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source: BOL/script_install/install_lmdz_new.sh @ 4215

Last change on this file since 4215 was 4215, checked in by lguez, 2 years ago
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[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.
	21	# In the present case, LMDZ, ORCHIDEE, and IOIPSL or XIOS (handling of input-outputs
	22	# using the NetCDF library).
	23	#
	24	# The script downloads various source files (including a version of NetCDF)
	25	# and utilities, compiles the model, and runs a test simulation in a
	26	# minimal configuration.
	27	#
	28	# Prerequisites : 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
	51	\cp -f -p /u/lmdz/WWW/LMDZ/pub/$1 .
	52	elif [ -f ~/LMDZ/pub/$1 ] ; then
	53	\cp -f -p ~/LMDZ/pub/$1 .
	54	else
	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 ; cp -r `basename $1` $dir
	59	fi
[4210]	60	fi
	61	}
	62
	63	# 04_2021 : tester si r4 marche encore !
	64	#real=r4
	65	real=r8
	66
	67
	68	#########################################################################
	69	# Valeur par défaut des parametres
	70	#########################################################################
	71	svn=""
	72	#version=trunk
	73	version=20220131.trunk
	74
	75	getlmdzor=1
[4211]	76	netcdf=0 # 1: for automatic installation;
[4215]	77	# or 0: do not install NetCDF and look for it in standard locations;
	78	# or absolute path: look for NetCDF there
[4210]	79	check_linux=1
	80	ioipsl=1
	81	bench=1
	82	pclinux=1
	83	pcmac=0 # default: not on a Mac
	84	compiler=gfortran
	85	SCM=0
	86	# surface/vegetation scheme treatment
	87	# controlled by the single variable veget which can have the following values
	88	# - NONE: bucket scheme (default)
	89	# - CMIP6: orchidee version used in CMIP exercise, rev 5661
	90	# - number: orchidee version number
	91	veget=NONE
	92	# choose the resolution for the bench runs
	93	# grid_resolution= 32x24x11 or 48x36x19 for tests (test without ORCHIDEE)
	94	# 96x71x19 standard configuration
	95	grid_resolution=144x142x79
	96	grid_resolution=96x95x39
	97	grid_resolution=48x36x19
	98	grid_resolution=32x32x39
	99	# choose the physiq version you want to test
	100	#physiq=NPv6.0.14splith
	101	physiq=
	102
	103	## parallel can take the values none/mpi/omp/mpi_omp
	104	parallel=mpi_omp
	105	parallel=none
	106	idris_acct=lmd
	107	OPT_GPROF=""
	108	OPT_MAKELMDZ=""
	109	MODEL=""
	110
	111	## also compile XIOS? (and more recent NetCDF/HDF5 libraries) Default=no
	112	with_xios="n"
	113	opt_makelmdz_xios=""
	114
	115	## compile with oldrad/rrtm/ecrad radiatif code (Default=rrtm)
	116	rad=rrtm
	117
	118	## compile_with_fcm=1 : use makelmdz_fcm (1) or makelmdz (0)
	119	compile_with_fcm=1
	120
	121	#Compilation with Cosp (cosp=NONE/v1/v2 ; default=NONE)
	122	cosp=NONE
	123	opt_cosp=""
	124
	125	# Check if on a Mac
	126	if [ `uname` = "Darwin" ]
	127	then
	128	pcmac=1
	129	export MAKE=make
	130	fi
	131	#echo "pcmac="$pcmac
	132
	133	env_file=""
	134
	135	#########################################################################
	136	# Options interactives
	137	#########################################################################
	138	while (($# > 0))
[4215]	139	do
	140	case $1 in
	141	"-h") cat <<........fin
[4210]	142	$0 [ -v version ] [ -r svn_release ]
	143	[ -parallel PARA ] [ -d GRID_RESOLUTION ] [ -bench 0/1 ]
	144	[-name LOCAL_MODEL_NAME] [-gprof] [-opt_makelmdz] [-rad RADIATIF]
	145
	146	-v "version" like 20150828.trunk
	147	see http://www.lmd.jussieu.fr/~lmdz/Distrib/LISMOI.trunk
	148
	149	-r "svn_release" : either the svn release number or "last"
	150
	151	-compiler gfortran\|ifort\|pgf90 (default: gfortran)
	152
	153	-parallel PARA : can be mpi_omp (mpi with openMP) or none (for sequential)
	154
	155	-d GRID_RESOLUTION should be among the available benchs if -bench 1
	156	among which : 48x36x19, 48x36x39
	157	if wanting to run a bench simulation in addition to compilation
	158	default : 48x36x19
	159
	160	-bench activating the bench or not (0/1). Default 1
	161
	162	-name LOCAL_MODEL_NAME : default = LMDZversion.release
	163
[4211]	164	-netcdf 0, 1 or PATH
	165	0: do not download NetCDF, look for it in standard locations
	166	1: download and compile NetCDF
	167	PATH: full path to an existing installed NetCDF library
[4210]	168
	169	-xios also download and compile the XIOS library
	170	(requires the NetCDF4-HDF5 library, also installed by default)
	171	(requires to also have -parallel mpi_omp)
	172
	173	-gprof to compile with -pg to enable profiling with gprof
	174
	175	-cosp to run without our with cospv1 or cospv2 [none/v1/v2]
	176
	177	-rad RADIATIF can be oldrad, rrtm or ecrad radiatif code
	178
	179	-nofcm to compile without fcm
	180
	181	-SCM install 1D version automatically
	182
	183	-debug compile everything in debug mode
	184
	185	-opt_makelmdz to call makelmdz or makelmdz_fcm with additional options
	186
	187	-physiq to choose which physics package to use
	188
	189	-env_file specify an arch.env file to overwrite the existing one
	190
	191	-veget surface model to run [NONE/CMIP6/xxxx]
	192
	193	........fin
[4215]	194	exit ;;
	195	"-v") version=$2 ; shift ; shift ;;
	196	"-r") svn=$2 ; shift ; shift ;;
	197	"-compiler") compiler=$2
	198	case $compiler in
	199	"gfortran"\|"ifort"\|"pgf90") compiler=$2 ; shift ; shift ;;
	200	*) echo "Only gfortran , ifort or pgf90 for the compiler option" ; exit
	201	esac ;;
	202	"-d") grid_resolution=$2 ; shift ; shift ;;
	203	"-gprof") OPT_GPROF="-pg" ; shift ;;
	204	"-cosp") cosp=$2
	205	case $cosp in
	206	"none"\|"v1"\|"v2") cosp=$2 ; shift ; shift ;;
	207	*) echo Only none v1 v2 for cosp option ; exit
	208	esac ;;
	209	"-nofcm") compile_with_fcm=0 ; shift ;;
	210	"-SCM") SCM=1 ; shift ;;
	211	"-opt_makelmdz") OPT_MAKELMDZ="$2" ; shift ; shift ;;
	212	"-rrtm") rrtm="$2" ; if [ "$2" = "false" ] ; then rad="oldrad" ; else rad="rrtm" ; fi ; shift ; shift ;;
	213	"-rad") rad=$2
	214	case $rad in
	215	"oldrad"\|"rrtm"\|"ecrad") rad=$2 ; shift ; shift ;;
	216	*) echo Only oldrad rrtm ecrad for rad option ; exit
	217	esac ;;
	218	"-parallel") parallel=$2
	219	case $parallel in
	220	"none"\|"mpi"\|"omp"\|"mpi_omp") parallel=$2 ; shift ; shift ;;
	221	*) echo Only none mpi omp mpi_omp for the parallel option ; exit
	222	esac ;;
	223	"-bench") bench=$2 ; shift ; shift ;;
	224	"-debug") optim=-debug ; shift ;;
	225	"-name") MODEL=$2 ; shift ; shift ;;
	226	"-netcdf") netcdf=$2 ; shift ; shift ;;
	227	"-physiq") physiq=$2 ; shift ; shift ;;
	228	"-xios") with_xios="y" ; shift ;;
	229	"-env_file") env_file=$2 ; shift ; shift ;;
	230	"-veget") veget=$2 ; shift ; shift ;;
	231	*) ./install_lmdz.sh -h ; exit
	232	esac
[4210]	233	done
	234
	235	# Option de compilation du rayonnement : depend de $mysvn ><= r4185, sera donc definie plus bas
