source: BOL/script_install_amaury/install_lmdz.sh @ 4890

Last change on this file since 4890 was 4890, checked in by abarral, 7 weeks ago

copy local arch to module arch dir
standardize none/NONE
  • Property svn:executable set to *
File size: 48.4 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: $mysvn"
302}
303
304function download_model_AMAURY {  # TODO
305    MODEL=$(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 install_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 $fcm_path"; exit 1
331        fi
332    fi
333
334    # check compiler
335    compiler=$(< "$fcm_path" grep "%COMPILER" | sed -e "s/%COMPILER\s*//")
336
337    # Copy arch to different components
338    # TODO check that this doesn't error if the source and destination are the same
339    \cp -f "$arch_dir/arch-$arch.fcm" "$MODEL/modipsl/modeles/IOIPSL/arch"
340    \cp -f "$arch_dir/arch-$arch.path" "$MODEL/modipsl/modeles/IOIPSL/arch"
341    \cp -f "$arch_dir/arch-$arch.fcm" "$MODEL/modipsl/modeles/ORCHIDEE/arch"
342    \cp -f "$arch_dir/arch-$arch.path" "$MODEL/modipsl/modeles/ORCHIDEE/arch"
343
344    # TODO TEMP compat w/ old orch version - make a proper case later
345    sed -i'' -e "s/-I//" -e "s/-L//" "$MODEL/modipsl/modeles/ORCHIDEE/arch/arch-$arch.path"  # /!\ we only replace first occurence on purpose
346}
347
348function install_netcdf {
349    echo "Installing Netcdf"
350
351    if [[ $netcdf = 0 ]]; then
352        ncdfdir=$(nc-config --prefix)
353    else
354        cd "$MODEL"
355
356        case $compiler in
357          gfortran) opt1="-compiler gnu"; opt2="-CC gcc -FC gfortran -CXX g++";;
358          ifort)  opt1="-compiler intel"; opt2="-CC icc -FC ifort -CXX icpc";;
359          pgf90)  opt1="-compiler pgf90"; opt2="-CC pgcc -FC pgf90 -CXX pgCC";;
360          *)      echo "unexpected compiler $compiler for netcdf"; exit 1
361        esac
362
363        case $with_xios in
364            n) script_install_netcdf="install_netcdf4_hdf5_seq.bash"
365               ncdfdir="netcdf4_hdf5_seq"
366               opt_="$opt1";;
367            y) script_install_netcdf="install_netcdf4_hdf5.bash"
368               ncdfdir="netcdf4_hdf5"
369               opt_="$opt2 -MPI $root_mpi";;
370            *) echo "with_xios=$with_xios, should be n or y"; exit 1
371        esac
372        if [[ $netcdf = 1 ]]; then
373           ncdfdir="$MODEL/$ncdfdir"
374        else
375           mkdir -p "$netcdf"; ncdfdir="$netcdf/$ncdfdir"
376        fi
377
378        echo "Repertoire netcdf $ncdfdir"
379        if [[ ! -d $ncdfdir ]]; then
380            netcdflog=$(pwd)/netcdf.log
381            echo "----------------------------------------------------------"
382            echo "Compiling the Netcdf library"
383            echo "----------------------------------------------------------"
384            echo "log file : $netcdflog"
385            myget script_install/$script_install_netcdf >> "$netcdflog" 2>&1
386            chmod u=rwx $script_install_netcdf
387            # shellcheck disable=SC2086
388            ./$script_install_netcdf -prefix "$ncdfdir" $opt_ >> "$netcdflog" 2>&1
389        fi
390
391        #----------------------------------------------------------------------------
392        # LF rajout d'une verrue, pour une raison non encore expliquee,
393        # la librairie est parfois rangée dans lib64 et non dans lib
394        # par certains compilateurs
395        if [[ ! -e lib && -d lib64 ]]; then ln -s lib64 lib; fi
396        #----------------------------------------------------------------------------
397
398        echo "install_lmdz.sh netcdf_OK $(date)"
399    fi
400
401    cat >test_netcdf90.f90 <<EOF
402    use netcdf
403    print *, "NetCDF library version: ", nf90_inq_libvers()
404    end
405EOF
406
407    if $compiler -I"$ncdfdir"/include test_netcdf90.f90 -L"$ncdfdir"/lib -lnetcdff \
408              -lnetcdf -Wl,-rpath="$ncdfdir"/lib && ./a.out
409    then
410        \rm test_netcdf90.f90 a.out
411    else
412        cat <<EOF
413Failed test program using NetCDF-Fortran. You can:
414- check that you have NetCDF-Fortran installed in your system
415- or specify an installation directory with option -netcdf of install_lmdz.sh
416- or download and compile NetCDF-Fortran with option -netcdf 1 of nstall_lmdz.sh
417EOF
418        exit 1
419    fi
420}
421
422function install_IOIPSL {  # via fcm
423    cd "$MODEL/modipsl/modeles/IOIPSL"
424    ioipsllog="$(pwd)/ioipsl.log"
425    echo "Compiling IOIPSL, the interface library with Netcdf $(date) (log: $ioipsllog)"
426
427    if ! ./makeioipsl_fcm -arch "$arch" -job 8 > "$ioipsllog" 2>&1; then
428        echo "IOIPSL compile failed, exiting"; exit 1
429    fi
430    cp lib/* ../../lib
431    echo "IOIPSL compiled $(date)"
432
433    export IOIPSL_LIBDIR="$MODEL/modipsl/modeles/IOIPSL/lib"
434    export IOIPSL_INCDIR="$MODEL/modipsl/modeles/IOIPSL/inc"
435}
436
437function install_XIOS {
