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source: BOL/script_install_amaury/install_lmdz.sh @ 4995

Last change on this file since 4995 was 4994, checked in by abarral, 4 months ago
add new JEANZAY arch fix env supplied in modipsl/config bugfix related to modipsl/config arch retrieval fix orcbranch only computed if svn rev doesnt match current fix orc&lmdz svn retrieval
Property svn:executable set to ``*
File size: 34.4 KB

Line
1	#!/bin/bash
2	set -eu # error on command failure, and on unset variables
3	export LC_ALL=C # standardize awk format
4
5	###########################################################################
6	# Author : Laurent Fairhead et Frédéric Hourdin
7	# Usage : install_lmdz.sh -help
8	#
9	# bash installation script of the LMDZ model on different computer types :
10	# Linux PC, "mesocentre" (IPSL-UPMC, IPSL-X), super-computer (IDRIS)
11	#
12	# The model is downloaded in the following directory tree
13	# $MODEL/modipsl/modeles/...
14	# using the "modipsl" infrastructure created by the "IPSL"
15	# for coupled (atmosphere/ocean/vegetation/chemistry) climate modeling
16	# activities.
17	# Here we only download atmospheric (LMDZ) and vegetation (ORCHIDEE)
18	# components.
19	#
20	# The sources of the models can be found in the "modeles" directory.
21	# In the present case, LMDZ, ORCHIDEE, and IOIPSL or XIOS (handling of
22	# input-outputs using the NetCDF library).
23	#
24	# The script downloads various source files (including a version of NetCDF)
25	# and utilities, compiles the model, and runs a test simulation in a
26	# minimal configuration.
27	#
28	# Prerequisites : gfortran, bash or ksh, wget, gunzip, tar, ...
29	#
30	# Modif 18/11/2011
31	# changes for option real 8.
32	# We compile with -r8 (or equivalent) and -DNC_DOUBLE for the GCM
33	# but with -r4 for netcdf. Variable real must be set to
34	# r4 or r8 at the beginning of the script below.
35	#
36	###########################################################################
37
38	### Functions
39
40	function myget {
41	# Get a file from LMDZ repository, make it executable if .(ba)sh
42	local url=$1
43
44	local filename
45	filename=$(basename "$url")
46
47	wget --no-check-certificate -nv "http://lmdz.lmd.jussieu.fr/pub/$url"
48	if [[ $filename =~ .*\.(ba)?sh ]]; then chmod +x "$filename"; fi
49	}
50
51	function 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 [only orch>2.0] (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	if [[ $aerosols = 1 && $rad != "rrtm" ]]; then
282	echo "STOP: For the time being, <aerosols=spla> requires <rad=rrtm>"; exit 1
283	fi
284	# TODO: vérifier quelles contraintes sont des contraintes lmdzsetup, et lesquelles sont des vraies contraintes
285	}
286
287	function check_available_software {
288	echo "################################################################"
289	echo "Check if required software is available"
290	echo "################################################################"
291	for logiciel in wget tar gzip make gcc cmake m4 c++; do
292	if [[ $(which "$logiciel") = "" ]]; then
293	echo "You must first install $logiciel on your system"; exit 1
294	fi
295	done
296
297	cat <<eod > tt.f90
298	print*,'coucou'
299	end
300	eod
301	$compiler tt.f90 \|\| a.out
302	./a.out >\| tt
303	if [[ $(< tt sed -e 's/ //g' ) != "coucou" ]]; then
304	echo "problem installing with compiler $compiler"; exit 1
305	fi
306	\rm tt a.out tt.f90
307	}
308
309	function download_model {
310	if [[ $clean_install = 1 ]]; then rm -rf "$MODEL"; fi
311
312	mkdir -p "$MODEL"
313	MODEL=$(readlink -e -f "$MODEL"); echo "$MODEL" # absolute path
314	if [[ ! -f "$MODEL/modipsl" ]]; then
315	echo "##########################################################"
316	echo "Download a slightly modified version of LMDZ"
317	echo "##########################################################"
318	cd "$MODEL"
319	getlog="$(pwd)/get.log"
320	echo "logfile : $getlog"
321	myget "src_archives/$trusting/modipsl.$version.tar.gz" >> get.log 2>&1
322	echo "install_lmdz.sh wget_OK $(date)"
323	gunzip "modipsl.$version.tar.gz" >> get.log 2>&1
324	tar xf "modipsl.$version.tar" >> get.log 2>&1
325	\rm "modipsl.$version.tar"
326	fi
327	}
328
329	function create_model_tar { # TODO TEMP while waiting for tar: we copy the base from a local path = IPSLCM7 + ORCH2.2 8504
330	if [[ ! -d ../MODEL_REF ]]; then
331	cd ..