	236	#opt_rad=""
	237	#case $rad in
	238	# rrtm) opt_rad="-rad rrtm" ;;
	239	# ecrad) opt_rad="-rad ecrad" ;;
	240	#esac
	241
	242
	243	# Option de compilation pour Cosp
	244	opt_cosp=""
	245	case cosp in
[4215]	246	v1) opt_cosp="-cosp true" ;;
	247	v2) opt_cosp="-cospv2 true" ;;
[4210]	248	esac
	249
	250	# Check on veget version
	251	#if [ "$veget" != 'NONE' -a "$veget" != "CMIP6" -a "$veget" != +([0-9]) ] ; then
	252	if [ $veget != 'NONE' -a $veget != "CMIP6" ] ; then
	253	re='^[0-9]+$'
	254	if ! [[ $veget =~ $re ]] ; then
	255	echo 'Valeur de l option veget non valable'
	256	exit
	257	fi
	258	fi
	259
	260	#Define veget-related suffix for gcm name
	261	if [ "$veget" = 'NONE' ] ; then
	262	suff_orc=''
	263	#For use with tutorial, orchidee_rev is also defined (will be written in surface_env at the end of the script)
	264	orchidee_rev=''
	265	else
	266	suff_orc='_orch'
	267	fi
	268
	269
	270	if [ $parallel = none ] ; then sequential=1; suff_exe='_seq' ; else sequential=0; suff_exe='_para_mem' ; fi
	271
	272	#Chemin pour placer le modele
	273	if [ "$MODEL" = "" ] ; then MODEL=./LMDZ$version$svn$optim ; fi
	274
	275
	276	arch=local
	277
	278
	279	if [ $compiler = g95 ] ; then echo g95 is not supported anymore ; exit ; fi
	280
	281	################################################################
	282	# Specificite des machines
	283	################################################################
	284
	285	hostname=`hostname`
	286	if [ "$pclinux" = 1 ] ; then o_ins_make="-t g95" ; else o_ins_make="" ; fi
	287
	288	case ${hostname:0:5} in
	289
[4215]	290	jean-) compiler="mpiifort" ;
	291	par_comp="mpiifort" ;
	292	o_ins_make="-t jeanzay" ;
	293	make=gmake ;
	294	module purge
	295	module load intel-compilers/19.0.4 ;
	296	#module load intel-mpi/19.0.4 ;
	297	#module load intel-mkl/19.0.4 ;
	298	module load hdf5/1.10.5-mpi ;
	299	module load netcdf/4.7.2-mpi ;
	300	module load netcdf-fortran/4.5.2-mpi ;
	301	module load subversion/1.9.7 ;
	302	export NETCDF_LIBDIR=./
	303	export NETCDFFORTRAN_INCDIR=./
	304	export NETCDFFORTRAN_LIBDIR=./
	305	arch=X64_JEANZAY ;;
[4210]	306
[4215]	307	cicla\|camel) compiler="gfortran" ;
	308	module load netcdf4/4.3.3.1-gfortran;
	309	netcdf=/opt/netcdf43/gfortran
[4211]	310
[4215]	311	if [ $parallel != none ] ; then
	312	module load openmpi/1.6.5-gfortran ;
	313	root_mpi=$MPI_HOME ;
	314	path_mpi=$root_mpi/bin ;
	315	par_comp=${path_mpi}/mpif90 ;
	316	mpirun=${path_mpi}/mpirun ;
	317	fi ;
	318	arch=local ;
	319	make=make ;
	320	o_ins_make="-t g95" ;;
[4210]	321
[4215]	322	*) if [ $parallel = none -o -f /usr/bin/mpif90 ] ; then
	323	path_mpi=`which mpif90 \| sed -e s:/mpif90::` ;
	324	if [ -d /usr/lib64/openmpi ] ; then
	325	root_mpi="/usr/lib64/openmpi"
	326	else
	327	root_mpi="/usr"
	328	fi
	329	else
	330	echo "Cannot find mpif90" ;
	331	if [ $parallel = none ] ; then exit ; fi ;
	332	fi ;
	333	if [ $parallel != none ] ; then
	334	root_mpi=$(which mpif90 \| sed -e s:/bin/mpif90::)
	335	path_mpi=$(which mpif90 \| sed -e s:/mpif90::)
	336	export LD_LIBRARY_PATH=${root_mpi}/lib:$LD_LIBRARY_PATH
	337	fi
	338	par_comp=${path_mpi}/mpif90 ;
	339	mpirun=${path_mpi}/mpirun ;
	340	arch=local ;
	341	make=make ;
	342	o_ins_make="-t g95"
[4210]	343	esac
	344
	345	# Flags for parallelism:
	346	if [ $parallel != none ] ; then
[4215]	347	# MPI_LD are the flags needed for linking with MPI
	348	MPI_LD="-L${root_mpi}/lib -lmpi"
	349	if [ "$compiler" = "gfortran" ] ; then
	350	# MPI_FLAGS are the flags needed for compilation with MPI
	351	MPI_FLAGS="-fcray-pointer"
	352	# OMP_FLAGS are the flags needed for compilation with OpenMP
	353	OMP_FLAGS="-fopenmp -fcray-pointer"
	354	# OMP_LD are the flags needed for linking with OpenMP
	355	OMP_LD="-fopenmp"
	356	elif [ "$compiler" = "ifort" ] ; then
	357	MPI_FLAGS=""
	358	OMP_FLAGS="-openmp"
	359	OMP_LD="-openmp"
	360	else # pgf90
	361	MPI_FLAGS=""
	362	OMP_FLAGS="-mp"
	363	OMP_LD="-mp"
	364	fi
[4210]	365	fi
	366
	367	#####################################################################
	368	# Test for old gfortran compilers
	369	# If the compiler is too old (older than 4.3.x) we test if the
	370	# temporary gfortran44 patch is available on the computer in which
	371	# case the compiler is changed from gfortran to gfortran44
	372	# Must be aware than parallelism can not be activated in this case
	373	#####################################################################
	374
	375	if [ "$compiler" = "gfortran" ] ; then
[4215]	376	gfortran=gfortran
	377	gfortranv=`gfortran --version \| \
[4210]	378	head -1 \| awk ' { print $NF } ' \| awk -F. ' { print $1 * 10 + $2 } '`
[4215]	379	if [ $gfortranv -le 43 ] ; then
	380	echo ERROR : Your gfortran compiler is too old
	381	echo 'Please choose a new one (ifort) and change the line'
	382	echo compiler=xxx
	383	echo in the install_lmdz.sh script and rerun it
	384	if [ `which gfortran44 \| wc -w` -ne 0 ] ; then
	385	gfortran=gfortran44
	386	else
	387	echo gfotran trop vieux ; exit
	388	fi
	389	fi
	390	compiler=$gfortran
[4210]	391	fi
	392	#####################################################################
	393
	394	## if also compiling XIOS, parallel must be mpi_omp
	395	if [ "$with_xios" = "y" -a "$parallel" != "mpi_omp" ] ; then
[4215]	396	echo "Error, you must set -parallel mpi_omp if you want XIOS"
	397	exit
[4210]	398	fi
	399
	400	if [ "$with_xios" = "y" ] ; then
[4215]	401	opt_makelmdz_xios="-io xios"
[4210]	402	fi
	403
	404	if [ "$cosp" = "v2" -a "$with_xios" = "n" ] ; then
[4215]	405	echo "Error, Cospv2 cannot run without Xios"
	406	exit
[4210]	407	fi
	408
	409	echo '################################################################'
	410	echo Choix des options de compilation
	411	echo '################################################################'
	412
	413	export FC=$compiler
	414	export F90=$compiler
	415	export F77=$compiler
	416	export CPPFLAGS=
	417	OPTIMNC=$OPTIM
	418	BASE_LD="$OPT_GPROF"
	419	OPTPREC="$OPT_GPROF"
	420	ARFLAGS="rs" ; if [ -f /etc/issue ] ; then if [ "`grep -i ubuntu /etc/issue`" != "" ] ; then if [ "`grep -i ubuntu /etc/issue \| awk ' { print $2 } ' \| cut -d. -f1`" -ge 16 ] ; then ARFLAGS="rU" ; fi ; fi ; fi
	421
	422
	423
	424	if [ "$compiler" = "$gfortran" ] ; then
[4215]	425	OPTIM='-O3'
	426	OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all -fbacktrace -finit-real=snan"
	427	OPTDEV="-Wall -fbounds-check"
	428	fmod='I '
	429	OPTPREC="$OPTPREC -cpp -ffree-line-length-0"
	430	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE" ; fi
	431	export F90FLAGS=" -ffree-form $OPTIMNC"
	432	export FFLAGS=" $OPTIMNC"
	433	export CC=gcc
	434	export CXX=g++
	435	export fpp_flags="-P -C -traditional -ffreestanding"
[4210]	436
	437	elif [ $compiler = mpif90 ] ; then
