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source: BOL/script_install_amaury/install_lmdz.sh @ 4934

Last change on this file since 4934 was 4934, checked in by abarral, 5 months ago
fix run for users w/o svn make sourceable as a lib
Property svn:executable set to ``*
File size: 31.7 KB

Line
1	#!/bin/bash
2	set -eu # error on command failure, and on unset variables
3	export LC_ALL=C # standardize awk format
4
5	###########################################################################
6	# Author : Laurent Fairhead et Frédéric Hourdin
7	# Usage : install_lmdz.sh -help
8	#
9	# bash installation script of the LMDZ model on different computer types :
10	# Linux PC, "mesocentre" (IPSL-UPMC, IPSL-X), super-computer (IDRIS)
11	#
12	# The model is downloaded in the following directory tree
13	# $MODEL/modipsl/modeles/...
14	# using the "modipsl" infrastructure created by the "IPSL"
15	# for coupled (atmosphere/ocean/vegetation/chemistry) climate modeling
16	# activities.
17	# Here we only download atmospheric (LMDZ) and vegetation (ORCHIDEE)
18	# components.
19	#
20	# The sources of the models can be found in the "modeles" directory.
21	# In the present case, LMDZ, ORCHIDEE, and IOIPSL or XIOS (handling of
22	# input-outputs using the NetCDF library).
23	#
24	# The script downloads various source files (including a version of NetCDF)
25	# and utilities, compiles the model, and runs a test simulation in a
26	# minimal configuration.
27	#
28	# Prerequisites : gfortran, bash or ksh, wget, gunzip, tar, ...
29	#
30	# Modif 18/11/2011
31	# changes for option real 8.
32	# We compile with -r8 (or equivalent) and -DNC_DOUBLE for the GCM
33	# but with -r4 for netcdf. Variable real must be set to
34	# r4 or r8 at the beginning of the script below.
35	#
36	###########################################################################
37
38	### Functions
39
40	function myget { # 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	SCM=0
58	veget="none"
59	grid_resolution="32x32x39"
60	physiq=""
61
62	parallel="none"
63	trusting="testing"
64	MODEL=""
65
66	with_xios=0
67	opt_makelmdz_xios=""
68
69	rad="rrtm"
70
71	compile_with_fcm=1
72
73	cosp="none"
74
75	make_j=8
76
77	# Check if on a Mac /!\ Probably doesn't work anymore, to fix one day...
78	if [[ $(uname) = "Darwin" ]]; then
79	export MAKE="make"
80	fi
81
82	optim_debug=""
83	arch="local"
84
85	local mpi_file
86	mpi_file=$(readlink -f "$(which mpif90)")
87	path_mpi=$(dirname "$mpi_file")
88	root_mpi=$(dirname "$path_mpi")
89
90	arch="local-gfortran"
91	arch_dir=""
92	}
93
94	function read_cmdline_args {
95	while (($# > 0)); do
96	case $1 in
97	"-h") cat <<........fin
98	$0 [ -v version ] [ -r svn_release ]
99	[ -parallel PARA ] [ -d GRID_RESOLUTION ] [ -bench 0/1 ]
100	[-name LOCAL_MODEL_NAME] [-rad RADIATIF]
101
102	-v "version" like 20150828.trunk, see http://www.lmd.jussieu.fr/~lmdz/Distrib/LISMOI.trunk (default <$version>)
103
104	-r "svn_release" : either the svn release number or "last" (default <$svn_lmdz>)
105
106	-parallel parallel support: mpi, omp, mpi_omp (mpi with openMP) or none (default: <$parallel>)
107
