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source: BOL/script_install_amaury/install_lmdz.sh @ 4989

Last change on this file since 4989 was 4985, checked in by abarral, 17 months ago
correct archs
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1	#!/bin/bash
2	set -eu # error on command failure, and on unset variables
3	export LC_ALL=C # standardize awk format
4
5	###########################################################################
6	# Author : Laurent Fairhead et Frédéric Hourdin
7	# Usage : install_lmdz.sh -help
8	#
9	# bash installation script of the LMDZ model on different computer types :
10	# Linux PC, "mesocentre" (IPSL-UPMC, IPSL-X), super-computer (IDRIS)
11	#
12	# The model is downloaded in the following directory tree
13	# $MODEL/modipsl/modeles/...
14	# using the "modipsl" infrastructure created by the "IPSL"
15	# for coupled (atmosphere/ocean/vegetation/chemistry) climate modeling
16	# activities.
17	# Here we only download atmospheric (LMDZ) and vegetation (ORCHIDEE)
18	# components.
19	#
20	# The sources of the models can be found in the "modeles" directory.
21	# In the present case, LMDZ, ORCHIDEE, and IOIPSL or XIOS (handling of
22	# input-outputs using the NetCDF library).
23	#
24	# The script downloads various source files (including a version of NetCDF)
25	# and utilities, compiles the model, and runs a test simulation in a
26	# minimal configuration.
27	#
28	# Prerequisites : gfortran, bash or ksh, wget, gunzip, tar, ...
29	#
30	# Modif 18/11/2011
31	# changes for option real 8.
32	# We compile with -r8 (or equivalent) and -DNC_DOUBLE for the GCM
33	# but with -r4 for netcdf. Variable real must be set to
34	# r4 or r8 at the beginning of the script below.
35	#
36	###########################################################################
37
38	### Functions
39
40	function myget {
41	# Get a file from LMDZ repository, make it executable if .(ba)sh
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_lmdz=""
54	version="20231022.trunk"
55
56	netcdf=1
57	bench=1
58	SCM=0
59	veget="none"
60	grid_resolution="32x32x39"
61	benchphysiq=""
62	compphysiq="lmd"
63
64	parallel="none"
65	trusting="testing"
66	MODEL=""
67
68	with_xios=0
69	opt_makelmdz_xios=""
70
71	rad="rrtm"
72
73	compile_with_fcm=1
74
75	cosp="none"
76	aerosols=0
77	inlandsis=0
78
79	make_j=8
80	clean_install=1
81
82	# Check if on a Mac /!\ Probably doesn't work anymore, to fix one day...
83	if [[ $(uname) = "Darwin" ]]; then
84	export MAKE="make"
85	fi
86
87	optim_debug=""
88	arch="local"
89
90	local mpi_file
91	mpi_file=$(readlink -e -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	$0 [ -v version ] [ -r svn_release ]
104	[ -parallel PARA ] [ -d GRID_RESOLUTION ] [ -bench 0/1 ]
105	[-name LOCAL_MODEL_NAME] [-rad RADIATIF]
106
107	-v "version" like 20150828.trunk, see http://www.lmd.jussieu.fr/~lmdz/Distrib/LISMOI.trunk (default <$version>)
108
109	-r "svn_release" : either the svn release number or "last" (default <$svn_lmdz>)
110
111	-parallel parallel support: mpi, omp, mpi_omp (mpi with openMP) or none (default: <$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	-unstable use unstable tar instead of testing
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	-benchphysiq to choose which physics.def package to use in the bench (default <$benchphysiq>)
136
137	-compilephysiq physics to compile the model with (default <$compphysiq>)
138
139	-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 $veget)
140
141	-spla activate interactive aerosols
142
143	-inlandsis activate new snow scheme
144
145	-arch name of the arch to use (default <$arch>)
146
147	-arch_dir where to find the arch files (default <$arch_dir>)
148
149	-make_j number of processes to parallelize installations (default <$make_j>)
150
151	-noclean will only download necessary files (but no thorough check is made on the integrity of existing files), and will recompile everything (very quick if it's already been compiled before)
