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source: BOL/script_install_amaury/install_lmdz.sh @ 5075

Last change on this file since 5075 was 5064, checked in by abarral, 2 months ago
fix arch for 1D bench
Property svn:executable set to ``*
File size: 35.2 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 set_default_params {
52	# Valeur par défaut des parametres
53	svn_lmdz=""
54	version="20240508.CM7"
55
56	netcdf=1
57	bench=1
58	SCM=0
59	veget="none"
60	grid_resolution="32x32x39"
61	benchphysiq=""
62	compphysiq="lmd"
63
64	parallel="none"
65	trusting="testing"
66	MODEL=""
67
68	with_xios=0
69	opt_makelmdz_xios=""
70
71	rad="rrtm"
72
73	compile_with_fcm=1
74
75	cosp="none"
76	aerosols=0
77	inlandsis=0
78
79	make_j=8
80	clean_install=1
81
82	# Check if on a Mac /!\ Probably doesn't work anymore, to fix one day...
83	if [[ $(uname) = "Darwin" ]]; then
84	export MAKE="make"
85	fi
86
87	optim_debug=""
88	arch="local"
89
90	arch="local-gfortran"
91	arch_dir=""
92
93	jobcmd=""
94	}
95
96	function read_cmdline_args {
97	while (($# > 0)); do
98	case $1 in
99	"-h") cat <<........fin
100	$0 [ -v version ] [ -r svn_release ]
101	[ -parallel PARA ] [ -d GRID_RESOLUTION ] [ -bench 0/1 ]
102	[-name LOCAL_MODEL_NAME] [-rad RADIATIF]
103
104	-v "version" like 20150828.trunk, see http://www.lmd.jussieu.fr/~lmdz/Distrib/LISMOI.trunk (default <$version>)
105
106	-r "svn_release" : either the svn release number or "last" (default <$svn_lmdz>)
107
108	-parallel parallel support: mpi, omp, mpi_omp (mpi with openMP) or none (default: <$parallel>)
109
110	-d "grid resolution": should be among the available benchs if -bench 1 (valid values: 48x36x19, 48x36x39) (default : <$grid_resolution>)
111
112	-bench activating the bench or not (0/1) (default: <$bench>)
113
114	-unstable use unstable tar instead of testing
115
116	-name name of the folder to install to (default <$MODEL>)
117
118	-netcdf 0, 1 or PATH. 0: do not download NetCDF, look for it in standard locations (/usr); 1: download and compile NetCDF; PATH: full path to an existing installed NetCDF library (default: <$netcdf>)
119
120	-xios use (download and compile) the XIOS library (will compile the parallel NetCDF4-HDF5 library) (requires to also have -parallel mpi_omp)
121
122	-cosp to run with cospv1 or cospv2 [none/v1/v2] (default <$cosp>)
123
124	-rad radiative code: oldrad, rrtm or ecrad (default <$rad>)
125
126	-nofcm to compile without fcm
127
128	-SCM install 1D version automatically
129
130	-debug compile everything in debug mode
131
132	-benchphysiq to choose which physics.def package to use in the bench (default <$benchphysiq>)
133
134	-compilephysiq physics to compile the model with (default <$compphysiq>)
135
136	-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 $veget)
137
138	-spla activate interactive aerosols
139
140	-inlandsis activate new snow scheme
141
142	-arch name of the arch to use (default <$arch>)
143
144	-arch_dir where to find the arch files (default <$arch_dir>)
145
146	-make_j number of processes to parallelize installations (default <$make_j>)
147
148	-jobcmd command prepended to fcm compile jobs, e.g. "srun" (default <$jobcmd>)
149
150	-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)
151
152	........fin
153	exit 1;;
154	"-v") version=$2; shift; shift;;
155	"-r") svn_lmdz=$2; shift; shift;;
156	"-d") grid_resolution=$2; shift; shift;;
157	"-unstable") trusting="unstable"; shift;;
158	"-cosp") cosp=$2
159	case $cosp in
160	"none"\|"v1"\|"v2") cosp=$2; shift; shift;;
161	*) echo "Only none v1 v2 for cosp option"; exit 1
162	esac;;
163	"-nofcm") compile_with_fcm=0; echo "This option will be reactivated soon (promesse du 8dec2022)"; exit 1; shift;;
164	"-SCM") SCM=1; shift;;
165	"-rad") rad=$2
166	case $rad in
167	"oldrad"\|"rrtm"\|"ecrad") rad=$2; shift; shift;;