108	-d "grid resolution": should be among the available benchs if -bench 1 (valid values: 48x36x19, 48x36x39) (default : <$grid_resolution>)
109
110	-bench activating the bench or not (0/1) (default: <$bench>)
111
112	-unstable use unstable tar instead of testing
113
114	-name name of the folder to install to (default <$MODEL>)
115
116	-netcdf 0, 1 or PATH. 0: do not download NetCDF, look for it in standard locations (/usr); 1: download and compile NetCDF; PATH: full path to an existing installed NetCDF library (default: <$netcdf>)
117
118	-xios use (download and compile) the XIOS library (will compile the parallel NetCDF4-HDF5 library) (requires to also have -parallel mpi_omp)
119
120	-cosp to run with cospv1 or cospv2 [none/v1/v2] (default <$cosp>)
121
122	-rad radiative code: oldrad, rrtm or ecrad (default <$rad>)
123
124	-nofcm to compile without fcm
125
126	-SCM install 1D version automatically
127
128	-debug compile everything in debug mode
129
130	-physiq to choose which physics package to use in the bench (default <$physiq>)
131
132	-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 $veget)
133
134	-arch name of the arch to use (default <$arch>)
135
136	-arch_dir where to find the arch files (default <$arch_dir>)
137
138	-make_j number of processes to parallelize installations (default <$make_j>)
139
140	........fin
141	exit 1;;
142	"-v") version=$2; shift; shift;;
143	"-r") svn_lmdz=$2; shift; shift;;
144	"-d") grid_resolution=$2; shift; shift;;
145	"-unstable") trusting="unstable"; shift;;
146	"-cosp") cosp=$2
147	case $cosp in
148	"none"\|"v1"\|"v2") cosp=$2; shift; shift;;
149	*) echo "Only none v1 v2 for cosp option"; exit 1
150	esac;;
151	"-nofcm") compile_with_fcm=0; echo "This option will be reactivated soon (promesse du 8dec2022)"; exit 1; shift;;
152	"-SCM") SCM=1; shift;;
153	"-rad") rad=$2
154	case $rad in
155	"oldrad"\|"rrtm"\|"ecrad") rad=$2; shift; shift;;
156	*) echo "Only oldrad rrtm ecrad for rad option"; exit 1
157	esac;;
158	"-parallel") parallel=$2
159	case $parallel in
160	"none"\|"mpi"\|"omp"\|"mpi_omp") parallel=$2; shift; shift;;
161	*) echo "Only none mpi omp mpi_omp for the parallel option"; exit 1
162	esac;;
163	"-bench") bench=$2; shift; shift;;
164	"-debug") optim_debug=-debug; shift;;
165	"-name") MODEL=$2; shift; shift;;
166	"-netcdf") netcdf=$2; shift; shift;;
167	"-physiq") physiq=$2; shift; shift;;
168	"-xios") with_xios=1; shift;;
169	"-arch") arch=$2; shift; shift;;
170	"-arch_dir") arch_dir=$2; shift; shift;;
171	"-veget") veget=$2; shift; shift;;
172	"-make_j") make_j=$2; shift; shift;;
173	*) bash install_lmdz.sh -h; exit 1
174	esac
175	done
176
177	# Option de compilation pour Cosp
178	case $cosp in
179	v1) opt_cosp="-cosp true";;
180	v2) opt_cosp="-cospv2 true";;
181	*) opt_cosp=""
182	esac
183
184	# Check on veget version
185	if [[ $veget != 'none' && $veget != "CMIP6" && $veget != "orch2.0" && $veget != "orch2.2" ]]; then
186	re='^[0-9]+$'
187	if ! [[ $veget =~ $re ]]; then
188	echo 'Valeur de l option veget non valable'; exit 1
189	fi
190	fi
191
192	#Define veget-related suffix for gcm name
193	if [[ $veget = 'none' ]]; then
194	suff_orc=''
195	else
196	suff_orc='_orch'
197	fi
198
199
200	if [[ $parallel = "none" ]]; then
201	suff_exe='_seq'