152
153	........fin
154	exit 1;;
155	"-v") version=$2; shift; shift;;
156	"-r") svn_lmdz=$2; shift; shift;;
157	"-d") grid_resolution=$2; shift; shift;;
158	"-unstable") trusting="unstable"; shift;;
159	"-cosp") cosp=$2
160	case $cosp in
161	"none"\|"v1"\|"v2") cosp=$2; shift; shift;;
162	*) echo "Only none v1 v2 for cosp option"; exit 1
163	esac;;
164	"-nofcm") compile_with_fcm=0; echo "This option will be reactivated soon (promesse du 8dec2022)"; exit 1; shift;;
165	"-SCM") SCM=1; shift;;
166	"-rad") rad=$2
167	case $rad in
168	"oldrad"\|"rrtm"\|"ecrad") rad=$2; shift; shift;;
169	*) echo "Only oldrad rrtm ecrad for rad option"; exit 1
170	esac;;
171	"-parallel") parallel=$2
172	case $parallel in
173	"none"\|"mpi"\|"omp"\|"mpi_omp") parallel=$2; shift; shift;;
174	*) echo "Only none mpi omp mpi_omp for the parallel option"; exit 1
175	esac;;
176	"-bench") bench=$2; shift; shift;;
177	"-debug") optim_debug=-debug; shift;;
178	"-name") MODEL=$2; shift; shift;;
179	"-netcdf") netcdf=$2; shift; shift;;
180	"-benchphysiq") benchphysiq=$2; shift; shift;;
181	"-compilephysiq") compphysiq=$2; shift; shift;;
182	"-xios") with_xios=1; shift;;
183	"-arch") arch=$2; shift; shift;;
184	"-arch_dir") arch_dir=$2; shift; shift;;
185	"-veget") veget=$2; shift; shift;;
186	"-spla") aerosols=1; shift;;
187	"-inlandsis") inlandsis=1; shift;;
188	"-make_j") make_j=$2; shift; shift;;
189	"-noclean") clean_install=0; shift;;
190	*) bash install_lmdz.sh -h; exit 1
191	esac
192	done
193
194	# Isotopes : Compile and run with isotopes if lmdz_phys="lmdiso" in main.sh
195	if [[ $compphysiq = "lmdiso" ]]; then isotopes=1; else isotopes=0; fi
196
197	# Option de compilation pour Cosp
198	case $cosp in
199	v1) opt_cosp="-cosp true";;
200	v2) opt_cosp="-cospv2 true";;
201	*) opt_cosp=""
202	esac
203
204	#Define veget-related suffix for gcm name
205	if [[ $veget = 'none' ]]; then
206	suff_orc=''
207	else
208	suff_orc='_orch'
209	fi
210
211
212	if [[ $parallel = "none" ]]; then
213	suff_para='_seq'
214	else
215	suff_para='_para_mem'
216	fi
217
218	if [[ $with_xios = 1 ]]; then opt_makelmdz_xios="-io xios"; fi
219
220	if [[ $aerosols = 1 ]]; then
221	opt_aer="-dust true"; suff_aer="_spla"
222	else
223	opt_aer=""; suff_aer=""
224	fi
225
226	if [[ $inlandsis = 1 ]]; then
227	opt_inlandsis="-inlandsis true"
228	else
229	opt_inlandsis=""
230	fi
231
232	if [[ $isotopes = 1 ]]; then
233	opt_isotopes="-isotopes true"; suff_iso="_iso"
234	else
235	opt_isotopes="" ; suff_iso=""
236	fi
237
238
239	# Name of the model's folder. The convention taken here is that models that requires different compilation sources should have a different names.
240	local xios_name=""
241	if [[ $with_xios = 1 ]]; then xios_name="XIOS"; fi
242	if [[ $MODEL = "" ]]; then MODEL="./LMDZ$version${svn_lmdz}OR$veget$xios_name"; fi
243
244	if [[ $arch_dir = "" ]]; then arch_dir="$MODEL/modipsl/config/IPSLCM7/ARCH/"; fi
245	}
246
247	function ensure_correct_option_combinations {
248	# Check on veget version
249	if [[ $veget != 'none' && $veget != "CMIP6" && $veget != "orch2.0" && $veget != "orch2.2" ]]; then
250	re='^[0-9]+$'
251	if ! [[ $veget =~ $re ]]; then
252	echo 'Valeur de l option veget non valable'; exit 1
253	fi
254	fi
255
256	## if also compiling XIOS, parallel must be mpi_omp
257	if [[ $with_xios = 1 && $parallel != "mpi_omp" ]]; then
258	echo "Error, you must set -parallel mpi_omp if you want XIOS"; exit 1
259	fi
260
261	if [[ $cosp = "v2" && $with_xios = 0 ]]; then
262	echo "Error, Cospv2 cannot run without Xios"; exit 1
263	fi
264
265	# STOP if trying to use both ORCHIDEE and Isotopes :
266	if [[ $isotopes = 1 && $veget != "none" ]]; then
267	echo "STOP: You cannot run LMDZ with ORCHIDEE and ISOtopes at the same time"; exit 1
268	fi
269
270	# STOP if trying to use both SPLA and Isotopes :
