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install_lmdz.sh

Last change on this file was 4961, checked in by abarral, 11 days ago
add MESOIPSL-GNU arch fix ncdf dir detection
Property svn:executable set to ``*
File size: 34.0 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 (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	cd ../../script_install
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 "Error: no arch dir $arch_dir"; exit 1
361	elif [[ ! -f $arch_dir/arch-$arch.path ]]; then
362	echo "Error: no arch-$arch.path in $arch_dir"; exit 1
363	fi
364
365	local fcm_path
366	if [[ -f $arch_dir/arch-$arch.fcm ]]; then
367	fcm_path="$arch_dir/arch-$arch.fcm"
368	else
369	fcm_path="$MODEL/modipsl/modeles/LMDZ/arch/arch-$arch.fcm"
370	if [[ ! -f $fcm_path ]]; then
371	echo "Error: no $fcm_path"; exit 1
372	fi
373	fi
374
375	# check compiler
376	compiler=$(< "$fcm_path" grep "%COMPILER" \| sed -e "s/%COMPILER\s*//")
377
378	# load env
379	local env_path=${fcm_path/.fcm/.env}
380	# shellcheck disable=SC1090
381	if [[ -f $env_path ]]; then source "$env_path"; fi
382	}
383
384	function install_arch {
385	local component=$1
386
387	if [[ ! -f "$MODEL/modipsl/modeles/$component/arch/arch-$arch.fcm" ]]; then
388	cp -f "$arch_dir/arch-$arch."{fcm,path,env} "$MODEL/modipsl/modeles/$component/arch"
389
390	if [[ $component = "XIOS" ]]; then
391	# Adapt for XIOS, which uses different naming conventions
392	sed -i'' -e "s/%COMPILER/%FCOMPILER/" -e "s/%LINK/%LINKER/" -e "s/-fdefault-real-8//" "$MODEL/modipsl/modeles/XIOS/arch/arch-$arch.fcm"
393	elif [[ $component = "ORCHIDEE" ]]; then
394	if [[ $orcbranch = "/tags/ORCHIDEE_2_0/ORCHIDEE" ]]; then # 2.0 and before have a different fcm convention
395	sed -i'' -e "s/-I//" -e "s/-L//" "$MODEL/modipsl/modeles/ORCHIDEE/arch/arch-$arch.path" # /!\ we only replace first occurence on purpose
396	fi
397	fi
398	fi
399	}
400
401	function install_netcdf {
402	echo "Installing Netcdf"
403	local ncdf_compiler="$compiler"
404
405	if [[ $netcdf = 0 ]]; then
406	ncdfdir=$(nf-config --prefix)
407	else
408	cd "$MODEL"
409
410	# Convert non-basic compiler
411	case $compiler in
412	mpif90) ncdf_compiler=$($compiler --version \| head -n 1 \| cut -d " " -f -1)
413	esac
414
415	case $ncdf_compiler in
416	gfortran \| GNU) ncdf_compiler="gfortran"; opt1="-compiler gnu"; opt2="-CC gcc -FC gfortran -CXX g++";;
417	*) echo "unexpected compiler $ncdf_compiler for netcdf"; exit 1
418	esac
419
420	case $with_xios in
421	0) script_install_netcdf="install_netcdf4_hdf5_seq.bash"
422	ncdfdir="netcdf4_hdf5_seq"
423	opt_="$opt1";;
424	1) script_install_netcdf="install_netcdf4_hdf5.bash"
425	ncdfdir="netcdf4_hdf5"
426	opt_="$opt2 -MPI $root_mpi";;
427	*) echo "with_xios=$with_xios, should be 0 or 1"; exit 1
428	esac
429	if [[ $netcdf = 1 ]]; then
430	ncdfdir="$MODEL/$ncdfdir"
431	else
432	mkdir -p "$netcdf"; ncdfdir="$netcdf/$ncdfdir"
433	fi
434
435	echo "Repertoire netcdf $ncdfdir"
436	if [[ ! -d $ncdfdir ]]; then
437	netcdflog=$(pwd)/netcdf.log
438	echo "----------------------------------------------------------"
439	echo "Compiling the Netcdf library"
440	echo "----------------------------------------------------------"
