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source: BOL/script_install/install_lmdz.sh @ 4930

Last change on this file since 4930 was 4919, checked in by Laurent Fairhead, 5 months ago
Switching from forge.ipsl.jussieu.fr to forge.ipsl.fr
Property svn:executable set to ``*
File size: 57.2 KB

Rev	Line
[4210]	1	#!/bin/bash
	2
	3	#set -vx
	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.
[4218]	21	# In the present case, LMDZ, ORCHIDEE, and IOIPSL or XIOS (handling of
	22	# input-outputs using the NetCDF library).
[4210]	23	#
	24	# The script downloads various source files (including a version of NetCDF)
	25	# and utilities, compiles the model, and runs a test simulation in a
	26	# minimal configuration.
	27	#
	28	# Prerequisites : pgf90/gfortran, bash or ksh, wget , gunzip, tar, ...
	29	#
	30	# Modif 18/11/2011
	31	# changes for option real 8.
	32	# We compile with -r8 (or equivalent) and -DNC_DOUBLE for the GCM
	33	# but with -r4 for netcdf. Variable real must be set to
	34	# r4 or r8 at the beginning of the script below.
	35	#
	36	###########################################################################
	37
	38	echo install_lmdz.sh DEBUT `date`
	39	set -e
	40
	41	################################################################
	42	# Choice of installation options
	43	################################################################
	44
	45	################################################################
	46	# A function to fetch files either locally or on the internet
	47	################################################################
	48	function myget { #1st and only argument should be file name
[4215]	49	# Path on local computer where to look for the datafile
	50	if [ -f /u/lmdz/WWW/LMDZ/pub/$1 ] ; then
[4405]	51	\cp -f -p /u/lmdz/WWW/LMDZ/pub/$1 .
[4215]	52	elif [ -f ~/LMDZ/pub/$1 ] ; then
[4405]	53	\cp -f -p ~/LMDZ/pub/$1 .
[4215]	54	else
[4405]	55	wget --no-check-certificate -nv http://lmdz.lmd.jussieu.fr/pub/$1
	56	save_pub_locally=0
	57	if [ $save_pub_locally = 1 ] ; then # saving wget files on ~/LMDZ/pub
	58	dir=~/LMDZ/pub/`dirname $1` ; mkdir -p $dir
	59	cp -r `basename $1` $dir
	60	fi
[4210]	61	fi
	62	}
	63
	64	# 04_2021 : tester si r4 marche encore !
	65	#real=r4
	66	real=r8
	67
	68
	69	#########################################################################
	70	# Valeur par défaut des parametres
	71	#########################################################################
	72	svn=""
	73	#version=trunk
[4731]	74	version=20231022.trunk
[4210]	75
	76	getlmdzor=1
[4237]	77	netcdf=1 # 1: for automatic installation;
[4267]	78	# or 0: do not install NetCDF and look for it in standard locations;
	79	# or absolute path: look for NetCDF there
[4210]	80	check_linux=1
	81	ioipsl=1
	82	bench=1
	83	pclinux=1
	84	pcmac=0 # default: not on a Mac
	85	compiler=gfortran
[4779]	86	if [ `gfortran -dumpversion \| cut -d. -f1` -ge 10 ] ; then allow_arg_mismatch="-fallow-argument-mismatch" ; fi
[4210]	87	SCM=0
	88	# surface/vegetation scheme treatment
	89	# controlled by the single variable veget which can have the following values
	90	# - NONE: bucket scheme (default)
	91	# - CMIP6: orchidee version used in CMIP exercise, rev 5661
	92	# - number: orchidee version number
	93	veget=NONE
	94	# choose the resolution for the bench runs
	95	# grid_resolution= 32x24x11 or 48x36x19 for tests (test without ORCHIDEE)
	96	# 96x71x19 standard configuration
	97	grid_resolution=144x142x79
	98	grid_resolution=96x95x39
	99	grid_resolution=48x36x19
	100	grid_resolution=32x32x39
	101	# choose the physiq version you want to test
	102	#physiq=NPv6.0.14splith
	103	physiq=
	104
	105	## parallel can take the values none/mpi/omp/mpi_omp
	106	parallel=mpi_omp
	107	parallel=none
	108	idris_acct=lmd
[4417]	109	trusting=testing
[4210]	110	OPT_GPROF=""
	111	OPT_MAKELMDZ=""
	112	MODEL=""
	113
	114	## also compile XIOS? (and more recent NetCDF/HDF5 libraries) Default=no
	115	with_xios="n"
	116	opt_makelmdz_xios=""
	117
	118	## compile with oldrad/rrtm/ecrad radiatif code (Default=rrtm)
	119	rad=rrtm
	120
	121	## compile_with_fcm=1 : use makelmdz_fcm (1) or makelmdz (0)
	122	compile_with_fcm=1
	123
	124	#Compilation with Cosp (cosp=NONE/v1/v2 ; default=NONE)
	125	cosp=NONE
	126	opt_cosp=""
	127
	128	# Check if on a Mac
	129	if [ `uname` = "Darwin" ]
	130	then
	131	pcmac=1
	132	export MAKE=make
	133	fi
	134	#echo "pcmac="$pcmac
	135
	136	env_file=""
	137
	138	#########################################################################
	139	# Options interactives
	140	#########################################################################
	141	while (($# > 0))
[4215]	142	do
	143	case $1 in
[4405]	144	"-h") cat <<........fin
[4210]	145	$0 [ -v version ] [ -r svn_release ]
	146	[ -parallel PARA ] [ -d GRID_RESOLUTION ] [ -bench 0/1 ]
	147	[-name LOCAL_MODEL_NAME] [-gprof] [-opt_makelmdz] [-rad RADIATIF]
	148
	149	-v "version" like 20150828.trunk
	150	see http://www.lmd.jussieu.fr/~lmdz/Distrib/LISMOI.trunk
	151
	152	-r "svn_release" : either the svn release number or "last"
	153
	154	-compiler gfortran\|ifort\|pgf90 (default: gfortran)
	155
	156	-parallel PARA : can be mpi_omp (mpi with openMP) or none (for sequential)
	157
	158	-d GRID_RESOLUTION should be among the available benchs if -bench 1
	159	among which : 48x36x19, 48x36x39
	160	if wanting to run a bench simulation in addition to compilation
	161	default : 48x36x19
	162
	163	-bench activating the bench or not (0/1). Default 1
	164
[4421]	165	-testing/unstable
[4417]	166
[4210]	167	-name LOCAL_MODEL_NAME : default = LMDZversion.release
	168
[4211]	169	-netcdf 0, 1 or PATH
[4405]	170	0: do not download NetCDF, look for it in standard locations
	171	1: download and compile NetCDF
	172	PATH: full path to an existing installed NetCDF library
[4210]	173
	174	-xios also download and compile the XIOS library
	175	(requires the NetCDF4-HDF5 library, also installed by default)
	176	(requires to also have -parallel mpi_omp)
	177
	178	-gprof to compile with -pg to enable profiling with gprof
	179
	180	-cosp to run without our with cospv1 or cospv2 [none/v1/v2]
	181
	182	-rad RADIATIF can be oldrad, rrtm or ecrad radiatif code
	183
	184	-nofcm to compile without fcm
	185
	186	-SCM install 1D version automatically
	187
	188	-debug compile everything in debug mode
	189
	190	-opt_makelmdz to call makelmdz or makelmdz_fcm with additional options
	191
	192	-physiq to choose which physics package to use
	193
	194	-env_file specify an arch.env file to overwrite the existing one
	195
	196	-veget surface model to run [NONE/CMIP6/xxxx]
	197
	198	........fin
[4405]	199	exit ;;
	200	"-v") version=$2 ; shift ; shift ;;
	201	"-r") svn=$2 ; shift ; shift ;;
	202	"-compiler") compiler=$2
[4215]	203	case $compiler in
[4405]	204	"gfortran"\|"ifort"\|"pgf90") compiler=$2 ; shift
	205	shift ;;
	206	*) echo "Only gfortran , ifort or pgf90 for the " \
	207	"compiler option"
	208	exit
[4215]	209	esac ;;
[4405]	210	"-d") grid_resolution=$2 ; shift ; shift ;;
	211	"-gprof") OPT_GPROF="-pg" ; shift ;;
[4417]	212	"-unstable"\|"-testing") trusting=`echo $1 \| cut -c2-` ; shift ;;
[4405]	213	"-cosp") cosp=$2
	214	case $cosp in
[4215]	215	"none"\|"v1"\|"v2") cosp=$2 ; shift ; shift ;;
	216	*) echo Only none v1 v2 for cosp option ; exit
[4405]	217	esac ;;
	218	"-nofcm") compile_with_fcm=0 ; echo This option will be reactivated soon '(promesse du 8dec2022)' ; exit 1 ; shift ;;
	219	"-SCM") SCM=1 ; shift ;;
	220	"-opt_makelmdz") OPT_MAKELMDZ="$2" ; shift ; shift ;;
	221	"-rrtm") rrtm="$2"
	222	if [ "$2" = "false" ] ; then
	223	rad="oldrad"
	224	else
	225	rad="rrtm"
	226	fi
	227	shift ; shift ;;
	228	"-rad") rad=$2
	229	case $rad in
[4215]	230	"oldrad"\|"rrtm"\|"ecrad") rad=$2 ; shift ; shift ;;
	231	*) echo Only oldrad rrtm ecrad for rad option ; exit
