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source: BOL/script_install_amaury/install_lmdz.sh @ 4952

Last change on this file since 4952 was 4941, checked in by abarral, 8 months ago
(WIP) add option top resume install from existing directory
Property svn:executable set to ``*
File size: 35.0 KB

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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="20231022.trunk"
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 [[ $(uname) = "Darwin" ]]; then
84	export MAKE="make"
85	fi
86
87	optim_debug=""
88	arch="local"
89
90	local mpi_file
91	mpi_file=$(readlink -e -f "$(which mpif90)")
92	path_mpi=$(dirname "$mpi_file")
93	root_mpi=$(dirname "$path_mpi")
94
95	arch="local-gfortran"
96	arch_dir=""
97	}
98
99	function read_cmdline_args {
100	while (($# > 0)); do
101	case $1 in
102	"-h") cat <<........fin
103	$0 [ -v version ] [ -r svn_release ]
104	[ -parallel PARA ] [ -d GRID_RESOLUTION ] [ -bench 0/1 ]
105	[-name LOCAL_MODEL_NAME] [-rad RADIATIF]
106
107	-v "version" like 20150828.trunk, see http://www.lmd.jussieu.fr/~lmdz/Distrib/LISMOI.trunk (default <$version>)
108
109	-r "svn_release" : either the svn release number or "last" (default <$svn_lmdz>)
110
111	-parallel parallel support: mpi, omp, mpi_omp (mpi with openMP) or none (default: <$parallel>)
112
113	-d "grid resolution": should be among the available benchs if -bench 1 (valid values: 48x36x19, 48x36x39) (default : <$grid_resolution>)
114
115	-bench activating the bench or not (0/1) (default: <$bench>)
116
117	-unstable use unstable tar instead of testing
118
119	-name name of the folder to install to (default <$MODEL>)
120
121	-netcdf 0, 1 or PATH. 0: do not download NetCDF, look for it in standard locations (/usr); 1: download and compile NetCDF; PATH: full path to an existing installed NetCDF library (default: <$netcdf>)
122
123	-xios use (download and compile) the XIOS library (will compile the parallel NetCDF4-HDF5 library) (requires to also have -parallel mpi_omp)
124
125	-cosp to run with cospv1 or cospv2 [none/v1/v2] (default <$cosp>)
126
127	-rad radiative code: oldrad, rrtm or ecrad (default <$rad>)
128
129	-nofcm to compile without fcm
130
131	-SCM install 1D version automatically
132
133	-debug compile everything in debug mode
134
135	-benchphysiq to choose which physics.def package to use in the bench (default <$benchphysiq>)
136
137	-compilephysiq physics to compile the model with (default <$compphysiq>)
138
139	-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 (default $veget)
140
141	-spla activate interactive aerosols
142
143	-inlandsis activate new snow scheme
144
145	-arch name of the arch to use (default <$arch>)
146
147	-arch_dir where to find the arch files (default <$arch_dir>)
148
149	-make_j number of processes to parallelize installations (default <$make_j>)
150
151	-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)
152
153	........fin
154	exit 1;;
155	"-v") version=$2; shift; shift;;
156	"-r") svn_lmdz=$2; shift; shift;;
157	"-d") grid_resolution=$2; shift; shift;;
158	"-unstable") trusting="unstable"; shift;;
159	"-cosp") cosp=$2
160	case $cosp in
161	"none"\|"v1"\|"v2") cosp=$2; shift; shift;;
162	*) echo "Only none v1 v2 for cosp option"; exit 1
163	esac;;
164	"-nofcm") compile_with_fcm=0; echo "This option will be reactivated soon (promesse du 8dec2022)"; exit 1; shift;;
165	"-SCM") SCM=1; shift;;
166	"-rad") rad=$2
167	case $rad in
168	"oldrad"\|"rrtm"\|"ecrad") rad=$2; shift; shift;;
169	*) echo "Only oldrad rrtm ecrad for rad option"; exit 1
170	esac;;
171	"-parallel") parallel=$2
172	case $parallel in
173	"none"\|"mpi"\|"omp"\|"mpi_omp") parallel=$2; shift; shift;;
174	*) echo "Only none mpi omp mpi_omp for the parallel option"; exit 1
175	esac;;
176	"-bench") bench=$2; shift; shift;;
177	"-debug") optim_debug=-debug; shift;;
178	"-name") MODEL=$2; shift; shift;;
179	"-netcdf") netcdf=$2; shift; shift;;
