source: BOL/script_install_amaury/install_lmdz.sh

Last change on this file was 4941, checked in by abarral, 3 weeks ago

(WIP)
add option top resume install from existing directory
  • 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="20231022.trunk"
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 [[ $(uname) = "Darwin" ]]; then
84        export MAKE="make"
85    fi
86
87    optim_debug=""
88    arch="local"
89
90    local mpi_file
91    mpi_file=$(readlink -e -f "$(which mpif90)")
92    path_mpi=$(dirname "$mpi_file")
93    root_mpi=$(dirname "$path_mpi")
94
95    arch="local-gfortran"
96    arch_dir=""
97}
98
99function read_cmdline_args {
100    while (($# > 0)); do
101        case $1 in
102            "-h") cat <<........fin
103        $0 [ -v version ] [ -r svn_release ]
104               [ -parallel PARA ] [ -d GRID_RESOLUTION ] [ -bench 0/1 ]
105               [-name LOCAL_MODEL_NAME] [-rad RADIATIF]
106
107        -v       "version" like 20150828.trunk, see http://www.lmd.jussieu.fr/~lmdz/Distrib/LISMOI.trunk (default <$version>)
108
109        -r       "svn_release" : either the svn release number or "last" (default <$svn_lmdz>)
110
111        -parallel parallel support: mpi, omp, mpi_omp (mpi with openMP) or none (default: <$parallel>)
112
113        -d        "grid resolution": should be among the available benchs if -bench 1 (valid values: 48x36x19, 48x36x39) (default : <$grid_resolution>)
114
115        -bench     activating the bench or not (0/1) (default: <$bench>)
116
117        -unstable  use unstable tar instead of testing
118
119        -name      name of the folder to install to (default <$MODEL>)
120
121        -netcdf    0, 1 or PATH. 0: do not download NetCDF, look for it in standard locations (/usr);  1: download and compile NetCDF; PATH: full path to an existing installed NetCDF library (default: <$netcdf>)
122
123        -xios      use (download and compile) the XIOS library (will compile the parallel NetCDF4-HDF5 library) (requires to also have -parallel mpi_omp)
124
125        -cosp       to run with cospv1 or cospv2 [none/v1/v2] (default <$cosp>)
126
127        -rad        radiative code: oldrad, rrtm or ecrad (default <$rad>)
128
129        -nofcm      to compile without fcm
130
131        -SCM        install 1D version automatically
132
133        -debug      compile everything in debug mode
134
135        -benchphysiq   to choose which physics.def package to use in the bench (default <$benchphysiq>)
136
137        -compilephysiq   physics to compile the model with (default <$compphysiq>)
138
139        -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 (default $veget)
140
141        -spla       activate interactive aerosols
142
143        -inlandsis  activate new snow scheme
144
145        -arch       name of the arch to use (default <$arch>)
146
147        -arch_dir   where to find the arch files (default <$arch_dir>)
148
149        -make_j     number of processes to parallelize installations (default <$make_j>)
150
151        -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)
152
153........fin
154                  exit 1;;
155            "-v") version=$2; shift; shift;;
156            "-r") svn_lmdz=$2; shift; shift;;
157            "-d") grid_resolution=$2; shift; shift;;
158            "-unstable") trusting="unstable"; shift;;
159            "-cosp") cosp=$2
160                     case $cosp in
161                         "none"|"v1"|"v2") cosp=$2; shift; shift;;
162                         *) echo "Only none v1 v2 for cosp option"; exit 1
163                     esac;;
164            "-nofcm") compile_with_fcm=0; echo "This option will be reactivated soon (promesse du 8dec2022)"; exit 1;  shift;;
165            "-SCM") SCM=1; shift;;
166            "-rad") rad=$2
167                    case $rad in
168                        "oldrad"|"rrtm"|"ecrad") rad=$2; shift; shift;;
169                        *) echo "Only oldrad rrtm ecrad for rad option"; exit 1
170                    esac;;
171            "-parallel") parallel=$2
172                         case $parallel in
173                             "none"|"mpi"|"omp"|"mpi_omp") parallel=$2; shift; shift;;
174                             *) echo "Only none mpi omp mpi_omp for the parallel option"; exit 1
175                         esac;;
176            "-bench") bench=$2; shift; shift;;
177            "-debug") optim_debug=-debug; shift;;
178            "-name") MODEL=$2; shift; shift;;
179            "-netcdf") netcdf=$2; shift; shift;;
180            "-benchphysiq") benchphysiq=$2; shift; shift;;
181            "-compilephysiq") compphysiq=$2; shift; shift;;
182            "-xios") with_xios=1; shift;;
183            "-arch") arch=$2; shift; shift;;
184            "-arch_dir") arch_dir=$2; shift; shift;;
185            "-veget") veget=$2; shift; shift;;
186            "-spla") aerosols=1; shift;;
187            "-inlandsis") inlandsis=1; shift;;
188            "-make_j") make_j=$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
239    # Name of the model's folder. The convention taken here is that models that requires different compilation sources should have a different names.
