source: BOL/script_install_amaury/install_lmdz.sh @ 4873

Last change on this file since 4873 was 4873, checked in by abarral, 8 weeks ago

(WIP)
write default param values in cmdline
remove obsolete arch params
dummy model DL with new modipsl sources
  • Property svn:executable set to *
File size: 47.9 KB
Line 
1#!/bin/bash
2set -eu  # error on command failure, and on unset variables
3export LC_ALL=C  # standardize awk format
4
5###########################################################################
6# Author : Laurent Fairhead et Frédéric Hourdin
7# Usage  : install_lmdz.sh -help
8#
9# bash installation script of the LMDZ model on different computer types :
10# Linux PC, "mesocentre" (IPSL-UPMC, IPSL-X), super-computer (IDRIS)
11#
12# The model is downloaded in the following directory tree
13# $MODEL/modipsl/modeles/...
14# using the "modipsl" infrastructure created by the "IPSL"
15# for coupled (atmosphere/ocean/vegetation/chemistry) climate modeling
16# activities.
17# Here we only download atmospheric (LMDZ) and vegetation (ORCHIDEE)
18# components.
19#
20# The sources of the models can be found in the "modeles" directory.
21# In the present case, LMDZ, ORCHIDEE, and IOIPSL or XIOS (handling of
22# input-outputs using the NetCDF library).
23#
24# The script downloads various source files (including a version of NetCDF)
25# and utilities, compiles the model, and runs a test simulation in a
26# minimal configuration.
27#
28# Prerequisites : pgf90/gfortran, bash or ksh, wget , gunzip, tar, ...
29#
30# Modif 18/11/2011
31#    changes for option real 8.
32#      We compile with -r8 (or equivalent) and -DNC_DOUBLE for the GCM
33#      but with -r4 for netcdf. Variable real must be set to
34#      r4 or r8 at the beginning of the script below.
35#
36###########################################################################
37
38### Functions
39
40function myget { # Get a file from LMDZ repository
41  local url=$1
42
43  local filename
44  filename=$(basename "$url")
45
46  wget --no-check-certificate -nv "http://lmdz.lmd.jussieu.fr/pub/$url"
47  if [[ $filename =~ .*\.(ba)?sh ]]; then chmod +x "$filename"; fi
48}
49
50function set_default_params {
51    # Valeur par défaut des parametres
52
53    # 04_2021 : tester si r4 marche encore !
54    real="r8"  # ou "r4"
55
56    svn=""
57    version="20231022.trunk"
58
59    netcdf=1   #  1: for automatic installation;
60    #          or 0: do not install NetCDF and look for it in standard locations;
61    #          or absolute path: look for NetCDF there
62    bench=1
63    pclinux=1
64    pcmac=0 # default: not on a Mac
65    SCM=0
66    # surface/vegetation scheme treatment
67    # controlled by the single variable veget which can have the following values
68    # - NONE: bucket scheme (default)
69    # - CMIP6: orchidee version used in CMIP exercise, rev 5661
70    # - number: orchidee version number
71    veget="NONE"
72    # choose the resolution for the bench runs
73    # grid_resolution= 32x24x11 or 48x36x19 for tests (test without ORCHIDEE)
74    #                  96x71x19  standard configuration
75    grid_resolution="32x32x39"  # "48x36x19", "96x95x39", "144x142x79"
76    # choose the physiq version you want to test
77    #physiq=NPv6.0.14splith
78    physiq=""
79
80    xios_branch="2.6"
81    xios_rev="2568"
82
83    ## parallel can take the values none/mpi/omp/mpi_omp
84    parallel="none"  # "mpi_omp"
85    idris_acct="lmd"
86    trusting="testing"
87    MODEL=""
88
89    ## also compile XIOS? (and more recent NetCDF/HDF5 libraries) Default=no
90    with_xios="n"
91    opt_makelmdz_xios=""
92
93    ## compile with oldrad/rrtm/ecrad radiatif code (Default=rrtm)
94    rad="rrtm"
95
96    ## compile_with_fcm=1 : use makelmdz_fcm (1) or makelmdz (0)
97    compile_with_fcm=1
98
99    #Compilation with Cosp (cosp=NONE/v1/v2; default=NONE)
100    cosp="NONE"
101    opt_cosp=""
102
103    # Check if on a Mac
104    if [[ $(uname) = "Darwin" ]]; then
105        pcmac=1
106        export MAKE="make"
107    fi
108
109    env_file=""
110    optim_debug=""
111    arch="local"
112
113    local mpi_file
114    mpi_file=$(readlink -f "$(which mpif90)")
115    path_mpi=$(dirname "$mpi_file")
116    root_mpi=$(dirname "$path_mpi")
117
118    arch="local-gfortran"
119    arch_dir=""
120}
121
122function read_cmdline_args {
123    while (($# > 0)); do
124        case $1 in
125            "-h") cat <<........fin
126        $0 [ -v version ] [ -r svn_release ]
127               [ -parallel PARA ] [ -d GRID_RESOLUTION ] [ -bench 0/1 ]
128               [-name LOCAL_MODEL_NAME] [-gprof] [-opt_makelmdz] [-rad RADIATIF]
129
130        -v       "version" like 20150828.trunk, see http://www.lmd.jussieu.fr/~lmdz/Distrib/LISMOI.trunk (default <$version>)
131
132        -r       "svn_release" : either the svn release number or "last" (default <$svn>)
133
134        -parallel parallel support: mpi, omp, mpi_omp (mpi with openMP) or none (default: <$parallel>)
135
136        -d        "grid resolution": should be among the available benchs if -bench 1 (valid values: 48x36x19, 48x36x39) (default : <$grid_resolution>)
137
138        -bench     activating the bench or not (0/1) (default: <$bench>)
139
140        -testing/unstable
141
142        -name      name of the folder to install to (default <$MODEL>)
143
144        -netcdf    0, 1 or PATH. 0: do not download NetCDF, look for it in standard locations (/usr);  1: download and compile NetCDF; PATH: full path to an existing installed NetCDF library (default: <$netcdf>)
145
146        -xios      use (download and compile) the XIOS library (will compile the parallel NetCDF4-HDF5 library) (requires to also have -parallel mpi_omp)
147
148        -cosp       to run with cospv1 or cospv2 [none/v1/v2] (default <$cosp>)
149
150        -rad        radiative code: oldrad, rrtm or ecrad (default <$rad>)
151
152        -nofcm      to compile without fcm
153
154        -SCM        install 1D version automatically
155
156        -debug      compile everything in debug mode
157
158        -physiq     to choose which physics package to use (default <$physiq>)
159
160        -veget      surface/vegetation scheme treatment controlled by the single variable veget which can have the following values: none: bucket scheme (default); CMIP6: orchidee version used in CMIP exercise, rev 5661; number: orchidee version number (default $veget)
161
162        -arch       name of the arch to use (default <$arch>)
163
164        -arch_dir   where to find the arch files (default <$arch_dir>)
165
166........fin
167                  exit 1;;
