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source: BOL/script_install_amaury/install_lmdz.sh @ 4861

Last change on this file since 4861 was 4861, checked in by abarral, 2 months ago
remove ksh support correct indentation fix build typo
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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	# $MODEL/modipsl/modeles/...
14	# using the "modipsl" infrastructure created by the "IPSL"
15	# for coupled (atmosphere/ocean/vegetation/chemistry) climate modeling
16	# activities.
17	# Here we only download atmospheric (LMDZ) and vegetation (ORCHIDEE)
18	# components.
19	#
20	# The sources of the models can be found in the "modeles" directory.
21	# In the present case, LMDZ, ORCHIDEE, and IOIPSL or XIOS (handling of
22	# input-outputs using the NetCDF library).
23	#
24	# The script downloads various source files (including a version of NetCDF)
25	# and utilities, compiles the model, and runs a test simulation in a
26	# minimal configuration.
27	#
28	# Prerequisites : pgf90/gfortran, bash or ksh, wget , gunzip, tar, ...
29	#
30	# Modif 18/11/2011
31	# changes for option real 8.
32	# We compile with -r8 (or equivalent) and -DNC_DOUBLE for the GCM
33	# but with -r4 for netcdf. Variable real must be set to
34	# r4 or r8 at the beginning of the script below.
35	#
36	###########################################################################
37
38	echo install_lmdz.sh DEBUT "$(date)"
39
40	################################################################
41	# Choice of installation options
42	################################################################
43
44	################################################################
45	# A function to fetch files either locally or on the internet
46	################################################################
47	function myget { #1st and only argument should be file name
48	# Path on local computer where to look for the datafile
49	if [[ -f /u/lmdz/WWW/LMDZ/pub/$1 ]]; then
50	\cp -f -p "/u/lmdz/WWW/LMDZ/pub/$1" .
51	elif [[ -f ~/LMDZ/pub/$1 ]]; then
52	\cp -f -p ~"/LMDZ/pub/$1" .
53	else
54	wget --no-check-certificate -nv "http://lmdz.lmd.jussieu.fr/pub/$1"
55	save_pub_locally=0
56	if [[ $save_pub_locally = 1 ]]; then # saving wget files on ~/LMDZ/pub
57	dir=~"/LMDZ/pub/$(dirname "$1")"; mkdir -p "$dir"
58	cp -r "$(basename "$1")" "$dir"
59	fi
60	fi
61	}
62
63	# 04_2021 : tester si r4 marche encore !
64	real="r8" # ou "r4"
65
66
67	#########################################################################
68	# Valeur par défaut des parametres
69	#########################################################################
70	svn=""
71	version="20231022.trunk"
72
73	getlmdzor=1
74	netcdf=1 # 1: for automatic installation;
75	# or 0: do not install NetCDF and look for it in standard locations;
76	# or absolute path: look for NetCDF there
77	check_software_linux=1
78	ioipsl=1
79	bench=1
80	pclinux=1
81	pcmac=0 # default: not on a Mac
82	compiler="gfortran"
83	if [[ $(gfortran -dumpversion \| cut -d. -f1) -ge 10 ]]; then allow_arg_mismatch="-fallow-argument-mismatch"; fi
84	SCM=0
85	# surface/vegetation scheme treatment
86	# controlled by the single variable veget which can have the following values
87	# - NONE: bucket scheme (default)
88	# - CMIP6: orchidee version used in CMIP exercise, rev 5661
89	# - number: orchidee version number
90	veget="NONE"
91	# choose the resolution for the bench runs
92	# grid_resolution= 32x24x11 or 48x36x19 for tests (test without ORCHIDEE)
93	# 96x71x19 standard configuration
94	grid_resolution="144x142x79"
95	grid_resolution="96x95x39"
96	grid_resolution="48x36x19"
97	grid_resolution="32x32x39"
98	# choose the physiq version you want to test
99	#physiq=NPv6.0.14splith
100	physiq=""
101
102	## parallel can take the values none/mpi/omp/mpi_omp
103	parallel="mpi_omp"
104	parallel="none"
105	idris_acct="lmd"
106	trusting="testing"
107	OPT_GPROF=""
108	OPT_MAKELMDZ=""
109	MODEL=""
110
111	## also compile XIOS? (and more recent NetCDF/HDF5 libraries) Default=no
112	with_xios="n"
113	opt_makelmdz_xios=""
114
115	## compile with oldrad/rrtm/ecrad radiatif code (Default=rrtm)
116	rad="rrtm"
117
118	## compile_with_fcm=1 : use makelmdz_fcm (1) or makelmdz (0)
119	compile_with_fcm=1
120
121	#Compilation with Cosp (cosp=NONE/v1/v2; default=NONE)
122	cosp="NONE"
123	opt_cosp=""
124
125	# Check if on a Mac
126	if [[ $(uname) = "Darwin" ]]; then
127	pcmac=1
128	export MAKE=make
129	fi
130
131	env_file=""
132	optim=""
133
134	#########################################################################
135	# Options interactives
136	#########################################################################
137	while (($# > 0))
138	do
139	case $1 in
140	"-h") cat <<........fin
141	$0 [ -v version ] [ -r svn_release ]
142	[ -parallel PARA ] [ -d GRID_RESOLUTION ] [ -bench 0/1 ]
143	[-name LOCAL_MODEL_NAME] [-gprof] [-opt_makelmdz] [-rad RADIATIF]
144
145	-v "version" like 20150828.trunk
146	see http://www.lmd.jussieu.fr/~lmdz/Distrib/LISMOI.trunk
147
148	-r "svn_release" : either the svn release number or "last"
149
150	-compiler gfortran\|ifort\|pgf90 (default: gfortran)
151
152	-parallel PARA : can be mpi_omp (mpi with openMP) or none (for sequential)
153
154	-d GRID_RESOLUTION should be among the available benchs if -bench 1
155	among which : 48x36x19, 48x36x39
156	if wanting to run a bench simulation in addition to compilation
