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source: BOL/script_install_amaury/install_lmdz.sh @ 4891

Last change on this file since 4891 was 4891, checked in by abarral, 6 weeks ago
fix orchidee & lmdz compilation explicit exported variables in compile.sh only compile orchidee once (seq OR par) standardize n/y vs 0/1 clean redundant comments in default args
Property svn:executable set to ``*
File size: 29.1 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	# TODO add make_j parallel argument -> check what is used for libigcm
40
41	function myget { # Get a file from LMDZ repository
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=""
54	version="20231022.trunk"
55
56	netcdf=1
57	bench=1
58	pcmac=0 # default: not on a Mac
59	SCM=0
60	veget="none"
61	grid_resolution="32x32x39"
62	physiq=""
63
64	xios_branch="2.6"
65	xios_rev="2568"
66
67	parallel="none"
68	trusting="testing"
69	MODEL=""
70
71	with_xios=0
72	opt_makelmdz_xios=""
73
74	rad="rrtm"
75
76	compile_with_fcm=1
77
78	cosp="none"
79	opt_cosp=""
80
81	# Check if on a Mac
82	if [[ $(uname) = "Darwin" ]]; then
83	pcmac=1
84	export MAKE="make"
85	fi
86
87	optim_debug=""
88	arch="local"
89
90	local mpi_file
91	mpi_file=$(readlink -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	$0 [ -v version ] [ -r svn_release ]
104	[ -parallel PARA ] [ -d GRID_RESOLUTION ] [ -bench 0/1 ]
105	[-name LOCAL_MODEL_NAME] [-gprof] [-opt_makelmdz] [-rad RADIATIF]
106
107	-v "version" like 20150828.trunk, see http://www.lmd.jussieu.fr/~lmdz/Distrib/LISMOI.trunk (default <$version>)
108
109	-r "svn_release" : either the svn release number or "last" (default <$svn>)
110
111	-parallel parallel support: mpi, omp, mpi_omp (mpi with openMP) or none (default: <$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	-testing/unstable
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	-physiq to choose which physics package to use (default <$physiq>)
136
137	-veget surface/vegetation scheme treatment controlled by the single variable veget which can have the following values: none: bucket scheme (default); CMIP6: orchidee version used in CMIP exercise, rev 5661; number: orchidee version number (default $veget)
138
139	-arch name of the arch to use (default <$arch>)
140
141	-arch_dir where to find the arch files (default <$arch_dir>)
142
143	........fin
144	exit 1;;
145	"-v") version=$2; shift; shift;;
146	"-r") svn=$2; shift; shift;;
147	"-d") grid_resolution=$2; shift; shift;;
148	"-unstable"\|"-testing") trusting=$(echo "$1" \| cut -c2-); shift;;
149	"-cosp") cosp=$2
150	case $cosp in
151	"none"\|"v1"\|"v2") cosp=$2; shift; shift;;
152	*) echo "Only none v1 v2 for cosp option"; exit 1
153	esac;;
154	"-nofcm") compile_with_fcm=0; echo "This option will be reactivated soon (promesse du 8dec2022)"; exit 1; shift;;
155	"-SCM") SCM=1; shift;;
156	"-rad") rad=$2
157	case $rad in
158	"oldrad"\|"rrtm"\|"ecrad") rad=$2; shift; shift;;
159	*) echo "Only oldrad rrtm ecrad for rad option"; exit 1
160	esac;;
161	"-parallel") parallel=$2
162	case $parallel in
163	"none"\|"mpi"\|"omp"\|"mpi_omp") parallel=$2; shift; shift;;