168            "-v") version=$2; shift; shift;;
169            "-r") svn=$2; shift; shift;;
170            "-d") grid_resolution=$2; shift; shift;;
171            "-unstable"|"-testing") trusting=$(echo "$1" | cut -c2-); shift;;
172            "-cosp") cosp=$2
173                     case $cosp in
174                         "none"|"v1"|"v2") cosp=$2; shift; shift;;
175                         *) echo "Only none v1 v2 for cosp option"; exit 1
176                     esac;;
177            "-nofcm") compile_with_fcm=0; echo "This option will be reactivated soon (promesse du 8dec2022)"; exit 1;  shift;;
178            "-SCM") SCM=1; shift;;
179            "-rad") rad=$2
180                    case $rad in
181                        "oldrad"|"rrtm"|"ecrad") rad=$2; shift; shift;;
182                        *) echo "Only oldrad rrtm ecrad for rad option"; exit 1
183                    esac;;
184            "-parallel") parallel=$2
185                         case $parallel in
186                             "none"|"mpi"|"omp"|"mpi_omp") parallel=$2; shift; shift;;
187                             *) echo "Only none mpi omp mpi_omp for the parallel option"; exit 1
188                         esac;;
189            "-bench") bench=$2; shift; shift;;
190            "-debug") optim_debug=-debug; shift;;
191            "-name") MODEL=$2; shift; shift;;
192            "-netcdf") netcdf=$2; shift; shift;;
193            "-physiq") physiq=$2; shift; shift;;
194            "-xios") with_xios="y"; shift;;
195            "-arch") arch=$2; shift; shift;;
196            "-arch_dir") arch_dir=$2; shift; shift;;
197            "-veget") veget=$2; shift; shift;;
198            *)  bash install_lmdz.sh -h; exit 1
199        esac
200    done
201
202    # Option de compilation pour Cosp
203    case $cosp in
204        v1) opt_cosp="-cosp true";;
205        v2) opt_cosp="-cospv2 true";;
206        *) opt_cosp=""
207    esac
208
209    # Check on veget version
210    if [[ $veget != 'NONE' && $veget != "CMIP6" ]]; then
211        re='^[0-9]+$'
212        if ! [[ $veget =~ $re ]]; then
213            echo 'Valeur de l option veget non valable'; exit 1
214        fi
215    fi
216
217    #Define veget-related suffix for gcm name
218    if [[ $veget = 'NONE' ]]; then
219        suff_orc=''
220        #For use with tutorial, orchidee_rev is also defined (will be
221        #written in surface_env at the end of the script)
222        orchidee_rev=''
223    else
224        suff_orc='_orch'
225    fi
226
227
228    if [[ $parallel = "none" ]]; then
229        sequential=1; suff_exe='_seq'
230    else
231        sequential=0; suff_exe='_para_mem'
232    fi
233
234    #Chemin pour placer le modele
235    if [[ $MODEL = "" ]]; then MODEL="./LMDZ$version$svn$optim_debug"; fi
236
237    ## if also compiling XIOS, parallel must be mpi_omp
238    if [[ $with_xios = "y" && $parallel != "mpi_omp" ]]; then
239        echo "Error, you must set -parallel mpi_omp if you want XIOS"; exit 1
240    fi
241
242    if [[ $with_xios = "y" ]]; then
243        opt_makelmdz_xios="-io xios"
244    fi
245
246    if [[ $cosp = "v2" && $with_xios = "n" ]]; then
247        echo "Error, Cospv2 cannot run without Xios"; exit 1
248    fi
249
250    if [[ $arch_dir = "" ]]; then
251        arch_dir="$MODEL/modipsl/config/IPSLCM7/ARCH/"
252    fi
253    arch_dir=$(readlink -f "$arch_dir")  # full path
254}
255
256function check_available_software {
257    echo "################################################################"
258    echo "Check if required software is available"
259    echo "################################################################"
260    for logiciel in wget tar gzip make gcc cmake m4 c++; do
261        if [[ $(which "$logiciel") = "" ]]; then
262            echo "You must first install $logiciel on your system"; exit 1
263        fi
264    done
265
266    cat <<eod > tt.f90
267print*,'coucou'
268end
269eod
270    $compiler tt.f90 || a.out
271    ./a.out >| tt
272    if [[ $(< tt sed -e 's/ //g' ) != "coucou" ]]; then
273        echo "problem installing with compiler $compiler"; exit 1
274    fi
275    \rm tt a.out tt.f90
276}
277
278function download_model {
279    mkdir -p "$MODEL"
280    MODEL=$(readlink -f "$MODEL"); echo "$MODEL"  # absolute path
281
282    rm -rf "$MODEL/modipsl"
283
284    echo "##########################################################"
285    echo "Download a slightly modified version of  LMDZ"
286    echo "##########################################################"
287    cd "$MODEL"
288    getlog="$(pwd)/get.log"
289    echo "logfile : $getlog"
290    myget "src_archives/$trusting/modipsl.$version.tar.gz" >> get.log 2>&1
291    echo "install_lmdz.sh wget_OK $(date)"
292    gunzip "modipsl.$version.tar.gz" >> get.log 2>&1
293    tar xf "modipsl.$version.tar" >> get.log 2>&1
294    \rm "modipsl.$version.tar"
295
296    if [[ $svn != "" ]]; then
297        mysvn=$svn
298    else
299        mysvn="$(grep 'Revision: [0-9]' "$MODEL"/Read*.md | awk ' { print $2 } ' 2>/dev/null)"
300    fi
301    echo "SVN revision used: $mysvn"
302}
303
304function download_model_AMAURY {
305    MODEL=$(readlink -f "$MODEL"); echo "$MODEL"  # absolute path
306
307    if [[ $svn != "" ]]; then
308        mysvn=$svn
309    else
310        mysvn="$(grep 'Revision: [0-9]' "$MODEL"/Read*.md | awk ' { print $2 } ' 2>/dev/null)"
311    fi
312    echo "SVN revision used: $mysvn"
313}
314
315function check_arch {
316    # TODO     if [[ $(gfortran -dumpversion | cut -d. -f1) -ge 10 ]]; then allow_arg_mismatch="-fallow-argument-mismatch"; fi
317
318    if [[ ! -d $arch_dir ]]; then
319        echo "Error: no arch dir $arch_dir"; exit 1
320    elif [[ ! -f $arch_dir/arch-$arch.path ]]; then
321        echo "Error: no arch-$arch.path in $arch_dir"; exit 1
322    fi
323
324    local fcm_path
325    if [[ -f $arch_dir/arch-$arch.fcm ]]; then
326        fcm_path="$arch_dir/arch-$arch.fcm"
327    else
328        fcm_path="$MODEL/modipsl/modeles/LMDZ/arch/arch-$arch.fcm"
329        if [[ ! -f $fcm_path ]]; then
330            echo "Error: no $fcm_path"; exit 1
331        fi
332    fi
333
334    # check compiler
335    compiler=$(< "$fcm_path" grep "%COMPILER" | sed -e "s/%COMPILER\s*//")
336}
337
338function install_netcdf {
339    echo "Installing Netcdf"
340
341    if [[ $netcdf = 0 ]]; then
342        ncdfdir=$(nc-config --prefix)
343    else
344        cd "$MODEL"
345
346        case $compiler in
347          gfortran) opt1="-compiler gnu"; opt2="-CC gcc -FC gfortran -CXX g++";;
348          ifort)  opt1="-compiler intel"; opt2="-CC icc -FC ifort -CXX icpc";;
