source: BOL/script_install/install_lmdz.sh @ 3928

Last change on this file since 3928 was 3922, checked in by Laurent Fairhead, 3 years ago

New install with updated CMIP6 vegetation by default
LF/AS
File size: 43.5 KB
Line 
1#!/bin/bash
2
3###########################################################################
4# Author : Laurent Fairhead et Frédéric Hourdin
5# Usage  : install_lmdz.sh -help
6#
7# bash installation script of the LMDZ model on different computer types :
8# Linux PC, "mesocentre" (IPSL-UPMC, IPSL-X), super-computer (IDRIS)
9#
10# The model is downloaded in the following directory tree
11# $MODEL/modipsl/modeles/...
12# using the "modipsl" infrastructure created by the "IPSL"
13# for coupled (atmosphere/ocean/vegetation/chemistry) climate modeling
14# activities.
15# Here we only download atmospheric (LMDZ) and vegetation (ORCHIDEE)
16# components.
17#
18# The sources of the models can be found in the "modeles" directory.
19# In the present case, LMDZ, ORCHIDEE, and IOIPSL or XIOS (handling of input-outputs
20# using the NetCDF library).
21#
22# The script downloads various source files (including a version of NetCDF)
23# and utilities, compiles the model, and runs a test simulation in a
24# minimal configuration.
25#
26# Prerequisites : pgf90/gfortran, bash or ksh, wget , gunzip, tar, ...
27#
28# Modif 18/11/2011
29#    changes for option real 8.
30#      We compile with -r8 (or equivalent) and -DNC_DOUBLE for the GCM
31#      but with -r4 for netcdf. Variable real must be set to
32#      r4 or r8 at the beginning of the script below.
33#
34###########################################################################
35
36echo install.sh DEBUT `date`
37
38set -e
39
40################################################################
41# Choice of installation options
42################################################################
43
44# A function to fetch files either locally or on the internet
45function myget { #1st and only argument should be file name
46  # Path on local computer where to look for the datafile
47  if [ -f /u/lmdz/WWW/LMDZ/pub/$1 ] ; then
48    \cp -f -p /u/lmdz/WWW/LMDZ/pub/$1 .
49  elif [ -f ~/LMDZ/pub/$1 ] ; then
50    \cp -f -p ~/LMDZ/pub/$1 .
51  else
52    wget -nv http://www.lmd.jussieu.fr/~lmdz/pub/$1
53    #dir=~/LMDZ/pub/`dirname $1` ; mkdir -p $dir ; cp -r `basename $1` $dir
54  fi
55}
56
57# 04_2021 : tester si r4 marche encore !
58#real=r4
59real=r8
60
61#########################################################################
62# Valeur par défaut des parametres
63#########################################################################
64svn=""
65#version=trunk
66version=20210320.trunk
67getlmdzor=1
68netcdf=1   #  1 for automatic installation
69           #  0 for no installation
70           #  /.../../netcdf-4.0.1 if wanting to link with an already
71           #  compiled netcdf library (implies to check option compatibility)
72check_linux=1
73ioipsl=1
74bench=1
75pclinux=1
76pcmac=0 # default: not on a Mac
77compiler=gfortran
78SCM=0
79# surface/vegetation scheme treatment
80# controlled by the single variable veget which can have the following values
81# - NONE: bucket scheme (default)
82# - CMIP6: orchidee version used in CMIP exercise, rev 5661
83# - number: orchidee version number (not yet implemented)
84veget=NONE
85# choose the resolution for the bench runs
86# grid_resolution= 32x24x11 or 48x36x19 for tests (test without ORCHIDEE)
87#                  96x71x19  standard configuration
88grid_resolution=144x142x79
89grid_resolution=96x95x39
90grid_resolution=48x36x19
91grid_resolution=32x32x39
92# choose the physiq version you want to test
93#physiq=NPv6.0.14splith
94physiq=
95
96## parallel can take the values none/mpi/omp/mpi_omp
97parallel=mpi_omp
98parallel=none
99idris_acct=lmd
100OPT_GPROF=""
101OPT_MAKELMDZ=""
102MODEL=""
103
104## also compile XIOS? (and more recent NetCDF/HDF5 libraries) Default=no
105with_xios="n"
106opt_makelmdz_xios=""
107
108## compile_with_fcm=1 : use makelmdz_fcm (1) or makelmdz (0)
109compile_with_fcm=1
110cosp=0 ; opt_cosp1=""
111cosp=0 ; opt_cosp2=""
112cosp=0 ; opt_cospv2=""
113opt_cosp=""
114
115# Check if on a Mac
116if [ `uname` = "Darwin" ]
117then
118    pcmac=1
119    export MAKE=make
120fi
121#echo "pcmac="$pcmac
122
123env_file=""
124
125#########################################################################
126#  Options interactives
127#########################################################################
128while (($# > 0))
129   do
130   case $1 in
131     "-h") cat <<........fin
132    $0 [ -v version ] [ -r svn_release ]
133           [ -parallel PARA ] [ -d GRID_RESOLUTION ] [ -bench 0/1 ]
134           [-name LOCAL_MODEL_NAME] [-gprof] [-opt_makelmdz]
135
136    -v       "version" like 20150828.trunk
137             see http://www.lmd.jussieu.fr/~lmdz/Distrib/LISMOI.trunk
138
139    -r       "svn_release" : either the svn release number or "last"
140   
141    -compiler gfortran|ifort|pgf90 (default: gfortran)
142
143    -parallel PARA : can be mpi_omp (mpi with openMP) or none (for sequential)
144
145    -d        GRID_RESOLUTION should be among the available benchs if -bench 1
146              among which : 48x36x19, 48x36x39
147              if wanting to run a bench simulation in addition to compilation
148              default : 48x36x19
149
150    -bench     activating the bench or not (0/1). Default 1
151
152    -name      LOCAL_MODEL_NAME : default = LMDZversion.release
153
154    -netcdf    PATH : full path to an existing installed NetCDF library
155               (without -netcdf: also download and install the NetCDF library) 
156   
157    -xios      also download and compile the XIOS library
158               (requires the NetCDF4-HDF5 library, also installed by default)
159               (requires to also have -parallel mpi_omp)
160
161    -gprof     to compile with -pg to enable profiling with gprof
162
163    -cosp      to compile with cosp(v1)
164 
165    -cosp2      to compile with cosp(1v2)
166
167    -cospv2      to compile with cosp(v2)
168
169    -nofcm     to compile without fcm
170
171    -SCM        install 1D version automatically
172
173    -debug      compile everything in debug mode
174
175    -opt_makelmdz     to call makelmdz or makelmdz_fcm with additional options
176
177    -physiq    to choose which physics package to use
178
179    -env_file  specify an arch.env file to overwrite the existing one
180
181    -veget surface model to run [NONE/CMIP6/xxxx]
182
183........fin
184     exit ;;
