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source: BOL/script_install_amaury/install_lmdz.sh @ 4870

Last change on this file since 4870 was 4862, checked in by abarral, 9 months ago
(WIP) turn blocks into functions auto-detect netcdf dir if -netcdf 0 compile IOIPSL via fcm
Property svn:executable set to ``*
File size: 47.4 KB

Line
1	#!/bin/bash
2	set -eu # error on command failure, and on unset variables
3	export LC_ALL=C # standardize awk format
4
5	###########################################################################
6	# Author : Laurent Fairhead et Frédéric Hourdin
7	# Usage : install_lmdz.sh -help
8	#
9	# bash installation script of the LMDZ model on different computer types :
10	# Linux PC, "mesocentre" (IPSL-UPMC, IPSL-X), super-computer (IDRIS)
11	#
12	# The model is downloaded in the following directory tree
13	# $MODEL/modipsl/modeles/...
14	# using the "modipsl" infrastructure created by the "IPSL"
15	# for coupled (atmosphere/ocean/vegetation/chemistry) climate modeling
16	# activities.
17	# Here we only download atmospheric (LMDZ) and vegetation (ORCHIDEE)
18	# components.
19	#
20	# The sources of the models can be found in the "modeles" directory.
21	# In the present case, LMDZ, ORCHIDEE, and IOIPSL or XIOS (handling of
22	# input-outputs using the NetCDF library).
23	#
24	# The script downloads various source files (including a version of NetCDF)
25	# and utilities, compiles the model, and runs a test simulation in a
26	# minimal configuration.
27	#
28	# Prerequisites : 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	### Functions
39
40	function myget {
41	# A function to fetch files either locally or on the internet
42
43	local file_name=$1
44	# Path on local computer where to look for the datafile
45	if [[ -f "/u/lmdz/WWW/LMDZ/pub/$file_name" ]]; then
46	\cp -f -p "/u/lmdz/WWW/LMDZ/pub/$file_name" .
47	elif [[ -f ~"/LMDZ/pub/$file_name" ]]; then
48	\cp -f -p ~"/LMDZ/pub/$file_name" .
49	else
50	wget --no-check-certificate -nv "http://lmdz.lmd.jussieu.fr/pub/$file_name"
51	fi
52	}
53
54	function set_default_params {
55	# Valeur par défaut des parametres
56
57	# 04_2021 : tester si r4 marche encore !
58	real="r8" # ou "r4"
59
60	svn=""
61	version="20231022.trunk"
62
63	getlmdzor=1
64	netcdf=1 # 1: for automatic installation;
65	# or 0: do not install NetCDF and look for it in standard locations;
66	# or absolute path: look for NetCDF there
67	check_software_linux=1
68	ioipsl=1
69	bench=1
70	pclinux=1
71	pcmac=0 # default: not on a Mac
72	compiler="gfortran"
73	if [[ $(gfortran -dumpversion \| cut -d. -f1) -ge 10 ]]; then allow_arg_mismatch="-fallow-argument-mismatch"; fi
74	SCM=0
75	# surface/vegetation scheme treatment
76	# controlled by the single variable veget which can have the following values
77	# - NONE: bucket scheme (default)
78	# - CMIP6: orchidee version used in CMIP exercise, rev 5661
79	# - number: orchidee version number
80	veget="NONE"
81	# choose the resolution for the bench runs
82	# grid_resolution= 32x24x11 or 48x36x19 for tests (test without ORCHIDEE)
83	# 96x71x19 standard configuration
84	grid_resolution="32x32x39" # "48x36x19", "96x95x39", "144x142x79"
85	# choose the physiq version you want to test
86	#physiq=NPv6.0.14splith
87	physiq=""
88
89	## parallel can take the values none/mpi/omp/mpi_omp
90	parallel="none" # "mpi_omp"
91	idris_acct="lmd"
92	trusting="testing"
93	OPT_GPROF=""
94	OPT_MAKELMDZ=""
95	MODEL=""
96
97	## also compile XIOS? (and more recent NetCDF/HDF5 libraries) Default=no
98	with_xios="n"
99	opt_makelmdz_xios=""
100
101	## compile with oldrad/rrtm/ecrad radiatif code (Default=rrtm)
102	rad="rrtm"
103
104	## compile_with_fcm=1 : use makelmdz_fcm (1) or makelmdz (0)
105	compile_with_fcm=1
106
107	#Compilation with Cosp (cosp=NONE/v1/v2; default=NONE)
108	cosp="NONE"
109	opt_cosp=""
110
111	# Check if on a Mac
112	if [[ $(uname) = "Darwin" ]]; then
113	pcmac=1
114	export MAKE="make"
115	fi
116
117	env_file=""
118	optim=""
119	arch="local"
120
121	local mpi_file
122	mpi_file=$(readlink -f "$(which mpif90)")
123	path_mpi=$(dirname "$mpi_file")
124	root_mpi=$(dirname "$path_mpi")
125	}
126
127	function read_cmdline_args {
128	while (($# > 0)); do
129	case $1 in
130	"-h") cat <<........fin
131	$0 [ -v version ] [ -r svn_release ]
132	[ -parallel PARA ] [ -d GRID_RESOLUTION ] [ -bench 0/1 ]
133	[-name LOCAL_MODEL_NAME] [-gprof] [-opt_makelmdz] [-rad RADIATIF]
134
135	-v "version" like 20150828.trunk
136	see http://www.lmd.jussieu.fr/~lmdz/Distrib/LISMOI.trunk
137
138	-r "svn_release" : either the svn release number or "last"
139
140	-compiler gfortran\|ifort\|pgf90 (default: gfortran)
141
142	-parallel PARA : can be mpi_omp (mpi with openMP) or none (for sequential)
143
144	-d GRID_RESOLUTION should be among the available benchs if -bench 1
145	among which : 48x36x19, 48x36x39
146	if wanting to run a bench simulation in addition to compilation
147	default : 48x36x19
148
149	-bench activating the bench or not (0/1). Default 1
150
151	-testing/unstable
152
153	-name LOCAL_MODEL_NAME : default = LMDZversion.release
154
155	-netcdf 0, 1 or PATH
156	0: do not download NetCDF, look for it in standard locations
157	1: download and compile NetCDF
158	PATH: full path to an existing installed NetCDF library
159
160	-xios also download and compile the XIOS library
161	(requires the NetCDF4-HDF5 library, also installed by default)
162	(requires to also have -parallel mpi_omp)
163
164	-gprof to compile with -pg to enable profiling with gprof
165
166	-cosp to run without our with cospv1 or cospv2 [none/v1/v2]
167
168	-rad RADIATIF can be oldrad, rrtm or ecrad radiatif code
169
170	-nofcm to compile without fcm
171
172	-SCM install 1D version automatically
173
174	-debug compile everything in debug mode
175
176	-opt_makelmdz to call makelmdz or makelmdz_fcm with additional options
177
178	-physiq to choose which physics package to use
179
180	-env_file specify an arch.env file to overwrite the existing one
181
182	-veget surface model to run [NONE/CMIP6/xxxx]
183
184	........fin
185	exit 1;;
186	"-v") version=$2; shift; shift;;
187	"-r") svn=$2; shift; shift;;
188	"-compiler") compiler=$2
189	case $compiler in
190	"gfortran"\|"ifort"\|"pgf90") compiler=$2; shift
191	shift;;
192	*) echo "Only gfortran , ifort or pgf90 for the " \
