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source: BOL/script_install/install_lmdz.sh @ 4542

Last change on this file since 4542 was 4542, checked in by asima, 17 months ago
Add treatment of "rebuild" tool for IOIPSLv_2_2_5, for "ioipsl=1" (similar to rev 4508 for "ioipsl=0 and Jean-Zay")
Property svn:executable set to ``*
File size: 57.4 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
[4520]	74	version=20230412.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
[4269]	86	if [ `gfortran -dumpversion \| cut -d. -f1` -ge 11 ] ; 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 ;;
	244	"-netcdf") case $2 in
[4398]	245	0\|1) netcdf=$2 ;;
	246	*) netcdf=`ls -d $2` ; if [ $? != 0 ] ; then echo No directory $2 ; exit 1 ; fi
	247	esac
	248	shift ; shift ;;
[4405]	249	"-physiq") physiq=$2 ; shift ; shift ;;
	250	"-xios") with_xios="y" ; shift ;;
	251	"-env_file") env_file=$2 ; shift ; shift ;;
	252	"-veget") veget=$2 ; shift ; shift ;;
	253	*) ./install_lmdz.sh -h ; exit
[4215]	254	esac
[4210]	255	done
	256
[4218]	257	# Option de compilation du rayonnement : depend de $mysvn ><= r4185,
	258	# sera donc definie plus bas
	259
[4210]	260	#opt_rad=""
	261	#case $rad in
	262	# rrtm) opt_rad="-rad rrtm" ;;
	263	# ecrad) opt_rad="-rad ecrad" ;;
	264	#esac
	265
	266
	267	# Option de compilation pour Cosp
	268	opt_cosp=""
	269	case cosp in
[4215]	270	v1) opt_cosp="-cosp true" ;;
	271	v2) opt_cosp="-cospv2 true" ;;
[4210]	272	esac
	273
	274	# Check on veget version
	275	#if [ "$veget" != 'NONE' -a "$veget" != "CMIP6" -a "$veget" != +([0-9]) ] ; then
	276	if [ $veget != 'NONE' -a $veget != "CMIP6" ] ; then
	277	re='^[0-9]+$'
	278	if ! [[ $veget =~ $re ]] ; then
[4405]	279	echo 'Valeur de l option veget non valable'
	280	exit
[4210]	281	fi
	282	fi
	283
	284	#Define veget-related suffix for gcm name
	285	if [ "$veget" = 'NONE' ] ; then
	286	suff_orc=''
[4218]	287	#For use with tutorial, orchidee_rev is also defined (will be
	288	#written in surface_env at the end of the script)
[4210]	289	orchidee_rev=''
	290	else
	291	suff_orc='_orch'
	292	fi
	293
	294
[4218]	295	if [ $parallel = none ] ; then
	296	sequential=1; suff_exe='_seq'
	297	else
	298	sequential=0; suff_exe='_para_mem'
	299	fi
[4210]	300
	301	#Chemin pour placer le modele
	302	if [ "$MODEL" = "" ] ; then MODEL=./LMDZ$version$svn$optim ; fi
	303
	304
	305	arch=local
	306
	307
	308	if [ $compiler = g95 ] ; then echo g95 is not supported anymore ; exit ; fi
	309
	310	################################################################
	311	# Specificite des machines
	312	################################################################
	313
	314	hostname=`hostname`
	315	if [ "$pclinux" = 1 ] ; then o_ins_make="-t g95" ; else o_ins_make="" ; fi
	316
	317	case ${hostname:0:5} in
	318
[4215]	319	jean-) compiler="mpiifort" ;
	320	par_comp="mpiifort" ;
	321	o_ins_make="-t jeanzay" ;
	322	make=gmake ;
	323	module purge
	324	module load intel-compilers/19.0.4 ;
	325	#module load intel-mpi/19.0.4 ;
	326	#module load intel-mkl/19.0.4 ;
	327	module load hdf5/1.10.5-mpi ;
	328	module load netcdf/4.7.2-mpi ;
	329	module load netcdf-fortran/4.5.2-mpi ;
	330	module load subversion/1.9.7 ;
[4503]	331	module load cmake
[4508]	332	export NETCDF_LIBDIR=./
[4215]	333	export NETCDFFORTRAN_INCDIR=./
	334	export NETCDFFORTRAN_LIBDIR=./
	335	arch=X64_JEANZAY ;;
[4210]	336
[4215]	337	cicla\|camel) compiler="gfortran" ;
[4405]	338	module purge
	339	module load gnu/10.2.0
	340	module load openmpi/4.0.5
	341	module load hdf5/1.10.7-mpi
	342	module load netcdf-c/4.7.4-mpi
	343	module load netcdf-fortran/4.5.3-mpi
	344	netcdf=/net/nfs/tools/PrgEnv/linux-scientific6-x86_64/gcc-10.2.0/netcdf-fortran-4.5.3-k3drgfqok3lip62hnm3tsyof4cjen5sk
	345	module load svn/1.14.0
[4211]	346
[4405]	347	if [ $parallel != none ] ; then
	348	root_mpi=/net/nfs/tools/meso-sl6/openmpi/4.0.5-gcc-10.2.0
	349	path_mpi=$root_mpi/bin ;
	350	par_comp=${path_mpi}/mpif90 ;
	351	mpirun=${path_mpi}/mpirun ;
	352	fi ;
	353	arch=local ;
	354	make=make ;
	355	o_ins_make="-t g95" ;;
[4210]	356
[4215]	357	*) if [ $parallel = none -o -f /usr/bin/mpif90 ] ; then
	358	path_mpi=`which mpif90 \| sed -e s:/mpif90::` ;
	359	if [ -d /usr/lib64/openmpi ] ; then
	360	root_mpi="/usr/lib64/openmpi"
	361	else
	362	root_mpi="/usr"
	363	fi
	364	else
[4405]	365	echo "Cannot find mpif90" ;
	366	if [ $parallel = none ] ; then exit ; fi ;
[4215]	367	fi ;
	368	if [ $parallel != none ] ; then
[4405]	369	root_mpi=$(which mpif90 \| sed -e s:/bin/mpif90::)
	370	path_mpi=$(which mpif90 \| sed -e s:/mpif90::)
	371	export LD_LIBRARY_PATH=${root_mpi}/lib:$LD_LIBRARY_PATH
[4215]	372	fi
	373	par_comp=${path_mpi}/mpif90 ;
	374	mpirun=${path_mpi}/mpirun ;
	375	arch=local ;
	376	make=make ;
	377	o_ins_make="-t g95"
[4210]	378	esac
	379
	380	# Flags for parallelism:
	381	if [ $parallel != none ] ; then
[4215]	382	# MPI_LD are the flags needed for linking with MPI
	383	MPI_LD="-L${root_mpi}/lib -lmpi"
	384	if [ "$compiler" = "gfortran" ] ; then
[4405]	385	# MPI_FLAGS are the flags needed for compilation with MPI
	386	MPI_FLAGS="-fcray-pointer"
	387	# OMP_FLAGS are the flags needed for compilation with OpenMP
	388	OMP_FLAGS="-fopenmp -fcray-pointer"
	389	# OMP_LD are the flags needed for linking with OpenMP
	390	OMP_LD="-fopenmp"
[4215]	391	elif [ "$compiler" = "ifort" ] ; then
[4405]	392	MPI_FLAGS=""
	393	OMP_FLAGS="-openmp"
	394	OMP_LD="-openmp"
[4215]	395	else # pgf90
[4405]	396	MPI_FLAGS=""
	397	OMP_FLAGS="-mp"
	398	OMP_LD="-mp"
[4215]	399	fi
[4210]	400	fi
	401
	402	#####################################################################
	403	# Test for old gfortran compilers
	404	# If the compiler is too old (older than 4.3.x) we test if the
	405	# temporary gfortran44 patch is available on the computer in which
	406	# case the compiler is changed from gfortran to gfortran44
	407	# Must be aware than parallelism can not be activated in this case