185     "-v") version=$2 ; shift ; shift ;;
186     "-r") svn=$2 ; shift ; shift ;;
187     "-compiler") compiler=$2
188                  case $compiler in
189                    "gfortran"|"ifort"|"pgf90") compiler=$2 ; shift ; shift ;;
190                    *) echo "Only gfortran , ifort or pgf90 for the compiler option" ; exit
191                  esac ;;
192     "-d") grid_resolution=$2 ; shift ; shift ;;
193     "-gprof") OPT_GPROF="-pg" ; shift ;;
194     "-cosp") cosp=1 ; opt_cosp1="-cosp true" ; shift ;;
195     "-cosp2") cosp2=1 ; opt_cosp2="-cosp2 true" ; shift ;;
196     "-cospv2") cospv2=1 ; opt_cospv2="-cospv2 true" ; shift ;;
197     "-nofcm") compile_with_fcm=0 ; shift ;;
198     "-SCM") SCM=1 ; shift ;;
199     "-opt_makelmdz") OPT_MAKELMDZ="$2" ; shift ; shift ;;
200     "-parallel") parallel=$2
201                  case $parallel in
202                    "none"|"mpi"|"omp"|"mpi_omp") parallel=$2 ; shift ; shift ;;
203                    *) echo Only none mpi omp mpi_omp for the parallel option ; exit
204                  esac ;;
205     "-bench") bench=$2 ; shift ; shift ;;
206     "-debug") optim=-debug ; shift ;;
207     "-name") MODEL=$2 ; shift ; shift ;;
208     "-netcdf") netcdf=$2 ; shift ; shift ;;
209     "-physiq") physiq=$2 ; shift ; shift ;;
210     "-xios") with_xios="y" ; shift ;;
211     "-env_file") env_file=$2 ; shift ; shift ;;
212     "-veget") veget=$2 ; shift ; shift ;;
213     *) ./install_lmdz.sh -h ; exit
214   esac
215done
216
217# Check on veget version
218#if [ "$veget" != 'NONE'  -a "$veget" != "CMIP6" -a "$veget" != +([0-9]) ] ; then
219if [ $veget != 'NONE'   -a $veget != "CMIP6" ] ; then
220    re='^[0-9]+$'
221    if ! [[ $veget =~ $re ]] ; then
222        echo 'Valeur de l option veget non valable' 
223        exit
224    fi
225fi
226
227#Define veget-related suffix for gcm name
228if [ "$veget" = 'NONE' ] ; then
229    suff_orc=''
230    #For use with tutorial, orchidee_rev is also defined (will be written in surface_env at the end of the script)
231    orchidee_rev=''
232else 
233    suff_orc='_orch' 
234fi
235
236
237if [ $parallel = none ] ; then sequential=1; suff_exe='_seq' ; else sequential=0; suff_exe='_para_mem' ; fi 
238
239#Chemin pour placer le modele
240if [ "$MODEL" = "" ] ; then MODEL=./LMDZ$version$svn$optim ; fi
241
242
243arch=local
244
245
246if [ $compiler = g95 ] ; then echo g95 is not supported anymore ; exit ; fi
247
248################################################################
249# Specificite des machines
250################################################################
251
252hostname=`hostname`
253if [ "$pclinux" = 1 ] ; then o_ins_make="-t g95" ; else o_ins_make="" ; fi
254
255case ${hostname:0:5} in
256
257   jean-)   compiler="mpiifort" ;
258            par_comp="mpiifort" ;
259            o_ins_make="-t jeanzay" ;
260            make=gmake ;
261            module purge
262            module load intel-compilers/19.0.4 ;
263            #module load intel-mpi/19.0.4 ;
264            #module load intel-mkl/19.0.4 ;
265            module load hdf5/1.10.5-mpi ;
266            module load netcdf/4.7.2-mpi ;
267            module load netcdf-fortran/4.5.2-mpi ;
268            module load subversion/1.9.7 ;
269            export NETCDF_LIBDIR=./
270            export NETCDFFORTRAN_INCDIR=./
271            export NETCDFFORTRAN_LIBDIR=./
272            arch=X64_JEANZAY ;;
273
274   cicla|camel)   compiler="gfortran" ;
275            if [ $parallel != none ] ; then
276              module load openmpi/1.6.5-gfortran ;
277              root_mpi=$MPI_HOME ;
278              path_mpi=$root_mpi/bin ;
279              par_comp=${path_mpi}/mpif90 ;
280              mpirun=${path_mpi}/mpirun ;
281            fi ;
282            arch=local  ;
283            make=make ;
284            o_ins_make="-t g95" ;;
285           
286   *)       if [ $parallel = none -o -f /usr/bin/mpif90 ] ; then
287                path_mpi=`which mpif90 | sed -e s:/mpif90::` ;
288                if [ -d /usr/lib64/openmpi ] ; then
289                  root_mpi="/usr/lib64/openmpi"
290                else
291                  root_mpi="/usr"
292                fi
293            # For Scientifique Linux with gfortran at LMD :
294            elif [ -f /usr/lib64/openmpi/1.4.5-gfortran/bin/mpif90 -a $compiler = "gfortran" ] ; then
295                path_mpi=/usr/lib64/openmpi/1.4.5-gfortran/bin ;
296                root_mpi=/usr/lib64/openmpi/1.4.5-gfortran ;
297                export LD_LIBRARY_PATH=${root_mpi}/lib:$LD_LIBRARY_PATH
298            # For Scientifique Linux with ifort at LMD :
299            elif [ -f /usr/lib64/openmpi/1.4.5-ifort/bin/mpif90 -a $compiler = "ifort" ] ; then
300                path_mpi=/usr/lib64/openmpi/1.4.5-ifort/bin ;
301                root_mpi=/usr/lib64/openmpi/1.4.5-ifort ;
302                export LD_LIBRARY_PATH=${root_mpi}/lib:$LD_LIBRARY_PATH
303            # For Scientifique Linux with pgf90 at LMD :
304            elif [ -f /usr/lib64/openmpi/1.4.5-ifort/bin/mpif90 -a $compiler = "pgf90" ] ; then
305                path_mpi=/usr/lib64/openmpi/1.4.5-pgf/bin ;
306                root_mpi=/usr/lib64/openmpi/1.4.5-pgf ;
307                export LD_LIBRARY_PATH=${root_mpi}/lib:$LD_LIBRARY_PATH
308            else
309               echo "Cannot find mpif90" ;
310               if [ $parallel = none ] ; then exit ; fi ;
311            fi ;
312            par_comp=${path_mpi}/mpif90 ;
313            mpirun=${path_mpi}/mpirun ;
314            arch=local  ;
315            make=make ;
316            o_ins_make="-t g95"
317esac
318
319# Flags for parallelism:
320if [ $parallel != none ] ; then
321  # MPI_LD are the flags needed for linking with MPI
322  MPI_LD="-L${root_mpi}/lib -lmpi"
323  if [ "$compiler" = "gfortran" ] ; then
324    # MPI_FLAGS are the flags needed for compilation with MPI
325    MPI_FLAGS="-fcray-pointer"
326    # OMP_FLAGS are the flags needed for compilation with OpenMP
327    OMP_FLAGS="-fopenmp -fcray-pointer"
328    # OMP_LD are the flags needed for linking with OpenMP
329    OMP_LD="-fopenmp"
330  elif [ "$compiler" = "ifort" ] ; then
331    MPI_FLAGS=""
332    OMP_FLAGS="-openmp"
333    OMP_LD="-openmp"
334  else # pgf90
335    MPI_FLAGS=""
336    OMP_FLAGS="-mp"
337    OMP_LD="-mp"
338  fi
339fi
340
341#####################################################################
342# Test for old gfortran compilers
343# If the compiler is too old (older than 4.3.x) we test if the
344# temporary gfortran44 patch is available on the computer in which
345# case the compiler is changed from gfortran to gfortran44