157	default : 48x36x19
158
159	-bench activating the bench or not (0/1). Default 1
160
161	-testing/unstable
162
163	-name LOCAL_MODEL_NAME : default = LMDZversion.release
164
165	-netcdf 0, 1 or PATH
166	0: do not download NetCDF, look for it in standard locations
167	1: download and compile NetCDF
168	PATH: full path to an existing installed NetCDF library
169
170	-xios also download and compile the XIOS library
171	(requires the NetCDF4-HDF5 library, also installed by default)
172	(requires to also have -parallel mpi_omp)
173
174	-gprof to compile with -pg to enable profiling with gprof
175
176	-cosp to run without our with cospv1 or cospv2 [none/v1/v2]
177
178	-rad RADIATIF can be oldrad, rrtm or ecrad radiatif code
179
180	-nofcm to compile without fcm
181
182	-SCM install 1D version automatically
183
184	-debug compile everything in debug mode
185
186	-opt_makelmdz to call makelmdz or makelmdz_fcm with additional options
187
188	-physiq to choose which physics package to use
189
190	-env_file specify an arch.env file to overwrite the existing one
191
192	-veget surface model to run [NONE/CMIP6/xxxx]
193
194	........fin
195	exit 1;;
196	"-v") version=$2; shift; shift;;
197	"-r") svn=$2; shift; shift;;
198	"-compiler") compiler=$2
199	case $compiler in
200	"gfortran"\|"ifort"\|"pgf90") compiler=$2; shift
201	shift;;
202	*) echo "Only gfortran , ifort or pgf90 for the " \
203	"compiler option"
204	exit 1
205	esac;;
206	"-d") grid_resolution=$2; shift; shift;;
207	"-gprof") OPT_GPROF="-pg"; shift;;
208	"-unstable"\|"-testing") trusting=$(echo "$1" \| cut -c2-) ; shift;;
209	"-cosp") cosp=$2
210	case $cosp in
211	"none"\|"v1"\|"v2") cosp=$2; shift; shift;;
212	*) echo Only none v1 v2 for cosp option; exit 1
213	esac;;
214	"-nofcm") compile_with_fcm=0; echo This option will be reactivated soon '(promesse du 8dec2022)'; exit 1; shift;;
215	"-SCM") SCM=1; shift;;
216	"-opt_makelmdz") OPT_MAKELMDZ="$2"; shift; shift;;
217	"-rrtm") if [[ $2 = "false" ]]; then
218	rad="oldrad"
219	else
220	rad="rrtm"
221	fi
222	shift; shift;;
223	"-rad") rad=$2
224	case $rad in
225	"oldrad"\|"rrtm"\|"ecrad") rad=$2; shift; shift;;
226	*) echo "Only oldrad rrtm ecrad for rad option"; exit 1
227	esac;;
228	"-parallel") parallel=$2
229	case $parallel in
230	"none"\|"mpi"\|"omp"\|"mpi_omp") parallel=$2; shift
231	shift;;
232	*) echo "Only none mpi omp mpi_omp for the parallel option"
233	exit 1
234	esac;;
235	"-bench") bench=$2; shift; shift;;
236	"-debug") optim=-debug; shift;;
237	"-name") MODEL=$2; shift; shift;;
238	"-netcdf") netcdf=$2; shift; shift;;
239	"-physiq") physiq=$2; shift; shift;;
240	"-xios") with_xios="y"; shift;;
241	"-env_file") env_file=$2; shift; shift;;
242	"-veget") veget=$2; shift; shift;;
243	*) bash install_lmdz.sh -h; exit 1
244	esac
245	done
246
247	# Option de compilation du rayonnement : depend de $mysvn ><= r4185,
248	# sera donc definie plus bas
249
250	#opt_rad=""
251	#case $rad in
252	# rrtm) opt_rad="-rad rrtm";;
253	# ecrad) opt_rad="-rad ecrad";;
254	#esac
255
256
257	# Option de compilation pour Cosp
258	opt_cosp=""
259	case $cosp in
260	v1) opt_cosp="-cosp true";;
261	v2) opt_cosp="-cospv2 true";;
262	esac
263
264	# Check on veget version
265	if [[ $veget != 'NONE' && $veget != "CMIP6" ]]; then
266	re='^[0-9]+$'
267	if ! [[ $veget =~ $re ]]; then
268	echo 'Valeur de l option veget non valable'
269	exit 1
270	fi
271	fi
272
273	#Define veget-related suffix for gcm name
274	if [[ $veget = 'NONE' ]]; then
275	suff_orc=''
276	#For use with tutorial, orchidee_rev is also defined (will be
277	#written in surface_env at the end of the script)
278	orchidee_rev=''
279	else
280	suff_orc='_orch'
281	fi
282
283
284	if [[ $parallel = none ]]; then
285	sequential=1; suff_exe='_seq'
286	else
287	sequential=0; suff_exe='_para_mem'
288	fi
289
290	#Chemin pour placer le modele
291	if [[ $MODEL = "" ]]; then MODEL=./LMDZ$version$svn$optim; fi
292
293
294	arch=local
295
296	################################################################
297	# Specificite des machines
298	################################################################
299
300	hostname=$(hostname)
301	if [[ $pclinux = 1 ]]; then o_ins_make="-t g95"; else o_ins_make=""; fi
302
303	case ${hostname:0:5} in
304
305	jean-) compiler="mpiifort";
306	par_comp="mpiifort";
307	o_ins_make="-t jeanzay";
308	make=gmake;
309	module purge
310	module load intel-compilers/19.0.4;
311	module load hdf5/1.10.5-mpi;
312	module load netcdf/4.7.2-mpi;
313	module load netcdf-fortran/4.5.2-mpi;
314	module load subversion/1.9.7;
315	module load cmake
316	export NETCDF_LIBDIR=./
317	export NETCDFFORTRAN_INCDIR=./
318	export NETCDFFORTRAN_LIBDIR=./
319	arch=X64_JEANZAY;;
320
321	cicla\|camel) compiler="gfortran";
322	module purge
323	module load gnu/10.2.0
324	module load openmpi/4.0.5
325	module load hdf5/1.10.7-mpi
326	module load netcdf-c/4.7.4-mpi
327	module load netcdf-fortran/4.5.3-mpi
328	netcdf=/net/nfs/tools/PrgEnv/linux-scientific6-x86_64/gcc-10.2.0/netcdf-fortran-4.5.3-k3drgfqok3lip62hnm3tsyof4cjen5sk
329	module load svn/1.14.0
330
331	if [[ $parallel != none ]]; then
332	root_mpi=/net/nfs/tools/meso-sl6/openmpi/4.0.5-gcc-10.2.0
333	path_mpi=$root_mpi/bin;
334	par_comp=${path_mpi}/mpif90;
335	mpirun=${path_mpi}/mpirun;
336	fi;
337	arch="local" ;
338	make="make";
339	o_ins_make="-t g95";;
340
341	*) if [[ $parallel = none \|\| -f /usr/bin/mpif90 ]]; then