240    local xios_name=""
241    if [[ $with_xios = 1 ]]; then xios_name="XIOS"; fi
242    if [[ $MODEL = "" ]]; then MODEL="./LMDZ$version${svn_lmdz}OR$veget$xios_name"; fi
243
244    if [[ $arch_dir = "" ]]; then arch_dir="$MODEL/modipsl/config/IPSLCM7/ARCH/"; fi
245}
246
247function ensure_correct_option_combinations {
248    # Check on veget version
249    if [[ $veget != 'none' && $veget != "CMIP6" && $veget != "orch2.0" && $veget != "orch2.2" ]]; then
250        re='^[0-9]+$'
251        if ! [[ $veget =~ $re ]]; then
252            echo 'Valeur de l option veget non valable'; exit 1
253        fi
254    fi
255
256    ## if also compiling XIOS, parallel must be mpi_omp
257    if [[ $with_xios = 1 && $parallel != "mpi_omp" ]]; then
258        echo "Error, you must set -parallel mpi_omp if you want XIOS"; exit 1
259    fi
260
261    if [[ $cosp = "v2" && $with_xios = 0 ]]; then
262        echo "Error, Cospv2 cannot run without Xios"; exit 1
263    fi
264
265    # STOP if trying to use both ORCHIDEE and Isotopes :
266    if [[ $isotopes = 1 && $veget != "NONE" ]]; then
267      echo "STOP: You cannot run LMDZ with ORCHIDEE and ISOtopes at the same time"; exit 1
268    fi
269
270    # STOP if trying to use both SPLA and Isotopes :
271    if [[ $isotopes = 1 && $aerosols = 1 ]]; then
272      echo "STOP: You cannot run LMDZ with Isotopes and aerosols=spla at the same time"; exit 1
273    fi
274
275    # (Temporary) STOP if trying to use Isotopes with XIOS :
276    # TODO Amaury: check if still relevant
277    if [[ $isotopes = 1 && $with_xios = 1 ]]; then
278      echo "STOP: Isotopes cannont yet be run with XIOS"; exit 1
279    fi
280
281    # (Temporary) Constraints for aerosols=spla :
282    # --> resolution 128x88x79 and rad=rrtm
283    if [[ $aerosols = 1 && $grid_resolution != "128x88x79" ]]; then
284      echo 'For now, <aerosols=spla> requires <resol=128x88x79>, and uses the zoomed grid from gcm.def_zNAfrica_BiJe, for which forcing & initial files are available'
285      echo "Right now resol=<$grid_resolution>"
286      exit 1
287    fi
288
289    if [[ $aerosols = 1 && $rad != "rrtm" ]]; then
290      echo "STOP: For the time being, <aerosols=spla> requires <rad=rrtm>"; exit 1
291    fi
292}
293
294function check_available_software {
295    echo "################################################################"
296    echo "Check if required software is available"
297    echo "################################################################"
298    for logiciel in wget tar gzip make gcc cmake m4 c++; do
299        if [[ $(which "$logiciel") = "" ]]; then
300            echo "You must first install $logiciel on your system"; exit 1
301        fi
302    done
303
304    cat <<eod > tt.f90
305print*,'coucou'
306end
307eod
308    $compiler tt.f90 || a.out
309    ./a.out >| tt
310    if [[ $(< tt sed -e 's/ //g' ) != "coucou" ]]; then
311        echo "problem installing with compiler $compiler"; exit 1
312    fi
313    \rm tt a.out tt.f90
314}
315
316function download_model {
317    if [[ $clean_install = 1 ]]; then rm -rf "$MODEL"; fi
318
319    mkdir -p "$MODEL"
320    MODEL=$(readlink -e -f "$MODEL"); echo "$MODEL"  # absolute path
321    if [[ ! -f "$MODEL/modipsl" ]]; then
322        echo "##########################################################"
323        echo "Download a slightly modified version of  LMDZ"
324        echo "##########################################################"
325        cd "$MODEL"
326        getlog="$(pwd)/get.log"
327        echo "logfile : $getlog"
328        myget "src_archives/$trusting/modipsl.$version.tar.gz" >> get.log 2>&1
329        echo "install_lmdz.sh wget_OK $(date)"
330        gunzip "modipsl.$version.tar.gz" >> get.log 2>&1
331        tar xf "modipsl.$version.tar" >> get.log 2>&1
332        \rm "modipsl.$version.tar"
333    fi
334}
335
336function create_model_tar {  # TODO TEMP while waiting for tar: we copy the base from a local path = IPSLCM7 + ORCH2.2 8504
337    if [[ ! -d ../MODEL_REF ]]; then
338        cd ..