271	if [[ $isotopes = 1 && $aerosols = 1 ]]; then
272	echo "STOP: You cannot run LMDZ with Isotopes and aerosols=spla at the same time"; exit 1
273	fi
274
275	# (Temporary) STOP if trying to use Isotopes with XIOS :
276	# TODO Amaury: check if still relevant
277	if [[ $isotopes = 1 && $with_xios = 1 ]]; then
278	echo "STOP: Isotopes cannont yet be run with XIOS"; exit 1
279	fi
280
281	if [[ $aerosols = 1 && $rad != "rrtm" ]]; then
282	echo "STOP: For the time being, <aerosols=spla> requires <rad=rrtm>"; exit 1
283	fi
284	# TODO: vérifier quelles contraintes sont des contraintes lmdzsetup, et lesquelles sont des vraies contraintes
285	}
286
287	function check_available_software {
288	echo "################################################################"
289	echo "Check if required software is available"
290	echo "################################################################"
291	for logiciel in wget tar gzip make gcc cmake m4 c++; do
292	if [[ $(which "$logiciel") = "" ]]; then
293	echo "You must first install $logiciel on your system"; exit 1
294	fi
295	done
296
297	cat <<eod > tt.f90
298	print*,'coucou'
299	end
300	eod
301	$compiler tt.f90 \|\| a.out
302	./a.out >\| tt
303	if [[ $(< tt sed -e 's/ //g' ) != "coucou" ]]; then
304	echo "problem installing with compiler $compiler"; exit 1
305	fi
306	\rm tt a.out tt.f90
307	}
308
309	function download_model {
310	if [[ $clean_install = 1 ]]; then rm -rf "$MODEL"; fi
311
312	mkdir -p "$MODEL"
313	MODEL=$(readlink -e -f "$MODEL"); echo "$MODEL" # absolute path
314	if [[ ! -f "$MODEL/modipsl" ]]; then
315	echo "##########################################################"
316	echo "Download a slightly modified version of LMDZ"
317	echo "##########################################################"
318	cd "$MODEL"
319	getlog="$(pwd)/get.log"
320	echo "logfile : $getlog"
321	myget "src_archives/$trusting/modipsl.$version.tar.gz" >> get.log 2>&1
322	echo "install_lmdz.sh wget_OK $(date)"
323	gunzip "modipsl.$version.tar.gz" >> get.log 2>&1
324	tar xf "modipsl.$version.tar" >> get.log 2>&1
325	\rm "modipsl.$version.tar"
326	fi
327	}
328
329	function create_model_tar { # TODO TEMP while waiting for tar: we copy the base from a local path = IPSLCM7 + ORCH2.2 8504
330	if [[ ! -d ../MODEL_REF ]]; then
331	cd ..
332	mkdir MODEL_REF
333	cd MODEL_REF
334	# Base is IPSLCM7
335	svn co --username icmc_users https://forge.ipsl.fr/igcmg/svn/modipsl/trunk modipsl
336	cd modipsl/util
337	./model IPSLCM7_work
338	# Remove unused components
339	rm -rf ../oasis3-mct
340	cd ../modeles
341	rm -rf ICOSA_LMDZ ORCHIDEE_4 ORCHIDEE_2_2 NEMO DYNAMICO XIOS INCA
342	# Retrieve orch version
343	svn co svn://forge.ipsl.fr/orchidee/branches/ORCHIDEE_2_2/ORCHIDEE -r 8504
344	# Correct orchidee bug in 8504
345	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
346
347	echo "STOP: INITIALIZED, PLEASE RELAUNCH ONCE"; exit 1
348	fi
349
350	if [[ ! -d "$MODEL" ]]; then
351	\cp -r ../MODEL_REF .
352	mv MODEL_REF "$MODEL"
353	fi
354	MODEL=$(readlink -e -f "$MODEL"); echo "$MODEL" # absolute path
355	}
356
357	function init_arch {
358	arch_dir=$(readlink -e -f "$arch_dir") # full path. readlink must be called after the path is created
359	if [[ ! -d $arch_dir ]]; then
360	echo "Error: no arch dir $arch_dir"; exit 1
361	elif [[ ! -f $arch_dir/arch-$arch.path ]]; then
362	echo "Error: no arch-$arch.path in $arch_dir"; exit 1
363	fi
364
365	local fcm_path
366	if [[ -f $arch_dir/arch-$arch.fcm ]]; then
367	fcm_path="$arch_dir/arch-$arch.fcm"
368	else
369	fcm_path="$MODEL/modipsl/modeles/LMDZ/arch/arch-$arch.fcm"
370	if [[ ! -f $fcm_path ]]; then
371	echo "Error: no $fcm_path"; exit 1
372	fi
373	fi
374
375	# check compiler
376	compiler=$(< "$fcm_path" grep "%COMPILER" \| sed -e "s/%COMPILER\s*//")
377
378	# load env
379	local env_path=${fcm_path/.fcm/.env}
380	# shellcheck disable=SC1090
381	if [[ -f $env_path ]]; then source "$env_path"; fi
