Changeset 4891


Ignore:
Timestamp:
Apr 5, 2024, 4:33:57 PM (4 weeks ago)
Author:
abarral
Message:

fix orchidee & lmdz compilation
explicit exported variables in compile.sh
only compile orchidee once (seq OR par)
standardize n/y vs 0/1
clean redundant comments in default args

File:
1 edited

Legend:

Unmodified
Added
Removed

  • BOL/script_install_amaury/install_lmdz.sh

    r4890 r4891  
    3737
    3838### Functions
     39# TODO add make_j parallel argument -> check what is used for libigcm
    3940
    4041function myget { # Get a file from LMDZ repository
    … …  
    5051function set_default_params {
    5152    # Valeur par défaut des parametres
    52 
    53     # 04_2021 : tester si r4 marche encore !
    54     real="r8"  # ou "r4"
    55 
    5653    svn=""
    5754    version="20231022.trunk"
    5855
    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
     56    netcdf=1
    6257    bench=1
    63     pclinux=1
    6458    pcmac=0 # default: not on a Mac
    6559    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
    7160    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
     61    grid_resolution="32x32x39"
    7862    physiq=""
    7963
    … …  
    8165    xios_rev="2568"
    8266
    83     ## parallel can take the values none/mpi/omp/mpi_omp
    84     parallel="none"  # "mpi_omp"
    85     idris_acct="lmd"
     67    parallel="none"
    8668    trusting="testing"
    8769    MODEL=""
    8870
    89     ## also compile XIOS? (and more recent NetCDF/HDF5 libraries) Default=no
    90     with_xios="n"
     71    with_xios=0
    9172    opt_makelmdz_xios=""
    9273
    93     ## compile with oldrad/rrtm/ecrad radiatif code (Default=rrtm)
    9474    rad="rrtm"
    9575
    96     ## compile_with_fcm=1 : use makelmdz_fcm (1) or makelmdz (0)
    9776    compile_with_fcm=1
    9877
    99     #Compilation with Cosp (cosp=none/v1/v2; default=none)
    10078    cosp="none"
    10179    opt_cosp=""
    … …  
    10785    fi
    10886
    109     env_file=""
    11087    optim_debug=""
    11188    arch="local"
    … …  
    192169            "-netcdf") netcdf=$2; shift; shift;;
    193170            "-physiq") physiq=$2; shift; shift;;
    194             "-xios") with_xios="y"; shift;;
     171            "-xios") with_xios=1; shift;;
    195172            "-arch") arch=$2; shift; shift;;
    196173            "-arch_dir") arch_dir=$2; shift; shift;;
    … …  
    227204
    228205    if [[ $parallel = "none" ]]; then
    229         sequential=1; suff_exe='_seq'
    230     else
    231         sequential=0; suff_exe='_para_mem'
     206        suff_exe='_seq'
     207    else
     208        suff_exe='_para_mem'
    232209    fi
    233210
    … …  
    236213
    237214    ## if also compiling XIOS, parallel must be mpi_omp
    238     if [[ $with_xios = "y" && $parallel != "mpi_omp" ]]; then
     215    if [[ $with_xios = 1 && $parallel != "mpi_omp" ]]; then
    239216        echo "Error, you must set -parallel mpi_omp if you want XIOS"; exit 1
    240217    fi
    241218
    242     if [[ $with_xios = "y" ]]; then
     219    if [[ $with_xios = 1 ]]; then
    243220        opt_makelmdz_xios="-io xios"
    244221    fi
    245222
    246     if [[ $cosp = "v2" && $with_xios = "n" ]]; then
     223    if [[ $cosp = "v2" && $with_xios = 0 ]]; then
    247224        echo "Error, Cospv2 cannot run without Xios"; exit 1
    248225    fi
    … …  
    314291
    315292function install_arch {
    316     # TODO     if [[ $(gfortran -dumpversion | cut -d. -f1) -ge 10 ]]; then allow_arg_mismatch="-fallow-argument-mismatch"; fi
    317 
    318293    if [[ ! -d $arch_dir ]]; then
    319294        echo "Error: no arch dir $arch_dir"; exit 1
    … …  