168	*) echo "Only oldrad rrtm ecrad for rad option"; exit 1
169	esac;;
170	"-parallel") parallel=$2
171	case $parallel in
172	"none"\|"mpi"\|"omp"\|"mpi_omp") parallel=$2; shift; shift;;
173	*) echo "Only none mpi omp mpi_omp for the parallel option"; exit 1
174	esac;;
175	"-bench") bench=$2; shift; shift;;
176	"-debug") optim_debug=-debug; shift;;
177	"-name") MODEL=$2; shift; shift;;
178	"-netcdf") netcdf=$2; shift; shift;;
179	"-benchphysiq") benchphysiq=$2; shift; shift;;
180	"-compilephysiq") compphysiq=$2; shift; shift;;
181	"-xios") with_xios=1; shift;;
182	"-arch") arch=$2; shift; shift;;
183	"-arch_dir") arch_dir=$2; shift; shift;;
184	"-veget") veget=$2; shift; shift;;
185	"-spla") aerosols=1; shift;;
186	"-inlandsis") inlandsis=1; shift;;
187	"-make_j") make_j=$2; shift; shift;;
188	"-jobcmd") jobcmd=$2; shift; shift;;
189	"-noclean") clean_install=0; shift;;
190	*) bash install_lmdz.sh -h; exit 1
191	esac
192	done
193
194	# Isotopes : Compile and run with isotopes if lmdz_phys="lmdiso" in main.sh
195	if [[ $compphysiq = "lmdiso" ]]; then isotopes=1; else isotopes=0; fi
196
197	# Option de compilation pour Cosp
198	case $cosp in
199	v1) opt_cosp="-cosp true";;
200	v2) opt_cosp="-cospv2 true";;
201	*) opt_cosp=""
202	esac
203
204	#Define veget-related suffix for gcm name
205	if [[ $veget = 'none' ]]; then
206	suff_orc=''
207	else
208	suff_orc='_orch'
209	fi
210
211
212	if [[ $parallel = "none" ]]; then
213	suff_para='_seq'
214	else
215	suff_para='_para_mem'
216	fi
217
218	if [[ $with_xios = 1 ]]; then opt_makelmdz_xios="-io xios"; fi
219
220	if [[ $aerosols = 1 ]]; then
221	opt_aer="-dust true"; suff_aer="_spla"
222	else
223	opt_aer=""; suff_aer=""
224	fi
225
226	if [[ $inlandsis = 1 ]]; then
227	opt_inlandsis="-inlandsis true"
228	else
229	opt_inlandsis=""
230	fi
231
232	if [[ $isotopes = 1 ]]; then
233	opt_isotopes="-isotopes true"; suff_iso="_iso"
234	else
235	opt_isotopes="" ; suff_iso=""
236	fi
237
238	# set default arch if parallel
239	if [[ $arch = "local-gfortran" && $parallel != "none" ]]; then
240	arch="local-gfortran-parallel"
241	echo "Switching default arch to $arch"
242	fi
243
244	# Name of the model's folder. The convention taken here is that models that requires different compilation sources should have a different names.
245	local xios_name=""
246	if [[ $with_xios = 1 ]]; then xios_name="XIOS"; fi
247	if [[ $MODEL = "" ]]; then MODEL="./LMDZ$version${svn_lmdz}OR$veget$xios_name"; fi
248
249	if [[ $arch_dir = "" ]]; then
250	arch_dir="$MODEL/modipsl/config/IPSLCM7/ARCH/";
251	elif ! readlink -fe "$arch_dir"; then
252	echo "STOP: no arch dir <$arch_dir>"; exit 1
253	fi
254	}
255
256	function ensure_correct_option_combinations {
257	# Check on veget version
258	if [[ $veget != 'none' && $veget != "CMIP6" && $veget != "orch2.0" && $veget != "orch2.2" ]]; then
259	re='^[0-9]+$'
260	if ! [[ $veget =~ $re ]]; then
261	echo 'Valeur de l option veget non valable'; exit 1
262	fi
263	fi
264
265	## if also compiling XIOS, parallel must be mpi_omp
266	if [[ $with_xios = 1 && $parallel != "mpi_omp" ]]; then
267	echo "Error, you must set -parallel mpi_omp if you want XIOS"; exit 1
268	fi
269
270	if [[ $cosp = "v2" && $with_xios = 0 ]]; then
271	echo "Error, Cospv2 cannot run without Xios"; exit 1
272	fi
273
274	# STOP if trying to use both ORCHIDEE and Isotopes :
275	if [[ $isotopes = 1 && $veget != "none" ]]; then
276	echo "STOP: You cannot run LMDZ with ORCHIDEE and ISOtopes at the same time"; exit 1
277	fi
278
279	# STOP if trying to use both SPLA and Isotopes :
280	if [[ $isotopes = 1 && $aerosols = 1 ]]; then
281	echo "STOP: You cannot run LMDZ with Isotopes and aerosols=spla at the same time"; exit 1
282	fi
283
284	# (Temporary) STOP if trying to use Isotopes with XIOS :
285	# TODO Amaury: check if still relevant
286	if [[ $isotopes = 1 && $with_xios = 1 ]]; then