438    if [[ $with_xios = "y" ]]; then
439        cd "$MODEL/modipsl/modeles"
440        xioslog="$(pwd)/xios.log"
441        echo "##########################################################"
442        echo "Compiling XIOS (log $xioslog) $(date)"
443        echo "##########################################################"
444
445        # Download XIOS
446        case $xios_branch in
447            "trunk")
448            xios_http="http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/trunk";;
449            "2.5")
450            xios_http="http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5";;
451            "2.6")
452            xios_http="http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS2/branches/xios-2.6";;
453            *) echo "XIOS: Error, bad argument for -branch ! Did not expect $xios_branch"; exit;;
454        esac
455       
456        cd "$MODEL/modipsl/modeles"
457        set +e; svn co --revision $xios_rev $xios_http XIOS; set -e
458
459        cd XIOS
460        if ! ./make_xios --arch "$arch" --job 8 --arch_path "$arch_dir" > "$xioslog" 2>&1; then
461            echo "XIOS compilation failed, exiting"; exit 1
462        fi
463
464        echo "Compiled XIOS $(date)"
465    fi
466}
467
468function get_orchidee_version {  # Set / Check ORCHIDEE version
469  if [[ $veget = "none" ]]; then
470    veget_version="false"
471  elif [[ $veget = "CMIP6" ]]; then
472    veget_version=orchidee2.0
473    orchidee_rev=6592
474  else # specific orchidee revision newer than CMIP6, on 2_1 or 2_2 branches
475    veget_version=orchidee2.1
476    orchidee_rev="$veget"
477    if [[ $veget -lt 4465 ]]; then
478      echo 'ORCHIDEE version must be >=4465, exiting'
479      exit 1
480    fi
481
482    set +e
483    svn upgrade
484    local orcbranch
485    orcbranch=$(svn log -v -q svn://forge.ipsl.jussieu.fr/orchidee/ -r "$veget" |grep ORCHIDEE |head -1| sed -e 's:ORCHIDEE/.*$:ORCHIDEE:' | awk '{print $2}')
486    echo "IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at orchidee-help@listes.ipsl.fr"
487    svn switch -r "$veget" --accept theirs-full "svn://forge.ipsl.jussieu.fr/orchidee/$orcbranch"
488    svn log -r "$veget" | grep "$veget"
489    if ! svn log -r "$veget" | grep "$veget"; then
490      echo 'Cannot update ORCHIDEE as not on the right branch for ORCHIDEE'
491      exit 1
492    fi
493    svn update -r "$veget"
494    set -e
495  fi
496}
497
498function compile_orchidee_seq {
499  get_orchidee_version
500
501  if [[ $veget != "none" ]]; then
502    cd "$MODEL/modipsl/modeles/ORCHIDEE"
503
504    orchideelog="$(pwd)/orchidee.log"
505    echo "Compiling ORCHIDEE, the continental surface model (log $orchideelog)"
506    echo "Start of the first compilation of orchidee, in sequential mode: $(date)"
507
508    ORCHPATH=$(pwd)
509    export ORCHPATH=$ORCHPATH
510
511    local xios_orchid opt_orc
512    if [[ $with_xios = "y" ]]; then
513      xios_orchid="-xios";
514    else
515      xios_orchid="-noxios"
516    fi
517    if [[ $optim_debug = "-debug" ]]; then
518      opt_orc="-debug";
519    else
520      opt_orc="-prod"
521    fi
522
523    if ! ./makeorchidee_fcm "$xios_orchid" "$opt_orc" -parallel none -arch "$arch" > "$orchideelog" 2>&1; then
524      echo "ORCHIDEE seq compilation failed, exiting"; exit 1
525    fi
526    echo "Compiled ORCHIDEE seq $(date)"
527  fi
528}
529
530echo "install_lmdz.sh DEBUT $(date)"
531
532set_default_params
533read_cmdline_args "$@"
534#download_model
535download_model_AMAURY
536install_arch
537check_available_software
538install_netcdf
539install_IOIPSL
540#install_XIOS  # TODO disabled for now, did not decide which flags/arch to use for compile
541compile_orchidee_seq
542
543exit 0
544
545
546
547
548################################################################
549# Specificite des machines
550################################################################
551
552hostname=$(hostname)
553#case ${hostname:0:5} in
554#    *)       if [[ $parallel = none || -f /usr/bin/mpif90 ]]; then
555#                 path_mpi=$(which mpif90 | sed -e s:/mpif90::);
556#                 if [[ -d /usr/lib64/openmpi ]]; then
557#                     root_mpi="/usr/lib64/openmpi"
558#                 else
559#                     root_mpi="/usr"
560#                 fi
561#             else
562#                 echo "Cannot find mpif90";
563#                 if [[ $parallel = none ]]; then exit 1; fi;
564#             fi;
565#             if [[ $parallel != none ]]; then
566#                 root_mpi=$(which mpif90 | sed -e s:/bin/mpif90::)
567#                 path_mpi=$(which mpif90 | sed -e s:/mpif90::)
568#                 export LD_LIBRARY_PATH=${root_mpi}/lib:$LD_LIBRARY_PATH
569#             fi
570#             par_comp=${path_mpi}/mpif90;
571#             mpirun=${path_mpi}/mpirun;
572#             arch="local";
573#             make="make";