    337312    # Copy arch to different components
    338313    # TODO check that this doesn't error if the source and destination are the same
    339     \cp -f "$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" "$MODEL/modipsl/modeles/ORCHIDEE/arch"
     314    for dir in "IOIPSL" "ORCHIDEE" "LMDZ"; do
     315        \cp -f "$arch_dir/arch-$arch.fcm" "$MODEL/modipsl/modeles/$dir/arch"
     316        \cp -f "$arch_dir/arch-$arch.path" "$MODEL/modipsl/modeles/$dir/arch"
     317    done
    343318
    344319    # TODO TEMP compat w/ old orch version - make a proper case later
    … …  
    362337
    363338        case $with_xios in
    364             n) script_install_netcdf="install_netcdf4_hdf5_seq.bash"
     339            0) script_install_netcdf="install_netcdf4_hdf5_seq.bash"
    365340               ncdfdir="netcdf4_hdf5_seq"
    366341               opt_="$opt1";;
    367             y) script_install_netcdf="install_netcdf4_hdf5.bash"
     342            1) script_install_netcdf="install_netcdf4_hdf5.bash"
    368343               ncdfdir="netcdf4_hdf5"
    369344               opt_="$opt2 -MPI $root_mpi";;
    370             *) echo "with_xios=$with_xios, should be n or y"; exit 1
     345            *) echo "with_xios=$with_xios, should be 0 or 1"; exit 1
    371346        esac
    372347        if [[ $netcdf = 1 ]]; then
    … …  
    418393        exit 1
    419394    fi
     395
     396    # Compile NetCDF95
     397    cd "$MODEL/modipsl/modeles/LMD"*
     398    echo "Installing NetCDF95"
     399    cd "$MODEL"
     400    myget src_archives/netcdf/NetCDF95-0.3.tar.gz
     401    tar -xf NetCDF95-0.3.tar.gz
     402    \rm NetCDF95-0.3.tar.gz
     403    cd NetCDF95-0.3
     404    mkdir -p build && cd build
     405    netCDF_INCLUDE_DIR=$(nc-config --includedir) netCDF_LIBRARY=$(nc-config --libdir) cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH="$ncdfdir" -DCMAKE_INSTALL_PREFIX="$MODEL/modipsl"
     406    make install
    420407}
    421408
    … …  
    431418    echo "IOIPSL compiled $(date)"
    432419
    433     export IOIPSL_LIBDIR="$MODEL/modipsl/modeles/IOIPSL/lib"
    434     export IOIPSL_INCDIR="$MODEL/modipsl/modeles/IOIPSL/inc"
     420    IOIPSL_LIBDIR_="$MODEL/modipsl/modeles/IOIPSL/lib"
     421    IOIPSL_INCDIR_="$MODEL/modipsl/modeles/IOIPSL/inc"
    435422}
    436423
    437424function install_XIOS {
    438     if [[ $with_xios = "y" ]]; then
     425    if [[ $with_xios = 1 ]]; then
    439426        cd "$MODEL/modipsl/modeles"
    440427        xioslog="$(pwd)/xios.log"
    … …  
    467454
    468455function 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
     456    if [[ $veget = "none" ]]; then
     457        veget_version="false"
     458    elif [[ $veget = "CMIP6" ]]; then
     459        veget_version=orchidee2.0
     460        orchidee_rev=6592
     461    else # specific orchidee revision newer than CMIP6, on 2_1 or 2_2 branches
     462        veget_version=orchidee2.1
     463        orchidee_rev="$veget"
     464        if [[ $veget -lt 4465 ]]; then
     465            echo 'ORCHIDEE version must be >=4465, exiting'
     466            exit 1
     467        fi
     468
     469        set +e
     470        svn upgrade
     471        local orcbranch
     472        orcbranch=$(svn log -v -q svn://forge.ipsl.jussieu.fr/orchidee/ -r "$veget" |grep ORCHIDEE |head -1| sed -e 's:ORCHIDEE/.*$:ORCHIDEE:' | awk '{print $2}')
     473        echo "IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at orchidee-help@listes.ipsl.fr"
     474        svn switch -r "$veget" --accept theirs-full "svn://forge.ipsl.jussieu.fr/orchidee/$orcbranch"
     475        svn log -r "$veget" | grep "$veget"
