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source: BOL/script_install_amaury/install_lmdz.sh @ 5027

Last change on this file since 5027 was 5027, checked in by abarral, 2 months ago
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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="20240508.CM7"
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 "$path_mpi")
94
95	arch="local-gfortran"
96	arch_dir=""
97
98	jobcmd=""
99	}
100
101	function read_cmdline_args {
102	while (($# > 0)); do
103	case $1 in
104	"-h") cat <<........fin
105	$0 [ -v version ] [ -r svn_release ]
106	[ -parallel PARA ] [ -d GRID_RESOLUTION ] [ -bench 0/1 ]
107	[-name LOCAL_MODEL_NAME] [-rad RADIATIF]
108
109	-v "version" like 20150828.trunk, see http://www.lmd.jussieu.fr/~lmdz/Distrib/LISMOI.trunk (default <$version>)
110
111	-r "svn_release" : either the svn release number or "last" (default <$svn_lmdz>)
112
113	-parallel parallel support: mpi, omp, mpi_omp (mpi with openMP) or none (default: <$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	-unstable use unstable tar instead of testing
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	-benchphysiq to choose which physics.def package to use in the bench (default <$benchphysiq>)
138
139	-compilephysiq physics to compile the model with (default <$compphysiq>)
140
141	-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 [only orch>2.0] (default $veget)
142
143	-spla activate interactive aerosols
144
145	-inlandsis activate new snow scheme
146
147	-arch name of the arch to use (default <$arch>)
148
149	-arch_dir where to find the arch files (default <$arch_dir>)
150
151	-make_j number of processes to parallelize installations (default <$make_j>)
152
153	-jobcmd command prepended to fcm compile jobs, e.g. "srun" (default <$jobcmd>)
154
155	-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)
156
157	........fin
158	exit 1;;
159	"-v") version=$2; shift; shift;;
160	"-r") svn_lmdz=$2; shift; shift;;
161	"-d") grid_resolution=$2; shift; shift;;
162	"-unstable") trusting="unstable"; shift;;
163	"-cosp") cosp=$2
164	case $cosp in
165	"none"\|"v1"\|"v2") cosp=$2; shift; shift;;
166	*) echo "Only none v1 v2 for cosp option"; exit 1
167	esac;;
168	"-nofcm") compile_with_fcm=0; echo "This option will be reactivated soon (promesse du 8dec2022)"; exit 1; shift;;
169	"-SCM") SCM=1; shift;;
170	"-rad") rad=$2
171	case $rad in
172	"oldrad"\|"rrtm"\|"ecrad") rad=$2; shift; shift;;
173	*) echo "Only oldrad rrtm ecrad for rad option"; exit 1
174	esac;;
175	"-parallel") parallel=$2
176	case $parallel in
177	"none"\|"mpi"\|"omp"\|"mpi_omp") parallel=$2; shift; shift;;
178	*) echo "Only none mpi omp mpi_omp for the parallel option"; exit 1
179	esac;;
180	"-bench") bench=$2; shift; shift;;
181	"-debug") optim_debug=-debug; shift;;
182	"-name") MODEL=$2; shift; shift;;
183	"-netcdf") netcdf=$2; shift; shift;;
184	"-benchphysiq") benchphysiq=$2; shift; shift;;
185	"-compilephysiq") compphysiq=$2; shift; shift;;
186	"-xios") with_xios=1; shift;;
187	"-arch") arch=$2; shift; shift;;
188	"-arch_dir") arch_dir=$2; shift; shift;;
189	"-veget") veget=$2; shift; shift;;
190	"-spla") aerosols=1; shift;;
191	"-inlandsis") inlandsis=1; shift;;
192	"-make_j") make_j=$2; shift; shift;;
193	"-jobcmd") jobcmd=$2; shift; shift;;
194	"-noclean") clean_install=0; shift;;
195	*) bash install_lmdz.sh -h; exit 1
196	esac
197	done
198
199	# Isotopes : Compile and run with isotopes if lmdz_phys="lmdiso" in main.sh
200	if [[ $compphysiq = "lmdiso" ]]; then isotopes=1; else isotopes=0; fi
201
202	# Option de compilation pour Cosp
203	case $cosp in
204	v1) opt_cosp="-cosp true";;
205	v2) opt_cosp="-cospv2 true";;
206	*) opt_cosp=""
207	esac
208
209	#Define veget-related suffix for gcm name
210	if [[ $veget = 'none' ]]; then
211	suff_orc=''
212	else
213	suff_orc='_orch'
214	fi
215
216
217	if [[ $parallel = "none" ]]; then
218	suff_para='_seq'
219	else
220	suff_para='_para_mem'
221	fi
222
223	if [[ $with_xios = 1 ]]; then opt_makelmdz_xios="-io xios"; fi
224
225	if [[ $aerosols = 1 ]]; then
226	opt_aer="-dust true"; suff_aer="_spla"
227	else
228	opt_aer=""; suff_aer=""
229	fi
230
231	if [[ $inlandsis = 1 ]]; then
232	opt_inlandsis="-inlandsis true"
233	else
234	opt_inlandsis=""
235	fi
236
237	if [[ $isotopes = 1 ]]; then
238	opt_isotopes="-isotopes true"; suff_iso="_iso"
239	else
240	opt_isotopes="" ; suff_iso=""
241	fi
242
243
244	# Name of the model's folder. The convention taken here is that models that requires different compilation sources should have a different names.