332	mkdir MODEL_REF
333	cd MODEL_REF
334	# Base is IPSLCM7
335	svn co --username icmc_users https://forge.ipsl.fr/igcmg/svn/modipsl/trunk modipsl
336	cd modipsl/util
337	./model IPSLCM7_work
338	# Remove unused components
339	rm -rf ../oasis3-mct
340	cd ../modeles
341	rm -rf ICOSA_LMDZ ORCHIDEE_4 ORCHIDEE_2_2 NEMO DYNAMICO XIOS INCA
342	# Retrieve orch version
343	svn co svn://forge.ipsl.fr/orchidee/branches/ORCHIDEE_2_2/ORCHIDEE -r 8504
344	# Correct orchidee bug in 8504
345	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
346
347	echo "STOP: INITIALIZED, PLEASE RELAUNCH ONCE"; exit 1
348	fi
349
350	if [[ ! -d "$MODEL" ]]; then
351	\cp -r ../MODEL_REF .
352	mv MODEL_REF "$MODEL"
353	fi
354	MODEL=$(readlink -e -f "$MODEL"); echo "$MODEL" # absolute path
355	}
356
357	function init_arch {
358	arch_dir=$(readlink -e -f "$arch_dir") # full path. readlink must be called after the path is created
359	if [[ ! -d $arch_dir ]]; then
360	echo "STOP: no arch dir $arch_dir"; exit 1
361	fi
362
363	local fcm_path
364	if [[ -f $arch_dir/arch-$arch.fcm ]]; then
365	fcm_path="$arch_dir/arch-$arch.fcm"
366	else
367	fcm_path="$MODEL/modipsl/modeles/LMDZ/arch/arch-$arch.fcm"
368	if [[ ! -f $fcm_path ]]; then
369	echo "STOP: no $fcm_path"; exit 1
370	fi
371	fi
372
373	local env_path
374	if [[ -f $arch_dir/arch-$arch.env ]]; then
375	env_path="$arch_dir/arch-$arch.env"
376	else
377	env_path="$MODEL/modipsl/modeles/LMDZ/arch/arch-$arch.env"
378	if [[ ! -f $env_path ]]; then
379	echo "STOP: no $env_path"; exit 1
380	fi
381	fi
382
383	# check compiler
384	compiler=$(< "$fcm_path" grep "%COMPILER" \| sed -e "s/%COMPILER\s*//")
385
386	# load env
387	# shellcheck disable=SC1090
388	if [[ -f $env_path ]]; then source "$env_path"; fi
389	}
390
391	function install_arch {
392	local component=$1
393
394	if [[ -f "$arch_dir/arch-$arch.env" ]]; then
395	cp -f "$arch_dir/arch-$arch."{fcm,path,env} "$MODEL/modipsl/modeles/$component/arch" &> /dev/null \|\| true # allow failure if doesn't exist
396
397	if [[ $component = "XIOS" ]]; then
398	# Adapt for XIOS, which uses different naming conventions
399	sed -i'' -e "s/%COMPILER/%FCOMPILER/" -e "s/%LINK/%LINKER/" -e "s/-fdefault-real-8//" "$MODEL/modipsl/modeles/XIOS/arch/arch-$arch.fcm"
400	elif [[ $component = "ORCHIDEE" ]]; then
401	if [[ $orcbranch = "/tags/ORCHIDEE_2_0/ORCHIDEE" ]]; then # 2.0 and before have a different fcm convention
402	sed -i'' -e "s/-I//" -e "s/-L//" "$MODEL/modipsl/modeles/ORCHIDEE/arch/arch-$arch.path" # /!\ we only replace first occurence on purpose
403	fi
404	fi
405	fi
406	}
407
408	function install_netcdf {
409	echo "Installing Netcdf"
410	local ncdf_compiler="$compiler"
411
412	if [[ $netcdf = 0 ]]; then
413	ncdfdir=$(nf-config --prefix)
414	else
415	cd "$MODEL"
416
417	# Convert non-basic compiler