339        mkdir MODEL_REF
340        cd MODEL_REF
341        # Base is IPSLCM7
342        svn co --username icmc_users https://forge.ipsl.fr/igcmg/svn/modipsl/trunk modipsl
343        cd modipsl/util
344        ./model IPSLCM7_work
345        # Remove unused components
346        rm -rf ../oasis3-mct
347        cd ../modeles
348        rm -rf ICOSA_LMDZ ORCHIDEE_4 ORCHIDEE_2_2 NEMO DYNAMICO XIOS INCA
349        # Retrieve orch version
350        svn co svn://forge.ipsl.fr/orchidee/branches/ORCHIDEE_2_2/ORCHIDEE -r 8504
351        # Correct orchidee bug in 8504
352        sed -i"" -e "s/ts.second=dt_routing/ts%second=dt_routing/" -e "380,390 s/USE grid/USE grid, temp_disabled => contfrac/" ORCHIDEE/src_sechiba/routing_native_flow.f90
353
354        cd ../../../script_install
355    fi
356
357    if [[ ! -d "$MODEL" ]]; then
358        \cp -r ../MODEL_REF .
359        mv MODEL_REF "$MODEL"
360    fi
361    MODEL=$(readlink -e -f "$MODEL"); echo "$MODEL"  # absolute path
362}
363
364function init_arch {
365    arch_dir=$(readlink -e -f "$arch_dir")  # full path. readlink must be called *after* the path is created
366    if [[ ! -d $arch_dir ]]; then
367        echo "Error: no arch dir $arch_dir"; exit 1
368    elif [[ ! -f $arch_dir/arch-$arch.path ]]; then
369        echo "Error: no arch-$arch.path in $arch_dir"; exit 1
370    fi
371
372    local fcm_path
373    if [[ -f $arch_dir/arch-$arch.fcm ]]; then
374        fcm_path="$arch_dir/arch-$arch.fcm"
375    else
376        fcm_path="$MODEL/modipsl/modeles/LMDZ/arch/arch-$arch.fcm"
377        if [[ ! -f $fcm_path ]]; then
378            echo "Error: no $fcm_path"; exit 1
379        fi
380    fi
381
382    # check compiler
383    compiler=$(< "$fcm_path" grep "%COMPILER" | sed -e "s/%COMPILER\s*//")
384
385    # load env
386    local env_path=${fcm_path/.fcm/.env}
387    # shellcheck disable=SC1090
388    if [[ -f $env_path ]]; then source "$env_path"; fi
389}
390
391function install_arch {
392    local component=$1
393
394    if [[ ! -f "$MODEL/modipsl/modeles/$component/arch/arch-$arch.fcm" ]]; then
395        \cp -f "$arch_dir/arch-$arch.fcm" "$MODEL/modipsl/modeles/$component/arch"
396        \cp -f "$arch_dir/arch-$arch.path" "$MODEL/modipsl/modeles/$component/arch"
397
398        if [[ $component = "XIOS" ]]; then
399            # Adapt for XIOS, which uses different naming conventions
400            sed -i'' -e "s/%COMPILER/%FCOMPILER/" -e "s/%LINK/%LINKER/" -e "s/-fdefault-real-8//" "$MODEL/modipsl/modeles/XIOS/arch/arch-$arch.fcm"
401        elif [[ $component = "ORCHIDEE" ]]; then
402            if [[ $orcbranch = "/tags/ORCHIDEE_2_0/ORCHIDEE" ]]; then  # 2.0 and before have a different fcm convention
403                sed -i'' -e "s/-I//" -e "s/-L//" "$MODEL/modipsl/modeles/ORCHIDEE/arch/arch-$arch.path"  # /!\ we only replace first occurence on purpose
404            fi
405        fi
406    fi
407}
408
409function install_netcdf {
410    echo "Installing Netcdf"
411    local ncdf_compiler="$compiler"
412
413    if [[ $netcdf = 0 ]]; then
414        ncdfdir=$(nc-config --prefix)
415    else
416        cd "$MODEL"
417
418        # Convert non-basic compiler
419        case $compiler in
420            mpif90) ncdf_compiler=$($compiler --version | head -n 1 | cut -d " " -f -1)
421        esac
422
423        case $ncdf_compiler in
424            gfortran | GNU) ncdf_compiler="gfortran"; opt1="-compiler gnu"; opt2="-CC gcc -FC gfortran -CXX g++";;
425            *)      echo "unexpected compiler $ncdf_compiler for netcdf"; exit 1
426        esac
427
428        case $with_xios in
429            0) script_install_netcdf="install_netcdf4_hdf5_seq.bash"
430               ncdfdir="netcdf4_hdf5_seq"
431               opt_="$opt1";;
432            1) script_install_netcdf="install_netcdf4_hdf5.bash"
433               ncdfdir="netcdf4_hdf5"
434               opt_="$opt2 -MPI $root_mpi";;
435            *) echo "with_xios=$with_xios, should be 0 or 1"; exit 1