193	"compiler option"
194	exit 1
195	esac;;
196	"-d") grid_resolution=$2; shift; shift;;
197	"-gprof") OPT_GPROF="-pg"; shift;;
198	"-unstable"\|"-testing") trusting=$(echo "$1" \| cut -c2-) ; shift;;
199	"-cosp") cosp=$2
200	case $cosp in
201	"none"\|"v1"\|"v2") cosp=$2; shift; shift;;
202	*) echo "Only none v1 v2 for cosp option"; exit 1
203	esac;;
204	"-nofcm") compile_with_fcm=0; echo "This option will be reactivated soon (promesse du 8dec2022)"; exit 1; shift;;
205	"-SCM") SCM=1; shift;;
206	"-opt_makelmdz") OPT_MAKELMDZ="$2"; shift; shift;;
207	"-rrtm") if [[ $2 = "false" ]]; then
208	rad="oldrad"
209	else
210	rad="rrtm"
211	fi
212	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 1
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 1
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	*) bash install_lmdz.sh -h; exit 1
232	esac
233	done
234
235	# Option de compilation pour Cosp
236	case $cosp in
237	v1) opt_cosp="-cosp true";;
238	v2) opt_cosp="-cospv2 true";;
239	*) opt_cosp=""
240	esac
241
242	# Check on veget version
243	if [[ $veget != 'NONE' && $veget != "CMIP6" ]]; then
244	re='^[0-9]+$'
245	if ! [[ $veget =~ $re ]]; then
246	echo 'Valeur de l option veget non valable'; exit 1
247	fi
248	fi
249
250	#Define veget-related suffix for gcm name
251	if [[ $veget = 'NONE' ]]; then
252	suff_orc=''
253	#For use with tutorial, orchidee_rev is also defined (will be
254	#written in surface_env at the end of the script)
255	orchidee_rev=''
256	else
257	suff_orc='_orch'
258	fi
259
260
261	if [[ $parallel = "none" ]]; then
262	sequential=1; suff_exe='_seq'
263	else
264	sequential=0; suff_exe='_para_mem'
265	fi
266
267	#Chemin pour placer le modele
268	if [[ $MODEL = "" ]]; then MODEL="./LMDZ$version$svn$optim"; fi
269
270	## if also compiling XIOS, parallel must be mpi_omp
271	if [[ $with_xios = "y" && $parallel != "mpi_omp" ]]; then
272	echo "Error, you must set -parallel mpi_omp if you want XIOS"; exit 1
273	fi
274
275	if [[ $with_xios = "y" ]]; then
276	opt_makelmdz_xios="-io xios"
277	fi
278
279	if [[ $cosp = "v2" && $with_xios = "n" ]]; then
280	echo "Error, Cospv2 cannot run without Xios"; exit 1
281	fi
282	}
283
284	function check_available_software {
285	if [[ $check_software_linux = 1 ]]; then
286	echo "################################################################"
287	echo "Check if required software is available"
288	echo "################################################################"
289
290	for logiciel in wget tar gzip make $compiler gcc cmake m4 c++; do
291	if [[ $(which "$logiciel") = "" ]]; then
292	echo "You must first install $logiciel on your system"; exit 1
293	fi
294	done
295
296	cat <<eod > tt.f90
297	print*,'coucou'
298	end
299	eod
300	$compiler tt.f90 \|\| a.out
301	./a.out >\| tt
302	if [[ $(< tt sed -e 's/ //g' ) != "coucou" ]]; then
303	echo "problem installing with compiler $compiler"; exit 1; fi
304	\rm tt a.out tt.f90
305	fi
306	}
307
308	function download_model {
309	mkdir -p "$MODEL"
310	MODEL=$(readlink -f "$MODEL"); echo "$MODEL" # absolute path
311
312	if [[ $getlmdzor = 1 && ! -d $MODEL/modipsl ]]; then
313	echo "##########################################################"
314	echo "Download a slightly modified version of LMDZ"
315	echo "##########################################################"
316	cd "$MODEL"
317	getlog="$(pwd)/get.log"
318	echo "logfile : $getlog"
319	myget "src_archives/$trusting/modipsl.$version.tar.gz" >> get.log 2>&1
320	echo "install_lmdz.sh wget_OK $(date)"
321	gunzip "modipsl.$version.tar.gz" >> get.log 2>&1
322	tar xf "modipsl.$version.tar" >> get.log 2>&1
323	\rm "modipsl.$version.tar"
324	fi
325	}
326
327	function install_netcdf {
328	echo "Installing Netcdf"
329
330	if [[ $netcdf = 0 ]]; then
331	ncdfdir=$(nc-config --prefix)
332	else
333	cd "$MODEL"
334
335	case $compiler in
336	gfortran) opt1="-compiler gnu"; opt2="-CC gcc -FC gfortran -CXX g++";;
337	ifort) opt1="-compiler intel"; opt2="-CC icc -FC ifort -CXX icpc";;
338	pgf90) opt1="-compiler pgf90"; opt2="-CC pgcc -FC pgf90 -CXX pgCC";;
339	*) echo "unexpected compiler $compiler" for netcdf; exit 1
340	esac
341
342	case $with_xios in
343	n) script_install_netcdf="install_netcdf4_hdf5_seq.bash"
344	ncdfdir="netcdf4_hdf5_seq"
345	opt_="$opt1";;
346	y) script_install_netcdf="install_netcdf4_hdf5.bash"
347	ncdfdir="netcdf4_hdf5"
348	opt_="$opt2 -MPI $root_mpi";;
349	*) echo "with_xios=$with_xios, should be n or y"; exit 1
350	esac
351	if [[ $netcdf = 1 ]]; then
352	ncdfdir="$MODEL/$ncdfdir"
353	else
354	mkdir -p "$netcdf"; ncdfdir="$netcdf/$ncdfdir"
355	fi
356
357	echo "Repertoire netcdf $ncdfdir"
358	if [[ ! -d $ncdfdir ]]; then
359	netcdflog=$(pwd)/netcdf.log
360	echo "----------------------------------------------------------"
361	echo "Compiling the Netcdf library"
362	echo "----------------------------------------------------------"
363	echo "log file : $netcdflog"
364	myget script_install/$script_install_netcdf >> "$netcdflog" 2>&1
365	chmod u=rwx $script_install_netcdf
366	# shellcheck disable=SC2086
367	./$script_install_netcdf -prefix "$ncdfdir" $opt_ >> "$netcdflog" 2>&1
368	fi
369
370	#----------------------------------------------------------------------------
371	# LF rajout d'une verrue, pour une raison non encore expliquee,
372	# la librairie est parfois rangée dans lib64 et non dans lib
373	# par certains compilateurs
374	if [[ ! -e lib && -d lib64 ]]; then ln -s lib64 lib; fi
375	#----------------------------------------------------------------------------
376
377	echo "install_lmdz.sh netcdf_OK $(date)"
378	fi
379
380	cat >test_netcdf90.f90 <<EOF
381	use netcdf
382	print *, "NetCDF library version: ", nf90_inq_libvers()
383	end
384	EOF
385
386	if $compiler -I"$ncdfdir"/include test_netcdf90.f90 -L"$ncdfdir"/lib -lnetcdff \
387	-lnetcdf -Wl,-rpath="$ncdfdir"/lib && ./a.out
388	then
389	\rm test_netcdf90.f90 a.out
390	else
391	cat <<EOF
392	Failed test program using NetCDF-Fortran. You can:
393	- check that you have NetCDF-Fortran installed in your system
394	- or specify an installation directory with option -netcdf of install_lmdz.sh
395	- or download and compile NetCDF-Fortran with option -netcdf 1 of nstall_lmdz.sh
396	EOF
397	exit 1
398	fi
399	}
400
401	function install_IOIPSL { # via fcm
402	if [[ ! -f $MODEL/modipsl/lib/libioipsl.a ]]; then