349          pgf90)  opt1="-compiler pgf90"; opt2="-CC pgcc -FC pgf90 -CXX pgCC";;
350          *)      echo "unexpected compiler $compiler" for netcdf; exit 1
351        esac
352
353        case $with_xios in
354            n) script_install_netcdf="install_netcdf4_hdf5_seq.bash"
355               ncdfdir="netcdf4_hdf5_seq"
356               opt_="$opt1";;
357            y) script_install_netcdf="install_netcdf4_hdf5.bash"
358               ncdfdir="netcdf4_hdf5"
359               opt_="$opt2 -MPI $root_mpi";;
360            *) echo "with_xios=$with_xios, should be n or y"; exit 1
361        esac
362        if [[ $netcdf = 1 ]]; then
363           ncdfdir="$MODEL/$ncdfdir"
364        else
365           mkdir -p "$netcdf"; ncdfdir="$netcdf/$ncdfdir"
366        fi
367
368        echo "Repertoire netcdf $ncdfdir"
369        if [[ ! -d $ncdfdir ]]; then
370            netcdflog=$(pwd)/netcdf.log
371            echo "----------------------------------------------------------"
372            echo "Compiling the Netcdf library"
373            echo "----------------------------------------------------------"
374            echo "log file : $netcdflog"
375            myget script_install/$script_install_netcdf >> "$netcdflog" 2>&1
376            chmod u=rwx $script_install_netcdf
377            # shellcheck disable=SC2086
378            ./$script_install_netcdf -prefix "$ncdfdir" $opt_ >> "$netcdflog" 2>&1
379        fi
380
381        #----------------------------------------------------------------------------
382        # LF rajout d'une verrue, pour une raison non encore expliquee,
383        # la librairie est parfois rangée dans lib64 et non dans lib
384        # par certains compilateurs
385        if [[ ! -e lib && -d lib64 ]]; then ln -s lib64 lib; fi
386        #----------------------------------------------------------------------------
387
388        echo "install_lmdz.sh netcdf_OK $(date)"
389    fi
390
391    cat >test_netcdf90.f90 <<EOF
392    use netcdf
393    print *, "NetCDF library version: ", nf90_inq_libvers()
394    end
395EOF
396
397    if $compiler -I"$ncdfdir"/include test_netcdf90.f90 -L"$ncdfdir"/lib -lnetcdff \
398              -lnetcdf -Wl,-rpath="$ncdfdir"/lib && ./a.out
399    then
400        \rm test_netcdf90.f90 a.out
401    else
402        cat <<EOF
403Failed test program using NetCDF-Fortran. You can:
404- check that you have NetCDF-Fortran installed in your system
405- or specify an installation directory with option -netcdf of install_lmdz.sh
406- or download and compile NetCDF-Fortran with option -netcdf 1 of nstall_lmdz.sh
407EOF
408        exit 1
409    fi
410}
411
412function install_IOIPSL {  # via fcm
413    cd "$MODEL/modipsl/modeles/IOIPSL"
414    ioipsllog="$(pwd)/ioipsl.log"
415    echo "Compiling IOIPSL, the interface library with Netcdf $(date) (log: $ioipsllog)"
416
417    if ! ./makeioipsl_fcm -arch "$arch" -arch_path "$arch_dir" -job 8 > "$ioipsllog" 2>&1; then
418    echo "IOIPSL compile failed, exiting"; exit 1
419    fi
420    cp lib/* ../../lib
421    echo "IOIPSL compiled $(date)"
422
423    export IOIPSL_LIBDIR="$MODEL/modipsl/modeles/IOIPSL/lib"
424    export IOIPSL_INCDIR="$MODEL/modipsl/modeles/IOIPSL/inc"
425}
426
427function install_XIOS {
428    if [[ $with_xios = "y" ]]; then
429        cd "$MODEL/modipsl/modeles"
430        xioslog="$(pwd)/xios.log"
431        echo "##########################################################"
432        echo "Compiling XIOS (log $xioslog) $(date)"
433        echo "##########################################################"
434
435        # Download XIOS
436        case $xios_branch in
437            "trunk")
438            xios_http="http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/trunk";;
439            "2.5")
440            xios_http="http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5";;
441            "2.6")
442            xios_http="http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS2/branches/xios-2.6";;
443            *) echo "XIOS: Error, bad argument for -branch ! Did not expect $xios_branch"; exit;;
444        esac
445       
446        cd "$MODEL/modipsl/modeles"
447        set +e; svn co --revision $xios_rev $xios_http XIOS; set -e
448
449        cd XIOS
450        if ! ./make_xios --arch "$arch" --job 8 --arch_path "$arch_dir" > "$xioslog" 2>&1; then
451            echo "XIOS compilation failed, exiting"; exit 1
452        fi
453
454        echo "Compiled XIOS $(date)"
455    fi
456}
457
458function get_orchidee_version {  # Set / Check ORCHIDEE version
459  if [[ $veget = "NONE" ]]; then
460    veget_version="false"
461  elif [[ $veget = "CMIP6" ]]; then
462    veget_version=orchidee2.0
463    orchidee_rev=6592
464  else # specific orchidee revision newer than CMIP6, on 2_1 or 2_2 branches
465    veget_version=orchidee2.1
466    orchidee_rev="$veget"
467    if [[ $veget -lt 4465 ]]; then
468      echo 'ORCHIDEE version must be >=4465, exiting'
469      exit 1
470    fi
471
472    set +e
473    svn upgrade
474    local orcbranch
475    orcbranch=$(svn log -v -q svn://forge.ipsl.jussieu.fr/orchidee/ -r "$veget" |grep ORCHIDEE |head -1| sed -e 's:ORCHIDEE/.*$:ORCHIDEE:' | awk '{print $2}')
476    echo "IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at orchidee-help@listes.ipsl.fr"
477    svn switch -r "$veget" --accept theirs-full "svn://forge.ipsl.jussieu.fr/orchidee/$orcbranch"
478    svn log -r "$veget" | grep "$veget"
479    if ! svn log -r "$veget" | grep "$veget"; then
480      echo 'Cannot update ORCHIDEE as not on the right branch for ORCHIDEE'
481      exit 1
482    fi
483    svn update -r "$veget"
484    set -e
485  fi
486}
487
488function compile_orchidee_seq {
489  get_orchidee_version
490
491  if [[ $veget != "NONE" ]]; then
492    cd "$MODEL/modipsl/modeles/ORCHIDEE"
493
494    orchideelog="$(pwd)/orchidee.log"
495    echo "Compiling ORCHIDEE, the continental surface model (log $orchideelog)"
496    echo "Start of the first compilation of orchidee, in sequential mode: $(date)"
497
498    ORCHPATH=$(pwd)
499    export ORCHPATH=$ORCHPATH
500
501    local xios_orchid opt_orc
502    if [[ $with_xios = "y" ]]; then
503      xios_orchid="-xios";
504    else
505      xios_orchid="-noxios"
506    fi
507    if [[ $optim_debug = "-debug" ]]; then
508      opt_orc="-debug";
509    else
510      opt_orc="-prod"
511    fi
512
513    # TODO debug
514    echo "./makeorchidee_fcm $xios_orchid $opt_orc -parallel none -arch $arch -arch_path $arch_dir"
515
516    if ! ./makeorchidee_fcm "$xios_orchid" "$opt_orc" -parallel none -arch "$arch" -arch_path "$arch_dir" > "$orchideelog" 2>&1; then
