and compile NetCDF; PATH: full path to an existing installed NetCDF library (default: <$netcdf>)
     157
     158        -xios      use (download and compile) the XIOS library (will compile the parallel NetCDF4-HDF5 library) (requires to also have -parallel mpi_omp)
     159
     160        -cosp       to run with cospv1 or cospv2 [none/v1/v2] (default <$cosp>)
     161
     162        -rad        radiative code: oldrad, rrtm or ecrad (default <$rad>)
     163
     164        -nofcm      to compile without fcm
     165
     166        -SCM        install 1D version automatically
     167
     168        -debug      compile everything in debug mode
     169
     170        -benchphysiq   to choose which physics.def package to use in the bench (default <$benchphysiq>)
     171
     172        -compilephysiq   physics to compile the model with (default <$compphysiq>)
     173
     174        -veget      surface/vegetation scheme treatment controlled by the single variable veget which can have the following values: none: bucket scheme (default); CMIP6 | veget2.0: orchidee version used in CMIP exercise, rev 5661; veget2.2: orchidee branch 2.2, rev 8529 (bundled); number: orchidee version number  [only orch>2.0] (default $veget)
     175
     176        -spla       activate interactive aerosols
     177
     178        -inlandsis  activate new snow scheme
     179
     180        -arch       name of the arch to use (default <$arch>)
     181
     182        -arch_dir   where to find the arch files (default <$arch_dir>)
     183
     184        -make_j     number of processes to parallelize installations (default <$make_j>)
     185
     186        -jobcmd     command prepended to fcm compile jobs, e.g. "srun" (default <$jobcmd>)
     187
     188        -noclean    will only download necessary files (but no thorough check is made on the integrity of existing files), and will recompile everything (very quick if it's already been compiled before)
     189
     190        -icolmdz    to compile the icolmdz executable as well as the lonlat one
     191
     192........fin
     193                  exit 1;;
     194            "-v") version=$2; shift; shift;;
     195            "-r") svn_lmdz=$2; shift; shift;;
     196            "-d") grid_resolution=$2; shift; shift;;
     197            "-unstable") trusting="unstable"; shift;;
     198            "-cosp") cosp=$2
     199                     case $cosp in
     200                         "none"|"v1"|"v2") cosp=$2; shift; shift;;
     201                         *) echo "Only none v1 v2 for cosp option"; exit 1
     202                     esac;;
     203            "-nofcm") compile_with_fcm=0; echo "This option will be reactivated soon (promesse du 8dec2022)"; exit 1;  shift;;
     204            "-SCM") SCM=1; shift;;
     205            "-rad") rad=$2
     206                    case $rad in
     207                        "oldrad"|"rrtm"|"ecrad") rad=$2; shift; shift;;
     208                        *) echo "Only oldrad rrtm ecrad for rad option"; exit 1
     209                    esac;;
     210            "-parallel") parallel=$2
     211                         case $parallel in
     212                             "none"|"mpi"|"omp"|"mpi_omp") parallel=$2; shift; shift;;
     213                             *) echo "Only none mpi omp mpi_omp for the parallel option"; exit 1
     214                         esac;;
     215            "-bench") bench=$2; shift; shift;;
     216            "-debug") optim_flag="-debug"; shift;;
     217            "-name") MODEL=$2; shift; shift;;
     218            "-netcdf") netcdf=$2; shift; shift;;
     219            "-benchphysiq") benchphysiq=$2; shift; shift;;
     220            "-compilephysiq") compphysiq=$2; shift; shift;;
     221            "-xios") with_xios=1; shift;;
     222            "-arch") arch=$2; shift; shift;;
     223            "-arch_dir") arch_dir=$2; shift; shift;;
     224            "-veget") veget=$2; shift; shift;;
     225            "-spla") aerosols=1; shift;;
     226            "-strataer") strataer=1; shift;;
     227            "-inlandsis") inlandsis=1; shift;;
     228            "-make_j") make_j=$2; shift; shift;;
     229            "-jobcmd") jobcmd=$2; shift; shift;;
     230            "-noclean") clean_install=0; shift;;
     231            "-icolmdz") icolmdz=1; shift;;
     232            *)  bash install_lmdz.sh -h; exit 1
     233        esac
     234    done
     235
     236    # Isotopes : Compile and run with isotopes if lmdz_phys="lmdiso" in main.sh
     237    if [[ $compphysiq = "lmdiso" ]]; then isotopes=1; else isotopes=0; fi
     238
     239    # Option de compilation pour Cosp
     240    case $cosp in
     241        v1) opt_cosp="-cosp true";;
     242        v2) opt_cosp="-cospv2 true";;
     243        *) opt_cosp=""
     244    esac
     245
     246    #Define veget-related suffix for gcm name
     247    if [[ $veget = 'none' ]]; then
     248        suff_orc=''
    54249    else
    55         wget --no-check-certificate -nv http://lmdz.lmd.jussieu.fr/pub/$1
    56         save_pub_locally=0
    57         if [ $save_pub_locally = 1 ] ; then # saving wget files on ~/LMDZ/pub
    58             dir=~/LMDZ/pub/`dirname $1` ; mkdir -p $dir
    59             cp -r `basename $1` $dir
    60         fi
    61     fi
    62 }
    63 
    64 # 04_2021 : tester si r4 marche encore !
    65 #real=r4
    66 real=r8
    67 
    68 
    69 #########################################################################
    70 # Valeur par défaut des parametres
    71 #########################################################################
    72 svn=""
    73 #version=trunk
    74 version=20231022.trunk
    75 
    76 getlmdzor=1
    77 netcdf=1   #  1: for automatic installation;
    78 #          or 0: do not install NetCDF and look for it in standard locations;
    79 #          or absolute path: look for NetCDF there
    80 check_linux=1
    81 ioipsl=1
    82 bench=1
    83 pclinux=1
    84 pcmac=0 # default: not on a Mac
    85 compiler=gfortran
    86 if [ `gfortran -dumpversion | cut -d. -f1` -ge 10 ] ; then allow_arg_mismatch="-fallow-argument-mismatch" ; fi
    87 SCM=0
    88 # surface/vegetation scheme treatment
    89 # controlled by the single variable veget which can have the following values
    90 # - NONE: bucket scheme (default)
    91 # - CMIP6: orchidee version used in CMIP exercise, rev 5661
    92 # - number: orchidee version number
    93 veget=NONE
    94 # choose the resolution for the bench runs
    95 # grid_resolution= 32x24x11 or 48x36x19 for tests (test without ORCHIDEE)
    96 #                  96x71x19  standard configuration
    97 grid_resolution=144x142x79
    98 grid_resolution=96x95x39
    99 grid_resolution=48x36x19
    100 grid_resolution=32x32x39
    101 # choose the physiq version you want to test
    102 #physiq=NPv6.0.14splith
    103 physiq=
    104 
    105 ## parallel can take the values none/mpi/omp/mpi_omp
    106 parallel=mpi_omp
    107 parallel=none
    108 idris_acct=lmd
    109 trusting=testing
    110 OPT_GPROF=""
    111 OPT_MAKELMDZ=""
    112 MODEL=""
    113 
    114 ## also compile XIOS? (and more recent NetCDF/HDF5 libraries) Default=no
    115 with_xios="n"
    116 opt_makelmdz_xios=""
    117 
    118 ## compile with oldrad/rrtm/ecrad radiatif code (Default=rrtm)
    119 rad=rrtm
    120 
    121 ## compile_with_fcm=1 : use makelmdz_fcm (1) or makelmdz (0)
    122 compile_with_fcm=1
    123 
    124 #Compilation with Cosp (cosp=NONE/v1/v2 ; default=NONE)
    125 cosp=NONE
    126 opt_cosp=""
    127 
    128 # Check if on a Mac
    129 if [ `uname` = "Darwin" ]
    130 then
    131     pcmac=1
    132     export MAKE=make
    133 fi
    134 #echo "pcmac="$pcmac
    135 
    136 env_file=""
    137 
    138 #########################################################################
    139 #  Options interactives
    140 #########################################################################
    141 while (($# > 0))
    142 do
    143     case $1 in
    144         "-h") cat <<........fin
    145     $0 [ -v version ] [ -r svn_release ]
    146            [ -parallel PARA ] [ -d GRID_RESOLUTION ] [ -bench 0/1 ]
    147            [-name LOCAL_MODEL_NAME] [-gprof] [-opt_makelmdz] [-rad RADIATIF]
    148 
    149     -v       "version" like 20150828.trunk
    150              see http://www.lmd.jussieu.fr/~lmdz/Distrib/LISMOI.trunk
    151 
    152     -r       "svn_release" : either the svn release number or "last"
    153 
    154     -compiler gfortran|ifort|pgf90 (default: gfortran)
    155 
    156     -parallel PARA : can be mpi_omp (mpi with openMP) or none (for sequential)
    157 
    158     -d        GRID_RESOLUTION should be among the available benchs if -bench 1
    159               among which : 48x36x19, 48x36x39
    160               if wanting to run a bench simulation in addition to compilation
    161               default : 48x36x19
    162 
    163     -bench     activating the bench or not (0/1). Default 1
    164 
    165     -testing/unstable
    166 
    167     -name      LOCAL_MODEL_NAME : default = LMDZversion.release
    168 
    169     -netcdf    0, 1 or PATH
    170                    0: do not download NetCDF, look for it in standard locations
    171                1: download and compile NetCDF
    172                    PATH: full path to an existing installed NetCDF library
    173 
    174     -xios      also download and compile the XIOS library
    175                (requires the NetCDF4-HDF5 library, also installed by default)
    176                (requires to also have -parallel mpi_omp)
    177 
    178     -gprof     to compile with -pg to enable profiling with gprof
    179 
    180     -cosp      to run without our with cospv1 or cospv2 [none/v1/v2]
    181 
    182     -rad RADIATIF can be oldrad, rrtm or ecrad radiatif code
    183 
    184     -nofcm     to compile without fcm
    185 
    186     -SCM        install 1D version automatically
    187 
    188     -debug      compile everything in debug mode
    189 
    190     -opt_makelmdz     to call makelmdz or makelmdz_fcm with additional options
    191 
    192     -physiq    to choose which physics package to use
    193 
    194     -env_file  specify an arch.env file to overwrite the existing one
    195 
    196     -veget surface model to run [NONE/CMIP6/xxxx]
    197 
    198 ........fin
    199               exit ;;
    200         "-v") version=$2 ; shift ; shift ;;
    201         "-r") svn=$2 ; shift ; shift ;;
    202         "-compiler") compiler=$2
    203                      case $compiler in
    204                          "gfortran"|"ifort"|"pgf90") compiler=$2 ; shift
    205                                                      shift ;;
    206                          *) echo "Only gfortran , ifort or pgf90 for the " \
    207                                  "compiler option"
    208                             exit
    209                      esac ;;
    210         "-d") grid_resolution=$2 ; shift ; shift ;;
    211         "-gprof") OPT_GPROF="-pg" ; shift ;;
    212         "-unstable"|"-testing") trusting=`echo $1 | cut -c2-`  ; shift ;;
    213         "-cosp") cosp=$2
    214                  case $cosp in
    215                      "none"|"v1"|"v2") cosp=$2 ; shift ; shift ;;
    216                      *) echo Only none v1 v2 for cosp option ; exit
    217                  esac ;;
    218         "-nofcm") compile_with_fcm=0 ; echo This option will be reactivated soon '(promesse du 8dec2022)' ; exit 1 ;  shift ;;
    219         "-SCM") SCM=1 ; shift ;;
    220         "-opt_makelmdz") OPT_MAKELMDZ="$2" ; shift ; shift ;;
    221         "-rrtm") rrtm="$2"
    222                  if [ "$2" = "false" ] ; then
    223                      rad="oldrad"
    224                  else
    225                      rad="rrtm"
    226                  fi
    227                  shift ; shift ;;
    228         "-rad") rad=$2
    229                 case $rad in
    230                     "oldrad"|"rrtm"|"ecrad") rad=$2 ; shift ; shift ;;
    231                     *) echo Only oldrad rrtm ecrad for rad option ; exit
    232                 esac ;;
    233         "-parallel") parallel=$2
    234                      case $parallel in
    235                          "none"|"mpi"|"omp"|"mpi_omp") parallel=$2 ; shift
    236                                                        shift ;;
    237                          *) echo Only none mpi omp mpi_omp for the parallel \
    238                                  option
    239                             exit
    240                      esac ;;
    241         "-bench") bench=$2 ; shift ; shift ;;
    242         "-debug") optim=-debug ; shift ;;
    243         "-name") MODEL=$2 ; shift ; shift ;;
    244         "-netcdf") netcdf=$2 ; shift ; shift ;;
    245         "-physiq") physiq=$2 ; shift ; shift ;;
    246         "-xios") with_xios="y" ; shift ;;
    247         "-env_file") env_file=$2 ; shift ; shift ;;
    248         "-veget") veget=$2 ; shift ; shift ;;
    249         *)  bash install_lmdz.sh -h ; exit
    250     esac
    251 done
    252 
    253 # Option de compilation du rayonnement : depend de $mysvn ><= r4185,
    254 # sera donc definie plus bas
    255 
    256 #opt_rad=""
    257 #case $rad in
    258 #   rrtm) opt_rad="-rad rrtm" ;;
    259 #   ecrad) opt_rad="-rad ecrad" ;;
    260 #esac
    261 
    262 
    263 # Option de compilation pour Cosp
    264 opt_cosp=""
    265 case $cosp in
    266     v1) opt_cosp="-cosp true" ;;
    267     v2) opt_cosp="-cospv2 true" ;;
    268 esac
    269 
    270 # Check on veget version
    271 #if [ "$veget" != 'NONE'  -a "$veget" != "CMIP6" -a "$veget" != +([0-9]) ] ; then
    272 if [ $veget != 'NONE'   -a $veget != "CMIP6" ] ; then
