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source: BOL/script_install_amaury/install_lmdz.sh @ 5047

Last change on this file since 5047 was 5044, checked in by abarral, 3 months ago
move mpi detection after env sourcing
Property svn:executable set to ``*
File size: 34.8 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
239	# Name of the model's folder. The convention taken here is that models that requires different compilation sources should have a different names.
240	local xios_name=""
241	if [[ $with_xios = 1 ]]; then xios_name="XIOS"; fi
242	if [[ $MODEL = "" ]]; then MODEL="./LMDZ$version${svn_lmdz}OR$veget$xios_name"; fi
243
244	if [[ $arch_dir = "" ]]; then
245	arch_dir="$MODEL/modipsl/config/IPSLCM7/ARCH/";
246	elif ! readlink -fe "$arch_dir"; then
247	echo "STOP: no arch dir <$arch_dir>"; exit 1
248	fi
249	}
250
251	function ensure_correct_option_combinations {
252	# Check on veget version
253	if [[ $veget != 'none' && $veget != "CMIP6" && $veget != "orch2.0" && $veget != "orch2.2" ]]; then
254	re='^[0-9]+$'
255	if ! [[ $veget =~ $re ]]; then
256	echo 'Valeur de l option veget non valable'; exit 1
257	fi
258	fi
259
260	## if also compiling XIOS, parallel must be mpi_omp
261	if [[ $with_xios = 1 && $parallel != "mpi_omp" ]]; then
262	echo "Error, you must set -parallel mpi_omp if you want XIOS"; exit 1
263	fi
264
265	if [[ $cosp = "v2" && $with_xios = 0 ]]; then
266	echo "Error, Cospv2 cannot run without Xios"; exit 1
267	fi
268
269	# STOP if trying to use both ORCHIDEE and Isotopes :
270	if [[ $isotopes = 1 && $veget != "none" ]]; then
271	echo "STOP: You cannot run LMDZ with ORCHIDEE and ISOtopes at the same time"; exit 1
272	fi
273
274	# STOP if trying to use both SPLA and Isotopes :
275	if [[ $isotopes = 1 && $aerosols = 1 ]]; then
276	echo "STOP: You cannot run LMDZ with Isotopes and aerosols=spla at the same time"; exit 1
277	fi
278
279	# (Temporary) STOP if trying to use Isotopes with XIOS :
280	# TODO Amaury: check if still relevant
281	if [[ $isotopes = 1 && $with_xios = 1 ]]; then
282	echo "STOP: Isotopes cannont yet be run with XIOS"; exit 1
283	fi
284
285	if [[ $aerosols = 1 && $rad != "rrtm" ]]; then
286	echo "STOP: For the time being, <aerosols=spla> requires <rad=rrtm>"; exit 1
287	fi
288	# TODO: vérifier quelles contraintes sont des contraintes lmdzsetup, et lesquelles sont des vraies contraintes
289	}
290
291	function check_available_software {
292	echo "################################################################"
293	echo "Check if required software is available"
294	echo "################################################################"
295	for logiciel in wget tar gzip make gcc cmake m4 c++; do
296	if [[ $(which "$logiciel") = "" ]]; then
297	echo "You must first install $logiciel on your system"; exit 1
298	fi
299	done
300
301	cat <<eod > tt.f90
302	print*,'coucou'
303	end
304	eod
305	$compiler tt.f90 \|\| a.out
306	./a.out >\| tt
307	if [[ $(< tt sed -e 's/ //g' ) != "coucou" ]]; then