287	echo "STOP: Isotopes cannont yet be run with XIOS"; exit 1
288	fi
289
290	if [[ $aerosols = 1 && $rad != "rrtm" ]]; then
291	echo "STOP: For the time being, <aerosols=spla> requires <rad=rrtm>"; exit 1
292	fi
293	# TODO: vérifier quelles contraintes sont des contraintes lmdzsetup, et lesquelles sont des vraies contraintes
294	}
295
296	function check_available_software {
297	echo "################################################################"
298	echo "Check if required software is available"
299	echo "################################################################"
300	for logiciel in wget tar gzip make gcc cmake m4 c++; do
301	if [[ $(which "$logiciel") = "" ]]; then
302	echo "You must first install $logiciel on your system"; exit 1
303	fi
304	done
305
306	cat <<eod > tt.f90
307	print*,'coucou'
308	end
309	eod
310	$compiler tt.f90 \|\| a.out
311	./a.out >\| tt
312	if [[ $(< tt sed -e 's/ //g' ) != "coucou" ]]; then
313	echo "problem installing with compiler $compiler"; exit 1
314	fi
315	\rm tt a.out tt.f90
316	}
317
318	function download_model {
319	if [[ $clean_install = 1 ]]; then rm -rf "$MODEL"; fi
320
321	mkdir -p "$MODEL"
322	MODEL=$(readlink -e -f "$MODEL"); echo "$MODEL" # absolute path
323	if [[ ! -d "$MODEL/modipsl" ]]; then
324	echo "##########################################################"
325	echo "Download a slightly modified version of LMDZ"
326	echo "##########################################################"
327	cd "$MODEL"
328	getlog="$(pwd)/get.log"
329	echo "logfile : $getlog"
330	myget "src_archives/$trusting/modipsl.$version.tar.gz" &>> get.log
331	echo "install_lmdz.sh wget_OK $(date)"
332	gunzip "modipsl.$version.tar.gz" &>> get.log
333	tar xf "modipsl.$version.tar" &>> get.log
334	\rm "modipsl.$version.tar"
335	cd - &> /dev/null
336	fi
337	}
338
339	function init_arch {
340	set +e; arch_dir=$(readlink -f "$arch_dir"); set -e # full path. readlink must be called after the path is created
341
342	# Check where default fcm, path, env are located - by default in $arch_path, instead in $MODEL/modipsl/modeles/LMDZ/arch/
343	local i fcm_path path_path env_path
344	for i in "path" "fcm" "env"; do
345	local varname=${i}_path
346	if [[ -f $arch_dir/arch-$arch.$i ]]; then
347	declare $varname="$arch_dir/arch-$arch.$i"
348	else
349	declare $varname="$MODEL/modipsl/modeles/LMDZ/arch/arch-$arch.$i"
350	if [[ ! -f ${!varname} ]]; then
351	echo "STOP: no ${!varname}"; exit 1
352	fi
353	fi
354	done
355	default_fcm_path=$fcm_path
356	default_path_path=$path_path
357	default_env_path=$env_path
358
359	# check compiler
360	compiler=$(< "$default_fcm_path" grep "%COMPILER" \| sed -e "s/%COMPILER\s*//")
361
362	# load env
363	# shellcheck disable=SC1090
364	if [[ -f $default_env_path ]]; then source "$default_env_path"; fi
365
366	local mpi_file # can't be done before as it depends on sourcing the env
367	mpi_file=$(readlink -e -f "$(which mpif90)")
368	path_mpi=$(dirname "$mpi_file")
369	root_mpi=$(dirname "$path_mpi")
370	}
371
372	function install_arch {
373	local component=$1
374
375	# Use same .env for all components (for module compatibility)
376	cp -f "$default_env_path" "$MODEL/modipsl/modeles/$component/arch" &> /dev/null \|\| true # allow failure if we're copying the file to itself
377
378	# Use local .path and .fcm is available, otherwise default
379	if [[ ! -f "$MODEL/modipsl/modeles/$component/arch/arch-$arch.path" ]]; then
380	cp -f "$default_path_path" "$MODEL/modipsl/modeles/$component/arch"
381
382	if [[ $component = "ORCHIDEE" ]]; then
383	if [[ $orcbranch = "/tags/ORCHIDEE_2_0/ORCHIDEE" ]]; then # 2.0 and before have a different fcm convention
384	sed -i'' -e "s/-I//" -e "s/-L//" "$MODEL/modipsl/modeles/ORCHIDEE/arch/arch-$arch.path" # /!\ we only replace first occurence on purpose
385	fi
386	fi
387	fi