180	"-benchphysiq") benchphysiq=$2; shift; shift;;
181	"-compilephysiq") compphysiq=$2; shift; shift;;
182	"-xios") with_xios=1; shift;;
183	"-arch") arch=$2; shift; shift;;
184	"-arch_dir") arch_dir=$2; shift; shift;;
185	"-veget") veget=$2; shift; shift;;
186	"-spla") aerosols=1; shift;;
187	"-inlandsis") inlandsis=1; shift;;
188	"-make_j") make_j=$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 [[ $arch_dir = "" ]]; then arch_dir="$MODEL/modipsl/config/IPSLCM7/ARCH/"; fi
245	}
246
247	function ensure_correct_option_combinations {
248	# Check on veget version
249	if [[ $veget != 'none' && $veget != "CMIP6" && $veget != "orch2.0" && $veget != "orch2.2" ]]; then
250	re='^[0-9]+$'
251	if ! [[ $veget =~ $re ]]; then
252	echo 'Valeur de l option veget non valable'; exit 1
253	fi
254	fi
255
256	## if also compiling XIOS, parallel must be mpi_omp
257	if [[ $with_xios = 1 && $parallel != "mpi_omp" ]]; then
258	echo "Error, you must set -parallel mpi_omp if you want XIOS"; exit 1
259	fi
260
261	if [[ $cosp = "v2" && $with_xios = 0 ]]; then
262	echo "Error, Cospv2 cannot run without Xios"; exit 1
263	fi
264
265	# STOP if trying to use both ORCHIDEE and Isotopes :
266	if [[ $isotopes = 1 && $veget != "NONE" ]]; then
267	echo "STOP: You cannot run LMDZ with ORCHIDEE and ISOtopes at the same time"; exit 1
268	fi
269
270	# STOP if trying to use both SPLA and Isotopes :
271	if [[ $isotopes = 1 && $aerosols = 1 ]]; then
272	echo "STOP: You cannot run LMDZ with Isotopes and aerosols=spla at the same time"; exit 1
273	fi
274
275	# (Temporary) STOP if trying to use Isotopes with XIOS :
276	# TODO Amaury: check if still relevant
277	if [[ $isotopes = 1 && $with_xios = 1 ]]; then
278	echo "STOP: Isotopes cannont yet be run with XIOS"; exit 1
279	fi
280
281	# (Temporary) Constraints for aerosols=spla :
282	# --> resolution 128x88x79 and rad=rrtm
283	if [[ $aerosols = 1 && $grid_resolution != "128x88x79" ]]; then
284	echo 'For now, <aerosols=spla> requires <resol=128x88x79>, and uses the zoomed grid from gcm.def_zNAfrica_BiJe, for which forcing & initial files are available'
285	echo "Right now resol=<$grid_resolution>"
286	exit 1
287	fi
288
289	if [[ $aerosols = 1 && $rad != "rrtm" ]]; then
290	echo "STOP: For the time being, <aerosols=spla> requires <rad=rrtm>"; exit 1
291	fi
292	}
293
294	function check_available_software {
295	echo "################################################################"
296	echo "Check if required software is available"
297	echo "################################################################"
298	for logiciel in wget tar gzip make gcc cmake m4 c++; do
299	if [[ $(which "$logiciel") = "" ]]; then
300	echo "You must first install $logiciel on your system"; exit 1
301	fi
302	done
303
304	cat <<eod > tt.f90
305	print*,'coucou'
306	end
307	eod
308	$compiler tt.f90 \|\| a.out
309	./a.out >\| tt
310	if [[ $(< tt sed -e 's/ //g' ) != "coucou" ]]; then
311	echo "problem installing with compiler $compiler"; exit 1
312	fi
313	\rm tt a.out tt.f90
314	}
315
316	function download_model {
317	if [[ $clean_install = 1 ]]; then rm -rf "$MODEL"; fi
318
319	mkdir -p "$MODEL"
320	MODEL=$(readlink -e -f "$MODEL"); echo "$MODEL" # absolute path
321	if [[ ! -f "$MODEL/modipsl" ]]; then
322	echo "##########################################################"
323	echo "Download a slightly modified version of LMDZ"
324	echo "##########################################################"
325	cd "$MODEL"
326	getlog="$(pwd)/get.log"
327	echo "logfile : $getlog"
328	myget "src_archives/$trusting/modipsl.$version.tar.gz" >> get.log 2>&1
329	echo "install_lmdz.sh wget_OK $(date)"
330	gunzip "modipsl.$version.tar.gz" >> get.log 2>&1
331	tar xf "modipsl.$version.tar" >> get.log 2>&1
332	\rm "modipsl.$version.tar"
333	fi
334	}
335
336	function create_model_tar { # TODO TEMP while waiting for tar: we copy the base from a local path = IPSLCM7 + ORCH2.2 8504
337	if [[ ! -d ../MODEL_REF ]]; then
338	cd ..