     476        if ! svn log -r "$veget" | grep "$veget"; then
     477            echo 'Cannot update ORCHIDEE as not on the right branch for ORCHIDEE'
     478            exit 1
     479        fi
     480        svn update -r "$veget"
     481        set -e
     482    fi
     483}
     484
     485function compile_orchidee {
     486    get_orchidee_version
     487    ORCHPATH=""
     488
     489
     490    if [[ $veget != "none" ]]; then
     491        cd "$MODEL/modipsl/modeles/ORCHIDEE"
     492        ORCHPATH=$(pwd)
     493
     494        orchideelog="$(pwd)/orchidee.log"
     495        echo "Compiling ORCHIDEE, the continental surface model (log $orchideelog) $(date)"
     496
     497        local xios_orchid opt_orc
     498        if [[ $with_xios = 1 ]]; then
     499            xios_orchid="-xios";
     500        else
     501            xios_orchid="-noxios"
     502        fi
     503        if [[ $optim_debug = "-debug" ]]; then
     504            opt_orc="-debug";
     505        else
     506            opt_orc="-prod"
     507        fi
     508
     509        # TODO check that this works with old orchidee versions (cf. -d tools)
     510        local varenv="IOIPSL_LIBDIR_=$IOIPSL_LIBDIR_ IOIPSL_INCDIR_=$IOIPSL_INCDIR_ ORCHPATH=$ORCHPATH"
     511        if [[ $parallel = "none" ]]; then
     512            echo "$varenv ./makeorchidee_fcm $xios_orchid $opt_orc -parallel none -arch $arch -j 8" > compile.sh
     513        else
     514            if [[ ! -d src_parallel ]]; then
     515               echo "Orchidee version too old for parallel support"; exit 1
     516            fi
     517            {
     518                echo "$varenv ./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc -parallel $parallel -arch $arch"
     519                echo "$varenv ./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel $parallel -arch $arch"
     520            } > compile.sh
     521        fi
     522        chmod +x compile.sh
     523        echo "Compiling ORCHIDEE using $(\cat compile.sh)"
     524        if ! ./compile.sh > "$orchideelog" 2>&1; then
     525            echo "ORCHIDEE compilation failed, exiting"; exit 1
     526        fi
     527        echo "Compiled ORCHIDEE $(date)"
     528    fi
     529
     530    ORCH_LIBDIR_="$MODEL/modipsl/modeles/ORCHIDEE/lib"
     531}
     532
     533function get_lmdz_version {
     534    LMDZPATH=$(readlink -f "$MODEL/modipsl/modeles/LMD"*)
     535    cd "$LMDZPATH"
     536    lmdzlog="$(pwd)/lmdz.log"
    481537
    482538    set +e
    483539    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"
     540    if [[ $svn = "last" ]]; then
     541        svnopt=""
     542    else
     543        svnopt="-r $svn"
     544    fi
     545    if [[ $svn != "" ]]; then
     546        if svn info | grep -q 'https:'; then svn switch --relocate https://svn.lmd.jussieu.fr/LMDZ http://svn.lmd.jussieu.fr/LMDZ; fi
     547        svn update "$svnopt"
     548    fi
     549    mysvn=$(svnversion . | grep -E -o "[0-9]+" 2>/dev/null)
    494550    set -e
    495   fi
    496 }
    497 
    498 function 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
     551
     552    if [[ $mysvn = "" ]]; then mysvn=$(grep 'Revision: [0-9]' "$MODEL"/Read*.md | awk ' { print $2 } ' 2>/dev/null); fi
     553    if [[ $mysvn = "" ]]; then mysvn=4190; fi
     554}
     555
     556function compile_lmdz {
     557    get_lmdz_version
     558
     559    exe_name="bin/gcm_${grid_resolution}_phylmd_${rad}${suff_exe}${suff_orc}.e"
     560
     561    local opt_rad
     562    case $rad in
     563        oldrad) iflag_rrtm=0; NSW=2; opt_rad="";;
     564        rrtm)   iflag_rrtm=1; NSW=6
     565            if [[ $mysvn -le 4185 ]]; then