441	echo "log file : $netcdflog"
442	myget script_install/$script_install_netcdf >> "$netcdflog" 2>&1
443	chmod u=rwx $script_install_netcdf
444	# shellcheck disable=SC2086
445	./$script_install_netcdf -prefix "$ncdfdir" $opt_ >> "$netcdflog" 2>&1
446	fi
447
448	# Add to path
449	export PATH="$ncdfdir/bin:$PATH"
450
451	#----------------------------------------------------------------------------
452	# LF rajout d'une verrue, pour une raison non encore expliquee,
453	# la librairie est parfois rangée dans lib64 et non dans lib
454	# par certains compilateurs
455	if [[ ! -e lib && -d lib64 ]]; then ln -s lib64 lib; fi
456	#----------------------------------------------------------------------------
457
458	echo "install_lmdz.sh netcdf_OK $(date)"
459	fi
460
461	cat >test_netcdf90.f90 <<EOF
462	use netcdf
463	print *, "NetCDF library version: ", nf90_inq_libvers()
464	end
465	EOF
466
467	if $ncdf_compiler -I"$ncdfdir"/include test_netcdf90.f90 -L"$ncdfdir"/lib -lnetcdff \
468	-lnetcdf -Wl,-rpath="$ncdfdir"/lib && ./a.out
469	then
470	\rm test_netcdf90.f90 a.out
471	else
472	cat <<EOF
473	Failed test program using NetCDF-Fortran. You can:
474	- check that you have NetCDF-Fortran installed in your system
475	- or specify an installation directory with option -netcdf of install_lmdz.sh
476	- or download and compile NetCDF-Fortran with option -netcdf 1 of nstall_lmdz.sh
477	EOF
478	exit 1
479	fi
480
481	# Compile NetCDF95
482	cd "$MODEL/modipsl/modeles/LMD"*
483	echo "Installing NetCDF95"
484	cd "$MODEL"
485	if [[ ! -d "NetCDF95-0.3" ]]; then
486	myget src_archives/netcdf/NetCDF95-0.3.tar.gz
487	tar -xf NetCDF95-0.3.tar.gz
488	\rm NetCDF95-0.3.tar.gz
489	cd NetCDF95-0.3
490	mkdir -p build && cd build
491	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"
492	make install
493	fi
494	}
495
496	function install_IOIPSL {
497	install_arch "IOIPSL"
498
499	cd "$MODEL/modipsl/modeles/IOIPSL"
500	ioipsllog="$(pwd)/ioipsl.log"
501	echo "Compiling IOIPSL, the interface library with Netcdf $(date) (log: $ioipsllog)"
502
503	if ! ./makeioipsl_fcm -arch "$arch" -job 8 > "$ioipsllog" 2>&1; then
504	echo "IOIPSL compile failed, exiting"; exit 1
505	fi
506
507	# Link to modipsl/bin
508	cp -f bin/* ../../bin
509
510	echo "IOIPSL compiled $(date)"
511	}
512
513	function install_XIOS {
514	if [[ $with_xios = 1 ]]; then
515	cd "$MODEL/modipsl/modeles"
516	xioslog="$(pwd)/XIOS/xios.log"
517	echo "##########################################################"
518	echo "Compiling XIOS (log $xioslog) $(date)"
519	echo "##########################################################"
520
521	# Download XIOS
522	local xios_http="http://forge.ipsl.fr/ioserver/svn/XIOS2/branches/xios-2.6"
523	local xios_rev="2568"
524
525	cd "$MODEL/modipsl/modeles"
526	set +e; svn co -r $xios_rev $xios_http XIOS; set -e
527
528	cd XIOS
529
530	install_arch "XIOS"
531
532	echo "Starting XIOS compilation"
533	if ! ./make_xios --arch "$arch" --job 8 > "$xioslog" 2>&1; then
534	echo "XIOS compilation failed, exiting"; exit 1
535	fi
536
537	echo "Compiled XIOS $(date)"
538	fi
539	}
540
541	function get_orchidee_version { # Set / Check ORCHIDEE version
542	local fetch_rev=""
543	orcbranch=""