	408	#####################################################################
	409
	410	if [ "$compiler" = "gfortran" ] ; then
[4215]	411	gfortran=gfortran
	412	gfortranv=`gfortran --version \| \
[4210]	413	head -1 \| awk ' { print $NF } ' \| awk -F. ' { print $1 * 10 + $2 } '`
[4215]	414	if [ $gfortranv -le 43 ] ; then
[4405]	415	echo ERROR : Your gfortran compiler is too old
	416	echo 'Please choose a new one (ifort) and change the line'
	417	echo compiler=xxx
	418	echo in the install_lmdz.sh script and rerun it
	419	if [ `which gfortran44 \| wc -w` -ne 0 ] ; then
[4215]	420	gfortran=gfortran44
[4405]	421	else
[4215]	422	echo gfotran trop vieux ; exit
[4405]	423	fi
[4215]	424	fi
	425	compiler=$gfortran
[4210]	426	fi
	427	#####################################################################
	428
	429	## if also compiling XIOS, parallel must be mpi_omp
	430	if [ "$with_xios" = "y" -a "$parallel" != "mpi_omp" ] ; then
[4215]	431	echo "Error, you must set -parallel mpi_omp if you want XIOS"
	432	exit
[4210]	433	fi
	434
	435	if [ "$with_xios" = "y" ] ; then
[4215]	436	opt_makelmdz_xios="-io xios"
[4210]	437	fi
	438
	439	if [ "$cosp" = "v2" -a "$with_xios" = "n" ] ; then
[4215]	440	echo "Error, Cospv2 cannot run without Xios"
	441	exit
[4210]	442	fi
	443
	444	echo '################################################################'
	445	echo Choix des options de compilation
	446	echo '################################################################'
	447
	448	export FC=$compiler
	449	export F90=$compiler
	450	export F77=$compiler
	451	export CPPFLAGS=
	452	OPTIMNC=$OPTIM
	453	BASE_LD="$OPT_GPROF"
	454	OPTPREC="$OPT_GPROF"
[4218]	455	ARFLAGS="rs"
[4418]	456	if [ "`lsb_release -i -s`" = "Ubuntu" ] ; then
[4398]	457	if [ "`lsb_release -r -s \| cut -d. -f1`" -ge 16 ] ; then
	458	ARFLAGS="rU"
[4218]	459	fi
	460	fi
[4210]	461
	462	if [ "$compiler" = "$gfortran" ] ; then
[4267]	463	OPTIM="-O3 $allow_arg_mismatch"
	464	OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all -fbacktrace -finit-real=snan $allow_arg_mismatch"
	465	OPTDEV="-Wall -fbounds-check $allow_arg_mismatch"
	466	fmod='I '
	467	OPTPREC="$OPTPREC -cpp -ffree-line-length-0"
	468	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE" ; fi
	469	export F90FLAGS=" -ffree-form $OPTIMNC"
	470	export FFLAGS=" $OPTIMNC"
	471	export CC=gcc
	472	export CXX=g++
	473	export fpp_flags="-P -C -traditional -ffreestanding"
[4210]	474
	475	elif [ $compiler = mpif90 ] ; then
[4215]	476	OPTIM='-O3'
	477	OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all"
	478	OPTDEV="-Wall -fbounds-check"
	479	BASE_LD="$BASE_LD -lblas"
	480	fmod='I '
[4218]	481	if [ $real = r8 ] ; then
[4405]	482	OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE -fcray-pointer"
[4218]	483	fi
[4215]	484	export F90FLAGS=" -ffree-form $OPTIMNC"
	485	export FFLAGS=" $OPTIMNC"
	486	export CC=gcc
	487	export CXX=g++
[4210]	488
	489	elif [ $compiler = pgf90 ] ; then
[4215]	490	OPTIM='-O2 -Mipa -Munroll -Mnoframe -Mautoinline -Mcache_align'
	491	OPTDEB='-g -Mdclchk -Mbounds -Mchkfpstk -Mchkptr -Minform=inform -Mstandard -Ktrap=fp -traceback'
	492	OPTDEV='-g -Mbounds -Ktrap=fp -traceback'
	493	fmod='module '
	494	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -r8 -DNC_DOUBLE" ; fi
	495	export CPPFLAGS="-DpgiFortran"
	496	export CC=pgcc
	497	export CFLAGS="-O2 -Msignextend"
	498	export CXX=pgCC
	499	export CXXFLAGS="-O2 -Msignextend"
	500	export FFLAGS="-O2 $OPTIMNC"
	501	export F90FLAGS="-O2 $OPTIMNC"
	502	compile_with_fcm=1
[4210]	503
[4221]	504	elif [[ $compiler = ifort \|\| $compiler = mpiifort ]] ; then
[4215]	505	OPTIM="-O2 -fp-model strict -ip -align all "
	506	OPTDEV="-p -g -O2 -traceback -fp-stack-check -ftrapuv -check"
	507	OPTDEB="-g -no-ftz -traceback -ftrapuv -fp-stack-check -check"
	508	fmod='module '
	509	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -real-size 64 -DNC_DOUBLE" ; fi
	510	export CPP="icc -E"
	511	export FFLAGS="-O2 -ip -fpic -mcmodel=large"
	512	export FCFLAGS="-O2 -ip -fpic -mcmodel=large"
	513	export CC=icc
	514	export CFLAGS="-O2 -ip -fpic -mcmodel=large"
	515	export CXX=icpc
	516	export CXXFLAGS="-O2 -ip -fpic -mcmodel=large"
	517	export fpp_flags="-P -traditional"
	518	# Pourquoi forcer la compilation fcm. Marche mieux sans
	519	#compile_with_fcm=1
[4210]	520	else
[4215]	521	echo unexpected compiler $compiler ; exit
[4210]	522	fi
	523
	524	OPTIMGCM="$OPTIM $OPTPREC"
	525
	526	hostname=`hostname`
	527
	528	##########################################################################
	529	# If installing on known machines such as Jean-Zay at IDRIS,
	530	# don't check for available software and don't install netcdf
	531	if [ ${hostname:0:5} = jean- ] ; then
[4215]	532	netcdf=0 # no need to recompile netcdf, alreday available
	533	check_linux=0
	534	pclinux=0
	535	ioipsl=0 # no need to recompile ioipsl, already available
	536	#netcdf="/smplocal/pub/NetCDF/4.1.3"
	537	compiler="mpiifort"
	538	fmod='module '
	539	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -i4 -r8 -DNC_DOUBLE" ; fi
	540	OPTIM="-auto -align all -O2 -fp-model strict -xHost "
	541	OPTIMGCM="$OPTIM $OPTPREC"
[4210]	542	fi
	543	##########################################################################
	544
	545
	546	mkdir -p $MODEL
	547	echo $MODEL
	548	MODEL=`( cd $MODEL ; pwd )` # to get absolute path, if necessary
	549
	550
	551	if [ "$check_linux" = 1 ] ; then
[4372]	552	echo '################################################################'
[4215]	553	echo Check if required software is available
	554	echo '################################################################'
[4210]	555
[4215]	556	#### Ehouarn: test if the required shell is available
	557	#### Maj FH-LF-AS 2021-04 : default=bash ; if bash missing, use ksh
	558	use_shell="bash" # default
	559	if [ "`which bash`" = "" ] ; then
[4405]	560	echo "no bash ; we will use ksh"
	561	use_shell="ksh"
	562	if [ "`which ksh`" = "" ] ; then
	563	echo "bash (or ksh) needed!! Install it!"