202	else
203	suff_exe='_para_mem'
204	fi
205
206	#Chemin pour placer le modele
207	if [[ $MODEL = "" ]]; then MODEL="./LMDZ$version$svn_lmdz$optim_debug"; fi
208
209	## if also compiling XIOS, parallel must be mpi_omp
210	if [[ $with_xios = 1 && $parallel != "mpi_omp" ]]; then
211	echo "Error, you must set -parallel mpi_omp if you want XIOS"; exit 1
212	fi
213
214	if [[ $with_xios = 1 ]]; then
215	opt_makelmdz_xios="-io xios"
216	fi
217
218	if [[ $cosp = "v2" && $with_xios = 0 ]]; then
219	echo "Error, Cospv2 cannot run without Xios"; exit 1
220	fi
221
222	if [[ $arch_dir = "" ]]; then
223	arch_dir="$MODEL/modipsl/config/IPSLCM7/ARCH/"
224	fi
225	arch_dir=$(readlink -f "$arch_dir") # full path
226	}
227
228	function check_available_software {
229	echo "################################################################"
230	echo "Check if required software is available"
231	echo "################################################################"
232	for logiciel in wget tar gzip make gcc cmake m4 c++; do
233	if [[ $(which "$logiciel") = "" ]]; then
234	echo "You must first install $logiciel on your system"; exit 1
235	fi
236	done
237
238	cat <<eod > tt.f90
239	print*,'coucou'
240	end
241	eod
242	$compiler tt.f90 \|\| a.out
243	./a.out >\| tt
244	if [[ $(< tt sed -e 's/ //g' ) != "coucou" ]]; then
245	echo "problem installing with compiler $compiler"; exit 1
246	fi
247	\rm tt a.out tt.f90
248	}
249
250	function download_model {
251	mkdir -p "$MODEL"
252	MODEL=$(readlink -f "$MODEL"); echo "$MODEL" # absolute path
253
254	rm -rf "$MODEL/modipsl"
255
256	echo "##########################################################"
257	echo "Download a slightly modified version of LMDZ"
258	echo "##########################################################"
259	cd "$MODEL"
260	getlog="$(pwd)/get.log"
261	echo "logfile : $getlog"
262	myget "src_archives/$trusting/modipsl.$version.tar.gz" >> get.log 2>&1
263	echo "install_lmdz.sh wget_OK $(date)"
264	gunzip "modipsl.$version.tar.gz" >> get.log 2>&1
265	tar xf "modipsl.$version.tar" >> get.log 2>&1
266	\rm "modipsl.$version.tar"
267	}
268
269	function create_model_tar { # TODO TEMP while waiting for tar: we copy the base from a local path = IPSLCM7 + ORCH2.2 8504
270	if [[ ! -d ../MODEL_REF ]]; then
271	cd ..
272	mkdir MODEL_REF
273	cd MODEL_REF
274	# Base is IPSLCM7
275	svn co --username icmc_users https://forge.ipsl.fr/igcmg/svn/modipsl/trunk modipsl
276	cd modipsl/util
277	./model IPSLCM7_work
278	# Remove unused components
279	rm -rf ../oasis3-mct
280	cd ../modeles
281	rm -rf ICOSA_LMDZ ORCHIDEE_4 ORCHIDEE_2_2 NEMO DYNAMICO XIOS INCA
282	# Retrieve orch version
283	svn co svn://forge.ipsl.fr/orchidee/branches/ORCHIDEE_2_2/ORCHIDEE -r 8504
284	# Correct orchidee bug in 8504
285	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
286
287	cd ../../../script_install
288	fi
289
290	if [[ ! -d "$MODEL" ]]; then
291	\cp -r ../MODEL_REF .
292	mv MODEL_REF "$MODEL"
293	fi
294	MODEL=$(readlink -f "$MODEL"); echo "$MODEL" # absolute path
295	}
296
297	function init_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 $fcm_path"; exit 1
311	fi
312	fi
313
314	# check compiler
