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source: BOL/script_install_amaury/install_lmdz.sh @ 5226

Last change on this file since 5226 was 5187, checked in by abarral, 2 months ago
minor cleanup
Property svn:executable set to ``*
File size: 36.4 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 : 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	# Get a file from LMDZ repository, make it executable if .(ba)sh
42	local url=$1
43
44	local filename
45	filename=$(basename "$url")
46
47	wget --no-check-certificate -nv "http://lmdz.lmd.jussieu.fr/pub/$url"
48	if [[ $filename =~ .*\.(ba)?sh ]]; then chmod +x "$filename"; fi
49	}
50
51	function get_svn_branch {
52	local url=$1
53	local rev=$2
54	local res
55
56	res=$(svn log -v -q "$url" -r "$rev" -l 1 \| cut -d "/" -f -4)
57	if echo "$res" \| grep -q "/trunk/"; then
58	res=$(echo "$res" \| grep "/trunk/" \| head -1 \| cut -d "/" -f 2-3)
59	elif echo "$res" \| grep -q "/branches/"; then
60	res=$(echo "$res" \| grep "/branches/" \| head -1 \| cut -d "/" -f 2-4)
61	else
62	echo "Could not determine svn branch for $url, r=$rev"
63	fi
64	echo "$res"
65	}
66
67	function set_default_params {
68	# Valeur par défaut des parametres
69	svn_lmdz=""
70	version="20240508.CM7"
71
72	netcdf=1
73	bench=1
74	SCM=0
75	veget="none"
76	grid_resolution="32x32x39"
77	benchphysiq=""
78	compphysiq="lmd"
79	is_1D="n"
80	fortran_file="gcm"
81
82	parallel="none"
83	trusting="testing"
84	MODEL=""
85
86	with_xios=0
87	opt_makelmdz_xios=""
88
89	rad="rrtm"
90
91	compile_with_fcm=1
92
93	cosp="none"
94	aerosols=0
95	inlandsis=0
96
97	make_j=8
98	clean_install=1
99
100	# Check if on a Mac /!\ Probably doesn't work anymore, to fix one day...
101	if [[ $(uname) = "Darwin" ]]; then
102	export MAKE="make"
103	fi
104
105	optim_flag="-prod"
106	arch="local"
107
108	arch="local-gfortran"
109	arch_dir=""
110
111	jobcmd=""
112	}
113
114	function read_cmdline_args {
115	while (($# > 0)); do
116	case $1 in
117	"-h") cat <<........fin
118	$0 [ -v version ] [ -r svn_release ]
119	[ -parallel PARA ] [ -d GRID_RESOLUTION ] [ -bench 0/1 ]
120	[-name LOCAL_MODEL_NAME] [-rad RADIATIF]
121
122	-v "version" like 20150828.trunk, see http://www.lmd.jussieu.fr/~lmdz/Distrib/LISMOI.trunk (default <$version>)
123
124	-r "svn_release" : either the svn release number or "last" (default <$svn_lmdz>)
125
126	-parallel parallel support: mpi, omp, mpi_omp (mpi with openMP) or none (default: <$parallel>)
127
128	-d "grid resolution": should be among the available benchs if -bench 1 (valid values: 48x36x19, 48x36x39) (default : <$grid_resolution>)
129
130	-bench activating the bench or not (0/1) (default: <$bench>)
131
132	-unstable use unstable tar instead of testing
133
134	-name name of the folder to install to (default <$MODEL>)
135
136	-netcdf 0, 1 or PATH. 0: do not download NetCDF, look for it in standard locations (/usr); 1: download and compile NetCDF; PATH: full path to an existing installed NetCDF library (default: <$netcdf>)
137
138	-xios use (download and compile) the XIOS library (will compile the parallel NetCDF4-HDF5 library) (requires to also have -parallel mpi_omp)
139
140	-cosp to run with cospv1 or cospv2 [none/v1/v2] (default <$cosp>)
141
142	-rad radiative code: oldrad, rrtm or ecrad (default <$rad>)
143
144	-nofcm to compile without fcm
145
146	-SCM install 1D version automatically
147
148	-debug compile everything in debug mode
149
150	-benchphysiq to choose which physics.def package to use in the bench (default <$benchphysiq>)
151
152	-compilephysiq physics to compile the model with (default <$compphysiq>)
153
154	-veget surface/vegetation scheme treatment controlled by the single variable veget which can have the following values: none: bucket scheme (default); CMIP6 \| veget2.0: orchidee version used in CMIP exercise, rev 5661; veget2.2: orchidee branch 2.2, rev 8529 (bundled); number: orchidee version number [only orch>2.0] (default $veget)
155
156	-spla activate interactive aerosols
157
158	-inlandsis activate new snow scheme
159
160	-arch name of the arch to use (default <$arch>)
161
162	-arch_dir where to find the arch files (default <$arch_dir>)
163
164	-make_j number of processes to parallelize installations (default <$make_j>)
165