436        esac
437        if [[ $netcdf = 1 ]]; then
438           ncdfdir="$MODEL/$ncdfdir"
439        else
440           mkdir -p "$netcdf"; ncdfdir="$netcdf/$ncdfdir"
441        fi
442
443        echo "Repertoire netcdf $ncdfdir"
444        if [[ ! -d $ncdfdir ]]; then
445            netcdflog=$(pwd)/netcdf.log
446            echo "----------------------------------------------------------"
447            echo "Compiling the Netcdf library"
448            echo "----------------------------------------------------------"
449            echo "log file : $netcdflog"
450            myget script_install/$script_install_netcdf >> "$netcdflog" 2>&1
451            chmod u=rwx $script_install_netcdf
452            # shellcheck disable=SC2086
453            ./$script_install_netcdf -prefix "$ncdfdir" $opt_ >> "$netcdflog" 2>&1
454        fi
455
456        # Add to path
457        export PATH="$ncdfdir/bin:$PATH"
458
459        #----------------------------------------------------------------------------
460        # LF rajout d'une verrue, pour une raison non encore expliquee,
461        # la librairie est parfois rangée dans lib64 et non dans lib
462        # par certains compilateurs
463        if [[ ! -e lib && -d lib64 ]]; then ln -s lib64 lib; fi
464        #----------------------------------------------------------------------------
465
466        echo "install_lmdz.sh netcdf_OK $(date)"
467    fi
468
469    cat >test_netcdf90.f90 <<EOF
470    use netcdf
471    print *, "NetCDF library version: ", nf90_inq_libvers()
472    end
473EOF
474
475    if $ncdf_compiler -I"$ncdfdir"/include test_netcdf90.f90 -L"$ncdfdir"/lib -lnetcdff \
476              -lnetcdf -Wl,-rpath="$ncdfdir"/lib && ./a.out
477    then
478        \rm test_netcdf90.f90 a.out
479    else
480        cat <<EOF
481Failed test program using NetCDF-Fortran. You can:
482- check that you have NetCDF-Fortran installed in your system
483- or specify an installation directory with option -netcdf of install_lmdz.sh
484- or download and compile NetCDF-Fortran with option -netcdf 1 of nstall_lmdz.sh
485EOF
486        exit 1
487    fi
488
489    # Compile NetCDF95
490    cd "$MODEL/modipsl/modeles/LMD"*
491    echo "Installing NetCDF95"
492    cd "$MODEL"
493    myget src_archives/netcdf/NetCDF95-0.3.tar.gz
494    tar -xf NetCDF95-0.3.tar.gz
495    \rm NetCDF95-0.3.tar.gz
496    cd NetCDF95-0.3
497    mkdir -p build && cd build
498    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"
499    make install
500}
501
502function install_IOIPSL {
503    install_arch "IOIPSL"
504
505    cd "$MODEL/modipsl/modeles/IOIPSL"
506    ioipsllog="$(pwd)/ioipsl.log"
507    echo "Compiling IOIPSL, the interface library with Netcdf $(date) (log: $ioipsllog)"
508
509    if ! ./makeioipsl_fcm -arch "$arch" -job 8 > "$ioipsllog" 2>&1; then
510        echo "IOIPSL compile failed, exiting"; exit 1
511    fi
512
513    # Link to modipsl/bin
514    cp -f bin/* ../../bin
515
516    echo "IOIPSL compiled $(date)"
517
518    IOIPSL_LIBDIR_="$MODEL/modipsl/modeles/IOIPSL/lib"
519    IOIPSL_INCDIR_="$MODEL/modipsl/modeles/IOIPSL/inc"
520}
521
522function install_XIOS {
523    if [[ $with_xios = 1 ]]; then
524        cd "$MODEL/modipsl/modeles"
525        xioslog="$(pwd)/XIOS/xios.log"
526        echo "##########################################################"
527        echo "Compiling XIOS (log $xioslog) $(date)"
528        echo "##########################################################"
529
530        # Download XIOS
531        local xios_http="http://forge.ipsl.fr/ioserver/svn/XIOS2/branches/xios-2.6"
532        local xios_rev="2568"
533       
534        cd "$MODEL/modipsl/modeles"
535        set +e; svn co -r $xios_rev $xios_http XIOS; set -e
536
537        cd XIOS
538
539        install_arch "XIOS"
540
541        echo "Starting XIOS compilation"
542        if ! ./make_xios --arch "$arch" --job 8 > "$xioslog" 2>&1; then