	564	exit
	565	fi
[4215]	566	fi
[4210]	567
[4372]	568	for logiciel in wget tar gzip make $compiler gcc cmake m4 c++ ; do
[4405]	569	if [ "`which $logiciel`" = "" ] ; then
	570	echo You must first install $logiciel on your system
	571	exit
	572	fi
[4215]	573	done
[4210]	574
[4215]	575	if [ $pclinux = 1 ] ; then
[4405]	576	cd $MODEL
	577	cat <<eod > tt.f90
[4210]	578	print*,'coucou'
	579	end
	580	eod
[4405]	581	$compiler tt.f90 -o a.out
	582	./a.out >\| tt
	583	if [ "`cat tt \| sed -e 's/ //g' `" != "coucou" ] ; then
	584	echo problem installing with compiler $compiler ; exit ; fi
	585	\rm tt a.out tt.f90
[4215]	586	fi
[4210]	587	fi
	588
	589	###########################################################################
	590	if [ $getlmdzor = 1 -a ! -d $MODEL/modipsl ] ; then
[4267]	591	###########################################################################
	592	echo '##########################################################'
	593	echo Download a slightly modified version of LMDZ
	594	echo '##########################################################'
	595	cd $MODEL
	596	getlog=`pwd`/get.log
	597	echo logfile : $getlog
[4417]	598	myget src_archives/$trusting/modipsl.$version.tar.gz >> get.log 2>&1
[4267]	599	echo install_lmdz.sh wget_OK `date`
	600	gunzip modipsl.$version.tar.gz >> get.log 2>&1
[4286]	601	tar xf modipsl.$version.tar >> get.log 2>&1
[4267]	602	\rm modipsl.$version.tar
[4210]	603	fi
	604
	605	###########################################################################
[4217]	606	if [ $netcdf = 1 ] ; then
[4405]	607	###########################################################################
[4215]	608	cd $MODEL
	609	netcdflog=`pwd`/netcdf.log
[4405]	610	echo '----------------------------------------------------------'
[4215]	611	echo Compiling the Netcdf library
[4405]	612	echo '----------------------------------------------------------'
[4215]	613	echo log file : $netcdflog
[4212]	614
[4405]	615	case $compiler in
	616	gfortran) opt1="-compiler gnu" ; opt2="-CC gcc -FC gfortran -CXX g++" ;;
	617	ifort) opt1="-compiler intel" ; opt2="-CC icc -FC ifort -CXX icpc" ;;
	618	pgf90) opt1="-compiler pgf90" ; opt2="-CC pgcc -FC pgf90 -CXX pgCC" ;;
	619	*) echo "unexpected compiler $compiler" for netcdf ; exit 1
	620	esac
[4212]	621
[4405]	622	case $with_xios in
	623	n) script_install_netcdf=install_netcdf4_hdf5_seq.bash
	624	ncdfdir=$MODEL/netcdf4_hdf5_seq
	625	opt_=$opt1 ;;
	626	y) script_install_netcdf=install_netcdf4_hdf5.bash
	627	ncdfdir=$MODEL/netcdf4_hdf5
	628	opt_="$opt2 -MPI $root_mpi" ;;
	629	*) echo with_xios=$with_xios, should be n or y ; exit 1
	630	esac
	631
	632	if [[ ! -d $ncdfdir ]] ; then
[4411]	633	myget script_install/$script_install_netcdf >> $netcdflog 2>&1
[4405]	634	chmod u=rwx $script_install_netcdf
	635	./$script_install_netcdf -prefix $ncdfdir $opt_ >> $netcdflog 2>&1
	636	fi
	637
	638	#----------------------------------------------------------------------------
	639	# LF rajout d'une verrue, pour une raison non encore expliquee,
	640	# la librairie est parfois rangée dans lib64 et non dans lib
	641	# par certains compilateurs
	642	if [ ! -e lib -a -d lib64 ] ; then ln -s lib64 lib; fi
	643	#----------------------------------------------------------------------------
	644
[4215]	645	echo install_lmdz.sh netcdf_OK `date`
[4210]	646
[4405]	647	elif [ $netcdf = 0 ] ; then
[4215]	648	ncdfdir=/usr
[4210]	649	else
[4215]	650	ncdfdir=$netcdf
[4210]	651	fi
	652
[4238]	653	cat >test_netcdf90.f90 <<EOF
[4239]	654	use netcdf
[4238]	655	print *, "NetCDF library version: ", nf90_inq_libvers()
	656	end
	657	EOF
	658
[4405]	659	$compiler -I$ncdfdir/include test_netcdf90.f90 -L$ncdfdir/lib -lnetcdff \
	660	-lnetcdf -Wl,-rpath=$ncdfdir/lib && ./a.out
[4238]	661
	662	if (($? == 0))
	663	then
	664	rm test_netcdf90.f90 a.out
	665	else
	666	echo "Failed test program using NetCDF-Fortran."
	667	echo "You can:"
	668	echo "- check that you have NetCDF-Fortran installed in your system"
	669	echo "- or specify an installation directory with option -netcdf of" \
[4405]	670	"install_lmdz.sh"
[4238]	671	echo "- or download and compile NetCDF-Fortran with option -netcdf 1 of" \
[4405]	672	"install_lmdz.sh"
[4238]	673	exit 1
	674	fi
	675
[4210]	676	#=========================================================================
	677	if [[ ! -f $MODEL/modipsl/lib/libioipsl.a ]]
	678	then
[4215]	679	if [ $ioipsl = 1 ] ; then
[4405]	680	#=====================================================================
	681	echo OK ioipsl=$ioipsl
	682	echo '##########################################################'
	683	echo 'Installing MODIPSL, the installation package manager for the '
	684	echo 'IPSL models and tools'
	685	echo '##########################################################'
	686	echo `date`
[4210]	687
[4405]	688	cd $MODEL/modipsl
	689	\rm -rf lib/*
	690	cd util
	691	cp AA_make.gdef AA_make.orig
	692	F_C="$compiler -c "
	693	if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ]
	694	then
	695	F_C="$compiler -c -cpp "
	696	fi
	697	if [ "$compiler" = "pgf90" ] ; then F_C="$compiler -c -Mpreprocess" ; fi
	698	sed -e 's/^\#..g95..\#.*.$/\#/' AA_make.gdef > tmp
	699	sed -e "s:F_L = g95:F_L = $compiler:" \
	700	-e "s:F_C = g95 -c -cpp:F_C = $F_C": \
	701	-e 's/g95..w_w..(F_D)/g95 w_w = '"$OPTIMGCM"'/' \
	702	-e 's:g95..NCDF_INC..$:g95 NCDF_INC= '"$ncdfdir"'/include:' \
	703	-e 's:g95..NCDF_LIB..$:g95 NCDF_LIB= -L'"$ncdfdir"'/lib -lnetcdff -lnetcdf:' \
	704	-e 's:g95 L_O =:g95 L_O = -Wl,-rpath='"$ncdfdir"'/lib:' \
	705	-e "s:-fmod=:-$fmod:" -e 's/-fno-second-underscore//' \
	706	-e 's:#-Q- g95 M_K = gmake:#-Q- g95 M_K = make:' \
	707	tmp >\| AA_make.gdef
[4210]	708
[4405]	709	if [ $pcmac == 1 ]
	710	then
	711	cp AA_make.gdef tmp
	712	sed -e 's/rpath=/rpath,/g' tmp > AA_make.gdef
	713	fi
[4210]	714
	715
[4405]	716	# We use lines for g95 even for the other compilers to run ins_make
	717	if [ "$use_shell" = "ksh" ] ; then
	718	./ins_make $o_ins_make
	719	else # bash
	720	sed -e s:/bin/ksh:/bin/bash:g ins_make > ins_make.bash
	721	if [ "`grep jeanzay AA_make.gdef`" = "" ] ; then
	722	# Bidouille pour compiler sur ada des vieux modipsl.tar
	723	echo 'Warning jean-zay not in AA_make.gdef'
	724	echo 'Think about updating'
	725	exit 1
	726	fi
[4210]	727
[4405]	728	chmod u=rwx ins_make.bash
	729	./ins_make.bash $o_ins_make
	730	fi # of if [ "$use_shell" = "ksh" ]
[4210]	731
[4405]	732	echo install_lmdz.sh MODIPSL_OK `date`
[4210]	733
[4405]	734	cd $MODEL/modipsl/modeles/IOIPSL/src
	735	ioipsllog=`pwd`/ioipsl.log
	736	echo '##########################################################'
	737	echo 'Compiling IOIPSL, the interface library with Netcdf'
	738	echo '##########################################################'
	739	echo `date`
	740	echo log file : $ioipsllog
[4210]	741
[4405]	742	if [ "$use_shell" = "bash" ] ; then
	743	cp Makefile Makefile.ksh
	744	sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile
	745	fi
[4508]	746	### if [ "$pclinux" = 1 ] ; then
[4405]	747	# Build IOIPSL modules and library
	748	$make clean
	749	$make > $ioipsllog 2>&1
	750	if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then
	751	# copy module files to lib
	752	cp -f *.mod ../../../lib
	753	fi
	754	# Build IOIPSL tools (ie: "rebuild", if present)
[4542]	755	# For IOIPSLv_2_2_2, "rebuild" files are in IOIPSL/tools
	756	rebuild_dir=""
[4508]	757	if [ -f $MODEL/modipsl/modeles/IOIPSL/tools/rebuild ] ; then
[4542]	758	rebuild_dir=$MODEL/modipsl/modeles/IOIPSL/tools
	759	elif [ -d $MODEL/modipsl/modeles/IOIPSL/rebuild ] ; then
