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source: BOL/script_install_amaury/install_lmdz.sh @ 4900

Last change on this file since 4900 was 4900, checked in by abarral, 5 weeks ago
change bundled veget version fix veget version update unbundle XIOS split init and install arch fix ORCHIDEE XIOS library forwarding fix local netcdf compil fix Makefile linking
Property svn:executable set to ``*
File size: 30.6 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 : pgf90/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=""
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 <$svn>)
111
112	-parallel parallel support: mpi, omp, mpi_omp (mpi with openMP) or none (default: <$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=$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$svn$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	if [[ $svn != "" ]]; then
275	mysvn=$svn
276	else
277	mysvn="$(grep 'Revision: [0-9]' "$MODEL"/Read*.md \| awk ' { print $2 } ' 2>/dev/null)"
278	fi
279	echo "SVN revision used: $mysvn"
280	}
281
282	function download_model_AMAURY { # TODO TEMP while waiting for tar: we copy the base from a local path = IPSLCM7 + ORCH2.2 latest
283	if [[ ! -d ../MODEL_REF ]]; then
284	cd ..
285	mkdir MODEL_REF
286	cd MODEL_REF
287	svn co --username icmc_users https://forge.ipsl.fr/igcmg/svn/modipsl/trunk modipsl
288	cd modipsl/util
289	./model IPSLCM7_work
290	rm -rf oasis3-mct
291	cd ../modeles
292	rm -rf ICOSA_LMDZ ORCHIDEE_4 ORCHIDEE_2_2 NEMO DYNAMICO XIOS INCA
293	svn co svn://forge.ipsl.fr/orchidee/branches/ORCHIDEE_2_2/ORCHIDEE
294	cd ../../../script_install
295	fi
296
297	if [[ ! -d "$MODEL" ]]; then
298	\cp -r ../MODEL_REF .
299	mv MODEL_REF "$MODEL"
300	fi
301	MODEL=$(readlink -f "$MODEL"); echo "$MODEL" # absolute path
302
303	if [[ $svn != "" ]]; then
304	mysvn=$svn
305	else
306	mysvn="$(grep 'Revision: [0-9]' "$MODEL"/Read*.md \| awk ' { print $2 } ' 2>/dev/null)"
307	fi
308	echo "SVN revision used: $mysvn"
309	}
310
311	function init_arch {
312	if [[ ! -d $arch_dir ]]; then
313	echo "Error: no arch dir $arch_dir"; exit 1
314	elif [[ ! -f $arch_dir/arch-$arch.path ]]; then
315	echo "Error: no arch-$arch.path in $arch_dir"; exit 1
316	fi
317
318	local fcm_path
319	if [[ -f $arch_dir/arch-$arch.fcm ]]; then
320	fcm_path="$arch_dir/arch-$arch.fcm"
321	else
322	fcm_path="$MODEL/modipsl/modeles/LMDZ/arch/arch-$arch.fcm"
323	if [[ ! -f $fcm_path ]]; then
324	echo "Error: no $fcm_path"; exit 1
325	fi
326	fi
327
328	# check compiler
329	compiler=$(< "$fcm_path" grep "%COMPILER" \| sed -e "s/%COMPILER\s*//")
330	}
331
332	function install_arch {
333	local component=$1
334
335	if [[ ! -f "$MODEL/modipsl/modeles/$component/arch/arch-$arch.fcm" ]]; then
336	\cp -f "$arch_dir/arch-$arch.fcm" "$MODEL/modipsl/modeles/$component/arch"
337	\cp -f "$arch_dir/arch-$arch.path" "$MODEL/modipsl/modeles/$component/arch"
338
339	if [[ $component = "XIOS" ]]; then