342	path_mpi=$(which mpif90 \| sed -e s:/mpif90::);
343	if [[ -d /usr/lib64/openmpi ]]; then
344	root_mpi="/usr/lib64/openmpi"
345	else
346	root_mpi="/usr"
347	fi
348	else
349	echo "Cannot find mpif90";
350	if [[ $parallel = none ]]; then exit 1; fi;
351	fi;
352	if [[ $parallel != none ]]; then
353	root_mpi=$(which mpif90 \| sed -e s:/bin/mpif90::)
354	path_mpi=$(which mpif90 \| sed -e s:/mpif90::)
355	export LD_LIBRARY_PATH=${root_mpi}/lib:$LD_LIBRARY_PATH
356	fi
357	par_comp=${path_mpi}/mpif90;
358	mpirun=${path_mpi}/mpirun;
359	arch="local" ;
360	make="make";
361	o_ins_make="-t g95"
362	esac
363
364	# Flags for parallelism:
365	if [[ $parallel != none ]]; then
366	# MPI_LD are the flags needed for linking with MPI
367	MPI_LD="-L${root_mpi}/lib -lmpi"
368	if [[ "$compiler" = "gfortran" ]]; then
369	# MPI_FLAGS are the flags needed for compilation with MPI
370	MPI_FLAGS="-fcray-pointer"
371	# OMP_FLAGS are the flags needed for compilation with OpenMP
372	OMP_FLAGS="-fopenmp -fcray-pointer"
373	# OMP_LD are the flags needed for linking with OpenMP
374	OMP_LD="-fopenmp"
375	elif [[ "$compiler" = "ifort" ]]; then
376	MPI_FLAGS=""
377	OMP_FLAGS="-openmp"
378	OMP_LD="-openmp"
379	else # pgf90
380	MPI_FLAGS=""
381	OMP_FLAGS="-mp"
382	OMP_LD="-mp"
383	fi
384	fi
385
386	## if also compiling XIOS, parallel must be mpi_omp
387	if [[ $with_xios = "y" && $parallel != "mpi_omp" ]]; then
388	echo "Error, you must set -parallel mpi_omp if you want XIOS"
389	exit 1
390	fi
391
392	if [[ $with_xios = "y" ]]; then
393	opt_makelmdz_xios="-io xios"
394	fi
395
396	if [[ $cosp = "v2" && $with_xios = "n" ]]; then
397	echo "Error, Cospv2 cannot run without Xios"
398	exit 1
399	fi
400
401	echo "################################################################"
402	echo "Choix des options de compilation"
403	echo "################################################################"
404
405	export FC=$compiler
406	export F90=$compiler
407	export F77=$compiler
408	export CPPFLAGS=
409	OPTIMNC=""
410	BASE_LD="$OPT_GPROF"
411	OPTPREC="$OPT_GPROF"
412	ARFLAGS="rs"
413	if [[ $(lsb_release -i -s) = "Ubuntu" ]]; then
414	if [[ $(lsb_release -r -s \| cut -d. -f1) -ge 16 ]]; then
415	ARFLAGS="rU"
416	fi
417	fi
418
419	if [[ $compiler = "gfortran" ]]; then
420	OPTIM="-O3 $allow_arg_mismatch"
421	OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all -fbacktrace -finit-real=snan $allow_arg_mismatch"
422	OPTDEV="-Wall -fbounds-check $allow_arg_mismatch"
423	fmod="I "
424	OPTPREC="$OPTPREC -cpp -ffree-line-length-0"
425	if [[ $real = r8 ]]; then OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE"; fi
426	export F90FLAGS=" -ffree-form $OPTIMNC"
427	export FFLAGS=" $OPTIMNC"
428	export CC=gcc
429	export CXX=g++
430	export fpp_flags="-P -C -traditional -ffreestanding"
431
432	elif [[ $compiler = mpif90 ]]; then
433	OPTIM="-O3"
434	OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all"
435	OPTDEV="-Wall -fbounds-check"
436	BASE_LD="$BASE_LD -lblas"
437	fmod="I "
438	if [[ $real = r8 ]]; then
439	OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE -fcray-pointer"
440	fi
441	export F90FLAGS=" -ffree-form $OPTIMNC"
442	export FFLAGS=" $OPTIMNC"
443	export CC=gcc
444	export CXX=g++
445
446	elif [[ $compiler = pgf90 ]]; then
447	OPTIM="-O2 -Mipa -Munroll -Mnoframe -Mautoinline -Mcache_align"
448	OPTDEB="-g -Mdclchk -Mbounds -Mchkfpstk -Mchkptr -Minform=inform -Mstandard -Ktrap=fp -traceback"
449	OPTDEV="-g -Mbounds -Ktrap=fp -traceback"
450	fmod="module "
451	if [[ $real = r8 ]]; then OPTPREC="$OPTPREC -r8 -DNC_DOUBLE"; fi
452	export CPPFLAGS="-DpgiFortran"
453	export CC=pgcc
454	export CFLAGS="-O2 -Msignextend"
455	export CXX=pgCC
456	export CXXFLAGS="-O2 -Msignextend"
457	export FFLAGS="-O2 $OPTIMNC"
458	export F90FLAGS="-O2 $OPTIMNC"
459	compile_with_fcm=1
460
461	elif [[ $compiler = ifort \|\| $compiler = mpiifort ]]; then
462	OPTIM="-O2 -fp-model strict -ip -align all "
463	OPTDEV="-p -g -O2 -traceback -fp-stack-check -ftrapuv -check"
464	OPTDEB="-g -no-ftz -traceback -ftrapuv -fp-stack-check -check"
465	fmod='module '
466	if [[ $real = r8 ]]; then OPTPREC="$OPTPREC -real-size 64 -DNC_DOUBLE"; fi
467	export CPP="icc -E"
468	export FFLAGS="-O2 -ip -fpic -mcmodel=large"
469	export FCFLAGS="-O2 -ip -fpic -mcmodel=large"
470	export CC=icc
471	export CFLAGS="-O2 -ip -fpic -mcmodel=large"
472	export CXX=icpc
473	export CXXFLAGS="-O2 -ip -fpic -mcmodel=large"
474	export fpp_flags="-P -traditional"
475	# Pourquoi forcer la compilation fcm. Marche mieux sans
476	#compile_with_fcm=1
477	else
478	echo "unexpected compiler $compiler"; exit 1
479	fi
480
481	OPTIMGCM="$OPTIM $OPTPREC"
482
483	hostname=$(hostname)
484
485	##########################################################################
486	# If installing on known machines such as Jean-Zay at IDRIS,
487	# don't check for available software and don't install netcdf
488	if [[ ${hostname:0:5} = "jean-" ]]; then
489	netcdf=0 # no need to recompile netcdf, alreday available
490	check_software_linux=0
491	pclinux=0
492	ioipsl=0 # no need to recompile ioipsl, already available
493	#netcdf="/smplocal/pub/NetCDF/4.1.3"
494	compiler="mpiifort"
495	fmod='module '
496	if [[ $real = r8 ]]; then OPTPREC="$OPTPREC -i4 -r8 -DNC_DOUBLE"; fi
497	OPTIM="-auto -align all -O2 -fp-model strict -xHost "
498	OPTIMGCM="$OPTIM $OPTPREC"
499	fi