418	case $compiler in
419	mpif90) ncdf_compiler=$($compiler --version \| head -n 1 \| cut -d " " -f -1)
420	esac
421
422	case $ncdf_compiler in
423	gfortran \| GNU) ncdf_compiler="gfortran"; opt1="-compiler gnu"; opt2="-CC gcc -FC gfortran -CXX g++";;
424	*) echo "unexpected compiler $ncdf_compiler for netcdf"; exit 1
425	esac
426
427	case $with_xios in
428	0) script_install_netcdf="install_netcdf4_hdf5_seq.bash"
429	ncdfdir="netcdf4_hdf5_seq"
430	opt_="$opt1";;
431	1) script_install_netcdf="install_netcdf4_hdf5.bash"
432	ncdfdir="netcdf4_hdf5"
433	opt_="$opt2 -MPI $root_mpi";;
434	*) echo "with_xios=$with_xios, should be 0 or 1"; exit 1
435	esac
436	if [[ $netcdf = 1 ]]; then
437	ncdfdir="$MODEL/$ncdfdir"
438	else
439	mkdir -p "$netcdf"; ncdfdir="$netcdf/$ncdfdir"
440	fi
441
442	echo "Repertoire netcdf $ncdfdir"
443	if [[ ! -d $ncdfdir ]]; then
444	netcdflog=$(pwd)/netcdf.log
445	echo "----------------------------------------------------------"
446	echo "Compiling the Netcdf library"
447	echo "----------------------------------------------------------"
448	echo "log file : $netcdflog"
449	myget script_install/$script_install_netcdf >> "$netcdflog" 2>&1
450	chmod u=rwx $script_install_netcdf
451	# shellcheck disable=SC2086
452	./$script_install_netcdf -prefix "$ncdfdir" $opt_ >> "$netcdflog" 2>&1
453	fi
454
455	# Add to path
456	export PATH="$ncdfdir/bin:$PATH"
457
458	#----------------------------------------------------------------------------
459	# LF rajout d'une verrue, pour une raison non encore expliquee,
460	# la librairie est parfois rangée dans lib64 et non dans lib
461	# par certains compilateurs
462	if [[ ! -e lib && -d lib64 ]]; then ln -s lib64 lib; fi
463	#----------------------------------------------------------------------------
464
465	echo "install_lmdz.sh netcdf_OK $(date)"
466	fi
467
468	cat >test_netcdf90.f90 <<EOF
469	use netcdf
470	print *, "NetCDF library version: ", nf90_inq_libvers()
471	end
472	EOF
473
474	if $ncdf_compiler -I"$ncdfdir"/include test_netcdf90.f90 -L"$ncdfdir"/lib -lnetcdff -lnetcdf -Wl,-rpath="$ncdfdir"/lib && ./a.out; then
475	\rm test_netcdf90.f90 a.out
476	else
477	cat <<EOF
478	Failed test program using NetCDF-Fortran. You can:
479	- check that you have NetCDF-Fortran installed in your system
480	- or specify an installation directory with option -netcdf of install_lmdz.sh
481	- or download and compile NetCDF-Fortran with option -netcdf 1 of install_lmdz.sh
482	EOF
483	exit 1
484	fi
485
486	# Compile NetCDF95
487	cd "$MODEL/modipsl/modeles/LMD"*
488	echo "Installing NetCDF95"
489	cd "$MODEL"
490	if [[ ! -d "NetCDF95-0.3" ]]; then
491	myget src_archives/netcdf/NetCDF95-0.3.tar.gz
492	tar -xf NetCDF95-0.3.tar.gz
493	\rm NetCDF95-0.3.tar.gz
494	cd NetCDF95-0.3
495	mkdir -p build && cd build