	760	rebuild_dir=$MODEL/modipsl/modeles/IOIPSL/rebuild
	761	fi
	762	if [ $rebuild_dir != "" ] ; then
	763	cd $rebuild_dir
[4405]	764	# adapt Makefile & rebuild script if in bash
	765	if [ "$use_shell" = "bash" ] ; then
	766	cp Makefile Makefile.ksh
	767	sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile
	768	cp rebuild rebuild.ksh
	769	sed -e 's:/bin/ksh:/bin/bash:g' \
	770	-e 's:print -u2:echo:g' \
	771	-e 's:print:echo:g' rebuild.ksh > rebuild
	772	fi
	773	$make clean
	774	$make > $ioipsllog 2>&1
	775	fi
[4508]	776	### fi # of if [ "$pclinux" = 1 ] which is commented out
[4210]	777
[4508]	778	else # of if [ $ioipsl = 1 ]
[4405]	779	if [ ${hostname:0:5} = jean- ] ; then
	780	cd $MODEL/modipsl
	781	cd util
[4215]	782	if [ "`grep jeanzay AA_make.gdef`" = "" ] ; then
[4405]	783	echo 'Warning jean-zay not in AA_make.gdef'
	784	echo 'Think about updating'
	785	exit 1
[4215]	786	fi
	787	./ins_make $o_ins_make
[4405]	788	# Compile IOIPSL on jean-zay
[4215]	789	cd $MODEL/modipsl/modeles/IOIPSL/src
	790	gmake > ioipsl.log
[4508]	791	# For IOIPSLv_2_2_2, "rebuild" files are in IOIPSL/tools, so "gmake" in IOIPSL/tools is enough
	792	# For IOIPSLv_2_2_5, "rebuild" files are in a separate IOIPSL/rebuild folder , while "tools" only contains "FCM"
	793	if [ -f $MODEL/modipsl/modeles/IOIPSL/tools/Makefile ] ; then
[4502]	794	cd $MODEL/modipsl/modeles/IOIPSL/tools
	795	gmake > ioipsl.log
	796	fi
[4508]	797	if [ -d $MODEL/modipsl/modeles/IOIPSL/rebuild ] ; then
	798	cd $MODEL/modipsl/modeles/IOIPSL/rebuild
	799	gmake > ioipsl.log
	800	fi
	801
[4405]	802	fi
	803	echo install_lmdz.sh ioipsl_OK `date`
[4215]	804	fi # of if [ $ioipsl = 1 ]
[4508]	805	fi # of if [[ ! -f $MODEL/modipsl/lib/libioipsl.a ]]
[4210]	806
	807	#=========================================================================
	808	if [ "$with_xios" = "y" ] ; then
[4215]	809	echo '##########################################################'
	810	echo 'Compiling XIOS'
	811	echo '##########################################################'
	812	cd $MODEL/modipsl/modeles
	813	xioslog=`pwd`/xios.log
	814	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/install_xios.bash
[4411]	815	myget script_install/install_xios.bash
[4215]	816	chmod u=rwx install_xios.bash
	817	if [ ${hostname:0:5} = jean- ] ; then
[4405]	818	svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5 \
	819	XIOS
	820	cd XIOS/arch
	821	svn update
	822	cd ..
	823	echo "Compiling XIOS, start" `date` \
	824	"(it takes about 20 min on Jean-Zay)"
	825	echo "log file: $xioslog"
	826	./make_xios --prod --arch $arch --job 4 > xios.log 2>&1
[4215]	827	else
[4405]	828	./install_xios.bash -prefix $MODEL/modipsl/modeles \
	829	-netcdf ${ncdfdir} -hdf5 ${ncdfdir} \
	830	-MPI $root_mpi -arch $arch > xios.log 2>&1
[4215]	831	fi # of case Jean-Zay
	832	if [ -f XIOS/lib/libxios.a ] ; then
[4405]	833	echo "XIOS library successfully generated"
	834	echo install_lmdz.sh XIOS_OK `date`
[4215]	835	fi
[4210]	836	fi
	837
	838	#============================================================================
	839	veget_version=false
	840	if [ "$veget" != 'NONE' ] ; then
[4215]	841	cd $MODEL/modipsl/modeles/ORCHIDEE
	842	set +e ; svn upgrade ; set -e
	843	if [ "$veget" = "CMIP6" ] ; then
[4405]	844	veget_version=orchidee2.0
	845	orchidee_rev=6592
[4215]	846	else # specific orchidee revision newer than CMIP6, on 2_1 or 2_2 branches
[4405]	847	veget_version=orchidee2.1
	848	orchidee_rev=$veget
	849	if [ $veget -lt 4465 ] ; then
	850	echo 'Stopping, ORCHIDEE version too old, script needs work on ' \
	851	'the CPP flags to pass to makelmdz'
	852	exit 1
	853	fi
	854	set +e
	855	# which branch is my version on?
	856	orcbranch=`svn log -v -q svn://forge.ipsl.jussieu.fr/orchidee/ -r $veget \|grep ORCHIDEE \|head -1\| sed -e 's:ORCHIDEE/.*$:ORCHIDEE:' \| awk '{print $2}'`
	857	# switch to that branch
	858	echo IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at \
	859	orchidee-help@listes.ipsl.fr
	860	svn switch -r $veget --accept theirs-full \
	861	svn://forge.ipsl.jussieu.fr/orchidee/$orcbranch
	862	svn log -r $veget \| grep $veget
	863	if [ $? -gt 0 ] ; then
[4218]	864	echo 'Cannot update ORCHIDEE as not on the right branch for ' \
[4405]	865	'ORCHIDEE'
[4215]	866	exit
[4405]	867	fi
	868	set -e
	869	set +e ; svn update -r $veget ; set -e
[4215]	870	fi
	871	# Correctif suite debug Jean-Zay
[4218]	872	sed -i -e 's/9010 FORMAT(A52,F17.14)/9010 FORMAT(A52,F20.14)/' \
[4405]	873	src_stomate/stomate.f90
[4215]	874	opt_orc="-prod" ; if [ "$optim" = "-debug" ] ; then opt_orc="-debug" ; fi
[4210]	875
[4215]	876	orchideelog=`pwd`/orchidee.log
	877	echo '########################################################'
	878	echo 'Compiling ORCHIDEE, the continental surface model '
	879	echo '########################################################'
	880	echo Start of the first compilation of orchidee, in sequential mode: `date`
	881	echo log file : $orchideelog
[4210]	882
[4215]	883	export ORCHPATH=`pwd`
	884	xios_orchid="-noxios"
	885	if [ "$with_xios" = "y" ] ; then
[4405]	886	xios_orchid="-xios"
[4215]	887	fi
	888	if [ -d tools ] ; then
[4405]	889	###################################################################
	890	# Pour les experts qui voudraient changer de version d'orchidee.
	891	# Attention : necessite d'avoir le password pour orchidee
[4210]	892
[4405]	893	# Correctif suite debug Jean-Zay
	894	if [ -f src_global/time.f90 ] ; then
	895	sed -i -e 's/CALL tlen2itau/\!CALL tlen2itau/' src_global/time.f90
	896	fi
	897	###################################################################
	898	if [ "$veget_version" == "false" ] ; then
	899	veget_version=orchidee2.0
	900	fi
	901	cd arch
	902	sed -e s:"%COMPILER .*.$":"%COMPILER $compiler":1 \
	903	-e s:"%LINK .*.$":"%LINK $compiler":1 \
	904	-e s:"%FPP_FLAGS .*.$":"%FPP_FLAGS $fpp_flags":1 \
	905	-e s:"%PROD_FFLAGS .*.$":"%PROD_FFLAGS $OPTIM":1 \
	906	-e s:"%DEV_FFLAGS .*.$":"%DEV_FFLAGS $OPTDEV":1 \
	907	-e s:"%DEBUG_FFLAGS .*.$":"%DEBUG_FFLAGS $OPTDEB":1 \
	908	-e s:"%BASE_FFLAGS .*.$":"%BASE_FFLAGS $OPTPREC":1 \
	909	-e s:"%BASE_LD .*.$":"%BASE_LD $BASE_LD":1 \
	910	-e s:"%ARFLAGS .*.$":"%ARFLAGS $ARFLAGS":1 \
	911	arch-gfortran.fcm > arch-local.fcm
	912	echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib -lnetcdff -lnetcdf\"" \
	913	> arch-local.path
	914	echo "NETCDF_INCDIR=${ncdfdir}/include" >> arch-local.path
	915	echo "IOIPSL_INCDIR=$ORCHPATH/../../lib" >> arch-local.path
	916	echo "IOIPSL_LIBDIR=$ORCHPATH/../../lib" >> arch-local.path
	917	echo 'XIOS_INCDIR=${ORCHDIR}/../XIOS/inc' >> arch-local.path
	918	echo 'XIOS_LIBDIR="${ORCHDIR}/../XIOS/lib -lxios"' >> arch-local.path
	919	cd ../
[4210]	920
[4405]	921	echo ./makeorchidee_fcm -j $xios_orchid $opt_orc -parallel none \
	922	-arch $arch
	923	./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel none \
	924	-arch $arch > $orchideelog 2>&1
	925	pwd
[4215]	926	else # of "if [ -d tools ]"
[4405]	927	if [ -d src_parallel ] ; then
	928	liste_src="parallel parameters global stomate sechiba driver"
	929	if [ "$veget_version" == "false" ] ; then
	930	veget_version=orchidee2.0
	931	fi
	932	fi
	933	for d in $liste_src ; do
	934	src_d=src_$d
	935	echo src_d $src_d
	936	echo ls ; ls
	937	if [ ! -d $src_d ] ; then
	938	echo Problem orchidee : no $src_d ; exit
	939	fi
	940	cd $src_d ; \rm -f *.mod make ; $make clean
	941	$make > $orchideelog 2>&1
	942	if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then
	943	cp -f *.mod ../../../lib
	944	fi
	945	cd ..