245	local xios_name=""
246	if [[ $with_xios = 1 ]]; then xios_name="XIOS"; fi
247	if [[ $MODEL = "" ]]; then MODEL="./LMDZ$version${svn_lmdz}OR$veget$xios_name"; fi
248
249	if [[ $arch_dir = "" ]]; then arch_dir="$MODEL/modipsl/config/IPSLCM7/ARCH/"; fi
250	}
251
252	function ensure_correct_option_combinations {
253	# Check on veget version
254	if [[ $veget != 'none' && $veget != "CMIP6" && $veget != "orch2.0" && $veget != "orch2.2" ]]; then
255	re='^[0-9]+$'
256	if ! [[ $veget =~ $re ]]; then
257	echo 'Valeur de l option veget non valable'; exit 1
258	fi
259	fi
260
261	## if also compiling XIOS, parallel must be mpi_omp
262	if [[ $with_xios = 1 && $parallel != "mpi_omp" ]]; then
263	echo "Error, you must set -parallel mpi_omp if you want XIOS"; exit 1
264	fi
265
266	if [[ $cosp = "v2" && $with_xios = 0 ]]; then
267	echo "Error, Cospv2 cannot run without Xios"; exit 1
268	fi
269
270	# STOP if trying to use both ORCHIDEE and Isotopes :
271	if [[ $isotopes = 1 && $veget != "none" ]]; then
272	echo "STOP: You cannot run LMDZ with ORCHIDEE and ISOtopes at the same time"; exit 1
273	fi
274
275	# STOP if trying to use both SPLA and Isotopes :
276	if [[ $isotopes = 1 && $aerosols = 1 ]]; then
277	echo "STOP: You cannot run LMDZ with Isotopes and aerosols=spla at the same time"; exit 1
278	fi
279
280	# (Temporary) STOP if trying to use Isotopes with XIOS :
281	# TODO Amaury: check if still relevant
282	if [[ $isotopes = 1 && $with_xios = 1 ]]; then
283	echo "STOP: Isotopes cannont yet be run with XIOS"; exit 1
284	fi
285
286	if [[ $aerosols = 1 && $rad != "rrtm" ]]; then
287	echo "STOP: For the time being, <aerosols=spla> requires <rad=rrtm>"; exit 1
288	fi
289	# TODO: vérifier quelles contraintes sont des contraintes lmdzsetup, et lesquelles sont des vraies contraintes
290	}
291
292	function check_available_software {
293	echo "################################################################"
294	echo "Check if required software is available"
295	echo "################################################################"
296	for logiciel in wget tar gzip make gcc cmake m4 c++; do
297	if [[ $(which "$logiciel") = "" ]]; then
298	echo "You must first install $logiciel on your system"; exit 1
299	fi
300	done
301
302	cat <<eod > tt.f90
303	print*,'coucou'
304	end
305	eod
306	$compiler tt.f90 \|\| a.out
307	./a.out >\| tt
308	if [[ $(< tt sed -e 's/ //g' ) != "coucou" ]]; then
309	echo "problem installing with compiler $compiler"; exit 1
310	fi
311	\rm tt a.out tt.f90
312	}
313
314	function download_model {
315	if [[ $clean_install = 1 ]]; then rm -rf "$MODEL"; fi
316
317	mkdir -p "$MODEL"
318	MODEL=$(readlink -e -f "$MODEL"); echo "$MODEL" # absolute path
319	if [[ ! -f "$MODEL/modipsl" ]]; then
320	echo "##########################################################"
321	echo "Download a slightly modified version of LMDZ"
322	echo "##########################################################"
323	cd "$MODEL"
324	getlog="$(pwd)/get.log"
325	echo "logfile : $getlog"
326	myget "src_archives/$trusting/modipsl.$version.tar.gz" &>> get.log
327	echo "install_lmdz.sh wget_OK $(date)"
328	gunzip "modipsl.$version.tar.gz" &>> get.log
329	tar xf "modipsl.$version.tar" &>> get.log
330	\rm "modipsl.$version.tar"
331	cd - &> /dev/null
