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source: BOL/script_install_amaury/install_lmdz.sh @ 4922

Last change on this file since 4922 was 4922, checked in by abarral, 3 weeks ago
merge rev 4877 & 4919 from trunk
Property svn:executable set to ``*
File size: 31.0 KB

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1	#!/bin/bash
2	set -eu # error on command failure, and on unset variables
3	export LC_ALL=C # standardize awk format
4
5	###########################################################################
6	# Author : Laurent Fairhead et Frédéric Hourdin
7	# Usage : install_lmdz.sh -help
8	#
9	# bash installation script of the LMDZ model on different computer types :
10	# Linux PC, "mesocentre" (IPSL-UPMC, IPSL-X), super-computer (IDRIS)
11	#
12	# The model is downloaded in the following directory tree
13	# $MODEL/modipsl/modeles/...
14	# using the "modipsl" infrastructure created by the "IPSL"
15	# for coupled (atmosphere/ocean/vegetation/chemistry) climate modeling
16	# activities.
17	# Here we only download atmospheric (LMDZ) and vegetation (ORCHIDEE)
18	# components.
19	#
20	# The sources of the models can be found in the "modeles" directory.
21	# In the present case, LMDZ, ORCHIDEE, and IOIPSL or XIOS (handling of
22	# input-outputs using the NetCDF library).
23	#
24	# The script downloads various source files (including a version of NetCDF)
25	# and utilities, compiles the model, and runs a test simulation in a
26	# minimal configuration.
27	#
28	# Prerequisites : gfortran, bash or ksh, wget, gunzip, tar, ...
29	#
30	# Modif 18/11/2011
31	# changes for option real 8.
32	# We compile with -r8 (or equivalent) and -DNC_DOUBLE for the GCM
33	# but with -r4 for netcdf. Variable real must be set to
34	# r4 or r8 at the beginning of the script below.
35	#
36	###########################################################################
37
38	### Functions
39
40	function myget { # Get a file from LMDZ repository
41	local url=$1
42
43	local filename
44	filename=$(basename "$url")
45
46	wget --no-check-certificate -nv "http://lmdz.lmd.jussieu.fr/pub/$url"
47	if [[ $filename =~ .*\.(ba)?sh ]]; then chmod +x "$filename"; fi
48	}
49
50	function set_default_params {
51	# Valeur par défaut des parametres
52	svn_lmdz=""
53	version="20231022.trunk"
54
55	netcdf=1
56	bench=1
57	pcmac=0 # default: not on a Mac
58	SCM=0
59	veget="none"
60	grid_resolution="32x32x39"
61	physiq=""
62
63	xios_branch="2.6"
64	xios_rev="2568"
65
66	parallel="none"
67	trusting="testing"
68	MODEL=""
69
70	with_xios=0
71	opt_makelmdz_xios=""
72
73	rad="rrtm"
74
75	compile_with_fcm=1
76
77	cosp="none"
78	opt_cosp=""
79
80	make_j=8
81
82	# Check if on a Mac
83	if [[ $(uname) = "Darwin" ]]; then
84	pcmac=1
85	export MAKE="make"
86	fi
87
88	optim_debug=""
89	arch="local"
90
91	local mpi_file
92	mpi_file=$(readlink -f "$(which mpif90)")
93	path_mpi=$(dirname "$mpi_file")
94	root_mpi=$(dirname "$path_mpi")
95
96	arch="local-gfortran"
97	arch_dir=""
98	}
99
100	function read_cmdline_args {
101	while (($# > 0)); do
102	case $1 in
103	"-h") cat <<........fin
104	$0 [ -v version ] [ -r svn_release ]
105	[ -parallel PARA ] [ -d GRID_RESOLUTION ] [ -bench 0/1 ]
106	[-name LOCAL_MODEL_NAME] [-gprof] [-opt_makelmdz] [-rad RADIATIF]
107
108	-v "version" like 20150828.trunk, see http://www.lmd.jussieu.fr/~lmdz/Distrib/LISMOI.trunk (default <$version>)
109
110	-r "svn_release" : either the svn release number or "last" (default <$svn_lmdz>)
111
112	-parallel parallel support: mpi, omp, mpi_omp (mpi with openMP) or none (default: <$parallel>)
113
114	-d "grid resolution": should be among the available benchs if -bench 1 (valid values: 48x36x19, 48x36x39) (default : <$grid_resolution>)
115
116	-bench activating the bench or not (0/1) (default: <$bench>)
117
118	-testing/unstable
119
120	-name name of the folder to install to (default <$MODEL>)
121
122	-netcdf 0, 1 or PATH. 0: do not download NetCDF, look for it in standard locations (/usr); 1: download and compile NetCDF; PATH: full path to an existing installed NetCDF library (default: <$netcdf>)
123
124	-xios use (download and compile) the XIOS library (will compile the parallel NetCDF4-HDF5 library) (requires to also have -parallel mpi_omp)
125
126	-cosp to run with cospv1 or cospv2 [none/v1/v2] (default <$cosp>)
127
128	-rad radiative code: oldrad, rrtm or ecrad (default <$rad>)
129
130	-nofcm to compile without fcm
131
132	-SCM install 1D version automatically
133
134	-debug compile everything in debug mode
135
136	-physiq to choose which physics package to use (default <$physiq>)