543            echo "XIOS compilation failed, exiting"; exit 1
544        fi
545
546        echo "Compiled XIOS $(date)"
547    fi
548
549    XIOS_LIBDIR_="$MODEL/modipsl/modeles/XIOS/lib"
550    XIOS_INCDIR_="$MODEL/modipsl/modeles/XIOS/inc"
551}
552
553function get_orchidee_version {  # Set / Check ORCHIDEE version
554    local fetch_rev=""
555    orcbranch=""
556    case $veget in
557        "none") fcm_veget_version="false";;
558        "orch2.0" | "CMIP6") fcm_veget_version=orchidee2.0; fetch_rev=7906;;  # in previous tar we used 6592 but with some modifications to xios_orchidee.f90, which got integrated in 7906
559        "orch2.2") fcm_veget_version=orchidee2.1; orcbranch="ORCHIDEE_2_2" ;; # the bundled version
560        *) fetch_rev=$veget
561    esac
562
563    if [[ -n $fetch_rev ]]; then
564        echo "Fetching orch $fetch_rev from the repository"
565        orcbranch=$(svn log -v -q svn://forge.ipsl.fr/orchidee/ -r "$fetch_rev" | grep ORCHIDEE | head -1 | sed -e 's:ORCHIDEE/.*$:ORCHIDEE:' | awk '{print $2}')
566        echo "branch is $orcbranch"
567        if [[ $fetch_rev -lt 4465 ]]; then echo 'ORCHIDEE version must be >=4465, exiting'; exit 1; fi
568        echo "IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at orchidee-help@listes.ipsl.fr"
569        cd "$MODEL/modipsl/modeles"
570        svn co -r "$fetch_rev" "svn://forge.ipsl.fr/orchidee/$orcbranch" || (rm -rf ORCHIDEE && svn co -r "$fetch_rev" "svn://forge.ipsl.fr/orchidee/$orcbranch")  # if orch dir exists and is from a different branch, need to delete it first (but we don't want to do this all the time, as it would require a recompile for the same code)
571        cd -
572    fi
573
574    # Check parallel LMDZ+ORCH
575    if [[ (! $veget = "none") && $parallel = "none" && ($used_lmdz_rev -lt 4894) ]]; then
576        echo "LMDZ revision must be >=4894 for orchidee without parallel support. Upgrade lmdz or use -parallel mpi_omp."; exit 1
577    fi
578}
579
580function compile_orchidee {
581    install_arch "ORCHIDEE"
582
583    if [[ $veget != "none" ]]; then
584        cd "$MODEL/modipsl/modeles/ORCHIDEE"
585
586        orchideelog="$(pwd)/orchidee.log"
587        echo "Compiling ORCHIDEE, the continental surface model (log $orchideelog) $(date)"
588
589        local xios_orchid opt_orc
590        if [[ $with_xios = 1 ]]; then
591            xios_orchid="-xios";
592        else
593            xios_orchid="-noxios"
594        fi
595        if [[ $optim_debug = "-debug" ]]; then
596            opt_orc="-debug";
597        else
598            opt_orc="-prod"
599        fi
600
601        local varenv="IOIPSL_LIBDIR_=$IOIPSL_LIBDIR_ IOIPSL_INCDIR_=$IOIPSL_INCDIR_ XIOS_INCDIR_=$XIOS_INCDIR_ XIOS_LIBDIR_=$XIOS_LIBDIR_"
602        if [[ $parallel = "none" ]]; then
603            echo "$varenv ./makeorchidee_fcm $xios_orchid $opt_orc -parallel none -arch $arch -j $make_j" > compile.sh
604        else
605            if [[ ! -d src_parallel ]]; then
606               echo "Orchidee version too old for parallel support"; exit 1
607            fi
608            {
609                echo "$varenv ./makeorchidee_fcm -j $make_j $xios_orchid $opt_orc -parallel $parallel -arch $arch"
610            } > compile.sh
611        fi
612        chmod +x compile.sh
613        echo "Compiling ORCHIDEE using $(\cat compile.sh)"
614        if ! ./compile.sh > "$orchideelog" 2>&1; then
615            echo "ORCHIDEE compilation failed, exiting"; exit 1
616        fi
617        echo "Compiled ORCHIDEE $(date)"
618    fi
619
620    ORCH_INCDIR_="$MODEL/modipsl/modeles/ORCHIDEE/inc"
621    ORCH_LIBDIR_="$MODEL/modipsl/modeles/ORCHIDEE/lib"
622}
623
624function get_lmdz_version {
625    LMDZPATH=$(readlink -e -f "$MODEL/modipsl/modeles/LMD"*)
626    cd "$LMDZPATH"
627    lmdzlog="$(pwd)/lmdz.log"
628
629    used_lmdz_rev=$svn_lmdz
630    if [[ -n $svn_lmdz ]]; then
631        local lmdzbranch
632        echo "Fetching LMDZ $svn_lmdz from the repository"