166	-jobcmd command prepended to fcm compile jobs, e.g. "srun" (default <$jobcmd>)
167
168	-noclean will only download necessary files (but no thorough check is made on the integrity of existing files), and will recompile everything (very quick if it's already been compiled before)
169
170	........fin
171	exit 1;;
172	"-v") version=$2; shift; shift;;
173	"-r") svn_lmdz=$2; shift; shift;;
174	"-d") grid_resolution=$2; shift; shift;;
175	"-unstable") trusting="unstable"; shift;;
176	"-cosp") cosp=$2
177	case $cosp in
178	"none"\|"v1"\|"v2") cosp=$2; shift; shift;;
179	*) echo "Only none v1 v2 for cosp option"; exit 1
180	esac;;
181	"-nofcm") compile_with_fcm=0; echo "This option will be reactivated soon (promesse du 8dec2022)"; exit 1; shift;;
182	"-SCM") SCM=1; shift;;
183	"-rad") rad=$2
184	case $rad in
185	"oldrad"\|"rrtm"\|"ecrad") rad=$2; shift; shift;;
186	*) echo "Only oldrad rrtm ecrad for rad option"; exit 1
187	esac;;
188	"-parallel") parallel=$2
189	case $parallel in
190	"none"\|"mpi"\|"omp"\|"mpi_omp") parallel=$2; shift; shift;;
191	*) echo "Only none mpi omp mpi_omp for the parallel option"; exit 1
192	esac;;
193	"-bench") bench=$2; shift; shift;;
194	"-debug") optim_flag="-debug"; shift;;
195	"-name") MODEL=$2; shift; shift;;
196	"-netcdf") netcdf=$2; shift; shift;;
197	"-benchphysiq") benchphysiq=$2; shift; shift;;
198	"-compilephysiq") compphysiq=$2; shift; shift;;
199	"-xios") with_xios=1; shift;;
200	"-arch") arch=$2; shift; shift;;
201	"-arch_dir") arch_dir=$2; shift; shift;;
202	"-veget") veget=$2; shift; shift;;
203	"-spla") aerosols=1; shift;;
204	"-inlandsis") inlandsis=1; shift;;
205	"-make_j") make_j=$2; shift; shift;;
206	"-jobcmd") jobcmd=$2; shift; shift;;
207	"-noclean") clean_install=0; shift;;
208	*) bash install_lmdz.sh -h; exit 1
209	esac
210	done
211
212	# Isotopes : Compile and run with isotopes if lmdz_phys="lmdiso" in main.sh
213	if [[ $compphysiq = "lmdiso" ]]; then isotopes=1; else isotopes=0; fi
214
215	# Option de compilation pour Cosp
216	case $cosp in
217	v1) opt_cosp="-cosp true";;
218	v2) opt_cosp="-cospv2 true";;
219	*) opt_cosp=""
220	esac
221
222	#Define veget-related suffix for gcm name
223	if [[ $veget = 'none' ]]; then
224	suff_orc=''
225	else
226	suff_orc='_orch'
227	fi
228
229
230	if [[ $parallel = "none" ]]; then
231	suff_para='_seq'
232	else
233	suff_para='_para_mem'
234	fi
235
236	if [[ $with_xios = 1 ]]; then opt_makelmdz_xios="-io xios"; fi
237
238	if [[ $aerosols = 1 ]]; then
239	opt_aer="-dust true"; suff_aer="_spla"
240	else
241	opt_aer=""; suff_aer=""
242	fi
243
244	if [[ $inlandsis = 1 ]]; then
245	opt_inlandsis="-inlandsis true"
246	else
247	opt_inlandsis=""
248	fi
249
250	if [[ $isotopes = 1 ]]; then
251	opt_isotopes="-isotopes true"; suff_iso="_iso"
252	else
253	opt_isotopes="" ; suff_iso=""
254	fi
255
256	# set default arch if parallel
257	if [[ $arch = "local-gfortran" && $parallel != "none" ]]; then
258	arch="local-gfortran-parallel"
259	echo "Switching default arch to $arch"
260	fi
261
262	# Name of the model's folder. The convention taken here is that models that requires different compilation sources should have a different names.
263	local xios_name=""
264	if [[ $with_xios = 1 ]]; then xios_name="XIOS"; fi
265	if [[ $MODEL = "" ]]; then MODEL="./LMDZ$version${svn_lmdz}OR$veget$xios_name"; fi
266
267	if [[ $arch_dir = "" ]]; then
268	arch_dir="$MODEL/modipsl/config/IPSLCM7/ARCH/";
269	elif ! readlink -fe "$arch_dir" >/dev/null; then
270	echo "STOP: no arch dir <$arch_dir>"; exit 1
271	fi
272
273	if ! (echo "$grid_resolution" \| grep -q "x"); then
274	is_1D="y"
275	fortran_file="lmdz1d"
276	fi
277	}
278
279	function ensure_correct_option_combinations {
280	# Check on veget version
281	if [[ $veget != 'none' && $veget != "CMIP6" && $veget != "orch2.0" && $veget != "orch2.2" ]]; then
282	re='^[0-9]+$'
283	if ! [[ $veget =~ $re ]]; then
284	echo 'Valeur de l option veget non valable'; exit 1
285	fi
286	fi
287
288	## if also compiling XIOS, parallel must be mpi_omp
289	if [[ $with_xios = 1 && $parallel != "mpi_omp" ]]; then
290	echo "Error, you must set -parallel mpi_omp if you want XIOS"; exit 1
291	fi
292
293	if [[ $cosp = "v2" && $with_xios = 0 ]]; then
294	echo "Error, Cospv2 cannot run without Xios"; exit 1
295	fi
296