496	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"
497	make install
498	fi
499	}
500
501	function install_IOIPSL {
502	install_arch "IOIPSL"
503
504	cd "$MODEL/modipsl/modeles/IOIPSL"
505	ioipsllog="$(pwd)/ioipsl.log"
506	echo "Compiling IOIPSL, the interface library with Netcdf $(date) (log: $ioipsllog)"
507
508	if ! ./makeioipsl_fcm -arch "$arch" -job 8 > "$ioipsllog" 2>&1; then
509	echo "IOIPSL compile failed, exiting"; exit 1
510	fi
511
512	# Link to modipsl/bin
513	cp -f bin/* ../../bin
514
515	echo "IOIPSL compiled $(date)"
516	}
517
518	function install_XIOS {
519	if [[ $with_xios = 1 ]]; then
520	cd "$MODEL/modipsl/modeles"
521	xioslog="$(pwd)/XIOS/xios.log"
522	echo "##########################################################"
523	echo "Compiling XIOS (log $xioslog) $(date)"
524	echo "##########################################################"
525
526	# Download XIOS
527	local xios_http="http://forge.ipsl.fr/ioserver/svn/XIOS2/branches/xios-2.6"
528	local xios_rev="2568"
529
530	cd "$MODEL/modipsl/modeles"
531	set +e; svn co -r $xios_rev $xios_http XIOS; set -e
532
533	cd XIOS
534
535	install_arch "XIOS"
536
537	echo "Starting XIOS compilation"
538	if ! ./make_xios --arch "$arch" --job 8 > "$xioslog" 2>&1; then
539	echo "XIOS compilation failed, exiting"; exit 1
540	fi
541
542	echo "Compiled XIOS $(date)"
543	fi
544	}
545
546	function get_orchidee_version { # Set / Check ORCHIDEE version
547	local fetch_rev=""
548	orcbranch=""
549	case $veget in
550	"none") fcm_veget_version="false";;
551	"orch2.0" \| "CMIP6") fcm_veget_version=orchidee2.0; fetch_rev=7906;; # in previous tar we used 6592 but with some modifications to xios_orchidee.f90, which got integrated in 7906
552	"orch2.2") fcm_veget_version=orchidee2.1; orcbranch="ORCHIDEE_2_2" ;; # the bundled version
553	*) fetch_rev=$veget; fcm_veget_version=orchidee2.1;; # /!\ arbitary rev only works for orch>=2.1
554	esac
555
556	if [[ -n $fetch_rev ]]; then
557	local curr_rev
558	curr_rev=$(svn info "$MODEL/modipsl/modeles/ORCHIDEE" \| grep Revision: \| cut -d ":" -f 2 \| cut -c 2-)
559	orcbranch=$(svn log -v -q svn://forge.ipsl.fr/orchidee/ -r "$fetch_rev" \| grep ORCHIDEE \| head -1 \| sed -e 's:ORCHIDEE/.*$:ORCHIDEE:' \| awk '{print $2}')
560	if [[ $fetch_rev != "$curr_rev" ]]; then
561	echo "Fetching orch $fetch_rev from the repository (curr: $curr_rev)"
562	echo "branch is $orcbranch"
563	if [[ $fetch_rev -lt 4465 ]]; then echo 'ORCHIDEE version must be >=4465, exiting'; exit 1; fi
564	echo "IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at orchidee-help@listes.ipsl.fr"
565	cd "$MODEL/modipsl/modeles"
566	rm -rf ORCHIDEE
567	svn co -r "$fetch_rev" "svn://forge.ipsl.fr/orchidee/$orcbranch"
568	cd - > /dev/null
569	fi
570	fi
571
572	# Check parallel LMDZ+ORCH