[4215]	438	OPTIM='-O3'
	439	OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all"
	440	OPTDEV="-Wall -fbounds-check"
	441	BASE_LD="$BASE_LD -lblas"
	442	fmod='I '
	443	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE -fcray-pointer" ; fi
	444	export F90FLAGS=" -ffree-form $OPTIMNC"
	445	export FFLAGS=" $OPTIMNC"
	446	export CC=gcc
	447	export CXX=g++
[4210]	448
	449	elif [ $compiler = pgf90 ] ; then
[4215]	450	OPTIM='-O2 -Mipa -Munroll -Mnoframe -Mautoinline -Mcache_align'
	451	OPTDEB='-g -Mdclchk -Mbounds -Mchkfpstk -Mchkptr -Minform=inform -Mstandard -Ktrap=fp -traceback'
	452	OPTDEV='-g -Mbounds -Ktrap=fp -traceback'
	453	fmod='module '
	454	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -r8 -DNC_DOUBLE" ; fi
	455	export CPPFLAGS="-DpgiFortran"
	456	export CC=pgcc
	457	export CFLAGS="-O2 -Msignextend"
	458	export CXX=pgCC
	459	export CXXFLAGS="-O2 -Msignextend"
	460	export FFLAGS="-O2 $OPTIMNC"
	461	export F90FLAGS="-O2 $OPTIMNC"
	462	compile_with_fcm=1
[4210]	463
	464	elif [ $compiler = ifort ] ; then
[4215]	465	OPTIM="-O2 -fp-model strict -ip -align all "
	466	OPTDEV="-p -g -O2 -traceback -fp-stack-check -ftrapuv -check"
	467	OPTDEB="-g -no-ftz -traceback -ftrapuv -fp-stack-check -check"
	468	fmod='module '
	469	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -real-size 64 -DNC_DOUBLE" ; fi
	470	export CPP="icc -E"
	471	export FFLAGS="-O2 -ip -fpic -mcmodel=large"
	472	export FCFLAGS="-O2 -ip -fpic -mcmodel=large"
	473	export CC=icc
	474	export CFLAGS="-O2 -ip -fpic -mcmodel=large"
	475	export CXX=icpc
	476	export CXXFLAGS="-O2 -ip -fpic -mcmodel=large"
	477	export fpp_flags="-P -traditional"
	478	# Pourquoi forcer la compilation fcm. Marche mieux sans
	479	#compile_with_fcm=1
[4210]	480
	481	elif [ $compiler = mpiifort ] ; then
[4215]	482	echo on ne fait rien la
	483	# Pourquoi forcer la compilation fcm. Marche mieux sans
	484	#compile_with_fcm=1
[4210]	485
	486	else
[4215]	487	echo unexpected compiler $compiler ; exit
[4210]	488	fi
	489
	490	OPTIMGCM="$OPTIM $OPTPREC"
	491
	492	hostname=`hostname`
	493
	494	##########################################################################
	495	# If installing on known machines such as Jean-Zay at IDRIS,
	496	# don't check for available software and don't install netcdf
	497	if [ ${hostname:0:5} = jean- ] ; then
[4215]	498	netcdf=0 # no need to recompile netcdf, alreday available
	499	check_linux=0
	500	pclinux=0
	501	ioipsl=0 # no need to recompile ioipsl, already available
	502	#netcdf="/smplocal/pub/NetCDF/4.1.3"
	503	compiler="mpiifort"
	504	fmod='module '
	505	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -i4 -r8 -DNC_DOUBLE" ; fi
	506	OPTIM="-auto -align all -O2 -fp-model strict -xHost "
	507	OPTIMGCM="$OPTIM $OPTPREC"
[4210]	508	fi
	509	##########################################################################
	510
	511
	512	mkdir -p $MODEL
	513	echo $MODEL
	514	MODEL=`( cd $MODEL ; pwd )` # to get absolute path, if necessary
	515
	516
	517	echo '################################################################'
	518	if [ "$check_linux" = 1 ] ; then
[4215]	519	echo Check if required software is available
	520	echo '################################################################'
[4210]	521
[4215]	522	#### Ehouarn: test if the required shell is available
	523	#### Maj FH-LF-AS 2021-04 : default=bash ; if bash missing, use ksh
	524	use_shell="bash" # default
	525	if [ "`which bash`" = "" ] ; then
	526	echo "no bash ; we will use ksh"
	527	use_shell="ksh"
	528	if [ "`which ksh`" = "" ] ; then
	529	echo "bash (or ksh) needed!! Install it!"
	530	exit
	531	fi
	532	fi
[4210]	533
[4215]	534	for logiciel in wget tar gzip make $compiler gcc cmake ; do
	535	if [ "`which $logiciel`" = "" ] ; then
	536	echo You must first install $logiciel on your system
	537	exit
	538	fi
	539	done
[4210]	540
[4215]	541	if [ $pclinux = 1 ] ; then
	542	cd $MODEL
	543	cat <<eod > tt.f90
[4210]	544	print*,'coucou'
	545	end
	546	eod
[4215]	547	$compiler tt.f90 -o a.out
	548	./a.out >\| tt
	549	if [ "`cat tt \| sed -e 's/ //g' `" != "coucou" ] ; then
	550	echo problem installing with compiler $compiler ; exit ; fi
	551	\rm tt a.out tt.f90
	552	fi
[4210]	553	fi
	554
	555	###########################################################################
	556	if [ $getlmdzor = 1 -a ! -d $MODEL/modipsl ] ; then
[4215]	557	###########################################################################
	558	echo '##########################################################'
	559	echo Download a slightly modified version of LMDZ
	560	echo '##########################################################'
	561	cd $MODEL
	562	myget src/modipsl.$version.tar.gz
	563	echo install_lmdz.sh wget_OK `date`
	564	gunzip modipsl.$version.tar.gz
	565	tar xf modipsl.$version.tar
	566	\rm modipsl.$version.tar
[4210]	567	fi
	568
	569	###########################################################################
	570	if [ $netcdf = 1 -a ! -d $MODEL/netcdf ] ; then
[4215]	571	###########################################################################
	572	cd $MODEL
	573	netcdflog=`pwd`/netcdf.log
	574	echo '##########################################################'
	575	echo Compiling the Netcdf library
	576	echo '##########################################################'
	577	echo log file : $netcdflog
	578	if [ "$with_xios" = "n" ] ; then
	579	myget import/install_netcdf4_hdf5_seq.bash
	580	chmod +x install_netcdf4_hdf5_seq.bash
[4212]	581
[4215]	582	if [ "$compiler" = "gfortran" ]
	583	then
	584	./install_netcdf4_hdf5_seq.bash -prefix $MODEL/netcdf4_hdf5_seq \
	585	-compiler gnu > $netcdflog 2>&1
	586	elif [ "$compiler" = "ifort" ]
	587	then
	588	./install_netcdf4_hdf5_seq.bash -prefix $MODEL/netcdf4_hdf5_seq \
	589	-compiler intel > $netcdflog 2>&1
	590	else
	591	echo "unexpected compiler $compiler" ; exit
	592	fi
[4212]	593
[4215]	594	# LF rajout d'une verrue, pour une raison non encore expliquee,
	595	# la librairie est parfois rangée dans lib64 et non dans lib
	596	# par certains compilateurs
	597	if [ ! -e lib -a -d lib64 ] ; then ln -s lib64 lib; fi
	598	else
	599	# download and compile hdf5 and netcdf, etc. using the install_netcdf4_hdf5.bash script
	600	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/install_netcdf4_hdf5.bash
	601	myget import/install_netcdf4_hdf5.bash
	602	chmod u=rwx install_netcdf4_hdf5.bash
	603	if [ "$compiler" = "gfortran" ] ; then
	604	./install_netcdf4_hdf5.bash -prefix $MODEL/netcdf4_hdf5 -CC gcc -FC gfortran -CXX g++ -MPI $root_mpi > $netcdflog 2>&1
	605	elif [ "$compiler" = "ifort" ] ; then
	606	./install_netcdf4_hdf5.bash -prefix $MODEL/netcdf4_hdf5 -CC icc -FC ifort -CXX icpc -MPI $root_mpi > $netcdflog 2>&1
	607	elif [ "$compiler" = "pgf90" ] ; then