[4405]	232	esac ;;
	233	"-parallel") parallel=$2
[4215]	234	case $parallel in
[4405]	235	"none"\|"mpi"\|"omp"\|"mpi_omp") parallel=$2 ; shift
	236	shift ;;
	237	*) echo Only none mpi omp mpi_omp for the parallel \
	238	option
	239	exit
[4215]	240	esac ;;
[4405]	241	"-bench") bench=$2 ; shift ; shift ;;
	242	"-debug") optim=-debug ; shift ;;
	243	"-name") MODEL=$2 ; shift ; shift ;;
[4546]	244	"-netcdf") netcdf=$2 ; shift ; shift ;;
[4405]	245	"-physiq") physiq=$2 ; shift ; shift ;;
	246	"-xios") with_xios="y" ; shift ;;
	247	"-env_file") env_file=$2 ; shift ; shift ;;
	248	"-veget") veget=$2 ; shift ; shift ;;
[4546]	249	*) bash install_lmdz.sh -h ; exit
[4215]	250	esac
[4210]	251	done
	252
[4218]	253	# Option de compilation du rayonnement : depend de $mysvn ><= r4185,
	254	# sera donc definie plus bas
	255
[4210]	256	#opt_rad=""
	257	#case $rad in
	258	# rrtm) opt_rad="-rad rrtm" ;;
	259	# ecrad) opt_rad="-rad ecrad" ;;
	260	#esac
	261
[4807]	262
[4210]	263	# Option de compilation pour Cosp
	264	opt_cosp=""
[4784]	265	case $cosp in
[4215]	266	v1) opt_cosp="-cosp true" ;;
	267	v2) opt_cosp="-cospv2 true" ;;
[4210]	268	esac
	269
	270	# Check on veget version
	271	#if [ "$veget" != 'NONE' -a "$veget" != "CMIP6" -a "$veget" != +([0-9]) ] ; then
	272	if [ $veget != 'NONE' -a $veget != "CMIP6" ] ; then
	273	re='^[0-9]+$'
	274	if ! [[ $veget =~ $re ]] ; then
[4405]	275	echo 'Valeur de l option veget non valable'
	276	exit
[4210]	277	fi
	278	fi
	279
	280	#Define veget-related suffix for gcm name
	281	if [ "$veget" = 'NONE' ] ; then
	282	suff_orc=''
[4218]	283	#For use with tutorial, orchidee_rev is also defined (will be
	284	#written in surface_env at the end of the script)
[4210]	285	orchidee_rev=''
	286	else
	287	suff_orc='_orch'
	288	fi
	289
	290
[4218]	291	if [ $parallel = none ] ; then
	292	sequential=1; suff_exe='_seq'
	293	else
	294	sequential=0; suff_exe='_para_mem'
	295	fi
[4210]	296
	297	#Chemin pour placer le modele
	298	if [ "$MODEL" = "" ] ; then MODEL=./LMDZ$version$svn$optim ; fi
	299
	300
	301	arch=local
	302
	303
	304	if [ $compiler = g95 ] ; then echo g95 is not supported anymore ; exit ; fi
	305
	306	################################################################
	307	# Specificite des machines
	308	################################################################
	309
	310	hostname=`hostname`
	311	if [ "$pclinux" = 1 ] ; then o_ins_make="-t g95" ; else o_ins_make="" ; fi
	312
	313	case ${hostname:0:5} in
	314
[4215]	315	jean-) compiler="mpiifort" ;
	316	par_comp="mpiifort" ;
	317	o_ins_make="-t jeanzay" ;
	318	make=gmake ;
	319	module purge
	320	module load intel-compilers/19.0.4 ;
	321	#module load intel-mpi/19.0.4 ;
	322	#module load intel-mkl/19.0.4 ;
	323	module load hdf5/1.10.5-mpi ;
	324	module load netcdf/4.7.2-mpi ;
	325	module load netcdf-fortran/4.5.2-mpi ;
	326	module load subversion/1.9.7 ;
[4503]	327	module load cmake
[4508]	328	export NETCDF_LIBDIR=./
[4215]	329	export NETCDFFORTRAN_INCDIR=./
	330	export NETCDFFORTRAN_LIBDIR=./
	331	arch=X64_JEANZAY ;;
[4210]	332
[4215]	333	cicla\|camel) compiler="gfortran" ;
[4405]	334	module purge
	335	module load gnu/10.2.0
	336	module load openmpi/4.0.5
	337	module load hdf5/1.10.7-mpi
	338	module load netcdf-c/4.7.4-mpi
	339	module load netcdf-fortran/4.5.3-mpi
	340	netcdf=/net/nfs/tools/PrgEnv/linux-scientific6-x86_64/gcc-10.2.0/netcdf-fortran-4.5.3-k3drgfqok3lip62hnm3tsyof4cjen5sk
	341	module load svn/1.14.0
[4211]	342
[4405]	343	if [ $parallel != none ] ; then
	344	root_mpi=/net/nfs/tools/meso-sl6/openmpi/4.0.5-gcc-10.2.0
	345	path_mpi=$root_mpi/bin ;
	346	par_comp=${path_mpi}/mpif90 ;
	347	mpirun=${path_mpi}/mpirun ;
	348	fi ;
	349	arch=local ;
	350	make=make ;
	351	o_ins_make="-t g95" ;;
[4210]	352
[4215]	353	*) if [ $parallel = none -o -f /usr/bin/mpif90 ] ; then
	354	path_mpi=`which mpif90 \| sed -e s:/mpif90::` ;
	355	if [ -d /usr/lib64/openmpi ] ; then
	356	root_mpi="/usr/lib64/openmpi"
	357	else
	358	root_mpi="/usr"
	359	fi
	360	else
[4405]	361	echo "Cannot find mpif90" ;
	362	if [ $parallel = none ] ; then exit ; fi ;
[4215]	363	fi ;
	364	if [ $parallel != none ] ; then
[4405]	365	root_mpi=$(which mpif90 \| sed -e s:/bin/mpif90::)
	366	path_mpi=$(which mpif90 \| sed -e s:/mpif90::)
	367	export LD_LIBRARY_PATH=${root_mpi}/lib:$LD_LIBRARY_PATH
[4215]	368	fi
	369	par_comp=${path_mpi}/mpif90 ;
	370	mpirun=${path_mpi}/mpirun ;
	371	arch=local ;
	372	make=make ;
	373	o_ins_make="-t g95"
[4210]	374	esac
	375
	376	# Flags for parallelism:
	377	if [ $parallel != none ] ; then
[4215]	378	# MPI_LD are the flags needed for linking with MPI
	379	MPI_LD="-L${root_mpi}/lib -lmpi"
	380	if [ "$compiler" = "gfortran" ] ; then
[4405]	381	# MPI_FLAGS are the flags needed for compilation with MPI
	382	MPI_FLAGS="-fcray-pointer"
	383	# OMP_FLAGS are the flags needed for compilation with OpenMP
	384	OMP_FLAGS="-fopenmp -fcray-pointer"
	385	# OMP_LD are the flags needed for linking with OpenMP
	386	OMP_LD="-fopenmp"
[4215]	387	elif [ "$compiler" = "ifort" ] ; then
[4405]	388	MPI_FLAGS=""
	389	OMP_FLAGS="-openmp"
	390	OMP_LD="-openmp"
[4215]	391	else # pgf90
[4405]	392	MPI_FLAGS=""
	393	OMP_FLAGS="-mp"
	394	OMP_LD="-mp"
[4215]	395	fi
[4210]	396	fi
	397
	398	#####################################################################
	399	# Test for old gfortran compilers
	400	# If the compiler is too old (older than 4.3.x) we test if the
	401	# temporary gfortran44 patch is available on the computer in which
	402	# case the compiler is changed from gfortran to gfortran44
	403	# Must be aware than parallelism can not be activated in this case
	404	#####################################################################
	405
	406	if [ "$compiler" = "gfortran" ] ; then
[4215]	407	gfortran=gfortran
	408	gfortranv=`gfortran --version \| \
[4210]	409	head -1 \| awk ' { print $NF } ' \| awk -F. ' { print $1 * 10 + $2 } '`
[4215]	410	if [ $gfortranv -le 43 ] ; then
[4405]	411	echo ERROR : Your gfortran compiler is too old
	412	echo 'Please choose a new one (ifort) and change the line'
	413	echo compiler=xxx
	414	echo in the install_lmdz.sh script and rerun it
	415	if [ `which gfortran44 \| wc -w` -ne 0 ] ; then
[4215]	416	gfortran=gfortran44
[4405]	417	else
[4215]	418	echo gfotran trop vieux ; exit
[4405]	419	fi
[4215]	420	fi
	421	compiler=$gfortran
[4210]	422	fi
	423	#####################################################################
	424
	425	## if also compiling XIOS, parallel must be mpi_omp
	426	if [ "$with_xios" = "y" -a "$parallel" != "mpi_omp" ] ; then
[4215]	427	echo "Error, you must set -parallel mpi_omp if you want XIOS"
	428	exit
[4210]	429	fi
	430
	431	if [ "$with_xios" = "y" ] ; then
[4215]	432	opt_makelmdz_xios="-io xios"
[4210]	433	fi
	434
	435	if [ "$cosp" = "v2" -a "$with_xios" = "n" ] ; then
[4215]	436	echo "Error, Cospv2 cannot run without Xios"
	437	exit
[4210]	438	fi
	439
	440	echo '################################################################'
	441	echo Choix des options de compilation
	442	echo '################################################################'
	443
	444	export FC=$compiler
	445	export F90=$compiler
	446	export F77=$compiler
	447	export CPPFLAGS=
	448	OPTIMNC=$OPTIM
	449	BASE_LD="$OPT_GPROF"
	450	OPTPREC="$OPT_GPROF"
[4218]	451	ARFLAGS="rs"
[4418]	452	if [ "`lsb_release -i -s`" = "Ubuntu" ] ; then
[4398]	453	if [ "`lsb_release -r -s \| cut -d. -f1`" -ge 16 ] ; then
	454	ARFLAGS="rU"
[4218]	455	fi
	456	fi
[4210]	457
	458	if [ "$compiler" = "$gfortran" ] ; then
[4267]	459	OPTIM="-O3 $allow_arg_mismatch"
	460	OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all -fbacktrace -finit-real=snan $allow_arg_mismatch"
	461	OPTDEV="-Wall -fbounds-check $allow_arg_mismatch"
	462	fmod='I '
	463	OPTPREC="$OPTPREC -cpp -ffree-line-length-0"