137
138	-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 $veget)
139
140	-arch name of the arch to use (default <$arch>)
141
142	-arch_dir where to find the arch files (default <$arch_dir>)
143
144	-make_j number of processes to parallelize installations (default <$make_j>)
145
146	........fin
147	exit 1;;
148	"-v") version=$2; shift; shift;;
149	"-r") svn_lmdz=$2; shift; shift;;
150	"-d") grid_resolution=$2; shift; shift;;
151	"-unstable"\|"-testing") trusting=$(echo "$1" \| cut -c2-); shift;;
152	"-cosp") cosp=$2
153	case $cosp in
154	"none"\|"v1"\|"v2") cosp=$2; shift; shift;;
155	*) echo "Only none v1 v2 for cosp option"; exit 1
156	esac;;
157	"-nofcm") compile_with_fcm=0; echo "This option will be reactivated soon (promesse du 8dec2022)"; exit 1; shift;;
158	"-SCM") SCM=1; shift;;
159	"-rad") rad=$2
160	case $rad in
161	"oldrad"\|"rrtm"\|"ecrad") rad=$2; shift; shift;;
162	*) echo "Only oldrad rrtm ecrad for rad option"; exit 1
163	esac;;
164	"-parallel") parallel=$2
165	case $parallel in
166	"none"\|"mpi"\|"omp"\|"mpi_omp") parallel=$2; shift; shift;;
167	*) echo "Only none mpi omp mpi_omp for the parallel option"; exit 1
168	esac;;
169	"-bench") bench=$2; shift; shift;;
170	"-debug") optim_debug=-debug; shift;;
171	"-name") MODEL=$2; shift; shift;;
172	"-netcdf") netcdf=$2; shift; shift;;
173	"-physiq") physiq=$2; shift; shift;;
174	"-xios") with_xios=1; shift;;
175	"-arch") arch=$2; shift; shift;;
176	"-arch_dir") arch_dir=$2; shift; shift;;
177	"-veget") veget=$2; shift; shift;;
178	"-make_j") make_j=$2; shift; shift;;
179	*) bash install_lmdz.sh -h; exit 1
180	esac
181	done
182
183	# Option de compilation pour Cosp
184	case $cosp in
185	v1) opt_cosp="-cosp true";;
186	v2) opt_cosp="-cospv2 true";;
187	*) opt_cosp=""
188	esac
189
190	# Check on veget version
191	if [[ $veget != 'none' && $veget != "CMIP6" && $veget != "orch2.0" && $veget != "orch2.2" ]]; then
192	re='^[0-9]+$'
193	if ! [[ $veget =~ $re ]]; then
194	echo 'Valeur de l option veget non valable'; exit 1
195	fi
196	fi
197
198	#Define veget-related suffix for gcm name
199	if [[ $veget = 'none' ]]; then
200	suff_orc=''
201	else
202	suff_orc='_orch'
203	fi
204
205
206	if [[ $parallel = "none" ]]; then
207	suff_exe='_seq'
208	else
209	suff_exe='_para_mem'
210	fi
211
212	#Chemin pour placer le modele
213	if [[ $MODEL = "" ]]; then MODEL="./LMDZ$version$svn_lmdz$optim_debug"; fi
214
215	## if also compiling XIOS, parallel must be mpi_omp
216	if [[ $with_xios = 1 && $parallel != "mpi_omp" ]]; then
217	echo "Error, you must set -parallel mpi_omp if you want XIOS"; exit 1
218	fi
219
220	if [[ $with_xios = 1 ]]; then
221	opt_makelmdz_xios="-io xios"
222	fi
223
224	if [[ $cosp = "v2" && $with_xios = 0 ]]; then
225	echo "Error, Cospv2 cannot run without Xios"; exit 1
226	fi
227
228	if [[ $arch_dir = "" ]]; then
229	arch_dir="$MODEL/modipsl/config/IPSLCM7/ARCH/"
230	fi
231	arch_dir=$(readlink -f "$arch_dir") # full path
232	}
233
234	function check_available_software {
235	echo "################################################################"
236	echo "Check if required software is available"
237	echo "################################################################"
238	for logiciel in wget tar gzip make gcc cmake m4 c++; do
239	if [[ $(which "$logiciel") = "" ]]; then
240	echo "You must first install $logiciel on your system"; exit 1
241	fi
242	done
243
244	cat <<eod > tt.f90
245	print*,'coucou'
246	end
247	eod
248	$compiler tt.f90 \|\| a.out
249	./a.out >\| tt
250	if [[ $(< tt sed -e 's/ //g' ) != "coucou" ]]; then
251	echo "problem installing with compiler $compiler"; exit 1
252	fi
253	\rm tt a.out tt.f90
254	}
255
256	function download_model {
257	mkdir -p "$MODEL"
258	MODEL=$(readlink -f "$MODEL"); echo "$MODEL" # absolute path
259
260	rm -rf "$MODEL/modipsl"
261
262	echo "##########################################################"
263	echo "Download a slightly modified version of LMDZ"
264	echo "##########################################################"
265	cd "$MODEL"
266	getlog="$(pwd)/get.log"
267	echo "logfile : $getlog"
268	myget "src_archives/$trusting/modipsl.$version.tar.gz" >> get.log 2>&1
269	echo "install_lmdz.sh wget_OK $(date)"
270	gunzip "modipsl.$version.tar.gz" >> get.log 2>&1
271	tar xf "modipsl.$version.tar" >> get.log 2>&1
272	\rm "modipsl.$version.tar"
273	}
274
275	function create_model_tar { # TODO TEMP while waiting for tar: we copy the base from a local path = IPSLCM7 + ORCH2.2 8504
276	if [[ ! -d ../MODEL_REF ]]; then
277	cd ..