    273     re='^[0-9]+$'
    274     if ! [[ $veget =~ $re ]] ; then
    275         echo 'Valeur de l option veget non valable'
    276         exit
    277     fi
    278 fi
    279 
    280 #Define veget-related suffix for gcm name
    281 if [ "$veget" = 'NONE' ] ; then
    282     suff_orc=''
    283     #For use with tutorial, orchidee_rev is also defined (will be
    284     #written in surface_env at the end of the script)
    285     orchidee_rev=''
    286 else
    287     suff_orc='_orch'
    288 fi
    289 
    290 
    291 if [ $parallel = none ] ; then
    292     sequential=1; suff_exe='_seq'
    293 else
    294     sequential=0; suff_exe='_para_mem'
    295 fi
    296 
    297 #Chemin pour placer le modele
    298 if [ "$MODEL" = "" ] ; then MODEL=./LMDZ$version$svn$optim ; fi
    299 
    300 
    301 arch=local
    302 
    303 
    304 if [ $compiler = g95 ] ; then echo g95 is not supported anymore ; exit ; fi
    305 
    306 ################################################################
    307 # Specificite des machines
    308 ################################################################
    309 
    310 hostname=`hostname`
    311 if [ "$pclinux" = 1 ] ; then o_ins_make="-t g95" ; else o_ins_make="" ; fi
    312 
    313 case ${hostname:0:5} in
    314 
    315     jean-)   compiler="mpiifort" ;
    316              par_comp="mpiifort" ;
    317              o_ins_make="-t jeanzay" ;
    318              make=gmake ;
    319              module purge
    320              module load gcc/6.5.0
    321              module load intel-compilers/19.0.4 ;
    322              #module load intel-mpi/19.0.4 ;
    323              #module load intel-mkl/19.0.4 ;
    324              module load hdf5/1.10.5-mpi ;
    325              module load netcdf/4.7.2-mpi ;
    326              module load netcdf-fortran/4.5.2-mpi ;
    327              module load subversion/1.9.7 ;
    328              module load cmake
    329              export NETCDF_LIBDIR=./
    330              export NETCDFFORTRAN_INCDIR=./
    331              export NETCDFFORTRAN_LIBDIR=./
    332              arch=X64_JEANZAY ;;
    333 
    334     cicla|camel)   compiler="gfortran" ;
    335                    module purge
    336                    module load gnu/10.2.0
    337                    module load openmpi/4.0.5
    338                    module load hdf5/1.10.7-mpi
    339                    module load netcdf-c/4.7.4-mpi
    340                    module load netcdf-fortran/4.5.3-mpi
    341                    netcdf=/net/nfs/tools/PrgEnv/linux-scientific6-x86_64/gcc-10.2.0/netcdf-fortran-4.5.3-k3drgfqok3lip62hnm3tsyof4cjen5sk
    342                    module load svn/1.14.0
    343 
    344                    if [ $parallel != none ] ; then
    345                        root_mpi=/net/nfs/tools/meso-sl6/openmpi/4.0.5-gcc-10.2.0
    346                        path_mpi=$root_mpi/bin ;
    347                        par_comp=${path_mpi}/mpif90 ;
    348                        mpirun=${path_mpi}/mpirun ;
    349                    fi ;
    350                    arch=local  ;
    351                    make=make ;
    352                    o_ins_make="-t g95" ;;
    353 
    354     *)       if [ $parallel = none -o -f /usr/bin/mpif90 ] ; then
    355                  path_mpi=`which mpif90 | sed -e s:/mpif90::` ;
    356                  if [ -d /usr/lib64/openmpi ] ; then
    357                      root_mpi="/usr/lib64/openmpi"
    358                  else
    359                      root_mpi="/usr"
    360                  fi
    361              else
    362                  echo "Cannot find mpif90" ;
    363                  if [ $parallel = none ] ; then exit ; fi ;
    364              fi ;
    365              if [ $parallel != none ] ; then
    366                  root_mpi=$(which mpif90 | sed -e s:/bin/mpif90::)
    367                  path_mpi=$(which mpif90 | sed -e s:/mpif90::)
    368                  export LD_LIBRARY_PATH=${root_mpi}/lib:$LD_LIBRARY_PATH
    369              fi
    370              par_comp=${path_mpi}/mpif90 ;
    371              mpirun=${path_mpi}/mpirun ;
    372              arch=local  ;
    373              make=make ;
    374              o_ins_make="-t g95"
    375 esac
    376 
    377 # Flags for parallelism:
    378 if [ $parallel != none ] ; then
    379     # MPI_LD are the flags needed for linking with MPI
    380     MPI_LD="-L${root_mpi}/lib -lmpi"
    381     if [ "$compiler" = "gfortran" ] ; then
    382         # MPI_FLAGS are the flags needed for compilation with MPI
    383         MPI_FLAGS="-fcray-pointer"
    384         # OMP_FLAGS are the flags needed for compilation with OpenMP
    385         OMP_FLAGS="-fopenmp -fcray-pointer"
    386         # OMP_LD are the flags needed for linking with OpenMP
    387         OMP_LD="-fopenmp"
    388     elif [ "$compiler" = "ifort" ] ; then
    389         MPI_FLAGS=""
    390         OMP_FLAGS="-openmp"
    391         OMP_LD="-openmp"
    392     else # pgf90
    393         MPI_FLAGS=""
    394         OMP_FLAGS="-mp"
    395         OMP_LD="-mp"
    396     fi
    397 fi
    398 
    399 #####################################################################
    400 # Test for old gfortran compilers
    401 # If the compiler is too old (older than 4.3.x) we test if the
    402 # temporary gfortran44 patch is available on the computer in which
    403 # case the compiler is changed from gfortran to gfortran44
    404 # Must be aware than parallelism can not be activated in this case
    405 #####################################################################
    406 
    407 if [ "$compiler" = "gfortran" ] ; then
    408     gfortran=gfortran
    409     gfortranv=`gfortran --version | \
    410    head -1 | awk ' { print $NF } ' | awk -F. ' { print $1 * 10 + $2 } '`
    411     if [ $gfortranv -le 43 ] ; then
    412         echo ERROR : Your gfortran compiler is too old
    413         echo 'Please choose a new one (ifort) and change the line'
    414         echo compiler=xxx
    415         echo in the install_lmdz.sh script and rerun it
    416         if [ `which gfortran44 | wc -w` -ne 0 ] ; then
    417             gfortran=gfortran44
    418         else
    419             echo gfotran trop vieux ; exit
    420         fi
    421     fi
    422     compiler=$gfortran
    423 fi
    424 #####################################################################
    425 
    426 ## if also compiling XIOS, parallel must be mpi_omp
    427 if [ "$with_xios" = "y" -a "$parallel" != "mpi_omp" ] ; then
    428     echo "Error, you must set -parallel mpi_omp if you want XIOS"
    429     exit
    430 fi
    431 
    432 if [ "$with_xios" = "y" ] ; then
    433     opt_makelmdz_xios="-io xios"
    434 fi
    435 
    436 if [ "$cosp" = "v2" -a "$with_xios" = "n" ] ; then
    437     echo "Error, Cospv2 cannot run without Xios"
    438     exit
    439 fi
    440 
    441 echo '################################################################'
    442 echo  Choix des options de compilation
    443 echo '################################################################'
    444 
    445 export FC=$compiler
    446 export F90=$compiler
    447 export F77=$compiler
    448 export CPPFLAGS=
    449 OPTIMNC=$OPTIM
    450 BASE_LD="$OPT_GPROF"
    451 OPTPREC="$OPT_GPROF"
    452 ARFLAGS="rs"
    453 if [ "`lsb_release -i -s`" = "Ubuntu" ] ; then
    454     if [ "`lsb_release -r -s | cut -d. -f1`" -ge 16 ] ; then
    455             ARFLAGS="rU"
    456     fi
    457 fi
    458 
    459 if [ "$compiler" = "$gfortran" ] ; then
    460    OPTIM="-O3 $allow_arg_mismatch"
    461    OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all -fbacktrace -finit-real=snan  $allow_arg_mismatch"
    462    OPTDEV="-Wall -fbounds-check  $allow_arg_mismatch"
    463    fmod='I '
    464    OPTPREC="$OPTPREC -cpp -ffree-line-length-0"
    465    if [ $real = r8 ] ; then OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE" ; fi
    466    export F90FLAGS=" -ffree-form $OPTIMNC"
    467    export FFLAGS=" $OPTIMNC"
    468    export CC=gcc
    469    export CXX=g++
    470    export fpp_flags="-P -C -traditional -ffreestanding"
    471 
    472 elif [ $compiler = mpif90 ] ; then
    473     OPTIM='-O3'
    474     OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all"
    475     OPTDEV="-Wall -fbounds-check"
    476     BASE_LD="$BASE_LD -lblas"
    477     fmod='I '
    478     if [ $real = r8 ] ; then
    479         OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE -fcray-pointer"
    480     fi
    481     export F90FLAGS=" -ffree-form $OPTIMNC"
    482     export FFLAGS=" $OPTIMNC"
    483     export CC=gcc
    484     export CXX=g++
    485 
    486 elif [ $compiler = pgf90 ] ; then
    487     OPTIM='-O2 -Mipa -Munroll -Mnoframe -Mautoinline -Mcache_align'
    488     OPTDEB='-g -Mdclchk -Mbounds -Mchkfpstk -Mchkptr -Minform=inform -Mstandard -Ktrap=fp -traceback'
    489     OPTDEV='-g -Mbounds -Ktrap=fp -traceback'
    490     fmod='module '
    491     if [ $real = r8 ] ; then OPTPREC="$OPTPREC -r8 -DNC_DOUBLE" ; fi
    492     export CPPFLAGS="-DpgiFortran"
    493     export CC=pgcc
    494     export CFLAGS="-O2 -Msignextend"
    495     export CXX=pgCC
    496     export CXXFLAGS="-O2 -Msignextend"
    497     export FFLAGS="-O2 $OPTIMNC"
    498     export F90FLAGS="-O2 $OPTIMNC"
    499     compile_with_fcm=1
    500 
    501 elif [[ $compiler = ifort || $compiler = mpiifort ]] ; then
    502     OPTIM="-O2 -fp-model strict -ip -align all "
    503     OPTDEV="-p -g -O2 -traceback -fp-stack-check -ftrapuv -check"
    504     OPTDEB="-g -no-ftz -traceback -ftrapuv -fp-stack-check -check"
    505     fmod='module '
    506     if [ $real = r8 ] ; then OPTPREC="$OPTPREC -real-size 64 -DNC_DOUBLE" ; fi
    507     export CPP="icc -E"
    508     export FFLAGS="-O2 -ip -fpic -mcmodel=large"
    509     export FCFLAGS="-O2 -ip -fpic -mcmodel=large"
    510     export CC=icc
    511     export CFLAGS="-O2 -ip -fpic -mcmodel=large"
    512     export CXX=icpc
    513     export CXXFLAGS="-O2 -ip -fpic -mcmodel=large"
    514     export fpp_flags="-P -traditional"
    515     # Pourquoi forcer la compilation fcm. Marche mieux sans
    516     #compile_with_fcm=1
    517 else
    518     echo unexpected compiler $compiler ; exit
    519 fi
    520 
    521 OPTIMGCM="$OPTIM $OPTPREC"
    522 
    523 hostname=`hostname`
    524 
    525 ##########################################################################
    526 # If installing on known machines such as Jean-Zay at IDRIS,
    527 # don't check for available software and don't install netcdf
    528 if [ ${hostname:0:5} = jean- ] ; then
    529     netcdf=0 # no need to recompile netcdf, alreday available
    530     check_linux=0
    531     pclinux=0
    532     ioipsl=0 # no need to recompile ioipsl, already available
    533     #netcdf="/smplocal/pub/NetCDF/4.1.3"
    534     compiler="mpiifort"
    535     fmod='module '
    536     if [ $real = r8 ] ; then OPTPREC="$OPTPREC -i4 -r8 -DNC_DOUBLE" ; fi
    537     OPTIM="-auto -align all -O2 -fp-model strict -xHost "
    538     OPTIMGCM="$OPTIM $OPTPREC"
    539 fi
    540 ##########################################################################
    541 
    542 
    543 mkdir -p $MODEL
    544 echo $MODEL
    545 MODEL=`( cd $MODEL ; pwd )` # to get absolute path, if necessary
    546 
    547 
    548 if [ "$check_linux" = 1 ] ; then
    549     echo '################################################################'
    550     echo   Check if required software is available
    551     echo '################################################################'
    552 
    553     #### Ehouarn: test if the required shell is available
    554     #### Maj FH-LF-AS 2021-04 : default=bash ; if bash missing, use ksh
    555     use_shell="bash" # default
    556     if [ "`which bash`" = "" ] ; then
    557         echo "no bash ; we will use ksh"
    558         use_shell="ksh"
    559         if [ "`which ksh`" = "" ] ; then
    560             echo "bash (or ksh) needed!! Install it!"
    561             exit
    562         fi
    563     fi
    564 
    565     for logiciel in wget tar gzip make $compiler gcc cmake m4 c++ ; do
    566         if [ "`which $logiciel`" = "" ] ; then
    567             echo You must first install $logiciel on your system
    568             exit
     250        suff_orc='_orch'
     251    fi
     252
     253
     254    if [[ $parallel = "none" ]]; then
     255        suff_para='_seq'
     256    else
     257        suff_para='_para_mem'
     258    fi
     259
     260    if [[ $with_xios = 1 ]]; then opt_makelmdz_xios="-io xios"; fi
     261
     262    if [[ $aerosols = 1 ]]; then
     263      opt_aer="-dust true"; suff_aer="_spla"
     264    else
     265      opt_aer=""; suff_aer=""
     266    fi
     267
     268    if [[ $strataer = 1 ]]; then
     269      opt_strataer="-strataer true"
     270    else
     271      opt_strataer=""
     272    fi
     273
     274    if [[ $inlandsis = 1 ]]; then
     275       opt_inlandsis="-inlandsis true"
     276    else
     277       opt_inlandsis=""
     278    fi
     279
     280    if [[ $isotopes = 1 ]]; then
     281      opt_isotopes="-isotopes true"; suff_iso="_iso"
     282    else
     283      opt_isotopes="" ; suff_iso=""
     284    fi
     285
     286    # set default arch if parallel
     287    if [[ $arch = "local-gfortran" && $parallel != "none" ]]; then
     288      arch="local-gfortran-parallel"
     289      echo "Switching default arch to $arch"
     290    fi
     291
     292    # Name of the model's folder. The convention taken here is that models that requires different compilation sources should have a different names.