	464	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE" ; fi
	465	export F90FLAGS=" -ffree-form $OPTIMNC"
	466	export FFLAGS=" $OPTIMNC"
	467	export CC=gcc
	468	export CXX=g++
	469	export fpp_flags="-P -C -traditional -ffreestanding"
[4210]	470
	471	elif [ $compiler = mpif90 ] ; then
[4215]	472	OPTIM='-O3'
	473	OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all"
	474	OPTDEV="-Wall -fbounds-check"
	475	BASE_LD="$BASE_LD -lblas"
	476	fmod='I '
[4218]	477	if [ $real = r8 ] ; then
[4405]	478	OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE -fcray-pointer"
[4218]	479	fi
[4215]	480	export F90FLAGS=" -ffree-form $OPTIMNC"
	481	export FFLAGS=" $OPTIMNC"
	482	export CC=gcc
	483	export CXX=g++
[4210]	484
	485	elif [ $compiler = pgf90 ] ; then
[4215]	486	OPTIM='-O2 -Mipa -Munroll -Mnoframe -Mautoinline -Mcache_align'
	487	OPTDEB='-g -Mdclchk -Mbounds -Mchkfpstk -Mchkptr -Minform=inform -Mstandard -Ktrap=fp -traceback'
	488	OPTDEV='-g -Mbounds -Ktrap=fp -traceback'
	489	fmod='module '
	490	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -r8 -DNC_DOUBLE" ; fi
	491	export CPPFLAGS="-DpgiFortran"
	492	export CC=pgcc
	493	export CFLAGS="-O2 -Msignextend"
	494	export CXX=pgCC
	495	export CXXFLAGS="-O2 -Msignextend"
	496	export FFLAGS="-O2 $OPTIMNC"
	497	export F90FLAGS="-O2 $OPTIMNC"
	498	compile_with_fcm=1
[4210]	499
[4221]	500	elif [[ $compiler = ifort \|\| $compiler = mpiifort ]] ; then
[4215]	501	OPTIM="-O2 -fp-model strict -ip -align all "
	502	OPTDEV="-p -g -O2 -traceback -fp-stack-check -ftrapuv -check"
	503	OPTDEB="-g -no-ftz -traceback -ftrapuv -fp-stack-check -check"
	504	fmod='module '
	505	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -real-size 64 -DNC_DOUBLE" ; fi
	506	export CPP="icc -E"
	507	export FFLAGS="-O2 -ip -fpic -mcmodel=large"
	508	export FCFLAGS="-O2 -ip -fpic -mcmodel=large"
	509	export CC=icc
	510	export CFLAGS="-O2 -ip -fpic -mcmodel=large"
	511	export CXX=icpc
	512	export CXXFLAGS="-O2 -ip -fpic -mcmodel=large"
	513	export fpp_flags="-P -traditional"
	514	# Pourquoi forcer la compilation fcm. Marche mieux sans
	515	#compile_with_fcm=1
[4210]	516	else
[4215]	517	echo unexpected compiler $compiler ; exit
[4210]	518	fi
	519
	520	OPTIMGCM="$OPTIM $OPTPREC"
	521
	522	hostname=`hostname`
	523
	524	##########################################################################
	525	# If installing on known machines such as Jean-Zay at IDRIS,
	526	# don't check for available software and don't install netcdf
	527	if [ ${hostname:0:5} = jean- ] ; then
[4215]	528	netcdf=0 # no need to recompile netcdf, alreday available
	529	check_linux=0
	530	pclinux=0
	531	ioipsl=0 # no need to recompile ioipsl, already available
	532	#netcdf="/smplocal/pub/NetCDF/4.1.3"
	533	compiler="mpiifort"
	534	fmod='module '
	535	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -i4 -r8 -DNC_DOUBLE" ; fi
	536	OPTIM="-auto -align all -O2 -fp-model strict -xHost "
	537	OPTIMGCM="$OPTIM $OPTPREC"
[4210]	538	fi
	539	##########################################################################
	540
	541
	542	mkdir -p $MODEL
	543	echo $MODEL
	544	MODEL=`( cd $MODEL ; pwd )` # to get absolute path, if necessary
	545
	546
	547	if [ "$check_linux" = 1 ] ; then
[4372]	548	echo '################################################################'
[4215]	549	echo Check if required software is available
	550	echo '################################################################'
[4210]	551
[4215]	552	#### Ehouarn: test if the required shell is available
	553	#### Maj FH-LF-AS 2021-04 : default=bash ; if bash missing, use ksh
	554	use_shell="bash" # default
	555	if [ "`which bash`" = "" ] ; then
[4405]	556	echo "no bash ; we will use ksh"
	557	use_shell="ksh"
	558	if [ "`which ksh`" = "" ] ; then
	559	echo "bash (or ksh) needed!! Install it!"
	560	exit
	561	fi
[4215]	562	fi
[4210]	563
[4372]	564	for logiciel in wget tar gzip make $compiler gcc cmake m4 c++ ; do
[4405]	565	if [ "`which $logiciel`" = "" ] ; then
	566	echo You must first install $logiciel on your system
	567	exit
	568	fi
[4215]	569	done
[4210]	570
[4215]	571	if [ $pclinux = 1 ] ; then
[4405]	572	cd $MODEL
	573	cat <<eod > tt.f90
[4210]	574	print*,'coucou'
	575	end
	576	eod
[4405]	577	$compiler tt.f90 -o a.out
	578	./a.out >\| tt
	579	if [ "`cat tt \| sed -e 's/ //g' `" != "coucou" ] ; then
	580	echo problem installing with compiler $compiler ; exit ; fi
	581	\rm tt a.out tt.f90
[4215]	582	fi
[4210]	583	fi
	584
	585	###########################################################################
	586	if [ $getlmdzor = 1 -a ! -d $MODEL/modipsl ] ; then
[4267]	587	###########################################################################
	588	echo '##########################################################'
	589	echo Download a slightly modified version of LMDZ
	590	echo '##########################################################'
	591	cd $MODEL
	592	getlog=`pwd`/get.log
	593	echo logfile : $getlog
[4417]	594	myget src_archives/$trusting/modipsl.$version.tar.gz >> get.log 2>&1
[4267]	595	echo install_lmdz.sh wget_OK `date`
	596	gunzip modipsl.$version.tar.gz >> get.log 2>&1
[4286]	597	tar xf modipsl.$version.tar >> get.log 2>&1
[4267]	598	\rm modipsl.$version.tar
[4210]	599	fi
	600
	601	###########################################################################
[4546]	602	echo Installing Netcdf
[4405]	603	###########################################################################
[4546]	604
	605	if [ $netcdf = 0 ] ; then
	606	ncdfdir=/usr
	607
	608	else
[4215]	609	cd $MODEL
[4212]	610
[4405]	611	case $compiler in
	612	gfortran) opt1="-compiler gnu" ; opt2="-CC gcc -FC gfortran -CXX g++" ;;
	613	ifort) opt1="-compiler intel" ; opt2="-CC icc -FC ifort -CXX icpc" ;;
	614	pgf90) opt1="-compiler pgf90" ; opt2="-CC pgcc -FC pgf90 -CXX pgCC" ;;
	615	*) echo "unexpected compiler $compiler" for netcdf ; exit 1
	616	esac
[4212]	617
[4405]	618	case $with_xios in
	619	n) script_install_netcdf=install_netcdf4_hdf5_seq.bash
[4546]	620	ncdfdir=netcdf4_hdf5_seq
[4405]	621	opt_=$opt1 ;;
	622	y) script_install_netcdf=install_netcdf4_hdf5.bash
[4546]	623	ncdfdir=netcdf4_hdf5
[4405]	624	opt_="$opt2 -MPI $root_mpi" ;;
	625	*) echo with_xios=$with_xios, should be n or y ; exit 1
	626	esac
[4546]	627	if [ $netcdf = 1 ] ; then
	628	ncdfdir=$MODEL/$ncdfdir
	629	else
	630	mkdir -p $netcdf ; ncdfdir=$netcdf/$ncdfdir
	631	fi
[4405]	632
[4546]	633	echo Repertoire netcdf $ncdfdir
	634	if [ ! -d $ncdfdir ] ; then
	635	netcdflog=`pwd`/netcdf.log
	636	echo '----------------------------------------------------------'
	637	echo Compiling the Netcdf library
	638	echo '----------------------------------------------------------'
	639	echo log file : $netcdflog
[4411]	640	myget script_install/$script_install_netcdf >> $netcdflog 2>&1
[4405]	641	chmod u=rwx $script_install_netcdf
	642	./$script_install_netcdf -prefix $ncdfdir $opt_ >> $netcdflog 2>&1
	643	fi
	644
	645	#----------------------------------------------------------------------------
	646	# LF rajout d'une verrue, pour une raison non encore expliquee,
	647	# la librairie est parfois rangée dans lib64 et non dans lib
	648	# par certains compilateurs
	649	if [ ! -e lib -a -d lib64 ] ; then ln -s lib64 lib; fi
	650	#----------------------------------------------------------------------------
	651
[4215]	652	echo install_lmdz.sh netcdf_OK `date`
[4210]	653
	654	fi
	655
[4238]	656	cat >test_netcdf90.f90 <<EOF
[4239]	657	use netcdf
[4238]	658	print *, "NetCDF library version: ", nf90_inq_libvers()
	659	end
	660	EOF
	661
[4405]	662	$compiler -I$ncdfdir/include test_netcdf90.f90 -L$ncdfdir/lib -lnetcdff \
	663	-lnetcdf -Wl,-rpath=$ncdfdir/lib && ./a.out
[4238]	664
	665	if (($? == 0))
	666	then
	667	rm test_netcdf90.f90 a.out
	668	else
	669	echo "Failed test program using NetCDF-Fortran."