382	}
383
384	function install_arch {
385	local component=$1
386
387	if [[ ! -f "$MODEL/modipsl/modeles/$component/arch/arch-$arch.fcm" ]]; then
388	cp -f "$arch_dir/arch-$arch."{fcm,path,env} "$MODEL/modipsl/modeles/$component/arch"
389
390	if [[ $component = "XIOS" ]]; then
391	# Adapt for XIOS, which uses different naming conventions
392	sed -i'' -e "s/%COMPILER/%FCOMPILER/" -e "s/%LINK/%LINKER/" -e "s/-fdefault-real-8//" "$MODEL/modipsl/modeles/XIOS/arch/arch-$arch.fcm"
393	elif [[ $component = "ORCHIDEE" ]]; then
394	if [[ $orcbranch = "/tags/ORCHIDEE_2_0/ORCHIDEE" ]]; then # 2.0 and before have a different fcm convention
395	sed -i'' -e "s/-I//" -e "s/-L//" "$MODEL/modipsl/modeles/ORCHIDEE/arch/arch-$arch.path" # /!\ we only replace first occurence on purpose
396	fi
397	fi
398	fi
399	}
400
401	function install_netcdf {
402	echo "Installing Netcdf"
403	local ncdf_compiler="$compiler"
404
405	if [[ $netcdf = 0 ]]; then
406	ncdfdir=$(nf-config --prefix)
407	else
408	cd "$MODEL"
409
410	# Convert non-basic compiler
411	case $compiler in
412	mpif90) ncdf_compiler=$($compiler --version \| head -n 1 \| cut -d " " -f -1)
413	esac
414
415	case $ncdf_compiler in
416	gfortran \| GNU) ncdf_compiler="gfortran"; opt1="-compiler gnu"; opt2="-CC gcc -FC gfortran -CXX g++";;
417	*) echo "unexpected compiler $ncdf_compiler for netcdf"; exit 1
418	esac
419
420	case $with_xios in
421	0) script_install_netcdf="install_netcdf4_hdf5_seq.bash"
422	ncdfdir="netcdf4_hdf5_seq"
423	opt_="$opt1";;
424	1) script_install_netcdf="install_netcdf4_hdf5.bash"
425	ncdfdir="netcdf4_hdf5"
426	opt_="$opt2 -MPI $root_mpi";;
427	*) echo "with_xios=$with_xios, should be 0 or 1"; exit 1
428	esac
429	if [[ $netcdf = 1 ]]; then
430	ncdfdir="$MODEL/$ncdfdir"
431	else
432	mkdir -p "$netcdf"; ncdfdir="$netcdf/$ncdfdir"
433	fi
434
435	echo "Repertoire netcdf $ncdfdir"
436	if [[ ! -d $ncdfdir ]]; then
437	netcdflog=$(pwd)/netcdf.log
438	echo "----------------------------------------------------------"
439	echo "Compiling the Netcdf library"
440	echo "----------------------------------------------------------"
441	echo "log file : $netcdflog"
442	myget script_install/$script_install_netcdf >> "$netcdflog" 2>&1
443	chmod u=rwx $script_install_netcdf
444	# shellcheck disable=SC2086
445	./$script_install_netcdf -prefix "$ncdfdir" $opt_ >> "$netcdflog" 2>&1
446	fi
447
448	# Add to path
449	export PATH="$ncdfdir/bin:$PATH"
450
451	#----------------------------------------------------------------------------
452	# LF rajout d'une verrue, pour une raison non encore expliquee,
453	# la librairie est parfois rangée dans lib64 et non dans lib
454	# par certains compilateurs
455	if [[ ! -e lib && -d lib64 ]]; then ln -s lib64 lib; fi
456	#----------------------------------------------------------------------------
457
458	echo "install_lmdz.sh netcdf_OK $(date)"
459	fi
460
461	cat >test_netcdf90.f90 <<EOF
462	use netcdf
463	print *, "NetCDF library version: ", nf90_inq_libvers()
464	end
465	EOF
466
467	if $ncdf_compiler -I"$ncdfdir"/include test_netcdf90.f90 -L"$ncdfdir"/lib -lnetcdff -lnetcdf -Wl,-rpath="$ncdfdir"/lib && ./a.out; then
468	\rm test_netcdf90.f90 a.out
469	else
470	cat <<EOF
471	Failed test program using NetCDF-Fortran. You can:
472	- check that you have NetCDF-Fortran installed in your system
473	- or specify an installation directory with option -netcdf of install_lmdz.sh
474	- or download and compile NetCDF-Fortran with option -netcdf 1 of install_lmdz.sh
475	EOF
476	exit 1
477	fi
478
479	# Compile NetCDF95
480	cd "$MODEL/modipsl/modeles/LMD"*
481	echo "Installing NetCDF95"
482	cd "$MODEL"
483	if [[ ! -d "NetCDF95-0.3" ]]; then
484	myget src_archives/netcdf/NetCDF95-0.3.tar.gz
485	tar -xf NetCDF95-0.3.tar.gz
486	\rm NetCDF95-0.3.tar.gz
487	cd NetCDF95-0.3
488	mkdir -p build && cd build
489	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"