574#             o_ins_make="-t g95"
575#esac
576
577## Flags for parallelism:
578#if [[ $parallel != none ]]; then
579#    # MPI_LD are the flags needed for linking with MPI
580#    MPI_LD="-L${root_mpi}/lib -lmpi"
581#    if [[ $compiler = "gfortran" ]]; then
582#        # MPI_FLAGS are the flags needed for compilation with MPI
583#        MPI_FLAGS="-fcray-pointer"
584#        # OMP_FLAGS are the flags needed for compilation with OpenMP
585#        OMP_FLAGS="-fopenmp -fcray-pointer"
586#        # OMP_LD are the flags needed for linking with OpenMP
587#        OMP_LD="-fopenmp"
588#    elif [[ $compiler = "ifort" ]]; then
589#        MPI_FLAGS=""
590#        OMP_FLAGS="-openmp"
591#        OMP_LD="-openmp"
592#    else # pgf90
593#        MPI_FLAGS=""
594#        OMP_FLAGS="-mp"
595#        OMP_LD="-mp"
596#    fi
597#fi
598#
599#
600#echo "################################################################"
601#echo  "Choix des options de compilation"
602#echo "################################################################"
603#
604#export FC=$compiler
605#export F90=$compiler
606#export F77=$compiler
607#export CPPFLAGS=
608#OPTIMNC=""
609#BASE_LD="$OPT_GPROF"
610#OPTPREC="$OPT_GPROF"
611#ARFLAGS="rs"
612#if [[ $(lsb_release -i -s) = "Ubuntu" ]]; then
613#    if [[ $(lsb_release -r -s | cut -d. -f1) -ge 16 ]]; then
614#        ARFLAGS="rU"
615#    fi
616#fi
617#
618#if [[ $compiler = "gfortran" ]]; then
619#   OPTIM="-O3 $allow_arg_mismatch"
620#   OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all -fbacktrace -finit-real=snan  $allow_arg_mismatch"
621#   OPTDEV="-Wall -fbounds-check  $allow_arg_mismatch"
622#   fmod="I "
623#   OPTPREC="$OPTPREC -cpp -ffree-line-length-0"
624#   if [[ $real = r8 ]]; then OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE"; fi
625#   export F90FLAGS=" -ffree-form $OPTIMNC"
626#   export FFLAGS=" $OPTIMNC"
627#   export CC=gcc
628#   export CXX=g++
629#   export fpp_flags="-P -C -traditional -ffreestanding"
630#
631#elif [[ $compiler = mpif90 ]]; then
632#    OPTIM="-O3"
633#    OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all"
634#    OPTDEV="-Wall -fbounds-check"
635#    BASE_LD="$BASE_LD -lblas"
636#    fmod="I "
637#    if [[ $real = r8 ]]; then
638#        OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE -fcray-pointer"
639#    fi
640#    export F90FLAGS=" -ffree-form $OPTIMNC"
641#    export FFLAGS=" $OPTIMNC"
642#    export CC=gcc
643#    export CXX=g++
644#
645#elif [[ $compiler = pgf90 ]]; then
646#    OPTIM="-O2 -Mipa -Munroll -Mnoframe -Mautoinline -Mcache_align"
647#    OPTDEB="-g -Mdclchk -Mbounds -Mchkfpstk -Mchkptr -Minform=inform -Mstandard -Ktrap=fp -traceback"
648#    OPTDEV="-g -Mbounds -Ktrap=fp -traceback"
649#    fmod="module "
650#    if [[ $real = r8 ]]; then OPTPREC="$OPTPREC -r8 -DNC_DOUBLE"; fi
651#    export CPPFLAGS="-DpgiFortran"
652#    export CC=pgcc
653#    export CFLAGS="-O2 -Msignextend"
654#    export CXX=pgCC
655#    export CXXFLAGS="-O2 -Msignextend"
656#    export FFLAGS="-O2 $OPTIMNC"
657#    export F90FLAGS="-O2 $OPTIMNC"
658#    compile_with_fcm=1
659#
660#elif [[ $compiler = ifort || $compiler = mpiifort ]]; then
661#    OPTIM="-O2 -fp-model strict -ip -align all "
662#    OPTDEV="-p -g -O2 -traceback -fp-stack-check -ftrapuv -check"
663#    OPTDEB="-g -no-ftz -traceback -ftrapuv -fp-stack-check -check"
664#    fmod='module '
665#    if [[ $real = r8 ]]; then OPTPREC="$OPTPREC -real-size 64 -DNC_DOUBLE"; fi
666#    export CPP="icc -E"
667#    export FFLAGS="-O2 -ip -fpic -mcmodel=large"
668#    export FCFLAGS="-O2 -ip -fpic -mcmodel=large"
669#    export CC=icc
670#    export CFLAGS="-O2 -ip -fpic -mcmodel=large"
671#    export CXX=icpc
672#    export CXXFLAGS="-O2 -ip -fpic -mcmodel=large"
673#    export fpp_flags="-P -traditional"
674#    # Pourquoi forcer la compilation fcm. Marche mieux sans
675#    #compile_with_fcm=1
676#else
677#    echo "unexpected compiler $compiler"; exit 1
678#fi
679#
680#OPTIMGCM="$OPTIM $OPTPREC"
681
682
683veget_version=false
684if [[ $veget != 'none' ]]; then
685    cd "$MODEL/modipsl/modeles/ORCHIDEE"
686
687    opt_orc="-prod"; if [[ "$optim_debug" = "-debug" ]]; then opt_orc="-debug"; fi
688
689    orchideelog=$(pwd)/orchidee.log
690    echo '########################################################'
691    echo 'Compiling ORCHIDEE, the continental surface model '
692    echo '########################################################'
693    echo "Start of the first compilation of orchidee, in sequential mode: $(date)"
694    echo "log file : $orchideelog"
695
696    ORCHPATH=$(pwd)
697    export ORCHPATH=$ORCHPATH
698    xios_orchid="-noxios"
699    if [[ "$with_xios" = "y" ]]; then
700        xios_orchid="-xios"
701    fi
702    if [[ -d tools ]]; then
703        ###################################################################
704        # Pour les experts qui voudraient changer de version d'orchidee.