403	cd "$MODEL/modipsl/modeles/IOIPSL"
404	ioipsllog="$(pwd)/ioipsl.log"
405	echo "Compiling IOIPSL, the interface library with Netcdf $(date) (log: $ioipsllog)"
406
407	if ! ./makeioipsl_fcm -job 8 > "$ioipsllog" 2>&1; then
408	echo "IOIPSL compile failed, exiting"; exit 1
409	fi
410	cp lib/* ../../lib
411	echo "IOIPSL compiled $(date)"
412	fi
413	}
414
415	echo "install_lmdz.sh DEBUT $(date)"
416
417	set_default_params
418	read_cmdline_args "$@"
419	check_available_software
420	download_model
421	install_netcdf
422	install_IOIPSL
423
424
425
426
427	################################################################
428	# Specificite des machines
429	################################################################
430
431	hostname=$(hostname)
432	#case ${hostname:0:5} in
433	# *) if [[ $parallel = none \|\| -f /usr/bin/mpif90 ]]; then
434	# path_mpi=$(which mpif90 \| sed -e s:/mpif90::);
435	# if [[ -d /usr/lib64/openmpi ]]; then
436	# root_mpi="/usr/lib64/openmpi"
437	# else
438	# root_mpi="/usr"
439	# fi
440	# else
441	# echo "Cannot find mpif90";
442	# if [[ $parallel = none ]]; then exit 1; fi;
443	# fi;
444	# if [[ $parallel != none ]]; then
445	# root_mpi=$(which mpif90 \| sed -e s:/bin/mpif90::)
446	# path_mpi=$(which mpif90 \| sed -e s:/mpif90::)
447	# export LD_LIBRARY_PATH=${root_mpi}/lib:$LD_LIBRARY_PATH
448	# fi
449	# par_comp=${path_mpi}/mpif90;
450	# mpirun=${path_mpi}/mpirun;
451	# arch="local" ;
452	# make="make";
453	# o_ins_make="-t g95"
454	#esac
455
456	## Flags for parallelism:
457	#if [[ $parallel != none ]]; then
458	# # MPI_LD are the flags needed for linking with MPI
459	# MPI_LD="-L${root_mpi}/lib -lmpi"
460	# if [[ $compiler = "gfortran" ]]; then
461	# # MPI_FLAGS are the flags needed for compilation with MPI
462	# MPI_FLAGS="-fcray-pointer"
463	# # OMP_FLAGS are the flags needed for compilation with OpenMP
464	# OMP_FLAGS="-fopenmp -fcray-pointer"
465	# # OMP_LD are the flags needed for linking with OpenMP
466	# OMP_LD="-fopenmp"
467	# elif [[ $compiler = "ifort" ]]; then
468	# MPI_FLAGS=""
469	# OMP_FLAGS="-openmp"
470	# OMP_LD="-openmp"
471	# else # pgf90
472	# MPI_FLAGS=""
473	# OMP_FLAGS="-mp"
474	# OMP_LD="-mp"
475	# fi
476	#fi
477	#
478	#
479	#echo "################################################################"
480	#echo "Choix des options de compilation"
481	#echo "################################################################"
482	#
483	#export FC=$compiler
484	#export F90=$compiler
485	#export F77=$compiler
486	#export CPPFLAGS=
487	#OPTIMNC=""
488	#BASE_LD="$OPT_GPROF"
489	#OPTPREC="$OPT_GPROF"
490	#ARFLAGS="rs"
491	#if [[ $(lsb_release -i -s) = "Ubuntu" ]]; then
492	# if [[ $(lsb_release -r -s \| cut -d. -f1) -ge 16 ]]; then
493	# ARFLAGS="rU"
494	# fi
495	#fi
496	#
497	#if [[ $compiler = "gfortran" ]]; then
498	# OPTIM="-O3 $allow_arg_mismatch"
499	# OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all -fbacktrace -finit-real=snan $allow_arg_mismatch"
500	# OPTDEV="-Wall -fbounds-check $allow_arg_mismatch"
501	# fmod="I "
502	# OPTPREC="$OPTPREC -cpp -ffree-line-length-0"
503	# if [[ $real = r8 ]]; then OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE"; fi
504	# export F90FLAGS=" -ffree-form $OPTIMNC"
505	# export FFLAGS=" $OPTIMNC"
506	# export CC=gcc
507	# export CXX=g++
508	# export fpp_flags="-P -C -traditional -ffreestanding"
509	#
510	#elif [[ $compiler = mpif90 ]]; then
511	# OPTIM="-O3"
512	# OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all"
513	# OPTDEV="-Wall -fbounds-check"
514	# BASE_LD="$BASE_LD -lblas"
515	# fmod="I "
516	# if [[ $real = r8 ]]; then
517	# OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE -fcray-pointer"
518	# fi
519	# export F90FLAGS=" -ffree-form $OPTIMNC"
520	# export FFLAGS=" $OPTIMNC"
521	# export CC=gcc
522	# export CXX=g++
523	#
524	#elif [[ $compiler = pgf90 ]]; then
525	# OPTIM="-O2 -Mipa -Munroll -Mnoframe -Mautoinline -Mcache_align"
526	# OPTDEB="-g -Mdclchk -Mbounds -Mchkfpstk -Mchkptr -Minform=inform -Mstandard -Ktrap=fp -traceback"
527	# OPTDEV="-g -Mbounds -Ktrap=fp -traceback"
528	# fmod="module "
529	# if [[ $real = r8 ]]; then OPTPREC="$OPTPREC -r8 -DNC_DOUBLE"; fi
530	# export CPPFLAGS="-DpgiFortran"
531	# export CC=pgcc
532	# export CFLAGS="-O2 -Msignextend"
533	# export CXX=pgCC
534	# export CXXFLAGS="-O2 -Msignextend"
535	# export FFLAGS="-O2 $OPTIMNC"
536	# export F90FLAGS="-O2 $OPTIMNC"
537	# compile_with_fcm=1
538	#
539	#elif [[ $compiler = ifort \|\| $compiler = mpiifort ]]; then
540	# OPTIM="-O2 -fp-model strict -ip -align all "
541	# OPTDEV="-p -g -O2 -traceback -fp-stack-check -ftrapuv -check"
542	# OPTDEB="-g -no-ftz -traceback -ftrapuv -fp-stack-check -check"
543	# fmod='module '
544	# if [[ $real = r8 ]]; then OPTPREC="$OPTPREC -real-size 64 -DNC_DOUBLE"; fi
545	# export CPP="icc -E"
546	# export FFLAGS="-O2 -ip -fpic -mcmodel=large"
547	# export FCFLAGS="-O2 -ip -fpic -mcmodel=large"
548	# export CC=icc
549	# export CFLAGS="-O2 -ip -fpic -mcmodel=large"
550	# export CXX=icpc
551	# export CXXFLAGS="-O2 -ip -fpic -mcmodel=large"
552	# export fpp_flags="-P -traditional"
553	# # Pourquoi forcer la compilation fcm. Marche mieux sans
554	# #compile_with_fcm=1
555	#else
556	# echo "unexpected compiler $compiler"; exit 1
557	#fi
558	#
559	#OPTIMGCM="$OPTIM $OPTPREC"
560
561
562
563
564	if [[ "$with_xios" = "y" ]]; then
565	echo '##########################################################'
566	echo 'Compiling XIOS'
567	echo '##########################################################'
568	cd "$MODEL/modipsl/modeles"
569	xioslog="$(pwd)/xios.log"
570	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/install_xios.bash
571	myget script_install/install_xios.bash
572	chmod u=rwx install_xios.bash
573	# following will be recalculated later on once LMDZ is updated
574	# mysvn=`svnversion LMDZ \| egrep \|\| "[0-9]+" 2>/dev/null`
575	mysvn=$(grep 'Revision: [0-9]' "$MODEL"/Read*.md \| awk ' { print $2 } ' 2>/dev/null)
576	if [[ $svn != "" ]]; then mysvn=$svn; fi
577	echo "mysvn $mysvn"
578
579	if [[ ${hostname:0:5} = jean- ]]; then
580	if [[ $mysvn -ge 4619 ]]; then
581	svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS2/branches/xios-2.6 XIOS
582	else
583	svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS2/branches/xios-2.5 XIOS
584	fi
585	cd XIOS/arch
586	svn update
587	cd ..