164	*) echo "Only none mpi omp mpi_omp for the parallel option"; exit 1
165	esac;;
166	"-bench") bench=$2; shift; shift;;
167	"-debug") optim_debug=-debug; shift;;
168	"-name") MODEL=$2; shift; shift;;
169	"-netcdf") netcdf=$2; shift; shift;;
170	"-physiq") physiq=$2; shift; shift;;
171	"-xios") with_xios=1; shift;;
172	"-arch") arch=$2; shift; shift;;
173	"-arch_dir") arch_dir=$2; shift; shift;;
174	"-veget") veget=$2; shift; shift;;
175	*) bash install_lmdz.sh -h; exit 1
176	esac
177	done
178
179	# Option de compilation pour Cosp
180	case $cosp in
181	v1) opt_cosp="-cosp true";;
182	v2) opt_cosp="-cospv2 true";;
183	*) opt_cosp=""
184	esac
185
186	# Check on veget version
187	if [[ $veget != 'none' && $veget != "CMIP6" ]]; then
188	re='^[0-9]+$'
189	if ! [[ $veget =~ $re ]]; then
190	echo 'Valeur de l option veget non valable'; exit 1
191	fi
192	fi
193
194	#Define veget-related suffix for gcm name
195	if [[ $veget = 'none' ]]; then
196	suff_orc=''
197	#For use with tutorial, orchidee_rev is also defined (will be
198	#written in surface_env at the end of the script)
199	orchidee_rev=''
200	else
201	suff_orc='_orch'
202	fi
203
204
205	if [[ $parallel = "none" ]]; then
206	suff_exe='_seq'
207	else
208	suff_exe='_para_mem'
209	fi
210
211	#Chemin pour placer le modele
212	if [[ $MODEL = "" ]]; then MODEL="./LMDZ$version$svn$optim_debug"; fi
213
214	## if also compiling XIOS, parallel must be mpi_omp
215	if [[ $with_xios = 1 && $parallel != "mpi_omp" ]]; then
216	echo "Error, you must set -parallel mpi_omp if you want XIOS"; exit 1
217	fi
218
219	if [[ $with_xios = 1 ]]; then
220	opt_makelmdz_xios="-io xios"
221	fi
222
223	if [[ $cosp = "v2" && $with_xios = 0 ]]; then
224	echo "Error, Cospv2 cannot run without Xios"; exit 1
225	fi
226
227	if [[ $arch_dir = "" ]]; then
228	arch_dir="$MODEL/modipsl/config/IPSLCM7/ARCH/"
229	fi
230	arch_dir=$(readlink -f "$arch_dir") # full path
231	}
232
233	function check_available_software {
234	echo "################################################################"
235	echo "Check if required software is available"
236	echo "################################################################"
237	for logiciel in wget tar gzip make gcc cmake m4 c++; do
238	if [[ $(which "$logiciel") = "" ]]; then
239	echo "You must first install $logiciel on your system"; exit 1
240	fi
241	done
242
243	cat <<eod > tt.f90
244	print*,'coucou'
245	end
246	eod
247	$compiler tt.f90 \|\| a.out
248	./a.out >\| tt
249	if [[ $(< tt sed -e 's/ //g' ) != "coucou" ]]; then
250	echo "problem installing with compiler $compiler"; exit 1
251	fi
252	\rm tt a.out tt.f90
253	}
254
255	function download_model {
256	mkdir -p "$MODEL"
257	MODEL=$(readlink -f "$MODEL"); echo "$MODEL" # absolute path
258
259	rm -rf "$MODEL/modipsl"
260
261	echo "##########################################################"
262	echo "Download a slightly modified version of LMDZ"
263	echo "##########################################################"
264	cd "$MODEL"
265	getlog="$(pwd)/get.log"
266	echo "logfile : $getlog"
267	myget "src_archives/$trusting/modipsl.$version.tar.gz" >> get.log 2>&1