297	# STOP if trying to use both ORCHIDEE and Isotopes :
298	if [[ $isotopes = 1 && $veget != "none" ]]; then
299	echo "STOP: You cannot run LMDZ with ORCHIDEE and ISOtopes at the same time"; exit 1
300	fi
301
302	# STOP if trying to use both SPLA and Isotopes :
303	if [[ $isotopes = 1 && $aerosols = 1 ]]; then
304	echo "STOP: You cannot run LMDZ with Isotopes and aerosols=spla at the same time"; exit 1
305	fi
306
307	# (Temporary) STOP if trying to use Isotopes with XIOS :
308	if [[ $isotopes = 1 && $with_xios = 1 ]]; then
309	echo "STOP: Isotopes cannont yet be run with XIOS"; exit 1
310	fi
311
312	if [[ $aerosols = 1 && $rad != "rrtm" ]]; then
313	echo "STOP: For the time being, <aerosols=spla> requires <rad=rrtm>"; exit 1
314	fi
315	}
316
317	function check_available_software {
318	local required_soft=("wget" "tar" "gzip" "make" "gcc" "cmake" "m4" "c++")
319	echo "Checking if required software is available (${required_soft[*]})"
320	for logiciel in "${required_soft[@]}"; do
321	if [[ $(which "$logiciel") = "" ]]; then
322	echo "You must first install $logiciel on your system"; exit 1
323	fi
324	done
325
326	cat <<eod > tt.f90
327	print*,'coucou'
328	end
329	eod
330	$compiler tt.f90 \|\| a.out
331	./a.out >\| tt
332	if [[ $(< tt sed -e 's/ //g' ) != "coucou" ]]; then
333	echo "problem installing with compiler $compiler"; exit 1
334	fi
335	rm tt a.out tt.f90
336	}
337
338	function download_model {
339	if [[ $clean_install = 1 ]]; then rm -rf "$MODEL"; fi
340
341	mkdir -p "$MODEL"
342	MODEL=$(readlink -e -f "$MODEL"); echo "MODEL: $MODEL" # absolute path
343	if [[ ! -d "$MODEL/modipsl" ]]; then
344	echo "Downloading a slightly modified version of modipsl+LMDZ"
345	cd "$MODEL"
346	getlog="$(pwd)/get.log"
347	echo "logfile : $getlog"
348	myget "src_archives/$trusting/modipsl.$version.tar.gz" &>> get.log
349	echo "install_lmdz.sh wget_OK $(date)"
350
351	gunzip "modipsl.$version.tar.gz" &>> get.log
352	tar xf "modipsl.$version.tar" &>> get.log
353	rm "modipsl.$version.tar"
354
355	cd - &> /dev/null
356	fi
357	}
358
359	function init_arch {
360	set +e; arch_dir=$(readlink -f "$arch_dir"); set -e # full path. readlink must be called after the path is created
361
362	# Check where default fcm, path, env are located - by default in $arch_path, instead in $MODEL/modipsl/modeles/LMDZ/arch/
363	local i fcm_path path_path env_path
364	for i in "path" "fcm" "env"; do
365	local varname=${i}_path
366	if [[ -f $arch_dir/arch-$arch.$i ]]; then
367	declare $varname="$arch_dir/arch-$arch.$i"
368	else
369	declare $varname="$MODEL/modipsl/modeles/LMDZ/arch/arch-$arch.$i"
370	if [[ ! -f ${!varname} ]]; then
371	echo "STOP: no ${!varname}"; exit 1
372	fi
373	fi
374	done
375	default_fcm_path=$fcm_path
376	default_path_path=$path_path
377	default_env_path=$env_path
378
379	# check compiler
380	compiler=$(< "$default_fcm_path" grep "%COMPILER" \| sed -e "s/%COMPILER\s*//")
381
382	# load env
383	# shellcheck disable=SC1090
384	if [[ -f $default_env_path ]]; then source "$default_env_path"; fi
385
386	local mpi_file # can't be done before as it depends on sourcing the env
387	mpi_file=$(readlink -e -f "$(which mpif90)")
388	path_mpi=$(dirname "$mpi_file")
389	root_mpi=$(dirname "$path_mpi")
390	}
391
392	function install_arch {
393	local component=$1
394
395	# Use same .env for all components (for module compatibility)
396	cp -f "$default_env_path" "$MODEL/modipsl/modeles/$component/arch" &> /dev/null \|\| true # allow failure if we're copying the file to itself
397
398	# Use local .path and .fcm is available, otherwise default
399	if [[ ! -f "$MODEL/modipsl/modeles/$component/arch/arch-$arch.path" ]]; then
400	cp -f "$default_path_path" "$MODEL/modipsl/modeles/$component/arch"
401
402	if [[ $component = "ORCHIDEE" ]]; then
403	if [[ $orcbranch = "/tags/ORCHIDEE_2_0/ORCHIDEE" ]]; then # 2.0 and before have a different fcm convention
404	sed -i'' -e "s/-I//" -e "s/-L//" "$MODEL/modipsl/modeles/ORCHIDEE/arch/arch-$arch.path" # /!\ we only replace first occurence on purpose
405	fi
406	fi
407	fi
408	if [[ ! -f "$MODEL/modipsl/modeles/$component/arch/arch-$arch.fcm" ]]; then
409	cp -f "$default_fcm_path" "$MODEL/modipsl/modeles/$component/arch"
410
411	if [[ $component = "XIOS" ]]; then