278	mkdir MODEL_REF
279	cd MODEL_REF
280	# Base is IPSLCM7
281	svn co --username icmc_users https://forge.ipsl.fr/igcmg/svn/modipsl/trunk modipsl
282	cd modipsl/util
283	./model IPSLCM7_work
284	# Remove unused components
285	rm -rf ../oasis3-mct
286	cd ../modeles
287	rm -rf ICOSA_LMDZ ORCHIDEE_4 ORCHIDEE_2_2 NEMO DYNAMICO XIOS INCA
288	# Retrieve orch version
289	svn co svn://forge.ipsl.fr/orchidee/branches/ORCHIDEE_2_2/ORCHIDEE -r 8504
290	# Correct orchidee bug in 8504
291	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
292
293	cd ../../../script_install
294	fi
295
296	if [[ ! -d "$MODEL" ]]; then
297	\cp -r ../MODEL_REF .
298	mv MODEL_REF "$MODEL"
299	fi
300	MODEL=$(readlink -f "$MODEL"); echo "$MODEL" # absolute path
301	}
302
303	function init_arch {
304	if [[ ! -d $arch_dir ]]; then
305	echo "Error: no arch dir $arch_dir"; exit 1
306	elif [[ ! -f $arch_dir/arch-$arch.path ]]; then
307	echo "Error: no arch-$arch.path in $arch_dir"; exit 1
308	fi
309
310	local fcm_path
311	if [[ -f $arch_dir/arch-$arch.fcm ]]; then
312	fcm_path="$arch_dir/arch-$arch.fcm"
313	else
314	fcm_path="$MODEL/modipsl/modeles/LMDZ/arch/arch-$arch.fcm"
315	if [[ ! -f $fcm_path ]]; then
316	echo "Error: no $fcm_path"; exit 1
317	fi
318	fi
319
320	# check compiler
321	compiler=$(< "$fcm_path" grep "%COMPILER" \| sed -e "s/%COMPILER\s*//")
322
323	# load env
324	local env_path=${fcm_path/.fcm/.env}
325	# shellcheck disable=SC1090
326	if [[ -f $env_path ]]; then source "$env_path"; fi
327	}
328
329	function install_arch {
330	local component=$1
331
332	if [[ ! -f "$MODEL/modipsl/modeles/$component/arch/arch-$arch.fcm" ]]; then
333	\cp -f "$arch_dir/arch-$arch.fcm" "$MODEL/modipsl/modeles/$component/arch"
334	\cp -f "$arch_dir/arch-$arch.path" "$MODEL/modipsl/modeles/$component/arch"
335
336	if [[ $component = "XIOS" ]]; then
337	# Adapt for XIOS, which uses different naming conventions
338	sed -i'' -e "s/%COMPILER/%FCOMPILER/" -e "s/%LINK/%LINKER/" -e "s/-fdefault-real-8//" "$MODEL/modipsl/modeles/XIOS/arch/arch-$arch.fcm"
339	elif [[ $component = "ORCHIDEE" ]]; then
340	if [[ $orcbranch = "/tags/ORCHIDEE_2_0/ORCHIDEE" ]]; then # 2.0 and before have a different fcm convention
341	sed -i'' -e "s/-I//" -e "s/-L//" "$MODEL/modipsl/modeles/ORCHIDEE/arch/arch-$arch.path" # /!\ we only replace first occurence on purpose
342	fi
343	fi
344	fi
345	}
346
347	function install_netcdf {
348	echo "Installing Netcdf"
349	local ncdf_compiler="$compiler"
350
351	if [[ $netcdf = 0 ]]; then
352	ncdfdir=$(nc-config --prefix)
353	else
354	cd "$MODEL"
355
356	# Convert non-basic compiler
357	case $compiler in
358	mpif90) ncdf_compiler=$($compiler --version \| head -n 1 \| cut -d " " -f -1)
359	esac
360
361	case $ncdf_compiler in
362	gfortran \| GNU) ncdf_compiler="gfortran"; opt1="-compiler gnu"; opt2="-CC gcc -FC gfortran -CXX g++";;
363	*) echo "unexpected compiler $ncdf_compiler for netcdf"; exit 1
364	esac
365
366	case $with_xios in
367	0) script_install_netcdf="install_netcdf4_hdf5_seq.bash"
368	ncdfdir="netcdf4_hdf5_seq"
369	opt_="$opt1";;
370	1) script_install_netcdf="install_netcdf4_hdf5.bash"
371	ncdfdir="netcdf4_hdf5"
372	opt_="$opt2 -MPI $root_mpi";;
373	*) echo "with_xios=$with_xios, should be 0 or 1"; exit 1
374	esac
375	if [[ $netcdf = 1 ]]; then