500	##########################################################################
501
502
503	mkdir -p "$MODEL"
504	echo "$MODEL"
505	MODEL=$( cd "$MODEL"; pwd ) # to get absolute path, if necessary
506
507
508	if [[ $check_software_linux = 1 ]]; then
509	echo "################################################################"
510	echo "Check if required software is available"
511	echo "################################################################"
512
513	for logiciel in wget tar gzip make $compiler gcc cmake m4 c++; do
514	if [[ $(which $logiciel) = "" ]]; then
515	echo "You must first install $logiciel on your system"
516	exit 1
517	fi
518	done
519
520	cd "$MODEL"
521	cat <<eod > tt.f90
522	print*,'coucou'
523	end
524	eod
525	$compiler tt.f90 \|\| a.out
526	./a.out >\| tt
527	if [[ $(< tt sed -e 's/ //g' ) != "coucou" ]]; then
528	echo "problem installing with compiler $compiler"; exit 1; fi
529	\rm tt a.out tt.f90
530	fi
531
532	###########################################################################
533	if [[ $getlmdzor = 1 && ! -d $MODEL/modipsl ]]; then
534	###########################################################################
535	echo "##########################################################"
536	echo "Download a slightly modified version of LMDZ"
537	echo "##########################################################"
538	cd "$MODEL"
539	getlog=$(pwd)/get.log
540	echo logfile : "$getlog"
541	myget "src_archives/$trusting/modipsl.$version.tar.gz" >> get.log 2>&1
542	echo install_lmdz.sh wget_OK "$(date)"
543	gunzip "modipsl.$version.tar.gz" >> get.log 2>&1
544	tar xf "modipsl.$version.tar" >> get.log 2>&1
545	\rm "modipsl.$version.tar"
546	fi
547
548	###########################################################################
549	echo "Installing Netcdf"
550	###########################################################################
551
552	if [[ $netcdf = 0 ]]; then
553	ncdfdir=/usr
554
555	else
556	cd "$MODEL"
557
558	case $compiler in
559	gfortran) opt1="-compiler gnu"; opt2="-CC gcc -FC gfortran -CXX g++";;
560	ifort) opt1="-compiler intel"; opt2="-CC icc -FC ifort -CXX icpc";;
561	pgf90) opt1="-compiler pgf90"; opt2="-CC pgcc -FC pgf90 -CXX pgCC";;
562	*) echo "unexpected compiler $compiler" for netcdf; exit 1
563	esac
564
565	case $with_xios in
566	n) script_install_netcdf=install_netcdf4_hdf5_seq.bash
567	ncdfdir=netcdf4_hdf5_seq
568	opt_=$opt1;;
569	y) script_install_netcdf=install_netcdf4_hdf5.bash
570	ncdfdir=netcdf4_hdf5
571	opt_="$opt2 -MPI $root_mpi";;
572	*) echo with_xios=$with_xios, should be n or y; exit 1
573	esac
574	if [[ $netcdf = 1 ]]; then
575	ncdfdir=$MODEL/$ncdfdir
576	else
577	mkdir -p $netcdf; ncdfdir=$netcdf/$ncdfdir
578	fi
579
580	echo "Repertoire netcdf $ncdfdir"
581	if [[ ! -d $ncdfdir ]]; then
582	netcdflog=$(pwd)/netcdf.log
583	echo "----------------------------------------------------------"
584	echo "Compiling the Netcdf library"
585	echo "----------------------------------------------------------"
586	echo "log file : $netcdflog"
587	myget script_install/$script_install_netcdf >> "$netcdflog" 2>&1
588	chmod u=rwx $script_install_netcdf
589	# shellcheck disable=SC2086
590	./$script_install_netcdf -prefix "$ncdfdir" $opt_ >> "$netcdflog" 2>&1
591	fi
592
593	#----------------------------------------------------------------------------
594	# LF rajout d'une verrue, pour une raison non encore expliquee,
595	# la librairie est parfois rang�e dans lib64 et non dans lib
596	# par certains compilateurs
597	if [[ ! -e lib && -d lib64 ]]; then ln -s lib64 lib; fi
598	#----------------------------------------------------------------------------
599
600	echo install_lmdz.sh netcdf_OK "$(date)"
601
602	fi
603
604	cat >test_netcdf90.f90 <<EOF
605	use netcdf
606	print *, "NetCDF library version: ", nf90_inq_libvers()
607	end
608	EOF
609
610	if $compiler -I"$ncdfdir"/include test_netcdf90.f90 -L"$ncdfdir"/lib -lnetcdff \
611	-lnetcdf -Wl,-rpath="$ncdfdir"/lib && ./a.out
612	then
613	rm test_netcdf90.f90 a.out
614	else
615	echo "Failed test program using NetCDF-Fortran."
616	echo "You can:"
617	echo "- check that you have NetCDF-Fortran installed in your system"
618	echo "- or specify an installation directory with option -netcdf of" \
619	"install_lmdz.sh"
620	echo "- or download and compile NetCDF-Fortran with option -netcdf 1 of" \
621	"install_lmdz.sh"
622	exit 1
623	fi
624
625	if [[ ! -f $MODEL/modipsl/lib/libioipsl.a ]]
626	then
627	if [[ $ioipsl = 1 ]]; then
628	cat <<EOF
629	OK ioipsl=$ioipsl
630	##########################################################
631	Installing MODIPSL, the installation package manager for the
632	IPSL models and tools
633	##########################################################
634	$(date)
635	EOF
636	cd "$MODEL/modipsl"
637	\rm -rf lib/*
638	cd util
639	cp AA_make.gdef AA_make.orig
640	F_C="$compiler -c "
641	if [[ $compiler = "gfortran" \|\| $compiler = "mpif90" ]]
642	then
643	F_C="$compiler -c -cpp "
644	fi
645	if [[ $compiler = "pgf90" ]]; then F_C="$compiler -c -Mpreprocess"; fi
646	sed -e 's/^\#..g95..\#.*.$/\#/' AA_make.gdef > tmp
647	sed -e "s:F_L = g95:F_L = $compiler:" \
648	-e "s:F_C = g95 -c -cpp:F_C = $F_C": \
649	-e 's/g95..w_w..(F_D)/g95 w_w = '"$OPTIMGCM"'/' \
650	-e 's:g95..NCDF_INC..$:g95 NCDF_INC= '"$ncdfdir"'/include:' \
651	-e 's:g95..NCDF_LIB..$:g95 NCDF_LIB= -L'"$ncdfdir"'/lib -lnetcdff -lnetcdf:' \
652	-e 's:g95 L_O =:g95 L_O = -Wl,-rpath='"$ncdfdir"'/lib:' \