705        # Attention : necessite d'avoir le password pour orchidee
706        ###################################################################
707        if [[ "$veget_version" == "false" ]]; then
708            veget_version=orchidee2.0
709        fi
710        cd arch
711        sed -e s:"%COMPILER        .*.$:%COMPILER            $compiler":1 \
712            -e s:"%LINK            .*.$:%LINK                $compiler":1 \
713            -e s:"%FPP_FLAGS       .*.$:%FPP_FLAGS           $fpp_flags":1 \
714            -e s:"%PROD_FFLAGS     .*.$:%PROD_FFLAGS         $OPTIM":1 \
715            -e s:"%DEV_FFLAGS      .*.$:%DEV_FFLAGS          $OPTDEV":1 \
716            -e s:"%DEBUG_FFLAGS    .*.$:%DEBUG_FFLAGS        $OPTDEB":1 \
717            -e s:"%BASE_FFLAGS     .*.$:%BASE_FFLAGS         $OPTPREC":1 \
718            -e s:"%BASE_LD         .*.$:%BASE_LD             $BASE_LD":1 \
719            -e s:"%ARFLAGS         .*.$:%ARFLAGS             $ARFLAGS":1 \
720            arch-gfortran.fcm > arch-local.fcm
721        cat <<EOF > arch-local.path
722NETCDF_LIBDIR="-L$ncdfdir/lib -lnetcdff -lnetcdf"
723NETCDF_INCDIR="$ncdfdir/include"
724IOIPSL_INCDIR="$ORCHPATH/../../lib"
725IOIPSL_LIBDIR="$ORCHPATH/../../lib"
726XIOS_INCDIR="\$ORCHDIR/../XIOS/inc"
727XIOS_LIBDIR="\$ORCHDIR/../XIOS/lib -lxios"
728EOF
729        cd ../
730
731        echo ./makeorchidee_fcm -j $xios_orchid $opt_orc -parallel none \
732             -arch $arch
733        ./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel none \
734                           -arch $arch > "$orchideelog" 2>&1
735        pwd
736    else # of "if [[ -d tools ]]"
737        if [[ -d src_parallel ]]; then
738            liste_src="parallel parameters global stomate sechiba driver"
739            if [[ "$veget_version" == "false" ]]; then
740                veget_version=orchidee2.0
741            fi
742        fi
743        for d in $liste_src; do
744            src_d=src_$d
745            echo src_d "$src_d"
746            echo ls; ls
747            if [[ ! -d $src_d ]]; then
748                echo "Problem orchidee : no $src_d"; exit 1
749            fi
750            cd "$src_d"; \rm -f -- *.mod make; $make clean
751            $make > "$orchideelog" 2>&1
752            if [[ "$compiler" = "gfortran" || "$compiler" = "mpif90" ]]; then
753                cp -f -- *.mod ../../../lib
754            fi
755            cd ..
756        done
757    fi # of "if [[ -d tools ]]"
758    echo "install_lmdz.sh orchidee_compil_seq_OK $(date)"
759fi # of if [[ "$veget" != 'none' ]]
760
761
762#============================================================================
763# Ehouarn: the directory name LMDZ* depends on version/tar file...
764if find . -name "$MODEL/modipsl/modeles/LMD*"; then
765    echo '###############################################################'
766    echo 'Preparing LMDZ compilation : arch file, svn switch if needed...'
767    echo '###############################################################'
768    cd "$MODEL/modipsl/modeles/"LMD*
769    LMDZPATH=$(pwd)
770else
771    echo "ERROR: No LMD* directory !!!"
772    exit 1
773fi
774
775
776###########################################################
777# For those who want to use fcm to compile via :
778#  makelmdz_fcm -arch local .....
779############################################################
780
781
782
783cd "$MODEL/modipsl/modeles"/LMDZ*
784lmdzlog=$(pwd)/lmdz.log
785
786##################################################################
787# Possibly update LMDZ if a specific svn release is requested
788##################################################################
789
790set +e; svn upgrade; set -e
791
792if [[ $svn = "last" ]]; then svnopt=""; else svnopt="-r $svn"; fi
793if [[ $svn != "" ]]; then
794    if set +e; svn info | grep -q 'https:'; then
795        svn switch --relocate https://svn.lmd.jussieu.fr/LMDZ \
796            http://svn.lmd.jussieu.fr/LMDZ
797    fi
798    svn update "$svnopt"
799    set -e
800fi
801
802#---------------------------------------------------------------------
803# Retrieve the final svn release number, and adjust compilation
804# options accordingly
805# If svn not available, will use the svn writen in $MODEL/Readm*md
806# For old version it assumes that it is before 4185 (the version
807# for which the test was introduced
808#---------------------------------------------------------------------
809
810set +e; mysvn=$(svnversion . | grep -E || "[0-9]+" 2>/dev/null); set -e
811if [[ "$mysvn" = "" ]]; then mysvn=$(grep 'Revision: [0-9]' "$MODEL"/Read*.md | awk ' { print $2 } ' 2>/dev/null); fi
812if [[ "$mysvn" = "" ]]; then mysvn=4190; fi
813
814if [[ "$pclinux" = "1" && ! -f arch/arch-local.path ]]; then
815
816    # create local 'arch' files (if on Linux PC):
817    cd arch
818    # arch-local.path file
819    # test for version as arch.pth file changed format with rev 4426
820    if [[ "$mysvn" -gt 4425 ]]; then
821      cat <<EOF > arch-local.path
822NETCDF_LIBDIR="-L$ncdfdir/lib"
823NETCDF_LIB="-lnetcdff -lnetcdf"
824NETCDF_INCDIR=-I$ncdfdir/include
825NETCDF95_INCDIR=-I\$LMDGCM/../../include
826NETCDF95_LIBDIR=-L\$LMDGCM/../../lib
827NETCDF95_LIB=-lnetcdf95
828IOIPSL_INCDIR=-I\$LMDGCM/../../lib
829IOIPSL_LIBDIR=-L\$LMDGCM/../../lib
830IOIPSL_LIB=-lioipsl
831XIOS_INCDIR=-I\$LMDGCM/../XIOS/inc
832XIOS_LIBDIR=-L\$LMDGCM/../XIOS/lib
833XIOS_LIB="-lxios -lstdc++"
834ORCH_INCDIR=-I\$LMDGCM/../../lib
835ORCH_LIBDIR=-L\$LMDGCM/../../lib
836EOF
837    else
838      cat <<EOF > arch-local.path
839NETCDF_LIBDIR="-L$ncdfdir/lib -lnetcdff -lnetcdf"
840NETCDF_INCDIR=-I$ncdfdir/include
841NETCDF95_INCDIR=\$LMDGCM/../../include
842NETCDF95_LIBDIR=\$LMDGCM/../../lib
843IOIPSL_INCDIR=\$LMDGCM/../../lib
844IOIPSL_LIBDIR=\$LMDGCM/../../lib
845XIOS_INCDIR=\$LMDGCM/../XIOS/inc
846XIOS_LIBDIR=\$LMDGCM/../XIOS/lib
847ORCH_INCDIR=\$LMDGCM/../../lib
848ORCH_LIBDIR=\$LMDGCM/../../lib
849EOF
850    fi 
851
852    if [[ $pcmac == 1 ]]; then
853        BASE_LD="$BASE_LD -Wl,-rpath,${ncdfdir}/lib"
854    else
855        BASE_LD="$BASE_LD -Wl,-rpath=${ncdfdir}/lib"
856    fi
857    # Arch-local.fcm file (adapted from arch-linux-32bit.fcm)
858
859    if [[ $real = r8 ]]; then FPP_DEF=NC_DOUBLE; else FPP_DEF=""; fi
860    sed -e s:"%COMPILER        .*.$:%COMPILER            $compiler":1 \
861        -e s:"%LINK            .*.$:%LINK                $compiler":1 \
862        -e s:"%PROD_FFLAGS     .*.$:%PROD_FFLAGS         $OPTIM":1 \
863        -e s:"%DEV_FFLAGS      .*.$:%DEV_FFLAGS          $OPTDEV":1 \
864        -e s:"%DEBUG_FFLAGS    .*.$:%DEBUG_FFLAGS        $OPTDEB":1 \
865        -e s:"%BASE_FFLAGS     .*.$:%BASE_FFLAGS         $OPTPREC":1 \
866        -e s:"%FPP_DEF         .*.$:%FPP_DEF             $FPP_DEF":1 \
867        -e s:"%BASE_LD         .*.$:%BASE_LD             $BASE_LD":1 \
868        -e s:"%ARFLAGS         .*.$:%ARFLAGS             $ARFLAGS":1 \
869        arch-linux-32bit.fcm > arch-local.fcm
870
871    cd ..