332	fi
333	}
334
335	function init_arch {
336	arch_dir=$(readlink -e -f "$arch_dir") # full path. readlink must be called after the path is created
337	if [[ ! -d $arch_dir ]]; then
338	echo "STOP: no arch dir $arch_dir"; exit 1
339	fi
340
341	local fcm_path
342	if [[ -f $arch_dir/arch-$arch.fcm ]]; then
343	fcm_path="$arch_dir/arch-$arch.fcm"
344	else
345	fcm_path="$MODEL/modipsl/modeles/LMDZ/arch/arch-$arch.fcm"
346	if [[ ! -f $fcm_path ]]; then
347	echo "STOP: no $fcm_path"; exit 1
348	fi
349	fi
350
351	local env_path
352	if [[ -f $arch_dir/arch-$arch.env ]]; then
353	env_path="$arch_dir/arch-$arch.env"
354	else
355	env_path="$MODEL/modipsl/modeles/LMDZ/arch/arch-$arch.env"
356	if [[ ! -f $env_path ]]; then
357	echo "STOP: no $env_path"; exit 1
358	fi
359	fi
360
361	# check compiler
362	compiler=$(< "$fcm_path" grep "%COMPILER" \| sed -e "s/%COMPILER\s*//")
363
364	# load env
365	# shellcheck disable=SC1090
366	if [[ -f $env_path ]]; then source "$env_path"; fi
367	}
368
369	function install_arch {
370	local component=$1
371
372	if [[ -f "$arch_dir/arch-$arch.env" ]]; then
373	cp -f "$arch_dir/arch-$arch."{fcm,path,env} "$MODEL/modipsl/modeles/$component/arch" &> /dev/null \|\| true # allow failure if doesn't exist
374
375	if [[ $component = "XIOS" ]]; then
376	# Adapt for XIOS, which uses different naming conventions
377	sed -i'' -e "s/%COMPILER/%FCOMPILER/" -e "s/%LINK/%LINKER/" -e "s/-fdefault-real-8//" "$MODEL/modipsl/modeles/XIOS/arch/arch-$arch.fcm"
378	elif [[ $component = "ORCHIDEE" ]]; then
379	if [[ $orcbranch = "/tags/ORCHIDEE_2_0/ORCHIDEE" ]]; then # 2.0 and before have a different fcm convention
380	sed -i'' -e "s/-I//" -e "s/-L//" "$MODEL/modipsl/modeles/ORCHIDEE/arch/arch-$arch.path" # /!\ we only replace first occurence on purpose
381	fi
382	fi
383	fi
384	}
385
386	function install_netcdf {
387	echo "Installing Netcdf"
388	local ncdf_compiler="$compiler"
389
390	if [[ $netcdf = 0 ]]; then
391	ncdfdir=$(nf-config --prefix)
392	else
393	cd "$MODEL"
394
395	# Convert non-basic compiler
396	case $compiler in
397	mpif90) ncdf_compiler=$($compiler --version \| head -n 1 \| cut -d " " -f -1)
398	esac
399
400	case $ncdf_compiler in
401	gfortran \| GNU) ncdf_compiler="gfortran"; opt1="-compiler gnu"; opt2="-CC gcc -FC gfortran -CXX g++";;
402	*) echo "unexpected compiler $ncdf_compiler for netcdf"; exit 1
403	esac
404
405	case $with_xios in
406	0) script_install_netcdf="install_netcdf4_hdf5_seq.bash"
407	ncdfdir="netcdf4_hdf5_seq"
408	opt_="$opt1";;
409	1) script_install_netcdf="install_netcdf4_hdf5.bash"
410	ncdfdir="netcdf4_hdf5"
411	opt_="$opt2 -MPI $root_mpi";;
412	*) echo "with_xios=$with_xios, should be 0 or 1"; exit 1
413	esac
414	if [[ $netcdf = 1 ]]; then
415	ncdfdir="$MODEL/$ncdfdir"
416	else
417	mkdir -p "$netcdf"; ncdfdir="$netcdf/$ncdfdir"
418	fi
419
420	echo "Repertoire netcdf $ncdfdir"
421	if [[ ! -d $ncdfdir ]]; then
422	netcdflog=$(pwd)/netcdf.log
423	echo "----------------------------------------------------------"
424	echo "Compiling the Netcdf library"
425	echo "----------------------------------------------------------"
426	echo "log file : $netcdflog"
427	myget script_install/$script_install_netcdf &>> "$netcdflog"
428	chmod u=rwx $script_install_netcdf
429	# shellcheck disable=SC2086