308	echo "problem installing with compiler $compiler"; exit 1
309	fi
310	\rm tt a.out tt.f90
311	}
312
313	function download_model {
314	if [[ $clean_install = 1 ]]; then rm -rf "$MODEL"; fi
315
316	mkdir -p "$MODEL"
317	MODEL=$(readlink -e -f "$MODEL"); echo "$MODEL" # absolute path
318	if [[ ! -d "$MODEL/modipsl" ]]; then
319	echo "##########################################################"
320	echo "Download a slightly modified version of LMDZ"
321	echo "##########################################################"
322	cd "$MODEL"
323	getlog="$(pwd)/get.log"
324	echo "logfile : $getlog"
325	myget "src_archives/$trusting/modipsl.$version.tar.gz" &>> get.log
326	echo "install_lmdz.sh wget_OK $(date)"
327	gunzip "modipsl.$version.tar.gz" &>> get.log
328	tar xf "modipsl.$version.tar" &>> get.log
329	\rm "modipsl.$version.tar"
330	cd - &> /dev/null
331	fi
332	}
333
334	function init_arch {
335	set +e; arch_dir=$(readlink -f "$arch_dir"); set -e # full path. readlink must be called after the path is created
336
337	# Check where default fcm, path, env are located - by default in $arch_path, instead in $MODEL/modipsl/modeles/LMDZ/arch/
338	local i fcm_path path_path env_path
339	for i in "path" "fcm" "env"; do
340	local varname=${i}_path
341	if [[ -f $arch_dir/arch-$arch.$i ]]; then
342	declare $varname="$arch_dir/arch-$arch.$i"
343	else
344	declare $varname="$MODEL/modipsl/modeles/LMDZ/arch/arch-$arch.$i"
345	if [[ ! -f ${!varname} ]]; then
346	echo "STOP: no ${!varname}"; exit 1
347	fi
348	fi
349	done
350	default_fcm_path=$fcm_path
351	default_path_path=$path_path
352	default_env_path=$env_path
353
354	# check compiler
355	compiler=$(< "$default_fcm_path" grep "%COMPILER" \| sed -e "s/%COMPILER\s*//")
356
357	# load env
358	# shellcheck disable=SC1090
359	if [[ -f $default_env_path ]]; then source "$default_env_path"; fi
360
361	local mpi_file # can't be done before as it depends on sourcing the env
362	mpi_file=$(readlink -e -f "$(which mpif90)")
363	path_mpi=$(dirname "$mpi_file")
364	root_mpi=$(dirname "$path_mpi")
365	}
366
367	function install_arch {
368	local component=$1
369
370	# Use same .env for all components (for module compatibility)
371	cp -f "$default_env_path" "$MODEL/modipsl/modeles/$component/arch" &> /dev/null \|\| true # allow failure if we're copying the file to itself
372
373	# Use local .path and .fcm is available, otherwise default
374	if [[ ! -f "$MODEL/modipsl/modeles/$component/arch/arch-$arch.path" ]]; then
375	cp -f "$default_path_path" "$MODEL/modipsl/modeles/$component/arch"
376
377	if [[ $component = "ORCHIDEE" ]]; then
378	if [[ $orcbranch = "/tags/ORCHIDEE_2_0/ORCHIDEE" ]]; then # 2.0 and before have a different fcm convention
379	sed -i'' -e "s/-I//" -e "s/-L//" "$MODEL/modipsl/modeles/ORCHIDEE/arch/arch-$arch.path" # /!\ we only replace first occurence on purpose
380	fi
381	fi
382	fi
383	if [[ ! -f "$MODEL/modipsl/modeles/$component/arch/arch-$arch.fcm" ]]; then
384	cp -f "$default_fcm_path" "$MODEL/modipsl/modeles/$component/arch"
385
