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source: BOL/script_install_amaury/install_lmdz.sh @ 4896

Last change on this file since 4896 was 4896, checked in by abarral, 5 weeks ago
Fix XIOS compile Fix mpif90 netcdf compile Fix local netcdf compile Fix missing rebuild
Property svn:executable set to ``*
File size: 29.8 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	make_j=8
82
83	# Check if on a Mac
84	if [[ $(uname) = "Darwin" ]]; then
85	pcmac=1
86	export MAKE="make"
87	fi
88
89	optim_debug=""
90	arch="local"
91
92	local mpi_file
93	mpi_file=$(readlink -f "$(which mpif90)")
94	path_mpi=$(dirname "$mpi_file")
95	root_mpi=$(dirname "$path_mpi")
96
97	arch="local-gfortran"
98	arch_dir=""
99	}
100
101	function read_cmdline_args {
102	while (($# > 0)); do
103	case $1 in
104	"-h") cat <<........fin
105	$0 [ -v version ] [ -r svn_release ]
106	[ -parallel PARA ] [ -d GRID_RESOLUTION ] [ -bench 0/1 ]
107	[-name LOCAL_MODEL_NAME] [-gprof] [-opt_makelmdz] [-rad RADIATIF]
108
109	-v "version" like 20150828.trunk, see http://www.lmd.jussieu.fr/~lmdz/Distrib/LISMOI.trunk (default <$version>)
110
111	-r "svn_release" : either the svn release number or "last" (default <$svn>)
112
113	-parallel parallel support: mpi, omp, mpi_omp (mpi with openMP) or none (default: <$parallel>)
114
115	-d "grid resolution": should be among the available benchs if -bench 1 (valid values: 48x36x19, 48x36x39) (default : <$grid_resolution>)
116
117	-bench activating the bench or not (0/1) (default: <$bench>)
118
119	-testing/unstable
120
121	-name name of the folder to install to (default <$MODEL>)
122
123	-netcdf 0, 1 or PATH. 0: do not download NetCDF, look for it in standard locations (/usr); 1: download and compile NetCDF; PATH: full path to an existing installed NetCDF library (default: <$netcdf>)
124
125	-xios use (download and compile) the XIOS library (will compile the parallel NetCDF4-HDF5 library) (requires to also have -parallel mpi_omp)
126
127	-cosp to run with cospv1 or cospv2 [none/v1/v2] (default <$cosp>)
128
129	-rad radiative code: oldrad, rrtm or ecrad (default <$rad>)
130
131	-nofcm to compile without fcm
132
133	-SCM install 1D version automatically
134
135	-debug compile everything in debug mode
136
137	-physiq to choose which physics package to use (default <$physiq>)
138
139	-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 $veget)
140
141	-arch name of the arch to use (default <$arch>)
142
143	-arch_dir where to find the arch files (default <$arch_dir>)
144
145	-make_j number of processes to parallelize installations (default <$make_j>)
146
147	........fin
148	exit 1;;
149	"-v") version=$2; shift; shift;;
150	"-r") svn=$2; shift; shift;;
151	"-d") grid_resolution=$2; shift; shift;;
152	"-unstable"\|"-testing") trusting=$(echo "$1" \| cut -c2-); shift;;
153	"-cosp") cosp=$2
154	case $cosp in
155	"none"\|"v1"\|"v2") cosp=$2; shift; shift;;
156	*) echo "Only none v1 v2 for cosp option"; exit 1
157	esac;;
158	"-nofcm") compile_with_fcm=0; echo "This option will be reactivated soon (promesse du 8dec2022)"; exit 1; shift;;
159	"-SCM") SCM=1; shift;;
160	"-rad") rad=$2
161	case $rad in
162	"oldrad"\|"rrtm"\|"ecrad") rad=$2; shift; shift;;