     293    local xios_name=""
     294    if [[ $with_xios = 1 ]]; then xios_name="XIOS"; fi
     295    if [[ $MODEL = "" ]]; then MODEL="./LMDZ$version${svn_lmdz}OR$veget$xios_name"; fi
     296
     297    if [[ $arch_dir = "" ]]; then
     298      arch_dir="$MODEL/modipsl/config/IPSLCM7/ARCH/";
     299    elif ! readlink -fe "$arch_dir" >/dev/null; then
     300      echo "STOP: no arch dir <$arch_dir>"; exit 1
     301    fi
     302
     303    if ! (echo "$grid_resolution" | grep -q "x"); then
     304      is_1D="y"
     305      fortran_file="lmdz1d"
     306    fi
     307}
     308
     309function ensure_correct_option_combinations {
     310    # Check on veget version
     311    if [[ $veget != 'none' && $veget != "CMIP6" && $veget != "orch2.0" && $veget != "orch2.2" ]]; then
     312        re='^[0-9]+$'
     313        if ! [[ $veget =~ $re ]]; then
     314            echo 'Valeur de l option veget non valable'; exit 1
     315        fi
     316    fi
     317
     318    ## if compiling icolmdz, XIOS must be set
     319    if [[ $icolmdz = 1 && $with_xios = 0 ]]; then
     320      echo "Error, you must set -xios to compile the icolmdz executable"; exit 1
     321    fi
     322    ## if also compiling XIOS, parallel must be mpi_omp
     323    if [[ $with_xios = 1 && $parallel != "mpi_omp" ]]; then
     324        echo "Error, you must set -parallel mpi_omp if you want XIOS"; exit 1
     325    fi
     326
     327    if [[ $cosp = "v2" && $with_xios = 0 ]]; then
     328        echo "Error, Cospv2 cannot run without Xios"; exit 1
     329    fi
     330
     331    # STOP if trying to use both ORCHIDEE and Isotopes :
     332    if [[ $isotopes = 1 && $veget != "none" ]]; then
     333      echo "STOP: You cannot run LMDZ with ORCHIDEE and ISOtopes at the same time"; exit 1
     334    fi
     335
     336    # STOP if trying to use both SPLA and Isotopes :
     337    if [[ $isotopes = 1 && $aerosols = 1 ]]; then
     338      echo "STOP: You cannot run LMDZ with Isotopes and aerosols=spla at the same time"; exit 1
     339    fi
     340
     341    # (Temporary) STOP if trying to use Isotopes with XIOS :
     342    if [[ $isotopes = 1 && $with_xios = 1 ]]; then
     343      echo "STOP: Isotopes cannont yet be run with XIOS"; exit 1
     344    fi
     345
     346    if [[ $aerosols = 1 && $rad != "rrtm" ]]; then
     347      echo "STOP: For the time being, <aerosols=spla> requires <rad=rrtm>"; exit 1
     348    fi
     349}
     350
     351function check_available_software {
     352    local required_soft=("wget" "tar" "gzip" "make" "gcc" "cmake" "m4" "c++")
     353    echo "Checking if required software is available (${required_soft[*]})"
     354    for logiciel in "${required_soft[@]}"; do
     355        if [[ $(which "$logiciel") = "" ]]; then
     356            echo "You must first install $logiciel on your system"; exit 1
    569357        fi
    570358    done
    571359
    572     if [ $pclinux = 1 ] ; then
    573         cd $MODEL
    574         cat <<eod > tt.f90
     360    cat <<eod > tt.f90
    575361print*,'coucou'
    576362end
    577363eod
    578         $compiler tt.f90 -o a.out
    579         ./a.out >| tt
    580         if [ "`cat tt | sed -e 's/ //g' `" != "coucou" ] ; then
    581             echo problem installing with compiler $compiler ; exit ; fi
    582         \rm tt a.out tt.f90
    583     fi
    584 fi
    585 
    586 ###########################################################################
    587 if [ $getlmdzor = 1 -a ! -d $MODEL/modipsl ] ; then
    588 ###########################################################################
    589    echo '##########################################################'
    590    echo  Download a slightly modified version of  LMDZ
    591    echo '##########################################################'
    592    cd $MODEL
    593    getlog=`pwd`/get.log
    594    echo logfile : $getlog
    595    myget src_archives/$trusting/modipsl.$version.tar.gz >> get.log 2>&1
    596    echo install_lmdz.sh wget_OK `date`
    597    gunzip modipsl.$version.tar.gz >> get.log 2>&1
    598    tar xf modipsl.$version.tar >> get.log 2>&1
    599    \rm modipsl.$version.tar
    600 fi
    601 
    602 ###########################################################################
    603 echo Installing Netcdf
    604 ###########################################################################
    605 
    606 if [ $netcdf = 0 ] ; then
    607     ncdfdir=/usr
    608 
    609 else
    610     cd $MODEL
    611 
    612     case $compiler in
    613       gfortran) opt1="-compiler gnu" ; opt2="-CC gcc -FC gfortran -CXX g++" ;;
    614       ifort)  opt1="-compiler intel" ; opt2="-CC icc -FC ifort -CXX icpc" ;;
    615       pgf90)  opt1="-compiler pgf90" ; opt2="-CC pgcc -FC pgf90 -CXX pgCC" ;;
    616       *)      echo "unexpected compiler $compiler" for netcdf ; exit 1
     364    $compiler tt.f90 || a.out
     365    ./a.out >| tt
     366    if [[ $(< tt sed -e 's/ //g' ) != "coucou" ]]; then
     367        echo "problem installing with compiler $compiler"; exit 1
     368    fi
     369    rm tt a.out tt.f90
     370}
     371
     372function download_modipsl_tar {
     373    if [[ $clean_install = 1 ]]; then rm -rf "$MODEL"; fi
     374
     375    mkdir -p "$MODEL"
     376    MODEL=$(readlink -e -f "$MODEL"); echo "MODEL: $MODEL"  # absolute path
     377    if [[ ! -d "$MODEL/modipsl" ]]; then
     378        echo "Downloading a slightly modified version of modipsl+LMDZ"
     379        cd "$MODEL"
     380        getlog="$(pwd)/get.log"
     381        echo "logfile : $getlog"
     382        myget "src_archives/$trusting/modipsl.$version.tar.gz" &>> get.log
     383        echo "install_lmdz.sh wget_OK $(date)"
     384
     385        gunzip "modipsl.$version.tar.gz" &>> get.log
     386        tar xf "modipsl.$version.tar" &>> get.log
     387        rm "modipsl.$version.tar"
     388    fi
     389}
     390
     391function init_arch {
     392    cd "$local"
     393    set +e; arch_dir=$(readlink -f "$arch_dir"); set -e  # full path. readlink must be called *after* the path is created
     394
     395    # Check where default fcm, path, env are located - by default in $arch_path, instead in $MODEL/modipsl/modeles/LMDZ/arch/
     396    local i fcm_path path_path env_path
     397    for i in "path" "fcm" "env"; do
     398      local varname=${i}_path
     399      if [[ -f $arch_dir/arch-$arch.$i ]]; then
     400          declare $varname="$arch_dir/arch-$arch.$i"
     401      else
     402          declare $varname="$MODEL/modipsl/modeles/LMDZ/arch/arch-$arch.$i"
     403          if [[ ! -f ${!varname} ]]; then
     404              echo "STOP: no ${!varname}"; exit 1
     405          fi
     406      fi
     407    done
     408    default_fcm_path=$fcm_path
     409    default_path_path=$path_path
     410    default_env_path=$env_path
     411
     412    # check compiler
     413    compiler=$(< "$default_fcm_path" grep "%COMPILER" | sed -e "s/%COMPILER\s*//")
     414
     415    # load env
     416    # shellcheck disable=SC1090
     417    if [[ -f $default_env_path ]]; then source "$default_env_path"; fi
     418
     419    local mpi_file  # can't be done before as it depends on sourcing the env
     420    mpi_file=$(readlink -e -f "$(which mpif90)")
     421    path_mpi=$(dirname "$mpi_file")
     422    root_mpi=$(dirname "$path_mpi")
     423}
     424
     425function install_arch {
     426    local component=$1
     427
     428    # Use same .env for all components (for module compatibility)
     429    cp -f "$default_env_path" "$MODEL/modipsl/modeles/$component/arch" &> /dev/null || true  # allow failure if we're copying the file to itself
     430
     431    # Use local .path and .fcm if available, otherwise default
     432    if [[ ! -f "$MODEL/modipsl/modeles/$component/arch/arch-$arch.path" ]]; then
     433        cp -f "$default_path_path" "$MODEL/modipsl/modeles/$component/arch"
     434
     435        if [[ $component = "ORCHIDEE" ]]; then
     436            if [[ $orcbranch = "/tags/ORCHIDEE_2_0/ORCHIDEE" ]]; then  # 2.0 and before have a different fcm convention
     437                sed -i'' -e "s/-I//" -e "s/-L//" "$MODEL/modipsl/modeles/ORCHIDEE/arch/arch-$arch.path"  # /!\ we only replace first occurence on purpose
     438            fi
     439        fi
     440    fi
     441    if [[ ! -f "$MODEL/modipsl/modeles/$component/arch/arch-$arch.fcm" ]]; then
     442        cp -f "$default_fcm_path"  "$MODEL/modipsl/modeles/$component/arch"
     443
     444        if [[ $component = "XIOS" ]]; then
     445            # Adapt for XIOS, which uses different naming conventions
     446            sed -i'' -e "s/%COMPILER/%FCOMPILER/" -e "s/%LINK/%LINKER/" -e "s/-fdefault-real-8//" "$MODEL/modipsl/modeles/XIOS/arch/arch-$arch.fcm"
     447        fi
     448    fi
     449}
     450
     451function install_netcdf {
     452    echo "Installing Netcdf"
     453    local ncdf_compiler="$compiler"
     454
     455    if [[ $netcdf = 0 ]]; then
     456        ncdfdir=$(nf-config --prefix)
     457    else
     458        cd "$MODEL"
     459
     460        # Convert non-basic compiler
     461        case $compiler in
     462            mpif90) ncdf_compiler=$($compiler --version | head -n 1 | cut -d " " -f -1)
     463        esac
     464
     465        case $ncdf_compiler in
     466            gfortran | GNU) ncdf_compiler="gfortran"; opt1="-compiler gnu"; opt2="-CC gcc -FC gfortran -CXX g++";;
     467            *)      echo "unexpected compiler $ncdf_compiler for netcdf"; exit 1
     468        esac
     469
     470        case $with_xios in
     471            0) script_install_netcdf="install_netcdf4_hdf5_seq.bash"
     472               ncdfdir="netcdf4_hdf5_seq"
     473               opt_="$opt1";;
     474            1) script_install_netcdf="install_netcdf4_hdf5.bash"
     475               ncdfdir="netcdf4_hdf5"
     476               opt_="$opt2 -MPI $root_mpi";;
     477            *) echo "with_xios=$with_xios, should be 0 or 1"; exit 1
     478        esac
     479        if [[ $netcdf = 1 ]]; then
     480           ncdfdir="$MODEL/$ncdfdir"
     481        else
     482           mkdir -p "$netcdf"; ncdfdir="$netcdf/$ncdfdir"
     483        fi
     484
     485        echo "Repertoire netcdf $ncdfdir"
     486        if [[ ! -d $ncdfdir ]]; then
     487            netcdflog=$(pwd)/netcdf.log
     488            echo "----------------------------------------------------------"
     489            echo "Compiling the Netcdf library"
     490            echo "----------------------------------------------------------"
     491            echo "log file : $netcdflog"
     492            myget script_install/$script_install_netcdf &>> "$netcdflog"
     493            chmod u=rwx $script_install_netcdf
     494            # shellcheck disable=SC2086
     495            ./$script_install_netcdf -prefix "$ncdfdir" $opt_ &>> "$netcdflog"
     496        fi
     497
     498        # Add to path
     499        export PATH="$ncdfdir/bin:$PATH"
     500        echo "Bin PATH" $PATH
     501
     502        #----------------------------------------------------------------------------
     503        # LF rajout d'une verrue, pour une raison non encore expliquee,
     504        # la librairie est parfois rangée dans lib64 et non dans lib
     505        # par certains compilateurs
     506        if [[ ! -e lib && -d lib64 ]]; then ln -s lib64 lib; fi
     507        #----------------------------------------------------------------------------
     508
     509        echo "install_lmdz.sh netcdf_OK $(date)"
     510    fi
     511
     512    cat >test_netcdf90.f90 <<EOF
     513    use netcdf
     514    print *, "NetCDF library version: ", nf90_inq_libvers()
     515    end
     516EOF
     517
     518    if $ncdf_compiler -I"$ncdfdir"/include test_netcdf90.f90 -L"$ncdfdir"/lib -lnetcdff -lnetcdf -Wl,-rpath="$ncdfdir"/lib && ./a.out; then
     519        rm test_netcdf90.f90 a.out
     520    else
     521        cat <<EOF
     522Failed test program using NetCDF-Fortran. You can:
     523- check that you have NetCDF-Fortran installed in your system
     524- or specify an installation directory with option -netcdf of install_lmdz.sh
     525- or download and compile NetCDF-Fortran with option -netcdf 1 of install_lmdz.sh
     526EOF
     527        exit 1
     528    fi
     529
     530    # Compile NetCDF95
     531    cd "$MODEL/modipsl/modeles/LMD"*
     532    echo "Installing NetCDF95"
     533    cd "$MODEL"
     534    if [[ ! -d "NetCDF95-0.3" ]]; then
     535        myget src_archives/netcdf/NetCDF95-0.3.tar.gz
     536        tar -xf NetCDF95-0.3.tar.gz
     537        rm NetCDF95-0.3.tar.gz
     538        cd NetCDF95-0.3
     539        mkdir -p build && cd build
     540        netCDF_INCLUDE_DIR=$(nc-config --includedir) netCDF_LIBRARY=$(nc-config --libdir) cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH="$ncdfdir" -DCMAKE_INSTALL_PREFIX="$MODEL/modipsl"
     541        make install
     542    fi
     543}
     544
     545function install_IOIPSL {
     546    install_arch "IOIPSL"
     547
     548    cd "$MODEL/modipsl/modeles/IOIPSL"
     549    ioipsllog="$(pwd)/ioipsl.log"
     550    echo "Compiling IOIPSL, the interface library with Netcdf $(date) (log: $ioipsllog)"
     551# in case ksh is not installed on the pc
     552    if [[ ! -x /bin/ksh ]]; then
     553      sed -i''  -e 's/ksh/bash/' ins_m_prec
     554    fi
     555    echo "$jobcmd ./makeioipsl_fcm -j $make_j -arch $arch $optim_flag" > compile.sh
     556    chmod +x compile.sh
     557    echo "Compiling IOIPSL using $(\cat compile.sh)"
     558    if ! ./compile.sh &> "$ioipsllog"; then
     559        echo "STOP: IOIPSL compile failed, exiting"; exit 1
     560    fi
     561
     562    # Link to modipsl/bin
     563    cp -f bin/* ../../bin
     564
     565    echo "IOIPSL compiled $(date)"
     566}
     567
     568function install_XIOS {
     569    if [[ $with_xios = 1 ]]; then
     570        cd "$MODEL/modipsl/modeles"
     571        xioslog="$(pwd)/XIOS/xios.log"
     572        echo "##########################################################"
     573        echo "Compiling XIOS (log $xioslog) $(date)"
     574        echo "##########################################################"
     575
     576        # Download XIOS
     577        local xios_http="http://forge.ipsl.fr/ioserver/svn/XIOS2/branches/xios-2.6"
     578        local xios_rev="2568"
     579       
     580        cd "$MODEL/modipsl/modeles"
     581        set +e; svn co -r $xios_rev $xios_http XIOS; set -e
     582
     583        cd XIOS
     584
     585        install_arch "XIOS"
     586        do_compile_sh "XIOS" "$jobcmd ./make_xios --job $make_j --arch $arch"
     587    fi
     588}
     589
     590function get_orchidee_version {  # Set / Check ORCHIDEE version
     591    echo "Checking Orchidee source version"
     592    local fetch_rev=""
     593    orcbranch=""
     594    case $veget in
     595        "none") fcm_veget_version="false";;
     596        "orch2.0" | "CMIP6") fcm_veget_version=orchidee2.0; fetch_rev=7906;;  # in previous tar we used 6592 but with some modifications to xios_orchidee.f90, which got integrated in 7906
     597        "orch2.2") fcm_veget_version=orchidee2.1; orcbranch="/branches/ORCHIDEE_2_2/ORCHIDEE" ;; # the bundled version
     598        *) fetch_rev=$veget; fcm_veget_version=orchidee2.1;;  # /!\ arbitary rev only works for orch>=2.1
     599          # /!\ Note: for orch>=4, we should be using fcm_vegt_version="orchideetrunk". Below copied comment by Adriana in LMDZ_Setup docs:
     600#          Avec orchidee2.1, on va compiler LMDZ avec le cle cpp ORCHIDEE_NOLIC. On ne va donc pas prendre en compte les avancements fait dans le trunk qui permet que les fractions lic soitent traité par ORCHIDEE. Ca marche très bien sans cela puisque dans tout façon c'est en cours de développement et ce n'est pas activé par default. En fait on devrait compiler le trunk avec -v orchideetrunk mais avec landice_opt>2, ce qui ne change rien par rapport à orchidee2.1
     601#Si on voudrait activer landice_opt=2 , il faut compiler avec -v orchideetrunk.