     566                opt_rad="-rrtm true"
     567            else
     568                opt_rad="-rad rrtm"
     569            fi;;
     570        ecrad)  iflag_rrtm=2; NSW=6; opt_rad="-rad ecrad";;
     571        *) echo "Only oldrad rrtm ecrad for rad option"; exit 1
     572    esac
     573    if [[ $mysvn -le 4185 && $rad = "ecrad" ]]; then
     574        echo "ecrad only available for LMDZ rev starting with 4186 "; exit 1
     575    fi
     576
     577    # Compile
     578    local varenv="IOIPSL_LIBDIR_=$IOIPSL_LIBDIR_ IOIPSL_INCDIR_=$IOIPSL_INCDIR_ ORCH_LIBDIR_=$ORCH_LIBDIR_ ORCHPATH=$ORCHPATH"
     579    makelmdz="makelmdz_fcm $optim_debug -arch $arch -j 8"
     580    if [[ $parallel = "none" ]]; then
     581        echo "$varenv ./$makelmdz $opt_rad $opt_cosp -d ${grid_resolution} -v $veget_version gcm " > compile.sh
     582    else
     583        echo "$varenv ./$makelmdz $opt_rad $opt_cosp $opt_makelmdz_xios -d ${grid_resolution} -v $veget_version -mem -parallel $parallel gcm" > compile.sh
     584    fi
     585    echo "Compiling lmdz using $(\cat compile.sh) (log: $lmdzlog) $(date)"
     586    chmod +x ./compile.sh
     587    if ! ./compile.sh > "$lmdzlog" 2>&1; then
     588        echo "LMDZ compilation failed, exiting"; exit 1
     589    fi
     590    echo "Finished LMDZ compilation $(date)"
     591
     592    # Check executable
     593    # TODO $mysev -ge 4186 => other name convention ! check original install
     594    if [[ ! -f $exe_name ]]; then
     595        echo "Compilation failed, can't find the executable"; exit 1
     596    else
     597        echo "Compilation successfull, the executable is $exe_name $(date)"
     598    fi
     599}
     600
     601function run_bench {
     602    cd "$MODEL/modipsl/modeles/LMDZ"*
     603
     604    if [[ $bench = "tuto" ]]; then
     605        myget Training/tutorial.tar; tar xf tutorial.tar; cd TUTORIAL
     606        ./init.sh
     607    elif [[ $bench = 1 ]]; then
     608        \rm -rf "BENCH${grid_resolution}"
     609        local bench=bench_lmdz_${grid_resolution}
     610        myget "3DBenchs/$bench.tar.gz"
     611        tar xf "$bench.tar.gz"
     612
     613        if [[ $cosp = "v1" || $cosp = "v2" ]]; then
     614            cd "BENCH${grid_resolution}"
     615            # copier les fichiers namelist input et output our COSP
     616            cp ../DefLists/cosp*_input_nl.txt .
     617            cp ../DefLists/cosp*_output_nl.txt .
     618            # Activer la cles ok_cosp pour tourner avec COSP
     619            sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp
     620            \mv -f tmp config.def
     621            cd ..
     622        fi
     623
     624        if [[ -n "$physiq" ]]; then
     625            cd "BENCH${grid_resolution}"
     626            if [[ -f "physiq.def_${physiq}" ]]; then
     627                cp "physiq.def_${physiq}" physiq.def
     628                echo "using physiq.def_${physiq}"
     629            else
     630                echo "using standard physiq.def"
     631            fi
     632            cd ..
     633        else
     634            echo "using standard physiq.def"
     635        fi
     636
     637        if [[ $with_xios = 1 ]]; then
     638            cd "BENCH${grid_resolution}"
     639            cp ../DefLists/iodef.xml .
     640            cp ../DefLists/context_lmdz.xml .
     641            cp ../DefLists/field_def_lmdz.xml .
     642            # A raffiner par la suite
     643            echo "A FAIRE : Copier les *xml en fonction de l option cosp"
     644            cp ../DefLists/field_def_cosp*.xml .
     645            cp ../DefLists/file_def_hist*xml .