386	if [[ $component = "XIOS" ]]; then
387	# Adapt for XIOS, which uses different naming conventions
388	sed -i'' -e "s/%COMPILER/%FCOMPILER/" -e "s/%LINK/%LINKER/" -e "s/-fdefault-real-8//" "$MODEL/modipsl/modeles/XIOS/arch/arch-$arch.fcm"
389	fi
390	fi
391	}
392
393	function install_netcdf {
394	echo "Installing Netcdf"
395	local ncdf_compiler="$compiler"
396
397	if [[ $netcdf = 0 ]]; then
398	ncdfdir=$(nf-config --prefix)
399	else
400	cd "$MODEL"
401
402	# Convert non-basic compiler
403	case $compiler in
404	mpif90) ncdf_compiler=$($compiler --version \| head -n 1 \| cut -d " " -f -1)
405	esac
406
407	case $ncdf_compiler in
408	gfortran \| GNU) ncdf_compiler="gfortran"; opt1="-compiler gnu"; opt2="-CC gcc -FC gfortran -CXX g++";;
409	*) echo "unexpected compiler $ncdf_compiler for netcdf"; exit 1
410	esac
411
412	case $with_xios in
413	0) script_install_netcdf="install_netcdf4_hdf5_seq.bash"
414	ncdfdir="netcdf4_hdf5_seq"
415	opt_="$opt1";;
416	1) script_install_netcdf="install_netcdf4_hdf5.bash"
417	ncdfdir="netcdf4_hdf5"
418	opt_="$opt2 -MPI $root_mpi";;
419	*) echo "with_xios=$with_xios, should be 0 or 1"; exit 1
420	esac
421	if [[ $netcdf = 1 ]]; then
422	ncdfdir="$MODEL/$ncdfdir"
423	else
424	mkdir -p "$netcdf"; ncdfdir="$netcdf/$ncdfdir"
425	fi
426
427	echo "Repertoire netcdf $ncdfdir"
428	if [[ ! -d $ncdfdir ]]; then
429	netcdflog=$(pwd)/netcdf.log
430	echo "----------------------------------------------------------"
431	echo "Compiling the Netcdf library"
432	echo "----------------------------------------------------------"
433	echo "log file : $netcdflog"
434	myget script_install/$script_install_netcdf &>> "$netcdflog"
435	chmod u=rwx $script_install_netcdf
436	# shellcheck disable=SC2086
437	./$script_install_netcdf -prefix "$ncdfdir" $opt_ &>> "$netcdflog"
438	fi
439
440	# Add to path
441	export PATH="$ncdfdir/bin:$PATH"
442
443	#----------------------------------------------------------------------------
444	# LF rajout d'une verrue, pour une raison non encore expliquee,
445	# la librairie est parfois rangée dans lib64 et non dans lib
446	# par certains compilateurs
447	if [[ ! -e lib && -d lib64 ]]; then ln -s lib64 lib; fi
448	#----------------------------------------------------------------------------
449
450	echo "install_lmdz.sh netcdf_OK $(date)"
451	fi
452
453	cat >test_netcdf90.f90 <<EOF
454	use netcdf
455	print *, "NetCDF library version: ", nf90_inq_libvers()
456	end
457	EOF
458
459	if $ncdf_compiler -I"$ncdfdir"/include test_netcdf90.f90 -L"$ncdfdir"/lib -lnetcdff -lnetcdf -Wl,-rpath="$ncdfdir"/lib && ./a.out; then
460	\rm test_netcdf90.f90 a.out
461	else
462	cat <<EOF
463	Failed test program using NetCDF-Fortran. You can:
464	- check that you have NetCDF-Fortran installed in your system
465	- or specify an installation directory with option -netcdf of install_lmdz.sh
466	- or download and compile NetCDF-Fortran with option -netcdf 1 of install_lmdz.sh
467	EOF
468	exit 1
469	fi
470
471	# Compile NetCDF95
472	cd "$MODEL/modipsl/modeles/LMD"*