268	echo "install_lmdz.sh wget_OK $(date)"
269	gunzip "modipsl.$version.tar.gz" >> get.log 2>&1
270	tar xf "modipsl.$version.tar" >> get.log 2>&1
271	\rm "modipsl.$version.tar"
272
273	if [[ $svn != "" ]]; then
274	mysvn=$svn
275	else
276	mysvn="$(grep 'Revision: [0-9]' "$MODEL"/Read*.md \| awk ' { print $2 } ' 2>/dev/null)"
277	fi
278	echo "SVN revision used: $mysvn"
279	}
280
281	function download_model_AMAURY { # TODO
282	MODEL=$(readlink -f "$MODEL"); echo "$MODEL" # absolute path
283
284	if [[ $svn != "" ]]; then
285	mysvn=$svn
286	else
287	mysvn="$(grep 'Revision: [0-9]' "$MODEL"/Read*.md \| awk ' { print $2 } ' 2>/dev/null)"
288	fi
289	echo "SVN revision used: $mysvn"
290	}
291
292	function install_arch {
293	if [[ ! -d $arch_dir ]]; then
294	echo "Error: no arch dir $arch_dir"; exit 1
295	elif [[ ! -f $arch_dir/arch-$arch.path ]]; then
296	echo "Error: no arch-$arch.path in $arch_dir"; exit 1
297	fi
298
299	local fcm_path
300	if [[ -f $arch_dir/arch-$arch.fcm ]]; then
301	fcm_path="$arch_dir/arch-$arch.fcm"
302	else
303	fcm_path="$MODEL/modipsl/modeles/LMDZ/arch/arch-$arch.fcm"
304	if [[ ! -f $fcm_path ]]; then
305	echo "Error: no $fcm_path"; exit 1
306	fi
307	fi
308
309	# check compiler
310	compiler=$(< "$fcm_path" grep "%COMPILER" \| sed -e "s/%COMPILER\s*//")
311
312	# Copy arch to different components
313	# TODO check that this doesn't error if the source and destination are the same
314	for dir in "IOIPSL" "ORCHIDEE" "LMDZ"; do
315	\cp -f "$arch_dir/arch-$arch.fcm" "$MODEL/modipsl/modeles/$dir/arch"
316	\cp -f "$arch_dir/arch-$arch.path" "$MODEL/modipsl/modeles/$dir/arch"
317	done
318
319	# TODO TEMP compat w/ old orch version - make a proper case later
320	sed -i'' -e "s/-I//" -e "s/-L//" "$MODEL/modipsl/modeles/ORCHIDEE/arch/arch-$arch.path" # /!\ we only replace first occurence on purpose
321	}
322
323	function install_netcdf {
324	echo "Installing Netcdf"
325
326	if [[ $netcdf = 0 ]]; then
327	ncdfdir=$(nc-config --prefix)
328	else
329	cd "$MODEL"
330
331	case $compiler in
332	gfortran) opt1="-compiler gnu"; opt2="-CC gcc -FC gfortran -CXX g++";;
333	ifort) opt1="-compiler intel"; opt2="-CC icc -FC ifort -CXX icpc";;
334	pgf90) opt1="-compiler pgf90"; opt2="-CC pgcc -FC pgf90 -CXX pgCC";;
335	*) echo "unexpected compiler $compiler for netcdf"; exit 1
336	esac
337
338	case $with_xios in
339	0) script_install_netcdf="install_netcdf4_hdf5_seq.bash"
340	ncdfdir="netcdf4_hdf5_seq"
341	opt_="$opt1";;
342	1) script_install_netcdf="install_netcdf4_hdf5.bash"
343	ncdfdir="netcdf4_hdf5"
344	opt_="$opt2 -MPI $root_mpi";;
345	*) echo "with_xios=$with_xios, should be 0 or 1"; exit 1
346	esac
347	if [[ $netcdf = 1 ]]; then
348	ncdfdir="$MODEL/$ncdfdir"
349	else
350	mkdir -p "$netcdf"; ncdfdir="$netcdf/$ncdfdir"
351	fi
352
353	echo "Repertoire netcdf $ncdfdir"
354	if [[ ! -d $ncdfdir ]]; then
355	netcdflog=$(pwd)/netcdf.log
356	echo "----------------------------------------------------------"
357	echo "Compiling the Netcdf library"
358	echo "----------------------------------------------------------"
359	echo "log file : $netcdflog"
360	myget script_install/$script_install_netcdf >> "$netcdflog" 2>&1