573	if [[ (! $veget = "none") && $parallel = "none" && ($used_lmdz_rev -lt 4894) ]]; then
574	echo "LMDZ revision must be >=4894 for orchidee without parallel support. Upgrade lmdz or use -parallel mpi_omp."; exit 1
575	fi
576	}
577
578	function compile_orchidee {
579	install_arch "ORCHIDEE"
580
581	if [[ $veget != "none" ]]; then
582	cd "$MODEL/modipsl/modeles/ORCHIDEE"
583
584	orchideelog="$(pwd)/orchidee.log"
585	echo "Compiling ORCHIDEE, the continental surface model (log $orchideelog) $(date)"
586
587	local xios_orchid opt_orc
588	if [[ $with_xios = 1 ]]; then
589	xios_orchid="-xios";
590	else
591	xios_orchid="-noxios"
592	fi
593	if [[ $optim_debug = "-debug" ]]; then
594	opt_orc="-debug";
595	else
596	opt_orc="-prod"
597	fi
598
599	if [[ $parallel = "none" ]]; then
600	echo "./makeorchidee_fcm $xios_orchid $opt_orc -parallel none -arch $arch -j $make_j" > compile.sh
601	else
602	if [[ ! -d src_parallel ]]; then
603	echo "Orchidee version too old for parallel support"; exit 1
604	fi
605	{
606	echo "./makeorchidee_fcm -j $make_j $xios_orchid $opt_orc -parallel $parallel -arch $arch"
607	} > compile.sh
608	fi
609	chmod +x compile.sh
610	echo "Compiling ORCHIDEE using $(\cat compile.sh)"
611	if ! ./compile.sh > "$orchideelog" 2>&1; then
612	echo "ORCHIDEE compilation failed, exiting"; exit 1
613	fi
614	echo "Compiled ORCHIDEE $(date)"
615	fi
616	}
617
618	function get_lmdz_version {
619	LMDZPATH=$(readlink -e -f "$MODEL/modipsl/modeles/LMD"*)
620	cd "$LMDZPATH"
621	lmdzlog="$(pwd)/lmdz.log"
622
623	if [[ -n $svn_lmdz ]]; then
624	local curr_rev
625	curr_rev=$(svn info "$MODEL/modipsl/modeles/LMD"* \| grep Revision: \| cut -d ":" -f 2)
626	if [[ $svn_lmdz != "$curr_rev" ]]; then
627	local lmdzbranch
628	echo "Fetching LMDZ $svn_lmdz from the repository"
629	lmdzbranch=$(svn log -v -q https://svn.lmd.jussieu.fr/LMDZ -r "$svn_lmdz" \| grep LMDZ \| head -1 \| sed -e 's:trunk/.*$:trunk:' \| awk '{print $2}')
630	cd "$MODEL/modipsl/modeles"
631	rm -rf LMD*
632	svn co -r "$svn_lmdz" "https://svn.lmd.jussieu.fr/LMDZ$lmdzbranch" LMDZ
633	cd - > /dev/null
634	fi
635	else # get svn from info
636	set +e; used_lmdz_rev=$(svn info \| grep "Last Changed Rev" \| cut -c 19-); set -e
637	if [[ -z $used_lmdz_rev ]]; then # svn info failed
638	used_lmdz_rev=$(grep 'Revision: [0-9]' "$MODEL"/Read*.md \| awk ' { print $2 } ' 2>/dev/null)
639	if [[ -z $used_lmdz_rev ]]; then echo "Could not determine lmdz version. This is likely an issue with the .tar itself, please report to LMDZ team."; exit 1; fi
640	fi
641	fi
642	}
643
644	function compile_lmdz {
645	install_arch "LMDZ"
646	cd "$LMDZPATH"
647
648	if [[ $used_lmdz_rev -le 4185 ]]; then
649	exe_name="bin/gcm_${grid_resolution}_phy${compphysiq}_${suff_para}${suff_orc}${suff_aer}${suff_iso}.e"
650	else