473	echo "Installing NetCDF95"
474	cd "$MODEL"
475	if [[ ! -d "NetCDF95-0.3" ]]; then
476	myget src_archives/netcdf/NetCDF95-0.3.tar.gz
477	tar -xf NetCDF95-0.3.tar.gz
478	rm NetCDF95-0.3.tar.gz
479	cd NetCDF95-0.3
480	mkdir -p build && cd build
481	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"
482	make install
483	fi
484	}
485
486	function install_IOIPSL {
487	install_arch "IOIPSL"
488
489	cd "$MODEL/modipsl/modeles/IOIPSL"
490	ioipsllog="$(pwd)/ioipsl.log"
491	echo "Compiling IOIPSL, the interface library with Netcdf $(date) (log: $ioipsllog)"
492
493	echo "$jobcmd ./makeioipsl_fcm -j $make_j -arch $arch" > compile.sh
494	chmod +x compile.sh
495	echo "Compiling IOIPSL using $(\cat compile.sh)"
496	if ! ./compile.sh &> "$ioipsllog"; then
497	echo "STOP: IOIPSL compile failed, exiting"; exit 1
498	fi
499
500	# Link to modipsl/bin
501	cp -f bin/* ../../bin
502
503	echo "IOIPSL compiled $(date)"
504	}
505
506	function install_XIOS {
507	if [[ $with_xios = 1 ]]; then
508	cd "$MODEL/modipsl/modeles"
509	xioslog="$(pwd)/XIOS/xios.log"
510	echo "##########################################################"
511	echo "Compiling XIOS (log $xioslog) $(date)"
512	echo "##########################################################"
513
514	# Download XIOS
515	local xios_http="http://forge.ipsl.fr/ioserver/svn/XIOS2/branches/xios-2.6"
516	local xios_rev="2568"
517
518	cd "$MODEL/modipsl/modeles"
519	set +e; svn co -r $xios_rev $xios_http XIOS; set -e
520
521	cd XIOS
522
523	install_arch "XIOS"
524
525	echo "$jobcmd ./make_xios --job $make_j --arch $arch" > compile.sh
526	chmod +x compile.sh
527	echo "$(date) Compiling XIOS using $(\cat compile.sh) (log in $xioslog)"
528	if ! ./compile.sh &> "$xioslog"; then
529	echo "STOP: XIOS compilation failed, exiting"; exit 1
530	fi
531
532	echo "Compiled XIOS $(date)"
533	fi
534	}
535
536	function get_orchidee_version { # Set / Check ORCHIDEE version
537	local fetch_rev=""
538	orcbranch=""
539	case $veget in
540	"none") fcm_veget_version="false";;
541	"orch2.0" \| "CMIP6") fcm_veget_version=orchidee2.0; fetch_rev=7906;; # in previous tar we used 6592 but with some modifications to xios_orchidee.f90, which got integrated in 7906
542	"orch2.2") fcm_veget_version=orchidee2.1; orcbranch="/branches/ORCHIDEE_2_2/ORCHIDEE" ;; # the bundled version
543	*) fetch_rev=$veget; fcm_veget_version=orchidee2.1;; # /!\ arbitary rev only works for orch>=2.1
544	# /!\ Note: for orch>=4, we should be using fcm_vegt_version="orchideetrunk". Below copied comment by Adriana in LMDZ_Setup docs:
545	# 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
546	#Si on voudrait activer landice_opt=2 , il faut compiler avec -v orchideetrunk.
547
548	esac
549
550	if [[ -n $fetch_rev ]]; then
551	local curr_rev
552	curr_rev=$(svn info "$MODEL/modipsl/modeles/ORCHIDEE" \| grep Revision: \| cut -d ":" -f 2 \| cut -c 2-)
553	orcbranch=$(svn log -v -q svn://forge.ipsl.fr/orchidee/ -r "$fetch_rev" \| grep ORCHIDEE \| head -1 \| sed -e 's:ORCHIDEE/.*$:ORCHIDEE:' \| awk '{print $2}')