361	chmod u=rwx $script_install_netcdf
362	# shellcheck disable=SC2086
363	./$script_install_netcdf -prefix "$ncdfdir" $opt_ >> "$netcdflog" 2>&1
364	fi
365
366	#----------------------------------------------------------------------------
367	# LF rajout d'une verrue, pour une raison non encore expliquee,
368	# la librairie est parfois rangée dans lib64 et non dans lib
369	# par certains compilateurs
370	if [[ ! -e lib && -d lib64 ]]; then ln -s lib64 lib; fi
371	#----------------------------------------------------------------------------
372
373	echo "install_lmdz.sh netcdf_OK $(date)"
374	fi
375
376	cat >test_netcdf90.f90 <<EOF
377	use netcdf
378	print *, "NetCDF library version: ", nf90_inq_libvers()
379	end
380	EOF
381
382	if $compiler -I"$ncdfdir"/include test_netcdf90.f90 -L"$ncdfdir"/lib -lnetcdff \
383	-lnetcdf -Wl,-rpath="$ncdfdir"/lib && ./a.out
384	then
385	\rm test_netcdf90.f90 a.out
386	else
387	cat <<EOF
388	Failed test program using NetCDF-Fortran. You can:
389	- check that you have NetCDF-Fortran installed in your system
390	- or specify an installation directory with option -netcdf of install_lmdz.sh
391	- or download and compile NetCDF-Fortran with option -netcdf 1 of nstall_lmdz.sh
392	EOF
393	exit 1
394	fi
395
396	# Compile NetCDF95
397	cd "$MODEL/modipsl/modeles/LMD"*
398	echo "Installing NetCDF95"
399	cd "$MODEL"
400	myget src_archives/netcdf/NetCDF95-0.3.tar.gz
401	tar -xf NetCDF95-0.3.tar.gz
402	\rm NetCDF95-0.3.tar.gz
403	cd NetCDF95-0.3
404	mkdir -p build && cd build
405	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"
406	make install
407	}
408
409	function install_IOIPSL { # via fcm
410	cd "$MODEL/modipsl/modeles/IOIPSL"
411	ioipsllog="$(pwd)/ioipsl.log"
412	echo "Compiling IOIPSL, the interface library with Netcdf $(date) (log: $ioipsllog)"
413
414	if ! ./makeioipsl_fcm -arch "$arch" -job 8 > "$ioipsllog" 2>&1; then
415	echo "IOIPSL compile failed, exiting"; exit 1
416	fi
417	cp lib/* ../../lib
418	echo "IOIPSL compiled $(date)"
419
420	IOIPSL_LIBDIR_="$MODEL/modipsl/modeles/IOIPSL/lib"
421	IOIPSL_INCDIR_="$MODEL/modipsl/modeles/IOIPSL/inc"
422	}
423
424	function install_XIOS {
425	if [[ $with_xios = 1 ]]; then
426	cd "$MODEL/modipsl/modeles"
427	xioslog="$(pwd)/xios.log"
428	echo "##########################################################"
429	echo "Compiling XIOS (log $xioslog) $(date)"
430	echo "##########################################################"
431
432	# Download XIOS
433	case $xios_branch in
434	"trunk")
435	xios_http="http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/trunk";;
436	"2.5")
437	xios_http="http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5";;
438	"2.6")
439	xios_http="http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS2/branches/xios-2.6";;
440	*) echo "XIOS: Error, bad argument for -branch ! Did not expect $xios_branch"; exit;;
441	esac
442
443	cd "$MODEL/modipsl/modeles"
444	set +e; svn co --revision $xios_rev $xios_http XIOS; set -e
445
446	cd XIOS
447	if ! ./make_xios --arch "$arch" --job 8 --arch_path "$arch_dir" > "$xioslog" 2>&1; then
448	echo "XIOS compilation failed, exiting"; exit 1