651	exe_name="bin/gcm_${grid_resolution}_phy${compphysiq}_${rad}${suff_para}${suff_orc}${suff_aer}${suff_iso}.e"
652	fi
653
654	local opt_rad
655	case $rad in
656	oldrad) iflag_rrtm=0; NSW=2; opt_rad="";;
657	rrtm) iflag_rrtm=1; NSW=6
658	if [[ $used_lmdz_rev -le 4185 ]]; then
659	opt_rad="-rrtm true"
660	else
661	opt_rad="-rad rrtm"
662	fi;;
663	ecrad) iflag_rrtm=2; NSW=6; opt_rad="-rad ecrad";;
664	*) echo "Only oldrad rrtm ecrad for rad option"; exit 1
665	esac
666	if [[ $used_lmdz_rev -le 4185 && $rad = "ecrad" ]]; then
667	echo "ecrad only available for LMDZ rev starting with 4186 "; exit 1
668	fi
669
670	# Compile
671	makelmdz="makelmdz_fcm $optim_debug -arch $arch -j $make_j"
672	local para_compile_opt="-mem -parallel $parallel"; if [[ $parallel = "none" ]]; then para_compile_opt=""; fi
673	echo "./$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
674	echo "Compiling lmdz using $(\cat compile.sh) (log: $lmdzlog) $(date)"
675	chmod +x ./compile.sh
676	if ! ./compile.sh > "$lmdzlog" 2>&1; then
677	echo "LMDZ compilation failed, exiting"; exit 1
678	fi
679	echo "Finished LMDZ compilation $(date)"
680
681	# Check executable
682	if [[ ! -f $exe_name ]]; then
683	echo "Compilation failed, can't find the executable"; exit 1
684	else
685	echo "Compilation successfull, the executable is $exe_name $(date)"
686	fi
687	}
688
689	function run_bench {
690	cd "$MODEL/modipsl/modeles/LMDZ"*
691
692	if [[ $bench = "tuto" ]]; then
693	myget "Training/tutorial.tar"; tar xf tutorial.tar; cd TUTORIAL
694	./init.sh
695	elif [[ $bench = 1 ]]; then
696	\rm -rf "BENCH${grid_resolution}"
697	local bench=bench_lmdz_${grid_resolution}
698	myget "3DBenchs/$bench.tar.gz"
699	tar xf "$bench.tar.gz"
700
701	if [[ $cosp = "v1" \|\| $cosp = "v2" ]]; then
702	cd "BENCH${grid_resolution}"
703	# copier les fichiers namelist input et output our COSP
704	cp ../DefLists/cosp*_input_nl.txt .
705	cp ../DefLists/cosp*_output_nl.txt .
706	# Activer la cles ok_cosp pour tourner avec COSP
707	sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp
708	\mv -f tmp config.def
709	cd ..
710	fi
711
712	if [[ -n "$benchphysiq" ]]; then
713	cd "BENCH${grid_resolution}"
714	if [[ -f "physiq.def_${benchphysiq}" ]]; then
715	cp "physiq.def_${benchphysiq}" benchphysiq.def
716	echo "using physiq.def_${benchphysiq}"
717	else
718	echo "using standard physiq.def"
719	fi
720	cd ..
721	else
722	echo "using standard physiq.def"
723	fi
724
725	if [[ $with_xios = 1 ]]; then
726	cd "BENCH${grid_resolution}"
727	cp ../DefLists/iodef.xml .
728	cp ../DefLists/context_lmdz.xml .
729	cp ../DefLists/field_def_lmdz.xml .
730	# A raffiner par la suite
731	echo "A FAIRE : Copier les *xml en fonction de l option cosp"
732	cp ../DefLists/field_def_cosp*.xml .
733	cp ../DefLists/file_def_hist*xml .
