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source: BOL/script_install_amaury/install_lmdz.sh @ 5008

Last change on this file since 5008 was 5008, checked in by abarral, 5 weeks ago
fix lmdz rev retrieval
Property svn:executable set to ``*
File size: 34.5 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 "$path_mpi")
94
95	arch="local-gfortran"
96	arch_dir=""
97
98	jobcmd=""
99	}
100
101	function read_cmdline_args {
102	while (($# > 0)); do
103	case $1 in
104	"-h") cat <<........fin
105	$0 [ -v version ] [ -r svn_release ]
106	[ -parallel PARA ] [ -d GRID_RESOLUTION ] [ -bench 0/1 ]
107	[-name LOCAL_MODEL_NAME] [-rad RADIATIF]
108
109	-v "version" like 20150828.trunk, see http://www.lmd.jussieu.fr/~lmdz/Distrib/LISMOI.trunk (default <$version>)
110
111	-r "svn_release" : either the svn release number or "last" (default <$svn_lmdz>)
112
113	-parallel parallel support: mpi, omp, mpi_omp (mpi with openMP) or none (default: <$parallel>)
114
115	-d "grid resolution": should be among the available benchs if -bench 1 (valid values: 48x36x19, 48x36x39) (default : <$grid_resolution>)
116
117	-bench activating the bench or not (0/1) (default: <$bench>)
118
119	-unstable use unstable tar instead of testing
120
121	-name name of the folder to install to (default <$MODEL>)
122
123	-netcdf 0, 1 or PATH. 0: do not download NetCDF, look for it in standard locations (/usr); 1: download and compile NetCDF; PATH: full path to an existing installed NetCDF library (default: <$netcdf>)
124
125	-xios use (download and compile) the XIOS library (will compile the parallel NetCDF4-HDF5 library) (requires to also have -parallel mpi_omp)
126
127	-cosp to run with cospv1 or cospv2 [none/v1/v2] (default <$cosp>)
128
129	-rad radiative code: oldrad, rrtm or ecrad (default <$rad>)
130
131	-nofcm to compile without fcm
132
133	-SCM install 1D version automatically
134
135	-debug compile everything in debug mode
136
137	-benchphysiq to choose which physics.def package to use in the bench (default <$benchphysiq>)
138
139	-compilephysiq physics to compile the model with (default <$compphysiq>)
140
141	-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 $veget)
142
143	-spla activate interactive aerosols
144
145	-inlandsis activate new snow scheme
146
147	-arch name of the arch to use (default <$arch>)
148
149	-arch_dir where to find the arch files (default <$arch_dir>)
150
151	-make_j number of processes to parallelize installations (default <$make_j>)
152
153	-jobcmd command prepended to fcm compile jobs, e.g. "srun" (default <$jobcmd>)
154
155	-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)
156
157	........fin
158	exit 1;;
159	"-v") version=$2; shift; shift;;
160	"-r") svn_lmdz=$2; shift; shift;;
161	"-d") grid_resolution=$2; shift; shift;;
162	"-unstable") trusting="unstable"; shift;;
163	"-cosp") cosp=$2
164	case $cosp in
165	"none"\|"v1"\|"v2") cosp=$2; shift; shift;;
166	*) echo "Only none v1 v2 for cosp option"; exit 1
167	esac;;
168	"-nofcm") compile_with_fcm=0; echo "This option will be reactivated soon (promesse du 8dec2022)"; exit 1; shift;;
169	"-SCM") SCM=1; shift;;
170	"-rad") rad=$2
