source: BOL/script_install_amaury/install_lmdz.sh @ 5098

Last change on this file since 5098 was 5083, checked in by abarral, 4 months ago

Ensure prod is default flag everywhere
  • Property svn:executable set to *
File size: 35.0 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 : 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 {
41  # Get a file from LMDZ repository, make it executable if .(ba)sh
42  local url=$1
43
44  local filename
45  filename=$(basename "$url")
46
47  wget --no-check-certificate -nv "http://lmdz.lmd.jussieu.fr/pub/$url"
48  if [[ $filename =~ .*\.(ba)?sh ]]; then chmod +x "$filename"; fi
49}
50
51function set_default_params {
52    # Valeur par défaut des parametres
53    svn_lmdz=""
54    version="20240508.CM7"
55
56    netcdf=1
57    bench=1
58    SCM=0
59    veget="none"
60    grid_resolution="32x32x39"
61    benchphysiq=""
62    compphysiq="lmd"
63
64    parallel="none"
65    trusting="testing"
66    MODEL=""
67
68    with_xios=0
69    opt_makelmdz_xios=""
70
71    rad="rrtm"
72
73    compile_with_fcm=1
74
75    cosp="none"
76    aerosols=0
77    inlandsis=0
78
79    make_j=8
80    clean_install=1
81
82    # Check if on a Mac /!\ Probably doesn't work anymore, to fix one day...
83    if [[ $(uname) = "Darwin" ]]; then
84        export MAKE="make"
85    fi
86
87    optim_flag="-prod"
88    arch="local"
89
90    arch="local-gfortran"
91    arch_dir=""
92
93    jobcmd=""
94}
95
96function read_cmdline_args {
97    while (($# > 0)); do
98        case $1 in
99            "-h") cat <<........fin
100        $0 [ -v version ] [ -r svn_release ]
101               [ -parallel PARA ] [ -d GRID_RESOLUTION ] [ -bench 0/1 ]
102               [-name LOCAL_MODEL_NAME] [-rad RADIATIF]
103
104        -v       "version" like 20150828.trunk, see http://www.lmd.jussieu.fr/~lmdz/Distrib/LISMOI.trunk (default <$version>)
105
106        -r       "svn_release" : either the svn release number or "last" (default <$svn_lmdz>)
107
108        -parallel parallel support: mpi, omp, mpi_omp (mpi with openMP) or none (default: <$parallel>)
109
110        -d        "grid resolution": should be among the available benchs if -bench 1 (valid values: 48x36x19, 48x36x39) (default : <$grid_resolution>)
111
112        -bench     activating the bench or not (0/1) (default: <$bench>)
113
114        -unstable  use unstable tar instead of testing
115
116        -name      name of the folder to install to (default <$MODEL>)
117
118        -netcdf    0, 1 or PATH. 0: do not download NetCDF, look for it in standard locations (/usr);  1: download and compile NetCDF; PATH: full path to an existing installed NetCDF library (default: <$netcdf>)
119
120        -xios      use (download and compile) the XIOS library (will compile the parallel NetCDF4-HDF5 library) (requires to also have -parallel mpi_omp)
121
122        -cosp       to run with cospv1 or cospv2 [none/v1/v2] (default <$cosp>)
123
124        -rad        radiative code: oldrad, rrtm or ecrad (default <$rad>)
125
126        -nofcm      to compile without fcm
127
128        -SCM        install 1D version automatically
129
130        -debug      compile everything in debug mode
131
132        -benchphysiq   to choose which physics.def package to use in the bench (default <$benchphysiq>)
133
134        -compilephysiq   physics to compile the model with (default <$compphysiq>)
135
136        -veget      surface/vegetation scheme treatment controlled by the single variable veget which can have the following values: none: bucket scheme (default); CMIP6 | veget2.0: orchidee version used in CMIP exercise, rev 5661; veget2.2: orchidee branch 2.2, rev 8529 (bundled); number: orchidee version number  [only orch>2.0] (default $veget)
137
138        -spla       activate interactive aerosols
139
140        -inlandsis  activate new snow scheme
141
142        -arch       name of the arch to use (default <$arch>)
143
144        -arch_dir   where to find the arch files (default <$arch_dir>)
145
146        -make_j     number of processes to parallelize installations (default <$make_j>)
147
148        -jobcmd     command prepended to fcm compile jobs, e.g. "srun" (default <$jobcmd>)
149
150        -noclean    will only download necessary files (but no thorough check is made on the integrity of existing files), and will recompile everything (very quick if it's already been compiled before)
151
152........fin
153                  exit 1;;
154            "-v") version=$2; shift; shift;;
155            "-r") svn_lmdz=$2; shift; shift;;
156            "-d") grid_resolution=$2; shift; shift;;