554	if [[ $fetch_rev != "$curr_rev" ]]; then
555	echo "Fetching orch $fetch_rev from the repository (curr: $curr_rev)"
556	echo "branch is $orcbranch"
557	if [[ $fetch_rev -lt 4465 ]]; then echo 'ORCHIDEE version must be >=4465, exiting'; exit 1; fi
558	echo "IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at orchidee-help@listes.ipsl.fr"
559	cd "$MODEL/modipsl/modeles"
560	rm -rf ORCHIDEE
561	svn co -r "$fetch_rev" "svn://forge.ipsl.fr/orchidee/$orcbranch"
562	cd - > /dev/null
563	fi
564	fi
565
566	# Check parallel LMDZ+ORCH
567	if [[ (! $veget = "none") && $parallel = "none" && ($used_lmdz_rev -lt 4894) ]]; then
568	echo "LMDZ revision must be >=4894 for orchidee without parallel support. Upgrade lmdz or use -parallel mpi_omp."; exit 1
569	fi
570	}
571
572	function compile_orchidee {
573	install_arch "ORCHIDEE"
574
575	if [[ $veget != "none" ]]; then
576	cd "$MODEL/modipsl/modeles/ORCHIDEE"
577
578	orchideelog="$(pwd)/orchidee.log"
579	echo "Compiling ORCHIDEE, the continental surface model (log $orchideelog) $(date)"
580
581	local xios_orchid opt_orc
582	if [[ $with_xios = 1 ]]; then
583	xios_orchid="-xios";
584	else
585	xios_orchid="-noxios"
586	fi
587	if [[ $optim_debug = "-debug" ]]; then
588	opt_orc="-debug";
589	else
590	opt_orc="-prod"
591	fi
592
593	if [[ $parallel != "none" && ! -d src_parallel ]]; then
594	echo "STOP: Orchidee version too old for parallel support"; exit 1
595	fi
596	echo "$jobcmd ./makeorchidee_fcm -j $make_j $xios_orchid $opt_orc -parallel $parallel -arch $arch" > compile.sh
597	chmod +x compile.sh
598	echo "Compiling ORCHIDEE using $(\cat compile.sh)"
599	if ! ./compile.sh &> "$orchideelog"; then
600	echo "STOP: ORCHIDEE compilation failed, exiting"; exit 1
601	fi
602	echo "Compiled ORCHIDEE $(date)"
603	fi
604	}
605
606	function get_lmdz_version {
607	LMDZPATH=$(readlink -e -f "$MODEL/modipsl/modeles/LMD"*)
608	cd "$LMDZPATH"
609	lmdzlog="$(pwd)/lmdz.log"
610
611	if [[ -n $svn_lmdz ]]; then
612	local curr_rev
613	curr_rev=$(svn info "$MODEL/modipsl/modeles/LMD"* \| grep Revision: \| cut -d ":" -f 2 \| cut -c 2-)
614	if [[ $svn_lmdz != "$curr_rev" ]]; then
615	local lmdzbranch
616	echo "Fetching LMDZ $svn_lmdz from the repository"
617	lmdzbranch=$(svn log -v -q https://svn.lmd.jussieu.fr/LMDZ -r "$svn_lmdz" \| grep LMDZ \| head -1 \| sed -e 's:trunk/.*$:trunk:' \| awk '{print $2}')
618	cd "$MODEL/modipsl/modeles"
619	rm -rf LMD*
620	svn co -r "$svn_lmdz" "https://svn.lmd.jussieu.fr/LMDZ$lmdzbranch" LMDZ
621	cd - > /dev/null
622	fi
623	used_lmdz_rev=$svn_lmdz
624	else # get svn from info
625	set +e; used_lmdz_rev=$(svn info \| grep "Last Changed Rev" \| cut -c 19-); set -e
626	if [[ -z $used_lmdz_rev ]]; then # svn info failed
627	used_lmdz_rev=$(grep 'Revision: [0-9]' "$MODEL"/Read*.md \| awk ' { print $2 } ' 2>/dev/null)
628	if [[ -z $used_lmdz_rev ]]; then echo "Could not determine lmdz version. This is likely an issue with the .tar itself, please report to LMDZ team."; exit 1; fi
629	fi
630	fi
631	}
632