     646            # adapt iodef.xml to use attached mode
     647            sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' \
     648                iodef.xml > tmp
     649            \mv -f tmp iodef.xml
     650
     651            # and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
     652            # except for histday
     653            for histfile in file_def_hist*xml
     654            do
     655                if [[ "$histfile" = "file_def_histday_lmdz.xml" ]]; then
     656                    sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' \
     657                        "$histfile" > tmp
     658                    \mv -f tmp "$histfile"
     659                    sed -e 's@output_level="_AUTO_"@output_level="5"@' "$histfile" \
     660                        > tmp
     661                    \mv -f tmp "$histfile"
     662                    sed -e 's@compression_level="2"@compression_level="0"@' \
     663                        "$histfile" > tmp
     664                    \mv -f tmp "$histfile"
     665                else
     666                    sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
     667                        "$histfile" > tmp
     668                    \mv -f tmp "$histfile"
     669                fi
     670            done
     671            # and add option "ok_all_xml=y" in config.def
     672            echo "### XIOS outputs" >> config.def
     673            echo 'ok_all_xml=.true.' >> config.def
     674
     675            #activer les sorties pour Cosp
     676            if [[ "$cosp" = "v1" ]]; then
     677                sed -i'' -e 's@enabled=".FALSE."@enabled=".TRUE."@' \
     678                         -e 's@output_level="_AUTO_"@output_level="5"@' \
     679                         -e 's@compression_level="2"@compression_level="0"@' \
     680                         file_def_histdayCOSP_lmdz.xml
     681            fi
     682            if [[ "$cosp" = "v2" ]]; then
     683                sed -e 's@compression_level="2"@compression_level="0"@' file_def_histdayCOSPv2_lmdz.xml
     684                for type_ in hf day mth; do
     685                    file=file_def_hist${type_}COSP
     686                    sed -i'' -e 's@src="./'${file}'_lmdz.xml"@src="./'${file}'v2_lmdz.xml"@' context_lmdz.xml
     687                done
     688                sed -i '' -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' field_def_lmdz.xml
     689            fi
     690
     691            cd ..
     692        fi
     693
     694        # Cas Bench avec ecrad
     695        if [[ $rad = "ecrad" ]]; then
     696            cd "BENCH${grid_resolution}"
     697            cp  ../DefLists/namelist_ecrad .
     698            cp -r ../libf/phylmd/ecrad/data .
     699            cd ..
     700        fi
     701
     702        # Adjusting bench physiq.def to radiative code chosen
     703        cd "BENCH${grid_resolution}"
     704        sed -e 's/iflag_rrtm=.*.$/iflag_rrtm='$iflag_rrtm'/' \
     705            -e 's/NSW=.*.$/NSW='$NSW'/' physiq.def > tmpdef
     706        \mv tmpdef physiq.def
     707        cd ..
     708
     709        cp "$exe_name" "BENCH${grid_resolution}/gcm.e"
     710        cd "BENCH${grid_resolution}"
     711
     712        if [[ ${parallel:0:3} = "mpi" ]]; then
     713            # Lancement avec deux procs mpi et 2 openMP
     714            echo "export OMP_STACKSIZE=800M" > bench.sh
     715            if [[ "${parallel:4:3}" = "omp" ]]; then
     716                echo "export OMP_NUM_THREADS=2" >> bench.sh
     717            fi
     718            if [[ "$cosp" = "v1" || "$cosp" = "v2" ]]; then
     719                echo "ulimit -s 200000" >> bench.sh
     720            else
     721                echo "ulimit -s unlimited" >> bench.sh
     722            fi
     723            echo "mpirun -np 2 gcm.e > listing  2>&1" >> bench.sh
     724            # Add rebuild, using reb.sh if it is there
     725            cat <<EOF >> bench.sh
     726    if [[ -f reb.sh ]]; then
     727      ./reb.sh histday; ./reb.sh histmth; ./reb.sh histhf;
     728      ./reb.sh histins; ./reb.sh stomate_history;
     729      ./reb.sh sechiba_history; ./reb.sh sechiba_out_2
     730    fi
     731EOF
     732        else
     733            echo "./gcm.e > listing  2>&1" > bench.sh
     734        fi
     735        # Getting orchidee stuff
     736        if [[ $veget = 'CMIP6' ]]; then
     737            echo 'myget 3DBenchs/BENCHCMIP6.tar.gz'
     738            myget 3DBenchs/BENCHCMIP6.tar.gz
     739            tar xvzf BENCHCMIP6.tar.gz
     740            sed -e "s:VEGET=n:VEGET=y:" config.def > tmp
     741            mv -f tmp config.def
     742            if [[ $with_xios = 1 ]]; then
     743                cp ../../ORCHIDEE/src_xml/context_orchidee.xml .