376	ncdfdir="$MODEL/$ncdfdir"
377	else
378	mkdir -p "$netcdf"; ncdfdir="$netcdf/$ncdfdir"
379	fi
380
381	echo "Repertoire netcdf $ncdfdir"
382	if [[ ! -d $ncdfdir ]]; then
383	netcdflog=$(pwd)/netcdf.log
384	echo "----------------------------------------------------------"
385	echo "Compiling the Netcdf library"
386	echo "----------------------------------------------------------"
387	echo "log file : $netcdflog"
388	myget script_install/$script_install_netcdf >> "$netcdflog" 2>&1
389	chmod u=rwx $script_install_netcdf
390	# shellcheck disable=SC2086
391	./$script_install_netcdf -prefix "$ncdfdir" $opt_ >> "$netcdflog" 2>&1
392	fi
393
394	# Add to path
395	export PATH="$ncdfdir/bin:$PATH"
396
397	#----------------------------------------------------------------------------
398	# LF rajout d'une verrue, pour une raison non encore expliquee,
399	# la librairie est parfois rangée dans lib64 et non dans lib
400	# par certains compilateurs
401	if [[ ! -e lib && -d lib64 ]]; then ln -s lib64 lib; fi
402	#----------------------------------------------------------------------------
403
404	echo "install_lmdz.sh netcdf_OK $(date)"
405	fi
406
407	cat >test_netcdf90.f90 <<EOF
408	use netcdf
409	print *, "NetCDF library version: ", nf90_inq_libvers()
410	end
411	EOF
412
413	if $ncdf_compiler -I"$ncdfdir"/include test_netcdf90.f90 -L"$ncdfdir"/lib -lnetcdff \
414	-lnetcdf -Wl,-rpath="$ncdfdir"/lib && ./a.out
415	then
416	\rm test_netcdf90.f90 a.out
417	else
418	cat <<EOF
419	Failed test program using NetCDF-Fortran. You can:
420	- check that you have NetCDF-Fortran installed in your system
421	- or specify an installation directory with option -netcdf of install_lmdz.sh
422	- or download and compile NetCDF-Fortran with option -netcdf 1 of nstall_lmdz.sh
423	EOF
424	exit 1
425	fi
426
427	# Compile NetCDF95
428	cd "$MODEL/modipsl/modeles/LMD"*
429	echo "Installing NetCDF95"
430	cd "$MODEL"
431	myget src_archives/netcdf/NetCDF95-0.3.tar.gz
432	tar -xf NetCDF95-0.3.tar.gz
433	\rm NetCDF95-0.3.tar.gz
434	cd NetCDF95-0.3
435	mkdir -p build && cd build
436	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"
437	make install
438	}
439
440	function install_IOIPSL {
441	install_arch "IOIPSL"
442
443	cd "$MODEL/modipsl/modeles/IOIPSL"
444	ioipsllog="$(pwd)/ioipsl.log"
445	echo "Compiling IOIPSL, the interface library with Netcdf $(date) (log: $ioipsllog)"
446
447	if ! ./makeioipsl_fcm -arch "$arch" -job 8 > "$ioipsllog" 2>&1; then
448	echo "IOIPSL compile failed, exiting"; exit 1
449	fi
450
451	# Link to modipsl/bin
452	cp -f bin/* ../../bin
453
454	echo "IOIPSL compiled $(date)"
455
456	IOIPSL_LIBDIR_="$MODEL/modipsl/modeles/IOIPSL/lib"
457	IOIPSL_INCDIR_="$MODEL/modipsl/modeles/IOIPSL/inc"
458	}
459
460	function install_XIOS {
461	if [[ $with_xios = 1 ]]; then
462	cd "$MODEL/modipsl/modeles"
463	xioslog="$(pwd)/XIOS/xios.log"
464	echo "##########################################################"
465	echo "Compiling XIOS (log $xioslog) $(date)"
466	echo "##########################################################"
467
468	# Download XIOS
469	case $xios_branch in
470	"trunk")
471	xios_http="http://forge.ipsl.fr/ioserver/svn/XIOS/trunk";;
472	"2.5")
473	xios_http="http://forge.ipsl.fr/ioserver/svn/XIOS2/branches/xios-2.5";;
474	"2.6")