633	function compile_lmdz {
634	install_arch "LMDZ"
635	cd "$LMDZPATH"
636
637	if [[ $used_lmdz_rev -le 4185 ]]; then
638	exe_name="bin/gcm_${grid_resolution}_phy${compphysiq}_${suff_para}${suff_orc}${suff_aer}${suff_iso}.e"
639	else
640	exe_name="bin/gcm_${grid_resolution}_phy${compphysiq}_${rad}${suff_para}${suff_orc}${suff_aer}${suff_iso}.e"
641	fi
642
643	local opt_rad
644	case $rad in
645	oldrad) iflag_rrtm=0; NSW=2; opt_rad="";;
646	rrtm) iflag_rrtm=1; NSW=6
647	if [[ $used_lmdz_rev -le 4185 ]]; then
648	opt_rad="-rrtm true"
649	else
650	opt_rad="-rad rrtm"
651	fi;;
652	ecrad) iflag_rrtm=2; NSW=6; opt_rad="-rad ecrad";;
653	*) echo "Only oldrad rrtm ecrad for rad option"; exit 1
654	esac
655	if [[ $used_lmdz_rev -le 4185 && $rad = "ecrad" ]]; then
656	echo "ecrad only available for LMDZ rev starting with 4186 "; exit 1
657	fi
658
659	# Compile
660	makelmdz="makelmdz_fcm $optim_debug -arch $arch -j $make_j"
661	local para_compile_opt="-mem -parallel $parallel"; if [[ $parallel = "none" ]]; then para_compile_opt=""; fi
662	echo "$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
663	echo "Compiling lmdz using $(\cat compile.sh) (log: $lmdzlog) $(date)"
664	chmod +x ./compile.sh
665	if ! ./compile.sh &> "$lmdzlog"; then
666	echo "STOP: LMDZ compilation failed, exiting"; exit 1
667	fi
668	echo "Finished LMDZ compilation $(date)"
669
670	# Check executable
671	if [[ ! -f $exe_name ]]; then
672	echo "STOP: Compilation failed, can't find the executable"; exit 1
673	else
674	echo "Compilation successfull, the executable is $exe_name $(date)"
675	fi
676	}
677
678	function run_bench {
679	cd "$MODEL/modipsl/modeles/LMDZ"*
680
681	if [[ $bench = "tuto" ]]; then
682	myget "Training/tutorial.tar"; tar xf tutorial.tar; cd TUTORIAL
683	./init.sh
684	elif [[ $bench = 1 ]]; then
685	\rm -rf "BENCH${grid_resolution}"
686	local bench=bench_lmdz_${grid_resolution}
687	myget "3DBenchs/$bench.tar.gz"
688	tar xf "$bench.tar.gz"
689
690	if [[ $cosp = "v1" \|\| $cosp = "v2" ]]; then
691	cd "BENCH${grid_resolution}"
692	# copier les fichiers namelist input et output our COSP
693	cp ../DefLists/cosp*_input_nl.txt .
694	cp ../DefLists/cosp*_output_nl.txt .
695	# Activer la cles ok_cosp pour tourner avec COSP
696	sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp
697	\mv -f tmp config.def
698	cd ..
699	fi
700
701	if [[ -n "$benchphysiq" ]]; then
702	cd "BENCH${grid_resolution}"
703	if [[ -f "physiq.def_${benchphysiq}" ]]; then
704	cp "physiq.def_${benchphysiq}" benchphysiq.def
705	echo "using physiq.def_${benchphysiq}"
706	else
707	echo "using standard physiq.def"
708	fi
709	cd ..
710	else
711	echo "using standard physiq.def"
712	fi
713
714	if [[ $with_xios = 1 ]]; then
715	cd "BENCH${grid_resolution}"
716	cp ../DefLists/iodef.xml .
717	cp ../DefLists/context_lmdz.xml .
718	cp ../DefLists/field_def_lmdz.xml .
719	# A raffiner par la suite
720	echo "A FAIRE : Copier les *xml en fonction de l option cosp"
721	cp ../DefLists/field_def_cosp*.xml .
722	cp ../DefLists/file_def_hist*xml .