	670	echo "You can:"
	671	echo "- check that you have NetCDF-Fortran installed in your system"
	672	echo "- or specify an installation directory with option -netcdf of" \
[4405]	673	"install_lmdz.sh"
[4238]	674	echo "- or download and compile NetCDF-Fortran with option -netcdf 1 of" \
[4405]	675	"install_lmdz.sh"
[4238]	676	exit 1
	677	fi
	678
[4210]	679	#=========================================================================
	680	if [[ ! -f $MODEL/modipsl/lib/libioipsl.a ]]
	681	then
[4215]	682	if [ $ioipsl = 1 ] ; then
[4405]	683	#=====================================================================
	684	echo OK ioipsl=$ioipsl
	685	echo '##########################################################'
	686	echo 'Installing MODIPSL, the installation package manager for the '
	687	echo 'IPSL models and tools'
	688	echo '##########################################################'
	689	echo `date`
[4210]	690
[4405]	691	cd $MODEL/modipsl
	692	\rm -rf lib/*
	693	cd util
	694	cp AA_make.gdef AA_make.orig
	695	F_C="$compiler -c "
	696	if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ]
	697	then
	698	F_C="$compiler -c -cpp "
	699	fi
	700	if [ "$compiler" = "pgf90" ] ; then F_C="$compiler -c -Mpreprocess" ; fi
	701	sed -e 's/^\#..g95..\#.*.$/\#/' AA_make.gdef > tmp
	702	sed -e "s:F_L = g95:F_L = $compiler:" \
	703	-e "s:F_C = g95 -c -cpp:F_C = $F_C": \
	704	-e 's/g95..w_w..(F_D)/g95 w_w = '"$OPTIMGCM"'/' \
	705	-e 's:g95..NCDF_INC..$:g95 NCDF_INC= '"$ncdfdir"'/include:' \
	706	-e 's:g95..NCDF_LIB..$:g95 NCDF_LIB= -L'"$ncdfdir"'/lib -lnetcdff -lnetcdf:' \
	707	-e 's:g95 L_O =:g95 L_O = -Wl,-rpath='"$ncdfdir"'/lib:' \
	708	-e "s:-fmod=:-$fmod:" -e 's/-fno-second-underscore//' \
	709	-e 's:#-Q- g95 M_K = gmake:#-Q- g95 M_K = make:' \
	710	tmp >\| AA_make.gdef
[4210]	711
[4405]	712	if [ $pcmac == 1 ]
	713	then
	714	cp AA_make.gdef tmp
	715	sed -e 's/rpath=/rpath,/g' tmp > AA_make.gdef
	716	fi
[4210]	717
	718
[4405]	719	# We use lines for g95 even for the other compilers to run ins_make
	720	if [ "$use_shell" = "ksh" ] ; then
	721	./ins_make $o_ins_make
	722	else # bash
	723	sed -e s:/bin/ksh:/bin/bash:g ins_make > ins_make.bash
	724	if [ "`grep jeanzay AA_make.gdef`" = "" ] ; then
	725	# Bidouille pour compiler sur ada des vieux modipsl.tar
	726	echo 'Warning jean-zay not in AA_make.gdef'
	727	echo 'Think about updating'
	728	exit 1
	729	fi
[4210]	730
[4405]	731	chmod u=rwx ins_make.bash
	732	./ins_make.bash $o_ins_make
	733	fi # of if [ "$use_shell" = "ksh" ]
[4210]	734
[4405]	735	echo install_lmdz.sh MODIPSL_OK `date`
[4210]	736
[4405]	737	cd $MODEL/modipsl/modeles/IOIPSL/src
	738	ioipsllog=`pwd`/ioipsl.log
	739	echo '##########################################################'
	740	echo 'Compiling IOIPSL, the interface library with Netcdf'
	741	echo '##########################################################'
	742	echo `date`
	743	echo log file : $ioipsllog
[4210]	744
[4405]	745	if [ "$use_shell" = "bash" ] ; then
	746	cp Makefile Makefile.ksh
	747	sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile
	748	fi
[4508]	749	### if [ "$pclinux" = 1 ] ; then
[4405]	750	# Build IOIPSL modules and library
	751	$make clean
	752	$make > $ioipsllog 2>&1
	753	if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then
	754	# copy module files to lib
	755	cp -f *.mod ../../../lib
	756	fi
	757	# Build IOIPSL tools (ie: "rebuild", if present)
[4542]	758	# For IOIPSLv_2_2_2, "rebuild" files are in IOIPSL/tools
	759	rebuild_dir=""
[4508]	760	if [ -f $MODEL/modipsl/modeles/IOIPSL/tools/rebuild ] ; then
[4542]	761	rebuild_dir=$MODEL/modipsl/modeles/IOIPSL/tools
	762	elif [ -d $MODEL/modipsl/modeles/IOIPSL/rebuild ] ; then
	763	rebuild_dir=$MODEL/modipsl/modeles/IOIPSL/rebuild
	764	fi
	765	if [ $rebuild_dir != "" ] ; then
	766	cd $rebuild_dir
[4405]	767	# adapt Makefile & rebuild script if in bash
	768	if [ "$use_shell" = "bash" ] ; then
	769	cp Makefile Makefile.ksh
	770	sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile
	771	cp rebuild rebuild.ksh
	772	sed -e 's:/bin/ksh:/bin/bash:g' \
	773	-e 's:print -u2:echo:g' \
	774	-e 's:print:echo:g' rebuild.ksh > rebuild
	775	fi
	776	$make clean
	777	$make > $ioipsllog 2>&1
	778	fi
[4508]	779	### fi # of if [ "$pclinux" = 1 ] which is commented out
[4210]	780
[4508]	781	else # of if [ $ioipsl = 1 ]
[4405]	782	if [ ${hostname:0:5} = jean- ] ; then
	783	cd $MODEL/modipsl
	784	cd util
[4215]	785	if [ "`grep jeanzay AA_make.gdef`" = "" ] ; then
[4405]	786	echo 'Warning jean-zay not in AA_make.gdef'
	787	echo 'Think about updating'
	788	exit 1
[4215]	789	fi
	790	./ins_make $o_ins_make
[4405]	791	# Compile IOIPSL on jean-zay
[4215]	792	cd $MODEL/modipsl/modeles/IOIPSL/src
	793	gmake > ioipsl.log
[4508]	794	# For IOIPSLv_2_2_2, "rebuild" files are in IOIPSL/tools, so "gmake" in IOIPSL/tools is enough
	795	# For IOIPSLv_2_2_5, "rebuild" files are in a separate IOIPSL/rebuild folder , while "tools" only contains "FCM"
	796	if [ -f $MODEL/modipsl/modeles/IOIPSL/tools/Makefile ] ; then
[4502]	797	cd $MODEL/modipsl/modeles/IOIPSL/tools
	798	gmake > ioipsl.log
	799	fi
[4508]	800	if [ -d $MODEL/modipsl/modeles/IOIPSL/rebuild ] ; then
	801	cd $MODEL/modipsl/modeles/IOIPSL/rebuild
	802	gmake > ioipsl.log
	803	fi
	804
[4405]	805	fi
	806	echo install_lmdz.sh ioipsl_OK `date`
[4215]	807	fi # of if [ $ioipsl = 1 ]
[4508]	808	fi # of if [[ ! -f $MODEL/modipsl/lib/libioipsl.a ]]
[4210]	809
	810	#=========================================================================
	811	if [ "$with_xios" = "y" ] ; then
[4215]	812	echo '##########################################################'
	813	echo 'Compiling XIOS'
	814	echo '##########################################################'
	815	cd $MODEL/modipsl/modeles
	816	xioslog=`pwd`/xios.log
	817	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/install_xios.bash
[4411]	818	myget script_install/install_xios.bash
[4215]	819	chmod u=rwx install_xios.bash
[4709]	820	# following will be recalculated later on once LMDZ is updated
	821	# mysvn=`svnversion LMDZ \| egrep -o "[0-9]+" 2>/dev/null`
	822	mysvn=`grep 'Revision: [0-9]' $MODEL/Read*.md \| awk ' { print $2 } ' 2>/dev/null`
	823	if [ "$svn" != "" ] ; then mysvn=$svn ; fi
	824	echo mysvn $mysvn
	825
[4215]	826	if [ ${hostname:0:5} = jean- ] ; then
[4708]	827	if [ $mysvn -ge 4619 ] ; then
[4919]	828	svn co http://forge.ipsl.fr/ioserver/svn/XIOS2/branches/xios-2.6 \
[4405]	829	XIOS
[4708]	830	else
[4919]	831	svn co http://forge.ipsl.fr/ioserver/svn/XIOS2/branches/xios-2.5 \
[4708]	832	XIOS
	833	fi
[4405]	834	cd XIOS/arch
	835	svn update
	836	cd ..