475	xios_http="http://forge.ipsl.fr/ioserver/svn/XIOS2/branches/xios-2.6";;
476	*) echo "XIOS: Error, bad argument for -branch ! Did not expect $xios_branch"; exit 1;;
477	esac
478
479	cd "$MODEL/modipsl/modeles"
480	set +e; svn co --revision $xios_rev $xios_http XIOS; set -e
481
482	cd XIOS
483
484	install_arch "XIOS"
485
486	echo "Starting XIOS compilation"
487	if ! ./make_xios --arch "$arch" --job 8 > "$xioslog" 2>&1; then
488	echo "XIOS compilation failed, exiting"; exit 1
489	fi
490
491	echo "Compiled XIOS $(date)"
492	fi
493
494	XIOS_LIBDIR_="$MODEL/modipsl/modeles/XIOS/lib"
495	XIOS_INCDIR_="$MODEL/modipsl/modeles/XIOS/inc"
496	}
497
498	function get_orchidee_version { # Set / Check ORCHIDEE version
499	local fetch_rev=""
500	orcbranch=""
501	case $veget in
502	"none") fcm_veget_version="false";;
503	"orch2.0" \| "CMIP6") fcm_veget_version=orchidee2.0; fetch_rev=7906;; # in previous tar we used 6592 but with some modifications to xios_orchidee.f90, which got integrated in 7906
504	"orch2.2") fcm_veget_version=orchidee2.1; orcbranch="ORCHIDEE_2_2" ;; # the bundled version
505	*) fetch_rev=$veget
506	esac
507
508	if [[ -n $fetch_rev ]]; then
509	echo "Fetching orch $fetch_rev from the repository"
510	orcbranch=$(svn log -v -q svn://forge.ipsl.fr/orchidee/ -r "$fetch_rev" \| grep ORCHIDEE \| head -1 \| sed -e 's:ORCHIDEE/.*$:ORCHIDEE:' \| awk '{print $2}')
511	echo "branch is $orcbranch"
512	if [[ $fetch_rev -lt 4465 ]]; then echo 'ORCHIDEE version must be >=4465, exiting'; exit 1; fi
513	\rm -rf "$MODEL/modipsl/modeles/ORCHIDEE"
514	echo "IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at orchidee-help@listes.ipsl.fr"
515	cd "$MODEL/modipsl/modeles"
516	set +e
517	svn co -r "$fetch_rev" "svn://forge.ipsl.fr/orchidee/$orcbranch"
518	set -e
519	cd -
520	fi
521
522
523	# Check parallel LMDZ+ORCH
524	if [[ (! $veget = "none") && $parallel = "none" && ($used_lmdz_rev -lt 4894) ]]; then
525	echo "LMDZ revision must be >=4894 for orchidee without parallel support. Upgrade lmdz or use -parallel mpi_omp."; exit 1
526	fi
527	}
528
529	function compile_orchidee {
530	install_arch "ORCHIDEE"
531
532	if [[ $veget != "none" ]]; then
533	cd "$MODEL/modipsl/modeles/ORCHIDEE"
534
535	orchideelog="$(pwd)/orchidee.log"
536	echo "Compiling ORCHIDEE, the continental surface model (log $orchideelog) $(date)"
537
538	local xios_orchid opt_orc
539	if [[ $with_xios = 1 ]]; then
540	xios_orchid="-xios";
541	else
542	xios_orchid="-noxios"
543	fi
544	if [[ $optim_debug = "-debug" ]]; then
545	opt_orc="-debug";
546	else
547	opt_orc="-prod"
548	fi
549
550	local varenv="IOIPSL_LIBDIR_=$IOIPSL_LIBDIR_ IOIPSL_INCDIR_=$IOIPSL_INCDIR_ XIOS_INCDIR_=$XIOS_INCDIR_ XIOS_LIBDIR_=$XIOS_LIBDIR_"
551	if [[ $parallel = "none" ]]; then
552	echo "$varenv ./makeorchidee_fcm $xios_orchid $opt_orc -parallel none -arch $arch -j $make_j" > compile.sh
553	else
554	if [[ ! -d src_parallel ]]; then
555	echo "Orchidee version too old for parallel support"; exit 1
556	fi
557	{
558	echo "$varenv ./makeorchidee_fcm -j $make_j $xios_orchid $opt_orc -parallel $parallel -arch $arch"
559	} > compile.sh
560	fi
561	chmod +x compile.sh
562	echo "Compiling ORCHIDEE using $(\cat compile.sh)"
563	if ! ./compile.sh > "$orchideelog" 2>&1; then
564	echo "ORCHIDEE compilation failed, exiting"; exit 1