339	mkdir MODEL_REF
340	cd MODEL_REF
341	# Base is IPSLCM7
342	svn co --username icmc_users https://forge.ipsl.fr/igcmg/svn/modipsl/trunk modipsl
343	cd modipsl/util
344	./model IPSLCM7_work
345	# Remove unused components
346	rm -rf ../oasis3-mct
347	cd ../modeles
348	rm -rf ICOSA_LMDZ ORCHIDEE_4 ORCHIDEE_2_2 NEMO DYNAMICO XIOS INCA
349	# Retrieve orch version
350	svn co svn://forge.ipsl.fr/orchidee/branches/ORCHIDEE_2_2/ORCHIDEE -r 8504
351	# Correct orchidee bug in 8504
352	sed -i"" -e "s/ts.second=dt_routing/ts%second=dt_routing/" -e "380,390 s/USE grid/USE grid, temp_disabled => contfrac/" ORCHIDEE/src_sechiba/routing_native_flow.f90
353
354	cd ../../../script_install
355	fi
356
357	if [[ ! -d "$MODEL" ]]; then
358	\cp -r ../MODEL_REF .
359	mv MODEL_REF "$MODEL"
360	fi
361	MODEL=$(readlink -e -f "$MODEL"); echo "$MODEL" # absolute path
362	}
363
364	function init_arch {
365	arch_dir=$(readlink -e -f "$arch_dir") # full path. readlink must be called after the path is created
366	if [[ ! -d $arch_dir ]]; then
367	echo "Error: no arch dir $arch_dir"; exit 1
368	elif [[ ! -f $arch_dir/arch-$arch.path ]]; then
369	echo "Error: no arch-$arch.path in $arch_dir"; exit 1
370	fi
371
372	local fcm_path
373	if [[ -f $arch_dir/arch-$arch.fcm ]]; then
374	fcm_path="$arch_dir/arch-$arch.fcm"
375	else
376	fcm_path="$MODEL/modipsl/modeles/LMDZ/arch/arch-$arch.fcm"
377	if [[ ! -f $fcm_path ]]; then
378	echo "Error: no $fcm_path"; exit 1
379	fi
380	fi
381
382	# check compiler
383	compiler=$(< "$fcm_path" grep "%COMPILER" \| sed -e "s/%COMPILER\s*//")
384
385	# load env
386	local env_path=${fcm_path/.fcm/.env}
387	# shellcheck disable=SC1090
388	if [[ -f $env_path ]]; then source "$env_path"; fi
389	}
390
391	function install_arch {
392	local component=$1
393
394	if [[ ! -f "$MODEL/modipsl/modeles/$component/arch/arch-$arch.fcm" ]]; then
395	\cp -f "$arch_dir/arch-$arch.fcm" "$MODEL/modipsl/modeles/$component/arch"
396	\cp -f "$arch_dir/arch-$arch.path" "$MODEL/modipsl/modeles/$component/arch"
397
398	if [[ $component = "XIOS" ]]; then
399	# Adapt for XIOS, which uses different naming conventions
400	sed -i'' -e "s/%COMPILER/%FCOMPILER/" -e "s/%LINK/%LINKER/" -e "s/-fdefault-real-8//" "$MODEL/modipsl/modeles/XIOS/arch/arch-$arch.fcm"
401	elif [[ $component = "ORCHIDEE" ]]; then
402	if [[ $orcbranch = "/tags/ORCHIDEE_2_0/ORCHIDEE" ]]; then # 2.0 and before have a different fcm convention
403	sed -i'' -e "s/-I//" -e "s/-L//" "$MODEL/modipsl/modeles/ORCHIDEE/arch/arch-$arch.path" # /!\ we only replace first occurence on purpose
404	fi
405	fi
406	fi
407	}
408
409	function install_netcdf {
410	echo "Installing Netcdf"
411	local ncdf_compiler="$compiler"
412
413	if [[ $netcdf = 0 ]]; then
414	ncdfdir=$(nc-config --prefix)
415	else
416	cd "$MODEL"
417
418	# Convert non-basic compiler
419	case $compiler in
420	mpif90) ncdf_compiler=$($compiler --version \| head -n 1 \| cut -d " " -f -1)
421	esac
422
423	case $ncdf_compiler in
424	gfortran \| GNU) ncdf_compiler="gfortran"; opt1="-compiler gnu"; opt2="-CC gcc -FC gfortran -CXX g++";;
425	*) echo "unexpected compiler $ncdf_compiler for netcdf"; exit 1
426	esac
427
428	case $with_xios in
429	0) script_install_netcdf="install_netcdf4_hdf5_seq.bash"
430	ncdfdir="netcdf4_hdf5_seq"
431	opt_="$opt1";;
432	1) script_install_netcdf="install_netcdf4_hdf5.bash"
433	ncdfdir="netcdf4_hdf5"
434	opt_="$opt2 -MPI $root_mpi";;
435	*) echo "with_xios=$with_xios, should be 0 or 1"; exit 1
436	esac
437	if [[ $netcdf = 1 ]]; then