	837	echo "Compiling XIOS, start" `date` \
	838	"(it takes about 20 min on Jean-Zay)"
	839	echo "log file: $xioslog"
	840	./make_xios --prod --arch $arch --job 4 > xios.log 2>&1
[4215]	841	else
[4405]	842	./install_xios.bash -prefix $MODEL/modipsl/modeles \
	843	-netcdf ${ncdfdir} -hdf5 ${ncdfdir} \
	844	-MPI $root_mpi -arch $arch > xios.log 2>&1
[4215]	845	fi # of case Jean-Zay
	846	if [ -f XIOS/lib/libxios.a ] ; then
[4405]	847	echo "XIOS library successfully generated"
	848	echo install_lmdz.sh XIOS_OK `date`
[4215]	849	fi
[4210]	850	fi
	851
	852	#============================================================================
	853	veget_version=false
	854	if [ "$veget" != 'NONE' ] ; then
[4215]	855	cd $MODEL/modipsl/modeles/ORCHIDEE
	856	set +e ; svn upgrade ; set -e
	857	if [ "$veget" = "CMIP6" ] ; then
[4405]	858	veget_version=orchidee2.0
	859	orchidee_rev=6592
[4215]	860	else # specific orchidee revision newer than CMIP6, on 2_1 or 2_2 branches
[4405]	861	veget_version=orchidee2.1
	862	orchidee_rev=$veget
	863	if [ $veget -lt 4465 ] ; then
	864	echo 'Stopping, ORCHIDEE version too old, script needs work on ' \
	865	'the CPP flags to pass to makelmdz'
	866	exit 1
	867	fi
	868	set +e
	869	# which branch is my version on?
[4919]	870	orcbranch=`svn log -v -q svn://forge.ipsl.fr/orchidee/ -r $veget \|grep ORCHIDEE \|head -1\| sed -e 's:ORCHIDEE/.*$:ORCHIDEE:' \| awk '{print $2}'`
[4405]	871	# switch to that branch
	872	echo IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at \
	873	orchidee-help@listes.ipsl.fr
	874	svn switch -r $veget --accept theirs-full \
[4919]	875	svn://forge.ipsl.fr/orchidee/$orcbranch
[4405]	876	svn log -r $veget \| grep $veget
	877	if [ $? -gt 0 ] ; then
[4218]	878	echo 'Cannot update ORCHIDEE as not on the right branch for ' \
[4405]	879	'ORCHIDEE'
[4215]	880	exit
[4405]	881	fi
	882	set -e
	883	set +e ; svn update -r $veget ; set -e
[4215]	884	fi
	885	# Correctif suite debug Jean-Zay
[4218]	886	sed -i -e 's/9010 FORMAT(A52,F17.14)/9010 FORMAT(A52,F20.14)/' \
[4405]	887	src_stomate/stomate.f90
[4215]	888	opt_orc="-prod" ; if [ "$optim" = "-debug" ] ; then opt_orc="-debug" ; fi
[4210]	889
[4215]	890	orchideelog=`pwd`/orchidee.log
	891	echo '########################################################'
	892	echo 'Compiling ORCHIDEE, the continental surface model '
	893	echo '########################################################'
	894	echo Start of the first compilation of orchidee, in sequential mode: `date`
	895	echo log file : $orchideelog
[4210]	896
[4215]	897	export ORCHPATH=`pwd`
	898	xios_orchid="-noxios"
	899	if [ "$with_xios" = "y" ] ; then
[4405]	900	xios_orchid="-xios"
[4215]	901	fi
	902	if [ -d tools ] ; then
[4405]	903	###################################################################
	904	# Pour les experts qui voudraient changer de version d'orchidee.
	905	# Attention : necessite d'avoir le password pour orchidee
[4210]	906
[4405]	907	# Correctif suite debug Jean-Zay
	908	if [ -f src_global/time.f90 ] ; then
	909	sed -i -e 's/CALL tlen2itau/\!CALL tlen2itau/' src_global/time.f90
	910	fi
	911	###################################################################
	912	if [ "$veget_version" == "false" ] ; then
	913	veget_version=orchidee2.0
	914	fi
	915	cd arch
	916	sed -e s:"%COMPILER .*.$":"%COMPILER $compiler":1 \
	917	-e s:"%LINK .*.$":"%LINK $compiler":1 \
	918	-e s:"%FPP_FLAGS .*.$":"%FPP_FLAGS $fpp_flags":1 \
	919	-e s:"%PROD_FFLAGS .*.$":"%PROD_FFLAGS $OPTIM":1 \
	920	-e s:"%DEV_FFLAGS .*.$":"%DEV_FFLAGS $OPTDEV":1 \
	921	-e s:"%DEBUG_FFLAGS .*.$":"%DEBUG_FFLAGS $OPTDEB":1 \
	922	-e s:"%BASE_FFLAGS .*.$":"%BASE_FFLAGS $OPTPREC":1 \
	923	-e s:"%BASE_LD .*.$":"%BASE_LD $BASE_LD":1 \
	924	-e s:"%ARFLAGS .*.$":"%ARFLAGS $ARFLAGS":1 \
	925	arch-gfortran.fcm > arch-local.fcm
	926	echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib -lnetcdff -lnetcdf\"" \
	927	> arch-local.path
	928	echo "NETCDF_INCDIR=${ncdfdir}/include" >> arch-local.path
	929	echo "IOIPSL_INCDIR=$ORCHPATH/../../lib" >> arch-local.path
	930	echo "IOIPSL_LIBDIR=$ORCHPATH/../../lib" >> arch-local.path
	931	echo 'XIOS_INCDIR=${ORCHDIR}/../XIOS/inc' >> arch-local.path
	932	echo 'XIOS_LIBDIR="${ORCHDIR}/../XIOS/lib -lxios"' >> arch-local.path
	933	cd ../
[4210]	934
[4405]	935	echo ./makeorchidee_fcm -j $xios_orchid $opt_orc -parallel none \
	936	-arch $arch
	937	./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel none \
	938	-arch $arch > $orchideelog 2>&1
	939	pwd
[4215]	940	else # of "if [ -d tools ]"
[4405]	941	if [ -d src_parallel ] ; then
	942	liste_src="parallel parameters global stomate sechiba driver"
	943	if [ "$veget_version" == "false" ] ; then
	944	veget_version=orchidee2.0
	945	fi
	946	fi
	947	for d in $liste_src ; do
	948	src_d=src_$d
	949	echo src_d $src_d
	950	echo ls ; ls
	951	if [ ! -d $src_d ] ; then
	952	echo Problem orchidee : no $src_d ; exit
	953	fi
	954	cd $src_d ; \rm -f *.mod make ; $make clean
	955	$make > $orchideelog 2>&1
	956	if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then
	957	cp -f *.mod ../../../lib
	958	fi
	959	cd ..
	960	done
[4215]	961	fi # of "if [ -d tools ]"
	962	echo install_lmdz.sh orchidee_compil_seq_OK `date`
[4210]	963	fi # of if [ "$veget" != 'NONE' ]
	964
	965
	966	#============================================================================
	967	# Ehouarn: the directory name LMDZ* depends on version/tar file...
	968	if [ -d $MODEL/modipsl/modeles/LMD* ] ; then
[4215]	969	echo '###############################################################'
	970	echo 'Preparing LMDZ compilation : arch file, svn switch if needed...'
	971	echo '###############################################################'
	972	cd $MODEL/modipsl/modeles/LMD*
	973	LMDZPATH=`pwd`
[4210]	974	else
[4215]	975	echo "ERROR: No LMD* directory !!!"
	976	exit
[4210]	977	fi
	978
	979	###########################################################
	980	# For those who want to use fcm to compile via :
	981	# makelmdz_fcm -arch local .....