872    ### Adapt "bld.cfg" (add the shell):
873    #whereisthatshell=$(which ${use_shell})
874    #echo "bld::tool::SHELL   $whereisthatshell" >> bld.cfg
875
876fi # of if [[ "$pclinux" = 1 ]]
877#---------------------------------------------------------------------
878# Option de compilation du rayonnement : depend de $mysvn ><= r4185
879#---------------------------------------------------------------------
880opt_rad=""
881
882case $rad in
883    oldrad) iflag_rrtm=0; NSW=2; opt_rad="";;
884    rrtm)   iflag_rrtm=1; NSW=6
885            if [[ $mysvn -le 4185 ]]; then
886                opt_rad="-rrtm true"
887            else
888                opt_rad="-rad rrtm"
889            fi;;
890    ecrad)  iflag_rrtm=2; NSW=6; opt_rad="-rad ecrad";;
891    *) echo "Only oldrad rrtm ecrad for rad option"; exit 1
892esac
893
894if [[ $mysvn -le 4185 && $rad = "ecrad" ]]; then
895    echo "ecrad only available for LMDZ rev starting with 4186 "; exit 1
896fi
897
898##################################################################
899
900
901if [[ ! -f libf/misc/netcdf95.F90 &&  ! -d $MODEL/NetCDF95-0.3 ]]; then
902    cd "$MODEL"
903    myget src_archives/netcdf/NetCDF95-0.3.tar.gz
904    tar -xf NetCDF95-0.3.tar.gz
905    rm NetCDF95-0.3.tar.gz
906    cd NetCDF95-0.3
907    mkdir build
908    cd build
909    cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH="$ncdfdir" \
910          -DCMAKE_INSTALL_PREFIX="$MODEL/modipsl"
911    make install
912    cd "$MODEL/modipsl/modeles/"LMDZ*
913fi
914
915echo '##################################################################'
916echo "Preparing script compile.sh for LMDZ compilation"
917echo "It will only be run automatically if bench=1/tuto"
918echo "Here bench=$bench"
919echo '##################################################################'
920
921if [[ $env_file != "" ]]; then
922    mv arch/arch-${arch}.env arch/arch-${arch}.orig
923    \cp -f "$env_file" arch/arch-${arch}.env
924fi
925
926if [[ $compile_with_fcm = 1 ]]; then
927    makelmdz="makelmdz_fcm $optim_debug -arch $arch -j 8 "
928else
929    makelmdz="makelmdz $optim_debug -arch $arch"
930fi
931
932# sequential compilation
933if [[ "$sequential" = 1 ]]; then
934    echo Sequential compilation command, saved in compile.sh:
935    echo "./$makelmdz $optim_debug $OPT_MAKELMDZ $optim_debug $opt_rad $opt_cosp " \
936         "-d ${grid_resolution} -v $veget_version gcm "
937    echo "./$makelmdz $optim_debug $OPT_MAKELMDZ $optim_debug $opt_rad $opt_cosp " \
938         "-d ${grid_resolution} -v $veget_version gcm " > compile.sh
939    chmod +x ./compile.sh
940    if [[ $bench = 1 ]]; then
941        echo "install_lmdz.sh start_lmdz_seq_compilation $(date)"
942        echo "log file: $lmdzlog"
943        ./compile.sh > "$lmdzlog" 2>&1
944        echo "install_lmdz.sh end_lmdz_seq_compilation $(date)"
945    fi
946fi # fin sequential
947
948# compiling in parallel mode
949if [[ $parallel != "none" ]]; then
950    echo '##########################################################'
951    echo ' Parallel compile '
952    echo '##########################################################'
953    echo "(after saving the sequential libs and binaries)"
954    cd "$MODEL/modipsl"
955    tar cf sequential.tar bin/ lib/
956    #
957    # Orchidee
958    #
959    cd "$ORCHPATH"
960    if [[ -d src_parallel && $veget != 'none' ]]; then
961        cd arch
962        sed  \
963            -e s:"%COMPILER.*.$:%COMPILER            $par_comp":1 \
964            -e s:"%LINK.*.$:%LINK                $par_comp":1 \
965            -e s:"%MPI_FFLAG.*.$:%MPI_FFLAGS          $MPI_FLAGS":1 \
966            -e s:"%OMP_FFLAG.*.$:%OMP_FFLAGS          $OMP_FLAGS":1 \
967            -e s:"%MPI_LD.*.$:%MPI_LD              $MPI_LD":1 \
968            -e s:"%OMP_LD.*.$:%OMP_LD              $OMP_LD":1 \
969            arch-local.fcm > tmp.fcm
970
971        mv tmp.fcm arch-local.fcm
972        cd ../
973        echo "Compiling ORCHIDEE in parallel mode $(date)"
974        echo "logfile $orchideelog"
975        echo "NOTE : to recompile it when necessary, use ./compile_orc.sh " \
976             "in modipsl/modeles/ORCHIDEE"
977        echo ./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc \
978             -parallel "$parallel" -arch $arch > compile_orc.sh
979        echo ./makeorchidee_fcm -j 8 $xios_orchid $opt_orc \
980             -parallel "$parallel" -arch $arch >> compile_orc.sh
981        echo echo Now you must also recompile LMDZ, by running ./compile.sh \
982             in modeles/LMDZ >> compile_orc.sh
983        chmod u+x compile_orc.sh
984        ./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc \
985                           -parallel "$parallel" -arch $arch > "$orchideelog" 2>&1
986        ./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel "$parallel" \
987                           -arch $arch >> "$orchideelog" 2>&1
988        echo "End of ORCHIDEE compilation in parallel mode $(date)"