412	# Adapt for XIOS, which uses different naming conventions
413	sed -i'' -e "s/%COMPILER/%FCOMPILER/" -e "s/%LINK/%LINKER/" -e "s/-fdefault-real-8//" "$MODEL/modipsl/modeles/XIOS/arch/arch-$arch.fcm"
414	fi
415	fi
416	}
417
418	function install_netcdf {
419	echo "Installing Netcdf"
420	local ncdf_compiler="$compiler"
421
422	if [[ $netcdf = 0 ]]; then
423	ncdfdir=$(nf-config --prefix)
424	else
425	cd "$MODEL"
426
427	# Convert non-basic compiler
428	case $compiler in
429	mpif90) ncdf_compiler=$($compiler --version \| head -n 1 \| cut -d " " -f -1)
430	esac
431
432	case $ncdf_compiler in
433	gfortran \| GNU) ncdf_compiler="gfortran"; opt1="-compiler gnu"; opt2="-CC gcc -FC gfortran -CXX g++";;
434	*) echo "unexpected compiler $ncdf_compiler for netcdf"; exit 1
435	esac
436
437	case $with_xios in
438	0) script_install_netcdf="install_netcdf4_hdf5_seq.bash"
439	ncdfdir="netcdf4_hdf5_seq"
440	opt_="$opt1";;
441	1) script_install_netcdf="install_netcdf4_hdf5.bash"
442	ncdfdir="netcdf4_hdf5"
443	opt_="$opt2 -MPI $root_mpi";;
444	*) echo "with_xios=$with_xios, should be 0 or 1"; exit 1
445	esac
446	if [[ $netcdf = 1 ]]; then
447	ncdfdir="$MODEL/$ncdfdir"
448	else
449	mkdir -p "$netcdf"; ncdfdir="$netcdf/$ncdfdir"
450	fi
451
452	echo "Repertoire netcdf $ncdfdir"
453	if [[ ! -d $ncdfdir ]]; then
454	netcdflog=$(pwd)/netcdf.log
455	echo "----------------------------------------------------------"
456	echo "Compiling the Netcdf library"
457	echo "----------------------------------------------------------"
458	echo "log file : $netcdflog"
459	myget script_install/$script_install_netcdf &>> "$netcdflog"
460	chmod u=rwx $script_install_netcdf
461	# shellcheck disable=SC2086
462	./$script_install_netcdf -prefix "$ncdfdir" $opt_ &>> "$netcdflog"
463	fi
464
465	# Add to path
466	export PATH="$ncdfdir/bin:$PATH"
467
468	#----------------------------------------------------------------------------
469	# LF rajout d'une verrue, pour une raison non encore expliquee,
470	# la librairie est parfois rangée dans lib64 et non dans lib
471	# par certains compilateurs
472	if [[ ! -e lib && -d lib64 ]]; then ln -s lib64 lib; fi
473	#----------------------------------------------------------------------------
474
475	echo "install_lmdz.sh netcdf_OK $(date)"
476	fi
477
478	cat >test_netcdf90.f90 <<EOF
479	use netcdf
480	print *, "NetCDF library version: ", nf90_inq_libvers()
481	end
482	EOF
483
484	if $ncdf_compiler -I"$ncdfdir"/include test_netcdf90.f90 -L"$ncdfdir"/lib -lnetcdff -lnetcdf -Wl,-rpath="$ncdfdir"/lib && ./a.out; then
485	rm test_netcdf90.f90 a.out
486	else
487	cat <<EOF
488	Failed test program using NetCDF-Fortran. You can:
489	- check that you have NetCDF-Fortran installed in your system
490	- or specify an installation directory with option -netcdf of install_lmdz.sh
491	- or download and compile NetCDF-Fortran with option -netcdf 1 of install_lmdz.sh
492	EOF
493	exit 1
494	fi
495
496	# Compile NetCDF95
497	cd "$MODEL/modipsl/modeles/LMD"*
498	echo "Installing NetCDF95"
499	cd "$MODEL"
500	if [[ ! -d "NetCDF95-0.3" ]]; then
501	myget src_archives/netcdf/NetCDF95-0.3.tar.gz
502	tar -xf NetCDF95-0.3.tar.gz
503	rm NetCDF95-0.3.tar.gz
504	cd NetCDF95-0.3
505	mkdir -p build && cd build
506	netCDF_INCLUDE_DIR=$(nc-config --includedir) netCDF_LIBRARY=$(nc-config --libdir) cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH="$ncdfdir" -DCMAKE_INSTALL_PREFIX="$MODEL/modipsl"
507	make install
508	fi
509	}
510
511	function install_IOIPSL {
512	install_arch "IOIPSL"
513
514	cd "$MODEL/modipsl/modeles/IOIPSL"
515	ioipsllog="$(pwd)/ioipsl.log"
516	echo "Compiling IOIPSL, the interface library with Netcdf $(date) (log: $ioipsllog)"
517
518	echo "$jobcmd ./makeioipsl_fcm -j $make_j -arch $arch $optim_flag" > compile.sh
519	chmod +x compile.sh
520	echo "Compiling IOIPSL using $(\cat compile.sh)"
521	if ! ./compile.sh &> "$ioipsllog"; then
522	echo "STOP: IOIPSL compile failed, exiting"; exit 1
523	fi
524
525	# Link to modipsl/bin
526	cp -f bin/* ../../bin
527
528	echo "IOIPSL compiled $(date)"
529	}
530
531	function install_XIOS {
532	if [[ $with_xios = 1 ]]; then
533	cd "$MODEL/modipsl/modeles"
534	xioslog="$(pwd)/XIOS/xios.log"
535	echo "##########################################################"