	608	./install_netcdf4_hdf5.bash -prefix $MODEL/netcdf4_hdf5 -CC pgcc -FC pgf90 -CXX pgCC -MPI $root_mpi > $netcdflog 2>&1
	609	else
	610	echo "unexpected compiler $compiler" ; exit
	611	fi
	612	fi # of if [ "$with_xios" = "n" ]
	613	echo install_lmdz.sh netcdf_OK `date`
[4210]	614	fi # of if [ $netcdf = 1 ]
	615
	616	# ncdfdir contains the directory where netcdf is installed
[4211]	617	if [ $netcdf = 1 ] ; then
[4215]	618	if [ "$with_xios" = "y" ] ; then
	619	ncdfdir=$MODEL/netcdf4_hdf5
	620	else
	621	ncdfdir=$MODEL/netcdf4_hdf5_seq
	622	fi
[4211]	623	elif [ $netcdf = 0 ]
	624	then
[4215]	625	ncdfdir=/usr
[4210]	626	else
[4215]	627	ncdfdir=$netcdf
[4210]	628	fi
	629
	630	#=========================================================================
	631	if [[ ! -f $MODEL/modipsl/lib/libioipsl.a ]]
	632	then
[4215]	633	if [ $ioipsl = 1 ] ; then
	634	#=========================================================================
	635	echo OK ioipsl=$ioipsl
	636	echo '##########################################################'
	637	echo 'Installing MODIPSL, the installation package manager for the '
	638	echo 'IPSL models and tools'
	639	echo '##########################################################'
	640	echo `date`
[4210]	641
[4215]	642	cd $MODEL/modipsl
	643	\rm -rf lib/*
	644	cd util
	645	cp AA_make.gdef AA_make.orig
	646	F_C="$compiler -c " ; if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then F_C="$compiler -c -cpp " ; fi
	647	if [ "$compiler" = "pgf90" ] ; then F_C="$compiler -c -Mpreprocess" ; fi
	648	sed -e 's/^\#..g95..\#.*.$/\#/' AA_make.gdef > tmp
	649	sed -e "s:F_L = g95:F_L = $compiler:" -e "s:F_C = g95 -c -cpp:F_C = $F_C": \
	650	-e 's/g95..w_w..(F_D)/g95 w_w = '"$OPTIMGCM"'/' \
	651	-e 's:g95..NCDF_INC..$:g95 NCDF_INC= '"$ncdfdir"'/include:' \
	652	-e 's:g95..NCDF_LIB..$:g95 NCDF_LIB= -L'"$ncdfdir"'/lib -lnetcdff -lnetcdf:' \
	653	-e 's:g95 L_O =:g95 L_O = -Wl,-rpath='"$ncdfdir"'/lib:' \
	654	-e "s:-fmod=:-$fmod:" -e 's/-fno-second-underscore//' \
	655	-e 's:#-Q- g95 M_K = gmake:#-Q- g95 M_K = make:' \
	656	tmp >\| AA_make.gdef
[4210]	657
[4215]	658	if [ $pcmac == 1 ]
	659	then
	660	cp AA_make.gdef tmp
	661	sed -e 's/rpath=/rpath,/g' tmp > AA_make.gdef
	662	fi
[4210]	663
	664
[4215]	665	# We use lines for g95 even for the other compilers to run ins_make
	666	if [ "$use_shell" = "ksh" ] ; then
	667	./ins_make $o_ins_make
	668	else # bash
	669	sed -e s:/bin/ksh:/bin/bash:g ins_make > ins_make.bash
	670	if [ "`grep jeanzay AA_make.gdef`" = "" ] ; then # Bidouille pour compiler sur ada des vieux modipsl.tar
	671	echo 'Warning jean-zay not in AA_make.gdef'
	672	echo 'Think about updating'
	673	exit 1
	674	fi
[4210]	675
[4215]	676	chmod u=rwx ins_make.bash
	677	./ins_make.bash $o_ins_make
	678	fi # of if [ "$use_shell" = "ksh" ]
[4210]	679
[4215]	680	echo install_lmdz.sh MODIPSL_OK `date`
[4210]	681
[4215]	682	cd $MODEL/modipsl/modeles/IOIPSL/src
	683	ioipsllog=`pwd`/ioipsl.log
	684	echo '##########################################################'
	685	echo 'Compiling IOIPSL, the interface library with Netcdf'
	686	echo '##########################################################'
	687	echo `date`
	688	echo log file : $ioipsllog
[4210]	689
[4215]	690	if [ "$use_shell" = "bash" ] ; then
	691	cp Makefile Makefile.ksh
	692	sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile
	693	fi
	694	# if [ "$pclinux" = 1 ] ; then
	695	# Build IOIPSL modules and library
	696	$make clean
	697	$make > $ioipsllog 2>&1
	698	if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then # copy module files to lib
	699	cp -f *.mod ../../../lib
	700	fi
	701	# Build IOIPSL tools (ie: "rebuild", if present)
	702	if [ -f $MODEL/modipsl/modeles/IOIPSL/tools/rebuild ] ; then
	703	cd $MODEL/modipsl/modeles/IOIPSL/tools
	704	# adapt Makefile & rebuild script if in bash
	705	if [ "$use_shell" = "bash" ] ; then
	706	cp Makefile Makefile.ksh
	707	sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile
	708	cp rebuild rebuild.ksh
	709	sed -e 's:/bin/ksh:/bin/bash:g' \
	710	-e 's:print -u2:echo:g' \
	711	-e 's:print:echo:g' rebuild.ksh > rebuild
	712	fi
	713	$make clean
	714	$make > $ioipsllog 2>&1
	715	fi
	716	# fi # of if [ "$pclinux" = 1 ]
[4210]	717
[4215]	718	else # of if [ $ioipsl = 1 ]
	719	if [ ${hostname:0:5} = jean- ] ; then
	720	cd $MODEL/modipsl
	721	cd util
	722	if [ "`grep jeanzay AA_make.gdef`" = "" ] ; then
	723	echo 'Warning jean-zay not in AA_make.gdef'
	724	echo 'Think about updating'
	725	exit 1
	726	fi
	727	./ins_make $o_ins_make
	728	# Compile IOIPSL on jean-zay
	729	cd $MODEL/modipsl/modeles/IOIPSL/src
	730	gmake > ioipsl.log
	731	cd $MODEL/modipsl/modeles/IOIPSL/tools
	732	gmake > ioipsl.log
[4210]	733
[4215]	734	fi
	735	echo install_lmdz.sh ioipsl_OK `date`
	736	fi # of if [ $ioipsl = 1 ]
[4210]	737	fi
	738	# Saving ioipsl lib for possible parallel compile
[4215]	739	cd $MODEL/modipsl
	740	tar cf ioipsl.tar lib/ bin/
[4210]	741
	742	#=========================================================================
	743	if [ "$with_xios" = "y" ] ; then
[4215]	744	echo '##########################################################'
	745	echo 'Compiling XIOS'
	746	echo '##########################################################'
	747	cd $MODEL/modipsl/modeles
	748	xioslog=`pwd`/xios.log
	749	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/install_xios.bash
	750	myget import/install_xios.bash
	751	chmod u=rwx install_xios.bash
	752	if [ ${hostname:0:5} = jean- ] ; then
	753	svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5 XIOS
	754	cd XIOS/arch
	755	svn update
	756	cd ..
	757	echo "Compiling XIOS, start" `date` "(it takes about 20 min on Jean-Zay)"
	758	echo "log file: $xioslog"
	759	./make_xios --prod --arch $arch --job 4 > xios.log 2>&1
	760	else
	761	./install_xios.bash -prefix $MODEL/modipsl/modeles \
	762	-netcdf ${ncdfdir} -hdf5 ${ncdfdir} \
	763	-MPI $root_mpi -arch $arch > xios.log 2>&1
	764	fi # of case Jean-Zay
	765	if [ -f XIOS/lib/libxios.a ] ; then
	766	echo "XIOS library successfully generated"
	767	echo install_lmdz.sh XIOS_OK `date`
	768	fi
[4210]	769	fi
	770
	771	#============================================================================
	772	veget_version=false
	773	if [ "$veget" != 'NONE' ] ; then
[4215]	774	cd $MODEL/modipsl/modeles/ORCHIDEE
	775	set +e ; svn upgrade ; set -e
	776	if [ "$veget" = "CMIP6" ] ; then
	777	veget_version=orchidee2.0
	778	orchidee_rev=6592
	779	else # specific orchidee revision newer than CMIP6, on 2_1 or 2_2 branches
	780	veget_version=orchidee2.1
	781	orchidee_rev=$veget
	782	if [ $veget -lt 4465 ] ; then
	783	echo 'Stopping, ORCHIDEE version too old, script needs work on the CPP flags to pass to makelmdz'
	784	exit 1
	785	fi
	786	set +e
	787	# which branch is my version on?