388	if [[ ! -f "$MODEL/modipsl/modeles/$component/arch/arch-$arch.fcm" ]]; then
389	cp -f "$default_fcm_path" "$MODEL/modipsl/modeles/$component/arch"
390
391	if [[ $component = "XIOS" ]]; then
392	# Adapt for XIOS, which uses different naming conventions
393	sed -i'' -e "s/%COMPILER/%FCOMPILER/" -e "s/%LINK/%LINKER/" -e "s/-fdefault-real-8//" "$MODEL/modipsl/modeles/XIOS/arch/arch-$arch.fcm"
394	fi
395	fi
396	}
397
398	function install_netcdf {
399	echo "Installing Netcdf"
400	local ncdf_compiler="$compiler"
401
402	if [[ $netcdf = 0 ]]; then
403	ncdfdir=$(nf-config --prefix)
404	else
405	cd "$MODEL"
406
407	# Convert non-basic compiler
408	case $compiler in
409	mpif90) ncdf_compiler=$($compiler --version \| head -n 1 \| cut -d " " -f -1)
410	esac
411
412	case $ncdf_compiler in
413	gfortran \| GNU) ncdf_compiler="gfortran"; opt1="-compiler gnu"; opt2="-CC gcc -FC gfortran -CXX g++";;
414	*) echo "unexpected compiler $ncdf_compiler for netcdf"; exit 1
415	esac
416
417	case $with_xios in
418	0) script_install_netcdf="install_netcdf4_hdf5_seq.bash"
419	ncdfdir="netcdf4_hdf5_seq"
420	opt_="$opt1";;
421	1) script_install_netcdf="install_netcdf4_hdf5.bash"
422	ncdfdir="netcdf4_hdf5"
423	opt_="$opt2 -MPI $root_mpi";;
424	*) echo "with_xios=$with_xios, should be 0 or 1"; exit 1
425	esac
426	if [[ $netcdf = 1 ]]; then
427	ncdfdir="$MODEL/$ncdfdir"
428	else
429	mkdir -p "$netcdf"; ncdfdir="$netcdf/$ncdfdir"
430	fi
431
432	echo "Repertoire netcdf $ncdfdir"
433	if [[ ! -d $ncdfdir ]]; then
434	netcdflog=$(pwd)/netcdf.log
435	echo "----------------------------------------------------------"
436	echo "Compiling the Netcdf library"
437	echo "----------------------------------------------------------"
438	echo "log file : $netcdflog"
439	myget script_install/$script_install_netcdf &>> "$netcdflog"
440	chmod u=rwx $script_install_netcdf
441	# shellcheck disable=SC2086
442	./$script_install_netcdf -prefix "$ncdfdir" $opt_ &>> "$netcdflog"
443	fi
444
445	# Add to path
446	export PATH="$ncdfdir/bin:$PATH"
447
448	#----------------------------------------------------------------------------
449	# LF rajout d'une verrue, pour une raison non encore expliquee,
450	# la librairie est parfois rangée dans lib64 et non dans lib
451	# par certains compilateurs
452	if [[ ! -e lib && -d lib64 ]]; then ln -s lib64 lib; fi
453	#----------------------------------------------------------------------------
454
455	echo "install_lmdz.sh netcdf_OK $(date)"
456	fi
457
458	cat >test_netcdf90.f90 <<EOF
459	use netcdf
460	print *, "NetCDF library version: ", nf90_inq_libvers()
461	end
462	EOF
463
464	if $ncdf_compiler -I"$ncdfdir"/include test_netcdf90.f90 -L"$ncdfdir"/lib -lnetcdff -lnetcdf -Wl,-rpath="$ncdfdir"/lib && ./a.out; then
465	\rm test_netcdf90.f90 a.out
466	else
467	cat <<EOF
468	Failed test program using NetCDF-Fortran. You can:
469	- check that you have NetCDF-Fortran installed in your system
470	- or specify an installation directory with option -netcdf of install_lmdz.sh
471	- or download and compile NetCDF-Fortran with option -netcdf 1 of install_lmdz.sh
472	EOF
473	exit 1
474	fi
475
476	# Compile NetCDF95
477	cd "$MODEL/modipsl/modeles/LMD"*
478	echo "Installing NetCDF95"
479	cd "$MODEL"
480	if [[ ! -d "NetCDF95-0.3" ]]; then
481	myget src_archives/netcdf/NetCDF95-0.3.tar.gz
482	tar -xf NetCDF95-0.3.tar.gz
483	rm NetCDF95-0.3.tar.gz
484	cd NetCDF95-0.3
485	mkdir -p build && cd build
486	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"
487	make install
488	fi
489	}
490
491	function install_IOIPSL {
492	install_arch "IOIPSL"
493
494	cd "$MODEL/modipsl/modeles/IOIPSL"
495	ioipsllog="$(pwd)/ioipsl.log"
496	echo "Compiling IOIPSL, the interface library with Netcdf $(date) (log: $ioipsllog)"
497
498	echo "$jobcmd ./makeioipsl_fcm -j $make_j -arch $arch" > compile.sh
499	chmod +x compile.sh
500	echo "Compiling IOIPSL using $(\cat compile.sh)"