157            "-unstable") trusting="unstable"; shift;;
158            "-cosp") cosp=$2
159                     case $cosp in
160                         "none"|"v1"|"v2") cosp=$2; shift; shift;;
161                         *) echo "Only none v1 v2 for cosp option"; exit 1
162                     esac;;
163            "-nofcm") compile_with_fcm=0; echo "This option will be reactivated soon (promesse du 8dec2022)"; exit 1;  shift;;
164            "-SCM") SCM=1; shift;;
165            "-rad") rad=$2
166                    case $rad in
167                        "oldrad"|"rrtm"|"ecrad") rad=$2; shift; shift;;
168                        *) echo "Only oldrad rrtm ecrad for rad option"; exit 1
169                    esac;;
170            "-parallel") parallel=$2
171                         case $parallel in
172                             "none"|"mpi"|"omp"|"mpi_omp") parallel=$2; shift; shift;;
173                             *) echo "Only none mpi omp mpi_omp for the parallel option"; exit 1
174                         esac;;
175            "-bench") bench=$2; shift; shift;;
176            "-debug") optim_flag="-debug"; shift;;
177            "-name") MODEL=$2; shift; shift;;
178            "-netcdf") netcdf=$2; shift; shift;;
179            "-benchphysiq") benchphysiq=$2; shift; shift;;
180            "-compilephysiq") compphysiq=$2; shift; shift;;
181            "-xios") with_xios=1; shift;;
182            "-arch") arch=$2; shift; shift;;
183            "-arch_dir") arch_dir=$2; shift; shift;;
184            "-veget") veget=$2; shift; shift;;
185            "-spla") aerosols=1; shift;;
186            "-inlandsis") inlandsis=1; shift;;
187            "-make_j") make_j=$2; shift; shift;;
188            "-jobcmd") jobcmd=$2; shift; shift;;
189            "-noclean") clean_install=0; shift;;
190            *)  bash install_lmdz.sh -h; exit 1
191        esac
192    done
193
194    # Isotopes : Compile and run with isotopes if lmdz_phys="lmdiso" in main.sh
195    if [[ $compphysiq = "lmdiso" ]]; then isotopes=1; else isotopes=0; fi
196
197    # Option de compilation pour Cosp
198    case $cosp in
199        v1) opt_cosp="-cosp true";;
200        v2) opt_cosp="-cospv2 true";;
201        *) opt_cosp=""
202    esac
203
204    #Define veget-related suffix for gcm name
205    if [[ $veget = 'none' ]]; then
206        suff_orc=''
207    else
208        suff_orc='_orch'
209    fi
210
211
212    if [[ $parallel = "none" ]]; then
213        suff_para='_seq'
214    else
215        suff_para='_para_mem'
216    fi
217
218    if [[ $with_xios = 1 ]]; then opt_makelmdz_xios="-io xios"; fi
219
220    if [[ $aerosols = 1 ]]; then
221      opt_aer="-dust true"; suff_aer="_spla"
222    else
223      opt_aer=""; suff_aer=""
224    fi
225
226    if [[ $inlandsis = 1 ]]; then
227       opt_inlandsis="-inlandsis true"
228    else
229       opt_inlandsis=""
230    fi
231
232    if [[ $isotopes = 1 ]]; then
233      opt_isotopes="-isotopes true"; suff_iso="_iso"
234    else
235      opt_isotopes="" ; suff_iso=""
236    fi
237
238    # set default arch if parallel
239    if [[ $arch = "local-gfortran" && $parallel != "none" ]]; then
240      arch="local-gfortran-parallel"
241      echo "Switching default arch to $arch"
242    fi
243
244    # Name of the model's folder. The convention taken here is that models that requires different compilation sources should have a different names.
245    local xios_name=""
246    if [[ $with_xios = 1 ]]; then xios_name="XIOS"; fi
247    if [[ $MODEL = "" ]]; then MODEL="./LMDZ$version${svn_lmdz}OR$veget$xios_name"; fi
248
249    if [[ $arch_dir = "" ]]; then
250      arch_dir="$MODEL/modipsl/config/IPSLCM7/ARCH/";
251    elif ! readlink -fe "$arch_dir"; then
252      echo "STOP: no arch dir <$arch_dir>"; exit 1
253    fi
254}
255
256function ensure_correct_option_combinations {
257    # Check on veget version
258    if [[ $veget != 'none' && $veget != "CMIP6" && $veget != "orch2.0" && $veget != "orch2.2" ]]; then
259        re='^[0-9]+$'
260        if ! [[ $veget =~ $re ]]; then
261            echo 'Valeur de l option veget non valable'; exit 1
262        fi
263    fi
264
265    ## if also compiling XIOS, parallel must be mpi_omp
266    if [[ $with_xios = 1 && $parallel != "mpi_omp" ]]; then
267        echo "Error, you must set -parallel mpi_omp if you want XIOS"; exit 1
268    fi
269
270    if [[ $cosp = "v2" && $with_xios = 0 ]]; then
271        echo "Error, Cospv2 cannot run without Xios"; exit 1
272    fi
273
274    # STOP if trying to use both ORCHIDEE and Isotopes :