430	./$script_install_netcdf -prefix "$ncdfdir" $opt_ &>> "$netcdflog"
431	fi
432
433	# Add to path
434	export PATH="$ncdfdir/bin:$PATH"
435
436	#----------------------------------------------------------------------------
437	# LF rajout d'une verrue, pour une raison non encore expliquee,
438	# la librairie est parfois rangée dans lib64 et non dans lib
439	# par certains compilateurs
440	if [[ ! -e lib && -d lib64 ]]; then ln -s lib64 lib; fi
441	#----------------------------------------------------------------------------
442
443	echo "install_lmdz.sh netcdf_OK $(date)"
444	fi
445
446	cat >test_netcdf90.f90 <<EOF
447	use netcdf
448	print *, "NetCDF library version: ", nf90_inq_libvers()
449	end
450	EOF
451
452	if $ncdf_compiler -I"$ncdfdir"/include test_netcdf90.f90 -L"$ncdfdir"/lib -lnetcdff -lnetcdf -Wl,-rpath="$ncdfdir"/lib && ./a.out; then
453	\rm test_netcdf90.f90 a.out
454	else
455	cat <<EOF
456	Failed test program using NetCDF-Fortran. You can:
457	- check that you have NetCDF-Fortran installed in your system
458	- or specify an installation directory with option -netcdf of install_lmdz.sh
459	- or download and compile NetCDF-Fortran with option -netcdf 1 of install_lmdz.sh
460	EOF
461	exit 1
462	fi
463
464	# Compile NetCDF95
465	cd "$MODEL/modipsl/modeles/LMD"*
466	echo "Installing NetCDF95"
467	cd "$MODEL"
468	if [[ ! -d "NetCDF95-0.3" ]]; then
469	myget src_archives/netcdf/NetCDF95-0.3.tar.gz
470	tar -xf NetCDF95-0.3.tar.gz
471	\rm NetCDF95-0.3.tar.gz
472	cd NetCDF95-0.3
473	mkdir -p build && cd build
474	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"
475	make install
476	fi
477	}
478
479	function install_IOIPSL {
480	install_arch "IOIPSL"
481
482	cd "$MODEL/modipsl/modeles/IOIPSL"
483	ioipsllog="$(pwd)/ioipsl.log"
484	echo "Compiling IOIPSL, the interface library with Netcdf $(date) (log: $ioipsllog)"
485
486	echo "$jobcmd ./makeioipsl_fcm -j $make_j -arch $arch" > compile.sh
487	chmod +x compile.sh
488	echo "Compiling IOIPSL using $(\cat compile.sh)"
489	if ! ./compile.sh &> "$ioipsllog"; then
490	echo "STOP: IOIPSL compile failed, exiting"; exit 1
491	fi
492
493	# Link to modipsl/bin
494	cp -f bin/* ../../bin
495
496	echo "IOIPSL compiled $(date)"
497	}
498
499	function install_XIOS {
500	if [[ $with_xios = 1 ]]; then
501	cd "$MODEL/modipsl/modeles"
502	xioslog="$(pwd)/XIOS/xios.log"
503	echo "##########################################################"
504	echo "Compiling XIOS (log $xioslog) $(date)"
505	echo "##########################################################"
506
507	# Download XIOS
508	local xios_http="http://forge.ipsl.fr/ioserver/svn/XIOS2/branches/xios-2.6"
509	local xios_rev="2568"
510
511	cd "$MODEL/modipsl/modeles"
512	set +e; svn co -r $xios_rev $xios_http XIOS; set -e
513
514	cd XIOS
515
516	install_arch "XIOS"
517
518	echo "Starting XIOS compilation"
519	if ! ./make_xios --arch "$arch" --job 8 &> "$xioslog"; then
520	echo "STOP: XIOS compilation failed, exiting"; exit 1
521	fi
522
523	echo "Compiled XIOS $(date)"
524	fi
525	}
526
527	function get_orchidee_version { # Set / Check ORCHIDEE version
528	local fetch_rev=""
529	orcbranch=""
530	case $veget in
531	"none") fcm_veget_version="false";;