	946	done
[4215]	947	fi # of "if [ -d tools ]"
	948	echo install_lmdz.sh orchidee_compil_seq_OK `date`
[4210]	949	fi # of if [ "$veget" != 'NONE' ]
	950
	951
	952	#============================================================================
	953	# Ehouarn: the directory name LMDZ* depends on version/tar file...
	954	if [ -d $MODEL/modipsl/modeles/LMD* ] ; then
[4215]	955	echo '###############################################################'
	956	echo 'Preparing LMDZ compilation : arch file, svn switch if needed...'
	957	echo '###############################################################'
	958	cd $MODEL/modipsl/modeles/LMD*
	959	LMDZPATH=`pwd`
[4210]	960	else
[4215]	961	echo "ERROR: No LMD* directory !!!"
	962	exit
[4210]	963	fi
	964
	965	###########################################################
	966	# For those who want to use fcm to compile via :
	967	# makelmdz_fcm -arch local .....
	968	############################################################
	969
	970
	971
	972	cd $MODEL/modipsl/modeles/LMDZ*
	973	lmdzlog=`pwd`/lmdz.log
	974
	975	##################################################################
	976	# Possibly update LMDZ if a specific svn release is requested
	977	##################################################################
	978
	979	set +e ; svn upgrade ; set -e
	980
	981	if [ "$svn" = "last" ] ; then svnopt="" ; else svnopt="-r $svn" ; fi
	982	if [ "$svn" != "" ] ; then
	983	set +e ; svn info \| grep -q 'http:'
	984	if [ $? = 0 ] ; then
[4218]	985	svn switch --relocate http://svn.lmd.jussieu.fr/LMDZ \
[4405]	986	https://svn.lmd.jussieu.fr/LMDZ
[4210]	987	fi
	988	svn update $svnopt
[4372]	989	set -e
[4210]	990	fi
	991
[4372]	992	#---------------------------------------------------------------------
[4218]	993	# Retrieve the final svn release number, and adjust compilation
	994	# options accordingly
[4372]	995	# If svn not available, will use the svn writen in $MODEL/Readm*md
	996	# For old version it assumes that it is before 4185 (the version
	997	# for which the test was introduced
	998	#---------------------------------------------------------------------
[4210]	999
[4372]	1000	set +e ; mysvn=`svnversion . \| egrep -o "[0-9]+" 2>/dev/null` ; set -e
	1001	if [ "$mysvn" = "" ] ; then mysvn=`grep 'Revision: [0-9]' $MODEL/Read*.md \| awk ' { print $2 } ' 2>/dev/null` ; fi
	1002	if [ "$mysvn" = "" ] ; then mysvn=4190 ; fi
	1003
[4427]	1004	if [[ "$pclinux" = "1" && ! -f arch/arch-local.path ]] ; then
	1005
	1006	# create local 'arch' files (if on Linux PC):
	1007	cd arch
	1008	# arch-local.path file
	1009	# test for version as arch.pth file changed format with rev 4426
	1010	if [ "$mysvn" -gt 4425 ] ; then
	1011	echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib \"" > arch-local.path
	1012	echo "NETCDF_LIB=\"-lnetcdff -lnetcdf\"" >> arch-local.path
	1013	echo "NETCDF_INCDIR=-I${ncdfdir}/include" >> arch-local.path
	1014	echo 'NETCDF95_INCDIR=-I$LMDGCM/../../include' >> arch-local.path
	1015	echo 'NETCDF95_LIBDIR=-L$LMDGCM/../../lib' >> arch-local.path
	1016	echo 'NETCDF95_LIB=-lnetcdf95' >> arch-local.path
	1017	echo 'IOIPSL_INCDIR=-I$LMDGCM/../../lib' >> arch-local.path
	1018	echo 'IOIPSL_LIBDIR=-L$LMDGCM/../../lib' >> arch-local.path
	1019	echo 'IOIPSL_LIB=-lioipsl' >> arch-local.path
	1020	echo 'XIOS_INCDIR=-I$LMDGCM/../XIOS/inc' >> arch-local.path
	1021	echo 'XIOS_LIBDIR=-L$LMDGCM/../XIOS/lib' >> arch-local.path
	1022	echo "XIOS_LIB=\"-lxios -lstdc++\"" >> arch-local.path
	1023	echo 'ORCH_INCDIR=-I$LMDGCM/../../lib' >> arch-local.path
	1024	echo 'ORCH_LIBDIR=-L$LMDGCM/../../lib' >> arch-local.path
	1025	else
	1026	echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib -lnetcdff -lnetcdf\"" \
	1027	> arch-local.path
	1028	echo "NETCDF_INCDIR=-I${ncdfdir}/include" >> arch-local.path
	1029	echo 'NETCDF95_INCDIR=$LMDGCM/../../include' >> arch-local.path
	1030	echo 'NETCDF95_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
	1031	echo 'IOIPSL_INCDIR=$LMDGCM/../../lib' >> arch-local.path
	1032	echo 'IOIPSL_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
	1033	echo 'XIOS_INCDIR=$LMDGCM/../XIOS/inc' >> arch-local.path
	1034	echo 'XIOS_LIBDIR=$LMDGCM/../XIOS/lib' >> arch-local.path
	1035	echo 'ORCH_INCDIR=$LMDGCM/../../lib' >> arch-local.path
	1036	echo 'ORCH_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
	1037	fi
	1038
	1039	if [ $pcmac == 1 ] ; then
	1040	BASE_LD="$BASE_LD -Wl,-rpath,${ncdfdir}/lib"
	1041	else
	1042	BASE_LD="$BASE_LD -Wl,-rpath=${ncdfdir}/lib"
	1043	fi
	1044	# Arch-local.fcm file (adapted from arch-linux-32bit.fcm)
	1045
	1046	if [ $real = r8 ] ; then FPP_DEF=NC_DOUBLE ; else FPP_DEF="" ; fi
	1047	sed -e s:"%COMPILER .*.$":"%COMPILER $compiler":1 \
	1048	-e s:"%LINK .*.$":"%LINK $compiler":1 \
	1049	-e s:"%PROD_FFLAGS .*.$":"%PROD_FFLAGS $OPTIM":1 \
	1050	-e s:"%DEV_FFLAGS .*.$":"%DEV_FFLAGS $OPTDEV":1 \
	1051	-e s:"%DEBUG_FFLAGS .*.$":"%DEBUG_FFLAGS $OPTDEB":1 \
	1052	-e s:"%BASE_FFLAGS .*.$":"%BASE_FFLAGS $OPTPREC":1 \
	1053	-e s:"%FPP_DEF .*.$":"%FPP_DEF $FPP_DEF":1 \
	1054	-e s:"%BASE_LD .*.$":"%BASE_LD $BASE_LD":1 \
	1055	-e s:"%ARFLAGS .*.$":"%ARFLAGS $ARFLAGS":1 \
	1056	arch-linux-32bit.fcm > arch-local.fcm
	1057
	1058	cd ..
