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source: BOL/script_install_amaury/install_lmdz.sh @ 5178

Last change on this file since 5178 was 5156, checked in by abarral, 3 months ago
Add 1D and iso bench Better svn branch detection for lmdz Add script to test convergence locally Lint check_version.sh
Property svn:executable set to ``*
File size: 36.7 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	# TODO Amaury: check if still relevant
309	if [[ $isotopes = 1 && $with_xios = 1 ]]; then
310	echo "STOP: Isotopes cannont yet be run with XIOS"; exit 1
311	fi
312
313	if [[ $aerosols = 1 && $rad != "rrtm" ]]; then
314	echo "STOP: For the time being, <aerosols=spla> requires <rad=rrtm>"; exit 1
315	fi
316	# TODO: vérifier quelles contraintes sont des contraintes lmdzsetup, et lesquelles sont des vraies contraintes
317	}
318
319	function check_available_software {
320	echo "################################################################"
321	echo "Check if required software is available"
322	echo "################################################################"
323	for logiciel in wget tar gzip make gcc cmake m4 c++; do
324	if [[ $(which "$logiciel") = "" ]]; then
325	echo "You must first install $logiciel on your system"; exit 1
326	fi
327	done
328
329	cat <<eod > tt.f90
330	print*,'coucou'
331	end
332	eod
333	$compiler tt.f90 \|\| a.out
334	./a.out >\| tt
335	if [[ $(< tt sed -e 's/ //g' ) != "coucou" ]]; then
336	echo "problem installing with compiler $compiler"; exit 1
337	fi
338	rm tt a.out tt.f90
339	}
340
341	function download_model {
342	if [[ $clean_install = 1 ]]; then rm -rf "$MODEL"; fi
343
344	mkdir -p "$MODEL"
345	MODEL=$(readlink -e -f "$MODEL"); echo "MODEL: $MODEL" # absolute path
346	if [[ ! -d "$MODEL/modipsl" ]]; then
347	echo "##########################################################"
348	echo "Downloading a slightly modified version of modipsl+LMDZ"
349	echo "##########################################################"
350	cd "$MODEL"
351	getlog="$(pwd)/get.log"
352	echo "logfile : $getlog"
353	myget "src_archives/$trusting/modipsl.$version.tar.gz" &>> get.log
354	echo "install_lmdz.sh wget_OK $(date)"
355	gunzip "modipsl.$version.tar.gz" &>> get.log
356	tar xf "modipsl.$version.tar" &>> get.log
357	rm "modipsl.$version.tar"
358	cd - &> /dev/null
359	fi
360	}
361
362	function init_arch {
363	set +e; arch_dir=$(readlink -f "$arch_dir"); set -e # full path. readlink must be called after the path is created
364
365	# Check where default fcm, path, env are located - by default in $arch_path, instead in $MODEL/modipsl/modeles/LMDZ/arch/
366	local i fcm_path path_path env_path
367	for i in "path" "fcm" "env"; do
368	local varname=${i}_path
369	if [[ -f $arch_dir/arch-$arch.$i ]]; then
370	declare $varname="$arch_dir/arch-$arch.$i"
371	else
372	declare $varname="$MODEL/modipsl/modeles/LMDZ/arch/arch-$arch.$i"
373	if [[ ! -f ${!varname} ]]; then
374	echo "STOP: no ${!varname}"; exit 1
375	fi
376	fi
377	done
378	default_fcm_path=$fcm_path
379	default_path_path=$path_path
380	default_env_path=$env_path
381
382	# check compiler
383	compiler=$(< "$default_fcm_path" grep "%COMPILER" \| sed -e "s/%COMPILER\s*//")
384
385	# load env
386	# shellcheck disable=SC1090
387	if [[ -f $default_env_path ]]; then source "$default_env_path"; fi
388
389	local mpi_file # can't be done before as it depends on sourcing the env