653	-e "s:-fmod=:-$fmod:" -e 's/-fno-second-underscore//' \
654	-e 's:#-Q- g95 M_K = gmake:#-Q- g95 M_K = make:' \
655	tmp >\| AA_make.gdef
656
657	if [[ $pcmac == 1 ]]
658	then
659	cp AA_make.gdef tmp
660	sed -e 's/rpath=/rpath,/g' tmp > AA_make.gdef
661	fi
662
663	# We use lines for g95 even for the other compilers to run ins_make
664	sed -e s:/bin/ksh:/bin/bash:g ins_make > ins_make.bash # Note Amaury: the case where the default shell isn't bash should be handled directly in ins_make (via ./ and #! directives)
665
666	chmod u=rwx ins_make.bash
667	# shellcheck disable=SC2086
668	./ins_make.bash $o_ins_make
669
670	echo "install_lmdz.sh MODIPSL_OK $(date)"
671
672	cd "$MODEL/modipsl/modeles/IOIPSL/src"
673	ioipsllog=$(pwd)/ioipsl.log
674	echo '##########################################################'
675	echo 'Compiling IOIPSL, the interface library with Netcdf'
676	echo '##########################################################'
677	echo "log file : $ioipsllog $(date)"
678
679	cp Makefile Makefile.ksh
680	sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile
681
682	# Build IOIPSL modules and library
683	$make clean
684	$make > "$ioipsllog" 2>&1
685	if [[ $compiler = "gfortran" \|\| $compiler = "mpif90" ]]; then
686	# copy module files to lib
687	cp -f -- *.mod ../../../lib
688	fi
689	# Build IOIPSL tools (ie: "rebuild", if present)
690	# For IOIPSLv_2_2_2, "rebuild" files are in IOIPSL/tools
691	rebuild_dir=""
692	if [[ -f $MODEL/modipsl/modeles/IOIPSL/tools/rebuild ]]; then
693	rebuild_dir=$MODEL/modipsl/modeles/IOIPSL/tools
694	elif [[ -d $MODEL/modipsl/modeles/IOIPSL/rebuild ]]; then
695	rebuild_dir=$MODEL/modipsl/modeles/IOIPSL/rebuild
696	fi
697	if [[ $rebuild_dir != "" ]]; then
698	cd "$rebuild_dir"
699	# adapt Makefile & rebuild script if in bash
700	cp Makefile Makefile.ksh
701	sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile
702	cp rebuild rebuild.ksh
703	sed -e 's:/bin/ksh:/bin/bash:g' \
704	-e 's:print -u2:echo:g' \
705	-e 's:print:echo:g' rebuild.ksh > rebuild
706	$make clean
707	$make > "$ioipsllog" 2>&1
708	fi
709
710	else # of if [[ $ioipsl = 1 ]]
711	if [[ ${hostname:0:5} = jean- ]]; then
712	cd "$MODEL/modipsl"
713	cd util
714	if [[ $(grep jeanzay AA_make.gdef) = "" ]]; then
715	echo 'Warning jean-zay not in AA_make.gdef'
716	echo 'Think about updating'
717	exit 1
718	fi
719	./ins_make "$o_ins_make"
720	# Compile IOIPSL on jean-zay
721	cd "$MODEL/modipsl/modeles/IOIPSL/src"
722	gmake > ioipsl.log
723	# For IOIPSLv_2_2_2, "rebuild" files are in IOIPSL/tools, so "gmake" in IOIPSL/tools is enough
724	# For IOIPSLv_2_2_5, "rebuild" files are in a separate IOIPSL/rebuild folder , while "tools" only contains "FCM"
725	if [[ -f $MODEL/modipsl/modeles/IOIPSL/tools/Makefile ]]; then
726	cd "$MODEL/modipsl/modeles/IOIPSL/tools"
727	gmake > ioipsl.log
728	fi
729	if [[ -d $MODEL/modipsl/modeles/IOIPSL/rebuild ]]; then
730	cd "$MODEL/modipsl/modeles/IOIPSL/rebuild"
731	gmake > ioipsl.log
732	fi
733
734	fi
735	echo "install_lmdz.sh ioipsl_OK $(date)"
736	fi # of if [[ $ioipsl = 1 ]]
737	fi # of if [[ ! -f $MODEL/modipsl/lib/libioipsl.a ]]
738
739	#=========================================================================
740	if [[ "$with_xios" = "y" ]]; then
741	echo '##########################################################'
742	echo 'Compiling XIOS'
743	echo '##########################################################'
744	cd "$MODEL/modipsl/modeles"
745	xioslog="$(pwd)/xios.log"
746	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/install_xios.bash
747	myget script_install/install_xios.bash
748	chmod u=rwx install_xios.bash
749	# following will be recalculated later on once LMDZ is updated
750	# mysvn=`svnversion LMDZ \| egrep \|\| "[0-9]+" 2>/dev/null`
751	mysvn=$(grep 'Revision: [0-9]' "$MODEL"/Read*.md \| awk ' { print $2 } ' 2>/dev/null)
752	if [[ $svn != "" ]]; then mysvn=$svn; fi
753	echo "mysvn $mysvn"
754
755	if [[ ${hostname:0:5} = jean- ]]; then
756	if [[ $mysvn -ge 4619 ]]; then
757	svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS2/branches/xios-2.6 XIOS
758	else
759	svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS2/branches/xios-2.5 XIOS
760	fi
761	cd XIOS/arch
762	svn update
763	cd ..
764	echo "Compiling XIOS, start $(date) (it takes about 20 min on Jean-Zay)"
765	echo "log file: $xioslog"
766	./make_xios --prod --arch $arch --job 4 > xios.log 2>&1
767	else
768	./install_xios.bash -prefix "$MODEL/modipsl/modeles" \
769	-netcdf "$ncdfdir" -hdf5 "$ncdfdir" \
770	-MPI "$root_mpi" -arch $arch > xios.log 2>&1
771	fi # of case Jean-Zay
772	if [[ -f XIOS/lib/libxios.a ]]; then
773	echo "XIOS library successfully generated"
774	echo install_lmdz.sh XIOS_OK "$(date)"
775	fi
776	fi
777
778	#============================================================================
779	veget_version=false
780	if [[ "$veget" != 'NONE' ]]; then
781	cd "$MODEL/modipsl/modeles/ORCHIDEE"
782	set +e; svn upgrade; set -e
783	if [[ "$veget" = "CMIP6" ]]; then
784	veget_version=orchidee2.0
785	orchidee_rev=6592
786	else # specific orchidee revision newer than CMIP6, on 2_1 or 2_2 branches
787	veget_version=orchidee2.1
788	orchidee_rev=$veget
789	if [[ $veget -lt 4465 ]]; then
790	echo 'Stopping, ORCHIDEE version too old, script needs work on ' \
791	'the CPP flags to pass to makelmdz'
792	exit 1
793	fi
794	set +e
795	# which branch is my version on?