517      echo "ORCHIDEE seq compilation failed, exiting"; exit 1
518    fi
519    echo "Compiled ORCHIDEE seq $(date)"
520  fi
521}
522
523echo "install_lmdz.sh DEBUT $(date)"
524
525set_default_params
526read_cmdline_args "$@"
527#download_model
528download_model_AMAURY
529check_arch
530check_available_software
531install_netcdf
532install_IOIPSL
533#install_XIOS  # TODO disabled for now, did not decide which flags/arch to use for compile
534compile_orchidee_seq
535
536exit 0
537
538
539
540
541################################################################
542# Specificite des machines
543################################################################
544
545hostname=$(hostname)
546#case ${hostname:0:5} in
547#    *)       if [[ $parallel = none || -f /usr/bin/mpif90 ]]; then
548#                 path_mpi=$(which mpif90 | sed -e s:/mpif90::);
549#                 if [[ -d /usr/lib64/openmpi ]]; then
550#                     root_mpi="/usr/lib64/openmpi"
551#                 else
552#                     root_mpi="/usr"
553#                 fi
554#             else
555#                 echo "Cannot find mpif90";
556#                 if [[ $parallel = none ]]; then exit 1; fi;
557#             fi;
558#             if [[ $parallel != none ]]; then
559#                 root_mpi=$(which mpif90 | sed -e s:/bin/mpif90::)
560#                 path_mpi=$(which mpif90 | sed -e s:/mpif90::)
561#                 export LD_LIBRARY_PATH=${root_mpi}/lib:$LD_LIBRARY_PATH
562#             fi
563#             par_comp=${path_mpi}/mpif90;
564#             mpirun=${path_mpi}/mpirun;
565#             arch="local";
566#             make="make";
567#             o_ins_make="-t g95"
568#esac
569
570## Flags for parallelism:
571#if [[ $parallel != none ]]; then
572#    # MPI_LD are the flags needed for linking with MPI
573#    MPI_LD="-L${root_mpi}/lib -lmpi"
574#    if [[ $compiler = "gfortran" ]]; then
575#        # MPI_FLAGS are the flags needed for compilation with MPI
576#        MPI_FLAGS="-fcray-pointer"
577#        # OMP_FLAGS are the flags needed for compilation with OpenMP
578#        OMP_FLAGS="-fopenmp -fcray-pointer"
579#        # OMP_LD are the flags needed for linking with OpenMP
580#        OMP_LD="-fopenmp"
581#    elif [[ $compiler = "ifort" ]]; then
582#        MPI_FLAGS=""
583#        OMP_FLAGS="-openmp"
584#        OMP_LD="-openmp"
585#    else # pgf90
586#        MPI_FLAGS=""
587#        OMP_FLAGS="-mp"
588#        OMP_LD="-mp"
589#    fi
590#fi
591#
592#
593#echo "################################################################"
594#echo  "Choix des options de compilation"
595#echo "################################################################"
596#
597#export FC=$compiler
598#export F90=$compiler
599#export F77=$compiler
600#export CPPFLAGS=
601#OPTIMNC=""
602#BASE_LD="$OPT_GPROF"
603#OPTPREC="$OPT_GPROF"
604#ARFLAGS="rs"
605#if [[ $(lsb_release -i -s) = "Ubuntu" ]]; then
606#    if [[ $(lsb_release -r -s | cut -d. -f1) -ge 16 ]]; then
607#        ARFLAGS="rU"
608#    fi
609#fi
610#
611#if [[ $compiler = "gfortran" ]]; then
612#   OPTIM="-O3 $allow_arg_mismatch"
613#   OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all -fbacktrace -finit-real=snan  $allow_arg_mismatch"
614#   OPTDEV="-Wall -fbounds-check  $allow_arg_mismatch"
615#   fmod="I "
616#   OPTPREC="$OPTPREC -cpp -ffree-line-length-0"
617#   if [[ $real = r8 ]]; then OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE"; fi
618#   export F90FLAGS=" -ffree-form $OPTIMNC"
619#   export FFLAGS=" $OPTIMNC"
620#   export CC=gcc
621#   export CXX=g++
622#   export fpp_flags="-P -C -traditional -ffreestanding"
623#
624#elif [[ $compiler = mpif90 ]]; then
625#    OPTIM="-O3"
626#    OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all"
627#    OPTDEV="-Wall -fbounds-check"
628#    BASE_LD="$BASE_LD -lblas"
629#    fmod="I "
630#    if [[ $real = r8 ]]; then
631#        OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE -fcray-pointer"
632#    fi
633#    export F90FLAGS=" -ffree-form $OPTIMNC"
634#    export FFLAGS=" $OPTIMNC"
635#    export CC=gcc
636#    export CXX=g++
637#
638#elif [[ $compiler = pgf90 ]]; then
639#    OPTIM="-O2 -Mipa -Munroll -Mnoframe -Mautoinline -Mcache_align"
640#    OPTDEB="-g -Mdclchk -Mbounds -Mchkfpstk -Mchkptr -Minform=inform -Mstandard -Ktrap=fp -traceback"
641#    OPTDEV="-g -Mbounds -Ktrap=fp -traceback"
642#    fmod="module "
643#    if [[ $real = r8 ]]; then OPTPREC="$OPTPREC -r8 -DNC_DOUBLE"; fi
644#    export CPPFLAGS="-DpgiFortran"
645#    export CC=pgcc
646#    export CFLAGS="-O2 -Msignextend"
647#    export CXX=pgCC
648#    export CXXFLAGS="-O2 -Msignextend"
649#    export FFLAGS="-O2 $OPTIMNC"
650#    export F90FLAGS="-O2 $OPTIMNC"
651#    compile_with_fcm=1
652#
653#elif [[ $compiler = ifort || $compiler = mpiifort ]]; then
654#    OPTIM="-O2 -fp-model strict -ip -align all "
655#    OPTDEV="-p -g -O2 -traceback -fp-stack-check -ftrapuv -check"
656#    OPTDEB="-g -no-ftz -traceback -ftrapuv -fp-stack-check -check"
657#    fmod='module '
658#    if [[ $real = r8 ]]; then OPTPREC="$OPTPREC -real-size 64 -DNC_DOUBLE"; fi
659#    export CPP="icc -E"
660#    export FFLAGS="-O2 -ip -fpic -mcmodel=large"
661#    export FCFLAGS="-O2 -ip -fpic -mcmodel=large"
662#    export CC=icc
663#    export CFLAGS="-O2 -ip -fpic -mcmodel=large"
664#    export CXX=icpc
665#    export CXXFLAGS="-O2 -ip -fpic -mcmodel=large"
666#    export fpp_flags="-P -traditional"
667#    # Pourquoi forcer la compilation fcm. Marche mieux sans
668#    #compile_with_fcm=1
669#else
670#    echo "unexpected compiler $compiler"; exit 1
671#fi
672#
673#OPTIMGCM="$OPTIM $OPTPREC"
674
675
676veget_version=false
677if [[ $veget != 'NONE' ]]; then
678    cd "$MODEL/modipsl/modeles/ORCHIDEE"
679
680    opt_orc="-prod"; if [[ "$optim_debug" = "-debug" ]]; then opt_orc="-debug"; fi
681
682    orchideelog=$(pwd)/orchidee.log
683    echo '########################################################'
684    echo 'Compiling ORCHIDEE, the continental surface model '
685    echo '########################################################'
686    echo "Start of the first compilation of orchidee, in sequential mode: $(date)"
687    echo "log file : $orchideelog"
688
689    ORCHPATH=$(pwd)
690    export ORCHPATH=$ORCHPATH
691    xios_orchid="-noxios"
692    if [[ "$with_xios" = "y" ]]; then
693        xios_orchid="-xios"
694    fi
695    if [[ -d tools ]]; then
696        ###################################################################
697        # Pour les experts qui voudraient changer de version d'orchidee.