390	mpi_file=$(readlink -e -f "$(which mpif90)")
391	path_mpi=$(dirname "$mpi_file")
392	root_mpi=$(dirname "$path_mpi")
393	}
394
395	function install_arch {
396	local component=$1
397
398	# Use same .env for all components (for module compatibility)
399	cp -f "$default_env_path" "$MODEL/modipsl/modeles/$component/arch" &> /dev/null \|\| true # allow failure if we're copying the file to itself
400
401	# Use local .path and .fcm is available, otherwise default
402	if [[ ! -f "$MODEL/modipsl/modeles/$component/arch/arch-$arch.path" ]]; then
403	cp -f "$default_path_path" "$MODEL/modipsl/modeles/$component/arch"
404
405	if [[ $component = "ORCHIDEE" ]]; then
406	if [[ $orcbranch = "/tags/ORCHIDEE_2_0/ORCHIDEE" ]]; then # 2.0 and before have a different fcm convention
407	sed -i'' -e "s/-I//" -e "s/-L//" "$MODEL/modipsl/modeles/ORCHIDEE/arch/arch-$arch.path" # /!\ we only replace first occurence on purpose
408	fi
409	fi
410	fi
411	if [[ ! -f "$MODEL/modipsl/modeles/$component/arch/arch-$arch.fcm" ]]; then
412	cp -f "$default_fcm_path" "$MODEL/modipsl/modeles/$component/arch"
413
414	if [[ $component = "XIOS" ]]; then
415	# Adapt for XIOS, which uses different naming conventions
416	sed -i'' -e "s/%COMPILER/%FCOMPILER/" -e "s/%LINK/%LINKER/" -e "s/-fdefault-real-8//" "$MODEL/modipsl/modeles/XIOS/arch/arch-$arch.fcm"
417	fi
418	fi
419	}
420
421	function install_netcdf {
422	echo "Installing Netcdf"
423	local ncdf_compiler="$compiler"
424
425	if [[ $netcdf = 0 ]]; then
426	ncdfdir=$(nf-config --prefix)
427	else
428	cd "$MODEL"
429
430	# Convert non-basic compiler
431	case $compiler in
432	mpif90) ncdf_compiler=$($compiler --version \| head -n 1 \| cut -d " " -f -1)
433	esac
434
435	case $ncdf_compiler in
436	gfortran \| GNU) ncdf_compiler="gfortran"; opt1="-compiler gnu"; opt2="-CC gcc -FC gfortran -CXX g++";;
437	*) echo "unexpected compiler $ncdf_compiler for netcdf"; exit 1
438	esac
439
440	case $with_xios in
441	0) script_install_netcdf="install_netcdf4_hdf5_seq.bash"
442	ncdfdir="netcdf4_hdf5_seq"
443	opt_="$opt1";;
444	1) script_install_netcdf="install_netcdf4_hdf5.bash"
445	ncdfdir="netcdf4_hdf5"
446	opt_="$opt2 -MPI $root_mpi";;
447	*) echo "with_xios=$with_xios, should be 0 or 1"; exit 1
448	esac
449	if [[ $netcdf = 1 ]]; then
450	ncdfdir="$MODEL/$ncdfdir"
451	else
452	mkdir -p "$netcdf"; ncdfdir="$netcdf/$ncdfdir"
453	fi
454
455	echo "Repertoire netcdf $ncdfdir"
456	if [[ ! -d $ncdfdir ]]; then
457	netcdflog=$(pwd)/netcdf.log
458	echo "----------------------------------------------------------"
459	echo "Compiling the Netcdf library"
460	echo "----------------------------------------------------------"
461	echo "log file : $netcdflog"
462	myget script_install/$script_install_netcdf &>> "$netcdflog"
463	chmod u=rwx $script_install_netcdf
464	# shellcheck disable=SC2086
465	./$script_install_netcdf -prefix "$ncdfdir" $opt_ &>> "$netcdflog"
466	fi
467
468	# Add to path
469	export PATH="$ncdfdir/bin:$PATH"
470
471	#----------------------------------------------------------------------------
472	# LF rajout d'une verrue, pour une raison non encore expliquee,
473	# la librairie est parfois rangée dans lib64 et non dans lib
474	# par certains compilateurs
475	if [[ ! -e lib && -d lib64 ]]; then ln -s lib64 lib; fi
476	#----------------------------------------------------------------------------
477
478	echo "install_lmdz.sh netcdf_OK $(date)"
479	fi
480