438	ncdfdir="$MODEL/$ncdfdir"
439	else
440	mkdir -p "$netcdf"; ncdfdir="$netcdf/$ncdfdir"
441	fi
442
443	echo "Repertoire netcdf $ncdfdir"
444	if [[ ! -d $ncdfdir ]]; then
445	netcdflog=$(pwd)/netcdf.log
446	echo "----------------------------------------------------------"
447	echo "Compiling the Netcdf library"
448	echo "----------------------------------------------------------"
449	echo "log file : $netcdflog"
450	myget script_install/$script_install_netcdf >> "$netcdflog" 2>&1
451	chmod u=rwx $script_install_netcdf
452	# shellcheck disable=SC2086
453	./$script_install_netcdf -prefix "$ncdfdir" $opt_ >> "$netcdflog" 2>&1
454	fi
455
456	# Add to path
457	export PATH="$ncdfdir/bin:$PATH"
458
459	#----------------------------------------------------------------------------
460	# LF rajout d'une verrue, pour une raison non encore expliquee,
461	# la librairie est parfois rangée dans lib64 et non dans lib
462	# par certains compilateurs
463	if [[ ! -e lib && -d lib64 ]]; then ln -s lib64 lib; fi
464	#----------------------------------------------------------------------------
465
466	echo "install_lmdz.sh netcdf_OK $(date)"
467	fi
468
469	cat >test_netcdf90.f90 <<EOF
470	use netcdf
471	print *, "NetCDF library version: ", nf90_inq_libvers()
472	end
473	EOF
474
475	if $ncdf_compiler -I"$ncdfdir"/include test_netcdf90.f90 -L"$ncdfdir"/lib -lnetcdff \
476	-lnetcdf -Wl,-rpath="$ncdfdir"/lib && ./a.out
477	then
478	\rm test_netcdf90.f90 a.out
479	else
480	cat <<EOF
481	Failed test program using NetCDF-Fortran. You can:
482	- check that you have NetCDF-Fortran installed in your system
483	- or specify an installation directory with option -netcdf of install_lmdz.sh
484	- or download and compile NetCDF-Fortran with option -netcdf 1 of nstall_lmdz.sh
485	EOF
486	exit 1
487	fi
488
489	# Compile NetCDF95
490	cd "$MODEL/modipsl/modeles/LMD"*
491	echo "Installing NetCDF95"
492	cd "$MODEL"
493	myget src_archives/netcdf/NetCDF95-0.3.tar.gz
494	tar -xf NetCDF95-0.3.tar.gz
495	\rm NetCDF95-0.3.tar.gz
496	cd NetCDF95-0.3
497	mkdir -p build && cd build
498	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"
499	make install
500	}
501
502	function install_IOIPSL {
503	install_arch "IOIPSL"
504
505	cd "$MODEL/modipsl/modeles/IOIPSL"
506	ioipsllog="$(pwd)/ioipsl.log"
507	echo "Compiling IOIPSL, the interface library with Netcdf $(date) (log: $ioipsllog)"
508
509	if ! ./makeioipsl_fcm -arch "$arch" -job 8 > "$ioipsllog" 2>&1; then
510	echo "IOIPSL compile failed, exiting"; exit 1
511	fi
512
513	# Link to modipsl/bin
514	cp -f bin/* ../../bin
515
516	echo "IOIPSL compiled $(date)"
517
518	IOIPSL_LIBDIR_="$MODEL/modipsl/modeles/IOIPSL/lib"
519	IOIPSL_INCDIR_="$MODEL/modipsl/modeles/IOIPSL/inc"
520	}
521
522	function install_XIOS {
523	if [[ $with_xios = 1 ]]; then
524	cd "$MODEL/modipsl/modeles"
525	xioslog="$(pwd)/XIOS/xios.log"
526	echo "##########################################################"
527	echo "Compiling XIOS (log $xioslog) $(date)"
528	echo "##########################################################"
529
530	# Download XIOS
531	local xios_http="http://forge.ipsl.fr/ioserver/svn/XIOS2/branches/xios-2.6"
532	local xios_rev="2568"
533
534	cd "$MODEL/modipsl/modeles"
535	set +e; svn co -r $xios_rev $xios_http XIOS; set -e
536
537	cd XIOS
538
539	install_arch "XIOS"
540
541	echo "Starting XIOS compilation"
542	if ! ./make_xios --arch "$arch" --job 8 > "$xioslog" 2>&1; then
543	echo "XIOS compilation failed, exiting"; exit 1
544	fi
545