698        # Attention : necessite d'avoir le password pour orchidee
699        ###################################################################
700        if [[ "$veget_version" == "false" ]]; then
701            veget_version=orchidee2.0
702        fi
703        cd arch
704        sed -e s:"%COMPILER        .*.$:%COMPILER            $compiler":1 \
705            -e s:"%LINK            .*.$:%LINK                $compiler":1 \
706            -e s:"%FPP_FLAGS       .*.$:%FPP_FLAGS           $fpp_flags":1 \
707            -e s:"%PROD_FFLAGS     .*.$:%PROD_FFLAGS         $OPTIM":1 \
708            -e s:"%DEV_FFLAGS      .*.$:%DEV_FFLAGS          $OPTDEV":1 \
709            -e s:"%DEBUG_FFLAGS    .*.$:%DEBUG_FFLAGS        $OPTDEB":1 \
710            -e s:"%BASE_FFLAGS     .*.$:%BASE_FFLAGS         $OPTPREC":1 \
711            -e s:"%BASE_LD         .*.$:%BASE_LD             $BASE_LD":1 \
712            -e s:"%ARFLAGS         .*.$:%ARFLAGS             $ARFLAGS":1 \
713            arch-gfortran.fcm > arch-local.fcm
714        cat <<EOF > arch-local.path
715NETCDF_LIBDIR="-L$ncdfdir/lib -lnetcdff -lnetcdf"
716NETCDF_INCDIR="$ncdfdir/include"
717IOIPSL_INCDIR="$ORCHPATH/../../lib"
718IOIPSL_LIBDIR="$ORCHPATH/../../lib"
719XIOS_INCDIR="\$ORCHDIR/../XIOS/inc"
720XIOS_LIBDIR="\$ORCHDIR/../XIOS/lib -lxios"
721EOF
722        cd ../
723
724        echo ./makeorchidee_fcm -j $xios_orchid $opt_orc -parallel none \
725             -arch $arch
726        ./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel none \
727                           -arch $arch > "$orchideelog" 2>&1
728        pwd
729    else # of "if [[ -d tools ]]"
730        if [[ -d src_parallel ]]; then
731            liste_src="parallel parameters global stomate sechiba driver"
732            if [[ "$veget_version" == "false" ]]; then
733                veget_version=orchidee2.0
734            fi
735        fi
736        for d in $liste_src; do
737            src_d=src_$d
738            echo src_d "$src_d"
739            echo ls; ls
740            if [[ ! -d $src_d ]]; then
741                echo "Problem orchidee : no $src_d"; exit 1
742            fi
743            cd "$src_d"; \rm -f -- *.mod make; $make clean
744            $make > "$orchideelog" 2>&1
745            if [[ "$compiler" = "gfortran" || "$compiler" = "mpif90" ]]; then
746                cp -f -- *.mod ../../../lib
747            fi
748            cd ..
749        done
750    fi # of "if [[ -d tools ]]"
751    echo "install_lmdz.sh orchidee_compil_seq_OK $(date)"
752fi # of if [[ "$veget" != 'NONE' ]]
753
754
755#============================================================================
756# Ehouarn: the directory name LMDZ* depends on version/tar file...
757if find . -name "$MODEL/modipsl/modeles/LMD*"; then
758    echo '###############################################################'
759    echo 'Preparing LMDZ compilation : arch file, svn switch if needed...'
760    echo '###############################################################'
761    cd "$MODEL/modipsl/modeles/"LMD*
762    LMDZPATH=$(pwd)
763else
764    echo "ERROR: No LMD* directory !!!"
765    exit 1
766fi
767
768
769###########################################################
770# For those who want to use fcm to compile via :
771#  makelmdz_fcm -arch local .....
772############################################################
773
774
775
776cd "$MODEL/modipsl/modeles"/LMDZ*
777lmdzlog=$(pwd)/lmdz.log
778
779##################################################################
780# Possibly update LMDZ if a specific svn release is requested
781##################################################################
782
783set +e; svn upgrade; set -e
784
785if [[ $svn = "last" ]]; then svnopt=""; else svnopt="-r $svn"; fi
786if [[ $svn != "" ]]; then
787    if set +e; svn info | grep -q 'https:'; then
788        svn switch --relocate https://svn.lmd.jussieu.fr/LMDZ \
789            http://svn.lmd.jussieu.fr/LMDZ
790    fi
791    svn update "$svnopt"
792    set -e
793fi
794
795#---------------------------------------------------------------------
796# Retrieve the final svn release number, and adjust compilation
797# options accordingly
798# If svn not available, will use the svn writen in $MODEL/Readm*md
799# For old version it assumes that it is before 4185 (the version
800# for which the test was introduced
801#---------------------------------------------------------------------
802
803set +e; mysvn=$(svnversion . | grep -E || "[0-9]+" 2>/dev/null); set -e
804if [[ "$mysvn" = "" ]]; then mysvn=$(grep 'Revision: [0-9]' "$MODEL"/Read*.md | awk ' { print $2 } ' 2>/dev/null); fi
805if [[ "$mysvn" = "" ]]; then mysvn=4190; fi
806
807if [[ "$pclinux" = "1" && ! -f arch/arch-local.path ]]; then
808
809    # create local 'arch' files (if on Linux PC):
810    cd arch
811    # arch-local.path file
812    # test for version as arch.pth file changed format with rev 4426
813    if [[ "$mysvn" -gt 4425 ]]; then
814      cat <<EOF > arch-local.path
815NETCDF_LIBDIR="-L$ncdfdir/lib"
816NETCDF_LIB="-lnetcdff -lnetcdf"
817NETCDF_INCDIR=-I$ncdfdir/include
818NETCDF95_INCDIR=-I\$LMDGCM/../../include
819NETCDF95_LIBDIR=-L\$LMDGCM/../../lib
820NETCDF95_LIB=-lnetcdf95
821IOIPSL_INCDIR=-I\$LMDGCM/../../lib
822IOIPSL_LIBDIR=-L\$LMDGCM/../../lib
823IOIPSL_LIB=-lioipsl
824XIOS_INCDIR=-I\$LMDGCM/../XIOS/inc
825XIOS_LIBDIR=-L\$LMDGCM/../XIOS/lib
826XIOS_LIB="-lxios -lstdc++"
827ORCH_INCDIR=-I\$LMDGCM/../../lib
828ORCH_LIBDIR=-L\$LMDGCM/../../lib
829EOF
830    else
831      cat <<EOF > arch-local.path
832NETCDF_LIBDIR="-L$ncdfdir/lib -lnetcdff -lnetcdf"
833NETCDF_INCDIR=-I$ncdfdir/include
834NETCDF95_INCDIR=\$LMDGCM/../../include
835NETCDF95_LIBDIR=\$LMDGCM/../../lib
836IOIPSL_INCDIR=\$LMDGCM/../../lib
837IOIPSL_LIBDIR=\$LMDGCM/../../lib
838XIOS_INCDIR=\$LMDGCM/../XIOS/inc
839XIOS_LIBDIR=\$LMDGCM/../XIOS/lib
840ORCH_INCDIR=\$LMDGCM/../../lib
841ORCH_LIBDIR=\$LMDGCM/../../lib
842EOF
843    fi 
844
845    if [[ $pcmac == 1 ]]; then
846        BASE_LD="$BASE_LD -Wl,-rpath,${ncdfdir}/lib"
847    else
848        BASE_LD="$BASE_LD -Wl,-rpath=${ncdfdir}/lib"
849    fi
850    # Arch-local.fcm file (adapted from arch-linux-32bit.fcm)
851
852    if [[ $real = r8 ]]; then FPP_DEF=NC_DOUBLE; else FPP_DEF=""; fi
853    sed -e s:"%COMPILER        .*.$:%COMPILER            $compiler":1 \
854        -e s:"%LINK            .*.$:%LINK                $compiler":1 \
855        -e s:"%PROD_FFLAGS     .*.$:%PROD_FFLAGS         $OPTIM":1 \
856        -e s:"%DEV_FFLAGS      .*.$:%DEV_FFLAGS          $OPTDEV":1 \
857        -e s:"%DEBUG_FFLAGS    .*.$:%DEBUG_FFLAGS        $OPTDEB":1 \
858        -e s:"%BASE_FFLAGS     .*.$:%BASE_FFLAGS         $OPTPREC":1 \
859        -e s:"%FPP_DEF         .*.$:%FPP_DEF             $FPP_DEF":1 \
860        -e s:"%BASE_LD         .*.$:%BASE_LD             $BASE_LD":1 \
861        -e s:"%ARFLAGS         .*.$:%ARFLAGS             $ARFLAGS":1 \
862        arch-linux-32bit.fcm > arch-local.fcm
863
864    cd ..