490	make install
491	fi
492	}
493
494	function install_IOIPSL {
495	install_arch "IOIPSL"
496
497	cd "$MODEL/modipsl/modeles/IOIPSL"
498	ioipsllog="$(pwd)/ioipsl.log"
499	echo "Compiling IOIPSL, the interface library with Netcdf $(date) (log: $ioipsllog)"
500
501	if ! ./makeioipsl_fcm -arch "$arch" -job 8 > "$ioipsllog" 2>&1; then
502	echo "IOIPSL compile failed, exiting"; exit 1
503	fi
504
505	# Link to modipsl/bin
506	cp -f bin/* ../../bin
507
508	echo "IOIPSL compiled $(date)"
509	}
510
511	function install_XIOS {
512	if [[ $with_xios = 1 ]]; then
513	cd "$MODEL/modipsl/modeles"
514	xioslog="$(pwd)/XIOS/xios.log"
515	echo "##########################################################"
516	echo "Compiling XIOS (log $xioslog) $(date)"
517	echo "##########################################################"
518
519	# Download XIOS
520	local xios_http="http://forge.ipsl.fr/ioserver/svn/XIOS2/branches/xios-2.6"
521	local xios_rev="2568"
522
523	cd "$MODEL/modipsl/modeles"
524	set +e; svn co -r $xios_rev $xios_http XIOS; set -e
525
526	cd XIOS
527
528	install_arch "XIOS"
529
530	echo "Starting XIOS compilation"
531	if ! ./make_xios --arch "$arch" --job 8 > "$xioslog" 2>&1; then
532	echo "XIOS compilation failed, exiting"; exit 1
533	fi
534
535	echo "Compiled XIOS $(date)"
536	fi
537	}
538
539	function get_orchidee_version { # Set / Check ORCHIDEE version
540	local fetch_rev=""
541	orcbranch=""
542	case $veget in
543	"none") fcm_veget_version="false";;
544	"orch2.0" \| "CMIP6") fcm_veget_version=orchidee2.0; fetch_rev=7906;; # in previous tar we used 6592 but with some modifications to xios_orchidee.f90, which got integrated in 7906
545	"orch2.2") fcm_veget_version=orchidee2.1; orcbranch="ORCHIDEE_2_2" ;; # the bundled version
546	*) fetch_rev=$veget
547	esac
548
549	if [[ -n $fetch_rev ]]; then
550	echo "Fetching orch $fetch_rev from the repository"
551	orcbranch=$(svn log -v -q svn://forge.ipsl.fr/orchidee/ -r "$fetch_rev" \| grep ORCHIDEE \| head -1 \| sed -e 's:ORCHIDEE/.*$:ORCHIDEE:' \| awk '{print $2}')
552	echo "branch is $orcbranch"
553	if [[ $fetch_rev -lt 4465 ]]; then echo 'ORCHIDEE version must be >=4465, exiting'; exit 1; fi
554	echo "IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at orchidee-help@listes.ipsl.fr"
555	cd "$MODEL/modipsl/modeles"
556	svn co -r "$fetch_rev" "svn://forge.ipsl.fr/orchidee/$orcbranch" \|\| (rm -rf ORCHIDEE && svn co -r "$fetch_rev" "svn://forge.ipsl.fr/orchidee/$orcbranch") # if orch dir exists and is from a different branch, need to delete it first (but we don't want to do this all the time, as it would require a recompile for the same code)
557	cd -
558	fi
559
560	# Check parallel LMDZ+ORCH
561	if [[ (! $veget = "none") && $parallel = "none" && ($used_lmdz_rev -lt 4894) ]]; then
562	echo "LMDZ revision must be >=4894 for orchidee without parallel support. Upgrade lmdz or use -parallel mpi_omp."; exit 1
563	fi
564	}
565
566	function compile_orchidee {
567	install_arch "ORCHIDEE"
568
569	if [[ $veget != "none" ]]; then
570	cd "$MODEL/modipsl/modeles/ORCHIDEE"
571
572	orchideelog="$(pwd)/orchidee.log"
573	echo "Compiling ORCHIDEE, the continental surface model (log $orchideelog) $(date)"
574
575	local xios_orchid opt_orc
576	if [[ $with_xios = 1 ]]; then
577	xios_orchid="-xios";
578	else
579	xios_orchid="-noxios"
580	fi
581	if [[ $optim_debug = "-debug" ]]; then
582	opt_orc="-debug";
583	else
584	opt_orc="-prod"
585	fi
586
587	if [[ $parallel = "none" ]]; then
588	echo "./makeorchidee_fcm $xios_orchid $opt_orc -parallel none -arch $arch -j $make_j" > compile.sh
589	else
590	if [[ ! -d src_parallel ]]; then
591	echo "Orchidee version too old for parallel support"; exit 1
592	fi
593	{
594	echo "./makeorchidee_fcm -j $make_j $xios_orchid $opt_orc -parallel $parallel -arch $arch"
595	} > compile.sh
596	fi
597	chmod +x compile.sh
598	echo "Compiling ORCHIDEE using $(\cat compile.sh)"