536	echo "Compiling XIOS (log $xioslog) $(date)"
537	echo "##########################################################"
538
539	# Download XIOS
540	local xios_http="http://forge.ipsl.fr/ioserver/svn/XIOS2/branches/xios-2.6"
541	local xios_rev="2568"
542
543	cd "$MODEL/modipsl/modeles"
544	set +e; svn co -r $xios_rev $xios_http XIOS; set -e
545
546	cd XIOS
547
548	install_arch "XIOS"
549
550	echo "$jobcmd ./make_xios --job $make_j --arch $arch" > compile.sh
551	chmod +x compile.sh
552	echo "$(date) Compiling XIOS using $(\cat compile.sh) (log in $xioslog)"
553	if ! ./compile.sh &> "$xioslog"; then
554	echo "STOP: XIOS compilation failed, exiting"; exit 1
555	fi
556
557	echo "Compiled XIOS $(date)"
558	fi
559	}
560
561	function get_orchidee_version { # Set / Check ORCHIDEE version
562	echo "Checking Orchidee source version"
563	local fetch_rev=""
564	orcbranch=""
565	case $veget in
566	"none") fcm_veget_version="false";;
567	"orch2.0" \| "CMIP6") fcm_veget_version=orchidee2.0; fetch_rev=7906;; # in previous tar we used 6592 but with some modifications to xios_orchidee.f90, which got integrated in 7906
568	"orch2.2") fcm_veget_version=orchidee2.1; orcbranch="/branches/ORCHIDEE_2_2/ORCHIDEE" ;; # the bundled version
569	*) fetch_rev=$veget; fcm_veget_version=orchidee2.1;; # /!\ arbitary rev only works for orch>=2.1
570	# /!\ Note: for orch>=4, we should be using fcm_vegt_version="orchideetrunk". Below copied comment by Adriana in LMDZ_Setup docs:
571	# Avec orchidee2.1, on va compiler LMDZ avec le cle cpp ORCHIDEE_NOLIC. On ne va donc pas prendre en compte les avancements fait dans le trunk qui permet que les fractions lic soitent traité par ORCHIDEE. Ca marche très bien sans cela puisque dans tout façon c'est en cours de développement et ce n'est pas activé par default. En fait on devrait compiler le trunk avec -v orchideetrunk mais avec landice_opt>2, ce qui ne change rien par rapport à orchidee2.1
572	#Si on voudrait activer landice_opt=2 , il faut compiler avec -v orchideetrunk.
573
574	esac
575
576	if [[ -n $fetch_rev ]]; then
577	echo "IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at orchidee-help@listes.ipsl.fr"
578	local curr_rev
579	curr_rev=$(svn info "$MODEL/modipsl/modeles/ORCHIDEE" \| grep Revision: \| cut -d ":" -f 2 \| cut -c 2-)
580	orcbranch=$(svn log -v -q svn://forge.ipsl.fr/orchidee/ -r "$fetch_rev" \| grep ORCHIDEE \| head -1 \| sed -e 's:ORCHIDEE/.*$:ORCHIDEE:' \| awk '{print $2}')
581	if [[ $fetch_rev != "$curr_rev" ]]; then
582	echo "Fetching orch $fetch_rev from the repository (curr: $curr_rev)"
583	echo "branch is $orcbranch"
584	if [[ $fetch_rev -lt 4465 ]]; then echo 'ORCHIDEE version must be >=4465, exiting'; exit 1; fi
585	cd "$MODEL/modipsl/modeles"
586	rm -rf ORCHIDEE
587	svn co -r "$fetch_rev" "svn://forge.ipsl.fr/orchidee/$orcbranch"
588	cd - > /dev/null
589	fi
590	fi
591
592	# Check parallel LMDZ+ORCH
593	if [[ (! $veget = "none") && $parallel = "none" && ($used_lmdz_rev -lt 4894) ]]; then
594	echo "LMDZ revision must be >=4894 for orchidee without parallel support. Upgrade lmdz or use -parallel mpi_omp."; exit 1
595	fi
596	}
597
598	function compile_orchidee {
599	install_arch "ORCHIDEE"
600
601	if [[ $veget != "none" ]]; then
602	cd "$MODEL/modipsl/modeles/ORCHIDEE"
603
604	orchideelog="$(pwd)/orchidee.log"
605	echo "Compiling ORCHIDEE, the continental surface model (log $orchideelog) $(date)"
606
607	local xios_orchid
608	if [[ $with_xios = 1 ]]; then
609	xios_orchid="-xios";
610	else
611	xios_orchid="-noxios"
612	fi
613
614	if [[ $parallel != "none" && ! -d src_parallel ]]; then
615	echo "STOP: Orchidee version too old for parallel support"; exit 1
616	fi
617	echo "$jobcmd ./makeorchidee_fcm -j $make_j $xios_orchid $optim_flag -parallel $parallel -arch $arch" > compile.sh
618	chmod +x compile.sh
619	echo "Compiling ORCHIDEE using $(\cat compile.sh)"
620	if ! ./compile.sh &> "$orchideelog"; then
621	echo "STOP: ORCHIDEE compilation failed, exiting"; exit 1
622	fi
623	echo "Compiled ORCHIDEE $(date)"
624	fi
625	}
626
627	function get_lmdz_version {
628	echo "Checking LMDZ source version"
629	LMDZPATH=$(readlink -e -f "$MODEL/modipsl/modeles/LMD"*)
630	cd "$LMDZPATH"
631	lmdzlog="$(pwd)/lmdz.log"
632
633	if [[ -n $svn_lmdz ]]; then
634	local curr_rev