340	# Adapt for XIOS, which uses different naming conventions
341	sed -i'' -e "s/%COMPILER/%FCOMPILER/" -e "s/%LINK/%LINKER/" -e "s/-fdefault-real-8//" "$MODEL/modipsl/modeles/XIOS/arch/arch-$arch.fcm"
342	elif [[ $component = "ORCHIDEE" ]]; then
343	if [[ $orcbranch = "/tags/ORCHIDEE_2_0/ORCHIDEE" ]]; then # 2.0 and before have a different fcm convention
344	sed -i'' -e "s/-I//" -e "s/-L//" "$MODEL/modipsl/modeles/ORCHIDEE/arch/arch-$arch.path" # /!\ we only replace first occurence on purpose
345	fi
346	fi
347	fi
348	}
349
350	function install_netcdf {
351	echo "Installing Netcdf"
352	local ncdf_compiler="$compiler"
353
354	if [[ $netcdf = 0 ]]; then
355	ncdfdir=$(nc-config --prefix)
356	else
357	cd "$MODEL"
358
359	# Convert non-basic compiler
360	case $compiler in # TODO check if it works with other base compilers
361	mpif90) ncdf_compiler=$($compiler --help \| head -n 1 \| cut -f 2 -d " ")
362	esac
363
364	case $ncdf_compiler in
365	gfortran) opt1="-compiler gnu"; opt2="-CC gcc -FC gfortran -CXX g++";;
366	ifort) opt1="-compiler intel"; opt2="-CC icc -FC ifort -CXX icpc";;
367	pgf90) opt1="-compiler pgf90"; opt2="-CC pgcc -FC pgf90 -CXX pgCC";;
368	*) echo "unexpected compiler $ncdf_compiler for netcdf"; exit 1
369	esac
370
371	case $with_xios in
372	0) script_install_netcdf="install_netcdf4_hdf5_seq.bash"
373	ncdfdir="netcdf4_hdf5_seq"
374	opt_="$opt1";;
375	1) script_install_netcdf="install_netcdf4_hdf5.bash"
376	ncdfdir="netcdf4_hdf5"
377	opt_="$opt2 -MPI $root_mpi";;
378	*) echo "with_xios=$with_xios, should be 0 or 1"; exit 1
379	esac
380	if [[ $netcdf = 1 ]]; then
381	ncdfdir="$MODEL/$ncdfdir"
382	else
383	mkdir -p "$netcdf"; ncdfdir="$netcdf/$ncdfdir"
384	fi
385
386	echo "Repertoire netcdf $ncdfdir"
387	if [[ ! -d $ncdfdir ]]; then
388	netcdflog=$(pwd)/netcdf.log
389	echo "----------------------------------------------------------"
390	echo "Compiling the Netcdf library"
391	echo "----------------------------------------------------------"
392	echo "log file : $netcdflog"
393	myget script_install/$script_install_netcdf >> "$netcdflog" 2>&1
394	chmod u=rwx $script_install_netcdf
395	# shellcheck disable=SC2086
396	./$script_install_netcdf -prefix "$ncdfdir" $opt_ >> "$netcdflog" 2>&1
397	fi
398
399	# Add to path
400	export PATH="$ncdfdir/bin:$PATH"
401
402	#----------------------------------------------------------------------------
403	# LF rajout d'une verrue, pour une raison non encore expliquee,
404	# la librairie est parfois rangée dans lib64 et non dans lib
405	# par certains compilateurs
406	if [[ ! -e lib && -d lib64 ]]; then ln -s lib64 lib; fi
407	#----------------------------------------------------------------------------
408
409	echo "install_lmdz.sh netcdf_OK $(date)"
410	fi
411
412	cat >test_netcdf90.f90 <<EOF
413	use netcdf
414	print *, "NetCDF library version: ", nf90_inq_libvers()
415	end
416	EOF
417
418	if $ncdf_compiler -I"$ncdfdir"/include test_netcdf90.f90 -L"$ncdfdir"/lib -lnetcdff \