532	"orch2.0" \| "CMIP6") fcm_veget_version=orchidee2.0; fetch_rev=7906;; # in previous tar we used 6592 but with some modifications to xios_orchidee.f90, which got integrated in 7906
533	"orch2.2") fcm_veget_version=orchidee2.1; orcbranch="/branches/ORCHIDEE_2_2/ORCHIDEE" ;; # the bundled version
534	*) fetch_rev=$veget; fcm_veget_version=orchidee2.1;; # /!\ arbitary rev only works for orch>=2.1
535	esac
536
537	if [[ -n $fetch_rev ]]; then
538	local curr_rev
539	curr_rev=$(svn info "$MODEL/modipsl/modeles/ORCHIDEE" \| grep Revision: \| cut -d ":" -f 2 \| cut -c 2-)
540	orcbranch=$(svn log -v -q svn://forge.ipsl.fr/orchidee/ -r "$fetch_rev" \| grep ORCHIDEE \| head -1 \| sed -e 's:ORCHIDEE/.*$:ORCHIDEE:' \| awk '{print $2}')
541	if [[ $fetch_rev != "$curr_rev" ]]; then
542	echo "Fetching orch $fetch_rev from the repository (curr: $curr_rev)"
543	echo "branch is $orcbranch"
544	if [[ $fetch_rev -lt 4465 ]]; then echo 'ORCHIDEE version must be >=4465, exiting'; exit 1; fi
545	echo "IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at orchidee-help@listes.ipsl.fr"
546	cd "$MODEL/modipsl/modeles"
547	rm -rf ORCHIDEE
548	svn co -r "$fetch_rev" "svn://forge.ipsl.fr/orchidee/$orcbranch"
549	cd - > /dev/null
550	fi
551	fi
552
553	# Check parallel LMDZ+ORCH
554	if [[ (! $veget = "none") && $parallel = "none" && ($used_lmdz_rev -lt 4894) ]]; then
555	echo "LMDZ revision must be >=4894 for orchidee without parallel support. Upgrade lmdz or use -parallel mpi_omp."; exit 1
556	fi
557	}
558
559	function compile_orchidee {
560	install_arch "ORCHIDEE"
561
562	if [[ $veget != "none" ]]; then
563	cd "$MODEL/modipsl/modeles/ORCHIDEE"
564
565	orchideelog="$(pwd)/orchidee.log"
566	echo "Compiling ORCHIDEE, the continental surface model (log $orchideelog) $(date)"
567
568	local xios_orchid opt_orc
569	if [[ $with_xios = 1 ]]; then
570	xios_orchid="-xios";
571	else
572	xios_orchid="-noxios"
573	fi
574	if [[ $optim_debug = "-debug" ]]; then
575	opt_orc="-debug";
576	else
577	opt_orc="-prod"
578	fi
579
580	if [[ $parallel != "none" && ! -d src_parallel ]]; then
581	echo "STOP: Orchidee version too old for parallel support"; exit 1
582	fi
583	echo "$jobcmd ./makeorchidee_fcm -j $make_j $xios_orchid $opt_orc -parallel $parallel -arch $arch" > compile.sh
584	chmod +x compile.sh
585	echo "Compiling ORCHIDEE using $(\cat compile.sh)"
586	if ! ./compile.sh &> "$orchideelog"; then
587	echo "STOP: ORCHIDEE compilation failed, exiting"; exit 1
588	fi
589	echo "Compiled ORCHIDEE $(date)"
590	fi
591	}
592
593	function get_lmdz_version {
594	LMDZPATH=$(readlink -e -f "$MODEL/modipsl/modeles/LMD"*)
595	cd "$LMDZPATH"
596	lmdzlog="$(pwd)/lmdz.log"
597
598	if [[ -n $svn_lmdz ]]; then
599	local curr_rev
600	curr_rev=$(svn info "$MODEL/modipsl/modeles/LMD"* \| grep Revision: \| cut -d ":" -f 2 \| cut -c 2-)
601	if [[ $svn_lmdz != "$curr_rev" ]]; then
602	local lmdzbranch
603	echo "Fetching LMDZ $svn_lmdz from the repository"
604	lmdzbranch=$(svn log -v -q https://svn.lmd.jussieu.fr/LMDZ -r "$svn_lmdz" \| grep LMDZ \| head -1 \| sed -e 's:trunk/.*$:trunk:' \| awk '{print $2}')
605	cd "$MODEL/modipsl/modeles"
606	rm -rf LMD*
607	svn co -r "$svn_lmdz" "https://svn.lmd.jussieu.fr/LMDZ$lmdzbranch" LMDZ
608	cd - > /dev/null
609	fi
610	used_lmdz_rev=$svn_lmdz
611	else # get svn from info