163	*) echo "Only oldrad rrtm ecrad for rad option"; exit 1
164	esac;;
165	"-parallel") parallel=$2
166	case $parallel in
167	"none"\|"mpi"\|"omp"\|"mpi_omp") parallel=$2; shift; shift;;
168	*) echo "Only none mpi omp mpi_omp for the parallel option"; exit 1
169	esac;;
170	"-bench") bench=$2; shift; shift;;
171	"-debug") optim_debug=-debug; shift;;
172	"-name") MODEL=$2; shift; shift;;
173	"-netcdf") netcdf=$2; shift; shift;;
174	"-physiq") physiq=$2; shift; shift;;
175	"-xios") with_xios=1; shift;;
176	"-arch") arch=$2; shift; shift;;
177	"-arch_dir") arch_dir=$2; shift; shift;;
178	"-veget") veget=$2; shift; shift;;
179	"-make_j") make_j=$2; shift; shift;;
180	*) bash install_lmdz.sh -h; exit 1
181	esac
182	done
183
184	# Option de compilation pour Cosp
185	case $cosp in
186	v1) opt_cosp="-cosp true";;
187	v2) opt_cosp="-cospv2 true";;
188	*) opt_cosp=""
189	esac
190
191	# Check on veget version
192	if [[ $veget != 'none' && $veget != "CMIP6" ]]; then
193	re='^[0-9]+$'
194	if ! [[ $veget =~ $re ]]; then
195	echo 'Valeur de l option veget non valable'; exit 1
196	fi
197	fi
198
199	#Define veget-related suffix for gcm name
200	if [[ $veget = 'none' ]]; then
201	suff_orc=''
202	#For use with tutorial, orchidee_rev is also defined (will be
203	#written in surface_env at the end of the script)
204	orchidee_rev=''
205	else
206	suff_orc='_orch'
207	fi
208
209
210	if [[ $parallel = "none" ]]; then
211	suff_exe='_seq'
212	else
213	suff_exe='_para_mem'
214	fi
215
216	#Chemin pour placer le modele
217	if [[ $MODEL = "" ]]; then MODEL="./LMDZ$version$svn$optim_debug"; fi
218
219	## if also compiling XIOS, parallel must be mpi_omp
220	if [[ $with_xios = 1 && $parallel != "mpi_omp" ]]; then
221	echo "Error, you must set -parallel mpi_omp if you want XIOS"; exit 1
222	fi
223
224	if [[ $with_xios = 1 ]]; then
225	opt_makelmdz_xios="-io xios"
226	fi
227
228	if [[ $cosp = "v2" && $with_xios = 0 ]]; then
229	echo "Error, Cospv2 cannot run without Xios"; exit 1
230	fi
231
232	if [[ $arch_dir = "" ]]; then
233	arch_dir="$MODEL/modipsl/config/IPSLCM7/ARCH/"
234	fi
235	arch_dir=$(readlink -f "$arch_dir") # full path
236	}
237
238	function check_available_software {
239	echo "################################################################"
240	echo "Check if required software is available"
241	echo "################################################################"
242	for logiciel in wget tar gzip make gcc cmake m4 c++; do
243	if [[ $(which "$logiciel") = "" ]]; then
244	echo "You must first install $logiciel on your system"; exit 1
245	fi
246	done
247
248	cat <<eod > tt.f90
249	print*,'coucou'
250	end
251	eod
252	$compiler tt.f90 \|\| a.out
253	./a.out >\| tt
254	if [[ $(< tt sed -e 's/ //g' ) != "coucou" ]]; then
255	echo "problem installing with compiler $compiler"; exit 1
256	fi
257	\rm tt a.out tt.f90
258	}
259
260	function download_model {
261	mkdir -p "$MODEL"
262	MODEL=$(readlink -f "$MODEL"); echo "$MODEL" # absolute path
263
264	rm -rf "$MODEL/modipsl"
265
266	echo "##########################################################"
267	echo "Download a slightly modified version of LMDZ"
268	echo "##########################################################"
269	cd "$MODEL"
270	getlog="$(pwd)/get.log"