599	if ! ./compile.sh > "$orchideelog" 2>&1; then
600	echo "ORCHIDEE compilation failed, exiting"; exit 1
601	fi
602	echo "Compiled ORCHIDEE $(date)"
603	fi
604	}
605
606	function get_lmdz_version {
607	LMDZPATH=$(readlink -e -f "$MODEL/modipsl/modeles/LMD"*)
608	cd "$LMDZPATH"
609	lmdzlog="$(pwd)/lmdz.log"
610
611	used_lmdz_rev=$svn_lmdz
612	if [[ -n $svn_lmdz ]]; then
613	local lmdzbranch
614	echo "Fetching LMDZ $svn_lmdz from the repository"
615	lmdzbranch=$(svn log -v -q https://svn.lmd.jussieu.fr/LMDZ -r "$svn_lmdz" \| grep LMDZ \| head -1 \| sed -e 's:trunk/.*$:trunk:' \| awk '{print $2}')
616	cd "$MODEL/modipsl/modeles"
617	svn co -r "$svn_lmdz" "https://svn.lmd.jussieu.fr/LMDZ$lmdzbranch" LMDZ \|\| (rm -rf LMD* && svn co -r "$svn_lmdz" "https://svn.lmd.jussieu.fr/LMDZ$lmdzbranch" LMDZ) # if lmdz dir exists and is from a different branch, need to delete it first (but we don't want to do this all the time, as it would require a recompile for the same code)
618	cd -
619	else # get svn from info
620	set +e; used_lmdz_rev=$(svn info \| grep "Last Changed Rev" \| cut -c 19-); set -e
621	if [[ -z $used_lmdz_rev ]]; then # svn info failed
622	used_lmdz_rev=$(grep 'Revision: [0-9]' "$MODEL"/Read*.md \| awk ' { print $2 } ' 2>/dev/null)
623	if [[ -z $used_lmdz_rev ]]; then echo "Could not determine lmdz version. This is likely an issue with the .tar itself, please report to LMDZ team."; exit 1; fi
624	fi
625	fi
626	}
627
628	function compile_lmdz {
629	install_arch "LMDZ"
630	cd "$LMDZPATH"
631
632	if [[ $used_lmdz_rev -le 4185 ]]; then
633	exe_name="bin/gcm_${grid_resolution}_phy${compphysiq}_${suff_para}${suff_orc}${suff_aer}${suff_iso}.e"
634	else
635	exe_name="bin/gcm_${grid_resolution}_phy${compphysiq}_${rad}${suff_para}${suff_orc}${suff_aer}${suff_iso}.e"
636	fi
637
638	local opt_rad
639	case $rad in
640	oldrad) iflag_rrtm=0; NSW=2; opt_rad="";;
641	rrtm) iflag_rrtm=1; NSW=6
642	if [[ $used_lmdz_rev -le 4185 ]]; then
643	opt_rad="-rrtm true"
644	else
645	opt_rad="-rad rrtm"
646	fi;;
647	ecrad) iflag_rrtm=2; NSW=6; opt_rad="-rad ecrad";;
648	*) echo "Only oldrad rrtm ecrad for rad option"; exit 1
649	esac
650	if [[ $used_lmdz_rev -le 4185 && $rad = "ecrad" ]]; then
651	echo "ecrad only available for LMDZ rev starting with 4186 "; exit 1
652	fi
653
654	# Compile
655	makelmdz="makelmdz_fcm $optim_debug -arch $arch -j $make_j"
656	local para_compile_opt="-mem -parallel $parallel"; if [[ $parallel = "none" ]]; then para_compile_opt=""; fi
657	echo "./$makelmdz $opt_rad $opt_cosp $opt_makelmdz_xios $opt_aer $opt_inlandsis $opt_isotopes -p $compphysiq -d ${grid_resolution} -v $fcm_veget_version $para_compile_opt gcm" > compile.sh
658	echo "Compiling lmdz using $(\cat compile.sh) (log: $lmdzlog) $(date)"
659	chmod +x ./compile.sh
660	if ! ./compile.sh > "$lmdzlog" 2>&1; then
661	echo "LMDZ compilation failed, exiting"; exit 1
662	fi
663	echo "Finished LMDZ compilation $(date)"
664
665	# Check executable
666	if [[ ! -f $exe_name ]]; then
667	echo "Compilation failed, can't find the executable"; exit 1
668	else
669	echo "Compilation successfull, the executable is $exe_name $(date)"
670	fi
671	}
672
673	function run_bench {
674	cd "$MODEL/modipsl/modeles/LMDZ"*
675
676	if [[ $bench = "tuto" ]]; then
677	myget "Training/tutorial.tar"; tar xf tutorial.tar; cd TUTORIAL
678	./init.sh
679	elif [[ $bench = 1 ]]; then
680	\rm -rf "BENCH${grid_resolution}"
681	local bench=bench_lmdz_${grid_resolution}
682	myget "3DBenchs/$bench.tar.gz"
683	tar xf "$bench.tar.gz"
684
685	if [[ $cosp = "v1" \|\| $cosp = "v2" ]]; then
686	cd "BENCH${grid_resolution}"
687	# copier les fichiers namelist input et output our COSP
688	cp ../DefLists/cosp*_input_nl.txt .
689	cp ../DefLists/cosp*_output_nl.txt .
690	# Activer la cles ok_cosp pour tourner avec COSP
691	sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp
692	\mv -f tmp config.def
693	cd ..