544	case $veget in
545	"none") fcm_veget_version="false";;
546	"orch2.0" \| "CMIP6") fcm_veget_version=orchidee2.0; fetch_rev=7906;; # in previous tar we used 6592 but with some modifications to xios_orchidee.f90, which got integrated in 7906
547	"orch2.2") fcm_veget_version=orchidee2.1; orcbranch="ORCHIDEE_2_2" ;; # the bundled version
548	*) fetch_rev=$veget
549	esac
550
551	if [[ -n $fetch_rev ]]; then
552	echo "Fetching orch $fetch_rev from the repository"
553	orcbranch=$(svn log -v -q svn://forge.ipsl.fr/orchidee/ -r "$fetch_rev" \| grep ORCHIDEE \| head -1 \| sed -e 's:ORCHIDEE/.*$:ORCHIDEE:' \| awk '{print $2}')
554	echo "branch is $orcbranch"
555	if [[ $fetch_rev -lt 4465 ]]; then echo 'ORCHIDEE version must be >=4465, exiting'; exit 1; fi
556	echo "IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at orchidee-help@listes.ipsl.fr"
557	cd "$MODEL/modipsl/modeles"
558	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)
559	cd -
560	fi
561
562	# Check parallel LMDZ+ORCH
563	if [[ (! $veget = "none") && $parallel = "none" && ($used_lmdz_rev -lt 4894) ]]; then
564	echo "LMDZ revision must be >=4894 for orchidee without parallel support. Upgrade lmdz or use -parallel mpi_omp."; exit 1
565	fi
566	}
567
568	function compile_orchidee {
569	install_arch "ORCHIDEE"
570
571	if [[ $veget != "none" ]]; then
572	cd "$MODEL/modipsl/modeles/ORCHIDEE"
573
574	orchideelog="$(pwd)/orchidee.log"
575	echo "Compiling ORCHIDEE, the continental surface model (log $orchideelog) $(date)"
576
577	local xios_orchid opt_orc
578	if [[ $with_xios = 1 ]]; then
579	xios_orchid="-xios";
580	else
581	xios_orchid="-noxios"
582	fi
583	if [[ $optim_debug = "-debug" ]]; then
584	opt_orc="-debug";
585	else
586	opt_orc="-prod"
587	fi
588
589	if [[ $parallel = "none" ]]; then
590	echo "./makeorchidee_fcm $xios_orchid $opt_orc -parallel none -arch $arch -j $make_j" > compile.sh
591	else
592	if [[ ! -d src_parallel ]]; then
593	echo "Orchidee version too old for parallel support"; exit 1
594	fi
595	{
596	echo "./makeorchidee_fcm -j $make_j $xios_orchid $opt_orc -parallel $parallel -arch $arch"
597	} > compile.sh
598	fi
599	chmod +x compile.sh
600	echo "Compiling ORCHIDEE using $(\cat compile.sh)"
601	if ! ./compile.sh > "$orchideelog" 2>&1; then
602	echo "ORCHIDEE compilation failed, exiting"; exit 1
603	fi
604	echo "Compiled ORCHIDEE $(date)"
605	fi
606	}
607
608	function get_lmdz_version {
609	LMDZPATH=$(readlink -e -f "$MODEL/modipsl/modeles/LMD"*)
610	cd "$LMDZPATH"
611	lmdzlog="$(pwd)/lmdz.log"
612
613	used_lmdz_rev=$svn_lmdz
614	if [[ -n $svn_lmdz ]]; then
615	local lmdzbranch
616	echo "Fetching LMDZ $svn_lmdz from the repository"
617	lmdzbranch=$(svn log -v -q https://svn.lmd.jussieu.fr/LMDZ -r "$svn_lmdz" \| grep LMDZ \| head -1 \| sed -e 's:trunk/.*$:trunk:' \| awk '{print $2}')
618	cd "$MODEL/modipsl/modeles"
619	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)
620	cd -
621	else # get svn from info
622	set +e; used_lmdz_rev=$(svn info \| grep "Last Changed Rev" \| cut -c 19-); set -e
623	if [[ -z $used_lmdz_rev ]]; then # svn info failed
624	used_lmdz_rev=$(grep 'Revision: [0-9]' "$MODEL"/Read*.md \| awk ' { print $2 } ' 2>/dev/null)