419	-lnetcdf -Wl,-rpath="$ncdfdir"/lib && ./a.out
420	then
421	\rm test_netcdf90.f90 a.out
422	else
423	cat <<EOF
424	Failed test program using NetCDF-Fortran. You can:
425	- check that you have NetCDF-Fortran installed in your system
426	- or specify an installation directory with option -netcdf of install_lmdz.sh
427	- or download and compile NetCDF-Fortran with option -netcdf 1 of nstall_lmdz.sh
428	EOF
429	exit 1
430	fi
431
432	# Compile NetCDF95
433	cd "$MODEL/modipsl/modeles/LMD"*
434	echo "Installing NetCDF95"
435	cd "$MODEL"
436	myget src_archives/netcdf/NetCDF95-0.3.tar.gz
437	tar -xf NetCDF95-0.3.tar.gz
438	\rm NetCDF95-0.3.tar.gz
439	cd NetCDF95-0.3
440	mkdir -p build && cd build
441	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"
442	make install
443	}
444
445	function install_IOIPSL {
446	install_arch "IOIPSL"
447
448	cd "$MODEL/modipsl/modeles/IOIPSL"
449	ioipsllog="$(pwd)/ioipsl.log"
450	echo "Compiling IOIPSL, the interface library with Netcdf $(date) (log: $ioipsllog)"
451
452	if ! ./makeioipsl_fcm -arch "$arch" -job 8 > "$ioipsllog" 2>&1; then
453	echo "IOIPSL compile failed, exiting"; exit 1
454	fi
455
456	# Link to modipsl/bin
457	cp -f bin/* ../../bin
458
459	echo "IOIPSL compiled $(date)"
460
461	IOIPSL_LIBDIR_="$MODEL/modipsl/modeles/IOIPSL/lib"
462	IOIPSL_INCDIR_="$MODEL/modipsl/modeles/IOIPSL/inc"
463	}
464
465	function install_XIOS {
466	if [[ $with_xios = 1 ]]; then
467	cd "$MODEL/modipsl/modeles"
468	xioslog="$(pwd)/XIOS/xios.log"
469	echo "##########################################################"
470	echo "Compiling XIOS (log $xioslog) $(date)"
471	echo "##########################################################"
472
473	# Download XIOS
474	case $xios_branch in
475	"trunk")
476	xios_http="http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/trunk";;
477	"2.5")
478	xios_http="http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5";;
479	"2.6")
480	xios_http="http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS2/branches/xios-2.6";;
481	*) echo "XIOS: Error, bad argument for -branch ! Did not expect $xios_branch"; exit;;
482	esac
483
484	cd "$MODEL/modipsl/modeles"
485	set +e; svn co --revision $xios_rev $xios_http XIOS; set -e
486
487	cd XIOS
488
489	install_arch "XIOS"
490
491	echo "Starting XIOS compilation"
492	if ! ./make_xios --arch "$arch" --job 8 > "$xioslog" 2>&1; then
493	echo "XIOS compilation failed, exiting"; exit 1
494	fi
495
496	echo "Compiled XIOS $(date)"
497	fi
498
499	XIOS_LIBDIR_="$MODEL/modipsl/modeles/XIOS/lib"
500	XIOS_INCDIR_="$MODEL/modipsl/modeles/XIOS/inc"
501	}
502
503	function get_orchidee_version { # Set / Check ORCHIDEE version
504	local fetch_rev=""
505	orcbranch=""
506	case $veget in
507	"none") fcm_veget_version="false";;
508	"orch2.0" \| "CMIP6") fcm_veget_version=orchidee2.0; fetch_rev=6592;;
509	"orch2.2") fcm_veget_version=orchidee2.1; orcbranch="ORCHIDEE_2_2" ;; # the bundled version
510	*) fetch_rev=$veget
511	esac