565	fi
566	echo "Compiled ORCHIDEE $(date)"
567	fi
568
569	ORCH_INCDIR_="$MODEL/modipsl/modeles/ORCHIDEE/inc"
570	ORCH_LIBDIR_="$MODEL/modipsl/modeles/ORCHIDEE/lib"
571	}
572
573	function get_lmdz_version {
574	LMDZPATH=$(readlink -f "$MODEL/modipsl/modeles/LMD"*)
575	cd "$LMDZPATH"
576	lmdzlog="$(pwd)/lmdz.log"
577
578	used_lmdz_rev=$svn_lmdz
579	if [[ -n $svn_lmdz ]]; then
580	local lmdzbranch
581	echo "Fetching LMDZ $svn_lmdz from the repository"
582	lmdzbranch=$(svn log -v -q https://svn.lmd.jussieu.fr/LMDZ -r "$svn_lmdz" \| grep LMDZ \| head -1 \| sed -e 's:trunk/.*$:trunk:' \| awk '{print $2}')
583	\rm -rf "$MODEL/modipsl/modeles/LMDZ"
584	cd "$MODEL/modipsl/modeles"
585	set +e
586	svn co -r "$svn_lmdz" "https://svn.lmd.jussieu.fr/LMDZ$lmdzbranch" LMDZ
587	set -e
588	cd -
589	else # get svn from info
590	used_lmdz_rev=$(svn info \| grep "Last Changed Rev" \| cut -c 19-)
591	fi
592	}
593
594	function compile_lmdz {
595	install_arch "LMDZ"
596	cd "$LMDZPATH"
597
598	exe_name="bin/gcm_${grid_resolution}_phylmd_${rad}${suff_exe}${suff_orc}.e"
599
600	local opt_rad
601	case $rad in
602	oldrad) iflag_rrtm=0; NSW=2; opt_rad="";;
603	rrtm) iflag_rrtm=1; NSW=6
604	if [[ $used_lmdz_rev -le 4185 ]]; then
605	opt_rad="-rrtm true"
606	else
607	opt_rad="-rad rrtm"
608	fi;;
609	ecrad) iflag_rrtm=2; NSW=6; opt_rad="-rad ecrad";;
610	*) echo "Only oldrad rrtm ecrad for rad option"; exit 1
611	esac
612	if [[ $used_lmdz_rev -le 4185 && $rad = "ecrad" ]]; then
613	echo "ecrad only available for LMDZ rev starting with 4186 "; exit 1
614	fi
615
616	# Compile
617	local varenv="IOIPSL_LIBDIR_=\"$IOIPSL_LIBDIR_\" IOIPSL_INCDIR_=\"$IOIPSL_INCDIR_\" ORCH_INCDIR_=\"$ORCH_INCDIR_\" ORCH_LIBDIR_=\"$ORCH_LIBDIR_\" XIOS_INCDIR_=\"$XIOS_INCDIR_\" XIOS_LIBDIR_=\"$XIOS_LIBDIR_\""
618	makelmdz="makelmdz_fcm $optim_debug -arch $arch -j $make_j"
619	if [[ $parallel = "none" ]]; then
620	echo "$varenv ./$makelmdz $opt_rad $opt_cosp -d ${grid_resolution} -v $fcm_veget_version gcm " > compile.sh
621	else
622	echo "$varenv ./$makelmdz $opt_rad $opt_cosp $opt_makelmdz_xios -d ${grid_resolution} -v $fcm_veget_version -mem -parallel $parallel gcm" > compile.sh
623	fi
624	echo "Compiling lmdz using $(\cat compile.sh) (log: $lmdzlog) $(date)"
625	chmod +x ./compile.sh
626	if ! ./compile.sh > "$lmdzlog" 2>&1; then
627	echo "LMDZ compilation failed, exiting"; exit 1
628	fi
629	echo "Finished LMDZ compilation $(date)"
630
631	# Check executable
632	# TODO $mysev -ge 4186 => other name convention ! check original install
633	if [[ ! -f $exe_name ]]; then
634	echo "Compilation failed, can't find the executable"; exit 1
635	else
636	echo "Compilation successfull, the executable is $exe_name $(date)"
637	fi
638	}
639
640	function run_bench {
641	cd "$MODEL/modipsl/modeles/LMDZ"*
642
643	if [[ $bench = "tuto" ]]; then
644	myget "Training/tutorial.tar"; tar xf tutorial.tar; cd TUTORIAL
645	./init.sh
646	elif [[ $bench = 1 ]]; then
647	\rm -rf "BENCH${grid_resolution}"
648	local bench=bench_lmdz_${grid_resolution}
649	myget "3DBenchs/$bench.tar.gz"
650	tar xf "$bench.tar.gz"
651
652	if [[ $cosp = "v1" \|\| $cosp = "v2" ]]; then
653	cd "BENCH${grid_resolution}"
654	# copier les fichiers namelist input et output our COSP
655	cp ../DefLists/cosp*_input_nl.txt .