	788	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}'`
	789	# switch to that branch
	790	echo IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at orchidee-help@listes.ipsl.fr
	791	svn switch -r $veget --accept theirs-full svn://forge.ipsl.jussieu.fr/orchidee/$orcbranch
	792	svn log -r $veget \| grep $veget
	793	if [ $? -gt 0 ] ; then
	794	echo 'Cannot update ORCHIDEE as not on the right branch for ORCHIDEE'
	795	exit
	796	fi
	797	set -e
	798	set +e ; svn update -r $veget ; set -e
	799	fi
	800	# Correctif suite debug Jean-Zay
	801	sed -i -e 's/9010 FORMAT(A52,F17.14)/9010 FORMAT(A52,F20.14)/' src_stomate/stomate.f90
	802	opt_orc="-prod" ; if [ "$optim" = "-debug" ] ; then opt_orc="-debug" ; fi
[4210]	803
[4215]	804	orchideelog=`pwd`/orchidee.log
	805	echo '########################################################'
	806	echo 'Compiling ORCHIDEE, the continental surface model '
	807	echo '########################################################'
	808	echo Start of the first compilation of orchidee, in sequential mode: `date`
	809	echo log file : $orchideelog
[4210]	810
[4215]	811	export ORCHPATH=`pwd`
	812	xios_orchid="-noxios"
	813	if [ "$with_xios" = "y" ] ; then
	814	xios_orchid="-xios"
	815	fi
	816	if [ -d tools ] ; then
	817	###################################################################
	818	# Pour les experts qui voudraient changer de version d'orchidee.
	819	# Attention : necessite d'avoir le password pour orchidee
[4210]	820
[4215]	821	# Correctif suite debug Jean-Zay
	822	if [ -f src_global/time.f90 ] ; then sed -i -e 's/CALL tlen2itau/\!CALL tlen2itau/' src_global/time.f90 ; fi
	823	###################################################################
	824	if [ "$veget_version" == "false" ] ; then veget_version=orchidee2.0 ; fi
	825	cd arch
	826	sed -e s:"%COMPILER .*.$":"%COMPILER $compiler":1 \
	827	-e s:"%LINK .*.$":"%LINK $compiler":1 \
	828	-e s:"%FPP_FLAGS .*.$":"%FPP_FLAGS $fpp_flags":1 \
	829	-e s:"%PROD_FFLAGS .*.$":"%PROD_FFLAGS $OPTIM":1 \
	830	-e s:"%DEV_FFLAGS .*.$":"%DEV_FFLAGS $OPTDEV":1 \
	831	-e s:"%DEBUG_FFLAGS .*.$":"%DEBUG_FFLAGS $OPTDEB":1 \
	832	-e s:"%BASE_FFLAGS .*.$":"%BASE_FFLAGS $OPTPREC":1 \
	833	-e s:"%BASE_LD .*.$":"%BASE_LD $BASE_LD":1 \
	834	-e s:"%ARFLAGS .*.$":"%ARFLAGS $ARFLAGS":1 \
	835	arch-gfortran.fcm > arch-local.fcm
	836	echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib -lnetcdff -lnetcdf\"" > arch-local.path
	837	echo "NETCDF_INCDIR=${ncdfdir}/include" >> arch-local.path
	838	echo "IOIPSL_INCDIR=$ORCHPATH/../../lib" >> arch-local.path
	839	echo "IOIPSL_LIBDIR=$ORCHPATH/../../lib" >> arch-local.path
	840	echo 'XIOS_INCDIR=${ORCHDIR}/../XIOS/inc' >> arch-local.path
	841	echo 'XIOS_LIBDIR="${ORCHDIR}/../XIOS/lib -lxios"' >> arch-local.path
	842	cd ../
[4210]	843
[4215]	844	echo ./makeorchidee_fcm -j $xios_orchid $opt_orc -parallel none -arch $arch
	845	./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel none -arch $arch > $orchideelog 2>&1
	846	pwd
	847	else # of "if [ -d tools ]"
	848	if [ -d src_parallel ] ; then
	849	liste_src="parallel parameters global stomate sechiba driver"
	850	if [ "$veget_version" == "false" ] ; then veget_version=orchidee2.0 ; fi
	851	fi
	852	for d in $liste_src ; do src_d=src_$d
	853	echo src_d $src_d
	854	echo ls ; ls
	855	if [ ! -d $src_d ] ; then echo Problem orchidee : no $src_d ; exit ; fi
	856	cd $src_d ; \rm -f *.mod make ; $make clean
	857	$make > $orchideelog 2>&1 ; if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then cp -f *.mod ../../../lib ; fi
	858	cd ..
	859	done
	860	fi # of "if [ -d tools ]"
	861	echo install_lmdz.sh orchidee_compil_seq_OK `date`
[4210]	862	fi # of if [ "$veget" != 'NONE' ]
	863
	864
	865	#============================================================================
	866	# Ehouarn: the directory name LMDZ* depends on version/tar file...
	867	if [ -d $MODEL/modipsl/modeles/LMD* ] ; then
[4215]	868	echo '###############################################################'
	869	echo 'Preparing LMDZ compilation : arch file, svn switch if needed...'
	870	echo '###############################################################'
	871	cd $MODEL/modipsl/modeles/LMD*
	872	LMDZPATH=`pwd`
[4210]	873	else
[4215]	874	echo "ERROR: No LMD* directory !!!"
	875	exit
[4210]	876	fi
	877
	878	###########################################################
	879	# For those who want to use fcm to compile via :
	880	# makelmdz_fcm -arch local .....
	881	############################################################
	882
[4214]	883	if [[ "$pclinux" = "1" && ! -f arch/arch-local.path ]] ; then
[4210]	884
[4215]	885	# create local 'arch' files (if on Linux PC):
	886	cd arch
	887	# arch-local.path file
	888	echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib -lnetcdff -lnetcdf\"" > arch-local.path
	889	echo "NETCDF_INCDIR=-I${ncdfdir}/include" >> arch-local.path
	890	echo 'NETCDF95_INCDIR=$LMDGCM/../../include' >> arch-local.path
	891	echo 'NETCDF95_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
	892	echo 'IOIPSL_INCDIR=$LMDGCM/../../lib' >> arch-local.path
	893	echo 'IOIPSL_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
	894	echo 'XIOS_INCDIR=$LMDGCM/../XIOS/inc' >> arch-local.path
	895	echo 'XIOS_LIBDIR=$LMDGCM/../XIOS/lib' >> arch-local.path
	896	echo 'ORCH_INCDIR=$LMDGCM/../../lib' >> arch-local.path
	897	echo 'ORCH_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
[4210]	898
[4215]	899	if [ $pcmac == 1 ] ; then
	900	BASE_LD="$BASE_LD -Wl,-rpath,${ncdfdir}/lib"
	901	else
	902	BASE_LD="$BASE_LD -Wl,-rpath=${ncdfdir}/lib"
	903	fi
	904	# Arch-local.fcm file (adapted from arch-linux-32bit.fcm)
[4210]	905
[4215]	906	if [ $real = r8 ] ; then FPP_DEF=NC_DOUBLE ; else FPP_DEF="" ; fi
	907	sed -e s:"%COMPILER .*.$":"%COMPILER $compiler":1 \
	908	-e s:"%LINK .*.$":"%LINK $compiler":1 \
	909	-e s:"%PROD_FFLAGS .*.$":"%PROD_FFLAGS $OPTIM":1 \
	910	-e s:"%DEV_FFLAGS .*.$":"%DEV_FFLAGS $OPTDEV":1 \
	911	-e s:"%DEBUG_FFLAGS .*.$":"%DEBUG_FFLAGS $OPTDEB":1 \
	912	-e s:"%BASE_FFLAGS .*.$":"%BASE_FFLAGS $OPTPREC":1 \
	913	-e s:"%FPP_DEF .*.$":"%FPP_DEF $FPP_DEF":1 \
	914	-e s:"%BASE_LD .*.$":"%BASE_LD $BASE_LD":1 \
	915	-e s:"%ARFLAGS .*.$":"%ARFLAGS $ARFLAGS":1 \
	916	arch-linux-32bit.fcm > arch-local.fcm
[4210]	917
[4215]	918	cd ..