633        lmdzbranch=$(svn log -v -q https://svn.lmd.jussieu.fr/LMDZ -r "$svn_lmdz" | grep LMDZ | head -1 | sed -e 's:trunk/.*$:trunk:' | awk '{print $2}')
634        cd "$MODEL/modipsl/modeles"
635        svn co -r "$svn_lmdz" "https://svn.lmd.jussieu.fr/LMDZ$lmdzbranch" LMDZ || (rm -rf LMD* && svn co -r "$svn_lmdz" "https://svn.lmd.jussieu.fr/LMDZ$lmdzbranch" LMDZ)  # if lmdz dir exists and is from a different branch, need to delete it first (but we don't want to do this all the time, as it would require a recompile for the same code)
636        cd -
637    else  # get svn from info
638         set +e; used_lmdz_rev=$(svn info | grep "Last Changed Rev" | cut -c 19-); set -e
639         if [[ -z $used_lmdz_rev ]]; then  # svn info failed
640            used_lmdz_rev=$(grep 'Revision: [0-9]' "$MODEL"/Read*.md | awk ' { print $2 } ' 2>/dev/null)
641            if [[ -z $used_lmdz_rev ]]; then echo "Could not determine lmdz version. This is likely an issue with the .tar itself, please report to LMDZ team."; exit 1; fi
642         fi
643    fi
644}
645
646function compile_lmdz {
647    install_arch "LMDZ"
648    cd "$LMDZPATH"
649
650    if [[ $used_lmdz_rev -le 4185 ]]; then
651        exe_name="bin/gcm_${grid_resolution}_phy${compphysiq}_${suff_para}${suff_orc}${suff_aer}${suff_iso}.e"
652    else
653        exe_name="bin/gcm_${grid_resolution}_phy${compphysiq}_${rad}${suff_para}${suff_orc}${suff_aer}${suff_iso}.e"
654    fi
655
656    local opt_rad
657    case $rad in
658        oldrad) iflag_rrtm=0; NSW=2; opt_rad="";;
659        rrtm)   iflag_rrtm=1; NSW=6
660            if [[ $used_lmdz_rev -le 4185 ]]; then
661                opt_rad="-rrtm true"
662            else
663                opt_rad="-rad rrtm"
664            fi;;
665        ecrad)  iflag_rrtm=2; NSW=6; opt_rad="-rad ecrad";;
666        *) echo "Only oldrad rrtm ecrad for rad option"; exit 1
667    esac
668    if [[ $used_lmdz_rev -le 4185 && $rad = "ecrad" ]]; then
669        echo "ecrad only available for LMDZ rev starting with 4186 "; exit 1
670    fi
671
672    # Compile
673    local varenv="IOIPSL_LIBDIR_=\"$IOIPSL_LIBDIR_\" IOIPSL_INCDIR_=\"$IOIPSL_INCDIR_\" ORCH_INCDIR_=\"$ORCH_INCDIR_\" ORCH_LIBDIR_=\"$ORCH_LIBDIR_\" XIOS_INCDIR_=\"$XIOS_INCDIR_\" XIOS_LIBDIR_=\"$XIOS_LIBDIR_\""
674    makelmdz="makelmdz_fcm $optim_debug -arch $arch -j $make_j"
675    local para_compile_opt="-mem -parallel $parallel"; if [[ $parallel = "none" ]]; then para_compile_opt=""; fi
676    echo "$varenv ./$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
677    echo "Compiling lmdz using $(\cat compile.sh) (log: $lmdzlog) $(date)"
678    chmod +x ./compile.sh
679    if ! ./compile.sh > "$lmdzlog" 2>&1; then
680        echo "LMDZ compilation failed, exiting"; exit 1
681    fi
682    echo "Finished LMDZ compilation $(date)"
683
684    # Check executable
685    if [[ ! -f $exe_name ]]; then
686        echo "Compilation failed, can't find the executable"; exit 1
687    else
688        echo "Compilation successfull, the executable is $exe_name $(date)"
689    fi
690}
691
692function run_bench {
693    cd "$MODEL/modipsl/modeles/LMDZ"*
694
695    if [[ $bench = "tuto" ]]; then
696        myget "Training/tutorial.tar"; tar xf tutorial.tar; cd TUTORIAL
697        ./init.sh
698    elif [[ $bench = 1 ]]; then
699        \rm -rf "BENCH${grid_resolution}"
700        local bench=bench_lmdz_${grid_resolution}
701        myget "3DBenchs/$bench.tar.gz"
702        tar xf "$bench.tar.gz"
703
704        if [[ $cosp = "v1" || $cosp = "v2" ]]; then
705            cd "BENCH${grid_resolution}"
706            # copier les fichiers namelist input et output our COSP
707            cp ../DefLists/cosp*_input_nl.txt .
708            cp ../DefLists/cosp*_output_nl.txt .
709            # Activer la cles ok_cosp pour tourner avec COSP
710            sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp
711            \mv -f tmp config.def
712            cd ..