512
513	if [[ -n $fetch_rev ]]; then
514	echo "Fetching orch $fetch_rev from the repository"
515	orcbranch=$(svn log -v -q svn://forge.ipsl.jussieu.fr/orchidee/ -r "$fetch_rev" \|grep ORCHIDEE \|head -1\| sed -e 's:ORCHIDEE/.*$:ORCHIDEE:' \| awk '{print $2}')
516	echo "branch is $orcbranch"
517	if [[ $fetch_rev -lt 4465 ]]; then echo 'ORCHIDEE version must be >=4465, exiting'; exit 1; fi
518	\rm -rf "$MODEL/modipsl/modeles/ORCHIDEE"
519	echo "IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at orchidee-help@listes.ipsl.fr"
520	cd "$MODEL/modipsl/modeles"
521	set +e
522	svn co -r "$fetch_rev" "svn://forge.ipsl.jussieu.fr/orchidee/$orcbranch"
523	set -e
524	cd -
525	fi
526	}
527
528	function compile_orchidee {
529	get_orchidee_version
530	install_arch "ORCHIDEE"
531
532	ORCHPATH=""
533
534
535	if [[ $veget != "none" ]]; then
536	cd "$MODEL/modipsl/modeles/ORCHIDEE"
537	ORCHPATH=$(pwd)
538
539	orchideelog="$(pwd)/orchidee.log"
540	echo "Compiling ORCHIDEE, the continental surface model (log $orchideelog) $(date)"
541
542	local xios_orchid opt_orc
543	if [[ $with_xios = 1 ]]; then
544	xios_orchid="-xios";
545	else
546	xios_orchid="-noxios"
547	fi
548	if [[ $optim_debug = "-debug" ]]; then
549	opt_orc="-debug";
550	else
551	opt_orc="-prod"
552	fi
553
554	local varenv="IOIPSL_LIBDIR_=$IOIPSL_LIBDIR_ IOIPSL_INCDIR_=$IOIPSL_INCDIR_ ORCHPATH=$ORCHPATH XIOS_INCDIR_=$XIOS_INCDIR_ XIOS_LIBDIR_=$XIOS_LIBDIR_"
555	if [[ $parallel = "none" ]]; then
556	echo "$varenv ./makeorchidee_fcm $xios_orchid $opt_orc -parallel none -arch $arch -j $make_j" > compile.sh
557	else
558	if [[ ! -d src_parallel ]]; then
559	echo "Orchidee version too old for parallel support"; exit 1
560	fi
561	{
562	echo "$varenv ./makeorchidee_fcm -j $make_j -clean $xios_orchid $opt_orc -parallel $parallel -arch $arch"
563	echo "$varenv ./makeorchidee_fcm -j $make_j $xios_orchid $opt_orc -parallel $parallel -arch $arch"
564	} > compile.sh
565	fi
566	chmod +x compile.sh
567	echo "Compiling ORCHIDEE using $(\cat compile.sh)"
568	if ! ./compile.sh > "$orchideelog" 2>&1; then
569	echo "ORCHIDEE compilation failed, exiting"; exit 1
570	fi
571	echo "Compiled ORCHIDEE $(date)"
572	fi
573
574	ORCH_LIBDIR_="$MODEL/modipsl/modeles/ORCHIDEE/lib"
575	}
576
577	function get_lmdz_version {
578	LMDZPATH=$(readlink -f "$MODEL/modipsl/modeles/LMD"*)
579	cd "$LMDZPATH"
580	lmdzlog="$(pwd)/lmdz.log"
581
582	set +e
583	svn upgrade
584	if [[ $svn = "last" ]]; then
585	svnopt=""
586	else
587	svnopt="-r $svn"
588	fi
589	if [[ $svn != "" ]]; then
590	if svn info \| grep -q 'https:'; then svn switch --relocate https://svn.lmd.jussieu.fr/LMDZ http://svn.lmd.jussieu.fr/LMDZ; fi
591	svn update "$svnopt"
592	fi
593	mysvn=$(svnversion . \| grep -E -o "[0-9]+" 2>/dev/null)
594	set -e
595
596	if [[ $mysvn = "" ]]; then mysvn=$(grep 'Revision: [0-9]' "$MODEL"/Read*.md \| awk ' { print $2 } ' 2>/dev/null); fi
597	if [[ $mysvn = "" ]]; then mysvn=4190; fi
598	}
599