989    elif [[ $veget != 'none' ]]; then
990        echo '##########################################################'
991        echo ' Orchidee version too old                                 '
992        echo ' Please update to new version                             '
993        echo '##########################################################'
994        exit 1
995    fi #�of [ -d src_parallel && $veget != 'none' ]
996
997    # LMDZ
998    cd "$LMDZPATH"
999    if [[ $arch = local ]]; then
1000        cd arch
1001        sed -e s:"%COMPILER.*.$:%COMPILER            $par_comp":1 \
1002            -e s:"%LINK.*.$:%LINK                $par_comp":1 \
1003            -e s:"%MPI_FFLAG.*.$:%MPI_FFLAGS          $MPI_FLAGS":1 \
1004            -e s:"%OMP_FFLAG.*.$:%OMP_FFLAGS          $OMP_FLAGS":1 \
1005            -e s:"%ARFLAGS.*.$:%ARFLAGS          $ARFLAGS":1 \
1006            -e "s§%BASE_LD.*.$§%BASE_LD             -Wl,-rpath=${root_mpi}/lib:${ncdfdir}/lib§1" \
1007            -e s:"%MPI_LD.*.$:%MPI_LD              $MPI_LD":1 \
1008            -e s:"%OMP_LD.*.$:%OMP_LD              $OMP_LD":1 \
1009            arch-local.fcm > tmp.fcm
1010        mv tmp.fcm arch-local.fcm
1011        cd ../
1012    fi
1013    rm -f compile.sh
1014    echo resol="$grid_resolution" >> compile.sh
1015    if [[ ${hostname:0:5} = jean- && "$cosp" = "v2" ]]; then
1016
1017        echo "LMDZ compilation command in parallel mode, saved in compile.sh, is :"
1018        echo "(ATTENTION le probleme de cospv2 sur jean-zay en mode prod " \
1019             "n est pas corrige ! )"
1020        # ATTENTION le probleme de cospv2 sur jean-zay en mode prod n
1021        # est pas corrige
1022        echo ./"$makelmdz" -dev $optim_debug "$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" -dev $optim_debug "$OPT_MAKELMDZ" "$opt_rad" "$opt_cosp" \
1026             "$opt_makelmdz_xios" -d \$resol -v $veget_version -mem \
1027             -parallel "$parallel" gcm
1028    else
1029        echo ./"$makelmdz" $optim_debug "$OPT_MAKELMDZ" "$opt_rad" "$opt_cosp" \
1030             "$opt_makelmdz_xios" -d \$resol -v $veget_version -mem \
1031             -parallel "$parallel" gcm >> compile.sh
1032        echo ./"$makelmdz" $optim_debug "$OPT_MAKELMDZ" "$opt_rad" "$opt_cosp" \
1033             "$opt_makelmdz_xios" -d \$resol -v $veget_version -mem \
1034             -parallel "$parallel" gcm
1035    fi
1036    chmod +x ./compile.sh
1037
1038    if [[ $bench = 1 ]]; then
1039        echo "Compiling LMDZ in parallel mode $(date),  LMDZ log file: $lmdzlog"
1040        ./compile.sh > "$lmdzlog" 2>&1
1041    fi
1042
1043fi # of if [[ $parallel != "none" ]]
1044
1045
1046##################################################################
1047# Verification du succes de la compilation
1048##################################################################
1049
1050# Recherche de l'executable dont le nom a change au fil du temps ...
1051# suffix contains radiative option starting with revision 4186
1052if [[ $mysvn -ge 4186 ]]; then suff_exe=_${rad}${suff_exe}; fi
1053gcm=""
1054
1055for exe in gcm.e bin/gcm_${grid_resolution}_phylmd${suff_exe}${suff_orc}.e
1056do
1057    if [[ -f $exe ]]; then gcm=$exe; fi
1058done
1059
1060if [[ "$gcm" = "" ]]; then
1061    if [[ $bench = 1 ]]; then
1062        echo 'Compilation failed !! Cannot run the benchmark;'
1063        exit 1
1064    else
1065        echo 'Compilation not done (only done when bench=1)'
1066    fi
1067else
1068    echo '##########################################################'
1069    echo "Compilation successfull !!  $(date)"
1070    echo '##########################################################'
1071    echo "The executable is $gcm"
1072fi
1073
1074##################################################################
1075# Below, we run a benchmark if bench=1 or tuto
1076##################################################################
1077
1078if [[ $bench = tuto ]]; then
1079    myget Training/tutorial.tar; tar xf tutorial.tar; cd TUTORIAL
1080    ./init.sh
1081
1082elif [[ $bench = 1 && ! -d BENCH${grid_resolution} ]]; then
1083    # TOUTE CETTE SECTION DEVRAIT DISPARAITRE POUR UNE COMMANDE
1084    # OU DES BENCHS PAR MOTS CLES COMME tuto
1085
1086    echo '##########################################################'
1087    echo ' Running a test run '
1088    echo '##########################################################'
1089
1090    \rm -rf "BENCH${grid_resolution}"
1091    bench=bench_lmdz_${grid_resolution}
1092    echo "install_lmdz.sh before bench download  $(date)"
1093    #wget http://www.lmd.jussieu.fr/~lmdz/Distrib/$bench.tar.gz
1094    myget "3DBenchs/$bench.tar.gz"
1095    echo "install_lmdz.sh after bench download  $(date)"
1096    tar xf "$bench.tar.gz"
1097
1098    if [[ "$cosp" = "v1" || "$cosp" = "v2" ]]; then
1099        cd "BENCH${grid_resolution}"
1100        # copier les fichiers namelist input et output our COSP
1101        cp ../DefLists/cosp*_input_nl.txt .