315	compiler=$(< "$fcm_path" grep "%COMPILER" \| sed -e "s/%COMPILER\s*//")
316
317	# load env
318	local env_path=${fcm_path/.fcm/.env}
319	# shellcheck disable=SC1090
320	if [[ -f $env_path ]]; then source "$env_path"; fi
321	}
322
323	function install_arch {
324	local component=$1
325
326	if [[ ! -f "$MODEL/modipsl/modeles/$component/arch/arch-$arch.fcm" ]]; then
327	\cp -f "$arch_dir/arch-$arch.fcm" "$MODEL/modipsl/modeles/$component/arch"
328	\cp -f "$arch_dir/arch-$arch.path" "$MODEL/modipsl/modeles/$component/arch"
329
330	if [[ $component = "XIOS" ]]; then
331	# Adapt for XIOS, which uses different naming conventions
332	sed -i'' -e "s/%COMPILER/%FCOMPILER/" -e "s/%LINK/%LINKER/" -e "s/-fdefault-real-8//" "$MODEL/modipsl/modeles/XIOS/arch/arch-$arch.fcm"
333	elif [[ $component = "ORCHIDEE" ]]; then
334	if [[ $orcbranch = "/tags/ORCHIDEE_2_0/ORCHIDEE" ]]; then # 2.0 and before have a different fcm convention
335	sed -i'' -e "s/-I//" -e "s/-L//" "$MODEL/modipsl/modeles/ORCHIDEE/arch/arch-$arch.path" # /!\ we only replace first occurence on purpose
336	fi
337	fi
338	fi
339	}
340
341	function install_netcdf {
342	echo "Installing Netcdf"
343	local ncdf_compiler="$compiler"
344
345	if [[ $netcdf = 0 ]]; then
346	ncdfdir=$(nc-config --prefix)
347	else
348	cd "$MODEL"
349
350	# Convert non-basic compiler
351	case $compiler in
352	mpif90) ncdf_compiler=$($compiler --version \| head -n 1 \| cut -d " " -f -1)
353	esac
354
355	case $ncdf_compiler in
356	gfortran \| GNU) ncdf_compiler="gfortran"; opt1="-compiler gnu"; opt2="-CC gcc -FC gfortran -CXX g++";;
357	*) echo "unexpected compiler $ncdf_compiler for netcdf"; exit 1
358	esac
359
360	case $with_xios in
361	0) script_install_netcdf="install_netcdf4_hdf5_seq.bash"
362	ncdfdir="netcdf4_hdf5_seq"
363	opt_="$opt1";;
364	1) script_install_netcdf="install_netcdf4_hdf5.bash"
365	ncdfdir="netcdf4_hdf5"
366	opt_="$opt2 -MPI $root_mpi";;
367	*) echo "with_xios=$with_xios, should be 0 or 1"; exit 1
368	esac
369	if [[ $netcdf = 1 ]]; then
370	ncdfdir="$MODEL/$ncdfdir"
371	else
372	mkdir -p "$netcdf"; ncdfdir="$netcdf/$ncdfdir"
373	fi
374
375	echo "Repertoire netcdf $ncdfdir"
376	if [[ ! -d $ncdfdir ]]; then
377	netcdflog=$(pwd)/netcdf.log
378	echo "----------------------------------------------------------"
379	echo "Compiling the Netcdf library"
380	echo "----------------------------------------------------------"
381	echo "log file : $netcdflog"
382	myget script_install/$script_install_netcdf >> "$netcdflog" 2>&1
383	chmod u=rwx $script_install_netcdf
384	# shellcheck disable=SC2086
385	./$script_install_netcdf -prefix "$ncdfdir" $opt_ >> "$netcdflog" 2>&1
386	fi
387
388	# Add to path
389	export PATH="$ncdfdir/bin:$PATH"
390
391	#----------------------------------------------------------------------------
392	# LF rajout d'une verrue, pour une raison non encore expliquee,
393	# la librairie est parfois rangée dans lib64 et non dans lib
394	# par certains compilateurs
395	if [[ ! -e lib && -d lib64 ]]; then ln -s lib64 lib; fi
396	#----------------------------------------------------------------------------
397
398	echo "install_lmdz.sh netcdf_OK $(date)"
399	fi
400
401	cat >test_netcdf90.f90 <<EOF
402	use netcdf