     602
    617603    esac
    618604
    619     case $with_xios in
    620         n) script_install_netcdf=install_netcdf4_hdf5_seq.bash
    621            ncdfdir=netcdf4_hdf5_seq
    622            opt_=$opt1 ;;
    623         y) script_install_netcdf=install_netcdf4_hdf5.bash
    624            ncdfdir=netcdf4_hdf5
    625            opt_="$opt2 -MPI $root_mpi" ;;
    626         *) echo with_xios=$with_xios, should be n or y ; exit 1
    627     esac
    628     if [ $netcdf = 1 ] ; then
    629        ncdfdir=$MODEL/$ncdfdir
     605    if [[ -n $fetch_rev ]]; then
     606        echo "IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at orchidee-help@listes.ipsl.fr"
     607        local curr_rev
     608        curr_rev=$(svn info "$MODEL/modipsl/modeles/ORCHIDEE" | grep Revision: | cut -d ":" -f 2 | cut -c 2-)
     609        orcbranch=$(svn log -v -q svn://forge.ipsl.fr/orchidee/ -r "$fetch_rev" | grep ORCHIDEE | head -1 | sed -e 's:ORCHIDEE/.*$:ORCHIDEE:' | awk '{print $2}')
     610        if [[ $fetch_rev != "$curr_rev" ]]; then
     611            echo "Fetching orch $fetch_rev from the repository (curr: $curr_rev)"
     612            echo "branch is $orcbranch"
     613            if [[ $fetch_rev -lt 4465 ]]; then echo 'ORCHIDEE version must be >=4465, exiting'; exit 1; fi
     614            cd "$MODEL/modipsl/modeles"
     615            rm -rf ORCHIDEE
     616            svn co -r "$fetch_rev" "svn://forge.ipsl.fr/orchidee/$orcbranch"
     617            cd - > /dev/null
     618        fi
     619    fi
     620
     621    # Check parallel LMDZ+ORCH
     622    if [[ (! $veget = "none") && $parallel = "none" && ($used_lmdz_rev -lt 4894) ]]; then
     623        echo "LMDZ revision must be >=4894 for orchidee without parallel support. Upgrade lmdz or use -parallel mpi_omp."; exit 1
     624    fi
     625}
     626
     627function compile_orchidee {
     628    install_arch "ORCHIDEE"
     629
     630    if [[ $veget != "none" ]]; then
     631        cd "$MODEL/modipsl/modeles/ORCHIDEE"
     632
     633        local xios_orchid
     634        if [[ $with_xios = 1 ]]; then
     635            xios_orchid="-xios";
     636        else
     637            xios_orchid="-noxios"
     638        fi
     639
     640        if [[ $parallel != "none" && ! -d src_parallel ]]; then
     641           echo "STOP: Orchidee version too old for parallel support"; exit 1
     642        fi
     643        do_compile_sh "ORCHIDEE" "$jobcmd ./makeorchidee_fcm -j $make_j $xios_orchid $optim_flag -parallel $parallel -arch $arch"
     644    fi
     645}
     646
     647function get_lmdz_version {
     648    echo "Checking LMDZ source version"
     649    LMDZPATH=$(readlink -e -f "$MODEL/modipsl/modeles/LMD"*)
     650    cd "$LMDZPATH"
     651
     652    if [[ -n $svn_lmdz ]]; then
     653        local curr_rev
     654        curr_rev=$(svn info "$MODEL/modipsl/modeles/LMD"* | grep Revision: | cut -d ":" -f 2 | cut -c 2-)
     655        if [[ $svn_lmdz != "$curr_rev" ]]; then
     656            local lmdzbranch
     657            echo "Fetching LMDZ $svn_lmdz from the repository"
     658            lmdzbranch=$(get_svn_branch "https://svn.lmd.jussieu.fr/LMDZ" "$svn_lmdz")
     659            echo "branch is $lmdzbranch"
     660            cd "$MODEL/modipsl/modeles"
     661            rm -rf LMD*
     662            svn co -r "$svn_lmdz" "https://svn.lmd.jussieu.fr/LMDZ/$lmdzbranch" LMDZ
     663            cd - > /dev/null
     664        fi
     665        used_lmdz_rev=$svn_lmdz
     666    else  # get svn from info
     667        set +e; used_lmdz_rev=$(svn info | grep "Last Changed Rev" | cut -c 19-); set -e
     668        if [[ -z $used_lmdz_rev ]]; then  # svn info failed
     669            used_lmdz_rev=$(grep 'Revision: [0-9]' "$MODEL"/Read*.md | awk ' { print $2 } ' 2>/dev/null)
     670            if [[ -z $used_lmdz_rev ]]; then echo "Could not determine lmdz version. This is likely an issue with the .tar itself, please report to LMDZ team."; exit 1; fi
     671        fi
     672    fi
     673}
     674
     675function compile_lmdz {
     676    install_arch "LMDZ"
     677    cd "$LMDZPATH"
     678
     679    if [[ $used_lmdz_rev -le 4185 ]]; then
     680        exe_name="bin/${fortran_file}_${grid_resolution}_phy${compphysiq}_${suff_para}${suff_orc}${suff_aer}${suff_iso}.e"
    630681    else
    631        mkdir -p $netcdf ; ncdfdir=$netcdf/$ncdfdir
    632     fi
    633          
    634     echo Repertoire netcdf $ncdfdir
    635     if [ ! -d $ncdfdir ] ; then
    636         netcdflog=`pwd`/netcdf.log
    637         echo '----------------------------------------------------------'
    638         echo Compiling the Netcdf library
    639         echo '----------------------------------------------------------'
    640         echo log file : $netcdflog
    641         myget script_install/$script_install_netcdf >> $netcdflog 2>&1
    642         chmod u=rwx $script_install_netcdf
    643         ./$script_install_netcdf -prefix $ncdfdir $opt_ >> $netcdflog 2>&1
    644     fi
    645 
    646     #----------------------------------------------------------------------------
    647     # LF rajout d'une verrue, pour une raison non encore expliquee,
    648     # la librairie est parfois rangée dans lib64 et non dans lib
    649     # par certains compilateurs
    650     if [ ! -e lib -a -d lib64 ] ; then ln -s lib64 lib; fi
    651     #----------------------------------------------------------------------------
    652 
    653     echo install_lmdz.sh netcdf_OK `date`
    654 
    655 fi
    656 
    657 cat >test_netcdf90.f90 <<EOF
    658 use netcdf
    659 print *, "NetCDF library version: ", nf90_inq_libvers()
    660 end
    661 EOF
    662 
    663 $compiler -I$ncdfdir/include test_netcdf90.f90 -L$ncdfdir/lib -lnetcdff \
    664           -lnetcdf -Wl,-rpath=$ncdfdir/lib && ./a.out
    665    
    666 if (($? == 0))
    667 then
    668     rm test_netcdf90.f90 a.out
    669 else
    670     echo "Failed test program using NetCDF-Fortran."
    671     echo "You can:"
    672     echo "- check that you have NetCDF-Fortran installed in your system"
    673     echo "- or specify an installation directory with option -netcdf of" \
    674          "install_lmdz.sh"
    675     echo "- or download and compile NetCDF-Fortran with option -netcdf 1 of" \
    676          "install_lmdz.sh"
    677     exit 1
    678 fi
    679 
    680 #=========================================================================
    681 if [[ ! -f $MODEL/modipsl/lib/libioipsl.a ]]
    682 then
    683     if [ $ioipsl = 1 ] ; then
    684         #=====================================================================
    685         echo OK ioipsl=$ioipsl
    686         echo '##########################################################'
    687         echo 'Installing MODIPSL, the installation package manager for the '
    688         echo 'IPSL models and tools'
    689         echo '##########################################################'
    690         echo `date`
    691 
    692         cd $MODEL/modipsl
    693         \rm -rf lib/*
    694         cd util
    695         cp AA_make.gdef AA_make.orig
    696         F_C="$compiler -c "
    697         if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ]
    698         then
    699             F_C="$compiler -c -cpp "
    700         fi
    701         if [ "$compiler" = "pgf90" ] ; then F_C="$compiler -c -Mpreprocess" ; fi
    702         sed -e 's/^\#.*.g95.*.\#.*.$/\#/' AA_make.gdef > tmp
    703         sed -e "s:F_L = g95:F_L = $compiler:" \
    704             -e "s:F_C = g95 -c -cpp:F_C = $F_C": \
    705             -e 's/g95.*.w_w.*.(F_D)/g95      w_w = '"$OPTIMGCM"'/' \
    706             -e 's:g95.*.NCDF_INC.*.$:g95      NCDF_INC= '"$ncdfdir"'/include:' \
    707             -e 's:g95.*.NCDF_LIB.*.$:g95      NCDF_LIB= -L'"$ncdfdir"'/lib -lnetcdff -lnetcdf:' \
    708             -e 's:g95      L_O =:g95      L_O = -Wl,-rpath='"$ncdfdir"'/lib:' \
    709             -e "s:-fmod=:-$fmod:" -e 's/-fno-second-underscore//' \
    710             -e 's:#-Q- g95      M_K = gmake:#-Q- g95      M_K = make:' \
    711             tmp >| AA_make.gdef
    712 
    713         if [ $pcmac == 1 ]
    714         then
    715             cp AA_make.gdef tmp
    716             sed -e 's/rpath=/rpath,/g' tmp > AA_make.gdef
    717         fi
    718 
    719 
    720         # We use lines for g95 even for the other compilers to run ins_make
    721         if [ "$use_shell" = "ksh" ] ; then
    722             ./ins_make $o_ins_make
    723         else # bash
    724             sed -e s:/bin/ksh:/bin/bash:g ins_make > ins_make.bash
    725             if [ "`grep jeanzay AA_make.gdef`" = "" ] ; then
    726                 # Bidouille pour compiler sur ada des vieux modipsl.tar
    727                 echo 'Warning jean-zay not in AA_make.gdef'
    728                 echo 'Think about updating'
    729                 exit 1
    730             fi
    731 
    732             chmod u=rwx ins_make.bash
    733             ./ins_make.bash $o_ins_make
    734         fi # of if [ "$use_shell" = "ksh" ]
    735 
    736         echo install_lmdz.sh MODIPSL_OK `date`
    737 
    738         cd $MODEL/modipsl/modeles/IOIPSL/src
    739         ioipsllog=`pwd`/ioipsl.log
    740         echo '##########################################################'
    741         echo 'Compiling IOIPSL, the interface library with Netcdf'
    742         echo '##########################################################'
    743         echo `date`
    744         echo log file : $ioipsllog
    745 
    746         if [ "$use_shell" = "bash" ] ; then
    747             cp Makefile Makefile.ksh
    748             sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile
    749         fi
    750         ### if [ "$pclinux" = 1 ] ; then
    751         # Build IOIPSL modules and library
    752         $make clean
    753         $make > $ioipsllog 2>&1
    754         if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then
    755             # copy module files to lib
    756             cp -f *.mod ../../../lib
    757         fi
    758         # Build IOIPSL tools (ie: "rebuild", if present)
    759           # For IOIPSLv_2_2_2, "rebuild" files are in IOIPSL/tools
    760         rebuild_dir=""
    761         if [ -f $MODEL/modipsl/modeles/IOIPSL/tools/rebuild ] ; then
    762             rebuild_dir=$MODEL/modipsl/modeles/IOIPSL/tools
    763         elif [ -d $MODEL/modipsl/modeles/IOIPSL/rebuild ] ; then
    764               rebuild_dir=$MODEL/modipsl/modeles/IOIPSL/rebuild
    765         fi
    766         if [ $rebuild_dir != "" ] ; then
    767             cd $rebuild_dir     
    768             # adapt Makefile & rebuild script if in bash
    769             if [ "$use_shell" = "bash" ] ; then
    770                 cp Makefile Makefile.ksh
    771                 sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile
    772                 cp rebuild rebuild.ksh
    773                 sed -e 's:/bin/ksh:/bin/bash:g' \
    774                     -e 's:print -u2:echo:g' \
    775                     -e 's:print:echo:g' rebuild.ksh > rebuild
    776             fi
    777             $make clean
    778             $make > $ioipsllog 2>&1
    779         fi
    780         ### fi # of if [ "$pclinux" = 1 ] which is commented out
    781 
    782     else # of if [ $ioipsl = 1 ]
    783         if [ ${hostname:0:5} = jean- ] ; then
    784             cd $MODEL/modipsl
    785             cd util
    786             if [ "`grep jeanzay AA_make.gdef`" = "" ] ; then
    787                 echo 'Warning jean-zay not in AA_make.gdef'
    788                 echo 'Think about updating'
    789                 exit 1
    790             fi
    791             ./ins_make $o_ins_make
    792             # Compile IOIPSL on jean-zay
    793             cd $MODEL/modipsl/modeles/IOIPSL/src
    794             gmake > ioipsl.log
    795             # For IOIPSLv_2_2_2, "rebuild" files are in IOIPSL/tools, so "gmake" in IOIPSL/tools is enough
    796             # For IOIPSLv_2_2_5, "rebuild" files are in a separate IOIPSL/rebuild folder , while "tools" only contains "FCM"
    797             if [ -f $MODEL/modipsl/modeles/IOIPSL/tools/Makefile ] ; then
    798               cd $MODEL/modipsl/modeles/IOIPSL/tools
    799               gmake > ioipsl.log
    800             fi
    801             if [ -d $MODEL/modipsl/modeles/IOIPSL/rebuild ] ; then
    802               cd $MODEL/modipsl/modeles/IOIPSL/rebuild
    803               gmake > ioipsl.log
    804             fi
    805 
    806         fi
    807         echo install_lmdz.sh ioipsl_OK `date`
    808     fi # of if [ $ioipsl = 1 ]
    809 fi # of if [[ ! -f $MODEL/modipsl/lib/libioipsl.a ]]
    810 
    811 #=========================================================================
    812 if [ "$with_xios" = "y" ] ; then
    813     echo '##########################################################'
    814     echo 'Compiling XIOS'
    815     echo '##########################################################'
    816     cd $MODEL/modipsl/modeles
    817     xioslog=`pwd`/XIOS/xios.log
    818     #wget http://www.lmd.jussieu.fr/~lmdz/Distrib/install_xios.bash
    819     myget script_install/install_xios.bash
    820     chmod u=rwx install_xios.bash
    821 # following will be recalculated later on once LMDZ is updated
    822 #    mysvn=`svnversion LMDZ | egrep -o "[0-9]+" 2>/dev/null`
    823     mysvn=`grep 'Revision: [0-9]' $MODEL/Read*.md | awk ' { print $2 } ' 2>/dev/null`
    824     if [ "$svn" != "" ] ; then mysvn=$svn ; fi
    825     echo mysvn $mysvn
    826 
    827     if [ ${hostname:0:5} = jean- ] ; then
    828         if [ $mysvn -ge 4619 ] ; then
    829           svn co http://forge.ipsl.fr/ioserver/svn/XIOS2/branches/xios-2.6 \
    830             XIOS
    831         else
    832           svn co http://forge.ipsl.fr/ioserver/svn/XIOS2/branches/xios-2.5 \
    833             XIOS
    834         fi
    835         cd XIOS/arch
    836         svn update
    837         cd ..