546	echo "Compiled XIOS $(date)"
547	fi
548
549	XIOS_LIBDIR_="$MODEL/modipsl/modeles/XIOS/lib"
550	XIOS_INCDIR_="$MODEL/modipsl/modeles/XIOS/inc"
551	}
552
553	function get_orchidee_version { # Set / Check ORCHIDEE version
554	local fetch_rev=""
555	orcbranch=""
556	case $veget in
557	"none") fcm_veget_version="false";;
558	"orch2.0" \| "CMIP6") fcm_veget_version=orchidee2.0; fetch_rev=7906;; # in previous tar we used 6592 but with some modifications to xios_orchidee.f90, which got integrated in 7906
559	"orch2.2") fcm_veget_version=orchidee2.1; orcbranch="ORCHIDEE_2_2" ;; # the bundled version
560	*) fetch_rev=$veget
561	esac
562
563	if [[ -n $fetch_rev ]]; then
564	echo "Fetching orch $fetch_rev from the repository"
565	orcbranch=$(svn log -v -q svn://forge.ipsl.fr/orchidee/ -r "$fetch_rev" \| grep ORCHIDEE \| head -1 \| sed -e 's:ORCHIDEE/.*$:ORCHIDEE:' \| awk '{print $2}')
566	echo "branch is $orcbranch"
567	if [[ $fetch_rev -lt 4465 ]]; then echo 'ORCHIDEE version must be >=4465, exiting'; exit 1; fi
568	echo "IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at orchidee-help@listes.ipsl.fr"
569	cd "$MODEL/modipsl/modeles"
570	svn co -r "$fetch_rev" "svn://forge.ipsl.fr/orchidee/$orcbranch" \|\| (rm -rf ORCHIDEE && svn co -r "$fetch_rev" "svn://forge.ipsl.fr/orchidee/$orcbranch") # if orch dir exists and is from a different branch, need to delete it first (but we don't want to do this all the time, as it would require a recompile for the same code)
571	cd -
572	fi
573
574	# Check parallel LMDZ+ORCH
575	if [[ (! $veget = "none") && $parallel = "none" && ($used_lmdz_rev -lt 4894) ]]; then
576	echo "LMDZ revision must be >=4894 for orchidee without parallel support. Upgrade lmdz or use -parallel mpi_omp."; exit 1
577	fi
578	}
579
580	function compile_orchidee {
581	install_arch "ORCHIDEE"
582
583	if [[ $veget != "none" ]]; then
584	cd "$MODEL/modipsl/modeles/ORCHIDEE"
585
586	orchideelog="$(pwd)/orchidee.log"
587	echo "Compiling ORCHIDEE, the continental surface model (log $orchideelog) $(date)"
588
589	local xios_orchid opt_orc
590	if [[ $with_xios = 1 ]]; then
591	xios_orchid="-xios";
592	else
593	xios_orchid="-noxios"
594	fi
595	if [[ $optim_debug = "-debug" ]]; then
596	opt_orc="-debug";
597	else
598	opt_orc="-prod"
599	fi
600
601	local varenv="IOIPSL_LIBDIR_=$IOIPSL_LIBDIR_ IOIPSL_INCDIR_=$IOIPSL_INCDIR_ XIOS_INCDIR_=$XIOS_INCDIR_ XIOS_LIBDIR_=$XIOS_LIBDIR_"
602	if [[ $parallel = "none" ]]; then
603	echo "$varenv ./makeorchidee_fcm $xios_orchid $opt_orc -parallel none -arch $arch -j $make_j" > compile.sh
604	else
605	if [[ ! -d src_parallel ]]; then
606	echo "Orchidee version too old for parallel support"; exit 1
607	fi
608	{
609	echo "$varenv ./makeorchidee_fcm -j $make_j $xios_orchid $opt_orc -parallel $parallel -arch $arch"
610	} > compile.sh
611	fi
612	chmod +x compile.sh
613	echo "Compiling ORCHIDEE using $(\cat compile.sh)"
614	if ! ./compile.sh > "$orchideelog" 2>&1; then
615	echo "ORCHIDEE compilation failed, exiting"; exit 1
616	fi
617	echo "Compiled ORCHIDEE $(date)"
618	fi
619
620	ORCH_INCDIR_="$MODEL/modipsl/modeles/ORCHIDEE/inc"
621	ORCH_LIBDIR_="$MODEL/modipsl/modeles/ORCHIDEE/lib"
622	}
623
624	function get_lmdz_version {
625	LMDZPATH=$(readlink -e -f "$MODEL/modipsl/modeles/LMD"*)
626	cd "$LMDZPATH"
627	lmdzlog="$(pwd)/lmdz.log"
628
629	used_lmdz_rev=$svn_lmdz
630	if [[ -n $svn_lmdz ]]; then
631	local lmdzbranch
632	echo "Fetching LMDZ $svn_lmdz from the repository"