713        fi
714
715        if [[ -n "$benchphysiq" ]]; then
716            cd "BENCH${grid_resolution}"
717            if [[ -f "physiq.def_${benchphysiq}" ]]; then
718                cp "physiq.def_${benchphysiq}" benchphysiq.def
719                echo "using physiq.def_${benchphysiq}"
720            else
721                echo "using standard physiq.def"
722            fi
723            cd ..
724        else
725            echo "using standard physiq.def"
726        fi
727
728        if [[ $with_xios = 1 ]]; then
729            cd "BENCH${grid_resolution}"
730            cp ../DefLists/iodef.xml .
731            cp ../DefLists/context_lmdz.xml .
732            cp ../DefLists/field_def_lmdz.xml .
733            # A raffiner par la suite
734            echo "A FAIRE : Copier les *xml en fonction de l option cosp"
735            cp ../DefLists/field_def_cosp*.xml .
736            cp ../DefLists/file_def_hist*xml .
737            # adapt iodef.xml to use attached mode
738            sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' \
739                iodef.xml > tmp
740            \mv -f tmp iodef.xml
741
742            # and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
743            # except for histday
744            for histfile in file_def_hist*xml; do
745                if [[ "$histfile" = "file_def_histday_lmdz.xml" ]]; then
746                    sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' \
747                        "$histfile" > tmp
748                    \mv -f tmp "$histfile"
749                    sed -e 's@output_level="_AUTO_"@output_level="5"@' "$histfile" \
750                        > tmp
751                    \mv -f tmp "$histfile"
752                    sed -e 's@compression_level="2"@compression_level="0"@' \
753                        "$histfile" > tmp
754                    \mv -f tmp "$histfile"
755                else
756                    sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
757                        "$histfile" > tmp
758                    \mv -f tmp "$histfile"
759                fi
760            done
761            # and add option "ok_all_xml=y" in config.def
762            echo "### XIOS outputs" >> config.def
763            echo 'ok_all_xml=.true.' >> config.def
764
765            #activer les sorties pour Cosp
766            if [[ "$cosp" = "v1" ]]; then
767                sed -i'' -e 's@enabled=".FALSE."@enabled=".TRUE."@' \
768                         -e 's@output_level="_AUTO_"@output_level="5"@' \
769                         -e 's@compression_level="2"@compression_level="0"@' \
770                         file_def_histdayCOSP_lmdz.xml
771            fi
772            if [[ "$cosp" = "v2" ]]; then
773                sed -i'' -e 's@compression_level="2"@compression_level="0"@' file_def_histdayCOSPv2_lmdz.xml
774                for type_ in hf day mth; do
775                    file=file_def_hist${type_}COSP
776                    sed -i'' -e 's@src="./'${file}'_lmdz.xml"@src="./'${file}'v2_lmdz.xml"@' context_lmdz.xml
777                done
778                sed -i'' -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' field_def_lmdz.xml
779            fi
780
781            cd ..
782        fi
783
784        # Cas Bench avec ecrad
785        if [[ $rad = "ecrad" ]]; then
786            cd "BENCH${grid_resolution}"
787            cp  ../DefLists/namelist_ecrad .
788            cp -r ../libf/phylmd/ecrad/data .
789            cd ..
790        fi
791
792        # Adjusting bench physiq.def to radiative code chosen
793        cd "BENCH${grid_resolution}"
794        sed -e 's/iflag_rrtm=.*.$/iflag_rrtm='$iflag_rrtm'/' \
795            -e 's/NSW=.*.$/NSW='$NSW'/' physiq.def > tmpdef
796        \mv tmpdef physiq.def
797        cd ..
798
799        cp "$exe_name" "BENCH${grid_resolution}/gcm.e"
800        cd "BENCH${grid_resolution}"
801
802        local bench_cmd="./bench.sh"
803        if [[ ${parallel:0:3} = "mpi" ]]; then
804            # Lancement avec deux procs mpi et 2 openMP
805            echo "export OMP_STACKSIZE=800M" > bench.sh
806            if [[ "${parallel:4:3}" = "omp" ]]; then
807                echo "export OMP_NUM_THREADS=2" >> bench.sh
808            fi
809            if [[ $cosp = "v1" || $cosp = "v2" ]]; then
810                echo "ulimit -s 200000" >> bench.sh
811            else
812                echo "ulimit -s unlimited" >> bench.sh
813            fi
814            if which mpirun > /dev/null 2>&1; then
815                echo "mpirun -np 2 gcm.e > listing 2>&1" >> bench.sh
816            elif grep -q "Adastra" /etc/motd; then
817                local account
818                account=$(/usr/sbin/my_project.py -l 2>&1 | head -1 | cut -d " " -f 3- | cut -c 5-)
819                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"
820                echo "./gcm.e > listing 2>&1" >> bench.sh
821            else
822                echo "Error: No command found to run parallel bench"; exit 1
823            fi
824            # Add rebuild, using reb.sh if it is there
825            cat <<EOF >> bench.sh
826if [[ -f reb.sh ]]; then
827  ./reb.sh histday; ./reb.sh histmth; ./reb.sh histhf;
828  ./reb.sh histins; ./reb.sh stomate_history;
829  ./reb.sh sechiba_history; ./reb.sh sechiba_out_2
830fi
831EOF
832        else
833            echo "./gcm.e > listing 2>&1" > bench.sh
834        fi
835        # Getting orchidee stuff
836        if [[ $veget = 'CMIP6' || $veget = "orch2.0" ]]; then  # TODO once we have a 2.2 bench, add it here (or in planned separate bench script)
837            echo 'myget 3DBenchs/BENCHCMIP6.tar.gz'
838            myget 3DBenchs/BENCHCMIP6.tar.gz
839            tar xvzf BENCHCMIP6.tar.gz
840            sed -e "s:VEGET=n:VEGET=y:" config.def > tmp
841            mv -f tmp config.def
842            if [[ $with_xios = 1 ]]; then
843                cp ../../ORCHIDEE/src_xml/context_orchidee.xml .