346# Must be aware than parallelism can not be activated in this case
347#####################################################################
348
349if [ "$compiler" = "gfortran" ] ; then
350   gfortran=gfortran
351   gfortranv=`gfortran --version | \
352   head -1 | awk ' { print $NF } ' | awk -F. ' { print $1 * 10 + $2 } '`
353   if [ $gfortranv -le 43 ] ; then
354       echo ERROR : Your gfortran compiler is too old
355       echo 'Please choose a new one (ifort) and change the line'
356       echo compiler=xxx
357       echo in the install.sh script and rerun it
358       if [ `which gfortran44 | wc -w` -ne 0 ] ; then
359          gfortran=gfortran44
360       else
361          echo gfotran trop vieux ; exit
362       fi
363   fi
364   compiler=$gfortran
365fi
366#####################################################################
367
368## if also compiling XIOS, parallel must be mpi_omp
369if [ "$with_xios" = "y" -a "$parallel" != "mpi_omp" ] ; then 
370  echo "Error, you must set -parallel mpi_omp if you want XIOS"
371  exit
372fi
373
374## We can't compile with -cosp and -cosp2
375if [ "$cosp" = 1 -a "$cosp2" = 1 ] ; then
376   echo "Error, you can't run with cosp1 and cosp2"
377   exit
378fi
379if [ "$cosp" = 1 ] ; then
380   opt_cosp="$opt_cosp1"
381fi
382if [ "$cosp2" = 1 ] ; then
383   opt_cosp="$opt_cosp2"
384fi
385if [ "$cospv2" = 1 ] ; then
386   opt_cosp="$opt_cospv2"
387fi
388
389## if also compiling XIOS, cosp must be activate to define axis in *.xml
390if [ "$with_xios" = "y" ] ; then
391  if [ "$cosp" = 0 -a  "$cosp2" = 0 -a "$cospv2" = 0 ] ; then
392   echo "Error, you must use -cosp option when compiling with -xios"
393   echo "You need to call Cosp in physical first step to define axis variables"
394   exit
395  fi
396  opt_makelmdz_xios="-io xios"
397fi
398
399if [ "$cospv2" = 1 -a "$with_xios" = "n" ] ; then
400  echo "Error, Cospv2 cannot run without Xios"
401  exit
402fi
403
404echo '################################################################'
405echo  Choix des options de compilation
406echo '################################################################'
407
408export FC=$compiler
409export F90=$compiler
410export F77=$compiler
411export CPPFLAGS=
412OPTIMNC=$OPTIM
413BASE_LD="$OPT_GPROF"
414OPTPREC="$OPT_GPROF"
415ARFLAGS="rs" ; if [ -f /etc/issue ] ; then if [ "`grep -i ubuntu /etc/issue`" != "" ] ; then if [ "`grep -i ubuntu /etc/issue | awk ' { print $2 } ' | cut -d. -f1`" -ge 16 ] ; then ARFLAGS="rU" ; fi ; fi ; fi
416
417
418
419if [ "$compiler" = "$gfortran" ] ; then
420   OPTIM='-O3'
421   OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all -fbacktrace -finit-real=nan"
422   OPTDEV="-Wall -fbounds-check"
423   fmod='I '
424   OPTPREC="$OPTPREC -cpp -ffree-line-length-0"
425   if [ $real = r8 ] ; then OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE" ; fi
426   export F90FLAGS=" -ffree-form $OPTIMNC"
427   export FFLAGS=" $OPTIMNC"
428   export CC=gcc
429   export CXX=g++
430   export fpp_flags="-P -C -traditional -ffreestanding"
431
432elif [ $compiler = mpif90 ] ; then
433   OPTIM='-O3'
434   OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all"
435   OPTDEV="-Wall -fbounds-check"
436   BASE_LD="$BASE_LD -lblas"
437   fmod='I '
438   if [ $real = r8 ] ; then OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE -fcray-pointer" ; fi
439   export F90FLAGS=" -ffree-form $OPTIMNC"
440   export FFLAGS=" $OPTIMNC"
441   export CC=gcc
442   export CXX=g++
443
444elif [ $compiler = pgf90 ] ; then
445   OPTIM='-O2 -Mipa -Munroll -Mnoframe -Mautoinline -Mcache_align'
446   OPTDEB='-g -Mdclchk -Mbounds -Mchkfpstk -Mchkptr -Minform=inform -Mstandard -Ktrap=fp -traceback'
447   OPTDEV='-g -Mbounds -Ktrap=fp -traceback'
448   fmod='module '
449   if [ $real = r8 ] ; then OPTPREC="$OPTPREC -r8 -DNC_DOUBLE" ; fi
450   export CPPFLAGS="-DpgiFortran"
451   export CC=pgcc
452   export CFLAGS="-O2 -Msignextend"
453   export CXX=pgCC
454   export CXXFLAGS="-O2 -Msignextend"
455   export FFLAGS="-O2 $OPTIMNC"
456   export F90FLAGS="-O2 $OPTIMNC"
457   compile_with_fcm=1
458
459elif [ $compiler = ifort ] ; then
460   OPTIM="-O2 -fp-model strict -ip -align all "
461   OPTDEV="-p -g -O2 -traceback -fp-stack-check -ftrapuv -check"
462   OPTDEB="-g -no-ftz -traceback -ftrapuv -fp-stack-check -check"
463   fmod='module '
464   if [ $real = r8 ] ; then OPTPREC="$OPTPREC -real-size 64 -DNC_DOUBLE" ; fi
465   export CPP="icc -E"
466   export FFLAGS="-O2 -ip -fpic -mcmodel=large"
467   export FCFLAGS="-O2 -ip -fpic -mcmodel=large"
468   export CC=icc
469   export CFLAGS="-O2 -ip -fpic -mcmodel=large"
470   export CXX=icpc
471   export CXXFLAGS="-O2 -ip -fpic -mcmodel=large"
472   export fpp_flags="-P -traditional"
473   # Pourquoi forcer la compilation fcm. Marche mieux sans
474   #compile_with_fcm=1
475
476elif [ $compiler = mpiifort ] ; then
477   echo on ne fait rien la
478   # Pourquoi forcer la compilation fcm. Marche mieux sans
479   #compile_with_fcm=1
480
481else
482   echo unexpected compiler $compiler ; exit
483fi
484
485OPTIMGCM="$OPTIM $OPTPREC"
486
487hostname=`hostname`
488
489##########################################################################
490# If installing on known machines such as Jean-Zay at IDRIS,
491# don't check for available software and don't install netcdf
492if [ ${hostname:0:5} = jean- ] ; then
493  netcdf=0 # no need to recompile netcdf, alreday available
494  check_linux=0
495  pclinux=0
496  ioipsl=0 # no need to recompile ioipsl, already available
497  #netcdf="/smplocal/pub/NetCDF/4.1.3"
498  compiler="mpiifort"
499  fmod='module '
500  if [ $real = r8 ] ; then OPTPREC="$OPTPREC -i4 -r8 -DNC_DOUBLE" ; fi
501  OPTIM="-auto -align all -O2 -fp-model strict -xHost "
502  OPTIMGCM="$OPTIM $OPTPREC"
503fi
504##########################################################################
505
506
507mkdir -p $MODEL
508echo $MODEL
509MODEL=`( cd $MODEL ; pwd )` # to get absolute path, if necessary
510
511
512echo '################################################################'
513if [ "$check_linux" = 1 ] ; then
514echo   Check if required software is available
515echo '################################################################'
516
517#### Ehouarn: test if the required shell is available
518#### Maj FH-LF-AS 2021-04 : default=bash ; if bash missing, use ksh
519use_shell="bash" # default
520if [ "`which bash`" = "" ] ; then
521  echo "no bash ; we will use ksh"
522  use_shell="ksh"
523  if [ "`which ksh`" = "" ] ; then
524    echo "bash (or ksh) needed!! Install it!"