588	echo "Compiling XIOS, start $(date) (it takes about 20 min on Jean-Zay)"
589	echo "log file: $xioslog"
590	./make_xios --prod --arch $arch --job 4 > xios.log 2>&1
591	else
592	./install_xios.bash -prefix "$MODEL/modipsl/modeles" \
593	-netcdf "$ncdfdir" -hdf5 "$ncdfdir" \
594	-MPI "$root_mpi" -arch $arch > xios.log 2>&1
595	fi # of case Jean-Zay
596	if [[ -f XIOS/lib/libxios.a ]]; then
597	echo "XIOS library successfully generated"
598	echo install_lmdz.sh XIOS_OK "$(date)"
599	fi
600	fi
601
602	#============================================================================
603	veget_version=false
604	if [[ "$veget" != 'NONE' ]]; then
605	cd "$MODEL/modipsl/modeles/ORCHIDEE"
606	set +e; svn upgrade; set -e
607	if [[ "$veget" = "CMIP6" ]]; then
608	veget_version=orchidee2.0
609	orchidee_rev=6592
610	else # specific orchidee revision newer than CMIP6, on 2_1 or 2_2 branches
611	veget_version=orchidee2.1
612	orchidee_rev=$veget
613	if [[ $veget -lt 4465 ]]; then
614	echo 'Stopping, ORCHIDEE version too old, script needs work on ' \
615	'the CPP flags to pass to makelmdz'
616	exit 1
617	fi
618	set +e
619	# which branch is my version on?
620	orcbranch=$(svn log -v -q svn://forge.ipsl.jussieu.fr/orchidee/ -r "$veget" \|grep ORCHIDEE \|head -1\| sed -e 's:ORCHIDEE/.*$:ORCHIDEE:' \| awk '{print $2}')
621	# switch to that branch
622	echo IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at \
623	orchidee-help@listes.ipsl.fr
624	svn switch -r "$veget" --accept theirs-full "svn://forge.ipsl.jussieu.fr/orchidee/$orcbranch"
625	if ! (svn log -r "$veget" \| grep "$veget"); then
626	echo 'Cannot update ORCHIDEE as not on the right branch for ORCHIDEE'
627	exit 1
628	fi
629	set -e
630	set +e; svn update -r "$veget"; set -e
631	fi
632	# Correctif suite debug Jean-Zay
633	sed -i -e 's/9010 FORMAT(A52,F17.14)/9010 FORMAT(A52,F20.14)/' \
634	src_stomate/stomate.f90
635	opt_orc="-prod"; if [[ "$optim" = "-debug" ]]; then opt_orc="-debug"; fi
636
637	orchideelog=$(pwd)/orchidee.log
638	echo '########################################################'
639	echo 'Compiling ORCHIDEE, the continental surface model '
640	echo '########################################################'
641	echo "Start of the first compilation of orchidee, in sequential mode: $(date)"
642	echo "log file : $orchideelog"
643
644	ORCHPATH=$(pwd)
645	export ORCHPATH=$ORCHPATH
646	xios_orchid="-noxios"
647	if [[ "$with_xios" = "y" ]]; then
648	xios_orchid="-xios"
649	fi
650	if [[ -d tools ]]; then
651	###################################################################
652	# Pour les experts qui voudraient changer de version d'orchidee.
653	# Attention : necessite d'avoir le password pour orchidee
654
655	# Correctif suite debug Jean-Zay
656	if [[ -f src_global/time.f90 ]]; then
657	sed -i -e 's/CALL tlen2itau/\!CALL tlen2itau/' src_global/time.f90
658	fi
659	###################################################################
660	if [[ "$veget_version" == "false" ]]; then
661	veget_version=orchidee2.0
662	fi
663	cd arch
664	sed -e s:"%COMPILER .*.$:%COMPILER $compiler":1 \
665	-e s:"%LINK .*.$:%LINK $compiler":1 \
666	-e s:"%FPP_FLAGS .*.$:%FPP_FLAGS $fpp_flags":1 \
667	-e s:"%PROD_FFLAGS .*.$:%PROD_FFLAGS $OPTIM":1 \
668	-e s:"%DEV_FFLAGS .*.$:%DEV_FFLAGS $OPTDEV":1 \
669	-e s:"%DEBUG_FFLAGS .*.$:%DEBUG_FFLAGS $OPTDEB":1 \
670	-e s:"%BASE_FFLAGS .*.$:%BASE_FFLAGS $OPTPREC":1 \
671	-e s:"%BASE_LD .*.$:%BASE_LD $BASE_LD":1 \
672	-e s:"%ARFLAGS .*.$:%ARFLAGS $ARFLAGS":1 \
673	arch-gfortran.fcm > arch-local.fcm
674	cat <<EOF > arch-local.path
675	NETCDF_LIBDIR="-L$ncdfdir/lib -lnetcdff -lnetcdf"
676	NETCDF_INCDIR="$ncdfdir/include"
677	IOIPSL_INCDIR="$ORCHPATH/../../lib"
678	IOIPSL_LIBDIR="$ORCHPATH/../../lib"
679	XIOS_INCDIR="\$ORCHDIR/../XIOS/inc"
680	XIOS_LIBDIR="\$ORCHDIR/../XIOS/lib -lxios"
681	EOF
682	cd ../
683
684	echo ./makeorchidee_fcm -j $xios_orchid $opt_orc -parallel none \
685	-arch $arch
686	./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel none \
687	-arch $arch > "$orchideelog" 2>&1
688	pwd
689	else # of "if [[ -d tools ]]"
690	if [[ -d src_parallel ]]; then
691	liste_src="parallel parameters global stomate sechiba driver"
692	if [[ "$veget_version" == "false" ]]; then
693	veget_version=orchidee2.0
694	fi
695	fi
696	for d in $liste_src; do
697	src_d=src_$d
698	echo src_d "$src_d"
699	echo ls; ls
700	if [[ ! -d $src_d ]]; then
701	echo "Problem orchidee : no $src_d"; exit 1
702	fi
703	cd "$src_d"; \rm -f -- *.mod make; $make clean
704	$make > "$orchideelog" 2>&1
705	if [[ "$compiler" = "gfortran" \|\| "$compiler" = "mpif90" ]]; then
706	cp -f -- *.mod ../../../lib
707	fi
708	cd ..