171	case $rad in
172	"oldrad"\|"rrtm"\|"ecrad") rad=$2; shift; shift;;
173	*) echo "Only oldrad rrtm ecrad for rad option"; exit 1
174	esac;;
175	"-parallel") parallel=$2
176	case $parallel in
177	"none"\|"mpi"\|"omp"\|"mpi_omp") parallel=$2; shift; shift;;
178	*) echo "Only none mpi omp mpi_omp for the parallel option"; exit 1
179	esac;;
180	"-bench") bench=$2; shift; shift;;
181	"-debug") optim_debug=-debug; shift;;
182	"-name") MODEL=$2; shift; shift;;
183	"-netcdf") netcdf=$2; shift; shift;;
184	"-benchphysiq") benchphysiq=$2; shift; shift;;
185	"-compilephysiq") compphysiq=$2; shift; shift;;
186	"-xios") with_xios=1; shift;;
187	"-arch") arch=$2; shift; shift;;
188	"-arch_dir") arch_dir=$2; shift; shift;;
189	"-veget") veget=$2; shift; shift;;
190	"-spla") aerosols=1; shift;;
191	"-inlandsis") inlandsis=1; shift;;
192	"-make_j") make_j=$2; shift; shift;;
193	"-jobcmd") jobcmd=$2; shift; shift;;
194	"-noclean") clean_install=0; shift;;
195	*) bash install_lmdz.sh -h; exit 1
196	esac
197	done
198
199	# Isotopes : Compile and run with isotopes if lmdz_phys="lmdiso" in main.sh
200	if [[ $compphysiq = "lmdiso" ]]; then isotopes=1; else isotopes=0; fi
201
202	# Option de compilation pour Cosp
203	case $cosp in
204	v1) opt_cosp="-cosp true";;
205	v2) opt_cosp="-cospv2 true";;
206	*) opt_cosp=""
207	esac
208
209	#Define veget-related suffix for gcm name
210	if [[ $veget = 'none' ]]; then
211	suff_orc=''
212	else
213	suff_orc='_orch'
214	fi
215
216
217	if [[ $parallel = "none" ]]; then
218	suff_para='_seq'
219	else
220	suff_para='_para_mem'
221	fi
222
223	if [[ $with_xios = 1 ]]; then opt_makelmdz_xios="-io xios"; fi
224
225	if [[ $aerosols = 1 ]]; then
226	opt_aer="-dust true"; suff_aer="_spla"
227	else
228	opt_aer=""; suff_aer=""
229	fi
230
231	if [[ $inlandsis = 1 ]]; then
232	opt_inlandsis="-inlandsis true"
233	else
234	opt_inlandsis=""
235	fi
236
237	if [[ $isotopes = 1 ]]; then
238	opt_isotopes="-isotopes true"; suff_iso="_iso"
239	else
240	opt_isotopes="" ; suff_iso=""
241	fi
242
243
244	# Name of the model's folder. The convention taken here is that models that requires different compilation sources should have a different names.
245	local xios_name=""
246	if [[ $with_xios = 1 ]]; then xios_name="XIOS"; fi
247	if [[ $MODEL = "" ]]; then MODEL="./LMDZ$version${svn_lmdz}OR$veget$xios_name"; fi
248
249	if [[ $arch_dir = "" ]]; then arch_dir="$MODEL/modipsl/config/IPSLCM7/ARCH/"; fi
250	}
251
252	function ensure_correct_option_combinations {
253	# Check on veget version
254	if [[ $veget != 'none' && $veget != "CMIP6" && $veget != "orch2.0" && $veget != "orch2.2" ]]; then
255	re='^[0-9]+$'
256	if ! [[ $veget =~ $re ]]; then
257	echo 'Valeur de l option veget non valable'; exit 1
258	fi
259	fi
260
261	## if also compiling XIOS, parallel must be mpi_omp
262	if [[ $with_xios = 1 && $parallel != "mpi_omp" ]]; then
263	echo "Error, you must set -parallel mpi_omp if you want XIOS"; exit 1
264	fi
265
266	if [[ $cosp = "v2" && $with_xios = 0 ]]; then
267	echo "Error, Cospv2 cannot run without Xios"; exit 1
268	fi
269
270	# STOP if trying to use both ORCHIDEE and Isotopes :