525    exit
526  fi
527fi
528
529for logiciel in wget tar gzip make $compiler gcc ; do
530if [ "`which $logiciel`" = "" ] ; then
531echo You must first install $logiciel on your system
532exit
533fi
534done
535
536if [ $pclinux = 1 ] ; then
537cd $MODEL
538cat <<eod > tt.f90
539print*,'coucou'
540end
541eod
542$compiler tt.f90 -o a.out
543./a.out >| tt
544if [ "`cat tt | sed -e 's/ //g' `" != "coucou" ] ; then
545echo problem installing with compiler $compiler ; exit ; fi
546\rm tt a.out tt.f90
547fi
548fi
549
550###########################################################################
551if [ $getlmdzor = 1 ] ; then
552echo '##########################################################'
553echo  Download a slightly modified version of  LMDZ
554echo '##########################################################'
555cd $MODEL
556myget src/modipsl_orc_cmip6.$version.tar.gz
557echo install.sh wget_OK `date`
558gunzip modipsl_orc_cmip6.$version.tar.gz
559tar xvf modipsl_orc_cmip6.$version.tar
560\rm modipsl_orc_cmip6.$version.tar
561fi
562
563echo OK1
564
565if [ $netcdf = 1 ] ; then
566cd $MODEL
567netcdflog=`pwd`/netcdf.log
568echo '##########################################################'
569echo Compiling the Netcdf library
570echo '##########################################################'
571echo log file : $netcdflog
572if [ "$with_xios" = "n" ] ; then
573  # keep it simple
574  #wget http://www.lmd.jussieu.fr/~lmdz/Distrib/netcdf-4.0.1.tar.gz
575  myget import/netcdf-4.0.1.tar.gz
576  gunzip netcdf-4.0.1.tar.gz
577  tar xvf netcdf-4.0.1.tar
578  \rm -f netcdf-4.0.1.tar
579
580  cd netcdf-4.0.1
581
582  localdir=`pwd -P`
583  ./configure --prefix=$localdir --enable-shared --disable-cxx
584  #sed -e 's/gfortran/'$gfortran'/g' Makefile >| tmp ; mv -f tmp Makefile
585  $make check > $netcdflog 2>&1
586  $make install >> $netcdflog 2>&1
587#LF rajout d'une verrue, pour une raison non encore expliquee, la librairie est parfois rangée dans lib64
588#   et non dans lib par certains compilateurs
589  if [ ! -e lib -a -d lib64 ] ; then ln -s lib64 lib; fi
590else
591  # download and compile hdf5 and netcdf, etc. using the install_netcdf4_hdf5.bash script
592  #wget http://www.lmd.jussieu.fr/~lmdz/Distrib/install_netcdf4_hdf5.bash
593  myget import/install_netcdf4_hdf5.bash
594  chmod u=rwx install_netcdf4_hdf5.bash
595  if [ "$compiler" = "gfortran" ] ; then
596  ./install_netcdf4_hdf5.bash -prefix $MODEL/netcdf4_hdf5 -CC gcc -FC gfortran -CXX g++ -MPI $root_mpi  > $netcdflog 2>&1
597  elif [ "$compiler" = "ifort" ] ; then
598  ./install_netcdf4_hdf5.bash -prefix $MODEL/netcdf4_hdf5 -CC icc -FC ifort -CXX icpc -MPI $root_mpi  > $netcdflog 2>&1
599  elif [ "$compiler" = "pgf90" ] ; then
600  ./install_netcdf4_hdf5.bash -prefix $MODEL/netcdf4_hdf5 -CC pgcc -FC pgf90 -CXX pgCC -MPI $root_mpi  > $netcdflog 2>&1
601  else
602    echo "unexpected compiler $compiler" ; exit
603  fi
604fi  # of if [ "$with_xios" = "n" ]
605echo install.sh netcdf_OK `date`
606fi # of if [ $netcdf = 1 ]
607
608#======================================================================================
609echo OK2 ioipsl=$ioipsl
610echo '##########################################################'
611echo 'Installing MODIPSL, the installation package manager for the '
612echo 'IPSL models and tools'
613echo '##########################################################'
614
615if [ $netcdf = 0 -o $netcdf = 1 ] ; then
616  if [ "$with_xios" = "y" ] ; then
617  ncdfdir=$MODEL/netcdf4_hdf5
618  else
619  ncdfdir=$MODEL/netcdf-4.0.1
620  fi
621else
622  ncdfdir=$netcdf
623fi
624
625if [ $ioipsl = 1 ] ; then
626  cd $MODEL/modipsl
627  \rm -rf lib/*
628
629  cd util
630
631  cp AA_make.gdef AA_make.orig
632  F_C="$compiler -c " ; if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then F_C="$compiler -c -cpp " ; fi
633  if [ "$compiler" = "pgf90" ] ; then F_C="$compiler -c -Mpreprocess" ; fi
634  sed -e 's/^\#.*.g95.*.\#.*.$/\#/' AA_make.gdef > tmp
635  sed -e "s:F_L = g95:F_L = $compiler:" -e "s:F_C = g95 -c -cpp:F_C = $F_C": \
636  -e 's/g95.*.w_w.*.(F_D)/g95      w_w = '"$OPTIMGCM"'/' \
637  -e 's:g95.*.NCDF_INC.*.$:g95      NCDF_INC= '"$ncdfdir"'/include:' \
638  -e 's:g95.*.NCDF_LIB.*.$:g95      NCDF_LIB= -L'"$ncdfdir"'/lib -lnetcdff -lnetcdf:' \
639  -e 's:g95      L_O =:g95      L_O = -Wl,-rpath='"$ncdfdir"'/lib:' \
640  -e "s:-fmod=:-$fmod:" -e 's/-fno-second-underscore//' \
641  -e 's:#-Q- g95      M_K = gmake:#-Q- g95      M_K = make:' \
642  tmp >| AA_make.gdef
643
644  if [ $pcmac == 1 ]
645  then
646      cp AA_make.gdef tmp
647      sed -e 's/rpath=/rpath,/g' tmp > AA_make.gdef
648  fi
649 
650
651# We use lines for g95 even for the other compilers to run ins_make
652  if [ "$use_shell" = "ksh" ] ; then
653    ./ins_make $o_ins_make
654  else # bash
655    sed -e s:/bin/ksh:/bin/bash:g ins_make > ins_make.bash
656    #if [ "`grep ada AA_make.gdef`" = "" ] ; then # Bidouille pour compiler sur ada des vieux modipsl.tar
657    #    \cp -f ~rdzt401/bin/AA_make.gdef .