709	done
710	fi # of "if [[ -d tools ]]"
711	echo "install_lmdz.sh orchidee_compil_seq_OK $(date)"
712	fi # of if [[ "$veget" != 'NONE' ]]
713
714
715	#============================================================================
716	# Ehouarn: the directory name LMDZ* depends on version/tar file...
717	if find . -name "$MODEL/modipsl/modeles/LMD*"; then
718	echo '###############################################################'
719	echo 'Preparing LMDZ compilation : arch file, svn switch if needed...'
720	echo '###############################################################'
721	cd "$MODEL/modipsl/modeles/"LMD*
722	LMDZPATH=$(pwd)
723	else
724	echo "ERROR: No LMD* directory !!!"
725	exit 1
726	fi
727
728
729	###########################################################
730	# For those who want to use fcm to compile via :
731	# makelmdz_fcm -arch local .....
732	############################################################
733
734
735
736	cd "$MODEL/modipsl/modeles"/LMDZ*
737	lmdzlog=$(pwd)/lmdz.log
738
739	##################################################################
740	# Possibly update LMDZ if a specific svn release is requested
741	##################################################################
742
743	set +e; svn upgrade; set -e
744
745	if [[ $svn = "last" ]]; then svnopt=""; else svnopt="-r $svn"; fi
746	if [[ $svn != "" ]]; then
747	if set +e; svn info \| grep -q 'https:'; then
748	svn switch --relocate https://svn.lmd.jussieu.fr/LMDZ \
749	http://svn.lmd.jussieu.fr/LMDZ
750	fi
751	svn update "$svnopt"
752	set -e
753	fi
754
755	#---------------------------------------------------------------------
756	# Retrieve the final svn release number, and adjust compilation
757	# options accordingly
758	# If svn not available, will use the svn writen in $MODEL/Readm*md
759	# For old version it assumes that it is before 4185 (the version
760	# for which the test was introduced
761	#---------------------------------------------------------------------
762
763	set +e; mysvn=$(svnversion . \| grep -E \|\| "[0-9]+" 2>/dev/null); set -e
764	if [[ "$mysvn" = "" ]]; then mysvn=$(grep 'Revision: [0-9]' "$MODEL"/Read*.md \| awk ' { print $2 } ' 2>/dev/null); fi
765	if [[ "$mysvn" = "" ]]; then mysvn=4190; fi
766
767	if [[ "$pclinux" = "1" && ! -f arch/arch-local.path ]]; then
768
769	# create local 'arch' files (if on Linux PC):
770	cd arch
771	# arch-local.path file
772	# test for version as arch.pth file changed format with rev 4426
773	if [[ "$mysvn" -gt 4425 ]]; then
774	cat <<EOF > arch-local.path
775	NETCDF_LIBDIR="-L$ncdfdir/lib"
776	NETCDF_LIB="-lnetcdff -lnetcdf"
777	NETCDF_INCDIR=-I$ncdfdir/include
778	NETCDF95_INCDIR=-I\$LMDGCM/../../include
779	NETCDF95_LIBDIR=-L\$LMDGCM/../../lib
780	NETCDF95_LIB=-lnetcdf95
781	IOIPSL_INCDIR=-I\$LMDGCM/../../lib
782	IOIPSL_LIBDIR=-L\$LMDGCM/../../lib
783	IOIPSL_LIB=-lioipsl
784	XIOS_INCDIR=-I\$LMDGCM/../XIOS/inc
785	XIOS_LIBDIR=-L\$LMDGCM/../XIOS/lib
786	XIOS_LIB="-lxios -lstdc++"
787	ORCH_INCDIR=-I\$LMDGCM/../../lib
788	ORCH_LIBDIR=-L\$LMDGCM/../../lib
789	EOF
790	else
791	cat <<EOF > arch-local.path
792	NETCDF_LIBDIR="-L$ncdfdir/lib -lnetcdff -lnetcdf"
793	NETCDF_INCDIR=-I$ncdfdir/include
794	NETCDF95_INCDIR=\$LMDGCM/../../include
795	NETCDF95_LIBDIR=\$LMDGCM/../../lib
796	IOIPSL_INCDIR=\$LMDGCM/../../lib
797	IOIPSL_LIBDIR=\$LMDGCM/../../lib
798	XIOS_INCDIR=\$LMDGCM/../XIOS/inc
799	XIOS_LIBDIR=\$LMDGCM/../XIOS/lib
800	ORCH_INCDIR=\$LMDGCM/../../lib
801	ORCH_LIBDIR=\$LMDGCM/../../lib
802	EOF
803	fi
804
805	if [[ $pcmac == 1 ]]; then
806	BASE_LD="$BASE_LD -Wl,-rpath,${ncdfdir}/lib"
807	else
808	BASE_LD="$BASE_LD -Wl,-rpath=${ncdfdir}/lib"
809	fi
810	# Arch-local.fcm file (adapted from arch-linux-32bit.fcm)
811
812	if [[ $real = r8 ]]; then FPP_DEF=NC_DOUBLE; else FPP_DEF=""; fi
813	sed -e s:"%COMPILER .*.$:%COMPILER $compiler":1 \
814	-e s:"%LINK .*.$:%LINK $compiler":1 \
815	-e s:"%PROD_FFLAGS .*.$:%PROD_FFLAGS $OPTIM":1 \
816	-e s:"%DEV_FFLAGS .*.$:%DEV_FFLAGS $OPTDEV":1 \
817	-e s:"%DEBUG_FFLAGS .*.$:%DEBUG_FFLAGS $OPTDEB":1 \
818	-e s:"%BASE_FFLAGS .*.$:%BASE_FFLAGS $OPTPREC":1 \
819	-e s:"%FPP_DEF .*.$:%FPP_DEF $FPP_DEF":1 \
820	-e s:"%BASE_LD .*.$:%BASE_LD $BASE_LD":1 \
821	-e s:"%ARFLAGS .*.$:%ARFLAGS $ARFLAGS":1 \
822	arch-linux-32bit.fcm > arch-local.fcm
823
824	cd ..