	982	############################################################
	983
	984
	985
	986	cd $MODEL/modipsl/modeles/LMDZ*
	987	lmdzlog=`pwd`/lmdz.log
	988
	989	##################################################################
	990	# Possibly update LMDZ if a specific svn release is requested
	991	##################################################################
	992
	993	set +e ; svn upgrade ; set -e
	994
	995	if [ "$svn" = "last" ] ; then svnopt="" ; else svnopt="-r $svn" ; fi
	996	if [ "$svn" != "" ] ; then
[4634]	997	set +e ; svn info \| grep -q 'https:'
[4210]	998	if [ $? = 0 ] ; then
[4634]	999	svn switch --relocate https://svn.lmd.jussieu.fr/LMDZ \
	1000	http://svn.lmd.jussieu.fr/LMDZ
[4210]	1001	fi
	1002	svn update $svnopt
[4372]	1003	set -e
[4210]	1004	fi
	1005
[4372]	1006	#---------------------------------------------------------------------
[4218]	1007	# Retrieve the final svn release number, and adjust compilation
	1008	# options accordingly
[4372]	1009	# If svn not available, will use the svn writen in $MODEL/Readm*md
	1010	# For old version it assumes that it is before 4185 (the version
	1011	# for which the test was introduced
	1012	#---------------------------------------------------------------------
[4210]	1013
[4372]	1014	set +e ; mysvn=`svnversion . \| egrep -o "[0-9]+" 2>/dev/null` ; set -e
	1015	if [ "$mysvn" = "" ] ; then mysvn=`grep 'Revision: [0-9]' $MODEL/Read*.md \| awk ' { print $2 } ' 2>/dev/null` ; fi
	1016	if [ "$mysvn" = "" ] ; then mysvn=4190 ; fi
	1017
[4427]	1018	if [[ "$pclinux" = "1" && ! -f arch/arch-local.path ]] ; then
	1019
	1020	# create local 'arch' files (if on Linux PC):
	1021	cd arch
	1022	# arch-local.path file
	1023	# test for version as arch.pth file changed format with rev 4426
	1024	if [ "$mysvn" -gt 4425 ] ; then
	1025	echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib \"" > arch-local.path
	1026	echo "NETCDF_LIB=\"-lnetcdff -lnetcdf\"" >> arch-local.path
	1027	echo "NETCDF_INCDIR=-I${ncdfdir}/include" >> arch-local.path
	1028	echo 'NETCDF95_INCDIR=-I$LMDGCM/../../include' >> arch-local.path
	1029	echo 'NETCDF95_LIBDIR=-L$LMDGCM/../../lib' >> arch-local.path
	1030	echo 'NETCDF95_LIB=-lnetcdf95' >> arch-local.path
	1031	echo 'IOIPSL_INCDIR=-I$LMDGCM/../../lib' >> arch-local.path
	1032	echo 'IOIPSL_LIBDIR=-L$LMDGCM/../../lib' >> arch-local.path
	1033	echo 'IOIPSL_LIB=-lioipsl' >> arch-local.path
	1034	echo 'XIOS_INCDIR=-I$LMDGCM/../XIOS/inc' >> arch-local.path
	1035	echo 'XIOS_LIBDIR=-L$LMDGCM/../XIOS/lib' >> arch-local.path
	1036	echo "XIOS_LIB=\"-lxios -lstdc++\"" >> arch-local.path
	1037	echo 'ORCH_INCDIR=-I$LMDGCM/../../lib' >> arch-local.path
	1038	echo 'ORCH_LIBDIR=-L$LMDGCM/../../lib' >> arch-local.path
	1039	else
	1040	echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib -lnetcdff -lnetcdf\"" \
	1041	> arch-local.path
	1042	echo "NETCDF_INCDIR=-I${ncdfdir}/include" >> arch-local.path
	1043	echo 'NETCDF95_INCDIR=$LMDGCM/../../include' >> arch-local.path
	1044	echo 'NETCDF95_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
	1045	echo 'IOIPSL_INCDIR=$LMDGCM/../../lib' >> arch-local.path
	1046	echo 'IOIPSL_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
	1047	echo 'XIOS_INCDIR=$LMDGCM/../XIOS/inc' >> arch-local.path
	1048	echo 'XIOS_LIBDIR=$LMDGCM/../XIOS/lib' >> arch-local.path
	1049	echo 'ORCH_INCDIR=$LMDGCM/../../lib' >> arch-local.path
	1050	echo 'ORCH_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
	1051	fi
	1052
	1053	if [ $pcmac == 1 ] ; then
	1054	BASE_LD="$BASE_LD -Wl,-rpath,${ncdfdir}/lib"
	1055	else
	1056	BASE_LD="$BASE_LD -Wl,-rpath=${ncdfdir}/lib"
	1057	fi
	1058	# Arch-local.fcm file (adapted from arch-linux-32bit.fcm)
	1059
	1060	if [ $real = r8 ] ; then FPP_DEF=NC_DOUBLE ; else FPP_DEF="" ; fi
	1061	sed -e s:"%COMPILER .*.$":"%COMPILER $compiler":1 \
	1062	-e s:"%LINK .*.$":"%LINK $compiler":1 \
	1063	-e s:"%PROD_FFLAGS .*.$":"%PROD_FFLAGS $OPTIM":1 \
	1064	-e s:"%DEV_FFLAGS .*.$":"%DEV_FFLAGS $OPTDEV":1 \
	1065	-e s:"%DEBUG_FFLAGS .*.$":"%DEBUG_FFLAGS $OPTDEB":1 \
	1066	-e s:"%BASE_FFLAGS .*.$":"%BASE_FFLAGS $OPTPREC":1 \
	1067	-e s:"%FPP_DEF .*.$":"%FPP_DEF $FPP_DEF":1 \
	1068	-e s:"%BASE_LD .*.$":"%BASE_LD $BASE_LD":1 \
	1069	-e s:"%ARFLAGS .*.$":"%ARFLAGS $ARFLAGS":1 \
	1070	arch-linux-32bit.fcm > arch-local.fcm
	1071
	1072	cd ..
	1073	### Adapt "bld.cfg" (add the shell):
	1074	#whereisthatshell=$(which ${use_shell})
	1075	#echo "bld::tool::SHELL $whereisthatshell" >> bld.cfg
	1076
	1077	fi # of if [ "$pclinux" = 1 ]
[4372]	1078	#---------------------------------------------------------------------
[4210]	1079	# Option de compilation du rayonnement : depend de $mysvn ><= r4185
[4372]	1080	#---------------------------------------------------------------------
[4210]	1081	opt_rad=""
	1082
	1083	case $rad in
	1084	oldrad) iflag_rrtm=0 ; NSW=2 ; opt_rad="" ;;
[4218]	1085	rrtm) iflag_rrtm=1 ; NSW=6
[4405]	1086	if [ $mysvn -le 4185 ] ; then
	1087	opt_rad="-rrtm true"
	1088	else
	1089	opt_rad="-rad rrtm"
	1090	fi ;;
[4210]	1091	ecrad) iflag_rrtm=2 ; NSW=6 ; opt_rad="-rad ecrad" ;;
	1092	*) echo Only oldrad rrtm ecrad for rad option ; exit
	1093	esac
	1094
[4218]	1095	if [ $mysvn -le 4185 -a $rad = "ecrad" ] ; then
	1096	echo "ecrad only available for LMDZ rev starting with 4186 " ; exit
	1097	fi
[4210]	1098
	1099	##################################################################
	1100
[4213]	1101
[4577]	1102	if [[ ! -f libf/misc/netcdf95.F90 && ! -d $MODEL/NetCDF95-0.3 ]]
[4213]	1103	then
	1104	cd $MODEL
[4577]	1105	myget src_archives/netcdf/NetCDF95-0.3.tar.gz
	1106	tar -xf NetCDF95-0.3.tar.gz
	1107	rm NetCDF95-0.3.tar.gz
	1108	cd NetCDF95-0.3
[4213]	1109	mkdir build
	1110	cd build
	1111	cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=$ncdfdir \
[4405]	1112	-DCMAKE_INSTALL_PREFIX=$MODEL/modipsl
[4213]	1113	make install
	1114	cd $MODEL/modipsl/modeles/LMDZ*
	1115	fi
	1116
[4210]	1117	echo '##################################################################'
	1118	echo "Preparing script compile.sh for LMDZ compilation"
	1119	echo "It will only be run automatically if bench=1/tuto"
	1120	echo Here bench=$bench
	1121	echo '##################################################################'
	1122
[4218]	1123	if [ "$env_file" != "" ] ; then
	1124	mv arch/arch-${arch}.env arch/arch-${arch}.orig
	1125	\cp -f $env_file arch/arch-${arch}.env
	1126	fi
[4210]	1127
[4218]	1128	if [ $compile_with_fcm = 1 ] ; then
	1129	makelmdz="makelmdz_fcm $optim -arch $arch -j 8 "
	1130	else
	1131	makelmdz="makelmdz $optim -arch $arch"
	1132	fi
[4210]	1133
	1134	# sequential compilation
	1135	if [ "$sequential" = 1 ] ; then
[4215]	1136	echo Sequential compilation command, saved in compile.sh:
[4218]	1137	echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp " \
[4405]	1138	"-d ${grid_resolution} -v $veget_version gcm "
[4218]	1139	echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp " \
[4405]	1140	"-d ${grid_resolution} -v $veget_version gcm " > compile.sh
[4215]	1141	chmod +x ./compile.sh
	1142	if [ $bench = 1 ] ; then
[4405]	1143	echo install_lmdz.sh start_lmdz_seq_compilation `date`
	1144	echo log file: $lmdzlog
	1145	./compile.sh > $lmdzlog 2>&1
	1146	echo install_lmdz.sh end_lmdz_seq_compilation `date`
[4215]	1147	fi
[4210]	1148	fi # fin sequential
	1149
	1150	# compiling in parallel mode
	1151	if [ $parallel != "none" ] ; then
	1152	echo '##########################################################'
[4215]	1153	echo ' Parallel compile '
[4210]	1154	echo '##########################################################'
[4215]	1155	echo "(after saving the sequential libs and binaries)"
	1156	cd $MODEL/modipsl
	1157	tar cf sequential.tar bin/ lib/
	1158	#
	1159	# Orchidee
	1160	#
	1161	cd $ORCHPATH
	1162	if [ -d src_parallel -a $veget != 'NONE' ] ; then
[4405]	1163	cd arch
	1164	sed \
	1165	-e s:"%COMPILER.*.$":"%COMPILER $par_comp":1 \
	1166	-e s:"%LINK.*.$":"%LINK $par_comp":1 \
	1167	-e s:"%MPI_FFLAG.*.$":"%MPI_FFLAGS $MPI_FLAGS":1 \
	1168	-e s:"%OMP_FFLAG.*.$":"%OMP_FFLAGS $OMP_FLAGS":1 \
	1169	-e s:"%MPI_LD.*.$":"%MPI_LD $MPI_LD":1 \
	1170	-e s:"%OMP_LD.*.$":"%OMP_LD $OMP_LD":1 \
	1171	arch-local.fcm > tmp.fcm
[4210]	1172
[4405]	1173	mv tmp.fcm arch-local.fcm
	1174	cd ../
	1175	echo Compiling ORCHIDEE in parallel mode `date`
	1176	echo logfile $orchideelog
	1177	echo "NOTE : to recompile it when necessary, use ./compile_orc.sh " \