658    #fi
659    if [ "`grep jeanzay AA_make.gdef`" = "" ] ; then # Bidouille pour compiler sur ada des vieux modipsl.tar
660        echo 'Warning jean-zay not in AA_make.gdef'
661        echo 'Think about updating'
662        exit 1
663    fi
664   
665    chmod u=rwx ins_make.bash
666    ./ins_make.bash $o_ins_make
667  fi # of if [ "$use_shell" = "ksh" ]
668
669#=======================================================================================
670  cd $MODEL/modipsl/modeles/IOIPSL/src
671  ioipsllog=`pwd`/ioipsl.log
672  echo '##########################################################'
673  echo 'Compiling IOIPSL, the interface library with Netcdf'
674  echo '##########################################################'
675  echo log file : $ioipsllog
676
677  if [ "$use_shell" = "bash" ] ; then
678    cp Makefile Makefile.ksh
679    sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile
680  fi
681# if [ "$pclinux" = 1 ] ; then
682    # Build IOIPSL modules and library
683    $make clean
684    $make > $ioipsllog 2>&1
685    if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then # copy module files to lib
686      cp -f *.mod ../../../lib
687    fi
688    # Build IOIPSL tools (ie: "rebuild", if present)
689    if [ -f $MODEL/modipsl/modeles/IOIPSL/tools/rebuild ] ; then
690      cd $MODEL/modipsl/modeles/IOIPSL/tools
691      # adapt Makefile & rebuild script if in bash
692      if [ "$use_shell" = "bash" ] ; then
693        cp Makefile Makefile.ksh
694        sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile
695        cp rebuild rebuild.ksh
696        sed -e 's:/bin/ksh:/bin/bash:g' \
697            -e 's:print -u2:echo:g' \
698            -e 's:print:echo:g' rebuild.ksh > rebuild
699      fi
700      $make clean
701      $make > $ioipsllog 2>&1
702    fi
703# fi # of if [ "$pclinux" = 1 ]
704
705else # of if [ $ioipsl = 1 ]
706  if [ ${hostname:0:5} = jean- ] ; then
707     cd $MODEL/modipsl
708     cd util
709       if [ "`grep jeanzay AA_make.gdef`" = "" ] ; then
710        echo 'Warning jean-zay not in AA_make.gdef'
711        echo 'Think about updating'
712        exit 1
713       fi
714       ./ins_make $o_ins_make
715# Compile IOIPSL on jean-zay
716       cd $MODEL/modipsl/modeles/IOIPSL/src
717       gmake > ioipsl.log
718       cd $MODEL/modipsl/modeles/IOIPSL/tools
719       gmake > ioipsl.log
720   
721  fi
722  echo install.sh ioipsl_OK `date`
723fi # of if [ $ioipsl = 1 ]
724# Saving ioipsl lib for possible parallel compile
725  cd $MODEL/modipsl
726  tar cf ioipsl.tar lib/ bin/
727
728#===========================================================================
729if [ "$with_xios" = "y" ] ; then
730  echo '##########################################################'
731  echo 'Compiling XIOS'
732  echo '##########################################################'
733  cd $MODEL/modipsl/modeles
734  xioslog=`pwd`/xios.log
735  echo "log file: $xioslog"
736  #wget http://www.lmd.jussieu.fr/~lmdz/Distrib/install_xios.bash
737  myget import/install_xios.bash
738  chmod u=rwx install_xios.bash
739   if [ ${hostname:0:5} = jean- ] ; then
740#    echo 'Need to work on install_xios implementation for jean-zay'
741#    exit
742   svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5 XIOS
743   cd XIOS/arch
744   svn update
745   cd ..
746   ./make_xios --prod --arch $arch --job 4 > xios.log 2>&1
747   else
748     ./install_xios.bash -prefix $MODEL/modipsl/modeles \
749                      -netcdf ${ncdfdir} -hdf5 ${ncdfdir} \
750                      -MPI $root_mpi -arch $arch > xios.log 2>&1
751   fi
752   if [ -f XIOS/lib/libxios.a ] ; then
753     echo "OK, XIOS library successfully generated"
754   fi
755fi
756
757#============================================================================
758veget_version=false
759if [ "$veget" != 'NONE' ] ; then
760  cd $MODEL/modipsl/modeles/ORCHIDEE
761  set +e ; svn upgrade ; set -e
762  if [ "$veget" = "CMIP6" ] ; then
763    veget_version=orchidee2.0 
764    orchidee_rev=6592
765  else # specific orchidee revision
766     set +e
767     svn log -r $veget | grep  $veget
768     if [  $? -gt 0 ] ; then
769          echo 'Cannot update ORCHIDEE as not on the right branch for ORCHIDEE'
770          exit
771      fi
772      set -e
773      set +e ; svn update -r $veget ; set -e 
774  fi
775  # Correctif suite debug Jean-Zay
776  sed -i -e 's/9010  FORMAT(A52,F17.14)/9010  FORMAT(A52,F20.14)/' src_stomate/stomate.f90
777  opt_orc="-prod" ; if [ "$optim" = "-debug" ] ; then opt_orc="-debug" ; fi
778
779  orchideelog=`pwd`/orchidee.log
780  echo '########################################################'
781  echo 'Compiling ORCHIDEE, the continental surfaces model '
782  echo '########################################################'
783  echo log file : $orchideelog
784  export ORCHPATH=`pwd`
785  if [ -d tools ] ; then
786###################################################################
787# Pour les experts qui voudraient changer de version d'orchidee.