271	echo "logfile : $getlog"
272	myget "src_archives/$trusting/modipsl.$version.tar.gz" >> get.log 2>&1
273	echo "install_lmdz.sh wget_OK $(date)"
274	gunzip "modipsl.$version.tar.gz" >> get.log 2>&1
275	tar xf "modipsl.$version.tar" >> get.log 2>&1
276	\rm "modipsl.$version.tar"
277
278	if [[ $svn != "" ]]; then
279	mysvn=$svn
280	else
281	mysvn="$(grep 'Revision: [0-9]' "$MODEL"/Read*.md \| awk ' { print $2 } ' 2>/dev/null)"
282	fi
283	echo "SVN revision used: $mysvn"
284	}
285
286	function download_model_AMAURY { # TODO
287	MODEL=$(readlink -f "$MODEL"); echo "$MODEL" # absolute path
288
289	if [[ $svn != "" ]]; then
290	mysvn=$svn
291	else
292	mysvn="$(grep 'Revision: [0-9]' "$MODEL"/Read*.md \| awk ' { print $2 } ' 2>/dev/null)"
293	fi
294	echo "SVN revision used: $mysvn"
295	}
296
297	function install_arch {
298	if [[ ! -d $arch_dir ]]; then
299	echo "Error: no arch dir $arch_dir"; exit 1
300	elif [[ ! -f $arch_dir/arch-$arch.path ]]; then
301	echo "Error: no arch-$arch.path in $arch_dir"; exit 1
302	fi
303
304	local fcm_path
305	if [[ -f $arch_dir/arch-$arch.fcm ]]; then
306	fcm_path="$arch_dir/arch-$arch.fcm"
307	else
308	fcm_path="$MODEL/modipsl/modeles/LMDZ/arch/arch-$arch.fcm"
309	if [[ ! -f $fcm_path ]]; then
310	echo "Error: no $fcm_path"; exit 1
311	fi
312	fi
313
314	# check compiler
315	compiler=$(< "$fcm_path" grep "%COMPILER" \| sed -e "s/%COMPILER\s*//")
316
317	# Copy arch to different components
318	# TODO check that this doesn't error if the source and destination are the same
319	for dir in "IOIPSL" "ORCHIDEE" "LMDZ" "XIOS"; do
320	\cp -f "$arch_dir/arch-$arch.fcm" "$MODEL/modipsl/modeles/$dir/arch"
321	\cp -f "$arch_dir/arch-$arch.path" "$MODEL/modipsl/modeles/$dir/arch"
322	done
323
324	# TODO TEMP compat w/ old orch version - make a proper case later
325	sed -i'' -e "s/-I//" -e "s/-L//" "$MODEL/modipsl/modeles/ORCHIDEE/arch/arch-$arch.path" # /!\ we only replace first occurence on purpose
326
327	# Adapt for XIOS, which uses different naming conventions
328	sed -i'' -e "s/%COMPILER/%FCOMPILER/" -e "s/%LINK/%LINKER/" -e "s/-fdefault-real-8//" "$MODEL/modipsl/modeles/XIOS/arch/arch-$arch.fcm"
329	}
330
331	function install_netcdf {
332	echo "Installing Netcdf"
333
334	if [[ $netcdf = 0 ]]; then
335	ncdfdir=$(nc-config --prefix)
336	else
337	cd "$MODEL"
338
339	# Convert non-basic compiler
340	local ncdf_compiler="$compiler"
341	case $compiler in # TODO check if it works with other base compilers
342	mpif90) ncdf_compiler=$($compiler --help \| head -n 1 \| cut -f 2 -d " ")
343	esac
344
345	case $ncdf_compiler in
346	gfortran) opt1="-compiler gnu"; opt2="-CC gcc -FC gfortran -CXX g++";;
347	ifort) opt1="-compiler intel"; opt2="-CC icc -FC ifort -CXX icpc";;
348	pgf90) opt1="-compiler pgf90"; opt2="-CC pgcc -FC pgf90 -CXX pgCC";;
349	*) echo "unexpected compiler $ncdf_compiler for netcdf"; exit 1
350	esac
351
352	case $with_xios in
353	0) script_install_netcdf="install_netcdf4_hdf5_seq.bash"
354	ncdfdir="netcdf4_hdf5_seq"
355	opt_="$opt1";;
356	1) script_install_netcdf="install_netcdf4_hdf5.bash"
357	ncdfdir="netcdf4_hdf5"
358	opt_="$opt2 -MPI $root_mpi";;
359	*) echo "with_xios=$with_xios, should be 0 or 1"; exit 1
360	esac