694	fi
695
696	if [[ -n "$benchphysiq" ]]; then
697	cd "BENCH${grid_resolution}"
698	if [[ -f "physiq.def_${benchphysiq}" ]]; then
699	cp "physiq.def_${benchphysiq}" benchphysiq.def
700	echo "using physiq.def_${benchphysiq}"
701	else
702	echo "using standard physiq.def"
703	fi
704	cd ..
705	else
706	echo "using standard physiq.def"
707	fi
708
709	if [[ $with_xios = 1 ]]; then
710	cd "BENCH${grid_resolution}"
711	cp ../DefLists/iodef.xml .
712	cp ../DefLists/context_lmdz.xml .
713	cp ../DefLists/field_def_lmdz.xml .
714	# A raffiner par la suite
715	echo "A FAIRE : Copier les *xml en fonction de l option cosp"
716	cp ../DefLists/field_def_cosp*.xml .
717	cp ../DefLists/file_def_hist*xml .
718	# adapt iodef.xml to use attached mode
719	sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' \
720	iodef.xml > tmp
721	\mv -f tmp iodef.xml
722
723	# and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
724	# except for histday
725	for histfile in file_def_hist*xml; do
726	if [[ "$histfile" = "file_def_histday_lmdz.xml" ]]; then
727	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' \
728	"$histfile" > tmp
729	\mv -f tmp "$histfile"
730	sed -e 's@output_level="_AUTO_"@output_level="5"@' "$histfile" \
731	> tmp
732	\mv -f tmp "$histfile"
733	sed -e 's@compression_level="2"@compression_level="0"@' \
734	"$histfile" > tmp
735	\mv -f tmp "$histfile"
736	else
737	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
738	"$histfile" > tmp
739	\mv -f tmp "$histfile"
740	fi
741	done
742	# and add option "ok_all_xml=y" in config.def
743	echo "### XIOS outputs" >> config.def
744	echo 'ok_all_xml=.true.' >> config.def
745
746	#activer les sorties pour Cosp
747	if [[ "$cosp" = "v1" ]]; then
748	sed -i'' -e 's@enabled=".FALSE."@enabled=".TRUE."@' \
749	-e 's@output_level="_AUTO_"@output_level="5"@' \
750	-e 's@compression_level="2"@compression_level="0"@' \
751	file_def_histdayCOSP_lmdz.xml
752	fi
753	if [[ "$cosp" = "v2" ]]; then
754	sed -i'' -e 's@compression_level="2"@compression_level="0"@' file_def_histdayCOSPv2_lmdz.xml
755	for type_ in hf day mth; do
756	file=file_def_hist${type_}COSP
757	sed -i'' -e 's@src="./'${file}'_lmdz.xml"@src="./'${file}'v2_lmdz.xml"@' context_lmdz.xml
758	done
759	sed -i'' -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' field_def_lmdz.xml
760	fi
761
762	cd ..
763	fi
764
765	# Cas Bench avec ecrad
766	if [[ $rad = "ecrad" ]]; then
767	cd "BENCH${grid_resolution}"
768	cp ../DefLists/namelist_ecrad .
769	cp -r ../libf/phylmd/ecrad/data .
770	cd ..
771	fi
772
773	# Adjusting bench physiq.def to radiative code chosen
774	cd "BENCH${grid_resolution}"
775	sed -e 's/iflag_rrtm=.*.$/iflag_rrtm='$iflag_rrtm'/' \
776	-e 's/NSW=.*.$/NSW='$NSW'/' physiq.def > tmpdef
777	\mv tmpdef physiq.def
778	cd ..
779
780	cp "$exe_name" "BENCH${grid_resolution}/gcm.e"
781	cd "BENCH${grid_resolution}"
782
783	local bench_cmd="./bench.sh"
784	if [[ ${parallel:0:3} = "mpi" ]]; then
785	# Lancement avec deux procs mpi et 2 openMP
786	echo "export OMP_STACKSIZE=800M" > bench.sh
787	if [[ "${parallel:4:3}" = "omp" ]]; then
788	echo "export OMP_NUM_THREADS=2" >> bench.sh
789	fi
790	if [[ $cosp = "v1" \|\| $cosp = "v2" ]]; then
791	echo "ulimit -s 200000" >> bench.sh
792	else
793	echo "ulimit -s unlimited" >> bench.sh
794	fi
795	if which mpirun > /dev/null 2>&1; then
796	echo "mpirun -np 2 gcm.e > listing 2>&1" >> bench.sh
797	elif grep -q "Adastra" /etc/motd; then
798	local account
799	account=$(/usr/sbin/my_project.py -l 2>&1 \| head -1 \| cut -d " " -f 3- \| cut -c 5-)
800	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"
801	echo "./gcm.e > listing 2>&1" >> bench.sh
802	else
803	echo "Error: No command found to run parallel bench"; exit 1
804	fi
805	if [[ $(hostname \| cut -c -6) = "spirit" ]]; then # ulimit unlimited segfaults on Spirit
806	sed -i'' "s/ulimit -s unlimited/ulimit -Ss 8000/" bench.sh
807	fi
808	# Add rebuild, using reb.sh if it is there
809	cat <<EOF >> bench.sh
810	if [[ -f reb.sh ]]; then
811	./reb.sh histday; ./reb.sh histmth; ./reb.sh histhf;
812	./reb.sh histins; ./reb.sh stomate_history;
813	./reb.sh sechiba_history; ./reb.sh sechiba_out_2
814	fi
815	EOF
816	else
817	echo "./gcm.e > listing 2>&1" > bench.sh
818	fi
819	# Getting orchidee stuff
820	if [[ $veget = 'CMIP6' \|\| $veget = "orch2.0" ]]; then # TODO once we have a 2.2 bench, add it here (or in planned separate bench script)
821	echo 'myget 3DBenchs/BENCHCMIP6.tar.gz'
822	myget 3DBenchs/BENCHCMIP6.tar.gz
823	tar xvzf BENCHCMIP6.tar.gz
824	sed -e "s:VEGET=n:VEGET=y:" config.def > tmp
825	mv -f tmp config.def
826	if [[ $with_xios = 1 ]]; then
827	cp ../../ORCHIDEE/src_xml/context_orchidee.xml .