825	### Adapt "bld.cfg" (add the shell):
826	#whereisthatshell=$(which ${use_shell})
827	#echo "bld::tool::SHELL $whereisthatshell" >> bld.cfg
828
829	fi # of if [[ "$pclinux" = 1 ]]
830	#---------------------------------------------------------------------
831	# Option de compilation du rayonnement : depend de $mysvn ><= r4185
832	#---------------------------------------------------------------------
833	opt_rad=""
834
835	case $rad in
836	oldrad) iflag_rrtm=0; NSW=2; opt_rad="";;
837	rrtm) iflag_rrtm=1; NSW=6
838	if [[ $mysvn -le 4185 ]]; then
839	opt_rad="-rrtm true"
840	else
841	opt_rad="-rad rrtm"
842	fi;;
843	ecrad) iflag_rrtm=2; NSW=6; opt_rad="-rad ecrad";;
844	*) echo "Only oldrad rrtm ecrad for rad option"; exit 1
845	esac
846
847	if [[ $mysvn -le 4185 && $rad = "ecrad" ]]; then
848	echo "ecrad only available for LMDZ rev starting with 4186 "; exit 1
849	fi
850
851	##################################################################
852
853
854	if [[ ! -f libf/misc/netcdf95.F90 && ! -d $MODEL/NetCDF95-0.3 ]]; then
855	cd "$MODEL"
856	myget src_archives/netcdf/NetCDF95-0.3.tar.gz
857	tar -xf NetCDF95-0.3.tar.gz
858	rm NetCDF95-0.3.tar.gz
859	cd NetCDF95-0.3
860	mkdir build
861	cd build
862	cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH="$ncdfdir" \
863	-DCMAKE_INSTALL_PREFIX="$MODEL/modipsl"
864	make install
865	cd "$MODEL/modipsl/modeles/"LMDZ*
866	fi
867
868	echo '##################################################################'
869	echo "Preparing script compile.sh for LMDZ compilation"
870	echo "It will only be run automatically if bench=1/tuto"
871	echo "Here bench=$bench"
872	echo '##################################################################'
873
874	if [[ $env_file != "" ]]; then
875	mv arch/arch-${arch}.env arch/arch-${arch}.orig
876	\cp -f "$env_file" arch/arch-${arch}.env
877	fi
878
879	if [[ $compile_with_fcm = 1 ]]; then
880	makelmdz="makelmdz_fcm $optim -arch $arch -j 8 "
881	else
882	makelmdz="makelmdz $optim -arch $arch"
883	fi
884
885	# sequential compilation
886	if [[ "$sequential" = 1 ]]; then
887	echo Sequential compilation command, saved in compile.sh:
888	echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp " \
889	"-d ${grid_resolution} -v $veget_version gcm "
890	echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp " \
891	"-d ${grid_resolution} -v $veget_version gcm " > compile.sh
892	chmod +x ./compile.sh
893	if [[ $bench = 1 ]]; then
894	echo "install_lmdz.sh start_lmdz_seq_compilation $(date)"
895	echo "log file: $lmdzlog"
896	./compile.sh > "$lmdzlog" 2>&1
897	echo "install_lmdz.sh end_lmdz_seq_compilation $(date)"
898	fi
899	fi # fin sequential
900
901	# compiling in parallel mode
902	if [[ $parallel != "none" ]]; then
903	echo '##########################################################'
904	echo ' Parallel compile '
905	echo '##########################################################'
906	echo "(after saving the sequential libs and binaries)"
907	cd "$MODEL/modipsl"
908	tar cf sequential.tar bin/ lib/
909	#
910	# Orchidee
911	#
912	cd "$ORCHPATH"
913	if [[ -d src_parallel && $veget != 'NONE' ]]; then
914	cd arch
915	sed \
916	-e s:"%COMPILER.*.$:%COMPILER $par_comp":1 \
917	-e s:"%LINK.*.$:%LINK $par_comp":1 \
918	-e s:"%MPI_FFLAG.*.$:%MPI_FFLAGS $MPI_FLAGS":1 \
919	-e s:"%OMP_FFLAG.*.$:%OMP_FFLAGS $OMP_FLAGS":1 \
920	-e s:"%MPI_LD.*.$:%MPI_LD $MPI_LD":1 \
921	-e s:"%OMP_LD.*.$:%OMP_LD $OMP_LD":1 \
922	arch-local.fcm > tmp.fcm
923
924	mv tmp.fcm arch-local.fcm
925	cd ../
926	echo "Compiling ORCHIDEE in parallel mode $(date)"
927	echo "logfile $orchideelog"
928	echo "NOTE : to recompile it when necessary, use ./compile_orc.sh " \
929	"in modipsl/modeles/ORCHIDEE"
930	echo ./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc \
931	-parallel "$parallel" -arch $arch > compile_orc.sh
932	echo ./makeorchidee_fcm -j 8 $xios_orchid $opt_orc \
933	-parallel "$parallel" -arch $arch >> compile_orc.sh
934	echo echo Now you must also recompile LMDZ, by running ./compile.sh \
935	in modeles/LMDZ >> compile_orc.sh
936	chmod u+x compile_orc.sh
937	./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc \
938	-parallel "$parallel" -arch $arch > "$orchideelog" 2>&1
939	./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel "$parallel" \
940	-arch $arch >> "$orchideelog" 2>&1
941	echo "End of ORCHIDEE compilation in parallel mode $(date)"
942	elif [[ $veget != 'NONE' ]]; then
943	echo '##########################################################'
944	echo ' Orchidee version too old '
945	echo ' Please update to new version '
946	echo '##########################################################'
947	exit 1
948	fi #�of [ -d src_parallel && $veget != 'NONE' ]
949
950	# LMDZ
951	cd "$LMDZPATH"
952	if [[ $arch = local ]]; then
953	cd arch
954	sed -e s:"%COMPILER.*.$:%COMPILER $par_comp":1 \
955	-e s:"%LINK.*.$:%LINK $par_comp":1 \
956	-e s:"%MPI_FFLAG.*.$:%MPI_FFLAGS $MPI_FLAGS":1 \
957	-e s:"%OMP_FFLAG.*.$:%OMP_FFLAGS $OMP_FLAGS":1 \
958	-e s:"%ARFLAGS.*.$:%ARFLAGS $ARFLAGS":1 \
959	-e "s§%BASE_LD.*.$§%BASE_LD -Wl,-rpath=${root_mpi}/lib:${ncdfdir}/lib§1" \
960	-e s:"%MPI_LD.*.$:%MPI_LD $MPI_LD":1 \
961	-e s:"%OMP_LD.*.$:%OMP_LD $OMP_LD":1 \
962	arch-local.fcm > tmp.fcm
963	mv tmp.fcm arch-local.fcm
964	cd ../
965	fi
966	rm -f compile.sh
967	echo resol="$grid_resolution" >> compile.sh
968	if [[ ${hostname:0:5} = jean- && "$cosp" = "v2" ]]; then
969
970	echo "LMDZ compilation command in parallel mode, saved in compile.sh, is :"
971	echo "(ATTENTION le probleme de cospv2 sur jean-zay en mode prod " \
972	"n est pas corrige ! )"
973	# ATTENTION le probleme de cospv2 sur jean-zay en mode prod n
974	# est pas corrige
975	echo ./"$makelmdz" -dev $optim "$OPT_MAKELMDZ" "$opt_rad" "$opt_cosp" \
976	"$opt_makelmdz_xios" -d \$resol -v $veget_version -mem \
977	-parallel "$parallel" gcm >> compile.sh
978	echo ./"$makelmdz" -dev $optim "$OPT_MAKELMDZ" "$opt_rad" "$opt_cosp" \
979	"$opt_makelmdz_xios" -d \$resol -v $veget_version -mem \
980	-parallel "$parallel" gcm
981	else
982	echo ./"$makelmdz" $optim "$OPT_MAKELMDZ" "$opt_rad" "$opt_cosp" \
983	"$opt_makelmdz_xios" -d \$resol -v $veget_version -mem \
984	-parallel "$parallel" gcm >> compile.sh
985	echo ./"$makelmdz" $optim "$OPT_MAKELMDZ" "$opt_rad" "$opt_cosp" \
986	"$opt_makelmdz_xios" -d \$resol -v $veget_version -mem \
987	-parallel "$parallel" gcm
988	fi
989	chmod +x ./compile.sh
990
991	if [[ $bench = 1 ]]; then
992	echo "Compiling LMDZ in parallel mode $(date), LMDZ log file: $lmdzlog"
993	./compile.sh > "$lmdzlog" 2>&1
994	fi
995
996	fi # of if [[ $parallel != "none" ]]
997
998
999	##################################################################
1000	# Verification du succes de la compilation
1001	##################################################################
1002
1003	# Recherche de l'executable dont le nom a change au fil du temps ...