361	if [[ $netcdf = 1 ]]; then
362	ncdfdir="$MODEL/$ncdfdir"
363	else
364	mkdir -p "$netcdf"; ncdfdir="$netcdf/$ncdfdir"
365	fi
366
367
368	echo "Repertoire netcdf $ncdfdir"
369	if [[ ! -d $ncdfdir ]]; then
370	netcdflog=$(pwd)/netcdf.log
371	echo "----------------------------------------------------------"
372	echo "Compiling the Netcdf library"
373	echo "----------------------------------------------------------"
374	echo "log file : $netcdflog"
375	myget script_install/$script_install_netcdf >> "$netcdflog" 2>&1
376	chmod u=rwx $script_install_netcdf
377	# shellcheck disable=SC2086
378	./$script_install_netcdf -prefix "$ncdfdir" $opt_ >> "$netcdflog" 2>&1
379	fi
380
381	# Add to path
382	export PATH="$ncdfdir/bin:$PATH"
383
384	#----------------------------------------------------------------------------
385	# LF rajout d'une verrue, pour une raison non encore expliquee,
386	# la librairie est parfois rangée dans lib64 et non dans lib
387	# par certains compilateurs
388	if [[ ! -e lib && -d lib64 ]]; then ln -s lib64 lib; fi
389	#----------------------------------------------------------------------------
390
391	echo "install_lmdz.sh netcdf_OK $(date)"
392	fi
393
394	cat >test_netcdf90.f90 <<EOF
395	use netcdf
396	print *, "NetCDF library version: ", nf90_inq_libvers()
397	end
398	EOF
399
400	if $ncdf_compiler -I"$ncdfdir"/include test_netcdf90.f90 -L"$ncdfdir"/lib -lnetcdff \
401	-lnetcdf -Wl,-rpath="$ncdfdir"/lib && ./a.out
402	then
403	\rm test_netcdf90.f90 a.out
404	else
405	cat <<EOF
406	Failed test program using NetCDF-Fortran. You can:
407	- check that you have NetCDF-Fortran installed in your system
408	- or specify an installation directory with option -netcdf of install_lmdz.sh
409	- or download and compile NetCDF-Fortran with option -netcdf 1 of nstall_lmdz.sh
410	EOF
411	exit 1
412	fi
413
414	# Compile NetCDF95
415	cd "$MODEL/modipsl/modeles/LMD"*
416	echo "Installing NetCDF95"
417	cd "$MODEL"
418	myget src_archives/netcdf/NetCDF95-0.3.tar.gz
419	tar -xf NetCDF95-0.3.tar.gz
420	\rm NetCDF95-0.3.tar.gz
421	cd NetCDF95-0.3
422	mkdir -p build && cd build
423	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"
424	make install
425	}
426
427	function install_IOIPSL {
428	cd "$MODEL/modipsl/modeles/IOIPSL"
429	ioipsllog="$(pwd)/ioipsl.log"
430	echo "Compiling IOIPSL, the interface library with Netcdf $(date) (log: $ioipsllog)"
431
432	if ! ./makeioipsl_fcm -arch "$arch" -job 8 > "$ioipsllog" 2>&1; then
433	echo "IOIPSL compile failed, exiting"; exit 1
434	fi
435
436	# Link to modipsl/bin
437	cp -f bin/* ../../bin
438
439	echo "IOIPSL compiled $(date)"
440
441	IOIPSL_LIBDIR_="$MODEL/modipsl/modeles/IOIPSL/lib"
442	IOIPSL_INCDIR_="$MODEL/modipsl/modeles/IOIPSL/inc"
443	}
444
445	function install_XIOS {
446	if [[ $with_xios = 1 ]]; then
447	cd "$MODEL/modipsl/modeles"
448	xioslog="$(pwd)/XIOS/xios.log"
449	echo "##########################################################"
450	echo "Compiling XIOS (log $xioslog) $(date)"
451	echo "##########################################################"
452
453	# Download XIOS
454	case $xios_branch in
455	"trunk")
456	xios_http="http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/trunk";;
457	"2.5")