275    if [[ $isotopes = 1 && $veget != "none" ]]; then
276      echo "STOP: You cannot run LMDZ with ORCHIDEE and ISOtopes at the same time"; exit 1
277    fi
278
279    # STOP if trying to use both SPLA and Isotopes :
280    if [[ $isotopes = 1 && $aerosols = 1 ]]; then
281      echo "STOP: You cannot run LMDZ with Isotopes and aerosols=spla at the same time"; exit 1
282    fi
283
284    # (Temporary) STOP if trying to use Isotopes with XIOS :
285    # TODO Amaury: check if still relevant
286    if [[ $isotopes = 1 && $with_xios = 1 ]]; then
287      echo "STOP: Isotopes cannont yet be run with XIOS"; exit 1
288    fi
289
290    if [[ $aerosols = 1 && $rad != "rrtm" ]]; then
291      echo "STOP: For the time being, <aerosols=spla> requires <rad=rrtm>"; exit 1
292    fi
293    # TODO: vérifier quelles contraintes sont des contraintes lmdzsetup, et lesquelles sont des vraies contraintes
294}
295
296function check_available_software {
297    echo "################################################################"
298    echo "Check if required software is available"
299    echo "################################################################"
300    for logiciel in wget tar gzip make gcc cmake m4 c++; do
301        if [[ $(which "$logiciel") = "" ]]; then
302            echo "You must first install $logiciel on your system"; exit 1
303        fi
304    done
305
306    cat <<eod > tt.f90
307print*,'coucou'
308end
309eod
310    $compiler tt.f90 || a.out
311    ./a.out >| tt
312    if [[ $(< tt sed -e 's/ //g' ) != "coucou" ]]; then
313        echo "problem installing with compiler $compiler"; exit 1
314    fi
315    \rm tt a.out tt.f90
316}
317
318function download_model {
319    if [[ $clean_install = 1 ]]; then rm -rf "$MODEL"; fi
320
321    mkdir -p "$MODEL"
322    MODEL=$(readlink -e -f "$MODEL"); echo "$MODEL"  # absolute path
323    if [[ ! -d "$MODEL/modipsl" ]]; then
324        echo "##########################################################"
325        echo "Download a slightly modified version of LMDZ"
326        echo "##########################################################"
327        cd "$MODEL"
328        getlog="$(pwd)/get.log"
329        echo "logfile : $getlog"
330        myget "src_archives/$trusting/modipsl.$version.tar.gz" &>> get.log
331        echo "install_lmdz.sh wget_OK $(date)"
332        gunzip "modipsl.$version.tar.gz" &>> get.log
333        tar xf "modipsl.$version.tar" &>> get.log
334        \rm "modipsl.$version.tar"
335        cd - &> /dev/null
336    fi
337}
338
339function init_arch {
340    set +e; arch_dir=$(readlink -f "$arch_dir"); set -e  # full path. readlink must be called *after* the path is created
341
342    # Check where default fcm, path, env are located - by default in $arch_path, instead in $MODEL/modipsl/modeles/LMDZ/arch/
343    local i fcm_path path_path env_path
344    for i in "path" "fcm" "env"; do
345      local varname=${i}_path
346      if [[ -f $arch_dir/arch-$arch.$i ]]; then
347          declare $varname="$arch_dir/arch-$arch.$i"
348      else
349          declare $varname="$MODEL/modipsl/modeles/LMDZ/arch/arch-$arch.$i"
350          if [[ ! -f ${!varname} ]]; then
351              echo "STOP: no ${!varname}"; exit 1
352          fi
353      fi
354    done
355    default_fcm_path=$fcm_path
356    default_path_path=$path_path
357    default_env_path=$env_path
358
359    # check compiler
360    compiler=$(< "$default_fcm_path" grep "%COMPILER" | sed -e "s/%COMPILER\s*//")
361
362    # load env
363    # shellcheck disable=SC1090
364    if [[ -f $default_env_path ]]; then source "$default_env_path"; fi
365
366    local mpi_file  # can't be done before as it depends on sourcing the env
367    mpi_file=$(readlink -e -f "$(which mpif90)")
368    path_mpi=$(dirname "$mpi_file")
369    root_mpi=$(dirname "$path_mpi")
370}
371
372function install_arch {
373    local component=$1
374
375    # Use same .env for all components (for module compatibility)
376    cp -f "$default_env_path" "$MODEL/modipsl/modeles/$component/arch" &> /dev/null || true  # allow failure if we're copying the file to itself
377
378    # Use local .path and .fcm is available, otherwise default
379    if [[ ! -f "$MODEL/modipsl/modeles/$component/arch/arch-$arch.path" ]]; then
380        cp -f "$default_path_path" "$MODEL/modipsl/modeles/$component/arch"
381
382        if [[ $component = "ORCHIDEE" ]]; then
383            if [[ $orcbranch = "/tags/ORCHIDEE_2_0/ORCHIDEE" ]]; then  # 2.0 and before have a different fcm convention