	919	### Adapt "bld.cfg" (add the shell):
	920	#whereisthatshell=$(which ${use_shell})
	921	#echo "bld::tool::SHELL $whereisthatshell" >> bld.cfg
[4210]	922
	923	fi # of if [ "$pclinux" = 1 ]
	924
	925
	926	cd $MODEL/modipsl/modeles/LMDZ*
	927	lmdzlog=`pwd`/lmdz.log
	928
	929	##################################################################
	930	# Possibly update LMDZ if a specific svn release is requested
	931	##################################################################
	932
	933	set +e ; svn upgrade ; set -e
	934
	935	if [ "$svn" = "last" ] ; then svnopt="" ; else svnopt="-r $svn" ; fi
	936	if [ "$svn" != "" ] ; then
	937	set +e ; svn info \| grep -q 'http:'
	938	if [ $? = 0 ] ; then
	939	svn switch --relocate http://svn.lmd.jussieu.fr/LMDZ https://svn.lmd.jussieu.fr/LMDZ
	940	fi
	941	svn update $svnopt
	942	fi
	943	set -e
	944
	945	##################################################################
	946	# Retrieve the final svn release number, and adjust compilation options accordingly
	947	mysvn=`svnversion . \| egrep -o "[0-9]+"`
	948
	949	# Option de compilation du rayonnement : depend de $mysvn ><= r4185
	950	opt_rad=""
	951
	952	case $rad in
	953	oldrad) iflag_rrtm=0 ; NSW=2 ; opt_rad="" ;;
	954	rrtm) iflag_rrtm=1 ; NSW=6 ; if [ $mysvn -le 4185 ] ; then opt_rad="-rrtm true" ; else opt_rad="-rad rrtm" ; fi ;;
	955	ecrad) iflag_rrtm=2 ; NSW=6 ; opt_rad="-rad ecrad" ;;
	956	*) echo Only oldrad rrtm ecrad for rad option ; exit
	957	esac
	958
	959	if [ $mysvn -le 4185 -a $rad = "ecrad" ] ; then echo "ecrad only available for LMDZ rev starting with 4186 " ; exit ; fi
	960
	961	##################################################################
	962
[4213]	963
	964	if [[ ! -f libf/misc/netcdf95.F90 && ! -d $MODEL/NetCDF95-0.2 ]]
	965	then
	966	cd $MODEL
	967	myget import/NetCDF95-0.2.tar.gz
	968	tar -xf NetCDF95-0.2.tar.gz
	969	rm NetCDF95-0.2.tar.gz
	970	cd NetCDF95-0.2
	971	mkdir build
	972	cd build
	973	cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=$ncdfdir \
	974	-DCMAKE_INSTALL_PREFIX=$MODEL/modipsl
	975	make install
	976	cd $MODEL/modipsl/modeles/LMDZ*
	977	fi
	978
[4210]	979	echo '##################################################################'
	980	echo "Preparing script compile.sh for LMDZ compilation"
	981	echo "It will only be run automatically if bench=1/tuto"
	982	echo Here bench=$bench
	983	echo '##################################################################'
	984
	985	if [ "$env_file" != "" ] ; then mv arch/arch-${arch}.env arch/arch-${arch}.orig ; \cp -f $env_file arch/arch-${arch}.env ; fi
	986
	987	if [ $compile_with_fcm = 1 ] ; then makelmdz="makelmdz_fcm $optim -arch $arch -j 8 " ; else makelmdz="makelmdz $optim -arch $arch" ; fi
	988
	989	# sequential compilation
	990	if [ "$sequential" = 1 ] ; then
[4215]	991	echo Sequential compilation command, saved in compile.sh:
	992	echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp -d ${grid_resolution} -v $veget_version gcm "
	993	echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp -d ${grid_resolution} -v $veget_version gcm " > compile.sh
	994	chmod +x ./compile.sh
	995	if [ $bench = 1 ] ; then
	996	echo install_lmdz.sh start_lmdz_seq_compilation `date`
	997	echo log file: $lmdzlog
	998	./compile.sh > $lmdzlog 2>&1
	999	echo install_lmdz.sh end_lmdz_seq_compilation `date`
	1000	fi
[4210]	1001	fi # fin sequential
	1002
	1003	# compiling in parallel mode
	1004	if [ $parallel != "none" ] ; then
	1005	echo '##########################################################'
[4215]	1006	echo ' Parallel compile '
[4210]	1007	echo '##########################################################'
[4215]	1008	echo "(after saving the sequential libs and binaries)"
	1009	cd $MODEL/modipsl
	1010	tar cf sequential.tar bin/ lib/
	1011	\rm -rf bin/ lib/
	1012	tar xf ioipsl.tar
	1013	#
	1014	# Orchidee
	1015	#
	1016	cd $ORCHPATH
	1017	if [ -d src_parallel -a $veget != 'NONE' ] ; then
	1018	cd arch
	1019	sed \
	1020	-e s:"%COMPILER.*.$":"%COMPILER $par_comp":1 \
	1021	-e s:"%LINK.*.$":"%LINK $par_comp":1 \
	1022	-e s:"%MPI_FFLAG.*.$":"%MPI_FFLAGS $MPI_FLAGS":1 \
	1023	-e s:"%OMP_FFLAG.*.$":"%OMP_FFLAGS $OMP_FLAGS":1 \
	1024	-e s:"%MPI_LD.*.$":"%MPI_LD $MPI_LD":1 \
	1025	-e s:"%OMP_LD.*.$":"%OMP_LD $OMP_LD":1 \
	1026	arch-local.fcm > tmp.fcm
[4210]	1027
[4215]	1028	mv tmp.fcm arch-local.fcm
	1029	cd ../
	1030	echo Compiling ORCHIDEE in parallel mode `date`
	1031	echo logfile $orchideelog
	1032	echo "NOTE : to recompile it when necessary, use ./compile_orc.sh in modipsl/modeles/ORCHIDEE"
	1033	echo ./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc -parallel $parallel -arch $arch > compile_orc.sh
	1034	echo ./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel $parallel -arch $arch >> compile_orc.sh
	1035	echo echo Now you must also recompile LMDZ, by running ./compile.sh in modeles/LMDZ >> compile_orc.sh
	1036	chmod u+x compile_orc.sh
	1037	./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc -parallel $parallel -arch $arch > $orchideelog 2>&1
	1038	./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel $parallel -arch $arch >> $orchideelog 2>&1
	1039	echo End of ORCHIDEE compilation in parallel mode `date`
	1040	elif [ $veget != 'NONE' ] ; then
	1041	echo '##########################################################'
	1042	echo ' Orchidee version too old '
	1043	echo ' Please update to new version '
	1044	echo '##########################################################'
	1045	exit
	1046	fi # of [ -d src_parallel -a $veget != 'NONE' ]
[4210]	1047
[4215]	1048	# LMDZ
	1049	cd $LMDZPATH
	1050	if [ $arch = local ] ; then
	1051	cd arch
	1052	sed -e s:"%COMPILER.*.$":"%COMPILER $par_comp":1 \
	1053	-e s:"%LINK.*.$":"%LINK $par_comp":1 \
	1054	-e s:"%MPI_FFLAG.*.$":"%MPI_FFLAGS $MPI_FLAGS":1 \
	1055	-e s:"%OMP_FFLAG.*.$":"%OMP_FFLAGS $OMP_FLAGS":1 \
	1056	-e s:"%ARFLAGS.*.$":"%ARFLAGS $ARFLAGS":1 \
	1057	-e s@"%BASE_LD.*.$"@"%BASE_LD -Wl,-rpath=${root_mpi}/lib:${ncdfdir}/lib"@1 \
	1058	-e s:"%MPI_LD.*.$":"%MPI_LD $MPI_LD":1 \
	1059	-e s:"%OMP_LD.*.$":"%OMP_LD $OMP_LD":1 \
	1060	arch-local.fcm > tmp.fcm
	1061	mv tmp.fcm arch-local.fcm
	1062	cd ../
	1063	fi
	1064	rm -f compile.sh
	1065	echo resol=${grid_resolution} >> compile.sh
	1066	if [ ${hostname:0:5} = jean- -a "$cosp" = "v2" ] ; then
[4210]	1067
[4215]	1068	echo LMDZ compilation command in parallel mode, saved in compile.sh, is :
	1069	echo "(ATTENTION le probleme de cospv2 sur jean-zay en mode prod n est pas corrige ! )"
	1070	# ATTENTION le probleme de cospv2 sur jean-zay en mode prod n est pas corrige
	1071	echo ./$makelmdz -dev $optim $OPT_MAKELMDZ $opt_rad $opt_cosp $opt_makelmdz_xios -d \$resol -v $veget_version -mem -parallel $parallel gcm >> compile.sh
	1072	echo ./$makelmdz -dev $optim $OPT_MAKELMDZ $opt_rad $opt_cosp $opt_makelmdz_xios -d \$resol -v $veget_version -mem -parallel $parallel gcm
	1073	else
	1074	echo ./$makelmdz $optim $OPT_MAKELMDZ $opt_rad $opt_cosp $opt_makelmdz_xios -d \$resol -v $veget_version -mem -parallel $parallel gcm >> compile.sh
	1075	echo ./$makelmdz $optim $OPT_MAKELMDZ $opt_rad $opt_cosp $opt_makelmdz_xios -d \$resol -v $veget_version -mem -parallel $parallel gcm
	1076	fi
	1077	chmod +x ./compile.sh
[4210]	1078
[4215]	1079	if [ $bench = 1 ] ; then
	1080	echo Compiling LMDZ in parallel mode `date`, LMDZ log file: $lmdzlog ; ./compile.sh > $lmdzlog 2>&1
	1081	fi
	1082
[4210]	1083	fi # of if [ $parallel != "none" ]
	1084
	1085
	1086	##################################################################
	1087	# Verification du succes de la compilation
	1088	##################################################################
	1089
	1090	# Recherche de l'executable dont le nom a change au fil du temps ...