481	cat >test_netcdf90.f90 <<EOF
482	use netcdf
483	print *, "NetCDF library version: ", nf90_inq_libvers()
484	end
485	EOF
486
487	if $ncdf_compiler -I"$ncdfdir"/include test_netcdf90.f90 -L"$ncdfdir"/lib -lnetcdff -lnetcdf -Wl,-rpath="$ncdfdir"/lib && ./a.out; then
488	rm test_netcdf90.f90 a.out
489	else
490	cat <<EOF
491	Failed test program using NetCDF-Fortran. You can:
492	- check that you have NetCDF-Fortran installed in your system
493	- or specify an installation directory with option -netcdf of install_lmdz.sh
494	- or download and compile NetCDF-Fortran with option -netcdf 1 of install_lmdz.sh
495	EOF
496	exit 1
497	fi
498
499	# Compile NetCDF95
500	cd "$MODEL/modipsl/modeles/LMD"*
501	echo "Installing NetCDF95"
502	cd "$MODEL"
503	if [[ ! -d "NetCDF95-0.3" ]]; then
504	myget src_archives/netcdf/NetCDF95-0.3.tar.gz
505	tar -xf NetCDF95-0.3.tar.gz
506	rm NetCDF95-0.3.tar.gz
507	cd NetCDF95-0.3
508	mkdir -p build && cd build
509	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"
510	make install
511	fi
512	}
513
514	function install_IOIPSL {
515	install_arch "IOIPSL"
516
517	cd "$MODEL/modipsl/modeles/IOIPSL"
518	ioipsllog="$(pwd)/ioipsl.log"
519	echo "Compiling IOIPSL, the interface library with Netcdf $(date) (log: $ioipsllog)"
520
521	echo "$jobcmd ./makeioipsl_fcm -j $make_j -arch $arch $optim_flag" > compile.sh
522	chmod +x compile.sh
523	echo "Compiling IOIPSL using $(\cat compile.sh)"
524	if ! ./compile.sh &> "$ioipsllog"; then
525	echo "STOP: IOIPSL compile failed, exiting"; exit 1
526	fi
527
528	# Link to modipsl/bin
529	cp -f bin/* ../../bin
530
531	echo "IOIPSL compiled $(date)"
532	}
533
534	function install_XIOS {
535	if [[ $with_xios = 1 ]]; then
536	cd "$MODEL/modipsl/modeles"
537	xioslog="$(pwd)/XIOS/xios.log"
538	echo "##########################################################"
539	echo "Compiling XIOS (log $xioslog) $(date)"
540	echo "##########################################################"
541
542	# Download XIOS
543	local xios_http="http://forge.ipsl.fr/ioserver/svn/XIOS2/branches/xios-2.6"
544	local xios_rev="2568"
545
546	cd "$MODEL/modipsl/modeles"
547	set +e; svn co -r $xios_rev $xios_http XIOS; set -e
548
549	cd XIOS
550
551	install_arch "XIOS"
552
553	echo "$jobcmd ./make_xios --job $make_j --arch $arch" > compile.sh
554	chmod +x compile.sh
555	echo "$(date) Compiling XIOS using $(\cat compile.sh) (log in $xioslog)"
556	if ! ./compile.sh &> "$xioslog"; then
557	echo "STOP: XIOS compilation failed, exiting"; exit 1
558	fi
559
560	echo "Compiled XIOS $(date)"
561	fi
562	}
563
564	function get_orchidee_version { # Set / Check ORCHIDEE version
565	local fetch_rev=""
566	orcbranch=""
567	case $veget in
568	"none") fcm_veget_version="false";;
569	"orch2.0" \| "CMIP6") fcm_veget_version=orchidee2.0; fetch_rev=7906;; # in previous tar we used 6592 but with some modifications to xios_orchidee.f90, which got integrated in 7906
570	"orch2.2") fcm_veget_version=orchidee2.1; orcbranch="/branches/ORCHIDEE_2_2/ORCHIDEE" ;; # the bundled version
571	*) fetch_rev=$veget; fcm_veget_version=orchidee2.1;; # /!\ arbitary rev only works for orch>=2.1
572	# /!\ Note: for orch>=4, we should be using fcm_vegt_version="orchideetrunk". Below copied comment by Adriana in LMDZ_Setup docs:
573	# 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
574	#Si on voudrait activer landice_opt=2 , il faut compiler avec -v orchideetrunk.