384                sed -i'' -e "s/-I//" -e "s/-L//" "$MODEL/modipsl/modeles/ORCHIDEE/arch/arch-$arch.path"  # /!\ we only replace first occurence on purpose
385            fi
386        fi
387    fi
388    if [[ ! -f "$MODEL/modipsl/modeles/$component/arch/arch-$arch.fcm" ]]; then
389        cp -f "$default_fcm_path"  "$MODEL/modipsl/modeles/$component/arch"
390
391        if [[ $component = "XIOS" ]]; then
392            # Adapt for XIOS, which uses different naming conventions
393            sed -i'' -e "s/%COMPILER/%FCOMPILER/" -e "s/%LINK/%LINKER/" -e "s/-fdefault-real-8//" "$MODEL/modipsl/modeles/XIOS/arch/arch-$arch.fcm"
394        fi
395    fi
396}
397
398function install_netcdf {
399    echo "Installing Netcdf"
400    local ncdf_compiler="$compiler"
401
402    if [[ $netcdf = 0 ]]; then
403        ncdfdir=$(nf-config --prefix)
404    else
405        cd "$MODEL"
406
407        # Convert non-basic compiler
408        case $compiler in
409            mpif90) ncdf_compiler=$($compiler --version | head -n 1 | cut -d " " -f -1)
410        esac
411
412        case $ncdf_compiler in
413            gfortran | GNU) ncdf_compiler="gfortran"; opt1="-compiler gnu"; opt2="-CC gcc -FC gfortran -CXX g++";;
414            *)      echo "unexpected compiler $ncdf_compiler for netcdf"; exit 1
415        esac
416
417        case $with_xios in
418            0) script_install_netcdf="install_netcdf4_hdf5_seq.bash"
419               ncdfdir="netcdf4_hdf5_seq"
420               opt_="$opt1";;
421            1) script_install_netcdf="install_netcdf4_hdf5.bash"
422               ncdfdir="netcdf4_hdf5"
423               opt_="$opt2 -MPI $root_mpi";;
424            *) echo "with_xios=$with_xios, should be 0 or 1"; exit 1
425        esac
426        if [[ $netcdf = 1 ]]; then
427           ncdfdir="$MODEL/$ncdfdir"
428        else
429           mkdir -p "$netcdf"; ncdfdir="$netcdf/$ncdfdir"
430        fi
431
432        echo "Repertoire netcdf $ncdfdir"
433        if [[ ! -d $ncdfdir ]]; then
434            netcdflog=$(pwd)/netcdf.log
435            echo "----------------------------------------------------------"
436            echo "Compiling the Netcdf library"
437            echo "----------------------------------------------------------"
438            echo "log file : $netcdflog"
439            myget script_install/$script_install_netcdf &>> "$netcdflog"
440            chmod u=rwx $script_install_netcdf
441            # shellcheck disable=SC2086
442            ./$script_install_netcdf -prefix "$ncdfdir" $opt_ &>> "$netcdflog"
443        fi
444
445        # Add to path
446        export PATH="$ncdfdir/bin:$PATH"
447
448        #----------------------------------------------------------------------------
449        # LF rajout d'une verrue, pour une raison non encore expliquee,
450        # la librairie est parfois rangée dans lib64 et non dans lib
451        # par certains compilateurs
452        if [[ ! -e lib && -d lib64 ]]; then ln -s lib64 lib; fi
453        #----------------------------------------------------------------------------
454
455        echo "install_lmdz.sh netcdf_OK $(date)"
456    fi
457
458    cat >test_netcdf90.f90 <<EOF
459    use netcdf
460    print *, "NetCDF library version: ", nf90_inq_libvers()
461    end
462EOF
463
464    if $ncdf_compiler -I"$ncdfdir"/include test_netcdf90.f90 -L"$ncdfdir"/lib -lnetcdff -lnetcdf -Wl,-rpath="$ncdfdir"/lib && ./a.out; then
465        \rm test_netcdf90.f90 a.out
466    else
467        cat <<EOF
468Failed test program using NetCDF-Fortran. You can:
469- check that you have NetCDF-Fortran installed in your system
470- or specify an installation directory with option -netcdf of install_lmdz.sh
471- or download and compile NetCDF-Fortran with option -netcdf 1 of install_lmdz.sh
472EOF
473        exit 1
474    fi
475
476    # Compile NetCDF95
477    cd "$MODEL/modipsl/modeles/LMD"*
478    echo "Installing NetCDF95"
479    cd "$MODEL"
480    if [[ ! -d "NetCDF95-0.3" ]]; then
481        myget src_archives/netcdf/NetCDF95-0.3.tar.gz
482        tar -xf NetCDF95-0.3.tar.gz
483        rm NetCDF95-0.3.tar.gz
484        cd NetCDF95-0.3
485        mkdir -p build && cd build
486        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"
487        make install
488    fi
489}
490
491function install_IOIPSL {
492    install_arch "IOIPSL"
493
494    cd "$MODEL/modipsl/modeles/IOIPSL"
495    ioipsllog="$(pwd)/ioipsl.log"
496    echo "Compiling IOIPSL, the interface library with Netcdf $(date) (log: $ioipsllog)"
497
498    echo "$jobcmd ./makeioipsl_fcm -j $make_j -arch $arch $optim_flag" > compile.sh
499    chmod +x compile.sh