	1059	### Adapt "bld.cfg" (add the shell):
	1060	#whereisthatshell=$(which ${use_shell})
	1061	#echo "bld::tool::SHELL $whereisthatshell" >> bld.cfg
	1062
	1063	fi # of if [ "$pclinux" = 1 ]
[4372]	1064	#---------------------------------------------------------------------
[4210]	1065	# Option de compilation du rayonnement : depend de $mysvn ><= r4185
[4372]	1066	#---------------------------------------------------------------------
[4210]	1067	opt_rad=""
	1068
	1069	case $rad in
	1070	oldrad) iflag_rrtm=0 ; NSW=2 ; opt_rad="" ;;
[4218]	1071	rrtm) iflag_rrtm=1 ; NSW=6
[4405]	1072	if [ $mysvn -le 4185 ] ; then
	1073	opt_rad="-rrtm true"
	1074	else
	1075	opt_rad="-rad rrtm"
	1076	fi ;;
[4210]	1077	ecrad) iflag_rrtm=2 ; NSW=6 ; opt_rad="-rad ecrad" ;;
	1078	*) echo Only oldrad rrtm ecrad for rad option ; exit
	1079	esac
	1080
[4218]	1081	if [ $mysvn -le 4185 -a $rad = "ecrad" ] ; then
	1082	echo "ecrad only available for LMDZ rev starting with 4186 " ; exit
	1083	fi
[4210]	1084
	1085	##################################################################
	1086
[4213]	1087
	1088	if [[ ! -f libf/misc/netcdf95.F90 && ! -d $MODEL/NetCDF95-0.2 ]]
	1089	then
	1090	cd $MODEL
[4417]	1091	myget src_archives/netcdf/NetCDF95-0.2.tar.gz
[4213]	1092	tar -xf NetCDF95-0.2.tar.gz
	1093	rm NetCDF95-0.2.tar.gz
	1094	cd NetCDF95-0.2
	1095	mkdir build
	1096	cd build
	1097	cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=$ncdfdir \
[4405]	1098	-DCMAKE_INSTALL_PREFIX=$MODEL/modipsl
[4213]	1099	make install
	1100	cd $MODEL/modipsl/modeles/LMDZ*
	1101	fi
	1102
[4210]	1103	echo '##################################################################'
	1104	echo "Preparing script compile.sh for LMDZ compilation"
	1105	echo "It will only be run automatically if bench=1/tuto"
	1106	echo Here bench=$bench
	1107	echo '##################################################################'
	1108
[4218]	1109	if [ "$env_file" != "" ] ; then
	1110	mv arch/arch-${arch}.env arch/arch-${arch}.orig
	1111	\cp -f $env_file arch/arch-${arch}.env
	1112	fi
[4210]	1113
[4218]	1114	if [ $compile_with_fcm = 1 ] ; then
	1115	makelmdz="makelmdz_fcm $optim -arch $arch -j 8 "
	1116	else
	1117	makelmdz="makelmdz $optim -arch $arch"
	1118	fi
[4210]	1119
	1120	# sequential compilation
	1121	if [ "$sequential" = 1 ] ; then
[4215]	1122	echo Sequential compilation command, saved in compile.sh:
[4218]	1123	echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp " \
[4405]	1124	"-d ${grid_resolution} -v $veget_version gcm "
[4218]	1125	echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp " \
[4405]	1126	"-d ${grid_resolution} -v $veget_version gcm " > compile.sh
[4215]	1127	chmod +x ./compile.sh
	1128	if [ $bench = 1 ] ; then
[4405]	1129	echo install_lmdz.sh start_lmdz_seq_compilation `date`
	1130	echo log file: $lmdzlog
	1131	./compile.sh > $lmdzlog 2>&1
	1132	echo install_lmdz.sh end_lmdz_seq_compilation `date`
[4215]	1133	fi
[4210]	1134	fi # fin sequential
	1135
	1136	# compiling in parallel mode
	1137	if [ $parallel != "none" ] ; then
	1138	echo '##########################################################'
[4215]	1139	echo ' Parallel compile '
[4210]	1140	echo '##########################################################'
[4215]	1141	echo "(after saving the sequential libs and binaries)"
	1142	cd $MODEL/modipsl
	1143	tar cf sequential.tar bin/ lib/
	1144	#
	1145	# Orchidee
	1146	#
	1147	cd $ORCHPATH
	1148	if [ -d src_parallel -a $veget != 'NONE' ] ; then
[4405]	1149	cd arch
	1150	sed \
	1151	-e s:"%COMPILER.*.$":"%COMPILER $par_comp":1 \
	1152	-e s:"%LINK.*.$":"%LINK $par_comp":1 \
	1153	-e s:"%MPI_FFLAG.*.$":"%MPI_FFLAGS $MPI_FLAGS":1 \
	1154	-e s:"%OMP_FFLAG.*.$":"%OMP_FFLAGS $OMP_FLAGS":1 \
	1155	-e s:"%MPI_LD.*.$":"%MPI_LD $MPI_LD":1 \
	1156	-e s:"%OMP_LD.*.$":"%OMP_LD $OMP_LD":1 \
	1157	arch-local.fcm > tmp.fcm
[4210]	1158
[4405]	1159	mv tmp.fcm arch-local.fcm
	1160	cd ../
	1161	echo Compiling ORCHIDEE in parallel mode `date`
	1162	echo logfile $orchideelog
	1163	echo "NOTE : to recompile it when necessary, use ./compile_orc.sh " \
	1164	"in modipsl/modeles/ORCHIDEE"
	1165	echo ./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc \
	1166	-parallel $parallel -arch $arch > compile_orc.sh
	1167	echo ./makeorchidee_fcm -j 8 $xios_orchid $opt_orc \
	1168	-parallel $parallel -arch $arch >> compile_orc.sh
	1169	echo echo Now you must also recompile LMDZ, by running ./compile.sh \
	1170	in modeles/LMDZ >> compile_orc.sh
	1171	chmod u+x compile_orc.sh
	1172	./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc \
	1173	-parallel $parallel -arch $arch > $orchideelog 2>&1
	1174	./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel $parallel \
	1175	-arch $arch >> $orchideelog 2>&1
	1176	echo End of ORCHIDEE compilation in parallel mode `date`
[4215]	1177	elif [ $veget != 'NONE' ] ; then
[4405]	1178	echo '##########################################################'
	1179	echo ' Orchidee version too old '
	1180	echo ' Please update to new version '
	1181	echo '##########################################################'
	1182	exit
[4215]	1183	fi # of [ -d src_parallel -a $veget != 'NONE' ]
[4210]	1184
[4215]	1185	# LMDZ
	1186	cd $LMDZPATH
	1187	if [ $arch = local ] ; then
[4405]	1188	cd arch
	1189	sed -e s:"%COMPILER.*.$":"%COMPILER $par_comp":1 \
	1190	-e s:"%LINK.*.$":"%LINK $par_comp":1 \
	1191	-e s:"%MPI_FFLAG.*.$":"%MPI_FFLAGS $MPI_FLAGS":1 \
	1192	-e s:"%OMP_FFLAG.*.$":"%OMP_FFLAGS $OMP_FLAGS":1 \
	1193	-e s:"%ARFLAGS.*.$":"%ARFLAGS $ARFLAGS":1 \
	1194	-e s@"%BASE_LD.*.$"@"%BASE_LD -Wl,-rpath=${root_mpi}/lib:${ncdfdir}/lib"@1 \
	1195	-e s:"%MPI_LD.*.$":"%MPI_LD $MPI_LD":1 \
	1196	-e s:"%OMP_LD.*.$":"%OMP_LD $OMP_LD":1 \
	1197	arch-local.fcm > tmp.fcm
	1198	mv tmp.fcm arch-local.fcm
	1199	cd ../
[4215]	1200	fi
	1201	rm -f compile.sh
	1202	echo resol=${grid_resolution} >> compile.sh
	1203	if [ ${hostname:0:5} = jean- -a "$cosp" = "v2" ] ; then
[4210]	1204
[4405]	1205	echo LMDZ compilation command in parallel mode, saved in compile.sh, \
	1206	is :
	1207	echo "(ATTENTION le probleme de cospv2 sur jean-zay en mode prod " \
	1208	"n est pas corrige ! )"
	1209	# ATTENTION le probleme de cospv2 sur jean-zay en mode prod n
	1210	# est pas corrige
	1211	echo ./$makelmdz -dev $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
	1212	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
	1213	-parallel $parallel gcm >> compile.sh
	1214	echo ./$makelmdz -dev $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
	1215	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
	1216	-parallel $parallel gcm
[4215]	1217	else
[4405]	1218	echo ./$makelmdz $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
	1219	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
	1220	-parallel $parallel gcm >> compile.sh
	1221	echo ./$makelmdz $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
	1222	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
	1223	-parallel $parallel gcm
[4215]	1224	fi
	1225	chmod +x ./compile.sh
[4210]	1226
[4215]	1227	if [ $bench = 1 ] ; then
[4405]	1228	echo Compiling LMDZ in parallel mode `date`, LMDZ log file: $lmdzlog
	1229	./compile.sh > $lmdzlog 2>&1
[4215]	1230	fi
	1231
[4210]	1232	fi # of if [ $parallel != "none" ]
	1233
	1234
	1235	##################################################################
	1236	# Verification du succes de la compilation
	1237	##################################################################
	1238
	1239	# Recherche de l'executable dont le nom a change au fil du temps ...