575
576	esac
577
578	if [[ -n $fetch_rev ]]; then
579	local curr_rev
580	curr_rev=$(svn info "$MODEL/modipsl/modeles/ORCHIDEE" \| grep Revision: \| cut -d ":" -f 2 \| cut -c 2-)
581	orcbranch=$(svn log -v -q svn://forge.ipsl.fr/orchidee/ -r "$fetch_rev" \| grep ORCHIDEE \| head -1 \| sed -e 's:ORCHIDEE/.*$:ORCHIDEE:' \| awk '{print $2}')
582	if [[ $fetch_rev != "$curr_rev" ]]; then
583	echo "Fetching orch $fetch_rev from the repository (curr: $curr_rev)"
584	echo "branch is $orcbranch"
585	if [[ $fetch_rev -lt 4465 ]]; then echo 'ORCHIDEE version must be >=4465, exiting'; exit 1; fi
586	echo "IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at orchidee-help@listes.ipsl.fr"
587	cd "$MODEL/modipsl/modeles"
588	rm -rf ORCHIDEE
589	svn co -r "$fetch_rev" "svn://forge.ipsl.fr/orchidee/$orcbranch"
590	cd - > /dev/null
591	fi
592	fi
593
594	# Check parallel LMDZ+ORCH
595	if [[ (! $veget = "none") && $parallel = "none" && ($used_lmdz_rev -lt 4894) ]]; then
596	echo "LMDZ revision must be >=4894 for orchidee without parallel support. Upgrade lmdz or use -parallel mpi_omp."; exit 1
597	fi
598	}
599
600	function compile_orchidee {
601	install_arch "ORCHIDEE"
602
603	if [[ $veget != "none" ]]; then
604	cd "$MODEL/modipsl/modeles/ORCHIDEE"
605
606	orchideelog="$(pwd)/orchidee.log"
607	echo "Compiling ORCHIDEE, the continental surface model (log $orchideelog) $(date)"
608
609	local xios_orchid
610	if [[ $with_xios = 1 ]]; then
611	xios_orchid="-xios";
612	else
613	xios_orchid="-noxios"
614	fi
615
616	if [[ $parallel != "none" && ! -d src_parallel ]]; then
617	echo "STOP: Orchidee version too old for parallel support"; exit 1
618	fi
619	echo "$jobcmd ./makeorchidee_fcm -j $make_j $xios_orchid $optim_flag -parallel $parallel -arch $arch" > compile.sh
620	chmod +x compile.sh
621	echo "Compiling ORCHIDEE using $(\cat compile.sh)"
622	if ! ./compile.sh &> "$orchideelog"; then
623	echo "STOP: ORCHIDEE compilation failed, exiting"; exit 1
624	fi
625	echo "Compiled ORCHIDEE $(date)"
626	fi
627	}
628
629	function get_lmdz_version {
630	LMDZPATH=$(readlink -e -f "$MODEL/modipsl/modeles/LMD"*)
631	cd "$LMDZPATH"
632	lmdzlog="$(pwd)/lmdz.log"
633
634	if [[ -n $svn_lmdz ]]; then
635	local curr_rev
636	curr_rev=$(svn info "$MODEL/modipsl/modeles/LMD"* \| grep Revision: \| cut -d ":" -f 2 \| cut -c 2-)
637	if [[ $svn_lmdz != "$curr_rev" ]]; then
638	local lmdzbranch
639	echo "Fetching LMDZ $svn_lmdz from the repository"
640	lmdzbranch=$(get_svn_branch "https://svn.lmd.jussieu.fr/LMDZ" "$svn_lmdz")
641	echo "branch is $lmdzbranch"
642	cd "$MODEL/modipsl/modeles"
643	rm -rf LMD*
644	svn co -r "$svn_lmdz" "https://svn.lmd.jussieu.fr/LMDZ/$lmdzbranch" LMDZ
645	cd - > /dev/null
646	fi
647	used_lmdz_rev=$svn_lmdz