271	if [[ $isotopes = 1 && $veget != "none" ]]; then
272	echo "STOP: You cannot run LMDZ with ORCHIDEE and ISOtopes at the same time"; exit 1
273	fi
274
275	# STOP if trying to use both SPLA and Isotopes :
276	if [[ $isotopes = 1 && $aerosols = 1 ]]; then
277	echo "STOP: You cannot run LMDZ with Isotopes and aerosols=spla at the same time"; exit 1
278	fi
279
280	# (Temporary) STOP if trying to use Isotopes with XIOS :
281	# TODO Amaury: check if still relevant
282	if [[ $isotopes = 1 && $with_xios = 1 ]]; then
283	echo "STOP: Isotopes cannont yet be run with XIOS"; exit 1
284	fi
285
286	if [[ $aerosols = 1 && $rad != "rrtm" ]]; then
287	echo "STOP: For the time being, <aerosols=spla> requires <rad=rrtm>"; exit 1
288	fi
289	# TODO: vérifier quelles contraintes sont des contraintes lmdzsetup, et lesquelles sont des vraies contraintes
290	}
291
292	function check_available_software {
293	echo "################################################################"
294	echo "Check if required software is available"
295	echo "################################################################"
296	for logiciel in wget tar gzip make gcc cmake m4 c++; do
297	if [[ $(which "$logiciel") = "" ]]; then
298	echo "You must first install $logiciel on your system"; exit 1
299	fi
300	done
301
302	cat <<eod > tt.f90
303	print*,'coucou'
304	end
305	eod
306	$compiler tt.f90 \|\| a.out
307	./a.out >\| tt
308	if [[ $(< tt sed -e 's/ //g' ) != "coucou" ]]; then
309	echo "problem installing with compiler $compiler"; exit 1
310	fi
311	\rm tt a.out tt.f90
312	}
313
314	function download_model {
315	if [[ $clean_install = 1 ]]; then rm -rf "$MODEL"; fi
316
317	mkdir -p "$MODEL"
318	MODEL=$(readlink -e -f "$MODEL"); echo "$MODEL" # absolute path
319	if [[ ! -f "$MODEL/modipsl" ]]; then
320	echo "##########################################################"
321	echo "Download a slightly modified version of LMDZ"
322	echo "##########################################################"
323	cd "$MODEL"
324	getlog="$(pwd)/get.log"
325	echo "logfile : $getlog"
326	myget "src_archives/$trusting/modipsl.$version.tar.gz" &>> get.log
327	echo "install_lmdz.sh wget_OK $(date)"
328	gunzip "modipsl.$version.tar.gz" &>> get.log
329	tar xf "modipsl.$version.tar" &>> get.log
330	\rm "modipsl.$version.tar"
331	fi
332	}
333
334	function create_model_tar { # TODO TEMP while waiting for tar: we copy the base from a local path = IPSLCM7 + ORCH2.2 8504
335	if [[ ! -d ../MODEL_REF ]]; then
336	cd ..
337	mkdir MODEL_REF
338	cd MODEL_REF
339	# Base is IPSLCM7
340	svn co --username icmc_users https://forge.ipsl.fr/igcmg/svn/modipsl/trunk modipsl
341	cd modipsl/util
342	./model IPSLCM7_work
343	# Remove unused components
344	rm -rf ../oasis3-mct
345	cd ../modeles
346	rm -rf ICOSA_LMDZ ORCHIDEE_4 ORCHIDEE_2_2 NEMO DYNAMICO XIOS INCA
347	# Retrieve orch version
348	svn co svn://forge.ipsl.fr/orchidee/branches/ORCHIDEE_2_2/ORCHIDEE -r 8504
349	# Correct orchidee bug in 8504
350	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
351
352	echo "STOP: INITIALIZED, PLEASE RELAUNCH ONCE"; exit 1
353	fi
354
355	if [[ ! -d "$MODEL" ]]; then
356	\cp -r ../MODEL_REF .