	1240	# suffix contains radiative option starting with revision 4186
	1241	if [ $mysvn -ge 4186 ] ; then suff_exe=_${rad}${suff_exe} ; fi
	1242	gcm=""
[4219]	1243
[4218]	1244	for exe in gcm.e bin/gcm_${grid_resolution}_phylmd${suff_exe}${suff_orc}.e
	1245	do
	1246	if [ -f $exe ] ; then gcm=$exe ; fi
[4210]	1247	done
	1248
	1249	if [ "$gcm" = "" ] ; then
[4215]	1250	if [ $bench = 1 ] ; then
[4405]	1251	echo 'Compilation failed !! Cannot run the benchmark;'
	1252	exit
[4215]	1253	else
[4405]	1254	echo 'Compilation not done (only done when bench=1)'
[4215]	1255	fi
[4210]	1256	else
[4215]	1257	echo '##########################################################'
	1258	echo 'Compilation successfull !! ' `date`
	1259	echo '##########################################################'
	1260	echo The executable is $gcm
[4210]	1261	fi
	1262
	1263	##################################################################
	1264	# Below, we run a benchmark if bench=1 or tuto
	1265	##################################################################
	1266
	1267	if [ $bench = tuto ] ; then
[4286]	1268	myget Training/tutorial.tar ; tar xf tutorial.tar ; cd TUTORIAL
[4218]	1269	./init.sh
[4210]	1270
	1271	elif [[ $bench = 1 && ! -d BENCH${grid_resolution} ]] ; then
[4215]	1272	# TOUTE CETTE SECTION DEVRAIT DISPARAITRE POUR UNE COMMANDE
	1273	# OU DES BENCHS PAR MOTS CLES COMME tuto
[4210]	1274
[4215]	1275	echo '##########################################################'
	1276	echo ' Running a test run '
	1277	echo '##########################################################'
[4210]	1278
[4215]	1279	\rm -rf BENCH${grid_resolution}
	1280	bench=bench_lmdz_${grid_resolution}
	1281	echo install_lmdz.sh before bench download `date`
	1282	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/$bench.tar.gz
	1283	myget 3DBenchs/$bench.tar.gz
	1284	echo install_lmdz.sh after bench download `date`
[4286]	1285	tar xf $bench.tar.gz
[4210]	1286
[4215]	1287	if [ "$cosp" = "v1" -o "$cosp" = "v2" ] ; then
[4405]	1288	cd BENCH${grid_resolution}
	1289	# copier les fichiers namelist input et output our COSP
	1290	cp ../DefLists/cosp*_input_nl.txt .
	1291	cp ../DefLists/cosp*_output_nl.txt .
	1292	# Activer la cles ok_cosp pour tourner avec COSP
	1293	sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp
	1294	\mv -f tmp config.def
	1295	cd ..
[4215]	1296	fi
[4210]	1297
[4215]	1298	if [ -n "$physiq" ]; then
[4405]	1299	cd BENCH${grid_resolution}
	1300	if [ -f physiq.def_${physiq} ]; then
	1301	cp physiq.def_${physiq} physiq.def
	1302	echo using physiq.def_${physiq}
	1303	else
	1304	echo using standard physiq.def
	1305	fi
	1306	cd ..
[4215]	1307	else
[4405]	1308	echo using standard physiq.def
[4215]	1309	fi
[4210]	1310
[4215]	1311	if [ "$with_xios" = "y" ] ; then
[4405]	1312	cd BENCH${grid_resolution}
	1313	cp ../DefLists/iodef.xml .
	1314	cp ../DefLists/context_lmdz.xml .
	1315	cp ../DefLists/field_def_lmdz.xml .
	1316	# A raffiner par la suite
	1317	echo A FAIRE : Copier les *xml en fonction de l option cosp
	1318	cp ../DefLists/field_def_cosp*.xml .
	1319	cp ../DefLists/file_def_hist*xml .
	1320	# adapt iodef.xml to use attached mode
	1321	sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' \
	1322	iodef.xml > tmp
	1323	\mv -f tmp iodef.xml
[4210]	1324
[4405]	1325	# and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
	1326	# except for histday
	1327	for histfile in file_def_hist*xml
	1328	do
	1329	if [ "$histfile" = "file_def_histday_lmdz.xml" ] ; then
	1330	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' \
	1331	$histfile > tmp
	1332	\mv -f tmp $histfile
	1333	sed -e 's@output_level="_AUTO_"@output_level="5"@' $histfile \
	1334	> tmp
	1335	\mv -f tmp $histfile
	1336	sed -e 's@compression_level="2"@compression_level="0"@' \
	1337	$histfile > tmp
	1338	\mv -f tmp $histfile
	1339	else
	1340	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
	1341	$histfile > tmp
	1342	\mv -f tmp $histfile
	1343	fi
	1344	done
	1345	# and add option "ok_all_xml=y" in config.def
	1346	echo "### XIOS outputs" >> config.def
	1347	echo 'ok_all_xml=.true.' >> config.def
[4210]	1348
[4405]	1349	#activer les sorties pour Cosp
	1350	if [ "$cosp" = "v1" ] ; then
	1351	histfile=file_def_histdayCOSP_lmdz.xml
	1352	sed -e 's@enabled=".FALSE."@enabled=".TRUE."@' $histfile > tmp
	1353	\mv -f tmp $histfile
	1354	sed -e 's@output_level="_AUTO_"@output_level="5"@' $histfile > tmp
	1355	\mv -f tmp $histfile
	1356	sed -e 's@compression_level="2"@compression_level="0"@' \
	1357	$histfile > tmp
	1358	\mv -f tmp $histfile
	1359	fi
	1360	if [ "$cosp" = "v2" ] ; then
	1361	histfile=file_def_histdayCOSPv2_lmdz.xml
	1362	sed -e 's@compression_level="2"@compression_level="0"@' \
	1363	$histfile > tmp
	1364	\mv -f tmp $histfile
	1365	contextfile=context_lmdz.xml
	1366	sed -e 's@src="./file_def_histdayCOSP_lmdz.xml"@src="./file_def_histdayCOSPv2_lmdz.xml"@' \
	1367	$contextfile > tmp
	1368	\mv -f tmp $contextfile
	1369	sed -e 's@src="./file_def_histmthCOSP_lmdz.xml"@src="./file_def_histmthCOSPv2_lmdz.xml"@' \
	1370	$contextfile > tmp
	1371	\mv -f tmp $contextfile
	1372	sed -e 's@src="./file_def_histhfCOSP_lmdz.xml"@src="./file_def_histhfCOSPv2_lmdz.xml"@' \
	1373	$contextfile > tmp
	1374	\mv -f tmp $contextfile
	1375	fieldfile=field_def_lmdz.xml
	1376	sed -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' $fieldfile \
	1377	> tmp
	1378	\mv -f tmp $fieldfile
	1379	fi
[4210]	1380
[4405]	1381	cd ..
[4215]	1382	fi
[4210]	1383
[4215]	1384	# Cas Bensh avec ecrad
	1385	if [ "$rad" = "ecrad" ] ; then
[4405]	1386	cd BENCH${grid_resolution}
	1387	cp ../DefLists/namelist_ecrad .
	1388	cp -r ../libf/phylmd/ecrad/data .
	1389	cd ..
[4215]	1390	fi
[4210]	1391
[4215]	1392	# Adjusting bench physiq.def to radiative code chosen
	1393	cd BENCH${grid_resolution}
[4218]	1394	sed -e 's/iflag_rrtm=.*.$/iflag_rrtm='$iflag_rrtm'/' \
[4405]	1395	-e 's/NSW=.*.$/NSW='$NSW'/' physiq.def > tmpdef
[4215]	1396	\mv tmpdef physiq.def
	1397	cd ..