501	if ! ./compile.sh &> "$ioipsllog"; then
502	echo "STOP: IOIPSL compile failed, exiting"; exit 1
503	fi
504
505	# Link to modipsl/bin
506	cp -f bin/* ../../bin
507
508	echo "IOIPSL compiled $(date)"
509	}
510
511	function install_XIOS {
512	if [[ $with_xios = 1 ]]; then
513	cd "$MODEL/modipsl/modeles"
514	xioslog="$(pwd)/XIOS/xios.log"
515	echo "##########################################################"
516	echo "Compiling XIOS (log $xioslog) $(date)"
517	echo "##########################################################"
518
519	# Download XIOS
520	local xios_http="http://forge.ipsl.fr/ioserver/svn/XIOS2/branches/xios-2.6"
521	local xios_rev="2568"
522
523	cd "$MODEL/modipsl/modeles"
524	set +e; svn co -r $xios_rev $xios_http XIOS; set -e
525
526	cd XIOS
527
528	install_arch "XIOS"
529
530	echo "$jobcmd ./make_xios --job $make_j --arch $arch" > compile.sh
531	chmod +x compile.sh
532	echo "$(date) Compiling XIOS using $(\cat compile.sh) (log in $xioslog)"
533	if ! ./compile.sh &> "$xioslog"; then
534	echo "STOP: XIOS compilation failed, exiting"; exit 1
535	fi
536
537	echo "Compiled XIOS $(date)"
538	fi
539	}
540
541	function get_orchidee_version { # Set / Check ORCHIDEE version
542	local fetch_rev=""
543	orcbranch=""
544	case $veget in
545	"none") fcm_veget_version="false";;
546	"orch2.0" \| "CMIP6") fcm_veget_version=orchidee2.0; fetch_rev=7906;; # in previous tar we used 6592 but with some modifications to xios_orchidee.f90, which got integrated in 7906
547	"orch2.2") fcm_veget_version=orchidee2.1; orcbranch="/branches/ORCHIDEE_2_2/ORCHIDEE" ;; # the bundled version
548	*) fetch_rev=$veget; fcm_veget_version=orchidee2.1;; # /!\ arbitary rev only works for orch>=2.1
549	# /!\ Note: for orch>=4, we should be using fcm_vegt_version="orchideetrunk". Below copied comment by Adriana in LMDZ_Setup docs:
550	# 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
551	#Si on voudrait activer landice_opt=2 , il faut compiler avec -v orchideetrunk.
552
553	esac
554
555	if [[ -n $fetch_rev ]]; then
556	local curr_rev
557	curr_rev=$(svn info "$MODEL/modipsl/modeles/ORCHIDEE" \| grep Revision: \| cut -d ":" -f 2 \| cut -c 2-)
558	orcbranch=$(svn log -v -q svn://forge.ipsl.fr/orchidee/ -r "$fetch_rev" \| grep ORCHIDEE \| head -1 \| sed -e 's:ORCHIDEE/.*$:ORCHIDEE:' \| awk '{print $2}')
559	if [[ $fetch_rev != "$curr_rev" ]]; then
560	echo "Fetching orch $fetch_rev from the repository (curr: $curr_rev)"
561	echo "branch is $orcbranch"
562	if [[ $fetch_rev -lt 4465 ]]; then echo 'ORCHIDEE version must be >=4465, exiting'; exit 1; fi
563	echo "IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at orchidee-help@listes.ipsl.fr"
564	cd "$MODEL/modipsl/modeles"
565	rm -rf ORCHIDEE
566	svn co -r "$fetch_rev" "svn://forge.ipsl.fr/orchidee/$orcbranch"
567	cd - > /dev/null
568	fi
569	fi
570
571	# Check parallel LMDZ+ORCH
572	if [[ (! $veget = "none") && $parallel = "none" && ($used_lmdz_rev -lt 4894) ]]; then
573	echo "LMDZ revision must be >=4894 for orchidee without parallel support. Upgrade lmdz or use -parallel mpi_omp."; exit 1
574	fi
575	}
576
577	function compile_orchidee {
578	install_arch "ORCHIDEE"
579
580	if [[ $veget != "none" ]]; then
581	cd "$MODEL/modipsl/modeles/ORCHIDEE"
582
583	orchideelog="$(pwd)/orchidee.log"
584	echo "Compiling ORCHIDEE, the continental surface model (log $orchideelog) $(date)"
585
586	local xios_orchid opt_orc
587	if [[ $with_xios = 1 ]]; then
588	xios_orchid="-xios";
589	else
590	xios_orchid="-noxios"
591	fi
592	if [[ $optim_debug = "-debug" ]]; then
593	opt_orc="-debug";
594	else
595	opt_orc="-prod"
596	fi
597
598	if [[ $parallel != "none" && ! -d src_parallel ]]; then
599	echo "STOP: Orchidee version too old for parallel support"; exit 1
600	fi
601	echo "$jobcmd ./makeorchidee_fcm -j $make_j $xios_orchid $opt_orc -parallel $parallel -arch $arch" > compile.sh