723	# adapt iodef.xml to use attached mode
724	sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' \
725	iodef.xml > tmp
726	\mv -f tmp iodef.xml
727
728	# and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
729	# except for histday
730	for histfile in file_def_hist*xml; do
731	if [[ "$histfile" = "file_def_histday_lmdz.xml" ]]; then
732	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' \
733	"$histfile" > tmp
734	\mv -f tmp "$histfile"
735	sed -e 's@output_level="_AUTO_"@output_level="5"@' "$histfile" \
736	> tmp
737	\mv -f tmp "$histfile"
738	sed -e 's@compression_level="2"@compression_level="0"@' \
739	"$histfile" > tmp
740	\mv -f tmp "$histfile"
741	else
742	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
743	"$histfile" > tmp
744	\mv -f tmp "$histfile"
745	fi
746	done
747	# and add option "ok_all_xml=y" in config.def
748	echo "### XIOS outputs" >> config.def
749	echo 'ok_all_xml=.true.' >> config.def
750
751	#activer les sorties pour Cosp
752	if [[ "$cosp" = "v1" ]]; then
753	sed -i'' -e 's@enabled=".FALSE."@enabled=".TRUE."@' \
754	-e 's@output_level="_AUTO_"@output_level="5"@' \
755	-e 's@compression_level="2"@compression_level="0"@' \
756	file_def_histdayCOSP_lmdz.xml
757	fi
758	if [[ "$cosp" = "v2" ]]; then
759	sed -i'' -e 's@compression_level="2"@compression_level="0"@' file_def_histdayCOSPv2_lmdz.xml
760	for type_ in hf day mth; do
761	file=file_def_hist${type_}COSP
762	sed -i'' -e 's@src="./'${file}'_lmdz.xml"@src="./'${file}'v2_lmdz.xml"@' context_lmdz.xml
763	done
764	sed -i'' -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' field_def_lmdz.xml
765	fi
766
767	cd ..
768	fi
769
770	# Cas Bench avec ecrad
771	if [[ $rad = "ecrad" ]]; then
772	cd "BENCH${grid_resolution}"
773	cp ../DefLists/namelist_ecrad .
774	cp -r ../libf/phylmd/ecrad/data .
775	cd ..
776	fi
777
778	# Adjusting bench physiq.def to radiative code chosen
779	cd "BENCH${grid_resolution}"
780	sed -e 's/iflag_rrtm=.*.$/iflag_rrtm='$iflag_rrtm'/' \
781	-e 's/NSW=.*.$/NSW='$NSW'/' physiq.def > tmpdef
782	\mv tmpdef physiq.def
783	cd ..
784
785	cp "$exe_name" "BENCH${grid_resolution}/gcm.e"
786	cd "BENCH${grid_resolution}"
787
788	local bench_cmd="./bench.sh"
789	if [[ ${parallel:0:3} = "mpi" ]]; then
790	# Lancement avec deux procs mpi et 2 openMP
791	echo "export OMP_STACKSIZE=800M" > bench.sh
792	if [[ "${parallel:4:3}" = "omp" ]]; then
793	echo "export OMP_NUM_THREADS=2" >> bench.sh
794	fi
795	if [[ $cosp = "v1" \|\| $cosp = "v2" ]]; then
796	echo "ulimit -s 200000" >> bench.sh
797	else
798	echo "ulimit -s unlimited" >> bench.sh
799	fi
800	if which mpirun &> /dev/null; then
801	echo "mpirun -np 2 gcm.e &> listing" >> bench.sh
802	elif grep -q "Adastra" /etc/motd; then
803	local account
804	account=$(/usr/sbin/my_project.py -l 2>&1 \| head -1 \| cut -d " " -f 3- \| cut -c 5-)
805	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"
806	echo "./gcm.e &> listing" >> bench.sh
807	else
808	echo "Error: No command found to run parallel bench"; exit 1
809	fi
810	if [[ $(hostname \| cut -c -6) = "spirit" ]]; then # ulimit unlimited segfaults on Spirit
811	sed -i'' "s/ulimit -s unlimited/ulimit -Ss 8000/" bench.sh
812	fi
813	# Add rebuild, using reb.sh if it is there
814	cat <<EOF >> bench.sh
815	if [[ -f reb.sh ]]; then
816	./reb.sh histday; ./reb.sh histmth; ./reb.sh histhf;
817	./reb.sh histins; ./reb.sh stomate_history;
818	./reb.sh sechiba_history; ./reb.sh sechiba_out_2
819	fi
820	EOF
821	else
822	echo "./gcm.e &> listing" > bench.sh
823	fi
824	# Getting orchidee stuff
825	if [[ $veget = 'CMIP6' \|\| $veget = "orch2.0" ]]; then # TODO once we have a 2.2 bench, add it here (or in planned separate bench script)
826	echo 'myget 3DBenchs/BENCHCMIP6.tar.gz'
827	myget 3DBenchs/BENCHCMIP6.tar.gz
828	tar xvzf BENCHCMIP6.tar.gz
829	sed -e "s:VEGET=n:VEGET=y:" config.def > tmp
830	mv -f tmp config.def
831	if [[ $with_xios = 1 ]]; then
832	cp ../../ORCHIDEE/src_xml/context_orchidee.xml .