648	else # get svn from info
649	set +e; used_lmdz_rev=$(svn info \| grep "Last Changed Rev" \| cut -c 19-); set -e
650	if [[ -z $used_lmdz_rev ]]; then # svn info failed
651	used_lmdz_rev=$(grep 'Revision: [0-9]' "$MODEL"/Read*.md \| awk ' { print $2 } ' 2>/dev/null)
652	if [[ -z $used_lmdz_rev ]]; then echo "Could not determine lmdz version. This is likely an issue with the .tar itself, please report to LMDZ team."; exit 1; fi
653	fi
654	fi
655	}
656
657	function compile_lmdz {
658	install_arch "LMDZ"
659	cd "$LMDZPATH"
660
661	if [[ $used_lmdz_rev -le 4185 ]]; then
662	exe_name="bin/${fortran_file}_${grid_resolution}_phy${compphysiq}_${suff_para}${suff_orc}${suff_aer}${suff_iso}.e"
663	else
664	exe_name="bin/${fortran_file}_${grid_resolution}_phy${compphysiq}_${rad}${suff_para}${suff_orc}${suff_aer}${suff_iso}.e"
665	fi
666
667	local opt_rad
668	case $rad in
669	oldrad) iflag_rrtm=0; NSW=2; opt_rad="";;
670	rrtm) iflag_rrtm=1; NSW=6
671	if [[ $used_lmdz_rev -le 4185 ]]; then
672	opt_rad="-rrtm true"
673	else
674	opt_rad="-rad rrtm"
675	fi;;
676	ecrad) iflag_rrtm=2; NSW=6; opt_rad="-rad ecrad";;
677	*) echo "Only oldrad rrtm ecrad for rad option"; exit 1
678	esac
679	if [[ $used_lmdz_rev -le 4185 && $rad = "ecrad" ]]; then
680	echo "ecrad only available for LMDZ rev starting with 4186 "; exit 1
681	fi
682
683	# Compile
684	makelmdz="makelmdz_fcm $optim_flag -arch $arch -j $make_j"
685	local para_compile_opt="-mem -parallel $parallel"; if [[ $parallel = "none" ]]; then para_compile_opt=""; fi
686	echo "$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
687	echo "Compiling lmdz using $(\cat compile.sh) (log: $lmdzlog) $(date)"
688	chmod +x ./compile.sh
689	if ! ./compile.sh &> "$lmdzlog"; then
690	echo "STOP: LMDZ compilation failed, exiting"; exit 1
691	fi
692	echo "Finished LMDZ compilation $(date)"
693
694	# Check executable
695	if [[ ! -f $exe_name ]]; then
696	echo "STOP: Compilation failed, can't find the executable"; exit 1
697	else
698	echo "Compilation successful, the executable is $exe_name $(date)"
699	fi
700	}
701
702	function run_bench {
703	local bench_cmd="./bench.sh"
704
705	cd "$MODEL/modipsl/modeles/LMDZ"*
706
707	if [[ $bench = "tuto" ]]; then
708	myget "Training/tutorial.tar"; tar xf tutorial.tar; cd TUTORIAL
709	./init.sh
710	elif [[ $bench = 1 ]]; then
711	rm -rf "BENCH${grid_resolution}"
712	local bench=bench_lmdz_${grid_resolution}
713	if [[ $compphysiq = "lmdiso" ]]; then bench=bench_lmdz_iso_${grid_resolution}; fi
714
715	if [[ $is_1D = "y" ]] ; then # 1D
716	myget "1D/1D.tar.gz"
717	mkdir -p "BENCH${grid_resolution}"
718	tar xf "1D.tar.gz" -C "BENCH${grid_resolution}" --strip-components=1
719	cd "BENCH${grid_resolution}"
720	# Below: ugly, but until we rewrite the 1D case...