788# Attention : necessite d'avoir le password pour orchidee
789
790      # Correctif suite debug Jean-Zay
791      if [ -f src_global/time.f90 ] ; then sed -i -e 's/CALL tlen2itau/\!CALL tlen2itau/' src_global/time.f90 ; fi
792###################################################################
793     if [ "$veget_version" == "false" ] ; then veget_version=orchidee2.0 ; fi
794      cd arch
795      sed -e s:"%COMPILER        .*.$":"%COMPILER            $compiler":1 \
796     -e s:"%LINK            .*.$":"%LINK                $compiler":1 \
797     -e s:"%FPP_FLAGS       .*.$":"%FPP_FLAGS           $fpp_flags":1 \
798     -e s:"%PROD_FFLAGS     .*.$":"%PROD_FFLAGS         $OPTIM":1 \
799     -e s:"%DEV_FFLAGS      .*.$":"%DEV_FFLAGS          $OPTDEV":1 \
800     -e s:"%DEBUG_FFLAGS    .*.$":"%DEBUG_FFLAGS        $OPTDEB":1 \
801     -e s:"%BASE_FFLAGS     .*.$":"%BASE_FFLAGS         $OPTPREC":1 \
802     -e s:"%BASE_LD         .*.$":"%BASE_LD             $BASE_LD":1 \
803     -e s:"%ARFLAGS         .*.$":"%ARFLAGS             $ARFLAGS":1 \
804     arch-gfortran.fcm > arch-local.fcm
805     echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib -lnetcdff -lnetcdf\"" > arch-local.path
806     echo "NETCDF_INCDIR=${ncdfdir}/include" >> arch-local.path
807     echo "IOIPSL_INCDIR=$ORCHPATH/../../lib" >> arch-local.path
808     echo "IOIPSL_LIBDIR=$ORCHPATH/../../lib" >> arch-local.path
809     echo 'XIOS_INCDIR=${ORCHDIR}/../XIOS/inc' >> arch-local.path
810     echo 'XIOS_LIBDIR="${ORCHDIR}/../XIOS/lib -lxios"' >> arch-local.path
811     cd ../
812# compiling ORCHIDEE sequential mode
813     ./makeorchidee_fcm -j 8 -noxios $opt_orc -parallel none -arch $arch > $orchideelog 2>&1
814     echo ./makeorchidee_fcm -j 8 -noxios $opt_orc -parallel none -arch $arch
815     echo End of the first compilation of orchidee ; pwd
816  else
817     if [ -d src_parallel ] ; then
818       liste_src="parallel parameters global stomate sechiba driver"
819       if [ "$veget_version" == "false" ] ; then veget_version=orchidee2.0 ; fi
820     fi
821     for d in $liste_src ; do src_d=src_$d
822        echo src_d $src_d
823        echo ls ; ls
824        if [ ! -d $src_d ] ; then echo Problem orchidee : no $src_d ; exit ; fi
825        cd $src_d ; \rm -f *.mod make ; $make clean
826        $make > $orchideelog 2>&1 ; if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then cp -f *.mod ../../../lib ; fi
827        cd ..
828     done
829  fi
830  echo install.sh orchidee_OK `date`
831fi # of if [ "$veget" = 1 ]
832
833
834#============================================================================
835# Ehouarn: the directory name LMDZ* depends on version/tar file...
836if [ -d $MODEL/modipsl/modeles/LMD* ] ; then
837  echo '##########################################################'
838  echo 'Compiling LMDZ'
839  echo '##########################################################'
840  cd $MODEL/modipsl/modeles/LMD*
841  LMDZPATH=`pwd`
842else
843  echo "ERROR: No LMD* directory !!!"
844  exit
845fi
846
847###########################################################
848# For those who want to use fcm to compile via :
849#  makelmdz_fcm -arch local .....
850############################################################
851
852if [ "$pclinux" = "1" ] ; then
853
854# create local 'arch' files (if on Linux PC):
855cd arch
856# arch-local.path file
857echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib -lnetcdff -lnetcdf\"" > arch-local.path
858echo "NETCDF_INCDIR=-I${ncdfdir}/include" >> arch-local.path
859echo 'IOIPSL_INCDIR=$LMDGCM/../../lib' >> arch-local.path
860echo 'IOIPSL_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
861echo 'XIOS_INCDIR=$LMDGCM/../XIOS/inc' >> arch-local.path
862echo 'XIOS_LIBDIR=$LMDGCM/../XIOS/lib' >> arch-local.path
863echo 'ORCH_INCDIR=$LMDGCM/../../lib' >> arch-local.path
864echo 'ORCH_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
865
866if [ $pcmac == 1 ] ; then
867    BASE_LD="$BASE_LD -Wl,-rpath,${ncdfdir}/lib"
868else
869    BASE_LD="$BASE_LD -Wl,-rpath=${ncdfdir}/lib"
870fi
871# Arch-local.fcm file (adapted from arch-linux-32bit.fcm)
872
873if [ $real = r8 ] ; then FPP_DEF=NC_DOUBLE ; else FPP_DEF="" ; fi
874sed -e s:"%COMPILER        .*.$":"%COMPILER            $compiler":1 \
875    -e s:"%LINK            .*.$":"%LINK                $compiler":1 \
876    -e s:"%PROD_FFLAGS     .*.$":"%PROD_FFLAGS         $OPTIM":1 \
877    -e s:"%DEV_FFLAGS      .*.$":"%DEV_FFLAGS          $OPTDEV":1 \
878    -e s:"%DEBUG_FFLAGS    .*.$":"%DEBUG_FFLAGS        $OPTDEB":1 \
879    -e s:"%BASE_FFLAGS     .*.$":"%BASE_FFLAGS         $OPTPREC":1 \
880    -e s:"%FPP_DEF         .*.$":"%FPP_DEF             $FPP_DEF":1 \
881    -e s:"%BASE_LD         .*.$":"%BASE_LD             $BASE_LD":1 \
882    -e s:"%ARFLAGS         .*.$":"%ARFLAGS             $ARFLAGS":1 \
883    arch-linux-32bit.fcm > arch-local.fcm
884
885cd ..
886### Adapt "bld.cfg" (add the shell):
887whereisthatshell=$(which ${use_shell})
888echo "bld::tool::SHELL   $whereisthatshell" >> bld.cfg
889
890fi # of if [ "$pclinux" = 1 ]
891
892
893cd $MODEL/modipsl/modeles/LMDZ*
894lmdzlog=`pwd`/lmdz.log
895
896##################################################################
897# Possibly update LMDZ if a specific svn release is requested
898##################################################################
899
900
901set +e ; svn upgrade ; set -e
902if [ "$svn" = "last" ] ; then svnopt="" ; else svnopt="-r $svn" ; fi
903if [ "$svn" != "" ] ; then
904    svn info | grep -q 'http:'
905    if [ $? = 0 ] ; then
906        svn switch --relocate http://svn.lmd.jussieu.fr/LMDZ https://svn.lmd.jussieu.fr/LMDZ
907    fi
908    svn update $svnopt
909fi
910set -e
911
912echo '##################################################################'
913echo Compile LMDZ
914echo '##################################################################'
915echo log file : $lmdzlog
916
917if [ "$env_file" != "" ] ; then mv arch/arch-${arch}.env arch/arch-${arch}.orig ; \cp -f $env_file arch/arch-${arch}.env ; fi
918
919echo install.sh avant_compilation `date`
920if [ $compile_with_fcm = 1 ] ; then makelmdz="makelmdz_fcm $optim -arch $arch -j 8 " ; else makelmdz="makelmdz $optim -arch $arch" ; fi
921
922# sequential compilation and bench
923if [ "$sequential" = 1 ] ; then
924echo "./$makelmdz $optim $OPT_MAKELMDZ $optim -rrtm true $opt_cosp -d ${grid_resolution} -v $veget_version gcm " >> compile.sh
925chmod +x ./compile.sh