     744                echo '<context id="orchidee" src="./context_orchidee.xml"/>' > add.tmp
     745                cp ../../ORCHIDEE/src_xml/field_def_orchidee.xml .
     746                cp ../../ORCHIDEE/src_xml/file_def_orchidee.xml .
     747                cp ../../ORCHIDEE/src_xml/file_def_input_orchidee.xml .
     748                if [[ -f ../../ORCHIDEE/src_xml/context_input_orchidee.xml ]]; then
     749                       cp ../../ORCHIDEE/src_xml/context_input_orchidee.xml .
     750                       echo '<context id="orchidee" src="./context_input_orchidee.xml"/>' >> add.tmp
     751                fi
     752                sed -e '/id="LMDZ"/r add.tmp' iodef.xml > tmp
     753                mv tmp iodef.xml
     754                sed -e'{/sechiba1/ s/enabled="_AUTO_"/type="one_file" enabled=".TRUE."/}' \
     755                    file_def_orchidee.xml > tmp
     756                \mv -f tmp file_def_orchidee.xml
     757                sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
     758                    file_def_orchidee.xml > tmp
     759                \mv -f tmp file_def_orchidee.xml
     760                sed -e 's@output_level="_AUTO_"@output_level="1"@' \
     761                    file_def_orchidee.xml > tmp
     762                \mv -f tmp file_def_orchidee.xml
     763                sed -e 's@output_freq="_AUTO_"@output_freq="1d"@' \
     764                    file_def_orchidee.xml > tmp
     765                \mv -f tmp file_def_orchidee.xml
     766                sed -e 's@compression_level="4"@compression_level="0"@' \
     767                    file_def_orchidee.xml > tmp
     768                \mv -f tmp file_def_orchidee.xml
     769                sed -e 's@XIOS_ORCHIDEE_OK = n@XIOS_ORCHIDEE_OK = y@' \
     770                    orchidee.def > tmp
     771                \mv -f tmp orchidee.def
     772            fi
     773        fi
     774
     775        if [[ -f ../arch.env ]]; then source ../arch.env; fi
     776
     777        echo "EXECUTION DU BENCH"
     778        date
     779        if (! ./bench.sh > out.bench 2>&1) || ! (tail -n 1 listing | grep "Everything is cool"); then
     780            tail listing
     781            echo "Bench FAILED, exiting"; exit 1
     782        fi
     783        date
     784        tail listing
     785    fi
     786
     787    # 1D case
     788    if [[ $SCM = 1 ]]; then
     789        cd "$MODEL"
     790        myget 1D/1D.tar.gz
     791        tar xf 1D.tar.gz
     792        cd 1D
     793        if [[ $rad = "oldrad" ]]; then
     794            sed -i'' -e 's/^rad=.*$/rad=oldrad/' run.sh
     795            sed -i'' -e 's/^rad=.*$/rad=oldrad/' bin/compile
     796        fi
     797        echo "Running 1D/run.sh, log in $(pwd)/run1d.log"
     798        ./run.sh > "$(pwd)/run1d.log" 2>&1
     799    fi
    528800}
    529801
    … …  
    539811install_IOIPSL
    540812#install_XIOS  # TODO disabled for now, did not decide which flags/arch to use for compile
    541 compile_orchidee_seq
    542 
    543 exit 0
    544 
    545 
    546 
    547 
    548 ################################################################
    549 # Specificite des machines
    550 ################################################################
    551 
    552 hostname=$(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 
    683 veget_version=false
    684 if [[ $veget != 'none' ]]; then
    685     cd "$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             $ARFLAGS":1 \
    720             arch-gfortran.fcm > arch-local.fcm
    721         cat <<EOF > arch-local.path
    722 NETCDF_LIBDIR="-L$ncdfdir/lib -lnetcdff -lnetcdf"
    723 NETCDF_INCDIR="$ncdfdir/include"
    724 IOIPSL_INCDIR="$ORCHPATH/../../lib"
    725 IOIPSL_LIBDIR="$ORCHPATH/../../lib"
    726 XIOS_INCDIR="\$ORCHDIR/../XIOS/inc"
    727 XIOS_LIBDIR="\$ORCHDIR/../XIOS/lib -lxios"
    728 EOF
    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 $(date)"
    759 fi # of if [[ "$veget" != 'none' ]]
    760 
    761 
    762 #============================================================================
    763 # Ehouarn: the directory name LMDZ* depends on version/tar file...