    838         echo "Compiling XIOS, start" `date` \
    839         echo "log file: $xioslog"
    840         #./make_xios --prod --arch $arch --job 4 > xios.log 2>&1
    841         cat > compile_xios.sh <<EOD
    842 ./make_xios --prod --arch X64_JEANZAY --full --job 4 > xios.log 2>&1
    843 EOD
    844 srun --pty --ntasks=1 --cpus-per-task=20 --hint=nomultithread -t 00:30:00 \
    845  --account=gzi@cpu --qos=qos_cpu-dev bash ./compile_xios.sh
    846 
    847     else
    848         ./install_xios.bash -prefix $MODEL/modipsl/modeles \
    849                             -netcdf ${ncdfdir} -hdf5 ${ncdfdir} \
    850                             -MPI $root_mpi -arch $arch > xios.log 2>&1
    851     fi # of case Jean-Zay
    852     if [ -f XIOS/lib/libxios.a ] ; then
    853         echo "XIOS library successfully generated"
    854         echo install_lmdz.sh XIOS_OK `date`
    855     fi
    856 fi
    857 
    858 #============================================================================
    859 veget_version=false
    860 if [ "$veget" != 'NONE' ] ; then
    861     cd $MODEL/modipsl/modeles/ORCHIDEE
    862     set +e ; svn upgrade ; set -e
    863     if [ "$veget" = "CMIP6" ] ; then
    864         veget_version=orchidee2.0
    865         orchidee_rev=6592
    866     else # specific orchidee revision newer than CMIP6, on 2_1 or 2_2 branches
    867         veget_version=orchidee2.1
    868         orchidee_rev=$veget
    869         if [ $veget -lt 4465 ] ; then
    870             echo 'Stopping, ORCHIDEE version too old, script needs work on ' \
    871                  'the CPP flags to pass to makelmdz'
    872             exit 1
    873         fi
    874         set +e
    875         # which branch is my version on?
    876         orcbranch=`svn log -v -q svn://forge.ipsl.fr/orchidee/ -r $veget |grep ORCHIDEE |head -1| sed -e 's:ORCHIDEE/.*$:ORCHIDEE:' | awk '{print $2}'`
    877         # switch to that branch
    878         echo IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at \
    879              orchidee-help@listes.ipsl.fr
    880         svn switch -r $veget --accept theirs-full \
    881             svn://forge.ipsl.fr/orchidee/$orcbranch
    882         svn log -r $veget | grep  $veget
    883         if [  $? -gt 0 ] ; then
    884             echo 'Cannot update ORCHIDEE as not on the right branch for ' \
    885                  'ORCHIDEE'
    886             exit
    887         fi
    888         set -e
    889         set +e ; svn update -r $veget ; set -e
    890     fi
    891     # Correctif suite debug Jean-Zay
    892     sed -i -e 's/9010  FORMAT(A52,F17.14)/9010  FORMAT(A52,F20.14)/' \
    893         src_stomate/stomate.f90
    894     opt_orc="-prod" ; if [ "$optim" = "-debug" ] ; then opt_orc="-debug" ; fi
    895 
    896     orchideelog=`pwd`/orchidee.log
    897     echo '########################################################'
    898     echo 'Compiling ORCHIDEE, the continental surface model '
    899     echo '########################################################'
    900     echo Start of the first compilation of orchidee, in sequential mode: `date`
    901     echo log file : $orchideelog
    902 
    903     export ORCHPATH=`pwd`
    904     xios_orchid="-noxios"
    905     if [ "$with_xios" = "y" ] ; then
    906         xios_orchid="-xios"
    907     fi
    908     if [ -d tools ] ; then
    909         ###################################################################
    910         # Pour les experts qui voudraient changer de version d'orchidee.
    911         # Attention : necessite d'avoir le password pour orchidee
    912 
    913         # Correctif suite debug Jean-Zay
    914         if [ -f src_global/time.f90 ] ; then
    915             sed -i -e 's/CALL tlen2itau/\!CALL tlen2itau/' src_global/time.f90
    916         fi
    917         ###################################################################
    918         if [ "$veget_version" == "false" ] ; then
    919             veget_version=orchidee2.0
    920         fi
    921         cd arch
    922         sed -e s:"%COMPILER        .*.$":"%COMPILER            $compiler":1 \
    923             -e s:"%LINK            .*.$":"%LINK                $compiler":1 \
    924             -e s:"%FPP_FLAGS       .*.$":"%FPP_FLAGS           $fpp_flags":1 \
    925             -e s:"%PROD_FFLAGS     .*.$":"%PROD_FFLAGS         $OPTIM":1 \
    926             -e s:"%DEV_FFLAGS      .*.$":"%DEV_FFLAGS          $OPTDEV":1 \
    927             -e s:"%DEBUG_FFLAGS    .*.$":"%DEBUG_FFLAGS        $OPTDEB":1 \
    928             -e s:"%BASE_FFLAGS     .*.$":"%BASE_FFLAGS         $OPTPREC":1 \
    929             -e s:"%BASE_LD         .*.$":"%BASE_LD             $BASE_LD":1 \
    930             -e s:"%ARFLAGS         .*.$":"%ARFLAGS             $ARFLAGS":1 \
    931             arch-gfortran.fcm > arch-local.fcm
    932         echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib -lnetcdff -lnetcdf\"" \
    933              > arch-local.path
    934         echo "NETCDF_INCDIR=${ncdfdir}/include" >> arch-local.path
    935         echo "IOIPSL_INCDIR=$ORCHPATH/../../lib" >> arch-local.path
    936         echo "IOIPSL_LIBDIR=$ORCHPATH/../../lib" >> arch-local.path
    937         echo 'XIOS_INCDIR=${ORCHDIR}/../XIOS/inc' >> arch-local.path
    938         echo 'XIOS_LIBDIR="${ORCHDIR}/../XIOS/lib -lxios"' >> arch-local.path
    939         cd ../
    940 
    941         echo ./makeorchidee_fcm -j $xios_orchid $opt_orc -parallel none \
    942              -arch $arch
    943         ./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel none \
    944                            -arch $arch > $orchideelog 2>&1
    945         pwd
    946     else # of "if [ -d tools ]"
    947         if [ -d src_parallel ] ; then
    948             liste_src="parallel parameters global stomate sechiba driver"
    949             if [ "$veget_version" == "false" ] ; then
    950                 veget_version=orchidee2.0
    951             fi
    952         fi
    953         for d in $liste_src ; do
    954             src_d=src_$d
    955             echo src_d $src_d
    956             echo ls ; ls
    957             if [ ! -d $src_d ] ; then
    958                 echo Problem orchidee : no $src_d ; exit
    959             fi
    960             cd $src_d ; \rm -f *.mod make ; $make clean
    961             $make > $orchideelog 2>&1
    962             if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then
    963                 cp -f *.mod ../../../lib
    964             fi
    965             cd ..
    966         done
    967     fi # of "if [ -d tools ]"
    968     echo install_lmdz.sh orchidee_compil_seq_OK `date`
    969 fi # of if [ "$veget" != 'NONE' ]
    970 
    971 
    972 #============================================================================
    973 # Ehouarn: the directory name LMDZ* depends on version/tar file...
    974 if [ -d $MODEL/modipsl/modeles/LMD* ] ; then
    975     echo '###############################################################'
    976     echo 'Preparing LMDZ compilation : arch file, svn switch if needed...'
    977     echo '###############################################################'
    978     cd $MODEL/modipsl/modeles/LMD*
    979     LMDZPATH=`pwd`
    980 else
    981     echo "ERROR: No LMD* directory !!!"
    982     exit
    983 fi
    984 
    985 ###########################################################
    986 # For those who want to use fcm to compile via :
    987 #  makelmdz_fcm -arch local .....
    988 ############################################################
    989 
    990 
    991 
    992 cd $MODEL/modipsl/modeles/LMDZ*
    993 lmdzlog=`pwd`/lmdz.log
    994 
    995 ##################################################################
    996 # Possibly update LMDZ if a specific svn release is requested
    997 ##################################################################
    998 
    999 set +e ; svn upgrade ; set -e
    1000 
    1001 if [ "$svn" = "last" ] ; then svnopt="" ; else svnopt="-r $svn" ; fi
    1002 if [ "$svn" != "" ] ; then
    1003     set +e ; svn info | grep -q 'https:'
    1004     if [ $? = 0 ] ; then
    1005         svn switch --relocate https://svn.lmd.jussieu.fr/LMDZ \
    1006             http://svn.lmd.jussieu.fr/LMDZ
    1007     fi
    1008     svn update $svnopt
    1009     set -e
    1010 fi
    1011 
    1012 #---------------------------------------------------------------------
    1013 # Retrieve the final svn release number, and adjust compilation
    1014 # options accordingly
    1015 # If svn not available, will use the svn writen in $MODEL/Readm*md
    1016 # For old version it assumes that it is before 4185 (the version
    1017 # for which the test was introduced
    1018 #---------------------------------------------------------------------
    1019 
    1020 set +e ; mysvn=`svnversion . | egrep -o "[0-9]+" 2>/dev/null` ; set -e
    1021 if [ "$mysvn" = "" ] ; then mysvn=`grep 'Revision: [0-9]' $MODEL/Read*.md | awk ' { print $2 } ' 2>/dev/null` ; fi
    1022 if [ "$mysvn" = "" ] ; then mysvn=4190 ; fi
    1023 
    1024 if [[ "$pclinux" = "1" && ! -f arch/arch-local.path ]] ; then
    1025 
    1026     # create local 'arch' files (if on Linux PC):
    1027     cd arch
    1028     # arch-local.path file
    1029     # test for version as arch.pth file changed format with rev 4426
    1030     if [ "$mysvn" -gt 4425 ] ; then
    1031       echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib \"" > arch-local.path
    1032       echo "NETCDF_LIB=\"-lnetcdff -lnetcdf\"" >> arch-local.path
    1033       echo "NETCDF_INCDIR=-I${ncdfdir}/include" >> arch-local.path
    1034       echo 'NETCDF95_INCDIR=-I$LMDGCM/../../include' >> arch-local.path
    1035       echo 'NETCDF95_LIBDIR=-L$LMDGCM/../../lib' >> arch-local.path
    1036       echo 'NETCDF95_LIB=-lnetcdf95' >> arch-local.path
    1037       echo 'IOIPSL_INCDIR=-I$LMDGCM/../../lib' >> arch-local.path
    1038       echo 'IOIPSL_LIBDIR=-L$LMDGCM/../../lib' >> arch-local.path
    1039       echo 'IOIPSL_LIB=-lioipsl' >> arch-local.path
    1040       echo 'XIOS_INCDIR=-I$LMDGCM/../XIOS/inc' >> arch-local.path
    1041       echo 'XIOS_LIBDIR=-L$LMDGCM/../XIOS/lib' >> arch-local.path
    1042       echo "XIOS_LIB=\"-lxios -lstdc++\"" >> arch-local.path
    1043       echo 'ORCH_INCDIR=-I$LMDGCM/../../lib' >> arch-local.path
    1044       echo 'ORCH_LIBDIR=-L$LMDGCM/../../lib' >> arch-local.path
    1045     else
    1046       echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib -lnetcdff -lnetcdf\"" \
    1047          > arch-local.path
    1048       echo "NETCDF_INCDIR=-I${ncdfdir}/include" >> arch-local.path
    1049       echo 'NETCDF95_INCDIR=$LMDGCM/../../include' >> arch-local.path
    1050       echo 'NETCDF95_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
    1051       echo 'IOIPSL_INCDIR=$LMDGCM/../../lib' >> arch-local.path
    1052       echo 'IOIPSL_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
    1053       echo 'XIOS_INCDIR=$LMDGCM/../XIOS/inc' >> arch-local.path
    1054       echo 'XIOS_LIBDIR=$LMDGCM/../XIOS/lib' >> arch-local.path
    1055       echo 'ORCH_INCDIR=$LMDGCM/../../lib' >> arch-local.path
    1056       echo 'ORCH_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
    1057     fi
    1058 
    1059     if [ $pcmac == 1 ] ; then
    1060         BASE_LD="$BASE_LD -Wl,-rpath,${ncdfdir}/lib"
    1061     else
    1062         BASE_LD="$BASE_LD -Wl,-rpath=${ncdfdir}/lib"
    1063     fi
    1064     # Arch-local.fcm file (adapted from arch-linux-32bit.fcm)
    1065 
    1066     if [ $real = r8 ] ; then FPP_DEF=NC_DOUBLE ; else FPP_DEF="" ; fi
    1067     sed -e s:"%COMPILER        .*.$":"%COMPILER            $compiler":1 \
    1068         -e s:"%LINK            .*.$":"%LINK                $compiler":1 \
    1069         -e s:"%PROD_FFLAGS     .*.$":"%PROD_FFLAGS         $OPTIM":1 \
    1070         -e s:"%DEV_FFLAGS      .*.$":"%DEV_FFLAGS          $OPTDEV":1 \
    1071         -e s:"%DEBUG_FFLAGS    .*.$":"%DEBUG_FFLAGS        $OPTDEB":1 \
    1072         -e s:"%BASE_FFLAGS     .*.$":"%BASE_FFLAGS         $OPTPREC":1 \
    1073         -e s:"%FPP_DEF         .*.$":"%FPP_DEF             $FPP_DEF":1 \
    1074         -e s:"%BASE_LD         .*.$":"%BASE_LD             $BASE_LD":1 \
    1075         -e s:"%ARFLAGS         .*.$":"%ARFLAGS             $ARFLAGS":1 \
    1076         arch-linux-32bit.fcm > arch-local.fcm
    1077 
    1078     cd ..