635	curr_rev=$(svn info "$MODEL/modipsl/modeles/LMD"* \| grep Revision: \| cut -d ":" -f 2 \| cut -c 2-)
636	if [[ $svn_lmdz != "$curr_rev" ]]; then
637	local lmdzbranch
638	echo "Fetching LMDZ $svn_lmdz from the repository"
639	lmdzbranch=$(get_svn_branch "https://svn.lmd.jussieu.fr/LMDZ" "$svn_lmdz")
640	echo "branch is $lmdzbranch"
641	cd "$MODEL/modipsl/modeles"
642	rm -rf LMD*
643	svn co -r "$svn_lmdz" "https://svn.lmd.jussieu.fr/LMDZ/$lmdzbranch" LMDZ
644	cd - > /dev/null
645	fi
646	used_lmdz_rev=$svn_lmdz
647	else # get svn from info
648	set +e; used_lmdz_rev=$(svn info \| grep "Last Changed Rev" \| cut -c 19-); set -e
649	if [[ -z $used_lmdz_rev ]]; then # svn info failed
650	used_lmdz_rev=$(grep 'Revision: [0-9]' "$MODEL"/Read*.md \| awk ' { print $2 } ' 2>/dev/null)
651	if [[ -z $used_lmdz_rev ]]; then echo "Could not determine lmdz version. This is likely an issue with the .tar itself, please report to LMDZ team."; exit 1; fi
652	fi
653	fi
654	}
655
656	function compile_lmdz {
657	install_arch "LMDZ"
658	cd "$LMDZPATH"
659
660	if [[ $used_lmdz_rev -le 4185 ]]; then
661	exe_name="bin/${fortran_file}_${grid_resolution}_phy${compphysiq}_${suff_para}${suff_orc}${suff_aer}${suff_iso}.e"
662	else
663	exe_name="bin/${fortran_file}_${grid_resolution}_phy${compphysiq}_${rad}${suff_para}${suff_orc}${suff_aer}${suff_iso}.e"
664	fi
665
666	local opt_rad
667	case $rad in
668	oldrad) iflag_rrtm=0; NSW=2; opt_rad="";;
669	rrtm) iflag_rrtm=1; NSW=6
670	if [[ $used_lmdz_rev -le 4185 ]]; then
671	opt_rad="-rrtm true"
672	else
673	opt_rad="-rad rrtm"
674	fi;;
675	ecrad) iflag_rrtm=2; NSW=6; opt_rad="-rad ecrad";;
676	*) echo "Only oldrad rrtm ecrad for rad option"; exit 1
677	esac
678	if [[ $used_lmdz_rev -le 4185 && $rad = "ecrad" ]]; then
679	echo "ecrad only available for LMDZ rev starting with 4186 "; exit 1
680	fi
681
682	# Compile
683	makelmdz="makelmdz_fcm $optim_flag -arch $arch -j $make_j"
684	local para_compile_opt="-mem -parallel $parallel"; if [[ $parallel = "none" ]]; then para_compile_opt=""; fi
685	echo "$jobcmd ./$makelmdz $opt_rad $opt_cosp $opt_makelmdz_xios $opt_aer $opt_inlandsis $opt_isotopes -p $compphysiq -d ${grid_resolution} -v $fcm_veget_version $para_compile_opt $fortran_file" > compile.sh
686	echo "Compiling lmdz using $(\cat compile.sh) (log: $lmdzlog) $(date)"
687	chmod +x ./compile.sh
688	if ! ./compile.sh &> "$lmdzlog"; then
689	echo "STOP: LMDZ compilation failed, exiting"; exit 1
690	fi
691	echo "Finished LMDZ compilation $(date)"
692
693	# Check executable
694	if [[ ! -f $exe_name ]]; then
695	echo "STOP: Compilation failed, can't find the executable"; exit 1
696	else
697	echo "Compilation successful, the executable is $exe_name $(date)"
698	fi
699	}
700
701	function run_bench {
702	local bench_cmd="./bench.sh"
703
704	cd "$MODEL/modipsl/modeles/LMDZ"*
705
706	if [[ $bench = "tuto" ]]; then
707	myget "Training/tutorial.tar"; tar xf tutorial.tar; cd TUTORIAL
708	./init.sh
709	elif [[ $bench = 1 ]]; then
710	rm -rf "BENCH${grid_resolution}"
711	local bench=bench_lmdz_${grid_resolution}
712	if [[ $compphysiq = "lmdiso" ]]; then bench=bench_lmdz_iso_${grid_resolution}; fi
713
714	if [[ $is_1D = "y" ]] ; then # 1D
715	myget "1D/1D.tar.gz"
716	mkdir -p "BENCH${grid_resolution}"
717	tar xf "1D.tar.gz" -C "BENCH${grid_resolution}" --strip-components=1
718	cd "BENCH${grid_resolution}"
719	# Below: ugly, but until we rewrite the 1D case...
720	sed -i'' -e "s:^listecas=.*$:listecas=ARMCU/REF:" -e "s:cd \$local/bin ; ./compile -L \$L:#cd \$local/bin ; ./compile -L \$L:" \
721	-e "s:./compile -L \$llm:#./compile -L \$llm:" -e "s:ln -sf \$bin/\\\\\${main}\${suffixe}.e .:ln -sf ../../../../../$exe_name \\\\\${main}\${suffixe}.e:" -e "s:gzip listing:cp listing restartphy.nc ../../../../; exit 0:" \
722	run.sh
723	cp "../$exe_name" bin/
724	bench_cmd="./run.sh -rad $rad" # suppress ferret commands that launch after bench is "over"
725	else
726	myget "3DBenchs/$bench.tar.gz"
727	mkdir "BENCH${grid_resolution}"
728	tar xf "$bench.tar.gz" -C "BENCH${grid_resolution}" --strip-components=1
729
730	if [[ $cosp = "v1" \|\| $cosp = "v2" ]]; then
731	cd "BENCH${grid_resolution}"
732	# copier les fichiers namelist input et output our COSP
733	cp ../DefLists/cosp*_input_nl.txt .