458	xios_http="http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5";;
459	"2.6")
460	xios_http="http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS2/branches/xios-2.6";;
461	*) echo "XIOS: Error, bad argument for -branch ! Did not expect $xios_branch"; exit;;
462	esac
463
464	cd "$MODEL/modipsl/modeles"
465	set +e; svn co --revision $xios_rev $xios_http XIOS; set -e
466
467	cd XIOS
468	if ! ./make_xios --arch "$arch" --job 8 > "$xioslog" 2>&1; then
469	echo "XIOS compilation failed, exiting"; exit 1
470	fi
471
472	echo "Compiled XIOS $(date)"
473	fi
474
475	XIOS_LIBDIR_="$MODEL/modipsl/modeles/XIOS/lib"
476	XIOS_INCDIR_="$MODEL/modipsl/modeles/XIOS/inc"
477	}
478
479	function get_orchidee_version { # Set / Check ORCHIDEE version
480	if [[ $veget = "none" ]]; then
481	veget_version="false"
482	elif [[ $veget = "CMIP6" ]]; then
483	veget_version=orchidee2.0
484	else # specific orchidee revision newer than CMIP6, on 2_1 or 2_2 branches
485	veget_version=orchidee2.1
486	if [[ $veget -lt 4465 ]]; then
487	echo 'ORCHIDEE version must be >=4465, exiting'
488	exit 1
489	fi
490
491	set +e
492	svn upgrade
493	local orcbranch
494	orcbranch=$(svn log -v -q svn://forge.ipsl.jussieu.fr/orchidee/ -r "$veget" \|grep ORCHIDEE \|head -1\| sed -e 's:ORCHIDEE/.*$:ORCHIDEE:' \| awk '{print $2}')
495	echo "IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at orchidee-help@listes.ipsl.fr"
496	svn switch -r "$veget" --accept theirs-full "svn://forge.ipsl.jussieu.fr/orchidee/$orcbranch"
497	svn log -r "$veget" \| grep "$veget"
498	if ! svn log -r "$veget" \| grep "$veget"; then
499	echo 'Cannot update ORCHIDEE as not on the right branch for ORCHIDEE'
500	exit 1
501	fi
502	svn update -r "$veget"
503	set -e
504	fi
505	}
506
507	function compile_orchidee {
508	get_orchidee_version
509	ORCHPATH=""
510
511
512	if [[ $veget != "none" ]]; then
513	cd "$MODEL/modipsl/modeles/ORCHIDEE"
514	ORCHPATH=$(pwd)
515
516	orchideelog="$(pwd)/orchidee.log"
517	echo "Compiling ORCHIDEE, the continental surface model (log $orchideelog) $(date)"
518
519	local xios_orchid opt_orc
520	if [[ $with_xios = 1 ]]; then
521	xios_orchid="-xios";
522	else
523	xios_orchid="-noxios"
524	fi
525	if [[ $optim_debug = "-debug" ]]; then
526	opt_orc="-debug";
527	else
528	opt_orc="-prod"
529	fi
530
531	# TODO check that this works with old orchidee versions (cf. -d tools)
532	local varenv="IOIPSL_LIBDIR_=$IOIPSL_LIBDIR_ IOIPSL_INCDIR_=$IOIPSL_INCDIR_ ORCHPATH=$ORCHPATH"
533	if [[ $parallel = "none" ]]; then
534	echo "$varenv ./makeorchidee_fcm $xios_orchid $opt_orc -parallel none -arch $arch -j $make_j" > compile.sh
535	else
536	if [[ ! -d src_parallel ]]; then
537	echo "Orchidee version too old for parallel support"; exit 1
538	fi
539	{
540	echo "$varenv ./makeorchidee_fcm -j $make_j -clean $xios_orchid $opt_orc -parallel $parallel -arch $arch"
541	echo "$varenv ./makeorchidee_fcm -j $make_j $xios_orchid $opt_orc -parallel $parallel -arch $arch"
542	} > compile.sh
543	fi
544	chmod +x compile.sh
545	echo "Compiling ORCHIDEE using $(\cat compile.sh)"
546	if ! ./compile.sh > "$orchideelog" 2>&1; then
547	echo "ORCHIDEE compilation failed, exiting"; exit 1
548	fi
549	echo "Compiled ORCHIDEE $(date)"
550	fi
551