721	sed -i'' -e "s:^listecas=.*$:listecas=ARMCU/REF:" -e "s:cd \$local/bin ; ./compile -L \$L:#cd \$local/bin ; ./compile -L \$L:" \
722	-e "s:./compile -L \$llm:#./compile -L \$llm:" -e "s:ln -sf \$bin/\\\\\${main}\${suffixe}.e .:ln -sf ../../../../../$exe_name \\\\\${main}\${suffixe}.e:" -e "s:gzip listing:cp listing restartphy.nc ../../../../; exit 0:" \
723	run.sh
724	cp "../$exe_name" bin/
725	bench_cmd="./run.sh -rad $rad" # suppress ferret commands that launch after bench is "over"
726	else
727	myget "3DBenchs/$bench.tar.gz"
728	mkdir "BENCH${grid_resolution}"
729	tar xf "$bench.tar.gz" -C "BENCH${grid_resolution}" --strip-components=1
730
731	if [[ $cosp = "v1" \|\| $cosp = "v2" ]]; then
732	cd "BENCH${grid_resolution}"
733	# copier les fichiers namelist input et output our COSP
734	cp ../DefLists/cosp*_input_nl.txt .
735	cp ../DefLists/cosp*_output_nl.txt .
736	# Activer la cles ok_cosp pour tourner avec COSP
737	sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp
738	\mv -f tmp config.def
739	cd ..
740	fi
741
742	if [[ -n "$benchphysiq" ]]; then
743	cd "BENCH${grid_resolution}"
744	if [[ -f "physiq.def_${benchphysiq}" ]]; then
745	cp "physiq.def_${benchphysiq}" benchphysiq.def
746	echo "using physiq.def_${benchphysiq}"
747	else
748	echo "using standard physiq.def"
749	fi
750	cd ..
751	else
752	echo "using standard physiq.def"
753	fi
754
755	if [[ $with_xios = 1 ]]; then
756	cd "BENCH${grid_resolution}"
757	cp ../DefLists/iodef.xml .
758	cp ../DefLists/context_lmdz.xml .
759	cp ../DefLists/field_def_lmdz.xml .
760	# A raffiner par la suite
761	echo "A FAIRE : Copier les *xml en fonction de l option cosp"
762	cp ../DefLists/field_def_cosp*.xml .
763	cp ../DefLists/file_def_hist*xml .
764	# adapt iodef.xml to use attached mode
765	sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' \
766	iodef.xml > tmp
767	\mv -f tmp iodef.xml
768
769	# and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
770	# except for histday
771	for histfile in file_def_hist*xml; do
772	if [[ "$histfile" = "file_def_histday_lmdz.xml" ]]; then
773	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' \
774	"$histfile" > tmp
775	\mv -f tmp "$histfile"
776	sed -e 's@output_level="_AUTO_"@output_level="5"@' "$histfile" \
777	> tmp
778	\mv -f tmp "$histfile"
779	sed -e 's@compression_level="2"@compression_level="0"@' \
780	"$histfile" > tmp
781	\mv -f tmp "$histfile"
782	else
783	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
784	"$histfile" > tmp
785	\mv -f tmp "$histfile"
786	fi
787	done
788	# and add option "ok_all_xml=y" in config.def
789	echo "### XIOS outputs" >> config.def
790	echo 'ok_all_xml=.true.' >> config.def
791
792	#activer les sorties pour Cosp
793	if [[ "$cosp" = "v1" ]]; then
794	sed -i'' -e 's@enabled=".FALSE."@enabled=".TRUE."@' \
795	-e 's@output_level="_AUTO_"@output_level="5"@' \
796	-e 's@compression_level="2"@compression_level="0"@' \
797	file_def_histdayCOSP_lmdz.xml
798	fi
799	if [[ "$cosp" = "v2" ]]; then
800	sed -i'' -e 's@compression_level="2"@compression_level="0"@' file_def_histdayCOSPv2_lmdz.xml
801	for type_ in hf day mth; do
802	file=file_def_hist${type_}COSP
803	sed -i'' -e 's@src="./'${file}'_lmdz.xml"@src="./'${file}'v2_lmdz.xml"@' context_lmdz.xml
804	done
805	sed -i'' -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' field_def_lmdz.xml
806	fi
807
808	cd ..