	1091	# suffix contains radiative option starting with revision 4186
	1092	if [ $mysvn -ge 4186 ] ; then suff_exe=_${rad}${suff_exe} ; fi
	1093	gcm=""
	1094	#for exe in gcm.e bin/gcm_${grid_resolution}_phylmd_seq_orch.e bin/gcm_${grid_resolution}_phylmd_seq.e bin/gcm_${grid_resolution}_phylmd_para_mem_orch.e bin/gcm_${grid_resolution}_phylmd_para_mem.e ; do
	1095	for exe in gcm.e bin/gcm_${grid_resolution}_phylmd${suff_exe}${suff_orc}.e ; do if [ -f $exe ] ; then gcm=$exe ; fi
	1096	done
	1097
	1098	if [ "$gcm" = "" ] ; then
[4215]	1099	if [ $bench = 1 ] ; then
	1100	echo 'Compilation failed !! Cannot run the benchmark;'
	1101	exit
	1102	else
	1103	echo 'Compilation not done (only done when bench=1)'
	1104	fi
[4210]	1105	else
[4215]	1106	echo '##########################################################'
	1107	echo 'Compilation successfull !! ' `date`
	1108	echo '##########################################################'
	1109	echo The executable is $gcm
[4210]	1110	fi
	1111
	1112	##################################################################
	1113	# Below, we run a benchmark if bench=1 or tuto
	1114	##################################################################
	1115
	1116	if [ $bench = tuto ] ; then
[4215]	1117	myget Training/tutorial.tar ; tar xvf tutorial.tar ; cd TUTORIAL ; ./init.sh
[4210]	1118
	1119	elif [[ $bench = 1 && ! -d BENCH${grid_resolution} ]] ; then
[4215]	1120	# TOUTE CETTE SECTION DEVRAIT DISPARAITRE POUR UNE COMMANDE
	1121	# OU DES BENCHS PAR MOTS CLES COMME tuto
[4210]	1122
[4215]	1123	echo '##########################################################'
	1124	echo ' Running a test run '
	1125	echo '##########################################################'
[4210]	1126
[4215]	1127	\rm -rf BENCH${grid_resolution}
	1128	bench=bench_lmdz_${grid_resolution}
	1129	echo install_lmdz.sh before bench download `date`
	1130	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/$bench.tar.gz
	1131	myget 3DBenchs/$bench.tar.gz
	1132	echo install_lmdz.sh after bench download `date`
	1133	tar xvf $bench.tar.gz
[4210]	1134
[4215]	1135	if [ "$cosp" = "v1" -o "$cosp" = "v2" ] ; then
	1136	cd BENCH${grid_resolution}
	1137	# copier les fichiers namelist input et output our COSP
	1138	cp ../DefLists/cosp*_input_nl.txt .
	1139	cp ../DefLists/cosp*_output_nl.txt .
	1140	# Activer la cles ok_cosp pour tourner avec COSP
	1141	sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp
	1142	\mv -f tmp config.def
	1143	cd ..
	1144	fi
[4210]	1145
[4215]	1146	if [ -n "$physiq" ]; then
	1147	cd BENCH${grid_resolution}
	1148	if [ -f physiq.def_${physiq} ]; then
	1149	cp physiq.def_${physiq} physiq.def
	1150	echo using physiq.def_${physiq}
	1151	else
	1152	echo using standard physiq.def
	1153	fi
	1154	cd ..
	1155	else
	1156	echo using standard physiq.def
	1157	fi
[4210]	1158
[4215]	1159	if [ "$with_xios" = "y" ] ; then
	1160	cd BENCH${grid_resolution}
	1161	cp ../DefLists/iodef.xml .
	1162	cp ../DefLists/context_lmdz.xml .
	1163	cp ../DefLists/field_def_lmdz.xml .
	1164	# A raffiner par la suite
	1165	echo A FAIRE : Copier les *xml en fonction de l option cosp
	1166	cp ../DefLists/field_def_cosp*.xml .
	1167	cp ../DefLists/file_def_hist*xml .
	1168	# adapt iodef.xml to use attached mode
	1169	sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' iodef.xml > tmp
	1170	\mv -f tmp iodef.xml
[4210]	1171
[4215]	1172	# and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
	1173	# except for histday
	1174	for histfile in file_def_hist*xml
	1175	do
	1176	if [ "$histfile" = "file_def_histday_lmdz.xml" ] ; then
	1177	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' $histfile > tmp ; \mv -f tmp $histfile
	1178	sed -e 's@output_level="_AUTO_"@output_level="5"@' $histfile > tmp ; \mv -f tmp $histfile
	1179	sed -e 's@compression_level="2"@compression_level="0"@' $histfile > tmp ; \mv -f tmp $histfile
	1180	else
	1181	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' $histfile > tmp ; \mv -f tmp $histfile
	1182	fi
	1183	done
	1184	# and add option "ok_all_xml=y" in config.def
	1185	echo "### XIOS outputs" >> config.def
	1186	echo 'ok_all_xml=.true.' >> config.def
[4210]	1187
[4215]	1188	#activer les sorties pour Cosp
	1189	if [ "$cosp" = "v1" ] ; then
	1190	histfile=file_def_histdayCOSP_lmdz.xml
	1191	sed -e 's@enabled=".FALSE."@enabled=".TRUE."@' $histfile > tmp ; \mv -f tmp $histfile
	1192	sed -e 's@output_level="_AUTO_"@output_level="5"@' $histfile > tmp ; \mv -f tmp $histfile
	1193	sed -e 's@compression_level="2"@compression_level="0"@' $histfile > tmp ; \mv -f tmp $histfile
	1194	fi
	1195	if [ "$cosp" = "v2" ] ; then
	1196	histfile=file_def_histdayCOSPv2_lmdz.xml
	1197	sed -e 's@compression_level="2"@compression_level="0"@' $histfile > tmp ; \mv -f tmp $histfile
	1198	contextfile=context_lmdz.xml
	1199	sed -e 's@src="./file_def_histdayCOSP_lmdz.xml"@src="./file_def_histdayCOSPv2_lmdz.xml"@' $contextfile > tmp ; \mv -f tmp $contextfile
	1200	sed -e 's@src="./file_def_histmthCOSP_lmdz.xml"@src="./file_def_histmthCOSPv2_lmdz.xml"@' $contextfile > tmp ; \mv -f tmp $contextfile
	1201	sed -e 's@src="./file_def_histhfCOSP_lmdz.xml"@src="./file_def_histhfCOSPv2_lmdz.xml"@' $contextfile > tmp ; \mv -f tmp $contextfile
	1202	fieldfile=field_def_lmdz.xml
	1203	sed -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' $fieldfile > tmp ; \mv -f tmp $fieldfile
	1204	fi
[4210]	1205
[4215]	1206	cd ..