500    echo "Compiling IOIPSL using $(\cat compile.sh)"
501    if ! ./compile.sh &> "$ioipsllog"; then
502        echo "STOP: IOIPSL compile failed, exiting"; exit 1
503    fi
504
505    # Link to modipsl/bin
506    cp -f bin/* ../../bin
507
508    echo "IOIPSL compiled $(date)"
509}
510
511function install_XIOS {
512    if [[ $with_xios = 1 ]]; then
513        cd "$MODEL/modipsl/modeles"
514        xioslog="$(pwd)/XIOS/xios.log"
515        echo "##########################################################"
516        echo "Compiling XIOS (log $xioslog) $(date)"
517        echo "##########################################################"
518
519        # Download XIOS
520        local xios_http="http://forge.ipsl.fr/ioserver/svn/XIOS2/branches/xios-2.6"
521        local xios_rev="2568"
522       
523        cd "$MODEL/modipsl/modeles"
524        set +e; svn co -r $xios_rev $xios_http XIOS; set -e
525
526        cd XIOS
527
528        install_arch "XIOS"
529
530        echo "$jobcmd ./make_xios --job $make_j --arch $arch" > compile.sh
531        chmod +x compile.sh
532        echo "$(date) Compiling XIOS using $(\cat compile.sh) (log in $xioslog)"
533        if ! ./compile.sh &> "$xioslog"; then
534            echo "STOP: XIOS compilation failed, exiting"; exit 1
535        fi
536
537        echo "Compiled XIOS $(date)"
538    fi
539}
540
541function get_orchidee_version {  # Set / Check ORCHIDEE version
542    local fetch_rev=""
543    orcbranch=""
544    case $veget in
545        "none") fcm_veget_version="false";;
546        "orch2.0" | "CMIP6") fcm_veget_version=orchidee2.0; fetch_rev=7906;;  # in previous tar we used 6592 but with some modifications to xios_orchidee.f90, which got integrated in 7906
547        "orch2.2") fcm_veget_version=orchidee2.1; orcbranch="/branches/ORCHIDEE_2_2/ORCHIDEE" ;; # the bundled version
548        *) fetch_rev=$veget; fcm_veget_version=orchidee2.1;;  # /!\ arbitary rev only works for orch>=2.1
549          # /!\ Note: for orch>=4, we should be using fcm_vegt_version="orchideetrunk". Below copied comment by Adriana in LMDZ_Setup docs:
550#          Avec orchidee2.1, on va compiler LMDZ avec le cle cpp ORCHIDEE_NOLIC. On ne va donc pas prendre en compte les avancements fait dans le trunk qui permet que les fractions lic soitent traité par ORCHIDEE. Ca marche très bien sans cela puisque dans tout façon c'est en cours de développement et ce n'est pas activé par default. En fait on devrait compiler le trunk avec -v orchideetrunk mais avec landice_opt>2, ce qui ne change rien par rapport à orchidee2.1
551#Si on voudrait activer landice_opt=2 , il faut compiler avec -v orchideetrunk.
552
553    esac
554
555    if [[ -n $fetch_rev ]]; then
556        local curr_rev
557        curr_rev=$(svn info "$MODEL/modipsl/modeles/ORCHIDEE" | grep Revision: | cut -d ":" -f 2 | cut -c 2-)
558        orcbranch=$(svn log -v -q svn://forge.ipsl.fr/orchidee/ -r "$fetch_rev" | grep ORCHIDEE | head -1 | sed -e 's:ORCHIDEE/.*$:ORCHIDEE:' | awk '{print $2}')
559        if [[ $fetch_rev != "$curr_rev" ]]; then
560            echo "Fetching orch $fetch_rev from the repository (curr: $curr_rev)"
561            echo "branch is $orcbranch"
562            if [[ $fetch_rev -lt 4465 ]]; then echo 'ORCHIDEE version must be >=4465, exiting'; exit 1; fi
563            echo "IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at orchidee-help@listes.ipsl.fr"
564            cd "$MODEL/modipsl/modeles"
565            rm -rf ORCHIDEE
566            svn co -r "$fetch_rev" "svn://forge.ipsl.fr/orchidee/$orcbranch"
567            cd - > /dev/null
568        fi
569    fi
570
571    # Check parallel LMDZ+ORCH
572    if [[ (! $veget = "none") && $parallel = "none" && ($used_lmdz_rev -lt 4894) ]]; then
573        echo "LMDZ revision must be >=4894 for orchidee without parallel support. Upgrade lmdz or use -parallel mpi_omp."; exit 1
574    fi
575}
576
577function compile_orchidee {
578    install_arch "ORCHIDEE"
579
580    if [[ $veget != "none" ]]; then
581        cd "$MODEL/modipsl/modeles/ORCHIDEE"
582
583        orchideelog="$(pwd)/orchidee.log"
584        echo "Compiling ORCHIDEE, the continental surface model (log $orchideelog) $(date)"
585
586        local xios_orchid
587        if [[ $with_xios = 1 ]]; then
588            xios_orchid="-xios";
589        else
590            xios_orchid="-noxios"
591        fi
592
593        if [[ $parallel != "none" && ! -d src_parallel ]]; then
594           echo "STOP: Orchidee version too old for parallel support"; exit 1
595        fi