625	if [[ -z $used_lmdz_rev ]]; then echo "Could not determine lmdz version. This is likely an issue with the .tar itself, please report to LMDZ team."; exit 1; fi
626	fi
627	fi
628	}
629
630	function compile_lmdz {
631	install_arch "LMDZ"
632	cd "$LMDZPATH"
633
634	if [[ $used_lmdz_rev -le 4185 ]]; then
635	exe_name="bin/gcm_${grid_resolution}_phy${compphysiq}_${suff_para}${suff_orc}${suff_aer}${suff_iso}.e"
636	else
637	exe_name="bin/gcm_${grid_resolution}_phy${compphysiq}_${rad}${suff_para}${suff_orc}${suff_aer}${suff_iso}.e"
638	fi
639
640	local opt_rad
641	case $rad in
642	oldrad) iflag_rrtm=0; NSW=2; opt_rad="";;
643	rrtm) iflag_rrtm=1; NSW=6
644	if [[ $used_lmdz_rev -le 4185 ]]; then
645	opt_rad="-rrtm true"
646	else
647	opt_rad="-rad rrtm"
648	fi;;
649	ecrad) iflag_rrtm=2; NSW=6; opt_rad="-rad ecrad";;
650	*) echo "Only oldrad rrtm ecrad for rad option"; exit 1
651	esac
652	if [[ $used_lmdz_rev -le 4185 && $rad = "ecrad" ]]; then
653	echo "ecrad only available for LMDZ rev starting with 4186 "; exit 1
654	fi
655
656	# Compile
657	makelmdz="makelmdz_fcm $optim_debug -arch $arch -j $make_j"
658	local para_compile_opt="-mem -parallel $parallel"; if [[ $parallel = "none" ]]; then para_compile_opt=""; fi
659	echo "./$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
660	echo "Compiling lmdz using $(\cat compile.sh) (log: $lmdzlog) $(date)"
661	chmod +x ./compile.sh
662	if ! ./compile.sh > "$lmdzlog" 2>&1; then
663	echo "LMDZ compilation failed, exiting"; exit 1
664	fi
665	echo "Finished LMDZ compilation $(date)"
666
667	# Check executable
668	if [[ ! -f $exe_name ]]; then
669	echo "Compilation failed, can't find the executable"; exit 1
670	else
671	echo "Compilation successfull, the executable is $exe_name $(date)"
672	fi
673	}
674
675	function run_bench {
676	cd "$MODEL/modipsl/modeles/LMDZ"*
677
678	if [[ $bench = "tuto" ]]; then
679	myget "Training/tutorial.tar"; tar xf tutorial.tar; cd TUTORIAL
680	./init.sh
681	elif [[ $bench = 1 ]]; then
682	\rm -rf "BENCH${grid_resolution}"
683	local bench=bench_lmdz_${grid_resolution}
684	myget "3DBenchs/$bench.tar.gz"
685	tar xf "$bench.tar.gz"
686
687	if [[ $cosp = "v1" \|\| $cosp = "v2" ]]; then
688	cd "BENCH${grid_resolution}"
689	# copier les fichiers namelist input et output our COSP
690	cp ../DefLists/cosp*_input_nl.txt .
691	cp ../DefLists/cosp*_output_nl.txt .
692	# Activer la cles ok_cosp pour tourner avec COSP
693	sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp
694	\mv -f tmp config.def
695	cd ..
696	fi
697
698	if [[ -n "$benchphysiq" ]]; then
699	cd "BENCH${grid_resolution}"
700	if [[ -f "physiq.def_${benchphysiq}" ]]; then
701	cp "physiq.def_${benchphysiq}" benchphysiq.def
702	echo "using physiq.def_${benchphysiq}"
703	else
704	echo "using standard physiq.def"
705	fi
706	cd ..
707	else
708	echo "using standard physiq.def"
709	fi
710
711	if [[ $with_xios = 1 ]]; then
712	cd "BENCH${grid_resolution}"
713	cp ../DefLists/iodef.xml .
714	cp ../DefLists/context_lmdz.xml .
715	cp ../DefLists/field_def_lmdz.xml .
716	# A raffiner par la suite
717	echo "A FAIRE : Copier les *xml en fonction de l option cosp"
718	cp ../DefLists/field_def_cosp*.xml .
719	cp ../DefLists/file_def_hist*xml .