	1207	fi
[4210]	1208
[4215]	1209	# Cas Bensh avec ecrad
	1210	if [ "$rad" = "ecrad" ] ; then
	1211	cd BENCH${grid_resolution}
	1212	cp ../DefLists/namelist_ecrad .
	1213	cp -r ../libf/phylmd/ecrad/data .
	1214	cd ..
	1215	fi
[4210]	1216
[4215]	1217	# Adjusting bench physiq.def to radiative code chosen
	1218	cd BENCH${grid_resolution}
	1219	sed -e 's/iflag_rrtm=..$/iflag_rrtm='$iflag_rrtm'/' -e 's/NSW=..$/NSW='$NSW'/' physiq.def > tmpdef
	1220	\mv tmpdef physiq.def
	1221	cd ..
[4210]	1222
[4215]	1223	cp $gcm BENCH${grid_resolution}/gcm.e
[4210]	1224
[4215]	1225	cd BENCH${grid_resolution}
	1226	# On cree le fichier bench.sh au besoin
	1227	# Dans le cas 48x36x39 le bench.sh existe deja en parallele
[4210]	1228
[4215]	1229	if [ "$grid_resolution" = "48x36x39" ] ; then
	1230	echo On ne touche pas au bench.sh
	1231	# But we have to adapt "run_local.sh" for $mpirun
	1232	sed -e "s@mpirun@$mpirun@g" run_local.sh > tmp
	1233	mv -f tmp run_local.sh
	1234	chmod u=rwx run_local.sh
	1235	elif [ "${parallel:0:3}" = "mpi" ] ; then
	1236	# Lancement avec deux procs mpi et 2 openMP
	1237	echo "export OMP_STACKSIZE=800M" > bench.sh
	1238	if [ "${parallel:4:3}" = "omp" ] ; then
	1239	echo "export OMP_NUM_THREADS=2" >> bench.sh
	1240	fi
	1241	if [ "$cosp" = "v1" -o "$cosp" = "v2" ] ; then
	1242	if [ ${hostname:0:5} = jean- ] ; then
	1243	chmod +x ../arch.env
	1244	../arch.env
	1245	echo "ulimit -s 2000000" >> bench.sh
	1246	else
	1247	echo "ulimit -s 200000" >> bench.sh
	1248	fi
	1249	else
	1250	echo "ulimit -s unlimited" >> bench.sh
	1251	fi
	1252	if [ ${hostname:0:5} = jean- ] ; then
	1253	. ../arch/arch-${arch}.env
	1254	echo "srun -n 2 -A $idris_acct@cpu gcm.e > listing 2>&1" >> bench.sh
	1255	else
	1256	echo "$mpirun -np 2 gcm.e > listing 2>&1" >> bench.sh
	1257	fi
	1258	# Add rebuild, using reb.sh if it is there
	1259	echo 'if [ -f reb.sh ] ; then' >> bench.sh
	1260	echo ' ./reb.sh histday ; ./reb.sh histmth ; ./reb.sh histhf ; ./reb.sh histins ; ./reb.sh stomate_history ; ./reb.sh sechiba_history ; ./reb.sh sechiba_out_2 ' >> bench.sh
	1261	echo 'fi' >> bench.sh
	1262	else
	1263	echo "./gcm.e > listing 2>&1" > bench.sh
	1264	fi
	1265	# Getting orchidee stuff
	1266	if [ $veget == 'CMIP6' ] ; then
	1267	#echo 'myget 3DBenchs/BENCHorch11.tar.gz'
	1268	#myget 3DBenchs/BENCHorch11.tar.gz
	1269	#tar xvzf BENCHorch11.tar.gz
	1270	echo 'myget 3DBenchs/BENCHCMIP6.tar.gz'
	1271	myget 3DBenchs/BENCHCMIP6.tar.gz
	1272	tar xvzf BENCHCMIP6.tar.gz
	1273	sed -e "s:VEGET=n:VEGET=y:" config.def > tmp
	1274	mv -f tmp config.def
	1275	if [ "$with_xios" = "y" ] ; then
	1276	cp ../../ORCHIDEE/src_xml/context_orchidee.xml .
	1277	echo '<context id="orchidee" src="./context_orchidee.xml"/>' > add.tmp
	1278	cp ../../ORCHIDEE/src_xml/field_def_orchidee.xml .
	1279	cp ../../ORCHIDEE/src_xml/file_def_orchidee.xml .
	1280	cp ../../ORCHIDEE/src_xml/file_def_input_orchidee.xml .
	1281	if [ -f ../../ORCHIDEE/src_xml/context_input_orchidee.xml ] ; then
	1282	cp ../../ORCHIDEE/src_xml/context_input_orchidee.xml .
	1283	echo '<context id="orchidee" src="./context_input_orchidee.xml"/>' >> add.tmp
	1284	fi
	1285	sed -e '/id="LMDZ"/r add.tmp' iodef.xml > tmp
	1286	mv tmp iodef.xml
	1287	sed -e'{/sechiba1/ s/enabled="_AUTO_"/type="one_file" enabled=".TRUE."/}' file_def_orchidee.xml > tmp ; \mv -f tmp file_def_orchidee.xml
	1288	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' file_def_orchidee.xml > tmp ; \mv -f tmp file_def_orchidee.xml
	1289	sed -e 's@output_level="_AUTO_"@output_level="1"@' file_def_orchidee.xml > tmp ; \mv -f tmp file_def_orchidee.xml
	1290	sed -e 's@output_freq="_AUTO_"@output_freq="1d"@' file_def_orchidee.xml > tmp ; \mv -f tmp file_def_orchidee.xml
	1291	sed -e 's@compression_level="4"@compression_level="0"@' file_def_orchidee.xml > tmp ; \mv -f tmp file_def_orchidee.xml
	1292	sed -e 's@XIOS_ORCHIDEE_OK = n@XIOS_ORCHIDEE_OK = y@' orchidee.def > tmp ; \mv -f tmp orchidee.def
	1293	fi
	1294	fi
	1295	echo EXECUTION DU BENCH
	1296	set +e
	1297	date ; ./bench.sh > out.bench 2>&1 ; date
	1298	set -e
	1299	tail listing
[4210]	1300
	1301
[4215]	1302	echo '##########################################################'
	1303	echo 'Simulation finished in' `pwd`
	1304	echo 'You have compiled with:'
	1305	cat ../compile.sh
	1306	if [ $parallel = "none" ] ; then
	1307	echo 'You may re-run it with : cd ' `pwd` ' ; gcm.e'
	1308	echo 'or ./bench.sh'
	1309	else
	1310	echo 'You may re-run it with : '
	1311	echo 'cd ' `pwd` '; ./bench.sh'
	1312	# echo 'ulimit -s unlimited'
	1313	# echo 'export OMP_NUM_THREADS=2'
	1314	# echo 'export OMP_STACKSIZE=800M'
	1315	# echo "$mpirun -np 2 gcm.e "
	1316	fi
	1317	echo '##########################################################'
[4210]	1318
	1319	fi # bench
	1320
	1321
	1322	#################################################################
	1323	# Installation eventuelle du 1D
	1324	#################################################################
	1325
	1326	if [ $SCM = 1 ] ; then
[4215]	1327	cd $MODEL
	1328	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/1D.tar.gz
	1329	myget 1D/1D.tar.gz
	1330	tar xvf 1D.tar.gz
	1331	cd 1D
	1332	./run.sh -rad $rad
[4210]	1333	fi
	1334	#set -vx
	1335
	1336	#################################################################
	1337	# sauvegarde des options veget pour utilisation eventuelle tutorial_prod
	1338	#################################################################
	1339	cd $MODEL/modipsl/modeles
	1340	#echo surface_env file created in $MODEL
	1341	echo 'veget='$veget > surface_env
	1342	#opt_veget="-v $veget_version"
	1343	#echo 'opt_veget="'$opt_veget\" >> surface_env
	1344	echo 'opt_veget="'-v $veget_version\" >> surface_env
	1345	echo 'orchidee_rev='$orchidee_rev >> surface_env
	1346	echo 'suforch='$suff_orc >> surface_env
	1347
	1348
	1349
	1350

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