1004	# suffix contains radiative option starting with revision 4186
1005	if [[ $mysvn -ge 4186 ]]; then suff_exe=_${rad}${suff_exe}; fi
1006	gcm=""
1007
1008	for exe in gcm.e bin/gcm_${grid_resolution}_phylmd${suff_exe}${suff_orc}.e
1009	do
1010	if [[ -f $exe ]]; then gcm=$exe; fi
1011	done
1012
1013	if [[ "$gcm" = "" ]]; then
1014	if [[ $bench = 1 ]]; then
1015	echo 'Compilation failed !! Cannot run the benchmark;'
1016	exit 1
1017	else
1018	echo 'Compilation not done (only done when bench=1)'
1019	fi
1020	else
1021	echo '##########################################################'
1022	echo "Compilation successfull !! $(date)"
1023	echo '##########################################################'
1024	echo "The executable is $gcm"
1025	fi
1026
1027	##################################################################
1028	# Below, we run a benchmark if bench=1 or tuto
1029	##################################################################
1030
1031	if [[ $bench = tuto ]]; then
1032	myget Training/tutorial.tar; tar xf tutorial.tar; cd TUTORIAL
1033	./init.sh
1034
1035	elif [[ $bench = 1 && ! -d BENCH${grid_resolution} ]]; then
1036	# TOUTE CETTE SECTION DEVRAIT DISPARAITRE POUR UNE COMMANDE
1037	# OU DES BENCHS PAR MOTS CLES COMME tuto
1038
1039	echo '##########################################################'
1040	echo ' Running a test run '
1041	echo '##########################################################'
1042
1043	\rm -rf "BENCH${grid_resolution}"
1044	bench=bench_lmdz_${grid_resolution}
1045	echo "install_lmdz.sh before bench download $(date)"
1046	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/$bench.tar.gz
1047	myget "3DBenchs/$bench.tar.gz"
1048	echo "install_lmdz.sh after bench download $(date)"
1049	tar xf "$bench.tar.gz"
1050
1051	if [[ "$cosp" = "v1" \|\| "$cosp" = "v2" ]]; then
1052	cd "BENCH${grid_resolution}"
1053	# copier les fichiers namelist input et output our COSP
1054	cp ../DefLists/cosp*_input_nl.txt .
1055	cp ../DefLists/cosp*_output_nl.txt .
1056	# Activer la cles ok_cosp pour tourner avec COSP
1057	sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp
1058	\mv -f tmp config.def
1059	cd ..
1060	fi
1061
1062	if [[ -n "$physiq" ]]; then
1063	cd "BENCH${grid_resolution}"
1064	if [[ -f "physiq.def_${physiq}" ]]; then
1065	cp "physiq.def_${physiq}" physiq.def
1066	echo using "physiq.def_${physiq}"
1067	else
1068	echo using standard physiq.def
1069	fi
1070	cd ..
1071	else
1072	echo using standard physiq.def
1073	fi
1074
1075	if [[ "$with_xios" = "y" ]]; then
1076	cd "BENCH${grid_resolution}"
1077	cp ../DefLists/iodef.xml .
1078	cp ../DefLists/context_lmdz.xml .
1079	cp ../DefLists/field_def_lmdz.xml .
1080	# A raffiner par la suite
1081	echo "A FAIRE : Copier les *xml en fonction de l option cosp"
1082	cp ../DefLists/field_def_cosp*.xml .
1083	cp ../DefLists/file_def_hist*xml .
1084	# adapt iodef.xml to use attached mode
1085	sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' \
1086	iodef.xml > tmp
1087	\mv -f tmp iodef.xml
1088
1089	# and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
1090	# except for histday
1091	for histfile in file_def_hist*xml
1092	do
1093	if [[ "$histfile" = "file_def_histday_lmdz.xml" ]]; then
1094	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' \
1095	"$histfile" > tmp
1096	\mv -f tmp "$histfile"
1097	sed -e 's@output_level="_AUTO_"@output_level="5"@' "$histfile" \
1098	> tmp
1099	\mv -f tmp "$histfile"
1100	sed -e 's@compression_level="2"@compression_level="0"@' \
1101	"$histfile" > tmp
1102	\mv -f tmp "$histfile"
1103	else
1104	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
1105	"$histfile" > tmp
1106	\mv -f tmp "$histfile"
1107	fi
1108	done
1109	# and add option "ok_all_xml=y" in config.def
1110	echo "### XIOS outputs" >> config.def
1111	echo 'ok_all_xml=.true.' >> config.def
1112
1113	#activer les sorties pour Cosp
1114	if [[ "$cosp" = "v1" ]]; then
1115	sed -i'' -e 's@enabled=".FALSE."@enabled=".TRUE."@' \
1116	-e 's@output_level="_AUTO_"@output_level="5"@' \
1117	-e 's@compression_level="2"@compression_level="0"@' \
1118	file_def_histdayCOSP_lmdz.xml
1119	fi
1120	if [[ "$cosp" = "v2" ]]; then
1121	sed -e 's@compression_level="2"@compression_level="0"@' file_def_histdayCOSPv2_lmdz.xml
1122	for type_ in hf day mth; do
1123	file=file_def_hist${type_}COSP
1124	sed -i'' -e 's@src="./'${file}'_lmdz.xml"@src="./'${file}'v2_lmdz.xml"@' context_lmdz.xml
1125	done
1126	sed -i '' -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' field_def_lmdz.xml
1127	fi
1128
1129	cd ..
1130	fi
1131
1132	# Cas Bensh avec ecrad
1133	if [[ "$rad" = "ecrad" ]]; then
1134	cd "BENCH${grid_resolution}"
1135	cp ../DefLists/namelist_ecrad .
1136	cp -r ../libf/phylmd/ecrad/data .
1137	cd ..
1138	fi
1139
1140	# Adjusting bench physiq.def to radiative code chosen
1141	cd "BENCH${grid_resolution}"
1142	sed -e 's/iflag_rrtm=.*.$/iflag_rrtm='$iflag_rrtm'/' \
1143	-e 's/NSW=.*.$/NSW='$NSW'/' physiq.def > tmpdef
1144	\mv tmpdef physiq.def
1145	cd ..