600	function compile_lmdz {
601	get_lmdz_version
602	install_arch "LMDZ"
603
604	exe_name="bin/gcm_${grid_resolution}_phylmd_${rad}${suff_exe}${suff_orc}.e"
605
606	local opt_rad
607	case $rad in
608	oldrad) iflag_rrtm=0; NSW=2; opt_rad="";;
609	rrtm) iflag_rrtm=1; NSW=6
610	if [[ $mysvn -le 4185 ]]; then
611	opt_rad="-rrtm true"
612	else
613	opt_rad="-rad rrtm"
614	fi;;
615	ecrad) iflag_rrtm=2; NSW=6; opt_rad="-rad ecrad";;
616	*) echo "Only oldrad rrtm ecrad for rad option"; exit 1
617	esac
618	if [[ $mysvn -le 4185 && $rad = "ecrad" ]]; then
619	echo "ecrad only available for LMDZ rev starting with 4186 "; exit 1
620	fi
621
622	# Compile
623	local varenv="IOIPSL_LIBDIR_=$IOIPSL_LIBDIR_ IOIPSL_INCDIR_=$IOIPSL_INCDIR_ ORCH_LIBDIR_=$ORCH_LIBDIR_ ORCHPATH=$ORCHPATH XIOS_INCDIR_=$XIOS_INCDIR_ XIOS_LIBDIR_=$XIOS_LIBDIR_"
624	makelmdz="makelmdz_fcm $optim_debug -arch $arch -j $make_j"
625	if [[ $parallel = "none" ]]; then
626	echo "$varenv ./$makelmdz $opt_rad $opt_cosp -d ${grid_resolution} -v $fcm_veget_version gcm " > compile.sh
627	else
628	echo "$varenv ./$makelmdz $opt_rad $opt_cosp $opt_makelmdz_xios -d ${grid_resolution} -v $fcm_veget_version -mem -parallel $parallel gcm" > compile.sh
629	fi
630	echo "Compiling lmdz using $(\cat compile.sh) (log: $lmdzlog) $(date)"
631	chmod +x ./compile.sh
632	if ! ./compile.sh > "$lmdzlog" 2>&1; then
633	echo "LMDZ compilation failed, exiting"; exit 1
634	fi
635	echo "Finished LMDZ compilation $(date)"
636
637	# Check executable
638	# TODO $mysev -ge 4186 => other name convention ! check original install
639	if [[ ! -f $exe_name ]]; then
640	echo "Compilation failed, can't find the executable"; exit 1
641	else
642	echo "Compilation successfull, the executable is $exe_name $(date)"
643	fi
644	}
645
646	function run_bench {
647	cd "$MODEL/modipsl/modeles/LMDZ"*
648
649	if [[ $bench = "tuto" ]]; then
650	myget "Training/tutorial.tar"; tar xf tutorial.tar; cd TUTORIAL
651	./init.sh
652	elif [[ $bench = 1 ]]; then
653	\rm -rf "BENCH${grid_resolution}"
654	local bench=bench_lmdz_${grid_resolution}
655	myget "3DBenchs/$bench.tar.gz"
656	tar xf "$bench.tar.gz"
657
658	if [[ $cosp = "v1" \|\| $cosp = "v2" ]]; then
659	cd "BENCH${grid_resolution}"
660	# copier les fichiers namelist input et output our COSP
661	cp ../DefLists/cosp*_input_nl.txt .
662	cp ../DefLists/cosp*_output_nl.txt .
663	# Activer la cles ok_cosp pour tourner avec COSP
664	sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp
665	\mv -f tmp config.def
666	cd ..
667	fi
668
669	if [[ -n "$physiq" ]]; then
670	cd "BENCH${grid_resolution}"
671	if [[ -f "physiq.def_${physiq}" ]]; then
672	cp "physiq.def_${physiq}" physiq.def
673	echo "using physiq.def_${physiq}"
674	else
675	echo "using standard physiq.def"
676	fi
677	cd ..
678	else
679	echo "using standard physiq.def"
680	fi
681
682	if [[ $with_xios = 1 ]]; then
683	cd "BENCH${grid_resolution}"
684	cp ../DefLists/iodef.xml .
685	cp ../DefLists/context_lmdz.xml .