    764 if 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=$(pwd)
    770 else
    771     echo "ERROR: No LMD* directory !!!"
    772     exit 1
    773 fi
    774 
    775 
    776 ###########################################################
    777 # For those who want to use fcm to compile via :
    778 #  makelmdz_fcm -arch local .....
    779 ############################################################
    780 
    781 
    782 
    783 cd "$MODEL/modipsl/modeles"/LMDZ*
    784 lmdzlog=$(pwd)/lmdz.log
    785 
    786 ##################################################################
    787 # Possibly update LMDZ if a specific svn release is requested
    788 ##################################################################
    789 
    790 set +e; svn upgrade; set -e
    791 
    792 if [[ $svn = "last" ]]; then svnopt=""; else svnopt="-r $svn"; fi
    793 if [[ $svn != "" ]]; then
    794     if set +e; svn info | grep -q 'https:'; then
    795         svn switch --relocate https://svn.lmd.jussieu.fr/LMDZ \
    796             http://svn.lmd.jussieu.fr/LMDZ
    797     fi
    798     svn update "$svnopt"
    799     set -e
    800 fi
    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 $MODEL/Readm*md
    806 # For old version it assumes that it is before 4185 (the version
    807 # for which the test was introduced
    808 #---------------------------------------------------------------------
    809 
    810 set +e; mysvn=$(svnversion . | grep -E || "[0-9]+" 2>/dev/null); set -e
    811 if [[ "$mysvn" = "" ]]; then mysvn=$(grep 'Revision: [0-9]' "$MODEL"/Read*.md | awk ' { print $2 } ' 2>/dev/null); fi
    812 if [[ "$mysvn" = "" ]]; then mysvn=4190; fi
    813 
    814 if [[ "$pclinux" = "1" && ! -f arch/arch-local.path ]]; then
    815 
    816     # create local 'arch' files (if on Linux PC):
    817     cd arch
    818     # arch-local.path file
    819     # test for version as arch.pth file changed format with rev 4426
    820     if [[ "$mysvn" -gt 4425 ]]; then
    821       cat <<EOF > arch-local.path
    822 NETCDF_LIBDIR="-L$ncdfdir/lib"
    823 NETCDF_LIB="-lnetcdff -lnetcdf"
    824 NETCDF_INCDIR=-I$ncdfdir/include
    825 NETCDF95_INCDIR=-I\$LMDGCM/../../include
    826 NETCDF95_LIBDIR=-L\$LMDGCM/../../lib
    827 NETCDF95_LIB=-lnetcdf95
    828 IOIPSL_INCDIR=-I\$LMDGCM/../../lib
    829 IOIPSL_LIBDIR=-L\$LMDGCM/../../lib
    830 IOIPSL_LIB=-lioipsl
    831 XIOS_INCDIR=-I\$LMDGCM/../XIOS/inc
    832 XIOS_LIBDIR=-L\$LMDGCM/../XIOS/lib
    833 XIOS_LIB="-lxios -lstdc++"
    834 ORCH_INCDIR=-I\$LMDGCM/../../lib
    835 ORCH_LIBDIR=-L\$LMDGCM/../../lib
    836 EOF
    837     else
    838       cat <<EOF > arch-local.path
    839 NETCDF_LIBDIR="-L$ncdfdir/lib -lnetcdff -lnetcdf"
    840 NETCDF_INCDIR=-I$ncdfdir/include
    841 NETCDF95_INCDIR=\$LMDGCM/../../include
    842 NETCDF95_LIBDIR=\$LMDGCM/../../lib
    843 IOIPSL_INCDIR=\$LMDGCM/../../lib
    844 IOIPSL_LIBDIR=\$LMDGCM/../../lib
    845 XIOS_INCDIR=\$LMDGCM/../XIOS/inc
    846 XIOS_LIBDIR=\$LMDGCM/../XIOS/lib
    847 ORCH_INCDIR=\$LMDGCM/../../lib
    848 ORCH_LIBDIR=\$LMDGCM/../../lib
    849 EOF
    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   $whereisthatshell" >> bld.cfg
    875 
    876 fi # of if [[ "$pclinux" = 1 ]]
    877 #---------------------------------------------------------------------
    878 # Option de compilation du rayonnement : depend de $mysvn ><= r4185
    879 #---------------------------------------------------------------------
    880 opt_rad=""
    881 
    882 case $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
    892 esac
    893 
    894 if [[ $mysvn -le 4185 && $rad = "ecrad" ]]; then
    895     echo "ecrad only available for LMDZ rev starting with 4186 "; exit 1
    896 fi