1146
1147	cp "$gcm" "BENCH${grid_resolution}/gcm.e"
1148
1149	cd "BENCH${grid_resolution}"
1150	# On cree le fichier bench.sh au besoin
1151	# Dans le cas 48x36x39 le bench.sh existe deja en parallele
1152
1153	if [[ "$grid_resolution" = "48x36x39" ]]; then
1154	echo On ne touche pas au bench.sh
1155	# But we have to adapt "run_local.sh" for $mpirun
1156	sed -e "s@mpirun@$mpirun@g" run_local.sh > tmp
1157	mv -f tmp run_local.sh
1158	chmod u=rwx run_local.sh
1159	elif [[ "${parallel:0:3}" = "mpi" ]]; then
1160	# Lancement avec deux procs mpi et 2 openMP
1161	echo "export OMP_STACKSIZE=800M" > bench.sh
1162	if [[ "${parallel:4:3}" = "omp" ]]; then
1163	echo "export OMP_NUM_THREADS=2" >> bench.sh
1164	fi
1165	if [[ "$cosp" = "v1" \|\| "$cosp" = "v2" ]]; then
1166	if [[ ${hostname:0:5} = jean- ]]; then
1167	chmod +x ../arch.env
1168	../arch.env
1169	echo "ulimit -s 2000000" >> bench.sh
1170	else
1171	echo "ulimit -s 200000" >> bench.sh
1172	fi
1173	else
1174	echo "ulimit -s unlimited" >> bench.sh
1175	fi
1176	if [[ ${hostname:0:5} = jean- ]]; then
1177	. ../arch/arch-${arch}.env
1178	echo "srun -n 2 && $idris_acct@cpu gcm.e > listing 2>&1" \
1179	>> bench.sh
1180	else
1181	echo "$mpirun -np 2 gcm.e > listing 2>&1" >> bench.sh
1182	fi
1183	# Add rebuild, using reb.sh if it is there
1184	cat <<EOF >> bench.sh
1185	if [[ -f reb.sh ]]; then
1186	./reb.sh histday; ./reb.sh histmth; ./reb.sh histhf;
1187	./reb.sh histins; ./reb.sh stomate_history;
1188	./reb.sh sechiba_history; ./reb.sh sechiba_out_2
1189	fi
1190	EOF
1191	else
1192	echo "./gcm.e > listing 2>&1" > bench.sh
1193	fi
1194	# Getting orchidee stuff
1195	if [[ $veget == 'CMIP6' ]]; then
1196	#echo 'myget 3DBenchs/BENCHorch11.tar.gz'
1197	#myget 3DBenchs/BENCHorch11.tar.gz
1198	#tar xvzf BENCHorch11.tar.gz
1199	echo 'myget 3DBenchs/BENCHCMIP6.tar.gz'
1200	myget 3DBenchs/BENCHCMIP6.tar.gz
1201	tar xvzf BENCHCMIP6.tar.gz
1202	sed -e "s:VEGET=n:VEGET=y:" config.def > tmp
1203	mv -f tmp config.def
1204	if [[ "$with_xios" = "y" ]]; then
1205	cp ../../ORCHIDEE/src_xml/context_orchidee.xml .
1206	echo '<context id="orchidee" src="./context_orchidee.xml"/>' \
1207	> add.tmp
1208	cp ../../ORCHIDEE/src_xml/field_def_orchidee.xml .
1209	cp ../../ORCHIDEE/src_xml/file_def_orchidee.xml .
1210	cp ../../ORCHIDEE/src_xml/file_def_input_orchidee.xml .
1211	if [[ -f ../../ORCHIDEE/src_xml/context_input_orchidee.xml ]]; then
1212	cp ../../ORCHIDEE/src_xml/context_input_orchidee.xml .
1213	echo '<context id="orchidee" ' \
1214	'src="./context_input_orchidee.xml"/>' >> add.tmp
1215	fi
1216	sed -e '/id="LMDZ"/r add.tmp' iodef.xml > tmp
1217	mv tmp iodef.xml
1218	sed -e'{/sechiba1/ s/enabled="_AUTO_"/type="one_file" enabled=".TRUE."/}' \
1219	file_def_orchidee.xml > tmp
1220	\mv -f tmp file_def_orchidee.xml
1221	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
1222	file_def_orchidee.xml > tmp
1223	\mv -f tmp file_def_orchidee.xml
1224	sed -e 's@output_level="_AUTO_"@output_level="1"@' \
1225	file_def_orchidee.xml > tmp
1226	\mv -f tmp file_def_orchidee.xml
1227	sed -e 's@output_freq="_AUTO_"@output_freq="1d"@' \
1228	file_def_orchidee.xml > tmp
1229	\mv -f tmp file_def_orchidee.xml
1230	sed -e 's@compression_level="4"@compression_level="0"@' \
1231	file_def_orchidee.xml > tmp
1232	\mv -f tmp file_def_orchidee.xml
1233	sed -e 's@XIOS_ORCHIDEE_OK = n@XIOS_ORCHIDEE_OK = y@' \
1234	orchidee.def > tmp
1235	\mv -f tmp orchidee.def
1236	fi
1237	fi
1238
1239	if [[ -f ../arch.env ]]
1240	then
1241	source ../arch.env
1242	fi
1243
1244	echo EXECUTION DU BENCH
1245	set +e
1246	date; ./bench.sh > out.bench 2>&1; date
1247	set -e
1248	tail listing
1249
1250
1251	echo "##########################################################"
1252	echo "Simulation finished in $(pwd)"
1253	echo "You have compiled with:"
1254	cat ../compile.sh
1255	if [[ $parallel = "none" ]]; then
1256	echo "You may re-run it with : cd $(pwd) ; gcm.e"
1257	echo "or ./bench.sh"
1258	else
1259	echo "You may re-run it with : "
1260	echo "cd $(pwd) ; ./bench.sh"
1261	# echo 'ulimit -s unlimited'
1262	# echo 'export OMP_NUM_THREADS=2'
1263	# echo 'export OMP_STACKSIZE=800M'
1264	# echo "$mpirun -np 2 gcm.e "
1265	fi
1266	echo '##########################################################'
1267
1268	fi # bench
1269
1270
1271	#################################################################
1272	# Installation eventuelle du 1D
1273	#################################################################
1274
1275	if [[ $SCM = 1 ]]; then
1276	cd "$MODEL"
1277	myget 1D/1D.tar.gz
1278	tar xf 1D.tar.gz
1279	cd 1D
1280	if [[ $rad = oldrad ]]; then
1281	sed -i'' -e 's/^rad=.*$/rad=oldrad/' run.sh
1282	sed -i'' -e 's/^rad=.*$/rad=oldrad/' bin/compile
1283	fi
1284	echo "Running 1D/run.sh, log in $(pwd)/run1d.log"
1285	./run.sh > "$(pwd)/run1d.log" 2>&1
1286	fi
1287
1288
1289	#################################################################
1290	# sauvegarde des options veget pour utilisation eventuelle tutorial_prod
1291	#################################################################
1292	cd "$MODEL/modipsl/modeles"
1293	#echo surface_env file created in $MODEL
1294	cat <<EOF >surface_env
1295	veget=$veget
1296	opt_veget="-v $veget_version"
1297	orchidee_rev=$orchidee_rev
1298	suforch=$suff_orc
1299	EOF

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