449	fi
450
451	echo "Compiled XIOS $(date)"
452	fi
453	}
454
455	function get_orchidee_version { # Set / Check ORCHIDEE version
456	if [[ $veget = "none" ]]; then
457	veget_version="false"
458	elif [[ $veget = "CMIP6" ]]; then
459	veget_version=orchidee2.0
460	orchidee_rev=6592
461	else # specific orchidee revision newer than CMIP6, on 2_1 or 2_2 branches
462	veget_version=orchidee2.1
463	orchidee_rev="$veget"
464	if [[ $veget -lt 4465 ]]; then
465	echo 'ORCHIDEE version must be >=4465, exiting'
466	exit 1
467	fi
468
469	set +e
470	svn upgrade
471	local orcbranch
472	orcbranch=$(svn log -v -q svn://forge.ipsl.jussieu.fr/orchidee/ -r "$veget" \|grep ORCHIDEE \|head -1\| sed -e 's:ORCHIDEE/.*$:ORCHIDEE:' \| awk '{print $2}')
473	echo "IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at orchidee-help@listes.ipsl.fr"
474	svn switch -r "$veget" --accept theirs-full "svn://forge.ipsl.jussieu.fr/orchidee/$orcbranch"
475	svn log -r "$veget" \| grep "$veget"
476	if ! svn log -r "$veget" \| grep "$veget"; then
477	echo 'Cannot update ORCHIDEE as not on the right branch for ORCHIDEE'
478	exit 1
479	fi
480	svn update -r "$veget"
481	set -e
482	fi
483	}
484
485	function compile_orchidee {
486	get_orchidee_version
487	ORCHPATH=""
488
489
490	if [[ $veget != "none" ]]; then
491	cd "$MODEL/modipsl/modeles/ORCHIDEE"
492	ORCHPATH=$(pwd)
493
494	orchideelog="$(pwd)/orchidee.log"
495	echo "Compiling ORCHIDEE, the continental surface model (log $orchideelog) $(date)"
496
497	local xios_orchid opt_orc
498	if [[ $with_xios = 1 ]]; then
499	xios_orchid="-xios";
500	else
501	xios_orchid="-noxios"
502	fi
503	if [[ $optim_debug = "-debug" ]]; then
504	opt_orc="-debug";
505	else
506	opt_orc="-prod"
507	fi
508
509	# TODO check that this works with old orchidee versions (cf. -d tools)
510	local varenv="IOIPSL_LIBDIR_=$IOIPSL_LIBDIR_ IOIPSL_INCDIR_=$IOIPSL_INCDIR_ ORCHPATH=$ORCHPATH"
511	if [[ $parallel = "none" ]]; then
512	echo "$varenv ./makeorchidee_fcm $xios_orchid $opt_orc -parallel none -arch $arch -j 8" > compile.sh
513	else
514	if [[ ! -d src_parallel ]]; then
515	echo "Orchidee version too old for parallel support"; exit 1
516	fi
517	{
518	echo "$varenv ./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc -parallel $parallel -arch $arch"
519	echo "$varenv ./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel $parallel -arch $arch"
520	} > compile.sh
521	fi
522	chmod +x compile.sh
523	echo "Compiling ORCHIDEE using $(\cat compile.sh)"
524	if ! ./compile.sh > "$orchideelog" 2>&1; then
525	echo "ORCHIDEE compilation failed, exiting"; exit 1
526	fi
527	echo "Compiled ORCHIDEE $(date)"
528	fi
529
530	ORCH_LIBDIR_="$MODEL/modipsl/modeles/ORCHIDEE/lib"
531	}
532
533	function get_lmdz_version {
534	LMDZPATH=$(readlink -f "$MODEL/modipsl/modeles/LMD"*)
535	cd "$LMDZPATH"
536	lmdzlog="$(pwd)/lmdz.log"
537
538	set +e
539	svn upgrade
540	if [[ $svn = "last" ]]; then
541	svnopt=""
542	else
543	svnopt="-r $svn"
544	fi
545	if [[ $svn != "" ]]; then
546	if svn info \| grep -q 'https:'; then svn switch --relocate https://svn.lmd.jussieu.fr/LMDZ http://svn.lmd.jussieu.fr/LMDZ; fi