734	# adapt iodef.xml to use attached mode
735	sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' \
736	iodef.xml > tmp
737	\mv -f tmp iodef.xml
738
739	# and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
740	# except for histday
741	for histfile in file_def_hist*xml; do
742	if [[ "$histfile" = "file_def_histday_lmdz.xml" ]]; then
743	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' \
744	"$histfile" > tmp
745	\mv -f tmp "$histfile"
746	sed -e 's@output_level="_AUTO_"@output_level="5"@' "$histfile" \
747	> tmp
748	\mv -f tmp "$histfile"
749	sed -e 's@compression_level="2"@compression_level="0"@' \
750	"$histfile" > tmp
751	\mv -f tmp "$histfile"
752	else
753	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
754	"$histfile" > tmp
755	\mv -f tmp "$histfile"
756	fi
757	done
758	# and add option "ok_all_xml=y" in config.def
759	echo "### XIOS outputs" >> config.def
760	echo 'ok_all_xml=.true.' >> config.def
761
762	#activer les sorties pour Cosp
763	if [[ "$cosp" = "v1" ]]; then
764	sed -i'' -e 's@enabled=".FALSE."@enabled=".TRUE."@' \
765	-e 's@output_level="_AUTO_"@output_level="5"@' \
766	-e 's@compression_level="2"@compression_level="0"@' \
767	file_def_histdayCOSP_lmdz.xml
768	fi
769	if [[ "$cosp" = "v2" ]]; then
770	sed -i'' -e 's@compression_level="2"@compression_level="0"@' file_def_histdayCOSPv2_lmdz.xml
771	for type_ in hf day mth; do
772	file=file_def_hist${type_}COSP
773	sed -i'' -e 's@src="./'${file}'_lmdz.xml"@src="./'${file}'v2_lmdz.xml"@' context_lmdz.xml
774	done
775	sed -i'' -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' field_def_lmdz.xml
776	fi
777
778	cd ..
779	fi
780
781	# Cas Bench avec ecrad
782	if [[ $rad = "ecrad" ]]; then
783	cd "BENCH${grid_resolution}"
784	cp ../DefLists/namelist_ecrad .
785	cp -r ../libf/phylmd/ecrad/data .
786	cd ..
787	fi
788
789	# Adjusting bench physiq.def to radiative code chosen
790	cd "BENCH${grid_resolution}"
791	sed -e 's/iflag_rrtm=.*.$/iflag_rrtm='$iflag_rrtm'/' \
792	-e 's/NSW=.*.$/NSW='$NSW'/' physiq.def > tmpdef
793	\mv tmpdef physiq.def
794	cd ..
795
796	cp "$exe_name" "BENCH${grid_resolution}/gcm.e"
797	cd "BENCH${grid_resolution}"
798
799	local bench_cmd="./bench.sh"
800	if [[ ${parallel:0:3} = "mpi" ]]; then
801	# Lancement avec deux procs mpi et 2 openMP
802	echo "export OMP_STACKSIZE=800M" > bench.sh
803	if [[ "${parallel:4:3}" = "omp" ]]; then
804	echo "export OMP_NUM_THREADS=2" >> bench.sh
805	fi
806	if [[ $cosp = "v1" \|\| $cosp = "v2" ]]; then
807	echo "ulimit -s 200000" >> bench.sh
808	else
809	echo "ulimit -s unlimited" >> bench.sh
810	fi
811	if which mpirun > /dev/null 2>&1; then
812	echo "mpirun -np 2 gcm.e > listing 2>&1" >> bench.sh
813	elif grep -q "Adastra" /etc/motd; then
814	local account
815	account=$(/usr/sbin/my_project.py -l 2>&1 \| head -1 \| cut -d " " -f 3- \| cut -c 5-)
816	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"
817	echo "./gcm.e > listing 2>&1" >> bench.sh
818	else
819	echo "Error: No command found to run parallel bench"; exit 1
820	fi
821	if [[ $(hostname \| cut -c -6) = "spirit" ]]; then # ulimit unlimited segfaults on Spirit
822	sed -i'' "s/ulimit -s unlimited/ulimit -Ss 8000/" bench.sh
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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