403	print *, "NetCDF library version: ", nf90_inq_libvers()
404	end
405	EOF
406
407	if $ncdf_compiler -I"$ncdfdir"/include test_netcdf90.f90 -L"$ncdfdir"/lib -lnetcdff \
408	-lnetcdf -Wl,-rpath="$ncdfdir"/lib && ./a.out
409	then
410	\rm test_netcdf90.f90 a.out
411	else
412	cat <<EOF
413	Failed test program using NetCDF-Fortran. You can:
414	- check that you have NetCDF-Fortran installed in your system
415	- or specify an installation directory with option -netcdf of install_lmdz.sh
416	- or download and compile NetCDF-Fortran with option -netcdf 1 of nstall_lmdz.sh
417	EOF
418	exit 1
419	fi
420
421	# Compile NetCDF95
422	cd "$MODEL/modipsl/modeles/LMD"*
423	echo "Installing NetCDF95"
424	cd "$MODEL"
425	myget src_archives/netcdf/NetCDF95-0.3.tar.gz
426	tar -xf NetCDF95-0.3.tar.gz
427	\rm NetCDF95-0.3.tar.gz
428	cd NetCDF95-0.3
429	mkdir -p build && cd build
430	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"
431	make install
432	}
433
434	function install_IOIPSL {
435	install_arch "IOIPSL"
436
437	cd "$MODEL/modipsl/modeles/IOIPSL"
438	ioipsllog="$(pwd)/ioipsl.log"
439	echo "Compiling IOIPSL, the interface library with Netcdf $(date) (log: $ioipsllog)"
440
441	if ! ./makeioipsl_fcm -arch "$arch" -job 8 > "$ioipsllog" 2>&1; then
442	echo "IOIPSL compile failed, exiting"; exit 1
443	fi
444
445	# Link to modipsl/bin
446	cp -f bin/* ../../bin
447
448	echo "IOIPSL compiled $(date)"
449
450	IOIPSL_LIBDIR_="$MODEL/modipsl/modeles/IOIPSL/lib"
451	IOIPSL_INCDIR_="$MODEL/modipsl/modeles/IOIPSL/inc"
452	}
453
454	function install_XIOS {
455	if [[ $with_xios = 1 ]]; then
456	cd "$MODEL/modipsl/modeles"
457	xioslog="$(pwd)/XIOS/xios.log"
458	echo "##########################################################"
459	echo "Compiling XIOS (log $xioslog) $(date)"
460	echo "##########################################################"
461
462	# Download XIOS
463	local xios_http="http://forge.ipsl.fr/ioserver/svn/XIOS2/branches/xios-2.6"
464	local xios_rev="2568"
465
466	cd "$MODEL/modipsl/modeles"
467	set +e; svn co -r $xios_rev $xios_http XIOS; set -e
468
469	cd XIOS
470
471	install_arch "XIOS"
472
473	echo "Starting XIOS compilation"
474	if ! ./make_xios --arch "$arch" --job 8 > "$xioslog" 2>&1; then
475	echo "XIOS compilation failed, exiting"; exit 1
476	fi
477
478	echo "Compiled XIOS $(date)"
479	fi
480
481	XIOS_LIBDIR_="$MODEL/modipsl/modeles/XIOS/lib"
482	XIOS_INCDIR_="$MODEL/modipsl/modeles/XIOS/inc"
483	}
484
485	function get_orchidee_version { # Set / Check ORCHIDEE version
486	local fetch_rev=""
487	orcbranch=""
488	case $veget in
489	"none") fcm_veget_version="false";;
490	"orch2.0" \| "CMIP6") fcm_veget_version=orchidee2.0; fetch_rev=7906;; # in previous tar we used 6592 but with some modifications to xios_orchidee.f90, which got integrated in 7906
491	"orch2.2") fcm_veget_version=orchidee2.1; orcbranch="ORCHIDEE_2_2" ;; # the bundled version
492	*) fetch_rev=$veget
493	esac
494
495	if [[ -n $fetch_rev ]]; then
496	echo "Fetching orch $fetch_rev from the repository"
497	orcbranch=$(svn log -v -q svn://forge.ipsl.fr/orchidee/ -r "$fetch_rev" \| grep ORCHIDEE \| head -1 \| sed -e 's:ORCHIDEE/.*$:ORCHIDEE:' \| awk '{print $2}')