596        echo "$jobcmd ./makeorchidee_fcm -j $make_j $xios_orchid $optim_flag -parallel $parallel -arch $arch" > compile.sh
597        chmod +x compile.sh
598        echo "Compiling ORCHIDEE using $(\cat compile.sh)"
599        if ! ./compile.sh &> "$orchideelog"; then
600            echo "STOP: ORCHIDEE compilation failed, exiting"; exit 1
601        fi
602        echo "Compiled ORCHIDEE $(date)"
603    fi
604}
605
606function get_lmdz_version {
607    LMDZPATH=$(readlink -e -f "$MODEL/modipsl/modeles/LMD"*)
608    cd "$LMDZPATH"
609    lmdzlog="$(pwd)/lmdz.log"
610
611    if [[ -n $svn_lmdz ]]; then
612        local curr_rev
613        curr_rev=$(svn info "$MODEL/modipsl/modeles/LMD"* | grep Revision: | cut -d ":" -f 2 | cut -c 2-)
614        if [[ $svn_lmdz != "$curr_rev" ]]; then
615            local lmdzbranch
616            echo "Fetching LMDZ $svn_lmdz from the repository"
617            lmdzbranch=$(svn log -v -q https://svn.lmd.jussieu.fr/LMDZ -r "$svn_lmdz" | grep LMDZ | head -1 | sed -e 's:trunk/.*$:trunk:' | awk '{print $2}')
618            cd "$MODEL/modipsl/modeles"
619            rm -rf LMD*
620            svn co -r "$svn_lmdz" "https://svn.lmd.jussieu.fr/LMDZ$lmdzbranch" LMDZ
621            cd - > /dev/null
622        fi
623        used_lmdz_rev=$svn_lmdz
624    else  # get svn from info
625        set +e; used_lmdz_rev=$(svn info | grep "Last Changed Rev" | cut -c 19-); set -e
626        if [[ -z $used_lmdz_rev ]]; then  # svn info failed
627            used_lmdz_rev=$(grep 'Revision: [0-9]' "$MODEL"/Read*.md | awk ' { print $2 } ' 2>/dev/null)
628            if [[ -z $used_lmdz_rev ]]; then echo "Could not determine lmdz version. This is likely an issue with the .tar itself, please report to LMDZ team."; exit 1; fi
629        fi
630    fi
631}
632
633function compile_lmdz {
634    install_arch "LMDZ"
635    cd "$LMDZPATH"
636
637    if [[ $used_lmdz_rev -le 4185 ]]; then
638        exe_name="bin/gcm_${grid_resolution}_phy${compphysiq}_${suff_para}${suff_orc}${suff_aer}${suff_iso}.e"
639    else
640        exe_name="bin/gcm_${grid_resolution}_phy${compphysiq}_${rad}${suff_para}${suff_orc}${suff_aer}${suff_iso}.e"
641    fi
642
643    local opt_rad
644    case $rad in
645        oldrad) iflag_rrtm=0; NSW=2; opt_rad="";;
646        rrtm)   iflag_rrtm=1; NSW=6
647            if [[ $used_lmdz_rev -le 4185 ]]; then
648                opt_rad="-rrtm true"
649            else
650                opt_rad="-rad rrtm"
651            fi;;
652        ecrad)  iflag_rrtm=2; NSW=6; opt_rad="-rad ecrad";;
653        *) echo "Only oldrad rrtm ecrad for rad option"; exit 1
654    esac
655    if [[ $used_lmdz_rev -le 4185 && $rad = "ecrad" ]]; then
656        echo "ecrad only available for LMDZ rev starting with 4186 "; exit 1
657    fi
658
659    # Compile
660    makelmdz="makelmdz_fcm $optim_flag -arch $arch -j $make_j"
661    local para_compile_opt="-mem -parallel $parallel"; if [[ $parallel = "none" ]]; then para_compile_opt=""; fi
662    echo "$jobcmd ./$makelmdz $opt_rad $opt_cosp $opt_makelmdz_xios $opt_aer $opt_inlandsis $opt_isotopes -p $compphysiq -d ${grid_resolution} -v $fcm_veget_version $para_compile_opt gcm" > compile.sh
663    echo "Compiling lmdz using $(\cat compile.sh) (log: $lmdzlog) $(date)"
664    chmod +x ./compile.sh
665    if ! ./compile.sh &> "$lmdzlog"; then
666        echo "STOP: LMDZ compilation failed, exiting"; exit 1
667    fi
668    echo "Finished LMDZ compilation $(date)"
669
670    # Check executable
671    if [[ ! -f $exe_name ]]; then
672        echo "STOP: Compilation failed, can't find the executable"; exit 1
673    else
674        echo "Compilation successful, the executable is $exe_name $(date)"
675    fi
676}
677
678function run_bench {
679    cd "$MODEL/modipsl/modeles/LMDZ"*
680
681    if [[ $bench = "tuto" ]]; then
682        myget "Training/tutorial.tar"; tar xf tutorial.tar; cd TUTORIAL
683        ./init.sh
684    elif [[ $bench = 1 ]]; then
685        \rm -rf "BENCH${grid_resolution}"
686        local bench=bench_lmdz_${grid_resolution}
687        myget "3DBenchs/$bench.tar.gz"
688        tar xf "$bench.tar.gz"
689
690        if [[ $cosp = "v1" || $cosp = "v2" ]]; then
691            cd "BENCH${grid_resolution}"
692            # copier les fichiers namelist input et output our COSP
693            cp ../DefLists/cosp*_input_nl.txt .
694            cp ../DefLists/cosp*_output_nl.txt .
695            # Activer la cles ok_cosp pour tourner avec COSP
696            sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp
697            \mv -f tmp config.def
698            cd ..