547	svn update "$svnopt"
548	fi
549	mysvn=$(svnversion . \| grep -E -o "[0-9]+" 2>/dev/null)
550	set -e
551
552	if [[ $mysvn = "" ]]; then mysvn=$(grep 'Revision: [0-9]' "$MODEL"/Read*.md \| awk ' { print $2 } ' 2>/dev/null); fi
553	if [[ $mysvn = "" ]]; then mysvn=4190; fi
554	}
555
556	function compile_lmdz {
557	get_lmdz_version
558
559	exe_name="bin/gcm_${grid_resolution}_phylmd_${rad}${suff_exe}${suff_orc}.e"
560
561	local opt_rad
562	case $rad in
563	oldrad) iflag_rrtm=0; NSW=2; opt_rad="";;
564	rrtm) iflag_rrtm=1; NSW=6
565	if [[ $mysvn -le 4185 ]]; then
566	opt_rad="-rrtm true"
567	else
568	opt_rad="-rad rrtm"
569	fi;;
570	ecrad) iflag_rrtm=2; NSW=6; opt_rad="-rad ecrad";;
571	*) echo "Only oldrad rrtm ecrad for rad option"; exit 1
572	esac
573	if [[ $mysvn -le 4185 && $rad = "ecrad" ]]; then
574	echo "ecrad only available for LMDZ rev starting with 4186 "; exit 1
575	fi
576
577	# Compile
578	local varenv="IOIPSL_LIBDIR_=$IOIPSL_LIBDIR_ IOIPSL_INCDIR_=$IOIPSL_INCDIR_ ORCH_LIBDIR_=$ORCH_LIBDIR_ ORCHPATH=$ORCHPATH"
579	makelmdz="makelmdz_fcm $optim_debug -arch $arch -j 8"
580	if [[ $parallel = "none" ]]; then
581	echo "$varenv ./$makelmdz $opt_rad $opt_cosp -d ${grid_resolution} -v $veget_version gcm " > compile.sh
582	else
583	echo "$varenv ./$makelmdz $opt_rad $opt_cosp $opt_makelmdz_xios -d ${grid_resolution} -v $veget_version -mem -parallel $parallel gcm" > compile.sh
584	fi
585	echo "Compiling lmdz using $(\cat compile.sh) (log: $lmdzlog) $(date)"
586	chmod +x ./compile.sh
587	if ! ./compile.sh > "$lmdzlog" 2>&1; then
588	echo "LMDZ compilation failed, exiting"; exit 1
589	fi
590	echo "Finished LMDZ compilation $(date)"
591
592	# Check executable
593	# TODO $mysev -ge 4186 => other name convention ! check original install
594	if [[ ! -f $exe_name ]]; then
595	echo "Compilation failed, can't find the executable"; exit 1
596	else
597	echo "Compilation successfull, the executable is $exe_name $(date)"
598	fi
599	}
600
601	function run_bench {
602	cd "$MODEL/modipsl/modeles/LMDZ"*
603
604	if [[ $bench = "tuto" ]]; then
605	myget Training/tutorial.tar; tar xf tutorial.tar; cd TUTORIAL
606	./init.sh
607	elif [[ $bench = 1 ]]; then
608	\rm -rf "BENCH${grid_resolution}"
609	local bench=bench_lmdz_${grid_resolution}
610	myget "3DBenchs/$bench.tar.gz"
611	tar xf "$bench.tar.gz"
612
613	if [[ $cosp = "v1" \|\| $cosp = "v2" ]]; then
614	cd "BENCH${grid_resolution}"
615	# copier les fichiers namelist input et output our COSP
616	cp ../DefLists/cosp*_input_nl.txt .
617	cp ../DefLists/cosp*_output_nl.txt .
618	# Activer la cles ok_cosp pour tourner avec COSP
619	sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp
620	\mv -f tmp config.def
621	cd ..
622	fi
623
624	if [[ -n "$physiq" ]]; then
625	cd "BENCH${grid_resolution}"
626	if [[ -f "physiq.def_${physiq}" ]]; then
627	cp "physiq.def_${physiq}" physiq.def
628	echo "using physiq.def_${physiq}"
629	else
630	echo "using standard physiq.def"
631	fi
632	cd ..
633	else
634	echo "using standard physiq.def"
635	fi
636
637	if [[ $with_xios = 1 ]]; then
638	cd "BENCH${grid_resolution}"
639	cp ../DefLists/iodef.xml .