865    ### Adapt "bld.cfg" (add the shell):
866    #whereisthatshell=$(which ${use_shell})
867    #echo "bld::tool::SHELL   $whereisthatshell" >> bld.cfg
868
869fi # of if [[ "$pclinux" = 1 ]]
870#---------------------------------------------------------------------
871# Option de compilation du rayonnement : depend de $mysvn ><= r4185
872#---------------------------------------------------------------------
873opt_rad=""
874
875case $rad in
876    oldrad) iflag_rrtm=0; NSW=2; opt_rad="";;
877    rrtm)   iflag_rrtm=1; NSW=6
878            if [[ $mysvn -le 4185 ]]; then
879                opt_rad="-rrtm true"
880            else
881                opt_rad="-rad rrtm"
882            fi;;
883    ecrad)  iflag_rrtm=2; NSW=6; opt_rad="-rad ecrad";;
884    *) echo "Only oldrad rrtm ecrad for rad option"; exit 1
885esac
886
887if [[ $mysvn -le 4185 && $rad = "ecrad" ]]; then
888    echo "ecrad only available for LMDZ rev starting with 4186 "; exit 1
889fi
890
891##################################################################
892
893
894if [[ ! -f libf/misc/netcdf95.F90 &&  ! -d $MODEL/NetCDF95-0.3 ]]; then
895    cd "$MODEL"
896    myget src_archives/netcdf/NetCDF95-0.3.tar.gz
897    tar -xf NetCDF95-0.3.tar.gz
898    rm NetCDF95-0.3.tar.gz
899    cd NetCDF95-0.3
900    mkdir build
901    cd build
902    cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH="$ncdfdir" \
903          -DCMAKE_INSTALL_PREFIX="$MODEL/modipsl"
904    make install
905    cd "$MODEL/modipsl/modeles/"LMDZ*
906fi
907
908echo '##################################################################'
909echo "Preparing script compile.sh for LMDZ compilation"
910echo "It will only be run automatically if bench=1/tuto"
911echo "Here bench=$bench"
912echo '##################################################################'
913
914if [[ $env_file != "" ]]; then
915    mv arch/arch-${arch}.env arch/arch-${arch}.orig
916    \cp -f "$env_file" arch/arch-${arch}.env
917fi
918
919if [[ $compile_with_fcm = 1 ]]; then
920    makelmdz="makelmdz_fcm $optim_debug -arch $arch -j 8 "
921else
922    makelmdz="makelmdz $optim_debug -arch $arch"
923fi
924
925# sequential compilation
926if [[ "$sequential" = 1 ]]; then
927    echo Sequential compilation command, saved in compile.sh:
928    echo "./$makelmdz $optim_debug $OPT_MAKELMDZ $optim_debug $opt_rad $opt_cosp " \
929         "-d ${grid_resolution} -v $veget_version gcm "
930    echo "./$makelmdz $optim_debug $OPT_MAKELMDZ $optim_debug $opt_rad $opt_cosp " \
931         "-d ${grid_resolution} -v $veget_version gcm " > compile.sh
932    chmod +x ./compile.sh
933    if [[ $bench = 1 ]]; then
934        echo "install_lmdz.sh start_lmdz_seq_compilation $(date)"
935        echo "log file: $lmdzlog"
936        ./compile.sh > "$lmdzlog" 2>&1
937        echo "install_lmdz.sh end_lmdz_seq_compilation $(date)"
938    fi
939fi # fin sequential
940
941# compiling in parallel mode
942if [[ $parallel != "none" ]]; then
943    echo '##########################################################'
944    echo ' Parallel compile '
945    echo '##########################################################'
946    echo "(after saving the sequential libs and binaries)"
947    cd "$MODEL/modipsl"
948    tar cf sequential.tar bin/ lib/
949    #
950    # Orchidee
951    #
952    cd "$ORCHPATH"
953    if [[ -d src_parallel && $veget != 'NONE' ]]; then
954        cd arch
955        sed  \
956            -e s:"%COMPILER.*.$:%COMPILER            $par_comp":1 \
957            -e s:"%LINK.*.$:%LINK                $par_comp":1 \
958            -e s:"%MPI_FFLAG.*.$:%MPI_FFLAGS          $MPI_FLAGS":1 \
959            -e s:"%OMP_FFLAG.*.$:%OMP_FFLAGS          $OMP_FLAGS":1 \
960            -e s:"%MPI_LD.*.$:%MPI_LD              $MPI_LD":1 \
961            -e s:"%OMP_LD.*.$:%OMP_LD              $OMP_LD":1 \
962            arch-local.fcm > tmp.fcm
963
964        mv tmp.fcm arch-local.fcm
965        cd ../
966        echo "Compiling ORCHIDEE in parallel mode $(date)"
967        echo "logfile $orchideelog"
968        echo "NOTE : to recompile it when necessary, use ./compile_orc.sh " \
969             "in modipsl/modeles/ORCHIDEE"
970        echo ./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc \
971             -parallel "$parallel" -arch $arch > compile_orc.sh
972        echo ./makeorchidee_fcm -j 8 $xios_orchid $opt_orc \
973             -parallel "$parallel" -arch $arch >> compile_orc.sh
974        echo echo Now you must also recompile LMDZ, by running ./compile.sh \
975             in modeles/LMDZ >> compile_orc.sh
976        chmod u+x compile_orc.sh
977        ./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc \
978                           -parallel "$parallel" -arch $arch > "$orchideelog" 2>&1
979        ./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel "$parallel" \
980                           -arch $arch >> "$orchideelog" 2>&1
981        echo "End of ORCHIDEE compilation in parallel mode $(date)"
982    elif [[ $veget != 'NONE' ]]; then
983        echo '##########################################################'
984        echo ' Orchidee version too old                                 '
985        echo ' Please update to new version                             '
986        echo '##########################################################'
987        exit 1
988    fi #�of [ -d src_parallel && $veget != 'NONE' ]
989
990    # LMDZ
991    cd "$LMDZPATH"
992    if [[ $arch = local ]]; then
993        cd arch
994        sed -e s:"%COMPILER.*.$:%COMPILER            $par_comp":1 \
995            -e s:"%LINK.*.$:%LINK                $par_comp":1 \
996            -e s:"%MPI_FFLAG.*.$:%MPI_FFLAGS          $MPI_FLAGS":1 \
997            -e s:"%OMP_FFLAG.*.$:%OMP_FFLAGS          $OMP_FLAGS":1 \
998            -e s:"%ARFLAGS.*.$:%ARFLAGS          $ARFLAGS":1 \
999            -e "s§%BASE_LD.*.$§%BASE_LD             -Wl,-rpath=${root_mpi}/lib:${ncdfdir}/lib§1" \
1000            -e s:"%MPI_LD.*.$:%MPI_LD              $MPI_LD":1 \
1001            -e s:"%OMP_LD.*.$:%OMP_LD              $OMP_LD":1 \
1002            arch-local.fcm > tmp.fcm
1003        mv tmp.fcm arch-local.fcm
1004        cd ../
1005    fi
1006    rm -f compile.sh
1007    echo resol="$grid_resolution" >> compile.sh
1008    if [[ ${hostname:0:5} = jean- && "$cosp" = "v2" ]]; then
1009
1010        echo "LMDZ compilation command in parallel mode, saved in compile.sh, is :"
1011        echo "(ATTENTION le probleme de cospv2 sur jean-zay en mode prod " \
1012             "n est pas corrige ! )"
1013        # ATTENTION le probleme de cospv2 sur jean-zay en mode prod n
1014        # est pas corrige
1015        echo ./"$makelmdz" -dev $optim_debug "$OPT_MAKELMDZ" "$opt_rad" "$opt_cosp" \
1016             "$opt_makelmdz_xios" -d \$resol -v $veget_version -mem \
1017             -parallel "$parallel" gcm >> compile.sh
1018        echo ./"$makelmdz" -dev $optim_debug "$OPT_MAKELMDZ" "$opt_rad" "$opt_cosp" \
1019             "$opt_makelmdz_xios" -d \$resol -v $veget_version -mem \
1020             -parallel "$parallel" gcm
1021    else
1022        echo ./"$makelmdz" $optim_debug "$OPT_MAKELMDZ" "$opt_rad" "$opt_cosp" \
1023             "$opt_makelmdz_xios" -d \$resol -v $veget_version -mem \
1024             -parallel "$parallel" gcm >> compile.sh
1025        echo ./"$makelmdz" $optim_debug "$OPT_MAKELMDZ" "$opt_rad" "$opt_cosp" \
1026             "$opt_makelmdz_xios" -d \$resol -v $veget_version -mem \
1027             -parallel "$parallel" gcm
1028    fi
1029    chmod +x ./compile.sh
1030
1031    if [[ $bench = 1 ]]; then
1032        echo "Compiling LMDZ in parallel mode $(date),  LMDZ log file: $lmdzlog"
1033        ./compile.sh > "$lmdzlog" 2>&1
1034    fi
1035
1036fi # of if [[ $parallel != "none" ]]
1037
1038
1039##################################################################
1040# Verification du succes de la compilation
1041##################################################################
1042
1043# Recherche de l'executable dont le nom a change au fil du temps ...