656	cp ../DefLists/cosp*_output_nl.txt .
657	# Activer la cles ok_cosp pour tourner avec COSP
658	sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp
659	\mv -f tmp config.def
660	cd ..
661	fi
662
663	if [[ -n "$physiq" ]]; then
664	cd "BENCH${grid_resolution}"
665	if [[ -f "physiq.def_${physiq}" ]]; then
666	cp "physiq.def_${physiq}" physiq.def
667	echo "using physiq.def_${physiq}"
668	else
669	echo "using standard physiq.def"
670	fi
671	cd ..
672	else
673	echo "using standard physiq.def"
674	fi
675
676	if [[ $with_xios = 1 ]]; then
677	cd "BENCH${grid_resolution}"
678	cp ../DefLists/iodef.xml .
679	cp ../DefLists/context_lmdz.xml .
680	cp ../DefLists/field_def_lmdz.xml .
681	# A raffiner par la suite
682	echo "A FAIRE : Copier les *xml en fonction de l option cosp"
683	cp ../DefLists/field_def_cosp*.xml .
684	cp ../DefLists/file_def_hist*xml .
685	# adapt iodef.xml to use attached mode
686	sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' \
687	iodef.xml > tmp
688	\mv -f tmp iodef.xml
689
690	# and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
691	# except for histday
692	for histfile in file_def_hist*xml
693	do
694	if [[ "$histfile" = "file_def_histday_lmdz.xml" ]]; then
695	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' \
696	"$histfile" > tmp
697	\mv -f tmp "$histfile"
698	sed -e 's@output_level="_AUTO_"@output_level="5"@' "$histfile" \
699	> tmp
700	\mv -f tmp "$histfile"
701	sed -e 's@compression_level="2"@compression_level="0"@' \
702	"$histfile" > tmp
703	\mv -f tmp "$histfile"
704	else
705	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
706	"$histfile" > tmp
707	\mv -f tmp "$histfile"
708	fi
709	done
710	# and add option "ok_all_xml=y" in config.def
711	echo "### XIOS outputs" >> config.def
712	echo 'ok_all_xml=.true.' >> config.def
713
714	#activer les sorties pour Cosp
715	if [[ "$cosp" = "v1" ]]; then
716	sed -i'' -e 's@enabled=".FALSE."@enabled=".TRUE."@' \
717	-e 's@output_level="_AUTO_"@output_level="5"@' \
718	-e 's@compression_level="2"@compression_level="0"@' \
719	file_def_histdayCOSP_lmdz.xml
720	fi
721	if [[ "$cosp" = "v2" ]]; then
722	sed -e 's@compression_level="2"@compression_level="0"@' file_def_histdayCOSPv2_lmdz.xml
723	for type_ in hf day mth; do
724	file=file_def_hist${type_}COSP
725	sed -i'' -e 's@src="./'${file}'_lmdz.xml"@src="./'${file}'v2_lmdz.xml"@' context_lmdz.xml
726	done
727	sed -i '' -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' field_def_lmdz.xml
728	fi
729
730	cd ..
731	fi
732
733	# Cas Bench avec ecrad
734	if [[ $rad = "ecrad" ]]; then
735	cd "BENCH${grid_resolution}"
736	cp ../DefLists/namelist_ecrad .
737	cp -r ../libf/phylmd/ecrad/data .
738	cd ..
739	fi
740
741	# Adjusting bench physiq.def to radiative code chosen
742	cd "BENCH${grid_resolution}"
743	sed -e 's/iflag_rrtm=.*.$/iflag_rrtm='$iflag_rrtm'/' \
744	-e 's/NSW=.*.$/NSW='$NSW'/' physiq.def > tmpdef
745	\mv tmpdef physiq.def
746	cd ..