357	mv MODEL_REF "$MODEL"
358	fi
359	MODEL=$(readlink -e -f "$MODEL"); echo "$MODEL" # absolute path
360	}
361
362	function init_arch {
363	arch_dir=$(readlink -e -f "$arch_dir") # full path. readlink must be called after the path is created
364	if [[ ! -d $arch_dir ]]; then
365	echo "STOP: no arch dir $arch_dir"; exit 1
366	fi
367
368	local fcm_path
369	if [[ -f $arch_dir/arch-$arch.fcm ]]; then
370	fcm_path="$arch_dir/arch-$arch.fcm"
371	else
372	fcm_path="$MODEL/modipsl/modeles/LMDZ/arch/arch-$arch.fcm"
373	if [[ ! -f $fcm_path ]]; then
374	echo "STOP: no $fcm_path"; exit 1
375	fi
376	fi
377
378	local env_path
379	if [[ -f $arch_dir/arch-$arch.env ]]; then
380	env_path="$arch_dir/arch-$arch.env"
381	else
382	env_path="$MODEL/modipsl/modeles/LMDZ/arch/arch-$arch.env"
383	if [[ ! -f $env_path ]]; then
384	echo "STOP: no $env_path"; exit 1
385	fi
386	fi
387
388	# check compiler
389	compiler=$(< "$fcm_path" grep "%COMPILER" \| sed -e "s/%COMPILER\s*//")
390
391	# load env
392	# shellcheck disable=SC1090
393	if [[ -f $env_path ]]; then source "$env_path"; fi
394	}
395
396	function install_arch {
397	local component=$1
398
399	if [[ -f "$arch_dir/arch-$arch.env" ]]; then
400	cp -f "$arch_dir/arch-$arch."{fcm,path,env} "$MODEL/modipsl/modeles/$component/arch" &> /dev/null \|\| true # allow failure if doesn't exist
401
402	if [[ $component = "XIOS" ]]; then
403	# Adapt for XIOS, which uses different naming conventions
404	sed -i'' -e "s/%COMPILER/%FCOMPILER/" -e "s/%LINK/%LINKER/" -e "s/-fdefault-real-8//" "$MODEL/modipsl/modeles/XIOS/arch/arch-$arch.fcm"
405	elif [[ $component = "ORCHIDEE" ]]; then
406	if [[ $orcbranch = "/tags/ORCHIDEE_2_0/ORCHIDEE" ]]; then # 2.0 and before have a different fcm convention
407	sed -i'' -e "s/-I//" -e "s/-L//" "$MODEL/modipsl/modeles/ORCHIDEE/arch/arch-$arch.path" # /!\ we only replace first occurence on purpose
408	fi
409	fi
410	fi
411	}
412
413	function install_netcdf {
414	echo "Installing Netcdf"
415	local ncdf_compiler="$compiler"
416
417	if [[ $netcdf = 0 ]]; then
418	ncdfdir=$(nf-config --prefix)
419	else
420	cd "$MODEL"
421
422	# Convert non-basic compiler
423	case $compiler in
424	mpif90) ncdf_compiler=$($compiler --version \| head -n 1 \| cut -d " " -f -1)
425	esac
426
427	case $ncdf_compiler in
428	gfortran \| GNU) ncdf_compiler="gfortran"; opt1="-compiler gnu"; opt2="-CC gcc -FC gfortran -CXX g++";;
429	*) echo "unexpected compiler $ncdf_compiler for netcdf"; exit 1
430	esac
431
432	case $with_xios in
433	0) script_install_netcdf="install_netcdf4_hdf5_seq.bash"
434	ncdfdir="netcdf4_hdf5_seq"
435	opt_="$opt1";;
436	1) script_install_netcdf="install_netcdf4_hdf5.bash"
437	ncdfdir="netcdf4_hdf5"
438	opt_="$opt2 -MPI $root_mpi";;
439	*) echo "with_xios=$with_xios, should be 0 or 1"; exit 1
440	esac
441	if [[ $netcdf = 1 ]]; then
442	ncdfdir="$MODEL/$ncdfdir"
443	else
444	mkdir -p "$netcdf"; ncdfdir="$netcdf/$ncdfdir"
445	fi
446
447	echo "Repertoire netcdf $ncdfdir"
448	if [[ ! -d $ncdfdir ]]; then
449	netcdflog=$(pwd)/netcdf.log
450	echo "----------------------------------------------------------"
451	echo "Compiling the Netcdf library"
452	echo "----------------------------------------------------------"
453	echo "log file : $netcdflog"