796	orcbranch=$(svn log -v -q svn://forge.ipsl.jussieu.fr/orchidee/ -r "$veget" \|grep ORCHIDEE \|head -1\| sed -e 's:ORCHIDEE/.*$:ORCHIDEE:' \| awk '{print $2}')
797	# switch to that branch
798	echo IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at \
799	orchidee-help@listes.ipsl.fr
800	svn switch -r "$veget" --accept theirs-full "svn://forge.ipsl.jussieu.fr/orchidee/$orcbranch"
801	if ! (svn log -r "$veget" \| grep "$veget"); then
802	echo 'Cannot update ORCHIDEE as not on the right branch for ORCHIDEE'
803	exit 1
804	fi
805	set -e
806	set +e; svn update -r "$veget"; set -e
807	fi
808	# Correctif suite debug Jean-Zay
809	sed -i -e 's/9010 FORMAT(A52,F17.14)/9010 FORMAT(A52,F20.14)/' \
810	src_stomate/stomate.f90
811	opt_orc="-prod"; if [[ "$optim" = "-debug" ]]; then opt_orc="-debug"; fi
812
813	orchideelog=$(pwd)/orchidee.log
814	echo '########################################################'
815	echo 'Compiling ORCHIDEE, the continental surface model '
816	echo '########################################################'
817	echo "Start of the first compilation of orchidee, in sequential mode: $(date)"
818	echo "log file : $orchideelog"
819
820	ORCHPATH=$(pwd)
821	export ORCHPATH=$ORCHPATH
822	xios_orchid="-noxios"
823	if [[ "$with_xios" = "y" ]]; then
824	xios_orchid="-xios"
825	fi
826	if [[ -d tools ]]; then
827	###################################################################
828	# Pour les experts qui voudraient changer de version d'orchidee.
829	# Attention : necessite d'avoir le password pour orchidee
830
831	# Correctif suite debug Jean-Zay
832	if [[ -f src_global/time.f90 ]]; then
833	sed -i -e 's/CALL tlen2itau/\!CALL tlen2itau/' src_global/time.f90
834	fi
835	###################################################################
836	if [[ "$veget_version" == "false" ]]; then
837	veget_version=orchidee2.0
838	fi
839	cd arch
840	sed -e s:"%COMPILER .*.$:%COMPILER $compiler":1 \
841	-e s:"%LINK .*.$:%LINK $compiler":1 \
842	-e s:"%FPP_FLAGS .*.$:%FPP_FLAGS $fpp_flags":1 \
843	-e s:"%PROD_FFLAGS .*.$:%PROD_FFLAGS $OPTIM":1 \
844	-e s:"%DEV_FFLAGS .*.$:%DEV_FFLAGS $OPTDEV":1 \
845	-e s:"%DEBUG_FFLAGS .*.$:%DEBUG_FFLAGS $OPTDEB":1 \
846	-e s:"%BASE_FFLAGS .*.$:%BASE_FFLAGS $OPTPREC":1 \
847	-e s:"%BASE_LD .*.$:%BASE_LD $BASE_LD":1 \
848	-e s:"%ARFLAGS .*.$:%ARFLAGS $ARFLAGS":1 \
849	arch-gfortran.fcm > arch-local.fcm
850	cat <<EOF > arch-local.path
851	NETCDF_LIBDIR="-L$ncdfdir/lib -lnetcdff -lnetcdf"
852	NETCDF_INCDIR="$ncdfdir/include"
853	IOIPSL_INCDIR="$ORCHPATH/../../lib"
854	IOIPSL_LIBDIR="$ORCHPATH/../../lib"
855	XIOS_INCDIR="\$ORCHDIR/../XIOS/inc"
856	XIOS_LIBDIR="\$ORCHDIR/../XIOS/lib -lxios"
857	EOF
858	cd ../
859
860	echo ./makeorchidee_fcm -j $xios_orchid $opt_orc -parallel none \
861	-arch $arch
862	./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel none \
863	-arch $arch > "$orchideelog" 2>&1
864	pwd
865	else # of "if [[ -d tools ]]"
866	if [[ -d src_parallel ]]; then
867	liste_src="parallel parameters global stomate sechiba driver"
868	if [[ "$veget_version" == "false" ]]; then
869	veget_version=orchidee2.0
870	fi
871	fi
872	for d in $liste_src; do
873	src_d=src_$d
874	echo src_d "$src_d"
875	echo ls; ls
876	if [[ ! -d $src_d ]]; then
877	echo "Problem orchidee : no $src_d"; exit 1
878	fi
879	cd "$src_d"; \rm -f -- *.mod make; $make clean
880	$make > "$orchideelog" 2>&1
881	if [[ "$compiler" = "gfortran" \|\| "$compiler" = "mpif90" ]]; then
882	cp -f -- *.mod ../../../lib
883	fi
884	cd ..
885	done
886	fi # of "if [[ -d tools ]]"
887	echo "install_lmdz.sh orchidee_compil_seq_OK $(date)"
888	fi # of if [[ "$veget" != 'NONE' ]]
889
890
891	#============================================================================
892	# Ehouarn: the directory name LMDZ* depends on version/tar file...
893	if find . -name "$MODEL/modipsl/modeles/LMD*"; then
894	echo '###############################################################'
895	echo 'Preparing LMDZ compilation : arch file, svn switch if needed...'
896	echo '###############################################################'
897	cd "$MODEL/modipsl/modeles/"LMD*
898	LMDZPATH=$(pwd)
899	else
900	echo "ERROR: No LMD* directory !!!"
901	exit 1
902	fi
903
904
905	###########################################################
906	# For those who want to use fcm to compile via :
907	# makelmdz_fcm -arch local .....