747
748	cp "$exe_name" "BENCH${grid_resolution}/gcm.e"
749	cd "BENCH${grid_resolution}"
750
751	if [[ ${parallel:0:3} = "mpi" ]]; then
752	# Lancement avec deux procs mpi et 2 openMP
753	echo "export OMP_STACKSIZE=800M" > bench.sh
754	if [[ "${parallel:4:3}" = "omp" ]]; then
755	echo "export OMP_NUM_THREADS=2" >> bench.sh
756	fi
757	if [[ "$cosp" = "v1" \|\| "$cosp" = "v2" ]]; then
758	echo "ulimit -s 200000" >> bench.sh
759	else
760	echo "ulimit -s unlimited" >> bench.sh
761	fi
762	echo "mpirun -np 2 gcm.e > listing 2>&1" >> bench.sh
763	# Add rebuild, using reb.sh if it is there
764	cat <<EOF >> bench.sh
765	if [[ -f reb.sh ]]; then
766	./reb.sh histday; ./reb.sh histmth; ./reb.sh histhf;
767	./reb.sh histins; ./reb.sh stomate_history;
768	./reb.sh sechiba_history; ./reb.sh sechiba_out_2
769	fi
770	EOF
771	else
772	echo "./gcm.e > listing 2>&1" > bench.sh
773	fi
774	# Getting orchidee stuff
775	if [[ $veget = 'CMIP6' \|\| $veget = "orch2.0" ]]; then # TODO once we have a 2.2 bench, add it here (or in planned separate bench script)
776	echo 'myget 3DBenchs/BENCHCMIP6.tar.gz'
777	myget 3DBenchs/BENCHCMIP6.tar.gz
778	tar xvzf BENCHCMIP6.tar.gz
779	sed -e "s:VEGET=n:VEGET=y:" config.def > tmp
780	mv -f tmp config.def
781	if [[ $with_xios = 1 ]]; then
782	cp ../../ORCHIDEE/src_xml/context_orchidee.xml .
783	echo '<context id="orchidee" src="./context_orchidee.xml"/>' > add.tmp
784	cp ../../ORCHIDEE/src_xml/field_def_orchidee.xml .
785	cp ../../ORCHIDEE/src_xml/file_def_orchidee.xml .
786	cp ../../ORCHIDEE/src_xml/file_def_input_orchidee.xml .
787	if [[ -f ../../ORCHIDEE/src_xml/context_input_orchidee.xml ]]; then
788	cp ../../ORCHIDEE/src_xml/context_input_orchidee.xml .
789	echo '<context id="orchidee" src="./context_input_orchidee.xml"/>' >> add.tmp
790	fi
791	sed -e '/id="LMDZ"/r add.tmp' iodef.xml > tmp
792	mv tmp iodef.xml
793	sed -e'{/sechiba1/ s/enabled="_AUTO_"/type="one_file" enabled=".TRUE."/}' \
794	file_def_orchidee.xml > tmp
795	\mv -f tmp file_def_orchidee.xml
796	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
797	file_def_orchidee.xml > tmp
798	\mv -f tmp file_def_orchidee.xml
799	sed -e 's@output_level="_AUTO_"@output_level="1"@' \
800	file_def_orchidee.xml > tmp
801	\mv -f tmp file_def_orchidee.xml
802	sed -e 's@output_freq="_AUTO_"@output_freq="1d"@' \
803	file_def_orchidee.xml > tmp
804	\mv -f tmp file_def_orchidee.xml
805	sed -e 's@compression_level="4"@compression_level="0"@' \
806	file_def_orchidee.xml > tmp
807	\mv -f tmp file_def_orchidee.xml
808	sed -e 's@XIOS_ORCHIDEE_OK = n@XIOS_ORCHIDEE_OK = y@' \
809	orchidee.def > tmp
810	\mv -f tmp orchidee.def
811	fi
812	fi
813
814	if [[ -f ../arch.env ]]; then source ../arch.env; fi
815
816	echo "EXECUTION DU BENCH"
817	date
818	if (! ./bench.sh > out.bench 2>&1) \|\| ! (tail -n 1 listing \| grep "Everything is cool"); then
819	tail listing
820	echo "Bench FAILED, exiting"; exit 1
821	fi
822	date
823	tail listing
824	fi
825
826	# 1D case
827	if [[ $SCM = 1 ]]; then
828	cd "$MODEL"
829	myget 1D/1D.tar.gz
830	tar xf 1D.tar.gz
831	cd 1D
832	if [[ $rad = "oldrad" ]]; then
833	sed -i'' -e 's/^rad=.*$/rad=oldrad/' run.sh
834	sed -i'' -e 's/^rad=.*$/rad=oldrad/' bin/compile
835	elif [[ $rad = ecrad ]] ; then
836	sed -i'' -e 's/^rad=.*$/rad=ecrad/' run.sh
837	sed -i'' -e 's/^rad=.*$/rad=ecrad/' bin/compile
838	fi
839	echo "Running 1D/run.sh, log in $(pwd)/run1d.log"
840	./run.sh > "$(pwd)/run1d.log" 2>&1
841	fi
842	}
843
844	echo "install_lmdz.sh DEBUT $(date)"
845
846	set_default_params
847	read_cmdline_args "$@"
848	#download_model
849	create_model_tar
850	init_arch
851	check_available_software
852	get_lmdz_version
853	get_orchidee_version
854	install_netcdf
855	install_IOIPSL
856	install_XIOS
857	compile_orchidee
858	compile_lmdz
859	run_bench

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