686	cp ../DefLists/field_def_lmdz.xml .
687	# A raffiner par la suite
688	echo "A FAIRE : Copier les *xml en fonction de l option cosp"
689	cp ../DefLists/field_def_cosp*.xml .
690	cp ../DefLists/file_def_hist*xml .
691	# adapt iodef.xml to use attached mode
692	sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' \
693	iodef.xml > tmp
694	\mv -f tmp iodef.xml
695
696	# and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
697	# except for histday
698	for histfile in file_def_hist*xml
699	do
700	if [[ "$histfile" = "file_def_histday_lmdz.xml" ]]; then
701	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' \
702	"$histfile" > tmp
703	\mv -f tmp "$histfile"
704	sed -e 's@output_level="_AUTO_"@output_level="5"@' "$histfile" \
705	> tmp
706	\mv -f tmp "$histfile"
707	sed -e 's@compression_level="2"@compression_level="0"@' \
708	"$histfile" > tmp
709	\mv -f tmp "$histfile"
710	else
711	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
712	"$histfile" > tmp
713	\mv -f tmp "$histfile"
714	fi
715	done
716	# and add option "ok_all_xml=y" in config.def
717	echo "### XIOS outputs" >> config.def
718	echo 'ok_all_xml=.true.' >> config.def
719
720	#activer les sorties pour Cosp
721	if [[ "$cosp" = "v1" ]]; then
722	sed -i'' -e 's@enabled=".FALSE."@enabled=".TRUE."@' \
723	-e 's@output_level="_AUTO_"@output_level="5"@' \
724	-e 's@compression_level="2"@compression_level="0"@' \
725	file_def_histdayCOSP_lmdz.xml
726	fi
727	if [[ "$cosp" = "v2" ]]; then
728	sed -e 's@compression_level="2"@compression_level="0"@' file_def_histdayCOSPv2_lmdz.xml
729	for type_ in hf day mth; do
730	file=file_def_hist${type_}COSP
731	sed -i'' -e 's@src="./'${file}'_lmdz.xml"@src="./'${file}'v2_lmdz.xml"@' context_lmdz.xml
732	done
733	sed -i '' -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' field_def_lmdz.xml
734	fi
735
736	cd ..
737	fi
738
739	# Cas Bench avec ecrad
740	if [[ $rad = "ecrad" ]]; then
741	cd "BENCH${grid_resolution}"
742	cp ../DefLists/namelist_ecrad .
743	cp -r ../libf/phylmd/ecrad/data .
744	cd ..
745	fi
746
747	# Adjusting bench physiq.def to radiative code chosen
748	cd "BENCH${grid_resolution}"
749	sed -e 's/iflag_rrtm=.*.$/iflag_rrtm='$iflag_rrtm'/' \
750	-e 's/NSW=.*.$/NSW='$NSW'/' physiq.def > tmpdef
751	\mv tmpdef physiq.def
752	cd ..
753
754	cp "$exe_name" "BENCH${grid_resolution}/gcm.e"
755	cd "BENCH${grid_resolution}"
756
757	if [[ ${parallel:0:3} = "mpi" ]]; then
758	# Lancement avec deux procs mpi et 2 openMP
759	echo "export OMP_STACKSIZE=800M" > bench.sh
760	if [[ "${parallel:4:3}" = "omp" ]]; then
761	echo "export OMP_NUM_THREADS=2" >> bench.sh
762	fi
763	if [[ "$cosp" = "v1" \|\| "$cosp" = "v2" ]]; then
764	echo "ulimit -s 200000" >> bench.sh
765	else
766	echo "ulimit -s unlimited" >> bench.sh
767	fi
768	echo "mpirun -np 2 gcm.e > listing 2>&1" >> bench.sh
769	# Add rebuild, using reb.sh if it is there
770	cat <<EOF >> bench.sh
771	if [[ -f reb.sh ]]; then
772	./reb.sh histday; ./reb.sh histmth; ./reb.sh histhf;
773	./reb.sh histins; ./reb.sh stomate_history;
774	./reb.sh sechiba_history; ./reb.sh sechiba_out_2
775	fi
776	EOF
777	else
778	echo "./gcm.e > listing 2>&1" > bench.sh
779	fi
780	# Getting orchidee stuff
781	if [[ $veget = 'CMIP6' ]]; then
782	echo 'myget 3DBenchs/BENCHCMIP6.tar.gz'
783	myget 3DBenchs/BENCHCMIP6.tar.gz
784	tar xvzf BENCHCMIP6.tar.gz
785	sed -e "s:VEGET=n:VEGET=y:" config.def > tmp
786	mv -f tmp config.def
787	if [[ $with_xios = 1 ]]; then
788	cp ../../ORCHIDEE/src_xml/context_orchidee.xml .