720	# adapt iodef.xml to use attached mode
721	sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' \
722	iodef.xml > tmp
723	\mv -f tmp iodef.xml
724
725	# and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
726	# except for histday
727	for histfile in file_def_hist*xml; do
728	if [[ "$histfile" = "file_def_histday_lmdz.xml" ]]; then
729	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' \
730	"$histfile" > tmp
731	\mv -f tmp "$histfile"
732	sed -e 's@output_level="_AUTO_"@output_level="5"@' "$histfile" \
733	> tmp
734	\mv -f tmp "$histfile"
735	sed -e 's@compression_level="2"@compression_level="0"@' \
736	"$histfile" > tmp
737	\mv -f tmp "$histfile"
738	else
739	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
740	"$histfile" > tmp
741	\mv -f tmp "$histfile"
742	fi
743	done
744	# and add option "ok_all_xml=y" in config.def
745	echo "### XIOS outputs" >> config.def
746	echo 'ok_all_xml=.true.' >> config.def
747
748	#activer les sorties pour Cosp
749	if [[ "$cosp" = "v1" ]]; then
750	sed -i'' -e 's@enabled=".FALSE."@enabled=".TRUE."@' \
751	-e 's@output_level="_AUTO_"@output_level="5"@' \
752	-e 's@compression_level="2"@compression_level="0"@' \
753	file_def_histdayCOSP_lmdz.xml
754	fi
755	if [[ "$cosp" = "v2" ]]; then
756	sed -i'' -e 's@compression_level="2"@compression_level="0"@' file_def_histdayCOSPv2_lmdz.xml
757	for type_ in hf day mth; do
758	file=file_def_hist${type_}COSP
759	sed -i'' -e 's@src="./'${file}'_lmdz.xml"@src="./'${file}'v2_lmdz.xml"@' context_lmdz.xml
760	done
761	sed -i'' -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' field_def_lmdz.xml
762	fi
763
764	cd ..
765	fi
766
767	# Cas Bench avec ecrad
768	if [[ $rad = "ecrad" ]]; then
769	cd "BENCH${grid_resolution}"
770	cp ../DefLists/namelist_ecrad .
771	cp -r ../libf/phylmd/ecrad/data .
772	cd ..
773	fi
774
775	# Adjusting bench physiq.def to radiative code chosen
776	cd "BENCH${grid_resolution}"
777	sed -e 's/iflag_rrtm=.*.$/iflag_rrtm='$iflag_rrtm'/' \
778	-e 's/NSW=.*.$/NSW='$NSW'/' physiq.def > tmpdef
779	\mv tmpdef physiq.def
780	cd ..
781
782	cp "$exe_name" "BENCH${grid_resolution}/gcm.e"
783	cd "BENCH${grid_resolution}"
784
785	local bench_cmd="./bench.sh"
786	if [[ ${parallel:0:3} = "mpi" ]]; then
787	# Lancement avec deux procs mpi et 2 openMP
788	echo "export OMP_STACKSIZE=800M" > bench.sh
789	if [[ "${parallel:4:3}" = "omp" ]]; then
790	echo "export OMP_NUM_THREADS=2" >> bench.sh
791	fi
792	if [[ $cosp = "v1" \|\| $cosp = "v2" ]]; then
793	echo "ulimit -s 200000" >> bench.sh
794	else
795	echo "ulimit -s unlimited" >> bench.sh
796	fi
797	if which mpirun > /dev/null 2>&1; then
798	echo "mpirun -np 2 gcm.e > listing 2>&1" >> bench.sh
799	elif grep -q "Adastra" /etc/motd; then
800	local account
801	account=$(/usr/sbin/my_project.py -l 2>&1 \| head -1 \| cut -d " " -f 3- \| cut -c 5-)
802	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"
803	echo "./gcm.e > listing 2>&1" >> bench.sh
804	else
805	echo "Error: No command found to run parallel bench"; exit 1
806	fi
807	# Add rebuild, using reb.sh if it is there
808	cat <<EOF >> bench.sh
809	if [[ -f reb.sh ]]; then
810	./reb.sh histday; ./reb.sh histmth; ./reb.sh histhf;
811	./reb.sh histins; ./reb.sh stomate_history;
812	./reb.sh sechiba_history; ./reb.sh sechiba_out_2
813	fi
814	EOF
815	else
816	echo "./gcm.e > listing 2>&1" > bench.sh
817	fi
818	# Getting orchidee stuff
819	if [[ $veget = 'CMIP6' \|\| $veget = "orch2.0" ]]; then # TODO once we have a 2.2 bench, add it here (or in planned separate bench script)
820	echo 'myget 3DBenchs/BENCHCMIP6.tar.gz'
821	myget 3DBenchs/BENCHCMIP6.tar.gz
822	tar xvzf BENCHCMIP6.tar.gz
823	sed -e "s:VEGET=n:VEGET=y:" config.def > tmp
824	mv -f tmp config.def
825	if [[ $with_xios = 1 ]]; then
826	cp ../../ORCHIDEE/src_xml/context_orchidee.xml .