    1079     ### Adapt "bld.cfg" (add the shell):
    1080     #whereisthatshell=$(which ${use_shell})
    1081     #echo "bld::tool::SHELL   $whereisthatshell" >> bld.cfg
    1082 
    1083 fi # of if [ "$pclinux" = 1 ]
    1084 #---------------------------------------------------------------------
    1085 # Option de compilation du rayonnement : depend de $mysvn ><= r4185
    1086 #---------------------------------------------------------------------
    1087 opt_rad=""
    1088 
    1089 case $rad in
    1090     oldrad) iflag_rrtm=0 ; NSW=2 ; opt_rad="" ;;
    1091     rrtm)   iflag_rrtm=1 ; NSW=6
    1092             if [ $mysvn -le 4185 ] ; then
     682        exe_name="bin/${fortran_file}_${grid_resolution}_phy${compphysiq}_${rad}${suff_para}${suff_orc}${suff_aer}${suff_iso}.e"
     683    fi
     684
     685    local opt_rad
     686    case $rad in
     687        oldrad) iflag_rrtm=0; NSW=2; opt_rad="";;
     688        rrtm)   iflag_rrtm=1; NSW=6
     689            if [[ $used_lmdz_rev -le 4185 ]]; then
    1093690                opt_rad="-rrtm true"
    1094691            else
    1095692                opt_rad="-rad rrtm"
    1096             fi ;;
    1097     ecrad)  iflag_rrtm=2 ; NSW=6 ; opt_rad="-rad ecrad" ;;
    1098     *) echo Only oldrad rrtm ecrad for rad option ; exit
    1099 esac
    1100 
    1101 if [ $mysvn -le 4185 -a $rad = "ecrad" ] ; then
    1102     echo "ecrad only available for LMDZ rev starting with 4186 " ; exit
     693            fi;;
     694        ecrad)  iflag_rrtm=2; NSW=6; opt_rad="-rad ecrad";;
     695        *) echo "Only oldrad rrtm ecrad for rad option"; exit 1
     696    esac
     697    if [[ $used_lmdz_rev -le 4185 && $rad = "ecrad" ]]; then
     698        echo "ecrad only available for LMDZ rev starting with 4186 "; exit 1
     699    fi
     700
     701    # Compile
     702    local makelmdz="makelmdz_fcm $optim_flag -arch $arch -j $make_j"
     703    local para_compile_opt="-mem -parallel $parallel"; if [[ $parallel = "none" ]]; then para_compile_opt=""; fi
     704    do_compile_sh "LMDZ" "$jobcmd ./$makelmdz $opt_rad $opt_cosp $opt_makelmdz_xios $opt_aer $opt_inlandsis $opt_strataer $opt_isotopes -p $compphysiq -d ${grid_resolution} -v $fcm_veget_version $para_compile_opt $fortran_file"
     705
     706    # Check executable
     707    if [[ ! -f $exe_name ]]; then
     708        echo "STOP: Compilation failed, can't find the executable"; exit 1
     709    else
     710        echo "Compilation successful, the executable is $exe_name $(date)"
     711    fi
     712}
     713
     714function get_dynamico_icosa_version {
     715  if [[ $icolmdz = 1 ]]; then
     716    echo "Checking DYNAMICO source version"
     717    cd "$MODEL/modipsl/modeles"
     718    if [[ ! -d DYNAMICO ]]; then
     719      git clone https://gitlab.in2p3.fr/ipsl/projets/dynamico/dynamico.git DYNAMICO
     720    fi
     721    cd DYNAMICO
     722    git checkout master && git checkout $dynamico_commit
     723    cd - > /dev/null
     724
     725    echo "Checking ICOSA_LMDZ source version"
     726    if [[ ! -d ICOSA_LMDZ ]]; then
     727      svn checkout http://svn.lmd.jussieu.fr/LMDZ/ICOSA_LMDZ
     728    fi
     729    cd ICOSA_LMDZ
     730    svn up -r 5320
     731  fi
     732}
     733
     734function compile_icolmdzor {
     735    if [[ $icolmdz = 1 ]]; then
     736      install_arch "ICOSA_LMDZ"
     737      local para_compile_opt="-parallel $parallel"; if [[ $parallel = "none" ]]; then para_compile_opt=""; fi
     738
     739      # LMDZ physics package library already available in LMDZ/config/lib directory
     740
     741      # Compile DYNAMICO
     742      cd "$MODEL/modipsl/modeles/DYNAMICO"
     743
     744      # Need to get rather than install the archs as DYNAMICO uses FCMv2 that does not understand the makefile syntax ($shell)
     745      cd arch
     746      wget "http://lmdz.lmd.jussieu.fr/pub/src_archives/misc/arch/DYNAMICO/arch-$arch.env"
     747      wget "http://lmdz.lmd.jussieu.fr/pub/src_archives/misc/arch/DYNAMICO/arch-$arch.fcm"
     748      wget "http://lmdz.lmd.jussieu.fr/pub/src_archives/misc/arch/DYNAMICO/arch-$arch.path"
     749      cd ..
     750
     751      do_compile_sh "DYNAMICO" "$jobcmd ./make_icosa $optim_flag -arch $arch -job $make_j $para_compile_opt -external_ioipsl -with_xios"
     752
     753      # Compile icosa_lmdz
     754      echo "Bin PATH before icosalmdz" "$PATH"
     755      cd "$MODEL/modipsl/modeles/ICOSA_LMDZ"
     756      do_compile_sh "ICOSA_LMDZ" "$jobcmd ./make_icosa_lmdz -arch $arch -j $make_j -nodeps -p lmd $optim_flag $para_compile_opt -with_orchidee"
     757      echo "# Running environment for icosa_lmdz" > icosalmdz.env
     758      echo "# "                                   >> icosalmdz.env
     759      if [[ -v LD_LIBRARY_PATH ]]; then 
     760        echo "export LD_LIBRARY_PATH=$ncdfdir/lib:$LD_LIBRARY_PATH" >> icosalmdz.env
     761      else
     762        echo "export LD_LIBRARY_PATH=$ncdfdir/lib" >> icosalmdz.env
     763      fi
     764    fi
     765}
     766
     767function run_bench {
     768    local bench_cmd="./bench.sh"
     769
     770    cd "$MODEL/modipsl/modeles/LMDZ"*
     771
     772    if [[ $bench = "tuto" ]]; then
     773        myget "Training/tutorial.tar"; tar xf tutorial.tar; cd TUTORIAL
     774        ./init.sh
     775    elif [[ $bench = 1 ]]; then
     776      rm -rf "BENCH${grid_resolution}"
     777      local bench=bench_lmdz_${grid_resolution}
     778      if [[ $compphysiq = "lmdiso" ]]; then bench=bench_lmdz_iso_${grid_resolution}; fi
     779
     780      if [[ $is_1D = "y" ]] ; then  # 1D
     781        myget "1D/1D.tar.gz"
     782        mkdir -p "BENCH${grid_resolution}"
     783        tar xf "1D.tar.gz" -C "BENCH${grid_resolution}" --strip-components=1
     784        cd "BENCH${grid_resolution}"
     785        # Below: ugly, but until we rewrite the 1D case...
     786        sed -i'' -e "s:^listecas=.*$:listecas=ARMCU/REF:" -e "s:cd \$local/bin ; ./compile -L \$L:#cd \$local/bin ; ./compile -L \$L:" \
     787            -e "s:./compile -L \$llm:#./compile -L \$llm:" -e "s:ln -sf \$bin/\\\\\${main}\${suffixe}.e .:ln -sf ../../../../../$exe_name \\\\\${main}\${suffixe}.e:" -e "s:gzip listing:cp listing restartphy.nc ../../../../; exit 0:" \
     788            run.sh
     789        cp "../$exe_name" bin/
     790        bench_cmd="./run.sh -rad $rad"  # suppress ferret commands that launch after bench is "over"
     791      else
     792        myget "3DBenchs/$bench.tar.gz"
     793        mkdir "BENCH${grid_resolution}"
     794        tar xf "$bench.tar.gz" -C "BENCH${grid_resolution}" --strip-components=1
     795
     796        if [[ $cosp = "v1" || $cosp = "v2" ]]; then
     797            cd "BENCH${grid_resolution}"
     798            # copier les fichiers namelist input et output our COSP
     799            cp ../DefLists/cosp*_input_nl.txt .
     800            cp ../DefLists/cosp*_output_nl.txt .
     801            # Activer la cles ok_cosp pour tourner avec COSP
     802            sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp
     803            \mv -f tmp config.def
     804            cd ..
     805        fi
     806
     807        if [[ -n "$benchphysiq" ]]; then
     808            cd "BENCH${grid_resolution}"
     809            if [[ -f "physiq.def_${benchphysiq}" ]]; then
     810                cp "physiq.def_${benchphysiq}" benchphysiq.def
     811                echo "using physiq.def_${benchphysiq}"
     812            else
     813                echo "using standard physiq.def"
     814            fi
     815            cd ..
     816        else
     817            echo "using standard physiq.def"
     818        fi
     819
     820        if [[ $with_xios = 1 ]]; then
     821            cd "BENCH${grid_resolution}"
     822            cp ../DefLists/iodef.xml .
     823            cp ../DefLists/context_lmdz.xml .
     824            cp ../DefLists/field_def_lmdz.xml .
     825            # A raffiner par la suite
     826            echo "A FAIRE : Copier les *xml en fonction de l option cosp"
     827            cp ../DefLists/field_def_cosp*.xml .
     828            cp ../DefLists/file_def_hist*xml .
     829            # adapt iodef.xml to use attached mode
     830            sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' \
     831                iodef.xml > tmp
     832            \mv -f tmp iodef.xml
     833
     834            # and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
     835            # except for histday
     836            for histfile in file_def_hist*xml; do
     837                if [[ "$histfile" = "file_def_histday_lmdz.xml" ]]; then
     838                    sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' \
     839                        "$histfile" > tmp
     840                    \mv -f tmp "$histfile"
     841                    sed -e 's@output_level="_AUTO_"@output_level="5"@' "$histfile" \
     842                        > tmp
     843                    \mv -f tmp "$histfile"
     844                    sed -e 's@compression_level="2"@compression_level="0"@' \
     845                        "$histfile" > tmp
     846                    \mv -f tmp "$histfile"
     847                else
     848                    sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
     849                        "$histfile" > tmp
     850                    \mv -f tmp "$histfile"
     851                fi
     852            done
     853            # and add option "ok_all_xml=y" in config.def
     854            echo "### XIOS outputs" >> config.def
     855            echo 'ok_all_xml=.true.' >> config.def
     856
     857            #activer les sorties pour Cosp
     858            if [[ "$cosp" = "v1" ]]; then
     859                sed -i'' -e 's@enabled=".FALSE."@enabled=".TRUE."@' \
     860                         -e 's@output_level="_AUTO_"@output_level="5"@' \
     861                         -e 's@compression_level="2"@compression_level="0"@' \
     862                         file_def_histdayCOSP_lmdz.xml
     863            fi
     864            if [[ "$cosp" = "v2" ]]; then
     865                sed -i'' -e 's@compression_level="2"@compression_level="0"@' file_def_histdayCOSPv2_lmdz.xml
     866                for type_ in hf day mth; do
     867                    file=file_def_hist${type_}COSP
     868                    sed -i'' -e 's@src="./'${file}'_lmdz.xml"@src="./'${file}'v2_lmdz.xml"@' context_lmdz.xml
     869                done
     870                sed -i'' -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' field_def_lmdz.xml
     871            fi
     872
     873            cd ..
     874        fi
     875
     876        # Cas Bench avec ecrad
     877        if [[ $rad = "ecrad" ]]; then
     878            cd "BENCH${grid_resolution}"
     879            cp  ../DefLists/namelist_ecrad .
     880            cp -r ../libf/phylmd/ecrad/data .
     881            cd ..
     882        fi
     883
     884        # Adjusting bench physiq.def to radiative code chosen
     885        cd "BENCH${grid_resolution}"
     886        sed -e 's/iflag_rrtm=.*.$/iflag_rrtm='$iflag_rrtm'/' \
     887            -e 's/NSW=.*.$/NSW='$NSW'/' physiq.def > tmpdef
     888        \mv tmpdef physiq.def
     889        cd ..