833	echo '<context id="orchidee" src="./context_orchidee.xml"/>' > add.tmp
834	cp ../../ORCHIDEE/src_xml/field_def_orchidee.xml .
835	cp ../../ORCHIDEE/src_xml/file_def_orchidee.xml .
836	cp ../../ORCHIDEE/src_xml/file_def_input_orchidee.xml .
837	if [[ -f ../../ORCHIDEE/src_xml/context_input_orchidee.xml ]]; then
838	cp ../../ORCHIDEE/src_xml/context_input_orchidee.xml .
839	echo '<context id="orchidee" src="./context_input_orchidee.xml"/>' >> add.tmp
840	fi
841	sed -e '/id="LMDZ"/r add.tmp' iodef.xml > tmp
842	mv tmp iodef.xml
843	sed -e'{/sechiba1/ s/enabled="_AUTO_"/type="one_file" enabled=".TRUE."/}' \
844	file_def_orchidee.xml > tmp
845	\mv -f tmp file_def_orchidee.xml
846	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
847	file_def_orchidee.xml > tmp
848	\mv -f tmp file_def_orchidee.xml
849	sed -e 's@output_level="_AUTO_"@output_level="1"@' \
850	file_def_orchidee.xml > tmp
851	\mv -f tmp file_def_orchidee.xml
852	sed -e 's@output_freq="_AUTO_"@output_freq="1d"@' \
853	file_def_orchidee.xml > tmp
854	\mv -f tmp file_def_orchidee.xml
855	sed -e 's@compression_level="4"@compression_level="0"@' \
856	file_def_orchidee.xml > tmp
857	\mv -f tmp file_def_orchidee.xml
858	sed -e 's@XIOS_ORCHIDEE_OK = n@XIOS_ORCHIDEE_OK = y@' \
859	orchidee.def > tmp
860	\mv -f tmp orchidee.def
861	fi
862	fi
863
864	if [[ -f ../arch.env ]]; then source ../arch.env; fi
865
866	echo "EXECUTION DU BENCH"
867	date
868	if (! $bench_cmd &> out.bench) \|\| ! (tail -n 1 listing \| grep "Everything is cool"); then
869	tail listing
870	echo "Bench FAILED, exiting"; exit 1
871	fi
872	date
873	tail listing
874	fi
875
876	# 1D case
877	if [[ $SCM = 1 ]]; then
878	cd "$MODEL"
879	myget 1D/1D.tar.gz
880	tar xf 1D.tar.gz
881	cd 1D
882	if [[ $rad = "oldrad" ]]; then
883	sed -i'' -e 's/^rad=.*$/rad=oldrad/' run.sh
884	sed -i'' -e 's/^rad=.*$/rad=oldrad/' bin/compile
885	elif [[ $rad = ecrad ]] ; then
886	sed -i'' -e 's/^rad=.*$/rad=ecrad/' run.sh
887	sed -i'' -e 's/^rad=.*$/rad=ecrad/' bin/compile
888	fi
889	echo "Running 1D/run.sh, log in $(pwd)/run1d.log"
890	./run.sh &> "$(pwd)/run1d.log"
891	fi
892	}
893
894	# If sourced: returns, else run setup
895	if [[ ! "${BASH_SOURCE[0]}" = "$0" ]]; then return 0; fi
896
897	echo "install_lmdz.sh DEBUT $(date)"
898
899	set_default_params
900	read_cmdline_args "$@"
901	ensure_correct_option_combinations
902	download_model
903	init_arch
904	check_available_software
905	get_lmdz_version
906	get_orchidee_version
907	install_netcdf
908	install_IOIPSL
909	install_XIOS
910	compile_orchidee
911	compile_lmdz
912	run_bench

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