612	set +e; used_lmdz_rev=$(svn info \| grep "Last Changed Rev" \| cut -c 19-); set -e
613	if [[ -z $used_lmdz_rev ]]; then # svn info failed
614	used_lmdz_rev=$(grep 'Revision: [0-9]' "$MODEL"/Read*.md \| awk ' { print $2 } ' 2>/dev/null)
615	if [[ -z $used_lmdz_rev ]]; then echo "Could not determine lmdz version. This is likely an issue with the .tar itself, please report to LMDZ team."; exit 1; fi
616	fi
617	fi
618	}
619
620	function compile_lmdz {
621	install_arch "LMDZ"
622	cd "$LMDZPATH"
623
624	if [[ $used_lmdz_rev -le 4185 ]]; then
625	exe_name="bin/gcm_${grid_resolution}_phy${compphysiq}_${suff_para}${suff_orc}${suff_aer}${suff_iso}.e"
626	else
627	exe_name="bin/gcm_${grid_resolution}_phy${compphysiq}_${rad}${suff_para}${suff_orc}${suff_aer}${suff_iso}.e"
628	fi
629
630	local opt_rad
631	case $rad in
632	oldrad) iflag_rrtm=0; NSW=2; opt_rad="";;
633	rrtm) iflag_rrtm=1; NSW=6
634	if [[ $used_lmdz_rev -le 4185 ]]; then
635	opt_rad="-rrtm true"
636	else
637	opt_rad="-rad rrtm"
638	fi;;
639	ecrad) iflag_rrtm=2; NSW=6; opt_rad="-rad ecrad";;
640	*) echo "Only oldrad rrtm ecrad for rad option"; exit 1
641	esac
642	if [[ $used_lmdz_rev -le 4185 && $rad = "ecrad" ]]; then
643	echo "ecrad only available for LMDZ rev starting with 4186 "; exit 1
644	fi
645
646	# Compile
647	makelmdz="makelmdz_fcm $optim_debug -arch $arch -j $make_j"
648	local para_compile_opt="-mem -parallel $parallel"; if [[ $parallel = "none" ]]; then para_compile_opt=""; fi
649	echo "$jobcmd ./$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
650	echo "Compiling lmdz using $(\cat compile.sh) (log: $lmdzlog) $(date)"
651	chmod +x ./compile.sh
652	if ! ./compile.sh &> "$lmdzlog"; then
653	echo "STOP: LMDZ compilation failed, exiting"; exit 1
654	fi
655	echo "Finished LMDZ compilation $(date)"
656
657	# Check executable
658	if [[ ! -f $exe_name ]]; then
659	echo "STOP: Compilation failed, can't find the executable"; exit 1
660	else
661	echo "Compilation successfull, the executable is $exe_name $(date)"
662	fi
663	}
664
665	function run_bench {
666	cd "$MODEL/modipsl/modeles/LMDZ"*
667
668	if [[ $bench = "tuto" ]]; then
669	myget "Training/tutorial.tar"; tar xf tutorial.tar; cd TUTORIAL
670	./init.sh
671	elif [[ $bench = 1 ]]; then
672	\rm -rf "BENCH${grid_resolution}"
673	local bench=bench_lmdz_${grid_resolution}
674	myget "3DBenchs/$bench.tar.gz"
675	tar xf "$bench.tar.gz"
676
677	if [[ $cosp = "v1" \|\| $cosp = "v2" ]]; then
678	cd "BENCH${grid_resolution}"
679	# copier les fichiers namelist input et output our COSP
680	cp ../DefLists/cosp*_input_nl.txt .
681	cp ../DefLists/cosp*_output_nl.txt .
682	# Activer la cles ok_cosp pour tourner avec COSP
683	sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp
684	\mv -f tmp config.def
685	cd ..
686	fi
687
688	if [[ -n "$benchphysiq" ]]; then
689	cd "BENCH${grid_resolution}"
690	if [[ -f "physiq.def_${benchphysiq}" ]]; then
691	cp "physiq.def_${benchphysiq}" benchphysiq.def
692	echo "using physiq.def_${benchphysiq}"
693	else
694	echo "using standard physiq.def"
695	fi
696	cd ..
697	else
698	echo "using standard physiq.def"
699	fi
700
701	if [[ $with_xios = 1 ]]; then
702	cd "BENCH${grid_resolution}"
703	cp ../DefLists/iodef.xml .
704	cp ../DefLists/context_lmdz.xml .
705	cp ../DefLists/field_def_lmdz.xml .