602	chmod +x compile.sh
603	echo "Compiling ORCHIDEE using $(\cat compile.sh)"
604	if ! ./compile.sh &> "$orchideelog"; then
605	echo "STOP: ORCHIDEE compilation failed, exiting"; exit 1
606	fi
607	echo "Compiled ORCHIDEE $(date)"
608	fi
609	}
610
611	function get_lmdz_version {
612	LMDZPATH=$(readlink -e -f "$MODEL/modipsl/modeles/LMD"*)
613	cd "$LMDZPATH"
614	lmdzlog="$(pwd)/lmdz.log"
615
616	if [[ -n $svn_lmdz ]]; then
617	local curr_rev
618	curr_rev=$(svn info "$MODEL/modipsl/modeles/LMD"* \| grep Revision: \| cut -d ":" -f 2 \| cut -c 2-)
619	if [[ $svn_lmdz != "$curr_rev" ]]; then
620	local lmdzbranch
621	echo "Fetching LMDZ $svn_lmdz from the repository"
622	lmdzbranch=$(svn log -v -q https://svn.lmd.jussieu.fr/LMDZ -r "$svn_lmdz" \| grep LMDZ \| head -1 \| sed -e 's:trunk/.*$:trunk:' \| awk '{print $2}')
623	cd "$MODEL/modipsl/modeles"
624	rm -rf LMD*
625	svn co -r "$svn_lmdz" "https://svn.lmd.jussieu.fr/LMDZ$lmdzbranch" LMDZ
626	cd - > /dev/null
627	fi
628	used_lmdz_rev=$svn_lmdz
629	else # get svn from info
630	set +e; used_lmdz_rev=$(svn info \| grep "Last Changed Rev" \| cut -c 19-); set -e
631	if [[ -z $used_lmdz_rev ]]; then # svn info failed
632	used_lmdz_rev=$(grep 'Revision: [0-9]' "$MODEL"/Read*.md \| awk ' { print $2 } ' 2>/dev/null)
633	if [[ -z $used_lmdz_rev ]]; then echo "Could not determine lmdz version. This is likely an issue with the .tar itself, please report to LMDZ team."; exit 1; fi
634	fi
635	fi
636	}
637
638	function compile_lmdz {
639	install_arch "LMDZ"
640	cd "$LMDZPATH"
641
642	if [[ $used_lmdz_rev -le 4185 ]]; then
643	exe_name="bin/gcm_${grid_resolution}_phy${compphysiq}_${suff_para}${suff_orc}${suff_aer}${suff_iso}.e"
644	else
645	exe_name="bin/gcm_${grid_resolution}_phy${compphysiq}_${rad}${suff_para}${suff_orc}${suff_aer}${suff_iso}.e"
646	fi
647
648	local opt_rad
649	case $rad in
650	oldrad) iflag_rrtm=0; NSW=2; opt_rad="";;
651	rrtm) iflag_rrtm=1; NSW=6
652	if [[ $used_lmdz_rev -le 4185 ]]; then
653	opt_rad="-rrtm true"
654	else
655	opt_rad="-rad rrtm"
656	fi;;
657	ecrad) iflag_rrtm=2; NSW=6; opt_rad="-rad ecrad";;
658	*) echo "Only oldrad rrtm ecrad for rad option"; exit 1
659	esac
660	if [[ $used_lmdz_rev -le 4185 && $rad = "ecrad" ]]; then
661	echo "ecrad only available for LMDZ rev starting with 4186 "; exit 1
662	fi
663
664	# Compile
665	makelmdz="makelmdz_fcm $optim_debug -arch $arch -j $make_j"
666	local para_compile_opt="-mem -parallel $parallel"; if [[ $parallel = "none" ]]; then para_compile_opt=""; fi
667	echo "$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 gcm" > compile.sh
668	echo "Compiling lmdz using $(\cat compile.sh) (log: $lmdzlog) $(date)"
669	chmod +x ./compile.sh
670	if ! ./compile.sh &> "$lmdzlog"; then
671	echo "STOP: LMDZ compilation failed, exiting"; exit 1
672	fi
673	echo "Finished LMDZ compilation $(date)"
674
675	# Check executable
676	if [[ ! -f $exe_name ]]; then
677	echo "STOP: Compilation failed, can't find the executable"; exit 1
678	else
679	echo "Compilation successfull, the executable is $exe_name $(date)"
680	fi
681	}
682
683	function run_bench {
684	cd "$MODEL/modipsl/modeles/LMDZ"*
685
686	if [[ $bench = "tuto" ]]; then
687	myget "Training/tutorial.tar"; tar xf tutorial.tar; cd TUTORIAL
688	./init.sh
689	elif [[ $bench = 1 ]]; then
690	\rm -rf "BENCH${grid_resolution}"
691	local bench=bench_lmdz_${grid_resolution}
692	myget "3DBenchs/$bench.tar.gz"
693	tar xf "$bench.tar.gz"
694
695	if [[ $cosp = "v1" \|\| $cosp = "v2" ]]; then
696	cd "BENCH${grid_resolution}"
697	# copier les fichiers namelist input et output our COSP
698	cp ../DefLists/cosp*_input_nl.txt .
699	cp ../DefLists/cosp*_output_nl.txt .
700	# Activer la cles ok_cosp pour tourner avec COSP
701	sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp
702	\mv -f tmp config.def
703	cd ..