640	cp ../DefLists/context_lmdz.xml .
641	cp ../DefLists/field_def_lmdz.xml .
642	# A raffiner par la suite
643	echo "A FAIRE : Copier les *xml en fonction de l option cosp"
644	cp ../DefLists/field_def_cosp*.xml .
645	cp ../DefLists/file_def_hist*xml .
646	# adapt iodef.xml to use attached mode
647	sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' \
648	iodef.xml > tmp
649	\mv -f tmp iodef.xml
650
651	# and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
652	# except for histday
653	for histfile in file_def_hist*xml
654	do
655	if [[ "$histfile" = "file_def_histday_lmdz.xml" ]]; then
656	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' \
657	"$histfile" > tmp
658	\mv -f tmp "$histfile"
659	sed -e 's@output_level="_AUTO_"@output_level="5"@' "$histfile" \
660	> tmp
661	\mv -f tmp "$histfile"
662	sed -e 's@compression_level="2"@compression_level="0"@' \
663	"$histfile" > tmp
664	\mv -f tmp "$histfile"
665	else
666	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
667	"$histfile" > tmp
668	\mv -f tmp "$histfile"
669	fi
670	done
671	# and add option "ok_all_xml=y" in config.def
672	echo "### XIOS outputs" >> config.def
673	echo 'ok_all_xml=.true.' >> config.def
674
675	#activer les sorties pour Cosp
676	if [[ "$cosp" = "v1" ]]; then
677	sed -i'' -e 's@enabled=".FALSE."@enabled=".TRUE."@' \
678	-e 's@output_level="_AUTO_"@output_level="5"@' \
679	-e 's@compression_level="2"@compression_level="0"@' \
680	file_def_histdayCOSP_lmdz.xml
681	fi
682	if [[ "$cosp" = "v2" ]]; then
683	sed -e 's@compression_level="2"@compression_level="0"@' file_def_histdayCOSPv2_lmdz.xml
684	for type_ in hf day mth; do
685	file=file_def_hist${type_}COSP
686	sed -i'' -e 's@src="./'${file}'_lmdz.xml"@src="./'${file}'v2_lmdz.xml"@' context_lmdz.xml
687	done
688	sed -i '' -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' field_def_lmdz.xml
689	fi
690
691	cd ..
692	fi
693
694	# Cas Bench avec ecrad
695	if [[ $rad = "ecrad" ]]; then
696	cd "BENCH${grid_resolution}"
697	cp ../DefLists/namelist_ecrad .
698	cp -r ../libf/phylmd/ecrad/data .
699	cd ..
700	fi
701
702	# Adjusting bench physiq.def to radiative code chosen
703	cd "BENCH${grid_resolution}"
704	sed -e 's/iflag_rrtm=.*.$/iflag_rrtm='$iflag_rrtm'/' \
705	-e 's/NSW=.*.$/NSW='$NSW'/' physiq.def > tmpdef
706	\mv tmpdef physiq.def
707	cd ..
708
709	cp "$exe_name" "BENCH${grid_resolution}/gcm.e"
710	cd "BENCH${grid_resolution}"
711
712	if [[ ${parallel:0:3} = "mpi" ]]; then
713	# Lancement avec deux procs mpi et 2 openMP
714	echo "export OMP_STACKSIZE=800M" > bench.sh
715	if [[ "${parallel:4:3}" = "omp" ]]; then
716	echo "export OMP_NUM_THREADS=2" >> bench.sh
717	fi
718	if [[ "$cosp" = "v1" \|\| "$cosp" = "v2" ]]; then
719	echo "ulimit -s 200000" >> bench.sh
720	else
721	echo "ulimit -s unlimited" >> bench.sh
722	fi
723	echo "mpirun -np 2 gcm.e > listing 2>&1" >> bench.sh
724	# Add rebuild, using reb.sh if it is there
725	cat <<EOF >> bench.sh
726	if [[ -f reb.sh ]]; then
727	./reb.sh histday; ./reb.sh histmth; ./reb.sh histhf;
728	./reb.sh histins; ./reb.sh stomate_history;
729	./reb.sh sechiba_history; ./reb.sh sechiba_out_2
730	fi
731	EOF
732	else
733	echo "./gcm.e > listing 2>&1" > bench.sh
734	fi
735	# Getting orchidee stuff
736	if [[ $veget = 'CMIP6' ]]; then
737	echo 'myget 3DBenchs/BENCHCMIP6.tar.gz'
738	myget 3DBenchs/BENCHCMIP6.tar.gz
739	tar xvzf BENCHCMIP6.tar.gz
740	sed -e "s:VEGET=n:VEGET=y:" config.def > tmp
741	mv -f tmp config.def
742	if [[ $with_xios = 1 ]]; then
743	cp ../../ORCHIDEE/src_xml/context_orchidee.xml .