552	ORCH_LIBDIR_="$MODEL/modipsl/modeles/ORCHIDEE/lib"
553	}
554
555	function get_lmdz_version {
556	LMDZPATH=$(readlink -f "$MODEL/modipsl/modeles/LMD"*)
557	cd "$LMDZPATH"
558	lmdzlog="$(pwd)/lmdz.log"
559
560	set +e
561	svn upgrade
562	if [[ $svn = "last" ]]; then
563	svnopt=""
564	else
565	svnopt="-r $svn"
566	fi
567	if [[ $svn != "" ]]; then
568	if svn info \| grep -q 'https:'; then svn switch --relocate https://svn.lmd.jussieu.fr/LMDZ http://svn.lmd.jussieu.fr/LMDZ; fi
569	svn update "$svnopt"
570	fi
571	mysvn=$(svnversion . \| grep -E -o "[0-9]+" 2>/dev/null)
572	set -e
573
574	if [[ $mysvn = "" ]]; then mysvn=$(grep 'Revision: [0-9]' "$MODEL"/Read*.md \| awk ' { print $2 } ' 2>/dev/null); fi
575	if [[ $mysvn = "" ]]; then mysvn=4190; fi
576	}
577
578	function compile_lmdz {
579	get_lmdz_version
580
581	exe_name="bin/gcm_${grid_resolution}_phylmd_${rad}${suff_exe}${suff_orc}.e"
582
583	local opt_rad
584	case $rad in
585	oldrad) iflag_rrtm=0; NSW=2; opt_rad="";;
586	rrtm) iflag_rrtm=1; NSW=6
587	if [[ $mysvn -le 4185 ]]; then
588	opt_rad="-rrtm true"
589	else
590	opt_rad="-rad rrtm"
591	fi;;
592	ecrad) iflag_rrtm=2; NSW=6; opt_rad="-rad ecrad";;
593	*) echo "Only oldrad rrtm ecrad for rad option"; exit 1
594	esac
595	if [[ $mysvn -le 4185 && $rad = "ecrad" ]]; then
596	echo "ecrad only available for LMDZ rev starting with 4186 "; exit 1
597	fi
598
599	# Compile
600	local varenv="IOIPSL_LIBDIR_=$IOIPSL_LIBDIR_ IOIPSL_INCDIR_=$IOIPSL_INCDIR_ ORCH_LIBDIR_=$ORCH_LIBDIR_ ORCHPATH=$ORCHPATH XIOS_INCDIR_=$XIOS_INCDIR_ XIOS_LIBDIR_=$XIOS_LIBDIR_"
601	makelmdz="makelmdz_fcm $optim_debug -arch $arch -j $make_j"
602	if [[ $parallel = "none" ]]; then
603	echo "$varenv ./$makelmdz $opt_rad $opt_cosp -d ${grid_resolution} -v $veget_version gcm " > compile.sh
604	else
605	echo "$varenv ./$makelmdz $opt_rad $opt_cosp $opt_makelmdz_xios -d ${grid_resolution} -v $veget_version -mem -parallel $parallel gcm" > compile.sh
606	fi
607	echo "Compiling lmdz using $(\cat compile.sh) (log: $lmdzlog) $(date)"
608	chmod +x ./compile.sh
609	if ! ./compile.sh > "$lmdzlog" 2>&1; then
610	echo "LMDZ compilation failed, exiting"; exit 1
611	fi
612	echo "Finished LMDZ compilation $(date)"
613
614	# Check executable
615	# TODO $mysev -ge 4186 => other name convention ! check original install
616	if [[ ! -f $exe_name ]]; then
617	echo "Compilation failed, can't find the executable"; exit 1
618	else
619	echo "Compilation successfull, the executable is $exe_name $(date)"
620	fi
621	}
622
623	function run_bench {
624	cd "$MODEL/modipsl/modeles/LMDZ"*
625
626	if [[ $bench = "tuto" ]]; then
627	myget "Training/tutorial.tar"; tar xf tutorial.tar; cd TUTORIAL
628	./init.sh
629	elif [[ $bench = 1 ]]; then
630	\rm -rf "BENCH${grid_resolution}"
631	local bench=bench_lmdz_${grid_resolution}
632	myget "3DBenchs/$bench.tar.gz"
633	tar xf "$bench.tar.gz"
634
635	if [[ $cosp = "v1" \|\| $cosp = "v2" ]]; then
636	cd "BENCH${grid_resolution}"
637	# copier les fichiers namelist input et output our COSP
638	cp ../DefLists/cosp*_input_nl.txt .
639	cp ../DefLists/cosp*_output_nl.txt .
640	# Activer la cles ok_cosp pour tourner avec COSP
641	sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp
642	\mv -f tmp config.def
643	cd ..