1044# suffix contains radiative option starting with revision 4186
1045if [[ $mysvn -ge 4186 ]]; then suff_exe=_${rad}${suff_exe}; fi
1046gcm=""
1047
1048for exe in gcm.e bin/gcm_${grid_resolution}_phylmd${suff_exe}${suff_orc}.e
1049do
1050    if [[ -f $exe ]]; then gcm=$exe; fi
1051done
1052
1053if [[ "$gcm" = "" ]]; then
1054    if [[ $bench = 1 ]]; then
1055        echo 'Compilation failed !! Cannot run the benchmark;'
1056        exit 1
1057    else
1058        echo 'Compilation not done (only done when bench=1)'
1059    fi
1060else
1061    echo '##########################################################'
1062    echo "Compilation successfull !!  $(date)"
1063    echo '##########################################################'
1064    echo "The executable is $gcm"
1065fi
1066
1067##################################################################
1068# Below, we run a benchmark if bench=1 or tuto
1069##################################################################
1070
1071if [[ $bench = tuto ]]; then
1072    myget Training/tutorial.tar; tar xf tutorial.tar; cd TUTORIAL
1073    ./init.sh
1074
1075elif [[ $bench = 1 && ! -d BENCH${grid_resolution} ]]; then
1076    # TOUTE CETTE SECTION DEVRAIT DISPARAITRE POUR UNE COMMANDE
1077    # OU DES BENCHS PAR MOTS CLES COMME tuto
1078
1079    echo '##########################################################'
1080    echo ' Running a test run '
1081    echo '##########################################################'
1082
1083    \rm -rf "BENCH${grid_resolution}"
1084    bench=bench_lmdz_${grid_resolution}
1085    echo "install_lmdz.sh before bench download  $(date)"
1086    #wget http://www.lmd.jussieu.fr/~lmdz/Distrib/$bench.tar.gz
1087    myget "3DBenchs/$bench.tar.gz"
1088    echo "install_lmdz.sh after bench download  $(date)"
1089    tar xf "$bench.tar.gz"
1090
1091    if [[ "$cosp" = "v1" || "$cosp" = "v2" ]]; then
1092        cd "BENCH${grid_resolution}"
1093        # copier les fichiers namelist input et output our COSP
1094        cp ../DefLists/cosp*_input_nl.txt .
1095        cp ../DefLists/cosp*_output_nl.txt .
1096        # Activer la cles ok_cosp pour tourner avec COSP
1097        sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp
1098        \mv -f tmp config.def
1099        cd ..
1100    fi
1101
1102    if [[ -n "$physiq" ]]; then
1103        cd "BENCH${grid_resolution}"
1104        if [[ -f "physiq.def_${physiq}" ]]; then
1105            cp "physiq.def_${physiq}" physiq.def
1106            echo using "physiq.def_${physiq}"
1107        else
1108            echo using standard physiq.def
1109        fi
1110        cd ..
1111    else
1112        echo using standard physiq.def
1113    fi
1114
1115    if [[ "$with_xios" = "y" ]]; then
1116        cd "BENCH${grid_resolution}"
1117        cp ../DefLists/iodef.xml .
1118        cp ../DefLists/context_lmdz.xml .
1119        cp ../DefLists/field_def_lmdz.xml .
1120        # A raffiner par la suite
1121        echo "A FAIRE : Copier les *xml en fonction de l option cosp"
1122        cp ../DefLists/field_def_cosp*.xml .
1123        cp ../DefLists/file_def_hist*xml .
1124        # adapt iodef.xml to use attached mode
1125        sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' \
1126            iodef.xml > tmp
1127        \mv -f tmp iodef.xml
1128
1129        # and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
1130        # except for histday
1131        for histfile in file_def_hist*xml
1132        do
1133            if [[ "$histfile" = "file_def_histday_lmdz.xml" ]]; then
1134                sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' \
1135                    "$histfile" > tmp
1136                \mv -f tmp "$histfile"
1137                sed -e 's@output_level="_AUTO_"@output_level="5"@' "$histfile" \
1138                    > tmp
1139                \mv -f tmp "$histfile"
1140                sed -e 's@compression_level="2"@compression_level="0"@' \
1141                    "$histfile" > tmp
1142                \mv -f tmp "$histfile"
1143            else
1144                sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
1145                    "$histfile" > tmp
1146                \mv -f tmp "$histfile"
1147            fi
1148        done
1149        # and add option "ok_all_xml=y" in config.def
1150        echo "### XIOS outputs" >> config.def
1151        echo 'ok_all_xml=.true.' >> config.def
1152
1153        #activer les sorties pour Cosp
1154        if [[ "$cosp" = "v1" ]]; then
1155            sed -i'' -e 's@enabled=".FALSE."@enabled=".TRUE."@' \
1156                     -e 's@output_level="_AUTO_"@output_level="5"@' \
1157                     -e 's@compression_level="2"@compression_level="0"@' \
1158                     file_def_histdayCOSP_lmdz.xml
1159        fi
1160        if [[ "$cosp" = "v2" ]]; then
1161            sed -e 's@compression_level="2"@compression_level="0"@' file_def_histdayCOSPv2_lmdz.xml
1162            for type_ in hf day mth; do
1163                file=file_def_hist${type_}COSP
1164                sed -i'' -e 's@src="./'${file}'_lmdz.xml"@src="./'${file}'v2_lmdz.xml"@' context_lmdz.xml
1165            done
1166            sed -i '' -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' field_def_lmdz.xml
1167        fi
1168
1169        cd ..
1170    fi
1171
1172    # Cas Bensh avec ecrad
1173    if [[ "$rad" = "ecrad" ]]; then
1174        cd "BENCH${grid_resolution}"
1175        cp  ../DefLists/namelist_ecrad .
1176        cp -r ../libf/phylmd/ecrad/data .
1177        cd ..