454	myget script_install/$script_install_netcdf &>> "$netcdflog"
455	chmod u=rwx $script_install_netcdf
456	# shellcheck disable=SC2086
457	./$script_install_netcdf -prefix "$ncdfdir" $opt_ &>> "$netcdflog"
458	fi
459
460	# Add to path
461	export PATH="$ncdfdir/bin:$PATH"
462
463	#----------------------------------------------------------------------------
464	# LF rajout d'une verrue, pour une raison non encore expliquee,
465	# la librairie est parfois rangée dans lib64 et non dans lib
466	# par certains compilateurs
467	if [[ ! -e lib && -d lib64 ]]; then ln -s lib64 lib; fi
468	#----------------------------------------------------------------------------
469
470	echo "install_lmdz.sh netcdf_OK $(date)"
471	fi
472
473	cat >test_netcdf90.f90 <<EOF
474	use netcdf
475	print *, "NetCDF library version: ", nf90_inq_libvers()
476	end
477	EOF
478
479	if $ncdf_compiler -I"$ncdfdir"/include test_netcdf90.f90 -L"$ncdfdir"/lib -lnetcdff -lnetcdf -Wl,-rpath="$ncdfdir"/lib && ./a.out; then
480	\rm test_netcdf90.f90 a.out
481	else
482	cat <<EOF
483	Failed test program using NetCDF-Fortran. You can:
484	- check that you have NetCDF-Fortran installed in your system
485	- or specify an installation directory with option -netcdf of install_lmdz.sh
486	- or download and compile NetCDF-Fortran with option -netcdf 1 of install_lmdz.sh
487	EOF
488	exit 1
489	fi
490
491	# Compile NetCDF95
492	cd "$MODEL/modipsl/modeles/LMD"*
493	echo "Installing NetCDF95"
494	cd "$MODEL"
495	if [[ ! -d "NetCDF95-0.3" ]]; then
496	myget src_archives/netcdf/NetCDF95-0.3.tar.gz
497	tar -xf NetCDF95-0.3.tar.gz
498	\rm NetCDF95-0.3.tar.gz
499	cd NetCDF95-0.3
500	mkdir -p build && cd build
501	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"
502	make install
503	fi
504	}
505
506	function install_IOIPSL {
507	install_arch "IOIPSL"
508
509	cd "$MODEL/modipsl/modeles/IOIPSL"
510	ioipsllog="$(pwd)/ioipsl.log"
511	echo "Compiling IOIPSL, the interface library with Netcdf $(date) (log: $ioipsllog)"
512
513	echo "$jobcmd ./makeioipsl_fcm -j $make_j -arch $arch" > compile.sh
514	chmod +x compile.sh
515	echo "Compiling IOIPSL using $(\cat compile.sh)"
516	if ! ./compile.sh &> "$ioipsllog"; then
517	echo "STOP: IOIPSL compile failed, exiting"; exit 1
518	fi
519
520	# Link to modipsl/bin
521	cp -f bin/* ../../bin
522
523	echo "IOIPSL compiled $(date)"
524	}
525
526	function install_XIOS {
527	if [[ $with_xios = 1 ]]; then
528	cd "$MODEL/modipsl/modeles"
529	xioslog="$(pwd)/XIOS/xios.log"
530	echo "##########################################################"
531	echo "Compiling XIOS (log $xioslog) $(date)"
532	echo "##########################################################"
533
534	# Download XIOS
535	local xios_http="http://forge.ipsl.fr/ioserver/svn/XIOS2/branches/xios-2.6"
536	local xios_rev="2568"
537
538	cd "$MODEL/modipsl/modeles"
539	set +e; svn co -r $xios_rev $xios_http XIOS; set -e
540
541	cd XIOS
542
543	install_arch "XIOS"
544
545	echo "Starting XIOS compilation"
546	if ! ./make_xios --arch "$arch" --job 8 &> "$xioslog"; then
547	echo "STOP: XIOS compilation failed, exiting"; exit 1
548	fi
549
550	echo "Compiled XIOS $(date)"
551	fi
552	}
553
554	function get_orchidee_version { # Set / Check ORCHIDEE version
555	local fetch_rev=""
556	orcbranch=""
557	case $veget in