744	echo '<context id="orchidee" src="./context_orchidee.xml"/>' > add.tmp
745	cp ../../ORCHIDEE/src_xml/field_def_orchidee.xml .
746	cp ../../ORCHIDEE/src_xml/file_def_orchidee.xml .
747	cp ../../ORCHIDEE/src_xml/file_def_input_orchidee.xml .
748	if [[ -f ../../ORCHIDEE/src_xml/context_input_orchidee.xml ]]; then
749	cp ../../ORCHIDEE/src_xml/context_input_orchidee.xml .
750	echo '<context id="orchidee" src="./context_input_orchidee.xml"/>' >> add.tmp
751	fi
752	sed -e '/id="LMDZ"/r add.tmp' iodef.xml > tmp
753	mv tmp iodef.xml
754	sed -e'{/sechiba1/ s/enabled="_AUTO_"/type="one_file" enabled=".TRUE."/}' \
755	file_def_orchidee.xml > tmp
756	\mv -f tmp file_def_orchidee.xml
757	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
758	file_def_orchidee.xml > tmp
759	\mv -f tmp file_def_orchidee.xml
760	sed -e 's@output_level="_AUTO_"@output_level="1"@' \
761	file_def_orchidee.xml > tmp
762	\mv -f tmp file_def_orchidee.xml
763	sed -e 's@output_freq="_AUTO_"@output_freq="1d"@' \
764	file_def_orchidee.xml > tmp
765	\mv -f tmp file_def_orchidee.xml
766	sed -e 's@compression_level="4"@compression_level="0"@' \
767	file_def_orchidee.xml > tmp
768	\mv -f tmp file_def_orchidee.xml
769	sed -e 's@XIOS_ORCHIDEE_OK = n@XIOS_ORCHIDEE_OK = y@' \
770	orchidee.def > tmp
771	\mv -f tmp orchidee.def
772	fi
773	fi
774
775	if [[ -f ../arch.env ]]; then source ../arch.env; fi
776
777	echo "EXECUTION DU BENCH"
778	date
779	if (! ./bench.sh > out.bench 2>&1) \|\| ! (tail -n 1 listing \| grep "Everything is cool"); then
780	tail listing
781	echo "Bench FAILED, exiting"; exit 1
782	fi
783	date
784	tail listing
785	fi
786
787	# 1D case
788	if [[ $SCM = 1 ]]; then
789	cd "$MODEL"
790	myget 1D/1D.tar.gz
791	tar xf 1D.tar.gz
792	cd 1D
793	if [[ $rad = "oldrad" ]]; then
794	sed -i'' -e 's/^rad=.*$/rad=oldrad/' run.sh
795	sed -i'' -e 's/^rad=.*$/rad=oldrad/' bin/compile
796	fi
797	echo "Running 1D/run.sh, log in $(pwd)/run1d.log"
798	./run.sh > "$(pwd)/run1d.log" 2>&1
799	fi
800	}
801
802	echo "install_lmdz.sh DEBUT $(date)"
803
804	set_default_params
805	read_cmdline_args "$@"
806	#download_model
807	download_model_AMAURY
808	install_arch
809	check_available_software
810	install_netcdf
811	install_IOIPSL
812	#install_XIOS # TODO disabled for now, did not decide which flags/arch to use for compile
813	compile_orchidee
814	compile_lmdz
815	run_bench

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