706	# A raffiner par la suite
707	echo "A FAIRE : Copier les *xml en fonction de l option cosp"
708	cp ../DefLists/field_def_cosp*.xml .
709	cp ../DefLists/file_def_hist*xml .
710	# adapt iodef.xml to use attached mode
711	sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' \
712	iodef.xml > tmp
713	\mv -f tmp iodef.xml
714
715	# and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
716	# except for histday
717	for histfile in file_def_hist*xml; do
718	if [[ "$histfile" = "file_def_histday_lmdz.xml" ]]; then
719	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' \
720	"$histfile" > tmp
721	\mv -f tmp "$histfile"
722	sed -e 's@output_level="_AUTO_"@output_level="5"@' "$histfile" \
723	> tmp
724	\mv -f tmp "$histfile"
725	sed -e 's@compression_level="2"@compression_level="0"@' \
726	"$histfile" > tmp
727	\mv -f tmp "$histfile"
728	else
729	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
730	"$histfile" > tmp
731	\mv -f tmp "$histfile"
732	fi
733	done
734	# and add option "ok_all_xml=y" in config.def
735	echo "### XIOS outputs" >> config.def
736	echo 'ok_all_xml=.true.' >> config.def
737
738	#activer les sorties pour Cosp
739	if [[ "$cosp" = "v1" ]]; then
740	sed -i'' -e 's@enabled=".FALSE."@enabled=".TRUE."@' \
741	-e 's@output_level="_AUTO_"@output_level="5"@' \
742	-e 's@compression_level="2"@compression_level="0"@' \
743	file_def_histdayCOSP_lmdz.xml
744	fi
745	if [[ "$cosp" = "v2" ]]; then
746	sed -i'' -e 's@compression_level="2"@compression_level="0"@' file_def_histdayCOSPv2_lmdz.xml
747	for type_ in hf day mth; do
748	file=file_def_hist${type_}COSP
749	sed -i'' -e 's@src="./'${file}'_lmdz.xml"@src="./'${file}'v2_lmdz.xml"@' context_lmdz.xml
750	done
751	sed -i'' -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' field_def_lmdz.xml
752	fi
753
754	cd ..
755	fi
756
757	# Cas Bench avec ecrad
758	if [[ $rad = "ecrad" ]]; then
759	cd "BENCH${grid_resolution}"
760	cp ../DefLists/namelist_ecrad .
761	cp -r ../libf/phylmd/ecrad/data .
762	cd ..
763	fi
764
765	# Adjusting bench physiq.def to radiative code chosen
766	cd "BENCH${grid_resolution}"
767	sed -e 's/iflag_rrtm=.*.$/iflag_rrtm='$iflag_rrtm'/' \
768	-e 's/NSW=.*.$/NSW='$NSW'/' physiq.def > tmpdef
769	\mv tmpdef physiq.def
770	cd ..
771
772	cp "$exe_name" "BENCH${grid_resolution}/gcm.e"
773	cd "BENCH${grid_resolution}"
774
775	local bench_cmd="./bench.sh"
776	if [[ ${parallel:0:3} = "mpi" ]]; then
777	# Lancement avec deux procs mpi et 2 openMP
778	echo "export OMP_STACKSIZE=800M" > bench.sh
779	if [[ "${parallel:4:3}" = "omp" ]]; then
780	echo "export OMP_NUM_THREADS=2" >> bench.sh
781	fi
782	if [[ $cosp = "v1" \|\| $cosp = "v2" ]]; then
783	echo "ulimit -s 200000" >> bench.sh
784	else
785	echo "ulimit -s unlimited" >> bench.sh
786	fi
787	if which mpirun &> /dev/null; then
788	echo "mpirun -np 2 gcm.e &> listing" >> bench.sh
789	elif grep -q "Adastra" /etc/motd; then
790	local account
791	account=$(/usr/sbin/my_project.py -l 2>&1 \| head -1 \| cut -d " " -f 3- \| cut -c 5-)
792	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"
793	echo "./gcm.e &> listing" >> bench.sh
794	else
795	echo "Error: No command found to run parallel bench"; exit 1
796	fi
797	if [[ $(hostname \| cut -c -6) = "spirit" ]]; then # ulimit unlimited segfaults on Spirit
798	sed -i'' "s/ulimit -s unlimited/ulimit -Ss 8000/" bench.sh
799	fi
800	# Add rebuild, using reb.sh if it is there
801	cat <<EOF >> bench.sh
802	if [[ -f reb.sh ]]; then
803	./reb.sh histday; ./reb.sh histmth; ./reb.sh histhf;
804	./reb.sh histins; ./reb.sh stomate_history;
805	./reb.sh sechiba_history; ./reb.sh sechiba_out_2
806	fi
807	EOF
808	else
809	echo "./gcm.e &> listing" > bench.sh
810	fi
811	# Getting orchidee stuff
812	if [[ $veget = 'CMIP6' \|\| $veget = "orch2.0" ]]; then # TODO once we have a 2.2 bench, add it here (or in planned separate bench script)
813	echo 'myget 3DBenchs/BENCHCMIP6.tar.gz'
814	myget 3DBenchs/BENCHCMIP6.tar.gz
815	tar xvzf BENCHCMIP6.tar.gz
816	sed -e "s:VEGET=n:VEGET=y:" config.def > tmp
817	mv -f tmp config.def
818	if [[ $with_xios = 1 ]]; then
819	cp ../../ORCHIDEE/src_xml/context_orchidee.xml .