	1178	"in modipsl/modeles/ORCHIDEE"
	1179	echo ./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc \
	1180	-parallel $parallel -arch $arch > compile_orc.sh
	1181	echo ./makeorchidee_fcm -j 8 $xios_orchid $opt_orc \
	1182	-parallel $parallel -arch $arch >> compile_orc.sh
	1183	echo echo Now you must also recompile LMDZ, by running ./compile.sh \
	1184	in modeles/LMDZ >> compile_orc.sh
	1185	chmod u+x compile_orc.sh
	1186	./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc \
	1187	-parallel $parallel -arch $arch > $orchideelog 2>&1
	1188	./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel $parallel \
	1189	-arch $arch >> $orchideelog 2>&1
	1190	echo End of ORCHIDEE compilation in parallel mode `date`
[4215]	1191	elif [ $veget != 'NONE' ] ; then
[4405]	1192	echo '##########################################################'
	1193	echo ' Orchidee version too old '
	1194	echo ' Please update to new version '
	1195	echo '##########################################################'
	1196	exit
[4215]	1197	fi # of [ -d src_parallel -a $veget != 'NONE' ]
[4210]	1198
[4215]	1199	# LMDZ
	1200	cd $LMDZPATH
	1201	if [ $arch = local ] ; then
[4405]	1202	cd arch
	1203	sed -e s:"%COMPILER.*.$":"%COMPILER $par_comp":1 \
	1204	-e s:"%LINK.*.$":"%LINK $par_comp":1 \
	1205	-e s:"%MPI_FFLAG.*.$":"%MPI_FFLAGS $MPI_FLAGS":1 \
	1206	-e s:"%OMP_FFLAG.*.$":"%OMP_FFLAGS $OMP_FLAGS":1 \
	1207	-e s:"%ARFLAGS.*.$":"%ARFLAGS $ARFLAGS":1 \
	1208	-e s@"%BASE_LD.*.$"@"%BASE_LD -Wl,-rpath=${root_mpi}/lib:${ncdfdir}/lib"@1 \
	1209	-e s:"%MPI_LD.*.$":"%MPI_LD $MPI_LD":1 \
	1210	-e s:"%OMP_LD.*.$":"%OMP_LD $OMP_LD":1 \
	1211	arch-local.fcm > tmp.fcm
	1212	mv tmp.fcm arch-local.fcm
	1213	cd ../
[4215]	1214	fi
	1215	rm -f compile.sh
	1216	echo resol=${grid_resolution} >> compile.sh
	1217	if [ ${hostname:0:5} = jean- -a "$cosp" = "v2" ] ; then
[4210]	1218
[4405]	1219	echo LMDZ compilation command in parallel mode, saved in compile.sh, \
	1220	is :
	1221	echo "(ATTENTION le probleme de cospv2 sur jean-zay en mode prod " \
	1222	"n est pas corrige ! )"
	1223	# ATTENTION le probleme de cospv2 sur jean-zay en mode prod n
	1224	# est pas corrige
	1225	echo ./$makelmdz -dev $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
	1226	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
	1227	-parallel $parallel gcm >> compile.sh
	1228	echo ./$makelmdz -dev $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
	1229	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
	1230	-parallel $parallel gcm
[4215]	1231	else
[4405]	1232	echo ./$makelmdz $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
	1233	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
	1234	-parallel $parallel gcm >> compile.sh
	1235	echo ./$makelmdz $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
	1236	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
	1237	-parallel $parallel gcm
[4215]	1238	fi
	1239	chmod +x ./compile.sh
[4210]	1240
[4215]	1241	if [ $bench = 1 ] ; then
[4405]	1242	echo Compiling LMDZ in parallel mode `date`, LMDZ log file: $lmdzlog
	1243	./compile.sh > $lmdzlog 2>&1
[4215]	1244	fi
	1245
[4210]	1246	fi # of if [ $parallel != "none" ]
	1247
	1248
	1249	##################################################################
	1250	# Verification du succes de la compilation
	1251	##################################################################
	1252
	1253	# Recherche de l'executable dont le nom a change au fil du temps ...
	1254	# suffix contains radiative option starting with revision 4186
	1255	if [ $mysvn -ge 4186 ] ; then suff_exe=_${rad}${suff_exe} ; fi
	1256	gcm=""
[4219]	1257
[4218]	1258	for exe in gcm.e bin/gcm_${grid_resolution}_phylmd${suff_exe}${suff_orc}.e
	1259	do
	1260	if [ -f $exe ] ; then gcm=$exe ; fi
[4210]	1261	done
	1262
	1263	if [ "$gcm" = "" ] ; then
[4215]	1264	if [ $bench = 1 ] ; then
[4405]	1265	echo 'Compilation failed !! Cannot run the benchmark;'
	1266	exit
[4215]	1267	else
[4405]	1268	echo 'Compilation not done (only done when bench=1)'
[4215]	1269	fi
[4210]	1270	else
[4215]	1271	echo '##########################################################'
	1272	echo 'Compilation successfull !! ' `date`
	1273	echo '##########################################################'
	1274	echo The executable is $gcm
[4210]	1275	fi
	1276
	1277	##################################################################
	1278	# Below, we run a benchmark if bench=1 or tuto
	1279	##################################################################
	1280
	1281	if [ $bench = tuto ] ; then
[4286]	1282	myget Training/tutorial.tar ; tar xf tutorial.tar ; cd TUTORIAL
[4218]	1283	./init.sh
[4210]	1284
	1285	elif [[ $bench = 1 && ! -d BENCH${grid_resolution} ]] ; then
[4215]	1286	# TOUTE CETTE SECTION DEVRAIT DISPARAITRE POUR UNE COMMANDE
	1287	# OU DES BENCHS PAR MOTS CLES COMME tuto
[4210]	1288
[4215]	1289	echo '##########################################################'
	1290	echo ' Running a test run '
	1291	echo '##########################################################'
[4210]	1292
[4215]	1293	\rm -rf BENCH${grid_resolution}
	1294	bench=bench_lmdz_${grid_resolution}
	1295	echo install_lmdz.sh before bench download `date`
	1296	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/$bench.tar.gz
	1297	myget 3DBenchs/$bench.tar.gz
	1298	echo install_lmdz.sh after bench download `date`
[4286]	1299	tar xf $bench.tar.gz
[4210]	1300
[4215]	1301	if [ "$cosp" = "v1" -o "$cosp" = "v2" ] ; then
[4405]	1302	cd BENCH${grid_resolution}
	1303	# copier les fichiers namelist input et output our COSP
	1304	cp ../DefLists/cosp*_input_nl.txt .
	1305	cp ../DefLists/cosp*_output_nl.txt .
	1306	# Activer la cles ok_cosp pour tourner avec COSP
	1307	sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp
	1308	\mv -f tmp config.def
	1309	cd ..
[4215]	1310	fi
[4210]	1311
[4215]	1312	if [ -n "$physiq" ]; then
[4405]	1313	cd BENCH${grid_resolution}
	1314	if [ -f physiq.def_${physiq} ]; then
	1315	cp physiq.def_${physiq} physiq.def
	1316	echo using physiq.def_${physiq}
	1317	else
	1318	echo using standard physiq.def
	1319	fi
	1320	cd ..
[4215]	1321	else
[4405]	1322	echo using standard physiq.def
[4215]	1323	fi
[4210]	1324
[4215]	1325	if [ "$with_xios" = "y" ] ; then
[4405]	1326	cd BENCH${grid_resolution}
	1327	cp ../DefLists/iodef.xml .
	1328	cp ../DefLists/context_lmdz.xml .
	1329	cp ../DefLists/field_def_lmdz.xml .
	1330	# A raffiner par la suite
	1331	echo A FAIRE : Copier les *xml en fonction de l option cosp
	1332	cp ../DefLists/field_def_cosp*.xml .
	1333	cp ../DefLists/file_def_hist*xml .
	1334	# adapt iodef.xml to use attached mode
	1335	sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' \
	1336	iodef.xml > tmp
	1337	\mv -f tmp iodef.xml
[4210]	1338
[4405]	1339	# and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
	1340	# except for histday
	1341	for histfile in file_def_hist*xml
	1342	do
	1343	if [ "$histfile" = "file_def_histday_lmdz.xml" ] ; then
	1344	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' \
	1345	$histfile > tmp
	1346	\mv -f tmp $histfile
	1347	sed -e 's@output_level="_AUTO_"@output_level="5"@' $histfile \
	1348	> tmp
	1349	\mv -f tmp $histfile
	1350	sed -e 's@compression_level="2"@compression_level="0"@' \
	1351	$histfile > tmp
	1352	\mv -f tmp $histfile
	1353	else
	1354	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
	1355	$histfile > tmp
	1356	\mv -f tmp $histfile
	1357	fi
	1358	done
	1359	# and add option "ok_all_xml=y" in config.def
	1360	echo "### XIOS outputs" >> config.def
	1361	echo 'ok_all_xml=.true.' >> config.def
[4210]	1362
[4405]	1363	#activer les sorties pour Cosp
	1364	if [ "$cosp" = "v1" ] ; then
[4807]	1365	sed -i'' -e 's@enabled=".FALSE."@enabled=".TRUE."@' \
	1366	-e 's@output_level="_AUTO_"@output_level="5"@' \
	1367	-e 's@compression_level="2"@compression_level="0"@' \
	1368	file_def_histdayCOSP_lmdz.xml
[4405]	1369	fi
	1370	if [ "$cosp" = "v2" ] ; then
[4807]	1371	sed -e 's@compression_level="2"@compression_level="0"@' file_def_histdayCOSPv2_lmdz.xml
	1372	for type_ in hf day mth ; do
	1373	file=file_def_hist${type_}COSP
	1374	sed -i'' -e 's@src="./'${file}'_lmdz.xml"@src="./'${file}'v2_lmdz.xml"@' context_lmdz.xml
	1375	done
	1376	sed -i '' -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' field_def_lmdz.xml
[4405]	1377	fi
[4210]	1378
[4405]	1379	cd ..