558	"none") fcm_veget_version="false";;
559	"orch2.0" \| "CMIP6") fcm_veget_version=orchidee2.0; fetch_rev=7906;; # in previous tar we used 6592 but with some modifications to xios_orchidee.f90, which got integrated in 7906
560	"orch2.2") fcm_veget_version=orchidee2.1; orcbranch="/branches/ORCHIDEE_2_2/ORCHIDEE" ;; # the bundled version
561	*) fetch_rev=$veget; fcm_veget_version=orchidee2.1;; # /!\ arbitary rev only works for orch>=2.1
562	esac
563
564	if [[ -n $fetch_rev ]]; then
565	local curr_rev
566	curr_rev=$(svn info "$MODEL/modipsl/modeles/ORCHIDEE" \| grep Revision: \| cut -d ":" -f 2 \| cut -c 2-)
567	orcbranch=$(svn log -v -q svn://forge.ipsl.fr/orchidee/ -r "$fetch_rev" \| grep ORCHIDEE \| head -1 \| sed -e 's:ORCHIDEE/.*$:ORCHIDEE:' \| awk '{print $2}')
568	if [[ $fetch_rev != "$curr_rev" ]]; then
569	echo "Fetching orch $fetch_rev from the repository (curr: $curr_rev)"
570	echo "branch is $orcbranch"
571	if [[ $fetch_rev -lt 4465 ]]; then echo 'ORCHIDEE version must be >=4465, exiting'; exit 1; fi
572	echo "IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at orchidee-help@listes.ipsl.fr"
573	cd "$MODEL/modipsl/modeles"
574	rm -rf ORCHIDEE
575	svn co -r "$fetch_rev" "svn://forge.ipsl.fr/orchidee/$orcbranch"
576	cd - > /dev/null
577	fi
578	fi
579
580	# Check parallel LMDZ+ORCH
581	if [[ (! $veget = "none") && $parallel = "none" && ($used_lmdz_rev -lt 4894) ]]; then
582	echo "LMDZ revision must be >=4894 for orchidee without parallel support. Upgrade lmdz or use -parallel mpi_omp."; exit 1
583	fi
584	}
585
586	function compile_orchidee {
587	install_arch "ORCHIDEE"
588
589	if [[ $veget != "none" ]]; then
590	cd "$MODEL/modipsl/modeles/ORCHIDEE"
591
592	orchideelog="$(pwd)/orchidee.log"
593	echo "Compiling ORCHIDEE, the continental surface model (log $orchideelog) $(date)"
594
595	local xios_orchid opt_orc
596	if [[ $with_xios = 1 ]]; then
597	xios_orchid="-xios";
598	else
599	xios_orchid="-noxios"
600	fi
601	if [[ $optim_debug = "-debug" ]]; then
602	opt_orc="-debug";
603	else
604	opt_orc="-prod"
605	fi
606
607	if [[ $parallel != "none" && ! -d src_parallel ]]; then
608	echo "STOP: Orchidee version too old for parallel support"; exit 1
609	fi
610	echo "$jobcmd ./makeorchidee_fcm -j $make_j $xios_orchid $opt_orc -parallel $parallel -arch $arch" > compile.sh
611	chmod +x compile.sh
612	echo "Compiling ORCHIDEE using $(\cat compile.sh)"
613	if ! ./compile.sh &> "$orchideelog"; then
614	echo "STOP: ORCHIDEE compilation failed, exiting"; exit 1
615	fi
616	echo "Compiled ORCHIDEE $(date)"
617	fi
618	}
619
620	function get_lmdz_version {
621	LMDZPATH=$(readlink -e -f "$MODEL/modipsl/modeles/LMD"*)
622	cd "$LMDZPATH"
623	lmdzlog="$(pwd)/lmdz.log"
624
625	if [[ -n $svn_lmdz ]]; then
626	local curr_rev
627	curr_rev=$(svn info "$MODEL/modipsl/modeles/LMD"* \| grep Revision: \| cut -d ":" -f 2 \| cut -c 2-)
628	if [[ $svn_lmdz != "$curr_rev" ]]; then
629	local lmdzbranch
630	echo "Fetching LMDZ $svn_lmdz from the repository"
631	lmdzbranch=$(svn log -v -q https://svn.lmd.jussieu.fr/LMDZ -r "$svn_lmdz" \| grep LMDZ \| head -1 \| sed -e 's:trunk/.*$:trunk:' \| awk '{print $2}')
632	cd "$MODEL/modipsl/modeles"
633	rm -rf LMD*
634	svn co -r "$svn_lmdz" "https://svn.lmd.jussieu.fr/LMDZ$lmdzbranch" LMDZ