633	lmdzbranch=$(svn log -v -q https://svn.lmd.jussieu.fr/LMDZ -r "$svn_lmdz" \| grep LMDZ \| head -1 \| sed -e 's:trunk/.*$:trunk:' \| awk '{print $2}')
634	cd "$MODEL/modipsl/modeles"
635	svn co -r "$svn_lmdz" "https://svn.lmd.jussieu.fr/LMDZ$lmdzbranch" LMDZ \|\| (rm -rf LMD* && svn co -r "$svn_lmdz" "https://svn.lmd.jussieu.fr/LMDZ$lmdzbranch" LMDZ) # if lmdz dir exists and is from a different branch, need to delete it first (but we don't want to do this all the time, as it would require a recompile for the same code)
636	cd -
637	else # get svn from info
638	set +e; used_lmdz_rev=$(svn info \| grep "Last Changed Rev" \| cut -c 19-); set -e
639	if [[ -z $used_lmdz_rev ]]; then # svn info failed
640	used_lmdz_rev=$(grep 'Revision: [0-9]' "$MODEL"/Read*.md \| awk ' { print $2 } ' 2>/dev/null)
641	if [[ -z $used_lmdz_rev ]]; then echo "Could not determine lmdz version. This is likely an issue with the .tar itself, please report to LMDZ team."; exit 1; fi
642	fi
643	fi
644	}
645
646	function compile_lmdz {
647	install_arch "LMDZ"
648	cd "$LMDZPATH"
649
650	if [[ $used_lmdz_rev -le 4185 ]]; then
651	exe_name="bin/gcm_${grid_resolution}_phy${compphysiq}_${suff_para}${suff_orc}${suff_aer}${suff_iso}.e"
652	else
653	exe_name="bin/gcm_${grid_resolution}_phy${compphysiq}_${rad}${suff_para}${suff_orc}${suff_aer}${suff_iso}.e"
654	fi
655
656	local opt_rad
657	case $rad in
658	oldrad) iflag_rrtm=0; NSW=2; opt_rad="";;
659	rrtm) iflag_rrtm=1; NSW=6
660	if [[ $used_lmdz_rev -le 4185 ]]; then
661	opt_rad="-rrtm true"
662	else
663	opt_rad="-rad rrtm"
664	fi;;
665	ecrad) iflag_rrtm=2; NSW=6; opt_rad="-rad ecrad";;
666	*) echo "Only oldrad rrtm ecrad for rad option"; exit 1
667	esac
668	if [[ $used_lmdz_rev -le 4185 && $rad = "ecrad" ]]; then
669	echo "ecrad only available for LMDZ rev starting with 4186 "; exit 1
670	fi
671
672	# Compile
673	local varenv="IOIPSL_LIBDIR_=\"$IOIPSL_LIBDIR_\" IOIPSL_INCDIR_=\"$IOIPSL_INCDIR_\" ORCH_INCDIR_=\"$ORCH_INCDIR_\" ORCH_LIBDIR_=\"$ORCH_LIBDIR_\" XIOS_INCDIR_=\"$XIOS_INCDIR_\" XIOS_LIBDIR_=\"$XIOS_LIBDIR_\""
674	makelmdz="makelmdz_fcm $optim_debug -arch $arch -j $make_j"
675	local para_compile_opt="-mem -parallel $parallel"; if [[ $parallel = "none" ]]; then para_compile_opt=""; fi
676	echo "$varenv ./$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
677	echo "Compiling lmdz using $(\cat compile.sh) (log: $lmdzlog) $(date)"
678	chmod +x ./compile.sh
679	if ! ./compile.sh > "$lmdzlog" 2>&1; then
680	echo "LMDZ compilation failed, exiting"; exit 1
681	fi
682	echo "Finished LMDZ compilation $(date)"
683
684	# Check executable
685	if [[ ! -f $exe_name ]]; then
686	echo "Compilation failed, can't find the executable"; exit 1
687	else
688	echo "Compilation successfull, the executable is $exe_name $(date)"
689	fi
690	}
691
692	function run_bench {
693	cd "$MODEL/modipsl/modeles/LMDZ"*
694
695	if [[ $bench = "tuto" ]]; then
696	myget "Training/tutorial.tar"; tar xf tutorial.tar; cd TUTORIAL
697	./init.sh
698	elif [[ $bench = 1 ]]; then
699	\rm -rf "BENCH${grid_resolution}"
700	local bench=bench_lmdz_${grid_resolution}
701	myget "3DBenchs/$bench.tar.gz"
702	tar xf "$bench.tar.gz"
703
704	if [[ $cosp = "v1" \|\| $cosp = "v2" ]]; then
705	cd "BENCH${grid_resolution}"
706	# copier les fichiers namelist input et output our COSP
707	cp ../DefLists/cosp*_input_nl.txt .
708	cp ../DefLists/cosp*_output_nl.txt .
709	# Activer la cles ok_cosp pour tourner avec COSP
710	sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp
711	\mv -f tmp config.def
712	cd ..