    897 
    898 ##################################################################
    899 
    900 
    901 if [[ ! -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 "$MODEL/modipsl/modeles/"LMDZ*
    913 fi
    914 
    915 echo '##################################################################'
    916 echo "Preparing script compile.sh for LMDZ compilation"
    917 echo "It will only be run automatically if bench=1/tuto"
    918 echo "Here bench=$bench"
    919 echo '##################################################################'
    920 
    921 if [[ $env_file != "" ]]; then
    922     mv arch/arch-${arch}.env arch/arch-${arch}.orig
    923     \cp -f "$env_file" arch/arch-${arch}.env
    924 fi
    925 
    926 if [[ $compile_with_fcm = 1 ]]; then
    927     makelmdz="makelmdz_fcm $optim_debug -arch $arch -j 8 "
    928 else
    929     makelmdz="makelmdz $optim_debug -arch $arch"
    930 fi
    931 
    932 # sequential compilation
    933 if [[ "$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
    946 fi # fin sequential
    947 
    948 # compiling in parallel mode
    949 if [[ $parallel != "none" ]]; then
    950     echo '##########################################################'
    951     echo ' Parallel compile '
    952     echo '##########################################################'
    953     echo "(after saving the sequential libs and binaries)"
    954     cd "$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 
    1043 fi # 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
    1052 if [[ $mysvn -ge 4186 ]]; then suff_exe=_${rad}${suff_exe}; fi
    1053 gcm=""
    1054 
    1055 for exe in gcm.e bin/gcm_${grid_resolution}_phylmd${suff_exe}${suff_orc}.e
    1056 do
    1057     if [[ -f $exe ]]; then gcm=$exe; fi
    1058 done
    1059 
    1060 if [[ "$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
    1067 else
    1068     echo '##########################################################'
    1069     echo "Compilation successfull !!  $(date)"
    1070     echo '##########################################################'
    1071     echo "The executable is $gcm"
    1072 fi
    1073 
    1074 ##################################################################
    1075 # Below, we run a benchmark if bench=1 or tuto
    1076 ##################################################################
    1077 
    1078 if [[ $bench = tuto ]]; then
    1079     myget Training/tutorial.tar; tar xf tutorial.tar; cd TUTORIAL
    1080     ./init.sh
    1081 
    1082 elif [[ $bench = 1 && ! -d BENCH${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
    1232 if [[ -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
    1236 fi
    1237 EOF
    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 
    1315 fi # bench
    1316 
    1317 
    1318 #################################################################
    1319 # Installation eventuelle du 1D
    1320 #################################################################
    1321 
    1322 if [[ $SCM = 1 ]]; then
    1323     cd "$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
    1333 fi
    1334 
    1335 
    1336 #################################################################
    1337 # sauvegarde des options veget pour utilisation eventuelle tutorial_prod
    1338 #################################################################
    1339 cd "$MODEL/modipsl/modeles"
    1340 #echo surface_env file created in $MODEL
    1341 cat <<EOF >surface_env
    1342 veget=$veget
    1343 opt_veget="-v $veget_version"
    1344 orchidee_rev=$orchidee_rev
    1345 suforch=$suff_orc
    1346 EOF
     813compile_orchidee
     814compile_lmdz
     815run_bench
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