734	cp ../DefLists/cosp*_output_nl.txt .
735	# Activer la cles ok_cosp pour tourner avec COSP
736	sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp
737	\mv -f tmp config.def
738	cd ..
739	fi
740
741	if [[ -n "$benchphysiq" ]]; then
742	cd "BENCH${grid_resolution}"
743	if [[ -f "physiq.def_${benchphysiq}" ]]; then
744	cp "physiq.def_${benchphysiq}" benchphysiq.def
745	echo "using physiq.def_${benchphysiq}"
746	else
747	echo "using standard physiq.def"
748	fi
749	cd ..
750	else
751	echo "using standard physiq.def"
752	fi
753
754	if [[ $with_xios = 1 ]]; then
755	cd "BENCH${grid_resolution}"
756	cp ../DefLists/iodef.xml .
757	cp ../DefLists/context_lmdz.xml .
758	cp ../DefLists/field_def_lmdz.xml .
759	# A raffiner par la suite
760	echo "A FAIRE : Copier les *xml en fonction de l option cosp"
761	cp ../DefLists/field_def_cosp*.xml .
762	cp ../DefLists/file_def_hist*xml .
763	# adapt iodef.xml to use attached mode
764	sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' \
765	iodef.xml > tmp
766	\mv -f tmp iodef.xml
767
768	# and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
769	# except for histday
770	for histfile in file_def_hist*xml; do
771	if [[ "$histfile" = "file_def_histday_lmdz.xml" ]]; then
772	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' \
773	"$histfile" > tmp
774	\mv -f tmp "$histfile"
775	sed -e 's@output_level="_AUTO_"@output_level="5"@' "$histfile" \
776	> tmp
777	\mv -f tmp "$histfile"
778	sed -e 's@compression_level="2"@compression_level="0"@' \
779	"$histfile" > tmp
780	\mv -f tmp "$histfile"
781	else
782	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
783	"$histfile" > tmp
784	\mv -f tmp "$histfile"
785	fi
786	done
787	# and add option "ok_all_xml=y" in config.def
788	echo "### XIOS outputs" >> config.def
789	echo 'ok_all_xml=.true.' >> config.def
790
791	#activer les sorties pour Cosp
792	if [[ "$cosp" = "v1" ]]; then
793	sed -i'' -e 's@enabled=".FALSE."@enabled=".TRUE."@' \
794	-e 's@output_level="_AUTO_"@output_level="5"@' \
795	-e 's@compression_level="2"@compression_level="0"@' \
796	file_def_histdayCOSP_lmdz.xml
797	fi
798	if [[ "$cosp" = "v2" ]]; then
799	sed -i'' -e 's@compression_level="2"@compression_level="0"@' file_def_histdayCOSPv2_lmdz.xml
800	for type_ in hf day mth; do
801	file=file_def_hist${type_}COSP
802	sed -i'' -e 's@src="./'${file}'_lmdz.xml"@src="./'${file}'v2_lmdz.xml"@' context_lmdz.xml
803	done
804	sed -i'' -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' field_def_lmdz.xml
805	fi
806
807	cd ..
808	fi
809
810	# Cas Bench avec ecrad
811	if [[ $rad = "ecrad" ]]; then
812	cd "BENCH${grid_resolution}"
813	cp ../DefLists/namelist_ecrad .
814	cp -r ../libf/phylmd/ecrad/data .
815	cd ..
816	fi
817
818	# Adjusting bench physiq.def to radiative code chosen
819	cd "BENCH${grid_resolution}"
820	sed -e 's/iflag_rrtm=.*.$/iflag_rrtm='$iflag_rrtm'/' \
821	-e 's/NSW=.*.$/NSW='$NSW'/' physiq.def > tmpdef
822	\mv tmpdef physiq.def
823	cd ..