1102        cp ../DefLists/cosp*_output_nl.txt .
1103        # Activer la cles ok_cosp pour tourner avec COSP
1104        sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp
1105        \mv -f tmp config.def
1106        cd ..
1107    fi
1108
1109    if [[ -n "$physiq" ]]; then
1110        cd "BENCH${grid_resolution}"
1111        if [[ -f "physiq.def_${physiq}" ]]; then
1112            cp "physiq.def_${physiq}" physiq.def
1113            echo using "physiq.def_${physiq}"
1114        else
1115            echo using standard physiq.def
1116        fi
1117        cd ..
1118    else
1119        echo using standard physiq.def
1120    fi
1121
1122    if [[ "$with_xios" = "y" ]]; then
1123        cd "BENCH${grid_resolution}"
1124        cp ../DefLists/iodef.xml .
1125        cp ../DefLists/context_lmdz.xml .
1126        cp ../DefLists/field_def_lmdz.xml .
1127        # A raffiner par la suite
1128        echo "A FAIRE : Copier les *xml en fonction de l option cosp"
1129        cp ../DefLists/field_def_cosp*.xml .
1130        cp ../DefLists/file_def_hist*xml .
1131        # adapt iodef.xml to use attached mode
1132        sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' \
1133            iodef.xml > tmp
1134        \mv -f tmp iodef.xml
1135
1136        # and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
1137        # except for histday
1138        for histfile in file_def_hist*xml
1139        do
1140            if [[ "$histfile" = "file_def_histday_lmdz.xml" ]]; then
1141                sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' \
1142                    "$histfile" > tmp
1143                \mv -f tmp "$histfile"
1144                sed -e 's@output_level="_AUTO_"@output_level="5"@' "$histfile" \
1145                    > tmp
1146                \mv -f tmp "$histfile"
1147                sed -e 's@compression_level="2"@compression_level="0"@' \
1148                    "$histfile" > tmp
1149                \mv -f tmp "$histfile"
1150            else
1151                sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
1152                    "$histfile" > tmp
1153                \mv -f tmp "$histfile"
1154            fi
1155        done
1156        # and add option "ok_all_xml=y" in config.def
1157        echo "### XIOS outputs" >> config.def
1158        echo 'ok_all_xml=.true.' >> config.def
1159
1160        #activer les sorties pour Cosp
1161        if [[ "$cosp" = "v1" ]]; then
1162            sed -i'' -e 's@enabled=".FALSE."@enabled=".TRUE."@' \
1163                     -e 's@output_level="_AUTO_"@output_level="5"@' \
1164                     -e 's@compression_level="2"@compression_level="0"@' \
1165                     file_def_histdayCOSP_lmdz.xml
1166        fi
1167        if [[ "$cosp" = "v2" ]]; then
1168            sed -e 's@compression_level="2"@compression_level="0"@' file_def_histdayCOSPv2_lmdz.xml
1169            for type_ in hf day mth; do
1170                file=file_def_hist${type_}COSP
1171                sed -i'' -e 's@src="./'${file}'_lmdz.xml"@src="./'${file}'v2_lmdz.xml"@' context_lmdz.xml
1172            done
1173            sed -i '' -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' field_def_lmdz.xml
1174        fi
1175
1176        cd ..
1177    fi
1178
1179    # Cas Bensh avec ecrad
1180    if [[ "$rad" = "ecrad" ]]; then
1181        cd "BENCH${grid_resolution}"
1182        cp  ../DefLists/namelist_ecrad .
1183        cp -r ../libf/phylmd/ecrad/data .
1184        cd ..
1185    fi
1186
1187    # Adjusting bench physiq.def to radiative code chosen
1188    cd "BENCH${grid_resolution}"
1189    sed -e 's/iflag_rrtm=.*.$/iflag_rrtm='$iflag_rrtm'/' \
1190        -e 's/NSW=.*.$/NSW='$NSW'/' physiq.def > tmpdef
1191    \mv tmpdef physiq.def
1192    cd ..