644	fi
645
646	if [[ -n "$physiq" ]]; then
647	cd "BENCH${grid_resolution}"
648	if [[ -f "physiq.def_${physiq}" ]]; then
649	cp "physiq.def_${physiq}" physiq.def
650	echo "using physiq.def_${physiq}"
651	else
652	echo "using standard physiq.def"
653	fi
654	cd ..
655	else
656	echo "using standard physiq.def"
657	fi
658
659	if [[ $with_xios = 1 ]]; then
660	cd "BENCH${grid_resolution}"
661	cp ../DefLists/iodef.xml .
662	cp ../DefLists/context_lmdz.xml .
663	cp ../DefLists/field_def_lmdz.xml .
664	# A raffiner par la suite
665	echo "A FAIRE : Copier les *xml en fonction de l option cosp"
666	cp ../DefLists/field_def_cosp*.xml .
667	cp ../DefLists/file_def_hist*xml .
668	# adapt iodef.xml to use attached mode
669	sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' \
670	iodef.xml > tmp
671	\mv -f tmp iodef.xml
672
673	# and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
674	# except for histday
675	for histfile in file_def_hist*xml
676	do
677	if [[ "$histfile" = "file_def_histday_lmdz.xml" ]]; then
678	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' \
679	"$histfile" > tmp
680	\mv -f tmp "$histfile"
681	sed -e 's@output_level="_AUTO_"@output_level="5"@' "$histfile" \
682	> tmp
683	\mv -f tmp "$histfile"
684	sed -e 's@compression_level="2"@compression_level="0"@' \
685	"$histfile" > tmp
686	\mv -f tmp "$histfile"
687	else
688	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
689	"$histfile" > tmp
690	\mv -f tmp "$histfile"
691	fi
692	done
693	# and add option "ok_all_xml=y" in config.def
694	echo "### XIOS outputs" >> config.def
695	echo 'ok_all_xml=.true.' >> config.def
696
697	#activer les sorties pour Cosp
698	if [[ "$cosp" = "v1" ]]; then
699	sed -i'' -e 's@enabled=".FALSE."@enabled=".TRUE."@' \
700	-e 's@output_level="_AUTO_"@output_level="5"@' \
701	-e 's@compression_level="2"@compression_level="0"@' \
702	file_def_histdayCOSP_lmdz.xml
703	fi
704	if [[ "$cosp" = "v2" ]]; then
705	sed -e 's@compression_level="2"@compression_level="0"@' file_def_histdayCOSPv2_lmdz.xml
706	for type_ in hf day mth; do
707	file=file_def_hist${type_}COSP
708	sed -i'' -e 's@src="./'${file}'_lmdz.xml"@src="./'${file}'v2_lmdz.xml"@' context_lmdz.xml
709	done
710	sed -i '' -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' field_def_lmdz.xml
711	fi
712
713	cd ..
714	fi
715
716	# Cas Bench avec ecrad
717	if [[ $rad = "ecrad" ]]; then
718	cd "BENCH${grid_resolution}"
719	cp ../DefLists/namelist_ecrad .
720	cp -r ../libf/phylmd/ecrad/data .
721	cd ..
722	fi
723
724	# Adjusting bench physiq.def to radiative code chosen
725	cd "BENCH${grid_resolution}"
726	sed -e 's/iflag_rrtm=.*.$/iflag_rrtm='$iflag_rrtm'/' \
727	-e 's/NSW=.*.$/NSW='$NSW'/' physiq.def > tmpdef
728	\mv tmpdef physiq.def
729	cd ..