498	echo "branch is $orcbranch"
499	if [[ $fetch_rev -lt 4465 ]]; then echo 'ORCHIDEE version must be >=4465, exiting'; exit 1; fi
500	\rm -rf "$MODEL/modipsl/modeles/ORCHIDEE"
501	echo "IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at orchidee-help@listes.ipsl.fr"
502	cd "$MODEL/modipsl/modeles"
503	set +e
504	svn co -r "$fetch_rev" "svn://forge.ipsl.fr/orchidee/$orcbranch"
505	set -e
506	cd -
507	fi
508
509
510	# Check parallel LMDZ+ORCH
511	if [[ (! $veget = "none") && $parallel = "none" && ($used_lmdz_rev -lt 4894) ]]; then
512	echo "LMDZ revision must be >=4894 for orchidee without parallel support. Upgrade lmdz or use -parallel mpi_omp."; exit 1
513	fi
514	}
515
516	function compile_orchidee {
517	install_arch "ORCHIDEE"
518
519	if [[ $veget != "none" ]]; then
520	cd "$MODEL/modipsl/modeles/ORCHIDEE"
521
522	orchideelog="$(pwd)/orchidee.log"
523	echo "Compiling ORCHIDEE, the continental surface model (log $orchideelog) $(date)"
524
525	local xios_orchid opt_orc
526	if [[ $with_xios = 1 ]]; then
527	xios_orchid="-xios";
528	else
529	xios_orchid="-noxios"
530	fi
531	if [[ $optim_debug = "-debug" ]]; then
532	opt_orc="-debug";
533	else
534	opt_orc="-prod"
535	fi
536
537	local varenv="IOIPSL_LIBDIR_=$IOIPSL_LIBDIR_ IOIPSL_INCDIR_=$IOIPSL_INCDIR_ XIOS_INCDIR_=$XIOS_INCDIR_ XIOS_LIBDIR_=$XIOS_LIBDIR_"
538	if [[ $parallel = "none" ]]; then
539	echo "$varenv ./makeorchidee_fcm $xios_orchid $opt_orc -parallel none -arch $arch -j $make_j" > compile.sh
540	else
541	if [[ ! -d src_parallel ]]; then
542	echo "Orchidee version too old for parallel support"; exit 1
543	fi
544	{
545	echo "$varenv ./makeorchidee_fcm -j $make_j $xios_orchid $opt_orc -parallel $parallel -arch $arch"
546	} > compile.sh
547	fi
548	chmod +x compile.sh
549	echo "Compiling ORCHIDEE using $(\cat compile.sh)"
550	if ! ./compile.sh > "$orchideelog" 2>&1; then
551	echo "ORCHIDEE compilation failed, exiting"; exit 1
552	fi
553	echo "Compiled ORCHIDEE $(date)"
554	fi
555
556	ORCH_INCDIR_="$MODEL/modipsl/modeles/ORCHIDEE/inc"
557	ORCH_LIBDIR_="$MODEL/modipsl/modeles/ORCHIDEE/lib"
558	}
559
560	function get_lmdz_version {
561	LMDZPATH=$(readlink -f "$MODEL/modipsl/modeles/LMD"*)
562	cd "$LMDZPATH"
563	lmdzlog="$(pwd)/lmdz.log"
564
565	used_lmdz_rev=$svn_lmdz
566	if [[ -n $svn_lmdz ]]; then
567	local lmdzbranch
568	echo "Fetching LMDZ $svn_lmdz from the repository"
569	lmdzbranch=$(svn log -v -q https://svn.lmd.jussieu.fr/LMDZ -r "$svn_lmdz" \| grep LMDZ \| head -1 \| sed -e 's:trunk/.*$:trunk:' \| awk '{print $2}')
570	\rm -rf "$MODEL/modipsl/modeles/LMDZ"
571	cd "$MODEL/modipsl/modeles"
572	set +e
573	svn co -r "$svn_lmdz" "https://svn.lmd.jussieu.fr/LMDZ$lmdzbranch" LMDZ
574	set -e
575	cd -
576	else # get svn from info
577	set +e; used_lmdz_rev=$(svn info \| grep "Last Changed Rev" \| cut -c 19-); set -e
578	if [[ -z $used_lmdz_rev ]]; then # svn info failed
579	used_lmdz_rev=$(grep 'Revision: [0-9]' "$MODEL"/Read*.md \| awk ' { print $2 } ' 2>/dev/null)
580	if [[ -z $used_lmdz_rev ]]; then echo "Could not determine lmdz version. This is likely an issue with the .tar itself, please report to LMDZ team."; exit 1; fi
581	fi
582	fi
583	}
584
585	function compile_lmdz {