1193
1194    cp "$gcm" "BENCH${grid_resolution}/gcm.e"
1195
1196    cd "BENCH${grid_resolution}"
1197    # On cree le fichier bench.sh au besoin
1198    # Dans le cas 48x36x39 le bench.sh existe deja en parallele
1199
1200    if [[ "$grid_resolution" = "48x36x39" ]]; then
1201        echo On ne touche pas au bench.sh
1202        # But we have to adapt "run_local.sh" for $mpirun
1203        sed -e "s@mpirun@$mpirun@g" run_local.sh > tmp
1204        mv -f tmp run_local.sh
1205        chmod u=rwx run_local.sh
1206    elif [[ "${parallel:0:3}" = "mpi" ]]; then
1207        # Lancement avec deux procs mpi et 2 openMP
1208        echo "export OMP_STACKSIZE=800M" > bench.sh
1209        if [[ "${parallel:4:3}" = "omp" ]]; then
1210            echo "export OMP_NUM_THREADS=2" >> bench.sh
1211        fi
1212        if [[ "$cosp" = "v1" || "$cosp" = "v2" ]]; then
1213            if [[ ${hostname:0:5} = jean- ]]; then
1214                   chmod +x ../arch.env
1215                ../arch.env       
1216                echo "ulimit -s 2000000" >> bench.sh
1217            else
1218                echo "ulimit -s 200000" >> bench.sh
1219            fi       
1220        else
1221            echo "ulimit -s unlimited" >> bench.sh
1222        fi
1223        if [[ ${hostname:0:5} = jean- ]]; then
1224            . ../arch/arch-${arch}.env
1225            echo "srun -n 2 && $idris_acct@cpu gcm.e > listing  2>&1" \
1226                 >> bench.sh
1227        else
1228            echo "$mpirun -np 2 gcm.e > listing  2>&1" >> bench.sh
1229        fi
1230        # Add rebuild, using reb.sh if it is there
1231        cat <<EOF >> bench.sh
1232if [[ -f reb.sh ]]; then
1233  ./reb.sh histday; ./reb.sh histmth; ./reb.sh histhf;
1234  ./reb.sh histins; ./reb.sh stomate_history;
1235  ./reb.sh sechiba_history; ./reb.sh sechiba_out_2
1236fi
1237EOF
1238    else
1239        echo "./gcm.e > listing  2>&1" > bench.sh
1240    fi
1241    # Getting orchidee stuff
1242    if [[ $veget == 'CMIP6' ]]; then
1243        #echo 'myget 3DBenchs/BENCHorch11.tar.gz'
1244        #myget 3DBenchs/BENCHorch11.tar.gz
1245        #tar xvzf BENCHorch11.tar.gz
1246        echo 'myget 3DBenchs/BENCHCMIP6.tar.gz'
1247        myget 3DBenchs/BENCHCMIP6.tar.gz
1248        tar xvzf BENCHCMIP6.tar.gz
1249        sed -e "s:VEGET=n:VEGET=y:" config.def > tmp
1250        mv -f tmp config.def
1251        if [[ "$with_xios" = "y" ]]; then
1252            cp ../../ORCHIDEE/src_xml/context_orchidee.xml .
1253            echo '<context id="orchidee" src="./context_orchidee.xml"/>' \
1254                 > add.tmp
1255            cp ../../ORCHIDEE/src_xml/field_def_orchidee.xml .
1256            cp ../../ORCHIDEE/src_xml/file_def_orchidee.xml .
1257            cp ../../ORCHIDEE/src_xml/file_def_input_orchidee.xml .
1258            if [[ -f ../../ORCHIDEE/src_xml/context_input_orchidee.xml ]]; then
1259                   cp ../../ORCHIDEE/src_xml/context_input_orchidee.xml .
1260                   echo '<context id="orchidee" ' \
1261                     'src="./context_input_orchidee.xml"/>' >> add.tmp
1262            fi
1263            sed -e '/id="LMDZ"/r add.tmp' iodef.xml > tmp
1264            mv tmp iodef.xml
1265            sed -e'{/sechiba1/ s/enabled="_AUTO_"/type="one_file" enabled=".TRUE."/}' \
1266                file_def_orchidee.xml > tmp
1267            \mv -f tmp file_def_orchidee.xml
1268            sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
1269                file_def_orchidee.xml > tmp
1270            \mv -f tmp file_def_orchidee.xml
1271            sed -e 's@output_level="_AUTO_"@output_level="1"@' \
1272                file_def_orchidee.xml > tmp
1273            \mv -f tmp file_def_orchidee.xml
1274            sed -e 's@output_freq="_AUTO_"@output_freq="1d"@' \
1275                file_def_orchidee.xml > tmp
1276            \mv -f tmp file_def_orchidee.xml
1277            sed -e 's@compression_level="4"@compression_level="0"@' \
1278                file_def_orchidee.xml > tmp
1279            \mv -f tmp file_def_orchidee.xml
1280            sed -e 's@XIOS_ORCHIDEE_OK = n@XIOS_ORCHIDEE_OK = y@' \
1281                orchidee.def > tmp
1282            \mv -f tmp orchidee.def
1283        fi
1284    fi
1285
1286    if [[ -f ../arch.env ]]
1287    then
1288        source ../arch.env
1289    fi
1290
1291    echo EXECUTION DU BENCH
1292    set +e
1293    date; ./bench.sh > out.bench 2>&1; date
1294    set -e
1295    tail listing
1296
1297
1298    echo "##########################################################"
1299    echo "Simulation finished in $(pwd)"
1300    echo "You have compiled with:"
1301    cat ../compile.sh
1302    if [[ $parallel = "none" ]]; then
1303        echo "You may re-run it with : cd  $(pwd); gcm.e"
1304        echo "or ./bench.sh"
1305    else
1306        echo "You may re-run it with : "
1307        echo "cd  $(pwd); ./bench.sh"
1308        #  echo 'ulimit -s unlimited'
1309        #  echo 'export OMP_NUM_THREADS=2'
1310        #  echo 'export OMP_STACKSIZE=800M'
1311        #  echo "$mpirun -np 2 gcm.e "
1312    fi
1313    echo '##########################################################'
1314
1315fi # bench
1316
1317
1318#################################################################
1319# Installation eventuelle du 1D
1320#################################################################
1321
1322if [[ $SCM = 1 ]]; then
1323    cd "$MODEL"
1324    myget 1D/1D.tar.gz
1325    tar xf 1D.tar.gz
1326    cd 1D
1327    if [[ $rad = oldrad ]]; then
1328        sed -i'' -e 's/^rad=.*$/rad=oldrad/' run.sh
1329        sed -i'' -e 's/^rad=.*$/rad=oldrad/' bin/compile
1330    fi
1331    echo "Running 1D/run.sh, log in $(pwd)/run1d.log"
1332    ./run.sh > "$(pwd)/run1d.log" 2>&1
1333fi
1334
1335
1336#################################################################
1337# sauvegarde des options veget pour utilisation eventuelle tutorial_prod
1338#################################################################
1339cd "$MODEL/modipsl/modeles"
1340#echo surface_env file created in $MODEL
1341cat <<EOF >surface_env
1342veget=$veget
1343opt_veget="-v $veget_version"
1344orchidee_rev=$orchidee_rev
1345suforch=$suff_orc
1346EOF
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