926if [ $bench != 0 ] ; then ./compile.sh > $lmdzlog 2>&1 ; fi
927echo install.sh apres_compilation `date`
928
929
930fi # fin sequential
931
932
933
934# compiling in parallel mode
935if [ $parallel != "none" ] ; then
936  echo '##########################################################'
937  echo ' Parallel compile '
938  echo '##########################################################'
939  # saving the sequential libs and binaries
940  cd $MODEL/modipsl
941  tar cf sequential.tar bin/ lib/
942  \rm -rf bin/ lib/
943  tar xf ioipsl.tar
944  #
945  # Orchidee
946  #
947  cd $ORCHPATH
948  if [ -d src_parallel -a $veget != 'NONE' ] ; then
949     cd arch
950     sed  \
951     -e s:"%COMPILER.*.$":"%COMPILER            $par_comp":1 \
952     -e s:"%LINK.*.$":"%LINK                $par_comp":1 \
953     -e s:"%MPI_FFLAG.*.$":"%MPI_FFLAGS          $MPI_FLAGS":1 \
954     -e s:"%OMP_FFLAG.*.$":"%OMP_FFLAGS          $OMP_FLAGS":1 \
955     -e s:"%MPI_LD.*.$":"%MPI_LD              $MPI_LD":1 \
956     -e s:"%OMP_LD.*.$":"%OMP_LD              $OMP_LD":1 \
957     arch-local.fcm > tmp.fcm
958
959     mv tmp.fcm arch-local.fcm
960     cd ../
961     echo compiling ORCHIDEE parallel mode
962     echo logfile $orchideelog
963     ./makeorchidee_fcm -j 8 -clean -noxios $opt_orc -parallel $parallel -arch $arch > $orchideelog 2>&1
964     ./makeorchidee_fcm -j 8 -noxios $opt_orc -parallel $parallel -arch $arch >> $orchideelog 2>&1
965     echo ./makeorchidee_fcm -j 8 -clean -noxios $opt_orc -parallel $parallel -arch $arch
966     echo ./makeorchidee_fcm -j 8 -noxios $opt_orc -parallel $parallel -arch $arch
967  elif [ $veget != 'NONE' ] ; then
968    echo '##########################################################'
969    echo ' Orchidee version too old                                 '
970    echo ' Please update to new version                             '
971    echo '##########################################################'
972    exit
973  fi # of if [ -d src_parallel ]
974  # LMDZ
975  cd $LMDZPATH
976  if [ $arch = local ] ; then
977    cd arch
978    sed -e s:"%COMPILER.*.$":"%COMPILER            $par_comp":1 \
979    -e s:"%LINK.*.$":"%LINK                $par_comp":1 \
980    -e s:"%MPI_FFLAG.*.$":"%MPI_FFLAGS          $MPI_FLAGS":1 \
981    -e s:"%OMP_FFLAG.*.$":"%OMP_FFLAGS          $OMP_FLAGS":1 \
982    -e s:"%ARFLAGS.*.$":"%ARFLAGS          $ARFLAGS":1 \
983    -e s@"%BASE_LD.*.$"@"%BASE_LD             -Wl,-rpath=${root_mpi}/lib:${ncdfdir}/lib"@1 \
984    -e s:"%MPI_LD.*.$":"%MPI_LD              $MPI_LD":1 \
985    -e s:"%OMP_LD.*.$":"%OMP_LD              $OMP_LD":1 \
986    arch-local.fcm > tmp.fcm
987    mv tmp.fcm arch-local.fcm
988    cd ../
989  fi
990  rm -f compile.sh
991  echo resol=${grid_resolution} >> compile.sh
992  if [ ${hostname:0:5} = jean- -a "$cospv2" = 1 ] ; then
993     echo ./$makelmdz -dev $optim $OPT_MAKELMDZ -rrtm true $opt_cosp $opt_makelmdz_xios -d \$resol -v $veget_version -mem -parallel $parallel gcm >> compile.sh
994     echo ./$makelmdz -dev $optim $OPT_MAKELMDZ -rrtm true $opt_cosp $opt_makelmdz_xios -d \$resol -v $veget_version -mem -parallel $parallel gcm
995  else   
996    echo ./$makelmdz $optim $OPT_MAKELMDZ -rrtm true $opt_cosp $opt_makelmdz_xios -d \$resol -v $veget_version -mem -parallel $parallel gcm >> compile.sh
997    echo ./$makelmdz $optim $OPT_MAKELMDZ -rrtm true $opt_cosp $opt_makelmdz_xios -d \$resol -v $veget_version -mem -parallel $parallel gcm
998  fi 
999  chmod +x ./compile.sh
1000  if [ $bench != 0 ] ; then ./compile.sh > $lmdzlog 2>&1 ; fi
1001
1002  echo "Compilation finished"
1003 
1004fi # of if [ $parallel != "none" ]
1005
1006
1007##################################################################
1008# Verification du succes de la compilation
1009##################################################################
1010
1011# Recherche de l'executable dont le nom a change au fil du temps ...
1012gcm=""
1013#for exe in gcm.e bin/gcm_${grid_resolution}_phylmd_seq_orch.e bin/gcm_${grid_resolution}_phylmd_seq.e bin/gcm_${grid_resolution}_phylmd_para_mem_orch.e bin/gcm_${grid_resolution}_phylmd_para_mem.e  ; do
1014for exe in gcm.e bin/gcm_${grid_resolution}_phylmd${suff_exe}${suff_orc}.e ; do   if [ -f $exe ] ; then gcm=$exe ; fi
1015done
1016
1017if [ "$gcm" = "" ] ; then
1018  if [ $bench != 0 ] ; then
1019    echo 'Compilation failed !! Cannot run the benchmark;'
1020    exit
1021  else
1022    echo 'Compilation not done (only done when bench=1)'
1023  fi
1024else
1025   echo '##########################################################'
1026   echo 'Compilation successfull !! '
1027   echo '##########################################################'
1028   echo The executable is $gcm
1029fi
1030
1031##################################################################
1032# Below, we run a benchmark test (if bench=0)
1033##################################################################
1034
1035if [ $bench != 0 ] ; then
1036
1037echo '##########################################################'
1038echo ' Running a test run '
1039echo '##########################################################'
1040
1041\rm -rf BENCH${grid_resolution}
1042bench=bench_lmdz_${grid_resolution}
1043echo install.sh before bench download  `date`
1044#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/$bench.tar.gz
1045myget 3DBenchs/$bench.tar.gz
1046echo install.sh after bench download  `date`
1047tar xvf $bench.tar.gz
1048
1049if [ "$cosp" = 1 -o "$cosp2" = 1 -o "$cospv2" = 1 ] ; then
1050  cd BENCH${grid_resolution}
1051# copier les fichiers namelist input et output our COSP
1052  cp ../DefLists/cosp*_input_nl.txt .
1053  cp ../DefLists/cosp*_output_nl.txt .
1054# Activer la cles ok_cosp pour tourner avec COSP
1055  sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp
1056   \mv -f tmp config.def
1057  cd ..
1058fi 
1059
1060if [ -n "$physiq" ]; then
1061  cd BENCH${grid_resolution}
1062  if [ -f physiq.def_${physiq} ]; then
1063    cp physiq.def_${physiq} physiq.def
1064    echo using physiq.def_${physiq}
1065  else
1066    echo using standard physiq.def
1067  fi
1068  cd ..
1069else
1070  echo using standard physiq.def
1071fi
1072
1073if [ "$with_xios" = "y" ] ; then
1074  cd BENCH${grid_resolution}
1075  cp ../DefLists/iodef.xml .
1076  cp ../DefLists/context_lmdz.xml .
1077  cp ../DefLists/field_def_lmdz.xml .
1078  cp ../DefLists/field_def_cosp*.xml .
1079  cp ../DefLists/file_def_hist*xml .