699        fi
700
701        if [[ -n "$benchphysiq" ]]; then
702            cd "BENCH${grid_resolution}"
703            if [[ -f "physiq.def_${benchphysiq}" ]]; then
704                cp "physiq.def_${benchphysiq}" benchphysiq.def
705                echo "using physiq.def_${benchphysiq}"
706            else
707                echo "using standard physiq.def"
708            fi
709            cd ..
710        else
711            echo "using standard physiq.def"
712        fi
713
714        if [[ $with_xios = 1 ]]; then
715            cd "BENCH${grid_resolution}"
716            cp ../DefLists/iodef.xml .
717            cp ../DefLists/context_lmdz.xml .
718            cp ../DefLists/field_def_lmdz.xml .
719            # A raffiner par la suite
720            echo "A FAIRE : Copier les *xml en fonction de l option cosp"
721            cp ../DefLists/field_def_cosp*.xml .
722            cp ../DefLists/file_def_hist*xml .
723            # adapt iodef.xml to use attached mode
724            sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' \
725                iodef.xml > tmp
726            \mv -f tmp iodef.xml
727
728            # and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
729            # except for histday
730            for histfile in file_def_hist*xml; do
731                if [[ "$histfile" = "file_def_histday_lmdz.xml" ]]; then
732                    sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' \
733                        "$histfile" > tmp
734                    \mv -f tmp "$histfile"
735                    sed -e 's@output_level="_AUTO_"@output_level="5"@' "$histfile" \
736                        > tmp
737                    \mv -f tmp "$histfile"
738                    sed -e 's@compression_level="2"@compression_level="0"@' \
739                        "$histfile" > tmp
740                    \mv -f tmp "$histfile"
741                else
742                    sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
743                        "$histfile" > tmp
744                    \mv -f tmp "$histfile"
745                fi
746            done
747            # and add option "ok_all_xml=y" in config.def
748            echo "### XIOS outputs" >> config.def
749            echo 'ok_all_xml=.true.' >> config.def
750
751            #activer les sorties pour Cosp
752            if [[ "$cosp" = "v1" ]]; then
753                sed -i'' -e 's@enabled=".FALSE."@enabled=".TRUE."@' \
754                         -e 's@output_level="_AUTO_"@output_level="5"@' \
755                         -e 's@compression_level="2"@compression_level="0"@' \
756                         file_def_histdayCOSP_lmdz.xml
757            fi
758            if [[ "$cosp" = "v2" ]]; then
759                sed -i'' -e 's@compression_level="2"@compression_level="0"@' file_def_histdayCOSPv2_lmdz.xml
760                for type_ in hf day mth; do
761                    file=file_def_hist${type_}COSP
762                    sed -i'' -e 's@src="./'${file}'_lmdz.xml"@src="./'${file}'v2_lmdz.xml"@' context_lmdz.xml
763                done
764                sed -i'' -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' field_def_lmdz.xml
765            fi
766
767            cd ..
768        fi
769
770        # Cas Bench avec ecrad
771        if [[ $rad = "ecrad" ]]; then
772            cd "BENCH${grid_resolution}"
773            cp  ../DefLists/namelist_ecrad .
774            cp -r ../libf/phylmd/ecrad/data .
775            cd ..
776        fi
777
778        # Adjusting bench physiq.def to radiative code chosen
779        cd "BENCH${grid_resolution}"
780        sed -e 's/iflag_rrtm=.*.$/iflag_rrtm='$iflag_rrtm'/' \
781            -e 's/NSW=.*.$/NSW='$NSW'/' physiq.def > tmpdef
782        \mv tmpdef physiq.def
783        cd ..
784
785        cp "$exe_name" "BENCH${grid_resolution}/gcm.e"
786        cd "BENCH${grid_resolution}"
787
788        local bench_cmd="./bench.sh"
789        if [[ ${parallel:0:3} = "mpi" ]]; then
790            # Lancement avec deux procs mpi et 2 openMP
791            echo "export OMP_STACKSIZE=800M" > bench.sh
792            if [[ "${parallel:4:3}" = "omp" ]]; then
793                echo "export OMP_NUM_THREADS=2" >> bench.sh
794            fi
795            if [[ $cosp = "v1" || $cosp = "v2" ]]; then
796                echo "ulimit -s 200000" >> bench.sh
797            else
798                echo "ulimit -s unlimited" >> bench.sh
799            fi
800            if which mpirun &> /dev/null; then
801                echo "mpirun -np 2 gcm.e &> listing" >> bench.sh
802            elif grep -q "Adastra" /etc/motd; then
803                local account
804                account=$(/usr/sbin/my_project.py -l 2>&1 | head -1 | cut -d " " -f 3- | cut -c 5-)
805                bench_cmd="srun --nodes=1 --ntasks=1 --cpus-per-task=2 --threads-per-core=2 --time=0:10:00 --constraint=GENOA --account=$account bash bench.sh"
806                echo "./gcm.e &> listing" >> bench.sh
807            else
808                echo "Error: No command found to run parallel bench"; exit 1
809            fi
810            if [[ $(hostname | cut -c -6) = "spirit" ]]; then  # ulimit unlimited segfaults on Spirit
811                sed -i'' "s/ulimit -s unlimited/ulimit -Ss 8000/" bench.sh
812            fi
813            # Add rebuild, using reb.sh if it is there
814            cat <<EOF >> bench.sh
815if [[ -f reb.sh ]]; then
816  ./reb.sh histday; ./reb.sh histmth; ./reb.sh histhf;
817  ./reb.sh histins; ./reb.sh stomate_history;
818  ./reb.sh sechiba_history; ./reb.sh sechiba_out_2
819fi
820EOF
821        else
822            echo "./gcm.e &> listing" > bench.sh
823        fi
824        # Getting orchidee stuff
825        if [[ $veget = 'CMIP6' || $veget = "orch2.0" ]]; then  # TODO once we have a 2.2 bench, add it here (or in planned separate bench script)
826            echo 'myget 3DBenchs/BENCHCMIP6.tar.gz'
827            myget 3DBenchs/BENCHCMIP6.tar.gz
828            tar xvzf BENCHCMIP6.tar.gz
829            sed -e "s:VEGET=n:VEGET=y:" config.def > tmp
830            mv -f tmp config.def
831            if [[ $with_xios = 1 ]]; then
832                cp ../../ORCHIDEE/src_xml/context_orchidee.xml .