789	echo '<context id="orchidee" src="./context_orchidee.xml"/>' > add.tmp
790	cp ../../ORCHIDEE/src_xml/field_def_orchidee.xml .
791	cp ../../ORCHIDEE/src_xml/file_def_orchidee.xml .
792	cp ../../ORCHIDEE/src_xml/file_def_input_orchidee.xml .
793	if [[ -f ../../ORCHIDEE/src_xml/context_input_orchidee.xml ]]; then
794	cp ../../ORCHIDEE/src_xml/context_input_orchidee.xml .
795	echo '<context id="orchidee" src="./context_input_orchidee.xml"/>' >> add.tmp
796	fi
797	sed -e '/id="LMDZ"/r add.tmp' iodef.xml > tmp
798	mv tmp iodef.xml
799	sed -e'{/sechiba1/ s/enabled="_AUTO_"/type="one_file" enabled=".TRUE."/}' \
800	file_def_orchidee.xml > tmp
801	\mv -f tmp file_def_orchidee.xml
802	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
803	file_def_orchidee.xml > tmp
804	\mv -f tmp file_def_orchidee.xml
805	sed -e 's@output_level="_AUTO_"@output_level="1"@' \
806	file_def_orchidee.xml > tmp
807	\mv -f tmp file_def_orchidee.xml
808	sed -e 's@output_freq="_AUTO_"@output_freq="1d"@' \
809	file_def_orchidee.xml > tmp
810	\mv -f tmp file_def_orchidee.xml
811	sed -e 's@compression_level="4"@compression_level="0"@' \
812	file_def_orchidee.xml > tmp
813	\mv -f tmp file_def_orchidee.xml
814	sed -e 's@XIOS_ORCHIDEE_OK = n@XIOS_ORCHIDEE_OK = y@' \
815	orchidee.def > tmp
816	\mv -f tmp orchidee.def
817	fi
818	fi
819
820	if [[ -f ../arch.env ]]; then source ../arch.env; fi
821
822	echo "EXECUTION DU BENCH"
823	date
824	if (! ./bench.sh > out.bench 2>&1) \|\| ! (tail -n 1 listing \| grep "Everything is cool"); then
825	tail listing
826	echo "Bench FAILED, exiting"; exit 1
827	fi
828	date
829	tail listing
830	fi
831
832	# 1D case
833	if [[ $SCM = 1 ]]; then
834	cd "$MODEL"
835	myget 1D/1D.tar.gz
836	tar xf 1D.tar.gz
837	cd 1D
838	if [[ $rad = "oldrad" ]]; then
839	sed -i'' -e 's/^rad=.*$/rad=oldrad/' run.sh
840	sed -i'' -e 's/^rad=.*$/rad=oldrad/' bin/compile
841	fi
842	echo "Running 1D/run.sh, log in $(pwd)/run1d.log"
843	./run.sh > "$(pwd)/run1d.log" 2>&1
844	fi
845	}
846
847	echo "install_lmdz.sh DEBUT $(date)"
848
849	set_default_params
850	read_cmdline_args "$@"
851	#download_model
852	download_model_AMAURY
853	init_arch
854	check_available_software
855	install_netcdf
856	install_IOIPSL
857	install_XIOS
858	compile_orchidee
859	compile_lmdz
860	run_bench

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