809	fi
810
811	# Cas Bench avec ecrad
812	if [[ $rad = "ecrad" ]]; then
813	cd "BENCH${grid_resolution}"
814	cp ../DefLists/namelist_ecrad .
815	cp -r ../libf/phylmd/ecrad/data .
816	cd ..
817	fi
818
819	# Adjusting bench physiq.def to radiative code chosen
820	cd "BENCH${grid_resolution}"
821	sed -e 's/iflag_rrtm=.*.$/iflag_rrtm='$iflag_rrtm'/' \
822	-e 's/NSW=.*.$/NSW='$NSW'/' physiq.def > tmpdef
823	\mv tmpdef physiq.def
824	cd ..
825
826	cp "$exe_name" "BENCH${grid_resolution}/gcm.e"
827	cd "BENCH${grid_resolution}"
828
829	if [[ ${parallel:0:3} = "mpi" ]]; then
830	# Lancement avec deux procs mpi et 2 openMP
831	echo "export OMP_STACKSIZE=800M" > bench.sh
832	if [[ "${parallel:4:3}" = "omp" ]]; then
833	echo "export OMP_NUM_THREADS=2" >> bench.sh
834	fi
835	if [[ $cosp = "v1" \|\| $cosp = "v2" ]]; then
836	echo "ulimit -s 200000" >> bench.sh
837	else
838	echo "ulimit -s unlimited" >> bench.sh
839	fi
840	if which mpirun &> /dev/null; then
841	echo "mpirun -np 2 gcm.e &> listing" >> bench.sh
842	elif grep -q "Adastra" /etc/motd; then
843	local account
844	account=$(/usr/sbin/my_project.py -l 2>&1 \| head -1 \| cut -d " " -f 3- \| cut -c 5-)
845	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"
846	echo "./gcm.e &> listing" >> bench.sh
847	else
848	echo "Error: No command found to run parallel bench"; exit 1
849	fi
850	if [[ $(hostname \| cut -c -6) = "spirit" ]]; then # ulimit unlimited segfaults on Spirit
851	sed -i'' "s/ulimit -s unlimited/ulimit -Ss 8000/" bench.sh
852	fi
853	# Add rebuild, using reb.sh if it is there
854	cat <<EOF >> bench.sh
855	if [[ -f reb.sh ]]; then
856	./reb.sh histday; ./reb.sh histmth; ./reb.sh histhf;
857	./reb.sh histins; ./reb.sh stomate_history;
858	./reb.sh sechiba_history; ./reb.sh sechiba_out_2
859	fi
860	EOF
861	else
862	echo "./gcm.e &> listing" > bench.sh
863	fi
864	chmod +x bench.sh
865	# Getting orchidee stuff
866	if [[ $veget = 'CMIP6' \|\| $veget = "orch2.0" ]]; then # TODO once we have a 2.2 bench, add it here (or in planned separate bench script)
867	echo 'myget 3DBenchs/BENCHCMIP6.tar.gz'
868	myget 3DBenchs/BENCHCMIP6.tar.gz
869	tar xvzf BENCHCMIP6.tar.gz
870	sed -e "s:VEGET=n:VEGET=y:" config.def > tmp
871	mv -f tmp config.def
872	if [[ $with_xios = 1 ]]; then
873	cp ../../ORCHIDEE/src_xml/context_orchidee.xml .