704	fi
705
706	if [[ -n "$benchphysiq" ]]; then
707	cd "BENCH${grid_resolution}"
708	if [[ -f "physiq.def_${benchphysiq}" ]]; then
709	cp "physiq.def_${benchphysiq}" benchphysiq.def
710	echo "using physiq.def_${benchphysiq}"
711	else
712	echo "using standard physiq.def"
713	fi
714	cd ..
715	else
716	echo "using standard physiq.def"
717	fi
718
719	if [[ $with_xios = 1 ]]; then
720	cd "BENCH${grid_resolution}"
721	cp ../DefLists/iodef.xml .
722	cp ../DefLists/context_lmdz.xml .
723	cp ../DefLists/field_def_lmdz.xml .
724	# A raffiner par la suite
725	echo "A FAIRE : Copier les *xml en fonction de l option cosp"
726	cp ../DefLists/field_def_cosp*.xml .
727	cp ../DefLists/file_def_hist*xml .
728	# adapt iodef.xml to use attached mode
729	sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' \
730	iodef.xml > tmp
731	\mv -f tmp iodef.xml
732
733	# and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
734	# except for histday
735	for histfile in file_def_hist*xml; do
736	if [[ "$histfile" = "file_def_histday_lmdz.xml" ]]; then
737	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' \
738	"$histfile" > tmp
739	\mv -f tmp "$histfile"
740	sed -e 's@output_level="_AUTO_"@output_level="5"@' "$histfile" \
741	> tmp
742	\mv -f tmp "$histfile"
743	sed -e 's@compression_level="2"@compression_level="0"@' \
744	"$histfile" > tmp
745	\mv -f tmp "$histfile"
746	else
747	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
748	"$histfile" > tmp
749	\mv -f tmp "$histfile"
750	fi
751	done
752	# and add option "ok_all_xml=y" in config.def
753	echo "### XIOS outputs" >> config.def
754	echo 'ok_all_xml=.true.' >> config.def
755
756	#activer les sorties pour Cosp
757	if [[ "$cosp" = "v1" ]]; then
758	sed -i'' -e 's@enabled=".FALSE."@enabled=".TRUE."@' \
759	-e 's@output_level="_AUTO_"@output_level="5"@' \
760	-e 's@compression_level="2"@compression_level="0"@' \
761	file_def_histdayCOSP_lmdz.xml
762	fi
763	if [[ "$cosp" = "v2" ]]; then
764	sed -i'' -e 's@compression_level="2"@compression_level="0"@' file_def_histdayCOSPv2_lmdz.xml
765	for type_ in hf day mth; do
766	file=file_def_hist${type_}COSP
767	sed -i'' -e 's@src="./'${file}'_lmdz.xml"@src="./'${file}'v2_lmdz.xml"@' context_lmdz.xml
768	done
769	sed -i'' -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' field_def_lmdz.xml
770	fi
771
772	cd ..
773	fi
774
775	# Cas Bench avec ecrad
776	if [[ $rad = "ecrad" ]]; then
777	cd "BENCH${grid_resolution}"
778	cp ../DefLists/namelist_ecrad .
779	cp -r ../libf/phylmd/ecrad/data .
780	cd ..
781	fi
782
783	# Adjusting bench physiq.def to radiative code chosen
784	cd "BENCH${grid_resolution}"
785	sed -e 's/iflag_rrtm=.*.$/iflag_rrtm='$iflag_rrtm'/' \
786	-e 's/NSW=.*.$/NSW='$NSW'/' physiq.def > tmpdef
787	\mv tmpdef physiq.def
788	cd ..
789
790	cp "$exe_name" "BENCH${grid_resolution}/gcm.e"
791	cd "BENCH${grid_resolution}"
792
793	local bench_cmd="./bench.sh"
794	if [[ ${parallel:0:3} = "mpi" ]]; then
795	# Lancement avec deux procs mpi et 2 openMP
796	echo "export OMP_STACKSIZE=800M" > bench.sh
797	if [[ "${parallel:4:3}" = "omp" ]]; then
798	echo "export OMP_NUM_THREADS=2" >> bench.sh
799	fi
800	if [[ $cosp = "v1" \|\| $cosp = "v2" ]]; then
801	echo "ulimit -s 200000" >> bench.sh
802	else
803	echo "ulimit -s unlimited" >> bench.sh
804	fi
805	if which mpirun &> /dev/null; then
806	echo "mpirun -np 2 gcm.e &> listing" >> bench.sh
807	elif grep -q "Adastra" /etc/motd; then
808	local account
809	account=$(/usr/sbin/my_project.py -l 2>&1 \| head -1 \| cut -d " " -f 3- \| cut -c 5-)
810	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"
811	echo "./gcm.e &> listing" >> bench.sh
812	else
813	echo "Error: No command found to run parallel bench"; exit 1
814	fi
815	if [[ $(hostname \| cut -c -6) = "spirit" ]]; then # ulimit unlimited segfaults on Spirit
816	sed -i'' "s/ulimit -s unlimited/ulimit -Ss 8000/" bench.sh
817	fi
818	# Add rebuild, using reb.sh if it is there
819	cat <<EOF >> bench.sh
820	if [[ -f reb.sh ]]; then
821	./reb.sh histday; ./reb.sh histmth; ./reb.sh histhf;
822	./reb.sh histins; ./reb.sh stomate_history;
823	./reb.sh sechiba_history; ./reb.sh sechiba_out_2
824	fi
825	EOF
826	else
827	echo "./gcm.e &> listing" > bench.sh
828	fi
829	# Getting orchidee stuff
830	if [[ $veget = 'CMIP6' \|\| $veget = "orch2.0" ]]; then # TODO once we have a 2.2 bench, add it here (or in planned separate bench script)
831	echo 'myget 3DBenchs/BENCHCMIP6.tar.gz'
832	myget 3DBenchs/BENCHCMIP6.tar.gz
833	tar xvzf BENCHCMIP6.tar.gz
834	sed -e "s:VEGET=n:VEGET=y:" config.def > tmp
835	mv -f tmp config.def
836	if [[ $with_xios = 1 ]]; then
837	cp ../../ORCHIDEE/src_xml/context_orchidee.xml .