1178    fi
1179
1180    # Adjusting bench physiq.def to radiative code chosen
1181    cd "BENCH${grid_resolution}"
1182    sed -e 's/iflag_rrtm=.*.$/iflag_rrtm='$iflag_rrtm'/' \
1183        -e 's/NSW=.*.$/NSW='$NSW'/' physiq.def > tmpdef
1184    \mv tmpdef physiq.def
1185    cd ..
1186
1187    cp "$gcm" "BENCH${grid_resolution}/gcm.e"
1188
1189    cd "BENCH${grid_resolution}"
1190    # On cree le fichier bench.sh au besoin
1191    # Dans le cas 48x36x39 le bench.sh existe deja en parallele
1192
1193    if [[ "$grid_resolution" = "48x36x39" ]]; then
1194        echo On ne touche pas au bench.sh
1195        # But we have to adapt "run_local.sh" for $mpirun
1196        sed -e "s@mpirun@$mpirun@g" run_local.sh > tmp
1197        mv -f tmp run_local.sh
1198        chmod u=rwx run_local.sh
1199    elif [[ "${parallel:0:3}" = "mpi" ]]; then
1200        # Lancement avec deux procs mpi et 2 openMP
1201        echo "export OMP_STACKSIZE=800M" > bench.sh
1202        if [[ "${parallel:4:3}" = "omp" ]]; then
1203            echo "export OMP_NUM_THREADS=2" >> bench.sh
1204        fi
1205        if [[ "$cosp" = "v1" || "$cosp" = "v2" ]]; then
1206            if [[ ${hostname:0:5} = jean- ]]; then
1207                   chmod +x ../arch.env
1208                ../arch.env       
1209                echo "ulimit -s 2000000" >> bench.sh
1210            else
1211                echo "ulimit -s 200000" >> bench.sh
1212            fi       
1213        else
1214            echo "ulimit -s unlimited" >> bench.sh
1215        fi
1216        if [[ ${hostname:0:5} = jean- ]]; then
1217            . ../arch/arch-${arch}.env
1218            echo "srun -n 2 && $idris_acct@cpu gcm.e > listing  2>&1" \
1219                 >> bench.sh
1220        else
1221            echo "$mpirun -np 2 gcm.e > listing  2>&1" >> bench.sh
1222        fi
1223        # Add rebuild, using reb.sh if it is there
1224        cat <<EOF >> bench.sh
1225if [[ -f reb.sh ]]; then
1226  ./reb.sh histday; ./reb.sh histmth; ./reb.sh histhf;
1227  ./reb.sh histins; ./reb.sh stomate_history;
1228  ./reb.sh sechiba_history; ./reb.sh sechiba_out_2
1229fi
1230EOF
1231    else
1232        echo "./gcm.e > listing  2>&1" > bench.sh
1233    fi
1234    # Getting orchidee stuff
1235    if [[ $veget == 'CMIP6' ]]; then
1236        #echo 'myget 3DBenchs/BENCHorch11.tar.gz'
1237        #myget 3DBenchs/BENCHorch11.tar.gz
1238        #tar xvzf BENCHorch11.tar.gz
1239        echo 'myget 3DBenchs/BENCHCMIP6.tar.gz'
1240        myget 3DBenchs/BENCHCMIP6.tar.gz
1241        tar xvzf BENCHCMIP6.tar.gz
1242        sed -e "s:VEGET=n:VEGET=y:" config.def > tmp
1243        mv -f tmp config.def
1244        if [[ "$with_xios" = "y" ]]; then
1245            cp ../../ORCHIDEE/src_xml/context_orchidee.xml .
1246            echo '<context id="orchidee" src="./context_orchidee.xml"/>' \
1247                 > add.tmp
1248            cp ../../ORCHIDEE/src_xml/field_def_orchidee.xml .
1249            cp ../../ORCHIDEE/src_xml/file_def_orchidee.xml .
1250            cp ../../ORCHIDEE/src_xml/file_def_input_orchidee.xml .
1251            if [[ -f ../../ORCHIDEE/src_xml/context_input_orchidee.xml ]]; then
1252                   cp ../../ORCHIDEE/src_xml/context_input_orchidee.xml .
1253                   echo '<context id="orchidee" ' \
1254                     'src="./context_input_orchidee.xml"/>' >> add.tmp
1255            fi
1256            sed -e '/id="LMDZ"/r add.tmp' iodef.xml > tmp
1257            mv tmp iodef.xml
1258            sed -e'{/sechiba1/ s/enabled="_AUTO_"/type="one_file" enabled=".TRUE."/}' \
1259                file_def_orchidee.xml > tmp
1260            \mv -f tmp file_def_orchidee.xml
1261            sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
1262                file_def_orchidee.xml > tmp
1263            \mv -f tmp file_def_orchidee.xml
1264            sed -e 's@output_level="_AUTO_"@output_level="1"@' \
1265                file_def_orchidee.xml > tmp
1266            \mv -f tmp file_def_orchidee.xml
1267            sed -e 's@output_freq="_AUTO_"@output_freq="1d"@' \
1268                file_def_orchidee.xml > tmp
1269            \mv -f tmp file_def_orchidee.xml
1270            sed -e 's@compression_level="4"@compression_level="0"@' \
1271                file_def_orchidee.xml > tmp
1272            \mv -f tmp file_def_orchidee.xml
1273            sed -e 's@XIOS_ORCHIDEE_OK = n@XIOS_ORCHIDEE_OK = y@' \
1274                orchidee.def > tmp
1275            \mv -f tmp orchidee.def
1276        fi
1277    fi
1278
1279    if [[ -f ../arch.env ]]
1280    then
1281        source ../arch.env
1282    fi
1283
1284    echo EXECUTION DU BENCH
1285    set +e
1286    date; ./bench.sh > out.bench 2>&1; date
1287    set -e
1288    tail listing
1289
1290
1291    echo "##########################################################"
1292    echo "Simulation finished in $(pwd)"
1293    echo "You have compiled with:"
1294    cat ../compile.sh
1295    if [[ $parallel = "none" ]]; then
1296        echo "You may re-run it with : cd  $(pwd); gcm.e"
1297        echo "or ./bench.sh"
1298    else
1299        echo "You may re-run it with : "
1300        echo "cd  $(pwd); ./bench.sh"
1301        #  echo 'ulimit -s unlimited'
1302        #  echo 'export OMP_NUM_THREADS=2'
1303        #  echo 'export OMP_STACKSIZE=800M'
1304        #  echo "$mpirun -np 2 gcm.e "
1305    fi
1306    echo '##########################################################'
1307
1308fi # bench
1309
1310
1311#################################################################
1312# Installation eventuelle du 1D
1313#################################################################
1314
1315if [[ $SCM = 1 ]]; then
1316    cd "$MODEL"
1317    myget 1D/1D.tar.gz
1318    tar xf 1D.tar.gz
1319    cd 1D
1320    if [[ $rad = oldrad ]]; then
1321        sed -i'' -e 's/^rad=.*$/rad=oldrad/' run.sh
1322        sed -i'' -e 's/^rad=.*$/rad=oldrad/' bin/compile
1323    fi
1324    echo "Running 1D/run.sh, log in $(pwd)/run1d.log"
1325    ./run.sh > "$(pwd)/run1d.log" 2>&1
1326fi
1327
1328
1329#################################################################
1330# sauvegarde des options veget pour utilisation eventuelle tutorial_prod
1331#################################################################
1332cd "$MODEL/modipsl/modeles"
1333#echo surface_env file created in $MODEL
1334cat <<EOF >surface_env
1335veget=$veget
1336opt_veget="-v $veget_version"
1337orchidee_rev=$orchidee_rev
1338suforch=$suff_orc
1339EOF
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