874	echo '<context id="orchidee" src="./context_orchidee.xml"/>' > add.tmp
875	cp ../../ORCHIDEE/src_xml/field_def_orchidee.xml .
876	cp ../../ORCHIDEE/src_xml/file_def_orchidee.xml .
877	cp ../../ORCHIDEE/src_xml/file_def_input_orchidee.xml .
878	if [[ -f ../../ORCHIDEE/src_xml/context_input_orchidee.xml ]]; then
879	cp ../../ORCHIDEE/src_xml/context_input_orchidee.xml .
880	echo '<context id="orchidee" src="./context_input_orchidee.xml"/>' >> add.tmp
881	fi
882	sed -e '/id="LMDZ"/r add.tmp' iodef.xml > tmp
883	mv tmp iodef.xml
884	sed -e'{/sechiba1/ s/enabled="_AUTO_"/type="one_file" enabled=".TRUE."/}' \
885	file_def_orchidee.xml > tmp
886	\mv -f tmp file_def_orchidee.xml
887	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
888	file_def_orchidee.xml > tmp
889	\mv -f tmp file_def_orchidee.xml
890	sed -e 's@output_level="_AUTO_"@output_level="1"@' \
891	file_def_orchidee.xml > tmp
892	\mv -f tmp file_def_orchidee.xml
893	sed -e 's@output_freq="_AUTO_"@output_freq="1d"@' \
894	file_def_orchidee.xml > tmp
895	\mv -f tmp file_def_orchidee.xml
896	sed -e 's@compression_level="4"@compression_level="0"@' \
897	file_def_orchidee.xml > tmp
898	\mv -f tmp file_def_orchidee.xml
899	sed -e 's@XIOS_ORCHIDEE_OK = n@XIOS_ORCHIDEE_OK = y@' \
900	orchidee.def > tmp
901	\mv -f tmp orchidee.def
902	fi
903	fi
904
905	fi
906
907	if [[ -f ../arch.env ]]; then source ../arch.env; fi
908
909	echo "STARTING BENCH"
910	date
911	if (! $bench_cmd &> out.bench) \|\| ! (tail -n 1 listing \| grep "Everything is cool"); then
912	tail listing
913	echo "Bench FAILED, exiting"; exit 1
914	fi
915	date
916	tail listing
917	fi
918
919	# 1D case
920	if [[ $SCM = 1 ]]; then
921	cd "$MODEL"
922	myget 1D/1D.tar.gz
923	tar xf 1D.tar.gz
924	cd 1D
925	for e in "fcm" "env" "path"; do
926	cp "$MODEL/modipsl/modeles/LMDZ/arch/arch-$arch.$e" "$MODEL/modipsl/modeles/LMDZ/arch/arch-local.$e"
927	done
928	if [[ $rad = "oldrad" ]]; then
929	sed -i'' -e 's/^rad=.*$/rad=oldrad/' run.sh
930	sed -i'' -e 's/^rad=.*$/rad=oldrad/' bin/compile
931	elif [[ $rad = ecrad ]] ; then
932	sed -i'' -e 's/^rad=.*$/rad=ecrad/' run.sh
933	sed -i'' -e 's/^rad=.*$/rad=ecrad/' bin/compile
934	fi
935	echo "Running 1D/run.sh, log in $(pwd)/run1d.log"
936	./run.sh &> "$(pwd)/run1d.log"
937	fi
938	}
939
940	# If sourced: returns, else run setup
941	if [[ ! "${BASH_SOURCE[0]}" = "$0" ]]; then return 0; fi
942
943	echo "install_lmdz.sh DEBUT $(date)"
944
945	set_default_params
946	read_cmdline_args "$@"
947	ensure_correct_option_combinations
948	download_model
949	init_arch
950	check_available_software
951	get_lmdz_version
952	get_orchidee_version
953	install_netcdf
954	install_IOIPSL
955	install_XIOS
956	compile_orchidee
957	compile_lmdz
958	run_bench

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