838	echo '<context id="orchidee" src="./context_orchidee.xml"/>' > add.tmp
839	cp ../../ORCHIDEE/src_xml/field_def_orchidee.xml .
840	cp ../../ORCHIDEE/src_xml/file_def_orchidee.xml .
841	cp ../../ORCHIDEE/src_xml/file_def_input_orchidee.xml .
842	if [[ -f ../../ORCHIDEE/src_xml/context_input_orchidee.xml ]]; then
843	cp ../../ORCHIDEE/src_xml/context_input_orchidee.xml .
844	echo '<context id="orchidee" src="./context_input_orchidee.xml"/>' >> add.tmp
845	fi
846	sed -e '/id="LMDZ"/r add.tmp' iodef.xml > tmp
847	mv tmp iodef.xml
848	sed -e'{/sechiba1/ s/enabled="_AUTO_"/type="one_file" enabled=".TRUE."/}' \
849	file_def_orchidee.xml > tmp
850	\mv -f tmp file_def_orchidee.xml
851	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
852	file_def_orchidee.xml > tmp
853	\mv -f tmp file_def_orchidee.xml
854	sed -e 's@output_level="_AUTO_"@output_level="1"@' \
855	file_def_orchidee.xml > tmp
856	\mv -f tmp file_def_orchidee.xml
857	sed -e 's@output_freq="_AUTO_"@output_freq="1d"@' \
858	file_def_orchidee.xml > tmp
859	\mv -f tmp file_def_orchidee.xml
860	sed -e 's@compression_level="4"@compression_level="0"@' \
861	file_def_orchidee.xml > tmp
862	\mv -f tmp file_def_orchidee.xml
863	sed -e 's@XIOS_ORCHIDEE_OK = n@XIOS_ORCHIDEE_OK = y@' \
864	orchidee.def > tmp
865	\mv -f tmp orchidee.def
866	fi
867	fi
868
869	if [[ -f ../arch.env ]]; then source ../arch.env; fi
870
871	echo "EXECUTION DU BENCH"
872	date
873	if (! $bench_cmd &> out.bench) \|\| ! (tail -n 1 listing \| grep "Everything is cool"); then
874	tail listing
875	echo "Bench FAILED, exiting"; exit 1
876	fi
877	date
878	tail listing
879	fi
880
881	# 1D case
882	if [[ $SCM = 1 ]]; then
883	cd "$MODEL"
884	myget 1D/1D.tar.gz
885	tar xf 1D.tar.gz
886	cd 1D
887	for e in "fcm" "env" "path"; do
888	cp "$MODEL/modipsl/modeles/LMDZ/arch/arch-$arch.$e" "$MODEL/modipsl/modeles/LMDZ/arch/arch-local.$e"
889	done
890	if [[ $rad = "oldrad" ]]; then
891	sed -i'' -e 's/^rad=.*$/rad=oldrad/' run.sh
892	sed -i'' -e 's/^rad=.*$/rad=oldrad/' bin/compile
893	elif [[ $rad = ecrad ]] ; then
894	sed -i'' -e 's/^rad=.*$/rad=ecrad/' run.sh
895	sed -i'' -e 's/^rad=.*$/rad=ecrad/' bin/compile
896	fi
897	echo "Running 1D/run.sh, log in $(pwd)/run1d.log"
898	./run.sh &> "$(pwd)/run1d.log"
899	fi
900	}
901
902	# If sourced: returns, else run setup
903	if [[ ! "${BASH_SOURCE[0]}" = "$0" ]]; then return 0; fi
904
905	echo "install_lmdz.sh DEBUT $(date)"
906
907	set_default_params
908	read_cmdline_args "$@"
909	ensure_correct_option_combinations
910	download_model
911	init_arch
912	check_available_software
913	get_lmdz_version
914	get_orchidee_version
915	install_netcdf
916	install_IOIPSL
917	install_XIOS
918	compile_orchidee
919	compile_lmdz
920	run_bench

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