635	cd - > /dev/null
636	fi
637	used_lmdz_rev=$svn_lmdz
638	else # get svn from info
639	set +e; used_lmdz_rev=$(svn info \| grep "Last Changed Rev" \| cut -c 19-); set -e
640	if [[ -z $used_lmdz_rev ]]; then # svn info failed
641	used_lmdz_rev=$(grep 'Revision: [0-9]' "$MODEL"/Read*.md \| awk ' { print $2 } ' 2>/dev/null)
642	if [[ -z $used_lmdz_rev ]]; then echo "Could not determine lmdz version. This is likely an issue with the .tar itself, please report to LMDZ team."; exit 1; fi
643	fi
644	fi
645	}
646
647	function compile_lmdz {
648	install_arch "LMDZ"
649	cd "$LMDZPATH"
650
651	if [[ $used_lmdz_rev -le 4185 ]]; then
652	exe_name="bin/gcm_${grid_resolution}_phy${compphysiq}_${suff_para}${suff_orc}${suff_aer}${suff_iso}.e"
653	else
654	exe_name="bin/gcm_${grid_resolution}_phy${compphysiq}_${rad}${suff_para}${suff_orc}${suff_aer}${suff_iso}.e"
655	fi
656
657	local opt_rad
658	case $rad in
659	oldrad) iflag_rrtm=0; NSW=2; opt_rad="";;
660	rrtm) iflag_rrtm=1; NSW=6
661	if [[ $used_lmdz_rev -le 4185 ]]; then
662	opt_rad="-rrtm true"
663	else
664	opt_rad="-rad rrtm"
665	fi;;
666	ecrad) iflag_rrtm=2; NSW=6; opt_rad="-rad ecrad";;
667	*) echo "Only oldrad rrtm ecrad for rad option"; exit 1
668	esac
669	if [[ $used_lmdz_rev -le 4185 && $rad = "ecrad" ]]; then
670	echo "ecrad only available for LMDZ rev starting with 4186 "; exit 1
671	fi
672
673	# Compile
674	makelmdz="makelmdz_fcm $optim_debug -arch $arch -j $make_j"
675	local para_compile_opt="-mem -parallel $parallel"; if [[ $parallel = "none" ]]; then para_compile_opt=""; fi
676	echo "$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
677	echo "Compiling lmdz using $(\cat compile.sh) (log: $lmdzlog) $(date)"
678	chmod +x ./compile.sh
679	if ! ./compile.sh &> "$lmdzlog"; then
680	echo "STOP: 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 "STOP: 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" \|\| $cosp = "v2" ]]; then
810	echo "ulimit -s 200000" >> bench.sh
811	else
812	echo "ulimit -s unlimited" >> bench.sh
813	fi
814	if which mpirun &> /dev/null; then
815	echo "mpirun -np 2 gcm.e &> listing" >> bench.sh
816	elif grep -q "Adastra" /etc/motd; then
817	local account
818	account=$(/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" >> bench.sh
821	else
822	echo "Error: No command found to run parallel bench"; exit 1
823	fi
824	if [[ $(hostname \| cut -c -6) = "spirit" ]]; then # ulimit unlimited segfaults on Spirit
825	sed -i'' "s/ulimit -s unlimited/ulimit -Ss 8000/" bench.sh
826	fi
827	# Add rebuild, using reb.sh if it is there
828	cat <<EOF >> bench.sh
829	if [[ -f reb.sh ]]; then
830	./reb.sh histday; ./reb.sh histmth; ./reb.sh histhf;
831	./reb.sh histins; ./reb.sh stomate_history;
832	./reb.sh sechiba_history; ./reb.sh sechiba_out_2
833	fi
834	EOF
835	else
836	echo "./gcm.e &> listing" > bench.sh
837	fi
838	# Getting orchidee stuff
839	if [[ $veget = 'CMIP6' \|\| $veget = "orch2.0" ]]; then # TODO once we have a 2.2 bench, add it here (or in planned separate bench script)
840	echo 'myget 3DBenchs/BENCHCMIP6.tar.gz'
841	myget 3DBenchs/BENCHCMIP6.tar.gz
842	tar xvzf BENCHCMIP6.tar.gz
843	sed -e "s:VEGET=n:VEGET=y:" config.def > tmp
844	mv -f tmp config.def
845	if [[ $with_xios = 1 ]]; then
846	cp ../../ORCHIDEE/src_xml/context_orchidee.xml .