828	echo '<context id="orchidee" src="./context_orchidee.xml"/>' > add.tmp
829	cp ../../ORCHIDEE/src_xml/field_def_orchidee.xml .
830	cp ../../ORCHIDEE/src_xml/file_def_orchidee.xml .
831	cp ../../ORCHIDEE/src_xml/file_def_input_orchidee.xml .
832	if [[ -f ../../ORCHIDEE/src_xml/context_input_orchidee.xml ]]; then
833	cp ../../ORCHIDEE/src_xml/context_input_orchidee.xml .
834	echo '<context id="orchidee" src="./context_input_orchidee.xml"/>' >> add.tmp
835	fi
836	sed -e '/id="LMDZ"/r add.tmp' iodef.xml > tmp
837	mv tmp iodef.xml
838	sed -e'{/sechiba1/ s/enabled="_AUTO_"/type="one_file" enabled=".TRUE."/}' \
839	file_def_orchidee.xml > tmp
840	\mv -f tmp file_def_orchidee.xml
841	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
842	file_def_orchidee.xml > tmp
843	\mv -f tmp file_def_orchidee.xml
844	sed -e 's@output_level="_AUTO_"@output_level="1"@' \
845	file_def_orchidee.xml > tmp
846	\mv -f tmp file_def_orchidee.xml
847	sed -e 's@output_freq="_AUTO_"@output_freq="1d"@' \
848	file_def_orchidee.xml > tmp
849	\mv -f tmp file_def_orchidee.xml
850	sed -e 's@compression_level="4"@compression_level="0"@' \
851	file_def_orchidee.xml > tmp
852	\mv -f tmp file_def_orchidee.xml
853	sed -e 's@XIOS_ORCHIDEE_OK = n@XIOS_ORCHIDEE_OK = y@' \
854	orchidee.def > tmp
855	\mv -f tmp orchidee.def
856	fi
857	fi
858
859	if [[ -f ../arch.env ]]; then source ../arch.env; fi
860
861	echo "EXECUTION DU BENCH"
862	date
863	if (! $bench_cmd > out.bench 2>&1) \|\| ! (tail -n 1 listing \| grep "Everything is cool"); then
864	tail listing
865	echo "Bench FAILED, exiting"; exit 1
866	fi
867	date
868	tail listing
869	fi
870
871	# 1D case
872	if [[ $SCM = 1 ]]; then
873	cd "$MODEL"
874	myget 1D/1D.tar.gz
875	tar xf 1D.tar.gz
876	cd 1D
877	if [[ $rad = "oldrad" ]]; then
878	sed -i'' -e 's/^rad=.*$/rad=oldrad/' run.sh
879	sed -i'' -e 's/^rad=.*$/rad=oldrad/' bin/compile
880	elif [[ $rad = ecrad ]] ; then
881	sed -i'' -e 's/^rad=.*$/rad=ecrad/' run.sh
882	sed -i'' -e 's/^rad=.*$/rad=ecrad/' bin/compile
883	fi
884	echo "Running 1D/run.sh, log in $(pwd)/run1d.log"
885	./run.sh > "$(pwd)/run1d.log" 2>&1
886	fi
887	}
888
889	# If sourced: returns, else run setup
890	if [[ ! "${BASH_SOURCE[0]}" = "$0" ]]; then return 0; fi
891
892	echo "install_lmdz.sh DEBUT $(date)"
893
894	set_default_params
895	read_cmdline_args "$@"
896	ensure_correct_option_combinations
897	#download_model
898	create_model_tar
899	init_arch
900	check_available_software
901	get_lmdz_version
902	get_orchidee_version
903	install_netcdf
904	install_IOIPSL
905	install_XIOS
906	compile_orchidee
907	compile_lmdz
908	run_bench

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