[4210]	1398
[4215]	1399	cp $gcm BENCH${grid_resolution}/gcm.e
[4210]	1400
[4215]	1401	cd BENCH${grid_resolution}
	1402	# On cree le fichier bench.sh au besoin
	1403	# Dans le cas 48x36x39 le bench.sh existe deja en parallele
[4210]	1404
[4215]	1405	if [ "$grid_resolution" = "48x36x39" ] ; then
[4405]	1406	echo On ne touche pas au bench.sh
	1407	# But we have to adapt "run_local.sh" for $mpirun
	1408	sed -e "s@mpirun@$mpirun@g" run_local.sh > tmp
	1409	mv -f tmp run_local.sh
	1410	chmod u=rwx run_local.sh
[4215]	1411	elif [ "${parallel:0:3}" = "mpi" ] ; then
[4405]	1412	# Lancement avec deux procs mpi et 2 openMP
	1413	echo "export OMP_STACKSIZE=800M" > bench.sh
	1414	if [ "${parallel:4:3}" = "omp" ] ; then
[4215]	1415	echo "export OMP_NUM_THREADS=2" >> bench.sh
[4405]	1416	fi
	1417	if [ "$cosp" = "v1" -o "$cosp" = "v2" ] ; then
[4215]	1418	if [ ${hostname:0:5} = jean- ] ; then
[4405]	1419	chmod +x ../arch.env
	1420	../arch.env
	1421	echo "ulimit -s 2000000" >> bench.sh
[4215]	1422	else
[4405]	1423	echo "ulimit -s 200000" >> bench.sh
	1424	fi
	1425	else
[4215]	1426	echo "ulimit -s unlimited" >> bench.sh
[4405]	1427	fi
	1428	if [ ${hostname:0:5} = jean- ] ; then
[4215]	1429	. ../arch/arch-${arch}.env
[4218]	1430	echo "srun -n 2 -A $idris_acct@cpu gcm.e > listing 2>&1" \
[4405]	1431	>> bench.sh
	1432	else
[4215]	1433	echo "$mpirun -np 2 gcm.e > listing 2>&1" >> bench.sh
[4405]	1434	fi
	1435	# Add rebuild, using reb.sh if it is there
	1436	echo 'if [ -f reb.sh ] ; then' >> bench.sh
	1437	echo ' ./reb.sh histday ; ./reb.sh histmth ; ./reb.sh histhf ; ' \
	1438	'./reb.sh histins ; ./reb.sh stomate_history ; ' \
	1439	'./reb.sh sechiba_history ; ./reb.sh sechiba_out_2 ' >> bench.sh
	1440	echo 'fi' >> bench.sh
[4215]	1441	else
[4405]	1442	echo "./gcm.e > listing 2>&1" > bench.sh
[4215]	1443	fi
	1444	# Getting orchidee stuff
	1445	if [ $veget == 'CMIP6' ] ; then
[4405]	1446	#echo 'myget 3DBenchs/BENCHorch11.tar.gz'
	1447	#myget 3DBenchs/BENCHorch11.tar.gz
	1448	#tar xvzf BENCHorch11.tar.gz
	1449	echo 'myget 3DBenchs/BENCHCMIP6.tar.gz'
	1450	myget 3DBenchs/BENCHCMIP6.tar.gz
	1451	tar xvzf BENCHCMIP6.tar.gz
	1452	sed -e "s:VEGET=n:VEGET=y:" config.def > tmp
	1453	mv -f tmp config.def
	1454	if [ "$with_xios" = "y" ] ; then
[4215]	1455	cp ../../ORCHIDEE/src_xml/context_orchidee.xml .
[4218]	1456	echo '<context id="orchidee" src="./context_orchidee.xml"/>' \
[4405]	1457	> add.tmp
[4215]	1458	cp ../../ORCHIDEE/src_xml/field_def_orchidee.xml .
	1459	cp ../../ORCHIDEE/src_xml/file_def_orchidee.xml .
	1460	cp ../../ORCHIDEE/src_xml/file_def_input_orchidee.xml .
	1461	if [ -f ../../ORCHIDEE/src_xml/context_input_orchidee.xml ] ; then
[4405]	1462	cp ../../ORCHIDEE/src_xml/context_input_orchidee.xml .
	1463	echo '<context id="orchidee" ' \
	1464	'src="./context_input_orchidee.xml"/>' >> add.tmp
[4215]	1465	fi
	1466	sed -e '/id="LMDZ"/r add.tmp' iodef.xml > tmp
	1467	mv tmp iodef.xml
[4218]	1468	sed -e'{/sechiba1/ s/enabled="_AUTO_"/type="one_file" enabled=".TRUE."/}' \
[4405]	1469	file_def_orchidee.xml > tmp
	1470	\mv -f tmp file_def_orchidee.xml
[4218]	1471	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
[4405]	1472	file_def_orchidee.xml > tmp
	1473	\mv -f tmp file_def_orchidee.xml
[4218]	1474	sed -e 's@output_level="_AUTO_"@output_level="1"@' \
[4405]	1475	file_def_orchidee.xml > tmp
	1476	\mv -f tmp file_def_orchidee.xml
[4218]	1477	sed -e 's@output_freq="_AUTO_"@output_freq="1d"@' \
[4405]	1478	file_def_orchidee.xml > tmp
	1479	\mv -f tmp file_def_orchidee.xml
[4218]	1480	sed -e 's@compression_level="4"@compression_level="0"@' \
[4405]	1481	file_def_orchidee.xml > tmp
	1482	\mv -f tmp file_def_orchidee.xml
[4218]	1483	sed -e 's@XIOS_ORCHIDEE_OK = n@XIOS_ORCHIDEE_OK = y@' \
[4405]	1484	orchidee.def > tmp
	1485	\mv -f tmp orchidee.def
	1486	fi
[4215]	1487	fi
[4220]	1488
	1489	if [[ -f ../arch.env ]]
	1490	then
[4405]	1491	source ../arch.env
[4220]	1492	fi
	1493
[4215]	1494	echo EXECUTION DU BENCH
	1495	set +e
	1496	date ; ./bench.sh > out.bench 2>&1 ; date
	1497	set -e
	1498	tail listing
[4210]	1499
	1500
[4215]	1501	echo '##########################################################'
	1502	echo 'Simulation finished in' `pwd`
	1503	echo 'You have compiled with:'
	1504	cat ../compile.sh
	1505	if [ $parallel = "none" ] ; then
[4405]	1506	echo 'You may re-run it with : cd ' `pwd` ' ; gcm.e'
	1507	echo 'or ./bench.sh'
[4215]	1508	else
[4405]	1509	echo 'You may re-run it with : '
	1510	echo 'cd ' `pwd` '; ./bench.sh'
	1511	# echo 'ulimit -s unlimited'
	1512	# echo 'export OMP_NUM_THREADS=2'
	1513	# echo 'export OMP_STACKSIZE=800M'
	1514	# echo "$mpirun -np 2 gcm.e "
[4215]	1515	fi
	1516	echo '##########################################################'
[4210]	1517
	1518	fi # bench
	1519
	1520
	1521	#################################################################
	1522	# Installation eventuelle du 1D
	1523	#################################################################
	1524
	1525	if [ $SCM = 1 ] ; then
[4215]	1526	cd $MODEL
	1527	myget 1D/1D.tar.gz
[4286]	1528	tar xf 1D.tar.gz
[4215]	1529	cd 1D
[4422]	1530	if [ $rad = oldrad ] ; then
	1531	sed -i'' -e 's/^rad=.*$/rad=oldrad/' run.sh
	1532	sed -i'' -e 's/^rad=.*$/rad=oldrad/' bin/compile
	1533	fi
[4409]	1534	echo Running 1D/run.sh, log in `pwd`/run1d.log
[4457]	1535	./run.sh > `pwd`/run1d.log 2>&1
[4210]	1536	fi
	1537
[4409]	1538
[4210]	1539	#################################################################
	1540	# sauvegarde des options veget pour utilisation eventuelle tutorial_prod
	1541	#################################################################
	1542	cd $MODEL/modipsl/modeles
	1543	#echo surface_env file created in $MODEL
	1544	echo 'veget='$veget > surface_env
	1545	#opt_veget="-v $veget_version"
	1546	#echo 'opt_veget="'$opt_veget\" >> surface_env
	1547	echo 'opt_veget="'-v $veget_version\" >> surface_env
	1548	echo 'orchidee_rev='$orchidee_rev >> surface_env
	1549	echo 'suforch='$suff_orc >> surface_env

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