827	echo '<context id="orchidee" src="./context_orchidee.xml"/>' > add.tmp
828	cp ../../ORCHIDEE/src_xml/field_def_orchidee.xml .
829	cp ../../ORCHIDEE/src_xml/file_def_orchidee.xml .
830	cp ../../ORCHIDEE/src_xml/file_def_input_orchidee.xml .
831	if [[ -f ../../ORCHIDEE/src_xml/context_input_orchidee.xml ]]; then
832	cp ../../ORCHIDEE/src_xml/context_input_orchidee.xml .
833	echo '<context id="orchidee" src="./context_input_orchidee.xml"/>' >> add.tmp
834	fi
835	sed -e '/id="LMDZ"/r add.tmp' iodef.xml > tmp
836	mv tmp iodef.xml
837	sed -e'{/sechiba1/ s/enabled="_AUTO_"/type="one_file" enabled=".TRUE."/}' \
838	file_def_orchidee.xml > tmp
839	\mv -f tmp file_def_orchidee.xml
840	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
841	file_def_orchidee.xml > tmp
842	\mv -f tmp file_def_orchidee.xml
843	sed -e 's@output_level="_AUTO_"@output_level="1"@' \
844	file_def_orchidee.xml > tmp
845	\mv -f tmp file_def_orchidee.xml
846	sed -e 's@output_freq="_AUTO_"@output_freq="1d"@' \
847	file_def_orchidee.xml > tmp
848	\mv -f tmp file_def_orchidee.xml
849	sed -e 's@compression_level="4"@compression_level="0"@' \
850	file_def_orchidee.xml > tmp
851	\mv -f tmp file_def_orchidee.xml
852	sed -e 's@XIOS_ORCHIDEE_OK = n@XIOS_ORCHIDEE_OK = y@' \
853	orchidee.def > tmp
854	\mv -f tmp orchidee.def
855	fi
856	fi
857
858	if [[ -f ../arch.env ]]; then source ../arch.env; fi
859
860	echo "EXECUTION DU BENCH"
861	date
862	if (! $bench_cmd > out.bench 2>&1) \|\| ! (tail -n 1 listing \| grep "Everything is cool"); then
863	tail listing
864	echo "Bench FAILED, exiting"; exit 1
865	fi
866	date
867	tail listing
868	fi
869
870	# 1D case
871	if [[ $SCM = 1 ]]; then
872	cd "$MODEL"
873	myget 1D/1D.tar.gz
874	tar xf 1D.tar.gz
875	cd 1D
876	if [[ $rad = "oldrad" ]]; then
877	sed -i'' -e 's/^rad=.*$/rad=oldrad/' run.sh
878	sed -i'' -e 's/^rad=.*$/rad=oldrad/' bin/compile
879	elif [[ $rad = ecrad ]] ; then
880	sed -i'' -e 's/^rad=.*$/rad=ecrad/' run.sh
881	sed -i'' -e 's/^rad=.*$/rad=ecrad/' bin/compile
882	fi
883	echo "Running 1D/run.sh, log in $(pwd)/run1d.log"
884	./run.sh > "$(pwd)/run1d.log" 2>&1
885	fi
886	}
887
888	# If sourced: returns, else run setup
889	if [[ ! "${BASH_SOURCE[0]}" = "$0" ]]; then return 0; fi
890
891	echo "install_lmdz.sh DEBUT $(date)"
892
893	set_default_params
894	read_cmdline_args "$@"
895	ensure_correct_option_combinations
896	#download_model
897	create_model_tar
898	init_arch
899	check_available_software
900	get_lmdz_version
901	get_orchidee_version
902	install_netcdf
903	install_IOIPSL
904	install_XIOS
905	compile_orchidee
906	compile_lmdz
907	run_bench

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