1080  # adapt iodef.xml to use attached mode
1081  sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' iodef.xml > tmp
1082  \mv -f tmp iodef.xml
1083
1084  # and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
1085  # except for histday
1086  for histfile in file_def_hist*xml
1087  do
1088    if [ "$histfile" = "file_def_histday_lmdz.xml" ] ; then
1089    sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' $histfile > tmp ; \mv -f tmp $histfile
1090    sed -e 's@output_level="_AUTO_"@output_level="5"@' $histfile > tmp ; \mv -f tmp $histfile
1091    sed -e 's@compression_level="2"@compression_level="0"@' $histfile > tmp ; \mv -f tmp $histfile
1092    else
1093    sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' $histfile > tmp ; \mv -f tmp $histfile
1094    fi
1095  done
1096  # and add option "ok_all_xml=y" in config.def
1097  echo "### XIOS outputs" >> config.def
1098  echo 'ok_all_xml=.true.' >> config.def
1099
1100  #activer les sorties pour Cosp
1101  if [ "$cosp" = 1 -o "$cosp2" = 1 ] ; then 
1102   histfile=file_def_histdayCOSP_lmdz.xml
1103   sed -e 's@enabled=".FALSE."@enabled=".TRUE."@' $histfile > tmp ; \mv -f tmp $histfile
1104   sed -e 's@output_level="_AUTO_"@output_level="5"@' $histfile > tmp ; \mv -f tmp $histfile
1105   sed -e 's@compression_level="2"@compression_level="0"@' $histfile > tmp ; \mv -f tmp $histfile
1106  fi
1107  if [ "$cospv2" = 1 ] ; then
1108   histfile=file_def_histdayCOSPv2_lmdz.xml
1109   sed -e 's@compression_level="2"@compression_level="0"@' $histfile > tmp ; \mv -f tmp $histfile
1110   contextfile=context_lmdz.xml
1111   sed -e 's@src="./file_def_histdayCOSP_lmdz.xml"@src="./file_def_histdayCOSPv2_lmdz.xml"@' $contextfile > tmp ; \mv -f tmp $contextfile
1112   fieldfile=field_def_lmdz.xml
1113   sed -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' $fieldfile > tmp ; \mv -f tmp $fieldfile
1114  fi
1115
1116  cd ..
1117fi
1118
1119cp $gcm BENCH${grid_resolution}/gcm.e
1120
1121cd BENCH${grid_resolution}
1122# On cree le fichier bench.sh au besoin
1123# Dans le cas 48x36x39 le bench.sh existe deja en parallele
1124
1125if [ "$grid_resolution" = "48x36x39" ] ; then
1126   echo On ne touche pas au bench.sh
1127   # But we have to adapt "run_local.sh" for $mpirun
1128   sed -e "s@mpirun@$mpirun@g" run_local.sh > tmp
1129   mv -f tmp run_local.sh
1130   chmod u=rwx run_local.sh
1131elif [ "${parallel:0:3}" = "mpi" ] ; then
1132   # Lancement avec deux procs mpi et 2 openMP
1133   echo "export OMP_STACKSIZE=800M" > bench.sh
1134   if [ "${parallel:4:3}" = "omp" ] ; then
1135     echo "export OMP_NUM_THREADS=2" >> bench.sh
1136   fi
1137   if [ "$cospv2" = 1 -o "$cosp" = 1 -o "$cosp2" = 1 ] ; then 
1138      if [ ${hostname:0:5} = jean- ] ; then   
1139        chmod +x ../arch.env
1140        ../arch.env     
1141        echo "ulimit -s 2000000" >> bench.sh
1142      else
1143        echo "ulimit -s 200000" >> bench.sh           
1144      fi       
1145   else
1146      echo "ulimit -s unlimited" >> bench.sh
1147   fi
1148   if [ ${hostname:0:5} = jean- ] ; then
1149     . ../arch/arch-${arch}.env 
1150     echo "srun -n 2 -A $idris_acct@cpu gcm.e > listing  2>&1" >> bench.sh
1151   else
1152     echo "$mpirun -np 2 gcm.e > listing  2>&1" >> bench.sh
1153   fi
1154   # Add rebuild, using reb.sh if it is there
1155   echo 'if [ -f reb.sh ] ; then' >> bench.sh
1156   echo '  ./reb.sh histday ; ./reb.sh histmth ; ./reb.sh histhf ; ./reb.sh histins ; ./reb.sh stomate_history ; ./reb.sh sechiba_history ; ./reb.sh sechiba_out_2 ' >> bench.sh
1157   echo 'fi' >> bench.sh
1158else
1159   echo "./gcm.e > listing  2>&1" > bench.sh
1160fi
1161# Getting orchidee stuff
1162if [ $veget == 'CMIP6' ] ; then
1163    #echo 'myget 3DBenchs/BENCHorch11.tar.gz'
1164    #myget 3DBenchs/BENCHorch11.tar.gz
1165    #tar xvzf BENCHorch11.tar.gz
1166    echo 'myget 3DBenchs/BENCHCMIP6.tar.gz'
1167    myget 3DBenchs/BENCHCMIP6.tar.gz
1168    tar xvzf BENCHCMIP6.tar.gz
1169    sed -e "s:VEGET=n:VEGET=y:" config.def > tmp
1170    mv -f tmp config.def
1171fi
1172echo EXECUTION DU BENCH
1173set +e
1174date ; ./bench.sh > out.bench 2>&1 ; date
1175set -e
1176tail listing
1177
1178
1179echo '##########################################################'
1180echo 'Simulation finished in' `pwd`
1181   echo 'You have compiled with:'
1182   cat ../compile.sh
1183if [ $parallel = "none" ] ; then
1184  echo 'You may re-run it with : cd ' `pwd` ' ; gcm.e'
1185  echo 'or ./bench.sh'
1186else
1187  echo 'You may re-run it with : '
1188  echo 'cd ' `pwd` '; ./bench.sh'
1189#  echo 'ulimit -s unlimited'
1190#  echo 'export OMP_NUM_THREADS=2'
1191#  echo 'export OMP_STACKSIZE=800M'
1192#  echo "$mpirun -np 2 gcm.e "
1193fi
1194echo '##########################################################'
1195
1196fi # bench
1197
1198
1199#################################################################
1200# Installation eventuelle du 1D
1201#################################################################
1202
1203if [ $SCM = 1 ] ; then
1204cd $MODEL
1205#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/1D.tar.gz
1206myget 1D/1D.tar.gz
1207tar xvf 1D.tar.gz
1208cd 1D
1209./run.sh
1210fi
1211set -vx
1212
1213#################################################################
1214# sauvegarde des options veget pour utilisation eventuelle tutorial_prod
1215#################################################################
1216cd $MODEL/modipsl/modeles
1217echo surface_env file created in $MODEL
1218echo 'veget='$veget > surface_env
1219#opt_veget="-v $veget_version"
1220#echo 'opt_veget="'$opt_veget\" >> surface_env
1221echo 'opt_veget="'-v $veget_version\" >> surface_env
1222echo 'orchidee_rev='$orchidee_rev >> surface_env
1223echo 'suforch='$suff_orc >> surface_env
1224   
1225
1226
1227
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