713	fi
714
715	if [[ -n "$benchphysiq" ]]; then
716	cd "BENCH${grid_resolution}"
717	if [[ -f "physiq.def_${benchphysiq}" ]]; then
718	cp "physiq.def_${benchphysiq}" benchphysiq.def
719	echo "using physiq.def_${benchphysiq}"
720	else
721	echo "using standard physiq.def"
722	fi
723	cd ..
724	else
725	echo "using standard physiq.def"
726	fi
727
728	if [[ $with_xios = 1 ]]; then
729	cd "BENCH${grid_resolution}"
730	cp ../DefLists/iodef.xml .
731	cp ../DefLists/context_lmdz.xml .
732	cp ../DefLists/field_def_lmdz.xml .
733	# A raffiner par la suite
734	echo "A FAIRE : Copier les *xml en fonction de l option cosp"
735	cp ../DefLists/field_def_cosp*.xml .
736	cp ../DefLists/file_def_hist*xml .
737	# adapt iodef.xml to use attached mode
738	sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' \
739	iodef.xml > tmp
740	\mv -f tmp iodef.xml
741
742	# and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
743	# except for histday
744	for histfile in file_def_hist*xml; do
745	if [[ "$histfile" = "file_def_histday_lmdz.xml" ]]; then
746	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' \
747	"$histfile" > tmp
748	\mv -f tmp "$histfile"
749	sed -e 's@output_level="_AUTO_"@output_level="5"@' "$histfile" \
750	> tmp
751	\mv -f tmp "$histfile"
752	sed -e 's@compression_level="2"@compression_level="0"@' \
753	"$histfile" > tmp
754	\mv -f tmp "$histfile"
755	else
756	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
757	"$histfile" > tmp
758	\mv -f tmp "$histfile"
759	fi
760	done
761	# and add option "ok_all_xml=y" in config.def
762	echo "### XIOS outputs" >> config.def
763	echo 'ok_all_xml=.true.' >> config.def
764
765	#activer les sorties pour Cosp
766	if [[ "$cosp" = "v1" ]]; then
767	sed -i'' -e 's@enabled=".FALSE."@enabled=".TRUE."@' \
768	-e 's@output_level="_AUTO_"@output_level="5"@' \
769	-e 's@compression_level="2"@compression_level="0"@' \
770	file_def_histdayCOSP_lmdz.xml
771	fi
772	if [[ "$cosp" = "v2" ]]; then
773	sed -i'' -e 's@compression_level="2"@compression_level="0"@' file_def_histdayCOSPv2_lmdz.xml
774	for type_ in hf day mth; do
775	file=file_def_hist${type_}COSP
776	sed -i'' -e 's@src="./'${file}'_lmdz.xml"@src="./'${file}'v2_lmdz.xml"@' context_lmdz.xml
777	done
778	sed -i'' -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' field_def_lmdz.xml
779	fi
780
781	cd ..
782	fi
783
784	# Cas Bench avec ecrad
785	if [[ $rad = "ecrad" ]]; then
786	cd "BENCH${grid_resolution}"
787	cp ../DefLists/namelist_ecrad .
788	cp -r ../libf/phylmd/ecrad/data .
789	cd ..
790	fi
791
792	# Adjusting bench physiq.def to radiative code chosen
793	cd "BENCH${grid_resolution}"
794	sed -e 's/iflag_rrtm=.*.$/iflag_rrtm='$iflag_rrtm'/' \
795	-e 's/NSW=.*.$/NSW='$NSW'/' physiq.def > tmpdef
796	\mv tmpdef physiq.def
797	cd ..
798
799	cp "$exe_name" "BENCH${grid_resolution}/gcm.e"
800	cd "BENCH${grid_resolution}"
801
802	local bench_cmd="./bench.sh"
803	if [[ ${parallel:0:3} = "mpi" ]]; then
804	# Lancement avec deux procs mpi et 2 openMP
805	echo "export OMP_STACKSIZE=800M" > bench.sh
806	if [[ "${parallel:4:3}" = "omp" ]]; then
807	echo "export OMP_NUM_THREADS=2" >> bench.sh
808	fi
809	if [[ $cosp = "v1" \|\| $cosp = "v2" ]]; then
810	echo "ulimit -s 200000" >> bench.sh
811	else
812	echo "ulimit -s unlimited" >> bench.sh
813	fi
814	if which mpirun > /dev/null 2>&1; then
815	echo "mpirun -np 2 gcm.e > listing 2>&1" >> bench.sh
816	elif grep -q "Adastra" /etc/motd; then
817	local account
818	account=$(/usr/sbin/my_project.py -l 2>&1 \| head -1 \| cut -d " " -f 3- \| cut -c 5-)
819	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"
820	echo "./gcm.e > listing 2>&1" >> bench.sh
821	else
822	echo "Error: No command found to run parallel bench"; exit 1
823	fi
824	# Add rebuild, using reb.sh if it is there
825	cat <<EOF >> bench.sh
826	if [[ -f reb.sh ]]; then
827	./reb.sh histday; ./reb.sh histmth; ./reb.sh histhf;
828	./reb.sh histins; ./reb.sh stomate_history;
829	./reb.sh sechiba_history; ./reb.sh sechiba_out_2
830	fi
831	EOF
832	else
833	echo "./gcm.e > listing 2>&1" > bench.sh
834	fi
835	# Getting orchidee stuff
836	if [[ $veget = 'CMIP6' \|\| $veget = "orch2.0" ]]; then # TODO once we have a 2.2 bench, add it here (or in planned separate bench script)
837	echo 'myget 3DBenchs/BENCHCMIP6.tar.gz'
838	myget 3DBenchs/BENCHCMIP6.tar.gz
839	tar xvzf BENCHCMIP6.tar.gz
840	sed -e "s:VEGET=n:VEGET=y:" config.def > tmp
841	mv -f tmp config.def
842	if [[ $with_xios = 1 ]]; then
843	cp ../../ORCHIDEE/src_xml/context_orchidee.xml .