     890
     891        cp "$exe_name" "BENCH${grid_resolution}/gcm.e"
     892        cd "BENCH${grid_resolution}"
     893
     894        if [[ ${parallel:0:3} = "mpi" ]]; then
     895            # Lancement avec deux procs mpi et 2 openMP
     896            echo "export OMP_STACKSIZE=800M" > bench.sh
     897            if [[ "${parallel:4:3}" = "omp" ]]; then
     898                echo "export OMP_NUM_THREADS=2" >> bench.sh
     899            fi
     900            if [[ $cosp = "v1" || $cosp = "v2" ]]; then
     901                echo "ulimit -s 200000" >> bench.sh
     902            else
     903                echo "ulimit -s unlimited" >> bench.sh
     904            fi
     905            if which mpirun &> /dev/null; then
     906                echo "mpirun -np 2 gcm.e &> listing" >> bench.sh
     907            elif grep -q "Adastra" /etc/motd; then
     908                local account
     909                account=$(/usr/sbin/my_project.py -l 2>&1 | head -1 | cut -d " " -f 3- | cut -c 5-)
     910                bench_cmd="srun --nodes=1 --ntasks=1 --cpus-per-task=2 --threads-per-core=2 --time=0:10:00 --constraint=GENOA --account=$account bash bench.sh"
     911                echo "./gcm.e &> listing" >> bench.sh
     912            else
     913                echo "Error: No command found to run parallel bench"; exit 1
     914            fi
     915            if [[ $(hostname | cut -c -6) = "spirit" ]]; then  # ulimit unlimited segfaults on Spirit
     916                sed -i'' "s/ulimit -s unlimited/ulimit -Ss 8000/" bench.sh
     917            fi
     918            # Add rebuild, using reb.sh if it is there
     919            cat <<EOF >> bench.sh
     920if [[ -f reb.sh ]]; then
     921  ./reb.sh histday; ./reb.sh histmth; ./reb.sh histhf;
     922  ./reb.sh histins; ./reb.sh stomate_history;
     923  ./reb.sh sechiba_history; ./reb.sh sechiba_out_2
    1103924fi
    1104 
    1105 ##################################################################
    1106 
    1107 
    1108 if [[ ! -f libf/misc/netcdf95.F90 &&  ! -d $MODEL/NetCDF95-0.3 ]]
    1109 then
    1110     cd $MODEL
    1111     myget src_archives/netcdf/NetCDF95-0.3.tar.gz
    1112     tar -xf NetCDF95-0.3.tar.gz
    1113     rm NetCDF95-0.3.tar.gz
    1114     cd NetCDF95-0.3
    1115     mkdir build
    1116     cd build
    1117     cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=$ncdfdir \
    1118           -DCMAKE_INSTALL_PREFIX=$MODEL/modipsl
    1119     make install
    1120     cd $MODEL/modipsl/modeles/LMDZ*
    1121 fi
    1122 
    1123 echo '##################################################################'
    1124 echo "Preparing script compile.sh for LMDZ compilation"
    1125 echo "It will only be run automatically if bench=1/tuto"
    1126 echo Here bench=$bench
    1127 echo '##################################################################'
    1128 
    1129 if [ "$env_file" != "" ] ; then
    1130     mv arch/arch-${arch}.env arch/arch-${arch}.orig
    1131     \cp -f $env_file arch/arch-${arch}.env
    1132 fi
    1133 
    1134 if [ $compile_with_fcm = 1 ] ; then
    1135     makelmdz="makelmdz_fcm $optim -arch $arch -j 8 "
    1136 else
    1137     makelmdz="makelmdz $optim -arch $arch"
    1138 fi
    1139 
    1140 # sequential compilation
    1141 if [ "$sequential" = 1 ] ; then
    1142     echo Sequential compilation command, saved in compile.sh:
    1143     echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp " \
    1144          "-d ${grid_resolution} -v $veget_version gcm "
    1145     echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp " \
    1146          "-d ${grid_resolution} -v $veget_version gcm " > compile.sh
    1147     chmod +x ./compile.sh
    1148     if [ $bench = 1 ] ; then
    1149         echo install_lmdz.sh start_lmdz_seq_compilation `date`
    1150         echo log file: $lmdzlog
    1151         ./compile.sh > $lmdzlog 2>&1
    1152         echo install_lmdz.sh end_lmdz_seq_compilation `date`
    1153     fi
    1154 fi # fin sequential
    1155 
    1156 # compiling in parallel mode
    1157 if [ $parallel != "none" ] ; then
    1158     echo '##########################################################'
    1159     echo ' Parallel compile '
    1160     echo '##########################################################'
    1161     echo "(after saving the sequential libs and binaries)"
    1162     cd $MODEL/modipsl
    1163     tar cf sequential.tar bin/ lib/
    1164     #
    1165     # Orchidee
    1166     #
    1167     cd $ORCHPATH
    1168     if [ -d src_parallel -a $veget != 'NONE' ] ; then
    1169         cd arch
    1170         sed  \
    1171             -e s:"%COMPILER.*.$":"%COMPILER            $par_comp":1 \
    1172             -e s:"%LINK.*.$":"%LINK                $par_comp":1 \
    1173             -e s:"%MPI_FFLAG.*.$":"%MPI_FFLAGS          $MPI_FLAGS":1 \
    1174             -e s:"%OMP_FFLAG.*.$":"%OMP_FFLAGS          $OMP_FLAGS":1 \
    1175             -e s:"%MPI_LD.*.$":"%MPI_LD              $MPI_LD":1 \
    1176             -e s:"%OMP_LD.*.$":"%OMP_LD              $OMP_LD":1 \
    1177             arch-local.fcm > tmp.fcm
    1178 
    1179         mv tmp.fcm arch-local.fcm
    1180         cd ../
    1181         echo Compiling ORCHIDEE in parallel mode `date`
    1182         echo logfile $orchideelog
    1183         echo "NOTE : to recompile it when necessary, use ./compile_orc.sh " \
    1184              "in modipsl/modeles/ORCHIDEE"
    1185         echo ./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc \
    1186              -parallel $parallel -arch $arch > compile_orc.sh
    1187         echo ./makeorchidee_fcm -j 8 $xios_orchid $opt_orc \
    1188              -parallel $parallel -arch $arch >> compile_orc.sh
    1189         echo echo Now you must also recompile LMDZ, by running ./compile.sh \
    1190              in modeles/LMDZ >> compile_orc.sh
    1191         chmod u+x compile_orc.sh
    1192         ./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc \
    1193                            -parallel $parallel -arch $arch > $orchideelog 2>&1
    1194         ./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel $parallel \
    1195                            -arch $arch >> $orchideelog 2>&1
    1196         echo End of ORCHIDEE compilation in parallel mode `date`
    1197     elif [ $veget != 'NONE' ] ; then
    1198         echo '##########################################################'
    1199         echo ' Orchidee version too old                                 '
    1200         echo ' Please update to new version                             '
    1201         echo '##########################################################'
    1202         exit
    1203     fi # of [ -d src_parallel -a $veget != 'NONE' ]
    1204 
    1205     # LMDZ
    1206     cd $LMDZPATH
    1207     if [ $arch = local ] ; then
    1208         cd arch
    1209         sed -e s:"%COMPILER.*.$":"%COMPILER            $par_comp":1 \
    1210             -e s:"%LINK.*.$":"%LINK                $par_comp":1 \
    1211             -e s:"%MPI_FFLAG.*.$":"%MPI_FFLAGS          $MPI_FLAGS":1 \
    1212             -e s:"%OMP_FFLAG.*.$":"%OMP_FFLAGS          $OMP_FLAGS":1 \
    1213             -e s:"%ARFLAGS.*.$":"%ARFLAGS          $ARFLAGS":1 \
    1214             -e s@"%BASE_LD.*.$"@"%BASE_LD             -Wl,-rpath=${root_mpi}/lib:${ncdfdir}/lib"@1 \
    1215             -e s:"%MPI_LD.*.$":"%MPI_LD              $MPI_LD":1 \
    1216             -e s:"%OMP_LD.*.$":"%OMP_LD              $OMP_LD":1 \
    1217             arch-local.fcm > tmp.fcm
    1218         mv tmp.fcm arch-local.fcm
    1219         cd ../
    1220     fi
    1221     rm -f compile.sh
    1222     echo resol=${grid_resolution} >> compile.sh
    1223     if [ ${hostname:0:5} = jean- -a "$cosp" = "v2" ] ; then
    1224 
    1225         echo LMDZ compilation command in parallel mode, saved in compile.sh, \
    1226              is :
    1227         echo "(ATTENTION le probleme de cospv2 sur jean-zay en mode prod " \
    1228              "n est pas corrige ! )"
    1229         # ATTENTION le probleme de cospv2 sur jean-zay en mode prod n
    1230         # est pas corrige
    1231         echo ./$makelmdz -dev $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
    1232              $opt_makelmdz_xios -d \$resol -v $veget_version -mem \
    1233              -parallel $parallel gcm >> compile.sh
    1234         echo ./$makelmdz -dev $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
    1235              $opt_makelmdz_xios -d \$resol -v $veget_version -mem \
    1236              -parallel $parallel gcm
    1237     else
    1238         echo ./$makelmdz $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
    1239              $opt_makelmdz_xios -d \$resol -v $veget_version -mem \
    1240              -parallel $parallel gcm >> compile.sh
    1241         echo ./$makelmdz $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
    1242              $opt_makelmdz_xios -d \$resol -v $veget_version -mem \
    1243              -parallel $parallel gcm
    1244     fi
    1245     chmod +x ./compile.sh
    1246 
    1247     if [ $bench = 1 ] ; then
    1248         echo Compiling LMDZ in parallel mode `date`,  LMDZ log file: $lmdzlog
    1249         ./compile.sh > $lmdzlog 2>&1
    1250     fi
    1251 
    1252 fi # of if [ $parallel != "none" ]
    1253 
    1254 
    1255 ##################################################################
    1256 # Verification du succes de la compilation
    1257 ##################################################################
    1258 
    1259 # Recherche de l'executable dont le nom a change au fil du temps ...
    1260 # suffix contains radiative option starting with revision 4186
    1261 if [ $mysvn -ge 4186 ] ; then suff_exe=_${rad}${suff_exe} ; fi
    1262 gcm=""
    1263 
    1264 for exe in gcm.e bin/gcm_${grid_resolution}_phylmd${suff_exe}${suff_orc}.e
    1265 do
    1266     if [ -f $exe ] ; then gcm=$exe ; fi
    1267 done
    1268 
    1269 if [ "$gcm" = "" ] ; then
    1270     if [ $bench = 1 ] ; then
    1271         echo 'Compilation failed !! Cannot run the benchmark;'
    1272         exit
    1273     else
    1274         echo 'Compilation not done (only done when bench=1)'
    1275     fi
    1276 else
    1277     echo '##########################################################'
    1278     echo 'Compilation successfull !! ' `date`
    1279     echo '##########################################################'
    1280     echo The executable is $gcm
    1281 fi
    1282 
    1283 ##################################################################
    1284 # Below, we run a benchmark if bench=1 or tuto
    1285 ##################################################################
    1286 
    1287 if [ $bench = tuto ] ; then
    1288     myget Training/tutorial.tar ; tar xf tutorial.tar ; cd TUTORIAL
    1289     ./init.sh
    1290 
    1291 elif [[ $bench = 1 && ! -d BENCH${grid_resolution} ]] ; then
    1292     # TOUTE CETTE SECTION DEVRAIT DISPARAITRE POUR UNE COMMANDE
    1293     # OU DES BENCHS PAR MOTS CLES COMME tuto
    1294 
    1295     echo '##########################################################'
    1296     echo ' Running a test run '
    1297     echo '##########################################################'
    1298 
    1299     \rm -rf BENCH${grid_resolution}
    1300     bench=bench_lmdz_${grid_resolution}
    1301     echo install_lmdz.sh before bench download  `date`
    1302     #wget http://www.lmd.jussieu.fr/~lmdz/Distrib/$bench.tar.gz
    1303     myget 3DBenchs/$bench.tar.gz
    1304     echo install_lmdz.sh after bench download  `date`
    1305     tar xf $bench.tar.gz
    1306 
    1307     if [ "$cosp" = "v1" -o "$cosp" = "v2" ] ; then
    1308         cd BENCH${grid_resolution}
    1309         # copier les fichiers namelist input et output our COSP
    1310         cp ../DefLists/cosp*_input_nl.txt .
    1311         cp ../DefLists/cosp*_output_nl.txt .
    1312         # Activer la cles ok_cosp pour tourner avec COSP
    1313         sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp
    1314         \mv -f tmp config.def
    1315         cd ..
    1316     fi
    1317 
    1318     if [ -n "$physiq" ]; then
    1319         cd BENCH${grid_resolution}
    1320         if [ -f physiq.def_${physiq} ]; then
    1321             cp physiq.def_${physiq} physiq.def
    1322             echo using physiq.def_${physiq}
     925EOF
    1323926        else
    1324             echo using standard physiq.def
    1325         fi
    1326         cd ..
    1327     else
    1328         echo using standard physiq.def
    1329     fi
    1330 
    1331     if [ "$with_xios" = "y" ] ; then
    1332         cd BENCH${grid_resolution}
    1333         cp ../DefLists/iodef.xml .
    1334         cp ../DefLists/context_lmdz.xml .
    1335         cp ../DefLists/field_def_lmdz.xml .
    1336         # A raffiner par la suite
    1337         echo A FAIRE : Copier les *xml en fonction de l option cosp
    1338         cp ../DefLists/field_def_cosp*.xml .
    1339         cp ../DefLists/file_def_hist*xml .
    1340         # adapt iodef.xml to use attached mode
    1341         sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' \
    1342             iodef.xml > tmp
    1343         \mv -f tmp iodef.xml
    1344 
    1345         # and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
    1346         # except for histday
    1347         for histfile in file_def_hist*xml
    1348         do
    1349             if [ "$histfile" = "file_def_histday_lmdz.xml" ] ; then
    1350                 sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' \
    1351                     $histfile > tmp
    1352                 \mv -f tmp $histfile
    1353                 sed -e 's@output_level="_AUTO_"@output_level="5"@' $histfile \
    1354                     > tmp
    1355                 \mv -f tmp $histfile
    1356                 sed -e 's@compression_level="2"@compression_level="0"@' \
    1357                     $histfile > tmp
    1358                 \mv -f tmp $histfile
    1359             else
     927            echo "./gcm.e &> listing" > bench.sh
     928        fi
     929        chmod +x bench.sh
     930        # Getting orchidee stuff
     931        if [[ $veget = 'CMIP6' || $veget = "orch2.0" ]]; then  # TODO once we have a 2.2 bench, add it here (or in planned separate bench script)
     932            echo 'myget 3DBenchs/BENCHCMIP6.tar.gz'
     933            myget 3DBenchs/BENCHCMIP6.tar.gz
     934            tar xvzf BENCHCMIP6.tar.gz
     935            sed -e "s:VEGET=n:VEGET=y:" config.def > tmp
     936            mv -f tmp config.def
     937            if [[ $with_xios = 1 ]]; then
     938                cp ../../ORCHIDEE/src_xml/context_orchidee.xml .
     939                echo '<context id="orchidee" src="./context_orchidee.xml"/>' > add.tmp
     940                cp ../../ORCHIDEE/src_xml/field_def_orchidee.xml .
     941                cp ../../ORCHIDEE/src_xml/file_def_orchidee.xml .
     942                cp ../../ORCHIDEE/src_xml/file_def_input_orchidee.xml .
     943                if [[ -f ../../ORCHIDEE/src_xml/context_input_orchidee.xml ]]; then
     944                       cp ../../ORCHIDEE/src_xml/context_input_orchidee.xml .