[4215]	1380	fi
[4210]	1381
[4215]	1382	# Cas Bensh avec ecrad
	1383	if [ "$rad" = "ecrad" ] ; then
[4405]	1384	cd BENCH${grid_resolution}
	1385	cp ../DefLists/namelist_ecrad .
	1386	cp -r ../libf/phylmd/ecrad/data .
	1387	cd ..
[4215]	1388	fi
[4210]	1389
[4215]	1390	# Adjusting bench physiq.def to radiative code chosen
	1391	cd BENCH${grid_resolution}
[4218]	1392	sed -e 's/iflag_rrtm=.*.$/iflag_rrtm='$iflag_rrtm'/' \
[4405]	1393	-e 's/NSW=.*.$/NSW='$NSW'/' physiq.def > tmpdef
[4215]	1394	\mv tmpdef physiq.def
	1395	cd ..
[4210]	1396
[4215]	1397	cp $gcm BENCH${grid_resolution}/gcm.e
[4210]	1398
[4215]	1399	cd BENCH${grid_resolution}
	1400	# On cree le fichier bench.sh au besoin
	1401	# Dans le cas 48x36x39 le bench.sh existe deja en parallele
[4210]	1402
[4215]	1403	if [ "$grid_resolution" = "48x36x39" ] ; then
[4405]	1404	echo On ne touche pas au bench.sh
	1405	# But we have to adapt "run_local.sh" for $mpirun
	1406	sed -e "s@mpirun@$mpirun@g" run_local.sh > tmp
	1407	mv -f tmp run_local.sh
	1408	chmod u=rwx run_local.sh
[4215]	1409	elif [ "${parallel:0:3}" = "mpi" ] ; then
[4405]	1410	# Lancement avec deux procs mpi et 2 openMP
	1411	echo "export OMP_STACKSIZE=800M" > bench.sh
	1412	if [ "${parallel:4:3}" = "omp" ] ; then
[4215]	1413	echo "export OMP_NUM_THREADS=2" >> bench.sh
[4405]	1414	fi
	1415	if [ "$cosp" = "v1" -o "$cosp" = "v2" ] ; then
[4215]	1416	if [ ${hostname:0:5} = jean- ] ; then
[4405]	1417	chmod +x ../arch.env
	1418	../arch.env
	1419	echo "ulimit -s 2000000" >> bench.sh
[4215]	1420	else
[4405]	1421	echo "ulimit -s 200000" >> bench.sh
	1422	fi
	1423	else
[4215]	1424	echo "ulimit -s unlimited" >> bench.sh
[4405]	1425	fi
	1426	if [ ${hostname:0:5} = jean- ] ; then
[4215]	1427	. ../arch/arch-${arch}.env
[4218]	1428	echo "srun -n 2 -A $idris_acct@cpu gcm.e > listing 2>&1" \
[4405]	1429	>> bench.sh
	1430	else
[4215]	1431	echo "$mpirun -np 2 gcm.e > listing 2>&1" >> bench.sh
[4405]	1432	fi
	1433	# Add rebuild, using reb.sh if it is there
	1434	echo 'if [ -f reb.sh ] ; then' >> bench.sh
	1435	echo ' ./reb.sh histday ; ./reb.sh histmth ; ./reb.sh histhf ; ' \
	1436	'./reb.sh histins ; ./reb.sh stomate_history ; ' \
	1437	'./reb.sh sechiba_history ; ./reb.sh sechiba_out_2 ' >> bench.sh
	1438	echo 'fi' >> bench.sh
[4215]	1439	else
[4405]	1440	echo "./gcm.e > listing 2>&1" > bench.sh
[4215]	1441	fi
	1442	# Getting orchidee stuff
	1443	if [ $veget == 'CMIP6' ] ; then
[4405]	1444	#echo 'myget 3DBenchs/BENCHorch11.tar.gz'
	1445	#myget 3DBenchs/BENCHorch11.tar.gz
	1446	#tar xvzf BENCHorch11.tar.gz
	1447	echo 'myget 3DBenchs/BENCHCMIP6.tar.gz'
	1448	myget 3DBenchs/BENCHCMIP6.tar.gz
	1449	tar xvzf BENCHCMIP6.tar.gz
	1450	sed -e "s:VEGET=n:VEGET=y:" config.def > tmp
	1451	mv -f tmp config.def
	1452	if [ "$with_xios" = "y" ] ; then
[4215]	1453	cp ../../ORCHIDEE/src_xml/context_orchidee.xml .
[4218]	1454	echo '<context id="orchidee" src="./context_orchidee.xml"/>' \
[4405]	1455	> add.tmp
[4215]	1456	cp ../../ORCHIDEE/src_xml/field_def_orchidee.xml .
	1457	cp ../../ORCHIDEE/src_xml/file_def_orchidee.xml .
	1458	cp ../../ORCHIDEE/src_xml/file_def_input_orchidee.xml .
	1459	if [ -f ../../ORCHIDEE/src_xml/context_input_orchidee.xml ] ; then
[4405]	1460	cp ../../ORCHIDEE/src_xml/context_input_orchidee.xml .
	1461	echo '<context id="orchidee" ' \
	1462	'src="./context_input_orchidee.xml"/>' >> add.tmp
[4215]	1463	fi
	1464	sed -e '/id="LMDZ"/r add.tmp' iodef.xml > tmp
	1465	mv tmp iodef.xml
[4218]	1466	sed -e'{/sechiba1/ s/enabled="_AUTO_"/type="one_file" enabled=".TRUE."/}' \
[4405]	1467	file_def_orchidee.xml > tmp
	1468	\mv -f tmp file_def_orchidee.xml
[4218]	1469	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
[4405]	1470	file_def_orchidee.xml > tmp
	1471	\mv -f tmp file_def_orchidee.xml
[4218]	1472	sed -e 's@output_level="_AUTO_"@output_level="1"@' \
[4405]	1473	file_def_orchidee.xml > tmp
	1474	\mv -f tmp file_def_orchidee.xml
[4218]	1475	sed -e 's@output_freq="_AUTO_"@output_freq="1d"@' \
[4405]	1476	file_def_orchidee.xml > tmp
	1477	\mv -f tmp file_def_orchidee.xml
[4218]	1478	sed -e 's@compression_level="4"@compression_level="0"@' \
[4405]	1479	file_def_orchidee.xml > tmp
	1480	\mv -f tmp file_def_orchidee.xml
[4218]	1481	sed -e 's@XIOS_ORCHIDEE_OK = n@XIOS_ORCHIDEE_OK = y@' \
[4405]	1482	orchidee.def > tmp
	1483	\mv -f tmp orchidee.def
	1484	fi
[4215]	1485	fi
[4220]	1486
	1487	if [[ -f ../arch.env ]]
	1488	then
[4405]	1489	source ../arch.env
[4220]	1490	fi
	1491
[4215]	1492	echo EXECUTION DU BENCH
	1493	set +e
	1494	date ; ./bench.sh > out.bench 2>&1 ; date
	1495	set -e
	1496	tail listing
[4210]	1497
	1498
[4215]	1499	echo '##########################################################'
	1500	echo 'Simulation finished in' `pwd`
	1501	echo 'You have compiled with:'
	1502	cat ../compile.sh
	1503	if [ $parallel = "none" ] ; then
[4405]	1504	echo 'You may re-run it with : cd ' `pwd` ' ; gcm.e'
	1505	echo 'or ./bench.sh'
[4215]	1506	else
[4405]	1507	echo 'You may re-run it with : '
	1508	echo 'cd ' `pwd` '; ./bench.sh'
	1509	# echo 'ulimit -s unlimited'
	1510	# echo 'export OMP_NUM_THREADS=2'
	1511	# echo 'export OMP_STACKSIZE=800M'
	1512	# echo "$mpirun -np 2 gcm.e "
[4215]	1513	fi
	1514	echo '##########################################################'
[4210]	1515
	1516	fi # bench
	1517
	1518
	1519	#################################################################
	1520	# Installation eventuelle du 1D
	1521	#################################################################
	1522
	1523	if [ $SCM = 1 ] ; then
[4215]	1524	cd $MODEL
	1525	myget 1D/1D.tar.gz
[4286]	1526	tar xf 1D.tar.gz
[4215]	1527	cd 1D
[4422]	1528	if [ $rad = oldrad ] ; then
	1529	sed -i'' -e 's/^rad=.*$/rad=oldrad/' run.sh
	1530	sed -i'' -e 's/^rad=.*$/rad=oldrad/' bin/compile
	1531	fi
[4877]	1532	if [ $rad = ecrad ] ; then
	1533	sed -i'' -e 's/^rad=.*$/rad=ecrad/' run.sh
	1534	sed -i'' -e 's/^rad=.*$/rad=ecrad/' bin/compile
	1535	fi
[4409]	1536	echo Running 1D/run.sh, log in `pwd`/run1d.log
[4457]	1537	./run.sh > `pwd`/run1d.log 2>&1
[4210]	1538	fi
	1539
[4409]	1540
[4210]	1541	#################################################################
	1542	# sauvegarde des options veget pour utilisation eventuelle tutorial_prod
	1543	#################################################################
	1544	cd $MODEL/modipsl/modeles
	1545	#echo surface_env file created in $MODEL
	1546	echo 'veget='$veget > surface_env
	1547	#opt_veget="-v $veget_version"
	1548	#echo 'opt_veget="'$opt_veget\" >> surface_env
	1549	echo 'opt_veget="'-v $veget_version\" >> surface_env
	1550	echo 'orchidee_rev='$orchidee_rev >> surface_env
	1551	echo 'suforch='$suff_orc >> surface_env

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