824
825	cp "$exe_name" "BENCH${grid_resolution}/gcm.e"
826	cd "BENCH${grid_resolution}"
827
828	if [[ ${parallel:0:3} = "mpi" ]]; then
829	# Lancement avec deux procs mpi et 2 openMP
830	echo "export OMP_STACKSIZE=800M" > bench.sh
831	if [[ "${parallel:4:3}" = "omp" ]]; then
832	echo "export OMP_NUM_THREADS=2" >> bench.sh
833	fi
834	if [[ $cosp = "v1" \|\| $cosp = "v2" ]]; then
835	echo "ulimit -s 200000" >> bench.sh
836	else
837	echo "ulimit -s unlimited" >> bench.sh
838	fi
839	if which mpirun &> /dev/null; then
840	echo "mpirun -np 2 gcm.e &> listing" >> bench.sh
841	elif grep -q "Adastra" /etc/motd; then
842	local account
843	account=$(/usr/sbin/my_project.py -l 2>&1 \| head -1 \| cut -d " " -f 3- \| cut -c 5-)
844	bench_cmd="srun --nodes=1 --ntasks=1 --cpus-per-task=2 --threads-per-core=2 --time=0:10:00 --constraint=GENOA --account=$account bash bench.sh"
845	echo "./gcm.e &> listing" >> bench.sh
846	else
847	echo "Error: No command found to run parallel bench"; exit 1
848	fi
849	if [[ $(hostname \| cut -c -6) = "spirit" ]]; then # ulimit unlimited segfaults on Spirit
850	sed -i'' "s/ulimit -s unlimited/ulimit -Ss 8000/" bench.sh
851	fi
852	# Add rebuild, using reb.sh if it is there
853	cat <<EOF >> bench.sh
854	if [[ -f reb.sh ]]; then
855	./reb.sh histday; ./reb.sh histmth; ./reb.sh histhf;
856	./reb.sh histins; ./reb.sh stomate_history;
857	./reb.sh sechiba_history; ./reb.sh sechiba_out_2
858	fi
859	EOF
860	else
861	echo "./gcm.e &> listing" > bench.sh
862	fi
863	chmod +x bench.sh
864	# Getting orchidee stuff
865	if [[ $veget = 'CMIP6' \|\| $veget = "orch2.0" ]]; then # TODO once we have a 2.2 bench, add it here (or in planned separate bench script)
866	echo 'myget 3DBenchs/BENCHCMIP6.tar.gz'
867	myget 3DBenchs/BENCHCMIP6.tar.gz
868	tar xvzf BENCHCMIP6.tar.gz
869	sed -e "s:VEGET=n:VEGET=y:" config.def > tmp
870	mv -f tmp config.def
871	if [[ $with_xios = 1 ]]; then
872	cp ../../ORCHIDEE/src_xml/context_orchidee.xml .
873	echo '<context id="orchidee" src="./context_orchidee.xml"/>' > add.tmp
874	cp ../../ORCHIDEE/src_xml/field_def_orchidee.xml .
875	cp ../../ORCHIDEE/src_xml/file_def_orchidee.xml .
876	cp ../../ORCHIDEE/src_xml/file_def_input_orchidee.xml .
877	if [[ -f ../../ORCHIDEE/src_xml/context_input_orchidee.xml ]]; then
878	cp ../../ORCHIDEE/src_xml/context_input_orchidee.xml .
879	echo '<context id="orchidee" src="./context_input_orchidee.xml"/>' >> add.tmp
880	fi
881	sed -e '/id="LMDZ"/r add.tmp' iodef.xml > tmp
882	mv tmp iodef.xml
883	sed -e'{/sechiba1/ s/enabled="_AUTO_"/type="one_file" enabled=".TRUE."/}' \
884	file_def_orchidee.xml > tmp
885	\mv -f tmp file_def_orchidee.xml
886	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
887	file_def_orchidee.xml > tmp
888	\mv -f tmp file_def_orchidee.xml
889	sed -e 's@output_level="_AUTO_"@output_level="1"@' \
890	file_def_orchidee.xml > tmp
891	\mv -f tmp file_def_orchidee.xml
892	sed -e 's@output_freq="_AUTO_"@output_freq="1d"@' \
893	file_def_orchidee.xml > tmp
894	\mv -f tmp file_def_orchidee.xml
895	sed -e 's@compression_level="4"@compression_level="0"@' \
896	file_def_orchidee.xml > tmp
897	\mv -f tmp file_def_orchidee.xml
898	sed -e 's@XIOS_ORCHIDEE_OK = n@XIOS_ORCHIDEE_OK = y@' \
899	orchidee.def > tmp
900	\mv -f tmp orchidee.def
901	fi
902	fi
903
904	fi
905
906	if [[ -f ../arch.env ]]; then source ../arch.env; fi
907
908	echo "STARTING BENCH"
909	date
910	if (! $bench_cmd &> out.bench) \|\| ! (tail -n 1 listing \| grep "Everything is cool"); then
911	tail listing
912	echo "Bench FAILED, exiting"; exit 1
913	fi
914	date
915	tail listing
916	fi
917
918	# 1D case
919	if [[ $SCM = 1 ]]; then
920	cd "$MODEL"
921	myget 1D/1D.tar.gz
922	tar xf 1D.tar.gz
923	cd 1D
924	for e in "fcm" "env" "path"; do
925	cp "$MODEL/modipsl/modeles/LMDZ/arch/arch-$arch.$e" "$MODEL/modipsl/modeles/LMDZ/arch/arch-local.$e"
926	done
927	if [[ $rad = "oldrad" ]]; then
928	sed -i'' -e 's/^rad=.*$/rad=oldrad/' run.sh
929	sed -i'' -e 's/^rad=.*$/rad=oldrad/' bin/compile
930	elif [[ $rad = ecrad ]] ; then
931	sed -i'' -e 's/^rad=.*$/rad=ecrad/' run.sh
932	sed -i'' -e 's/^rad=.*$/rad=ecrad/' bin/compile
933	fi
934	echo "Running 1D/run.sh, log in $(pwd)/run1d.log"
935	./run.sh &> "$(pwd)/run1d.log"
936	fi
937	}
938
939	# If sourced: returns, else run setup
940	if [[ ! "${BASH_SOURCE[0]}" = "$0" ]]; then return 0; fi
941
942	echo "install_lmdz.sh DEBUT $(date)"
943
944	set_default_params
945	read_cmdline_args "$@"
946	ensure_correct_option_combinations
947	download_model
948	init_arch
949	check_available_software
950	get_lmdz_version
951	get_orchidee_version
952	install_netcdf
953	install_IOIPSL
954	install_XIOS
955	compile_orchidee
956	compile_lmdz
957	run_bench

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