730
731	cp "$exe_name" "BENCH${grid_resolution}/gcm.e"
732	cd "BENCH${grid_resolution}"
733
734	if [[ ${parallel:0:3} = "mpi" ]]; then
735	# Lancement avec deux procs mpi et 2 openMP
736	echo "export OMP_STACKSIZE=800M" > bench.sh
737	if [[ "${parallel:4:3}" = "omp" ]]; then
738	echo "export OMP_NUM_THREADS=2" >> bench.sh
739	fi
740	if [[ "$cosp" = "v1" \|\| "$cosp" = "v2" ]]; then
741	echo "ulimit -s 200000" >> bench.sh
742	else
743	echo "ulimit -s unlimited" >> bench.sh
744	fi
745	echo "mpirun -np 2 gcm.e > listing 2>&1" >> bench.sh
746	# Add rebuild, using reb.sh if it is there
747	cat <<EOF >> bench.sh
748	if [[ -f reb.sh ]]; then
749	./reb.sh histday; ./reb.sh histmth; ./reb.sh histhf;
750	./reb.sh histins; ./reb.sh stomate_history;
751	./reb.sh sechiba_history; ./reb.sh sechiba_out_2
752	fi
753	EOF
754	else
755	echo "./gcm.e > listing 2>&1" > bench.sh
756	fi
757	# Getting orchidee stuff
758	if [[ $veget = 'CMIP6' ]]; then
759	echo 'myget 3DBenchs/BENCHCMIP6.tar.gz'
760	myget 3DBenchs/BENCHCMIP6.tar.gz
761	tar xvzf BENCHCMIP6.tar.gz
762	sed -e "s:VEGET=n:VEGET=y:" config.def > tmp
763	mv -f tmp config.def
764	if [[ $with_xios = 1 ]]; then
765	cp ../../ORCHIDEE/src_xml/context_orchidee.xml .
766	echo '<context id="orchidee" src="./context_orchidee.xml"/>' > add.tmp
767	cp ../../ORCHIDEE/src_xml/field_def_orchidee.xml .
768	cp ../../ORCHIDEE/src_xml/file_def_orchidee.xml .
769	cp ../../ORCHIDEE/src_xml/file_def_input_orchidee.xml .
770	if [[ -f ../../ORCHIDEE/src_xml/context_input_orchidee.xml ]]; then
771	cp ../../ORCHIDEE/src_xml/context_input_orchidee.xml .
772	echo '<context id="orchidee" src="./context_input_orchidee.xml"/>' >> add.tmp
773	fi
774	sed -e '/id="LMDZ"/r add.tmp' iodef.xml > tmp
775	mv tmp iodef.xml
776	sed -e'{/sechiba1/ s/enabled="_AUTO_"/type="one_file" enabled=".TRUE."/}' \
777	file_def_orchidee.xml > tmp
778	\mv -f tmp file_def_orchidee.xml
779	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
780	file_def_orchidee.xml > tmp
781	\mv -f tmp file_def_orchidee.xml
782	sed -e 's@output_level="_AUTO_"@output_level="1"@' \
783	file_def_orchidee.xml > tmp
784	\mv -f tmp file_def_orchidee.xml
785	sed -e 's@output_freq="_AUTO_"@output_freq="1d"@' \
786	file_def_orchidee.xml > tmp
787	\mv -f tmp file_def_orchidee.xml
788	sed -e 's@compression_level="4"@compression_level="0"@' \
789	file_def_orchidee.xml > tmp
790	\mv -f tmp file_def_orchidee.xml
791	sed -e 's@XIOS_ORCHIDEE_OK = n@XIOS_ORCHIDEE_OK = y@' \
792	orchidee.def > tmp
793	\mv -f tmp orchidee.def
794	fi
795	fi
796
797	if [[ -f ../arch.env ]]; then source ../arch.env; fi
798
799	echo "EXECUTION DU BENCH"
800	date
801	if (! ./bench.sh > out.bench 2>&1) \|\| ! (tail -n 1 listing \| grep "Everything is cool"); then
802	tail listing
803	echo "Bench FAILED, exiting"; exit 1
804	fi
805	date
806	tail listing
807	fi
808
809	# 1D case
810	if [[ $SCM = 1 ]]; then
811	cd "$MODEL"
812	myget 1D/1D.tar.gz
813	tar xf 1D.tar.gz
814	cd 1D
815	if [[ $rad = "oldrad" ]]; then
816	sed -i'' -e 's/^rad=.*$/rad=oldrad/' run.sh
817	sed -i'' -e 's/^rad=.*$/rad=oldrad/' bin/compile
818	fi
819	echo "Running 1D/run.sh, log in $(pwd)/run1d.log"
820	./run.sh > "$(pwd)/run1d.log" 2>&1
821	fi
822	}
823
824	echo "install_lmdz.sh DEBUT $(date)"
825
826	set_default_params
827	read_cmdline_args "$@"
828	#download_model
829	download_model_AMAURY
830	install_arch
831	check_available_software
832	install_netcdf
833	install_IOIPSL
834	install_XIOS
835	compile_orchidee
836	compile_lmdz
837	run_bench

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