844                echo '<context id="orchidee" src="./context_orchidee.xml"/>' > add.tmp
845                cp ../../ORCHIDEE/src_xml/field_def_orchidee.xml .
846                cp ../../ORCHIDEE/src_xml/file_def_orchidee.xml .
847                cp ../../ORCHIDEE/src_xml/file_def_input_orchidee.xml .
848                if [[ -f ../../ORCHIDEE/src_xml/context_input_orchidee.xml ]]; then
849                       cp ../../ORCHIDEE/src_xml/context_input_orchidee.xml .
850                       echo '<context id="orchidee" src="./context_input_orchidee.xml"/>' >> add.tmp
851                fi
852                sed -e '/id="LMDZ"/r add.tmp' iodef.xml > tmp
853                mv tmp iodef.xml
854                sed -e'{/sechiba1/ s/enabled="_AUTO_"/type="one_file" enabled=".TRUE."/}' \
855                    file_def_orchidee.xml > tmp
856                \mv -f tmp file_def_orchidee.xml
857                sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
858                    file_def_orchidee.xml > tmp
859                \mv -f tmp file_def_orchidee.xml
860                sed -e 's@output_level="_AUTO_"@output_level="1"@' \
861                    file_def_orchidee.xml > tmp
862                \mv -f tmp file_def_orchidee.xml
863                sed -e 's@output_freq="_AUTO_"@output_freq="1d"@' \
864                    file_def_orchidee.xml > tmp
865                \mv -f tmp file_def_orchidee.xml
866                sed -e 's@compression_level="4"@compression_level="0"@' \
867                    file_def_orchidee.xml > tmp
868                \mv -f tmp file_def_orchidee.xml
869                sed -e 's@XIOS_ORCHIDEE_OK = n@XIOS_ORCHIDEE_OK = y@' \
870                    orchidee.def > tmp
871                \mv -f tmp orchidee.def
872            fi
873        fi
874
875        if [[ -f ../arch.env ]]; then source ../arch.env; fi
876
877        echo "EXECUTION DU BENCH"
878        date
879        if (! $bench_cmd > out.bench 2>&1) || ! (tail -n 1 listing | grep "Everything is cool"); then
880            tail listing
881            echo "Bench FAILED, exiting"; exit 1
882        fi
883        date
884        tail listing
885    fi
886
887    # 1D case
888    if [[ $SCM = 1 ]]; then
889        cd "$MODEL"
890        myget 1D/1D.tar.gz
891        tar xf 1D.tar.gz
892        cd 1D
893        if [[ $rad = "oldrad" ]]; then
894            sed -i'' -e 's/^rad=.*$/rad=oldrad/' run.sh
895            sed -i'' -e 's/^rad=.*$/rad=oldrad/' bin/compile
896        elif [[ $rad = ecrad ]] ; then
897                        sed -i'' -e 's/^rad=.*$/rad=ecrad/' run.sh
898                        sed -i'' -e 's/^rad=.*$/rad=ecrad/' bin/compile
899                    fi
900        echo "Running 1D/run.sh, log in $(pwd)/run1d.log"
901        ./run.sh > "$(pwd)/run1d.log" 2>&1
902    fi
903}
904
905# If sourced: returns, else run setup
906if [[ ! "${BASH_SOURCE[0]}" = "$0" ]]; then return 0; fi
907
908echo "install_lmdz.sh DEBUT $(date)"
909
910set_default_params
911read_cmdline_args "$@"
912ensure_correct_option_combinations
913#download_model
914create_model_tar
915init_arch
916check_available_software
917get_lmdz_version
918get_orchidee_version
919install_netcdf
920install_IOIPSL
921install_XIOS
922compile_orchidee
923compile_lmdz
924run_bench
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