847	echo '<context id="orchidee" src="./context_orchidee.xml"/>' > add.tmp
848	cp ../../ORCHIDEE/src_xml/field_def_orchidee.xml .
849	cp ../../ORCHIDEE/src_xml/file_def_orchidee.xml .
850	cp ../../ORCHIDEE/src_xml/file_def_input_orchidee.xml .
851	if [[ -f ../../ORCHIDEE/src_xml/context_input_orchidee.xml ]]; then
852	cp ../../ORCHIDEE/src_xml/context_input_orchidee.xml .
853	echo '<context id="orchidee" src="./context_input_orchidee.xml"/>' >> add.tmp
854	fi
855	sed -e '/id="LMDZ"/r add.tmp' iodef.xml > tmp
856	mv tmp iodef.xml
857	sed -e'{/sechiba1/ s/enabled="_AUTO_"/type="one_file" enabled=".TRUE."/}' \
858	file_def_orchidee.xml > tmp
859	\mv -f tmp file_def_orchidee.xml
860	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
861	file_def_orchidee.xml > tmp
862	\mv -f tmp file_def_orchidee.xml
863	sed -e 's@output_level="_AUTO_"@output_level="1"@' \
864	file_def_orchidee.xml > tmp
865	\mv -f tmp file_def_orchidee.xml
866	sed -e 's@output_freq="_AUTO_"@output_freq="1d"@' \
867	file_def_orchidee.xml > tmp
868	\mv -f tmp file_def_orchidee.xml
869	sed -e 's@compression_level="4"@compression_level="0"@' \
870	file_def_orchidee.xml > tmp
871	\mv -f tmp file_def_orchidee.xml
872	sed -e 's@XIOS_ORCHIDEE_OK = n@XIOS_ORCHIDEE_OK = y@' \
873	orchidee.def > tmp
874	\mv -f tmp orchidee.def
875	fi
876	fi
877
878	if [[ -f ../arch.env ]]; then source ../arch.env; fi
879
880	echo "EXECUTION DU BENCH"
881	date
882	if (! $bench_cmd &> out.bench) \|\| ! (tail -n 1 listing \| grep "Everything is cool"); then
883	tail listing
884	echo "Bench FAILED, exiting"; exit 1
885	fi
886	date
887	tail listing
888	fi
889
890	# 1D case
891	if [[ $SCM = 1 ]]; then
892	cd "$MODEL"
893	myget 1D/1D.tar.gz
894	tar xf 1D.tar.gz
895	cd 1D
896	if [[ $rad = "oldrad" ]]; then
897	sed -i'' -e 's/^rad=.*$/rad=oldrad/' run.sh
898	sed -i'' -e 's/^rad=.*$/rad=oldrad/' bin/compile
899	elif [[ $rad = ecrad ]] ; then
900	sed -i'' -e 's/^rad=.*$/rad=ecrad/' run.sh
901	sed -i'' -e 's/^rad=.*$/rad=ecrad/' bin/compile
902	fi
903	echo "Running 1D/run.sh, log in $(pwd)/run1d.log"
904	./run.sh &> "$(pwd)/run1d.log"
905	fi
906	}
907
908	# If sourced: returns, else run setup
909	if [[ ! "${BASH_SOURCE[0]}" = "$0" ]]; then return 0; fi
910
911	echo "install_lmdz.sh DEBUT $(date)"
912
913	set_default_params
914	read_cmdline_args "$@"
915	ensure_correct_option_combinations
916	#download_model
917	create_model_tar
918	init_arch
919	check_available_software
920	get_lmdz_version
921	get_orchidee_version
922	install_netcdf
923	install_IOIPSL
924	install_XIOS
925	compile_orchidee
926	compile_lmdz
927	run_bench

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