586	install_arch "LMDZ"
587	cd "$LMDZPATH"
588
589	exe_name="bin/gcm_${grid_resolution}_phylmd_${rad}${suff_exe}${suff_orc}.e"
590
591	local opt_rad
592	case $rad in
593	oldrad) iflag_rrtm=0; NSW=2; opt_rad="";;
594	rrtm) iflag_rrtm=1; NSW=6
595	if [[ $used_lmdz_rev -le 4185 ]]; then
596	opt_rad="-rrtm true"
597	else
598	opt_rad="-rad rrtm"
599	fi;;
600	ecrad) iflag_rrtm=2; NSW=6; opt_rad="-rad ecrad";;
601	*) echo "Only oldrad rrtm ecrad for rad option"; exit 1
602	esac
603	if [[ $used_lmdz_rev -le 4185 && $rad = "ecrad" ]]; then
604	echo "ecrad only available for LMDZ rev starting with 4186 "; exit 1
605	fi
606
607	# Compile
608	local varenv="IOIPSL_LIBDIR_=\"$IOIPSL_LIBDIR_\" IOIPSL_INCDIR_=\"$IOIPSL_INCDIR_\" ORCH_INCDIR_=\"$ORCH_INCDIR_\" ORCH_LIBDIR_=\"$ORCH_LIBDIR_\" XIOS_INCDIR_=\"$XIOS_INCDIR_\" XIOS_LIBDIR_=\"$XIOS_LIBDIR_\""
609	makelmdz="makelmdz_fcm $optim_debug -arch $arch -j $make_j"
610	if [[ $parallel = "none" ]]; then
611	echo "$varenv ./$makelmdz $opt_rad $opt_cosp -d ${grid_resolution} -v $fcm_veget_version gcm " > compile.sh
612	else
613	echo "$varenv ./$makelmdz $opt_rad $opt_cosp $opt_makelmdz_xios -d ${grid_resolution} -v $fcm_veget_version -mem -parallel $parallel gcm" > compile.sh
614	fi
615	echo "Compiling lmdz using $(\cat compile.sh) (log: $lmdzlog) $(date)"
616	chmod +x ./compile.sh
617	if ! ./compile.sh > "$lmdzlog" 2>&1; then
618	echo "LMDZ compilation failed, exiting"; exit 1
619	fi
620	echo "Finished LMDZ compilation $(date)"
621
622	# Check executable
623	# TODO $mysev -ge 4186 => other name convention ! check original install
624	if [[ ! -f $exe_name ]]; then
625	echo "Compilation failed, can't find the executable"; exit 1
626	else
627	echo "Compilation successfull, the executable is $exe_name $(date)"
628	fi
629	}
630
631	function run_bench {
632	cd "$MODEL/modipsl/modeles/LMDZ"*
633
634	if [[ $bench = "tuto" ]]; then
635	myget "Training/tutorial.tar"; tar xf tutorial.tar; cd TUTORIAL
636	./init.sh
637	elif [[ $bench = 1 ]]; then
638	\rm -rf "BENCH${grid_resolution}"
639	local bench=bench_lmdz_${grid_resolution}
640	myget "3DBenchs/$bench.tar.gz"
641	tar xf "$bench.tar.gz"
642
643	if [[ $cosp = "v1" \|\| $cosp = "v2" ]]; then
644	cd "BENCH${grid_resolution}"
645	# copier les fichiers namelist input et output our COSP
646	cp ../DefLists/cosp*_input_nl.txt .
647	cp ../DefLists/cosp*_output_nl.txt .
648	# Activer la cles ok_cosp pour tourner avec COSP
649	sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp
650	\mv -f tmp config.def
651	cd ..
652	fi
653
654	if [[ -n "$physiq" ]]; then
655	cd "BENCH${grid_resolution}"
656	if [[ -f "physiq.def_${physiq}" ]]; then
657	cp "physiq.def_${physiq}" physiq.def
658	echo "using physiq.def_${physiq}"
659	else
660	echo "using standard physiq.def"
661	fi
662	cd ..
663	else
664	echo "using standard physiq.def"
665	fi
666
667	if [[ $with_xios = 1 ]]; then
668	cd "BENCH${grid_resolution}"
669	cp ../DefLists/iodef.xml .
670	cp ../DefLists/context_lmdz.xml .
671	cp ../DefLists/field_def_lmdz.xml .
672	# A raffiner par la suite
673	echo "A FAIRE : Copier les *xml en fonction de l option cosp"
674	cp ../DefLists/field_def_cosp*.xml .
675	cp ../DefLists/file_def_hist*xml .