820	echo '<context id="orchidee" src="./context_orchidee.xml"/>' > add.tmp
821	cp ../../ORCHIDEE/src_xml/field_def_orchidee.xml .
822	cp ../../ORCHIDEE/src_xml/file_def_orchidee.xml .
823	cp ../../ORCHIDEE/src_xml/file_def_input_orchidee.xml .
824	if [[ -f ../../ORCHIDEE/src_xml/context_input_orchidee.xml ]]; then
825	cp ../../ORCHIDEE/src_xml/context_input_orchidee.xml .
826	echo '<context id="orchidee" src="./context_input_orchidee.xml"/>' >> add.tmp
827	fi
828	sed -e '/id="LMDZ"/r add.tmp' iodef.xml > tmp
829	mv tmp iodef.xml
830	sed -e'{/sechiba1/ s/enabled="_AUTO_"/type="one_file" enabled=".TRUE."/}' \
831	file_def_orchidee.xml > tmp
832	\mv -f tmp file_def_orchidee.xml
833	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
834	file_def_orchidee.xml > tmp
835	\mv -f tmp file_def_orchidee.xml
836	sed -e 's@output_level="_AUTO_"@output_level="1"@' \
837	file_def_orchidee.xml > tmp
838	\mv -f tmp file_def_orchidee.xml
839	sed -e 's@output_freq="_AUTO_"@output_freq="1d"@' \
840	file_def_orchidee.xml > tmp
841	\mv -f tmp file_def_orchidee.xml
842	sed -e 's@compression_level="4"@compression_level="0"@' \
843	file_def_orchidee.xml > tmp
844	\mv -f tmp file_def_orchidee.xml
845	sed -e 's@XIOS_ORCHIDEE_OK = n@XIOS_ORCHIDEE_OK = y@' \
846	orchidee.def > tmp
847	\mv -f tmp orchidee.def
848	fi
849	fi
850
851	if [[ -f ../arch.env ]]; then source ../arch.env; fi
852
853	echo "EXECUTION DU BENCH"
854	date
855	if (! $bench_cmd &> out.bench) \|\| ! (tail -n 1 listing \| grep "Everything is cool"); then
856	tail listing
857	echo "Bench FAILED, exiting"; exit 1
858	fi
859	date
860	tail listing
861	fi
862
863	# 1D case
864	if [[ $SCM = 1 ]]; then
865	cd "$MODEL"
866	myget 1D/1D.tar.gz
867	tar xf 1D.tar.gz
868	cd 1D
869	if [[ $rad = "oldrad" ]]; then
870	sed -i'' -e 's/^rad=.*$/rad=oldrad/' run.sh
871	sed -i'' -e 's/^rad=.*$/rad=oldrad/' bin/compile
872	elif [[ $rad = ecrad ]] ; then
873	sed -i'' -e 's/^rad=.*$/rad=ecrad/' run.sh
874	sed -i'' -e 's/^rad=.*$/rad=ecrad/' bin/compile
875	fi
876	echo "Running 1D/run.sh, log in $(pwd)/run1d.log"
877	./run.sh &> "$(pwd)/run1d.log"
878	fi
879	}
880
881	# If sourced: returns, else run setup
882	if [[ ! "${BASH_SOURCE[0]}" = "$0" ]]; then return 0; fi
883
884	echo "install_lmdz.sh DEBUT $(date)"
885
886	set_default_params
887	read_cmdline_args "$@"
888	ensure_correct_option_combinations
889	download_model
890	init_arch
891	check_available_software
892	get_lmdz_version
893	get_orchidee_version
894	install_netcdf
895	install_IOIPSL
896	install_XIOS
897	compile_orchidee
898	compile_lmdz
899	run_bench

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