844	echo '<context id="orchidee" src="./context_orchidee.xml"/>' > add.tmp
845	cp ../../ORCHIDEE/src_xml/field_def_orchidee.xml .
846	cp ../../ORCHIDEE/src_xml/file_def_orchidee.xml .
847	cp ../../ORCHIDEE/src_xml/file_def_input_orchidee.xml .
848	if [[ -f ../../ORCHIDEE/src_xml/context_input_orchidee.xml ]]; then
849	cp ../../ORCHIDEE/src_xml/context_input_orchidee.xml .
850	echo '<context id="orchidee" src="./context_input_orchidee.xml"/>' >> add.tmp
851	fi
852	sed -e '/id="LMDZ"/r add.tmp' iodef.xml > tmp
853	mv tmp iodef.xml
854	sed -e'{/sechiba1/ s/enabled="_AUTO_"/type="one_file" enabled=".TRUE."/}' \
855	file_def_orchidee.xml > tmp
856	\mv -f tmp file_def_orchidee.xml
857	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
858	file_def_orchidee.xml > tmp
859	\mv -f tmp file_def_orchidee.xml
860	sed -e 's@output_level="_AUTO_"@output_level="1"@' \
861	file_def_orchidee.xml > tmp
862	\mv -f tmp file_def_orchidee.xml
863	sed -e 's@output_freq="_AUTO_"@output_freq="1d"@' \
864	file_def_orchidee.xml > tmp
865	\mv -f tmp file_def_orchidee.xml
866	sed -e 's@compression_level="4"@compression_level="0"@' \
867	file_def_orchidee.xml > tmp
868	\mv -f tmp file_def_orchidee.xml
869	sed -e 's@XIOS_ORCHIDEE_OK = n@XIOS_ORCHIDEE_OK = y@' \
870	orchidee.def > tmp
871	\mv -f tmp orchidee.def
872	fi
873	fi
874
875	if [[ -f ../arch.env ]]; then source ../arch.env; fi
876
877	echo "EXECUTION DU BENCH"
878	date
879	if (! $bench_cmd > out.bench 2>&1) \|\| ! (tail -n 1 listing \| grep "Everything is cool"); then
880	tail listing
881	echo "Bench FAILED, exiting"; exit 1
882	fi
883	date
884	tail listing
885	fi
886
887	# 1D case
888	if [[ $SCM = 1 ]]; then
889	cd "$MODEL"
890	myget 1D/1D.tar.gz
891	tar xf 1D.tar.gz
892	cd 1D
893	if [[ $rad = "oldrad" ]]; then
894	sed -i'' -e 's/^rad=.*$/rad=oldrad/' run.sh
895	sed -i'' -e 's/^rad=.*$/rad=oldrad/' bin/compile
896	elif [[ $rad = ecrad ]] ; then
897	sed -i'' -e 's/^rad=.*$/rad=ecrad/' run.sh
898	sed -i'' -e 's/^rad=.*$/rad=ecrad/' bin/compile
899	fi
900	echo "Running 1D/run.sh, log in $(pwd)/run1d.log"
901	./run.sh > "$(pwd)/run1d.log" 2>&1
902	fi
903	}
904
905	# If sourced: returns, else run setup
906	if [[ ! "${BASH_SOURCE[0]}" = "$0" ]]; then return 0; fi
907
908	echo "install_lmdz.sh DEBUT $(date)"
909
910	set_default_params
911	read_cmdline_args "$@"
912	ensure_correct_option_combinations
913	#download_model
914	create_model_tar
915	init_arch
916	check_available_software
917	get_lmdz_version
918	get_orchidee_version
919	install_netcdf
920	install_IOIPSL
921	install_XIOS
922	compile_orchidee
923	compile_lmdz
924	run_bench

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