833                echo '<context id="orchidee" src="./context_orchidee.xml"/>' > add.tmp
834                cp ../../ORCHIDEE/src_xml/field_def_orchidee.xml .
835                cp ../../ORCHIDEE/src_xml/file_def_orchidee.xml .
836                cp ../../ORCHIDEE/src_xml/file_def_input_orchidee.xml .
837                if [[ -f ../../ORCHIDEE/src_xml/context_input_orchidee.xml ]]; then
838                       cp ../../ORCHIDEE/src_xml/context_input_orchidee.xml .
839                       echo '<context id="orchidee" src="./context_input_orchidee.xml"/>' >> add.tmp
840                fi
841                sed -e '/id="LMDZ"/r add.tmp' iodef.xml > tmp
842                mv tmp iodef.xml
843                sed -e'{/sechiba1/ s/enabled="_AUTO_"/type="one_file" enabled=".TRUE."/}' \
844                    file_def_orchidee.xml > tmp
845                \mv -f tmp file_def_orchidee.xml
846                sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
847                    file_def_orchidee.xml > tmp
848                \mv -f tmp file_def_orchidee.xml
849                sed -e 's@output_level="_AUTO_"@output_level="1"@' \
850                    file_def_orchidee.xml > tmp
851                \mv -f tmp file_def_orchidee.xml
852                sed -e 's@output_freq="_AUTO_"@output_freq="1d"@' \
853                    file_def_orchidee.xml > tmp
854                \mv -f tmp file_def_orchidee.xml
855                sed -e 's@compression_level="4"@compression_level="0"@' \
856                    file_def_orchidee.xml > tmp
857                \mv -f tmp file_def_orchidee.xml
858                sed -e 's@XIOS_ORCHIDEE_OK = n@XIOS_ORCHIDEE_OK = y@' \
859                    orchidee.def > tmp
860                \mv -f tmp orchidee.def
861            fi
862        fi
863
864        if [[ -f ../arch.env ]]; then source ../arch.env; fi
865
866        echo "EXECUTION DU BENCH"
867        date
868        if (! $bench_cmd &> out.bench) || ! (tail -n 1 listing | grep "Everything is cool"); then
869            tail listing
870            echo "Bench FAILED, exiting"; exit 1
871        fi
872        date
873        tail listing
874    fi
875
876    # 1D case
877    if [[ $SCM = 1 ]]; then
878        cd "$MODEL"
879        myget 1D/1D.tar.gz
880        tar xf 1D.tar.gz
881        cd 1D
882        for e in "fcm" "env" "path"; do
883          cp "$MODEL/modipsl/modeles/LMDZ/arch/arch-$arch.$e" "$MODEL/modipsl/modeles/LMDZ/arch/arch-local.$e"
884        done
885        if [[ $rad = "oldrad" ]]; then
886            sed -i'' -e 's/^rad=.*$/rad=oldrad/' run.sh
887            sed -i'' -e 's/^rad=.*$/rad=oldrad/' bin/compile
888        elif [[ $rad = ecrad ]] ; then
889                        sed -i'' -e 's/^rad=.*$/rad=ecrad/' run.sh
890                        sed -i'' -e 's/^rad=.*$/rad=ecrad/' bin/compile
891                    fi
892        echo "Running 1D/run.sh, log in $(pwd)/run1d.log"
893        ./run.sh &> "$(pwd)/run1d.log"
894    fi
895}
896
897# If sourced: returns, else run setup
898if [[ ! "${BASH_SOURCE[0]}" = "$0" ]]; then return 0; fi
899
900echo "install_lmdz.sh DEBUT $(date)"
901
902set_default_params
903read_cmdline_args "$@"
904ensure_correct_option_combinations
905download_model
906init_arch
907check_available_software
908get_lmdz_version
909get_orchidee_version
910install_netcdf
911install_IOIPSL
912install_XIOS
913compile_orchidee
914compile_lmdz
915run_bench
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