     945                       echo '<context id="orchidee" src="./context_input_orchidee.xml"/>' >> add.tmp
     946                fi
     947                sed -e '/id="LMDZ"/r add.tmp' iodef.xml > tmp
     948                mv tmp iodef.xml
     949                sed -e'{/sechiba1/ s/enabled="_AUTO_"/type="one_file" enabled=".TRUE."/}' \
     950                    file_def_orchidee.xml > tmp
     951                \mv -f tmp file_def_orchidee.xml
    1360952                sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
    1361                     $histfile > tmp
    1362                 \mv -f tmp $histfile
     953                    file_def_orchidee.xml > tmp
     954                \mv -f tmp file_def_orchidee.xml
     955                sed -e 's@output_level="_AUTO_"@output_level="1"@' \
     956                    file_def_orchidee.xml > tmp
     957                \mv -f tmp file_def_orchidee.xml
     958                sed -e 's@output_freq="_AUTO_"@output_freq="1d"@' \
     959                    file_def_orchidee.xml > tmp
     960                \mv -f tmp file_def_orchidee.xml
     961                sed -e 's@compression_level="4"@compression_level="0"@' \
     962                    file_def_orchidee.xml > tmp
     963                \mv -f tmp file_def_orchidee.xml
     964                sed -e 's@XIOS_ORCHIDEE_OK = n@XIOS_ORCHIDEE_OK = y@' \
     965                    orchidee.def > tmp
     966                \mv -f tmp orchidee.def
    1363967            fi
     968        fi
     969
     970        fi
     971
     972        if [[ -f ../arch.env ]]; then source ../arch.env; fi
     973
     974        echo "STARTING BENCH"
     975        date
     976        if (! $bench_cmd &> out.bench) || ! (tail -n 1 listing | grep "Everything is cool"); then
     977            tail listing
     978            echo "Bench FAILED, exiting"; exit 1
     979        fi
     980        date
     981        tail listing
     982    fi
     983
     984    # 1D case
     985    if [[ $SCM = 1 ]]; then
     986        cd "$MODEL"
     987        myget 1D/1D.tar.gz
     988        tar xf 1D.tar.gz
     989        cd 1D
     990        for e in "fcm" "env" "path"; do
     991          cp "$MODEL/modipsl/modeles/LMDZ/arch/arch-$arch.$e" "$MODEL/modipsl/modeles/LMDZ/arch/arch-local.$e"
    1364992        done
    1365         # and add option "ok_all_xml=y" in config.def
    1366         echo "### XIOS outputs" >> config.def
    1367         echo 'ok_all_xml=.true.' >> config.def
    1368 
    1369         #activer les sorties pour Cosp
    1370         if [ "$cosp" = "v1" ] ; then
    1371             sed -i'' -e 's@enabled=".FALSE."@enabled=".TRUE."@' \
    1372                      -e 's@output_level="_AUTO_"@output_level="5"@' \
    1373                      -e 's@compression_level="2"@compression_level="0"@' \
    1374                      file_def_histdayCOSP_lmdz.xml
    1375         fi
    1376         if [ "$cosp" = "v2" ] ; then
    1377             sed -e 's@compression_level="2"@compression_level="0"@' file_def_histdayCOSPv2_lmdz.xml
    1378             for type_ in hf day mth ; do
    1379                 file=file_def_hist${type_}COSP
    1380                 sed -i'' -e 's@src="./'${file}'_lmdz.xml"@src="./'${file}'v2_lmdz.xml"@' context_lmdz.xml
    1381             done
    1382             sed -i '' -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' field_def_lmdz.xml
    1383         fi
    1384 
    1385         cd ..
    1386     fi
    1387 
    1388     # Cas Bensh avec ecrad
    1389     if [ "$rad" = "ecrad" ] ; then
    1390         cd BENCH${grid_resolution}
    1391         cp  ../DefLists/namelist_ecrad .
    1392         cp -r ../libf/phylmd/ecrad/data .
    1393         cd ..
    1394     fi
    1395 
    1396     # Adjusting bench physiq.def to radiative code chosen
    1397     cd BENCH${grid_resolution}
    1398     sed -e 's/iflag_rrtm=.*.$/iflag_rrtm='$iflag_rrtm'/' \
    1399         -e 's/NSW=.*.$/NSW='$NSW'/' physiq.def > tmpdef
    1400     \mv tmpdef physiq.def
    1401     cd ..
    1402 
    1403     cp $gcm BENCH${grid_resolution}/gcm.e
    1404 
    1405     cd BENCH${grid_resolution}
    1406     # On cree le fichier bench.sh au besoin
    1407     # Dans le cas 48x36x39 le bench.sh existe deja en parallele
    1408 
    1409     if [ "$grid_resolution" = "48x36x39" ] ; then
    1410         echo On ne touche pas au bench.sh
    1411         # But we have to adapt "run_local.sh" for $mpirun
    1412         sed -e "s@mpirun@$mpirun@g" run_local.sh > tmp
    1413         mv -f tmp run_local.sh
    1414         chmod u=rwx run_local.sh
    1415     elif [ "${parallel:0:3}" = "mpi" ] ; then
    1416         # Lancement avec deux procs mpi et 2 openMP
    1417         echo "export OMP_STACKSIZE=800M" > bench.sh
    1418         if [ "${parallel:4:3}" = "omp" ] ; then
    1419             echo "export OMP_NUM_THREADS=2" >> bench.sh
    1420         fi
    1421         if [ "$cosp" = "v1" -o "$cosp" = "v2" ] ; then
    1422             if [ ${hostname:0:5} = jean- ] ; then
    1423                    chmod +x ../arch.env
    1424                 ../arch.env       
    1425                 echo "ulimit -s 2000000" >> bench.sh
    1426             else
    1427                 echo "ulimit -s 200000" >> bench.sh
    1428             fi       
    1429         else
    1430             echo "ulimit -s unlimited" >> bench.sh
    1431         fi
    1432         if [ ${hostname:0:5} = jean- ] ; then
    1433             . ../arch/arch-${arch}.env
    1434             echo "srun -n 2 -A $idris_acct@cpu gcm.e > listing  2>&1" \
    1435                  >> bench.sh
    1436         else
    1437             echo "$mpirun -np 2 gcm.e > listing  2>&1" >> bench.sh
    1438         fi
    1439         # Add rebuild, using reb.sh if it is there
    1440         echo 'if [ -f reb.sh ] ; then' >> bench.sh
    1441         echo '  ./reb.sh histday ; ./reb.sh histmth ; ./reb.sh histhf ; ' \
    1442              './reb.sh histins ; ./reb.sh stomate_history ; ' \
    1443              './reb.sh sechiba_history ; ./reb.sh sechiba_out_2 ' >> bench.sh
    1444         echo 'fi' >> bench.sh
    1445     else
    1446         echo "./gcm.e > listing  2>&1" > bench.sh
    1447     fi
    1448     # Getting orchidee stuff
    1449     if [ $veget == 'CMIP6' ] ; then
    1450         #echo 'myget 3DBenchs/BENCHorch11.tar.gz'
    1451         #myget 3DBenchs/BENCHorch11.tar.gz
    1452         #tar xvzf BENCHorch11.tar.gz
    1453         echo 'myget 3DBenchs/BENCHCMIP6.tar.gz'
    1454         myget 3DBenchs/BENCHCMIP6.tar.gz
    1455         tar xvzf BENCHCMIP6.tar.gz
    1456         sed -e "s:VEGET=n:VEGET=y:" config.def > tmp
    1457         mv -f tmp config.def
    1458         if [ "$with_xios" = "y" ] ; then
    1459             cp ../../ORCHIDEE/src_xml/context_orchidee.xml .
    1460             echo '<context id="orchidee" src="./context_orchidee.xml"/>' \
    1461                  > add.tmp
    1462             cp ../../ORCHIDEE/src_xml/field_def_orchidee.xml .
    1463             cp ../../ORCHIDEE/src_xml/file_def_orchidee.xml .
    1464             cp ../../ORCHIDEE/src_xml/file_def_input_orchidee.xml .
    1465             if [ -f ../../ORCHIDEE/src_xml/context_input_orchidee.xml ] ; then
    1466                    cp ../../ORCHIDEE/src_xml/context_input_orchidee.xml .
    1467                    echo '<context id="orchidee" ' \
    1468                      'src="./context_input_orchidee.xml"/>' >> add.tmp
    1469             fi
    1470             sed -e '/id="LMDZ"/r add.tmp' iodef.xml > tmp
    1471             mv tmp iodef.xml
    1472             sed -e'{/sechiba1/ s/enabled="_AUTO_"/type="one_file" enabled=".TRUE."/}' \
    1473                 file_def_orchidee.xml > tmp
    1474             \mv -f tmp file_def_orchidee.xml
    1475             sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
    1476                 file_def_orchidee.xml > tmp
    1477             \mv -f tmp file_def_orchidee.xml
    1478             sed -e 's@output_level="_AUTO_"@output_level="1"@' \
    1479                 file_def_orchidee.xml > tmp
    1480             \mv -f tmp file_def_orchidee.xml
    1481             sed -e 's@output_freq="_AUTO_"@output_freq="1d"@' \
    1482                 file_def_orchidee.xml > tmp
    1483             \mv -f tmp file_def_orchidee.xml
    1484             sed -e 's@compression_level="4"@compression_level="0"@' \
    1485                 file_def_orchidee.xml > tmp
    1486             \mv -f tmp file_def_orchidee.xml
    1487             sed -e 's@XIOS_ORCHIDEE_OK = n@XIOS_ORCHIDEE_OK = y@' \
    1488                 orchidee.def > tmp
    1489             \mv -f tmp orchidee.def
    1490         fi
    1491     fi
    1492 
    1493     if [[ -f ../arch.env ]]
    1494     then
    1495         source ../arch.env
    1496     fi
    1497 
    1498     echo EXECUTION DU BENCH
    1499     set +e
    1500     date ; ./bench.sh > out.bench 2>&1 ; date
    1501     set -e
    1502     tail listing
    1503 
    1504 
    1505     echo '##########################################################'
    1506     echo 'Simulation finished in' `pwd`
    1507     echo 'You have compiled with:'
    1508     cat ../compile.sh
    1509     if [ $parallel = "none" ] ; then
    1510         echo 'You may re-run it with : cd ' `pwd` ' ; gcm.e'
    1511         echo 'or ./bench.sh'
    1512     else
    1513         echo 'You may re-run it with : '
    1514         echo 'cd ' `pwd` '; ./bench.sh'
    1515         #  echo 'ulimit -s unlimited'
    1516         #  echo 'export OMP_NUM_THREADS=2'
    1517         #  echo 'export OMP_STACKSIZE=800M'
    1518         #  echo "$mpirun -np 2 gcm.e "
    1519     fi
    1520     echo '##########################################################'
    1521 
    1522 fi # bench
    1523 
    1524 
    1525 #################################################################
    1526 # Installation eventuelle du 1D
    1527 #################################################################
    1528 
    1529 if [ $SCM = 1 ] ; then
    1530     cd $MODEL
    1531     myget 1D/1D.tar.gz
    1532     tar xf 1D.tar.gz
    1533     cd 1D
    1534     if [ $rad = oldrad ] ; then
    1535         sed -i'' -e 's/^rad=.*$/rad=oldrad/' run.sh
    1536         sed -i'' -e 's/^rad=.*$/rad=oldrad/' bin/compile
    1537     fi
    1538     if [ $rad = ecrad ] ; then
    1539         sed -i'' -e 's/^rad=.*$/rad=ecrad/' run.sh
    1540         sed -i'' -e 's/^rad=.*$/rad=ecrad/' bin/compile
    1541     fi
    1542     echo Running 1D/run.sh, log in `pwd`/run1d.log
    1543     ./run.sh > `pwd`/run1d.log 2>&1
    1544 fi
    1545 
    1546 
    1547 #################################################################
    1548 # sauvegarde des options veget pour utilisation eventuelle tutorial_prod
    1549 #################################################################
    1550 cd $MODEL/modipsl/modeles
    1551 #echo surface_env file created in $MODEL
    1552 echo 'veget='$veget > surface_env
    1553 #opt_veget="-v $veget_version"
    1554 #echo 'opt_veget="'$opt_veget\" >> surface_env
    1555 echo 'opt_veget="'-v $veget_version\" >> surface_env
    1556 echo 'orchidee_rev='$orchidee_rev >> surface_env
    1557 echo 'suforch='$suff_orc >> surface_env
     993        if [[ $rad = "oldrad" ]]; then
     994            sed -i'' -e 's/^rad=.*$/rad=oldrad/' run.sh
     995            sed -i'' -e 's/^rad=.*$/rad=oldrad/' bin/compile
     996        elif [[ $rad = ecrad ]] ; then
     997                        sed -i'' -e 's/^rad=.*$/rad=ecrad/' run.sh
     998                        sed -i'' -e 's/^rad=.*$/rad=ecrad/' bin/compile
     999                    fi
     1000        echo "Running 1D/run.sh, log in $(pwd)/run1d.log"
     1001        ./run.sh &> "$(pwd)/run1d.log"
     1002    fi
     1003}
     1004
     1005function run_bench_icosa {
     1006    local bench_cmd="./bench.sh"
     1007
     1008    if [[ $icolmdz = 1 ]]; then
     1009      cd "$MODEL/modipsl/modeles/ICOSA_LMDZ"
     1010      if [[ $bench = 1 ]]; then
     1011        namebench="bench_icolmdz_nbp10_79"
     1012        rm -rf $namebench
     1013        myget "3DBenchs/$namebench.tar.gz"
     1014        mkdir -p $namebench
     1015        tar xf "$namebench.tar.gz" -C "$namebench" --strip-components=1
     1016        cd $namebench
     1017        # copy executables
     1018        if [[ ! -x ../bin/icosa_lmdz.exe ]]; then
     1019          echo "STOP in icosa_lmdz bench, icosa_lmdz.exe executable not present"; exit 1
     1020        fi
     1021        cp ../bin/icosa_lmdz.exe .
     1022         if [[ ! -x ../../XIOS/bin/xios_server.exe ]]; then
     1023          echo "STOP in icosa_lmdz bench, XIOS executable not present"; exit 1
     1024        fi
     1025        cp ../../XIOS/bin/xios_server.exe .
     1026        echo "STARTING ICOSA_LMDZ BENCH"
     1027        date
     1028        if (! $bench_cmd &> out.bench) || ! ( grep "Time elapsed" listing); then
     1029            tail listing
     1030            echo "ICOSA_LMDZ bench FAILED, exiting"; exit 1
     1031        fi
     1032        date
     1033        echo "ICOSA_LMDZ bench finished"
     1034      fi
     1035    fi
     1036
     1037}
     1038# If sourced: returns, else run setup
     1039if [[ ! "${BASH_SOURCE[0]}" = "$0" ]]; then return 0; fi
     1040
     1041echo "install_lmdz.sh DEBUT $(date)"
     1042
     1043set_default_params
     1044read_cmdline_args "$@"
     1045ensure_correct_option_combinations
     1046download_modipsl_tar
     1047init_arch
     1048check_available_software
     1049get_lmdz_version
     1050get_dynamico_icosa_version
     1051get_orchidee_version
     1052install_netcdf
     1053install_IOIPSL
     1054install_XIOS
     1055compile_orchidee
     1056compile_lmdz
     1057compile_icolmdzor
     1058run_bench
     1059run_bench_icosa
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