676	# adapt iodef.xml to use attached mode
677	sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' \
678	iodef.xml > tmp
679	\mv -f tmp iodef.xml
680
681	# and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
682	# except for histday
683	for histfile in file_def_hist*xml; do
684	if [[ "$histfile" = "file_def_histday_lmdz.xml" ]]; then
685	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' \
686	"$histfile" > tmp
687	\mv -f tmp "$histfile"
688	sed -e 's@output_level="_AUTO_"@output_level="5"@' "$histfile" \
689	> tmp
690	\mv -f tmp "$histfile"
691	sed -e 's@compression_level="2"@compression_level="0"@' \
692	"$histfile" > tmp
693	\mv -f tmp "$histfile"
694	else
695	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
696	"$histfile" > tmp
697	\mv -f tmp "$histfile"
698	fi
699	done
700	# and add option "ok_all_xml=y" in config.def
701	echo "### XIOS outputs" >> config.def
702	echo 'ok_all_xml=.true.' >> config.def
703
704	#activer les sorties pour Cosp
705	if [[ "$cosp" = "v1" ]]; then
706	sed -i'' -e 's@enabled=".FALSE."@enabled=".TRUE."@' \
707	-e 's@output_level="_AUTO_"@output_level="5"@' \
708	-e 's@compression_level="2"@compression_level="0"@' \
709	file_def_histdayCOSP_lmdz.xml
710	fi
711	if [[ "$cosp" = "v2" ]]; then
712	sed -i'' -e 's@compression_level="2"@compression_level="0"@' file_def_histdayCOSPv2_lmdz.xml
713	for type_ in hf day mth; do
714	file=file_def_hist${type_}COSP
715	sed -i'' -e 's@src="./'${file}'_lmdz.xml"@src="./'${file}'v2_lmdz.xml"@' context_lmdz.xml
716	done
717	sed -i'' -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' field_def_lmdz.xml
718	fi
719
720	cd ..
721	fi
722
723	# Cas Bench avec ecrad
724	if [[ $rad = "ecrad" ]]; then
725	cd "BENCH${grid_resolution}"
726	cp ../DefLists/namelist_ecrad .
727	cp -r ../libf/phylmd/ecrad/data .
728	cd ..
729	fi
730
731	# Adjusting bench physiq.def to radiative code chosen
732	cd "BENCH${grid_resolution}"
733	sed -e 's/iflag_rrtm=.*.$/iflag_rrtm='$iflag_rrtm'/' \
734	-e 's/NSW=.*.$/NSW='$NSW'/' physiq.def > tmpdef
735	\mv tmpdef physiq.def
736	cd ..
737
738	cp "$exe_name" "BENCH${grid_resolution}/gcm.e"
739	cd "BENCH${grid_resolution}"
740
741	local bench_cmd="./bench.sh"
742	if [[ ${parallel:0:3} = "mpi" ]]; then
743	# Lancement avec deux procs mpi et 2 openMP
744	echo "export OMP_STACKSIZE=800M" > bench.sh
745	if [[ "${parallel:4:3}" = "omp" ]]; then
746	echo "export OMP_NUM_THREADS=2" >> bench.sh
747	fi
748	if [[ $cosp = "v1" \|\| $cosp = "v2" ]]; then
749	echo "ulimit -s 200000" >> bench.sh
750	else
751	echo "ulimit -s unlimited" >> bench.sh
752	fi
753	if which mpirun > /dev/null 2>&1; then
754	echo "mpirun -np 2 gcm.e > listing 2>&1" >> bench.sh
755	elif grep -q "Adastra" /etc/motd; then
756	local account
757	account=$(/usr/sbin/my_project.py -l 2>&1 \| head -1 \| cut -d " " -f 3- \| cut -c 5-)
758	bench_cmd="srun --nodes=1 --ntasks=1 --cpus-per-task=2 --threads-per-core=2 --time=0:10:00 --constraint=GENOA --account=$account bash bench.sh"
759	echo "./gcm.e > listing 2>&1" >> bench.sh
760	else
761	echo "Error: No command found to run parallel bench"; exit 1
762	fi
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_cmd > 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	# If sourced: returns, else run setup
845	if [[ ! "${BASH_SOURCE[0]}" = "$0" ]]; then return 0; fi
846
847	echo "install_lmdz.sh DEBUT $(date)"
848
849	set_default_params
850	read_cmdline_args "$@"
851	#download_model
852	create_model_tar
853	init_arch
854	check_available_software
855	get_lmdz_version
856	get_orchidee_version
857	install_netcdf
858	install_IOIPSL
859	install_XIOS
860	compile_orchidee
861	compile_lmdz
862	run_bench

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