908	############################################################
909
910
911
912	cd "$MODEL/modipsl/modeles"/LMDZ*
913	lmdzlog=$(pwd)/lmdz.log
914
915	##################################################################
916	# Possibly update LMDZ if a specific svn release is requested
917	##################################################################
918
919	set +e; svn upgrade; set -e
920
921	if [[ $svn = "last" ]]; then svnopt=""; else svnopt="-r $svn"; fi
922	if [[ $svn != "" ]]; then
923	if set +e; svn info \| grep -q 'https:'; then
924	svn switch --relocate https://svn.lmd.jussieu.fr/LMDZ \
925	http://svn.lmd.jussieu.fr/LMDZ
926	fi
927	svn update "$svnopt"
928	set -e
929	fi
930
931	#---------------------------------------------------------------------
932	# Retrieve the final svn release number, and adjust compilation
933	# options accordingly
934	# If svn not available, will use the svn writen in $MODEL/Readm*md
935	# For old version it assumes that it is before 4185 (the version
936	# for which the test was introduced
937	#---------------------------------------------------------------------
938
939	set +e; mysvn=$(svnversion . \| grep -E \|\| "[0-9]+" 2>/dev/null); set -e
940	if [[ "$mysvn" = "" ]]; then mysvn=$(grep 'Revision: [0-9]' "$MODEL"/Read*.md \| awk ' { print $2 } ' 2>/dev/null); fi
941	if [[ "$mysvn" = "" ]]; then mysvn=4190; fi
942
943	if [[ "$pclinux" = "1" && ! -f arch/arch-local.path ]]; then
944
945	# create local 'arch' files (if on Linux PC):
946	cd arch
947	# arch-local.path file
948	# test for version as arch.pth file changed format with rev 4426
949	if [[ "$mysvn" -gt 4425 ]]; then
950	cat <<EOF > arch-local.path
951	NETCDF_LIBDIR="-L$ncdfdir/lib"
952	NETCDF_LIB="-lnetcdff -lnetcdf"
953	NETCDF_INCDIR=-I$ncdfdir/include
954	NETCDF95_INCDIR=-I\$LMDGCM/../../include
955	NETCDF95_LIBDIR=-L\$LMDGCM/../../lib
956	NETCDF95_LIB=-lnetcdf95
957	IOIPSL_INCDIR=-I\$LMDGCM/../../lib
958	IOIPSL_LIBDIR=-L\$LMDGCM/../../lib
959	IOIPSL_LIB=-lioipsl
960	XIOS_INCDIR=-I\$LMDGCM/../XIOS/inc
961	XIOS_LIBDIR=-L\$LMDGCM/../XIOS/lib
962	XIOS_LIB="-lxios -lstdc++"
963	ORCH_INCDIR=-I\$LMDGCM/../../lib
964	ORCH_LIBDIR=-L\$LMDGCM/../../lib
965	EOF
966	else
967	cat <<EOF > arch-local.path
968	NETCDF_LIBDIR="-L$ncdfdir/lib -lnetcdff -lnetcdf"
969	NETCDF_INCDIR=-I$ncdfdir/include
970	NETCDF95_INCDIR=\$LMDGCM/../../include
971	NETCDF95_LIBDIR=\$LMDGCM/../../lib
972	IOIPSL_INCDIR=\$LMDGCM/../../lib
973	IOIPSL_LIBDIR=\$LMDGCM/../../lib
974	XIOS_INCDIR=\$LMDGCM/../XIOS/inc
975	XIOS_LIBDIR=\$LMDGCM/../XIOS/lib
976	ORCH_INCDIR=\$LMDGCM/../../lib
977	ORCH_LIBDIR=\$LMDGCM/../../lib
978	EOF
979	fi
980
981	if [[ $pcmac == 1 ]]; then
982	BASE_LD="$BASE_LD -Wl,-rpath,${ncdfdir}/lib"
983	else
984	BASE_LD="$BASE_LD -Wl,-rpath=${ncdfdir}/lib"
985	fi
986	# Arch-local.fcm file (adapted from arch-linux-32bit.fcm)
987
988	if [[ $real = r8 ]]; then FPP_DEF=NC_DOUBLE; else FPP_DEF=""; fi
989	sed -e s:"%COMPILER .*.$:%COMPILER $compiler":1 \
990	-e s:"%LINK .*.$:%LINK $compiler":1 \
991	-e s:"%PROD_FFLAGS .*.$:%PROD_FFLAGS $OPTIM":1 \
992	-e s:"%DEV_FFLAGS .*.$:%DEV_FFLAGS $OPTDEV":1 \
993	-e s:"%DEBUG_FFLAGS .*.$:%DEBUG_FFLAGS $OPTDEB":1 \
994	-e s:"%BASE_FFLAGS .*.$:%BASE_FFLAGS $OPTPREC":1 \
995	-e s:"%FPP_DEF .*.$:%FPP_DEF $FPP_DEF":1 \
996	-e s:"%BASE_LD .*.$:%BASE_LD $BASE_LD":1 \
997	-e s:"%ARFLAGS .*.$:%ARFLAGS $ARFLAGS":1 \
998	arch-linux-32bit.fcm > arch-local.fcm
999
1000	cd ..
1001	### Adapt "bld.cfg" (add the shell):
1002	#whereisthatshell=$(which ${use_shell})
1003	#echo "bld::tool::SHELL $whereisthatshell" >> bld.cfg
1004
1005	fi # of if [[ "$pclinux" = 1 ]]
1006	#---------------------------------------------------------------------
1007	# Option de compilation du rayonnement : depend de $mysvn ><= r4185
1008	#---------------------------------------------------------------------
1009	opt_rad=""
1010
1011	case $rad in
1012	oldrad) iflag_rrtm=0; NSW=2; opt_rad="";;
1013	rrtm) iflag_rrtm=1; NSW=6
1014	if [[ $mysvn -le 4185 ]]; then
1015	opt_rad="-rrtm true"
1016	else
1017	opt_rad="-rad rrtm"
1018	fi;;
1019	ecrad) iflag_rrtm=2; NSW=6; opt_rad="-rad ecrad";;
1020	*) echo "Only oldrad rrtm ecrad for rad option"; exit 1
1021	esac
1022
1023	if [[ $mysvn -le 4185 && $rad = "ecrad" ]]; then
1024	echo "ecrad only available for LMDZ rev starting with 4186 "; exit 1
1025	fi
1026
1027	##################################################################
1028
1029
1030	if [[ ! -f libf/misc/netcdf95.F90 && ! -d $MODEL/NetCDF95-0.3 ]]; then
1031	cd "$MODEL"
1032	myget src_archives/netcdf/NetCDF95-0.3.tar.gz
1033	tar -xf NetCDF95-0.3.tar.gz
1034	rm NetCDF95-0.3.tar.gz
1035	cd NetCDF95-0.3
1036	mkdir build
1037	cd build
1038	cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH="$ncdfdir" \
1039	-DCMAKE_INSTALL_PREFIX="$MODEL/modipsl"
1040	make install
1041	cd "$MODEL/modipsl/modeles/"LMDZ*
1042	fi
1043
1044	echo '##################################################################'
1045	echo "Preparing script compile.sh for LMDZ compilation"
1046	echo "It will only be run automatically if bench=1/tuto"
1047	echo "Here bench=$bench"
1048	echo '##################################################################'
1049
1050	if [[ $env_file != "" ]]; then
1051	mv arch/arch-${arch}.env arch/arch-${arch}.orig
1052	\cp -f "$env_file" arch/arch-${arch}.env
1053	fi
1054
1055	if [[ $compile_with_fcm = 1 ]]; then
1056	makelmdz="makelmdz_fcm $optim -arch $arch -j 8 "
1057	else
1058	makelmdz="makelmdz $optim -arch $arch"
1059	fi
1060
1061	# sequential compilation
1062	if [[ "$sequential" = 1 ]]; then
1063	echo Sequential compilation command, saved in compile.sh:
1064	echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp " \
1065	"-d ${grid_resolution} -v $veget_version gcm "
1066	echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp " \
1067	"-d ${grid_resolution} -v $veget_version gcm " > compile.sh
1068	chmod +x ./compile.sh
1069	if [[ $bench = 1 ]]; then
1070	echo "install_lmdz.sh start_lmdz_seq_compilation $(date)"
1071	echo "log file: $lmdzlog"
1072	./compile.sh > "$lmdzlog" 2>&1
1073	echo "install_lmdz.sh end_lmdz_seq_compilation $(date)"
1074	fi
1075	fi # fin sequential
1076
1077	# compiling in parallel mode
1078	if [[ $parallel != "none" ]]; then
1079	echo '##########################################################'
1080	echo ' Parallel compile '
1081	echo '##########################################################'
1082	echo "(after saving the sequential libs and binaries)"
1083	cd "$MODEL/modipsl"
1084	tar cf sequential.tar bin/ lib/
1085	#
1086	# Orchidee
1087	#
1088	cd "$ORCHPATH"
1089	if [[ -d src_parallel && $veget != 'NONE' ]]; then
1090	cd arch
1091	sed \
1092	-e s:"%COMPILER.*.$:%COMPILER $par_comp":1 \
1093	-e s:"%LINK.*.$:%LINK $par_comp":1 \
1094	-e s:"%MPI_FFLAG.*.$:%MPI_FFLAGS $MPI_FLAGS":1 \
1095	-e s:"%OMP_FFLAG.*.$:%OMP_FFLAGS $OMP_FLAGS":1 \
1096	-e s:"%MPI_LD.*.$:%MPI_LD $MPI_LD":1 \
1097	-e s:"%OMP_LD.*.$:%OMP_LD $OMP_LD":1 \
1098	arch-local.fcm > tmp.fcm
1099
1100	mv tmp.fcm arch-local.fcm
1101	cd ../
1102	echo "Compiling ORCHIDEE in parallel mode $(date)"
1103	echo "logfile $orchideelog"
1104	echo "NOTE : to recompile it when necessary, use ./compile_orc.sh " \
1105	"in modipsl/modeles/ORCHIDEE"
1106	echo ./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc \
1107	-parallel "$parallel" -arch $arch > compile_orc.sh
1108	echo ./makeorchidee_fcm -j 8 $xios_orchid $opt_orc \
1109	-parallel "$parallel" -arch $arch >> compile_orc.sh
1110	echo echo Now you must also recompile LMDZ, by running ./compile.sh \
1111	in modeles/LMDZ >> compile_orc.sh
1112	chmod u+x compile_orc.sh
1113	./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc \
1114	-parallel "$parallel" -arch $arch > "$orchideelog" 2>&1
1115	./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel "$parallel" \
1116	-arch $arch >> "$orchideelog" 2>&1
1117	echo "End of ORCHIDEE compilation in parallel mode $(date)"
1118	elif [[ $veget != 'NONE' ]]; then
1119	echo '##########################################################'
1120	echo ' Orchidee version too old '
1121	echo ' Please update to new version '
1122	echo '##########################################################'
1123	exit 1
1124	fi #�of [ -d src_parallel && $veget != 'NONE' ]
1125
1126	# LMDZ
1127	cd "$LMDZPATH"
1128	if [[ $arch = local ]]; then
1129	cd arch
1130	sed -e s:"%COMPILER.*.$:%COMPILER $par_comp":1 \
1131	-e s:"%LINK.*.$:%LINK $par_comp":1 \
1132	-e s:"%MPI_FFLAG.*.$:%MPI_FFLAGS $MPI_FLAGS":1 \
1133	-e s:"%OMP_FFLAG.*.$:%OMP_FFLAGS $OMP_FLAGS":1 \
1134	-e s:"%ARFLAGS.*.$:%ARFLAGS $ARFLAGS":1 \
1135	-e "s§%BASE_LD.*.$§%BASE_LD -Wl,-rpath=${root_mpi}/lib:${ncdfdir}/lib§1" \
1136	-e s:"%MPI_LD.*.$:%MPI_LD $MPI_LD":1 \
1137	-e s:"%OMP_LD.*.$:%OMP_LD $OMP_LD":1 \
1138	arch-local.fcm > tmp.fcm
1139	mv tmp.fcm arch-local.fcm
1140	cd ../
1141	fi
1142	rm -f compile.sh
1143	echo resol="$grid_resolution" >> compile.sh
1144	if [[ ${hostname:0:5} = jean- && "$cosp" = "v2" ]]; then
1145
1146	echo "LMDZ compilation command in parallel mode, saved in compile.sh, is :"
1147	echo "(ATTENTION le probleme de cospv2 sur jean-zay en mode prod " \
1148	"n est pas corrige ! )"
1149	# ATTENTION le probleme de cospv2 sur jean-zay en mode prod n
1150	# est pas corrige
1151	echo ./"$makelmdz" -dev $optim "$OPT_MAKELMDZ" "$opt_rad" "$opt_cosp" \
1152	"$opt_makelmdz_xios" -d \$resol -v $veget_version -mem \
1153	-parallel "$parallel" gcm >> compile.sh
1154	echo ./"$makelmdz" -dev $optim "$OPT_MAKELMDZ" "$opt_rad" "$opt_cosp" \
1155	"$opt_makelmdz_xios" -d \$resol -v $veget_version -mem \
1156	-parallel "$parallel" gcm
1157	else
1158	echo ./"$makelmdz" $optim "$OPT_MAKELMDZ" "$opt_rad" "$opt_cosp" \
1159	"$opt_makelmdz_xios" -d \$resol -v $veget_version -mem \
1160	-parallel "$parallel" gcm >> compile.sh
1161	echo ./"$makelmdz" $optim "$OPT_MAKELMDZ" "$opt_rad" "$opt_cosp" \
1162	"$opt_makelmdz_xios" -d \$resol -v $veget_version -mem \
1163	-parallel "$parallel" gcm
1164	fi
1165	chmod +x ./compile.sh
1166
1167	if [[ $bench = 1 ]]; then
1168	echo "Compiling LMDZ in parallel mode $(date), LMDZ log file: $lmdzlog"
1169	./compile.sh > "$lmdzlog" 2>&1
1170	fi
1171
1172	fi # of if [[ $parallel != "none" ]]
1173
1174
1175	##################################################################
1176	# Verification du succes de la compilation
1177	##################################################################
1178
1179	# Recherche de l'executable dont le nom a change au fil du temps ...
1180	# suffix contains radiative option starting with revision 4186
1181	if [[ $mysvn -ge 4186 ]]; then suff_exe=_${rad}${suff_exe}; fi
1182	gcm=""
1183
1184	for exe in gcm.e bin/gcm_${grid_resolution}_phylmd${suff_exe}${suff_orc}.e
1185	do
1186	if [[ -f $exe ]]; then gcm=$exe; fi
1187	done
1188
1189	if [[ "$gcm" = "" ]]; then
1190	if [[ $bench = 1 ]]; then
1191	echo 'Compilation failed !! Cannot run the benchmark;'
1192	exit 1
1193	else
1194	echo 'Compilation not done (only done when bench=1)'
1195	fi
1196	else
1197	echo '##########################################################'
1198	echo "Compilation successfull !! $(date)"
1199	echo '##########################################################'
1200	echo "The executable is $gcm"
1201	fi
1202
1203	##################################################################
1204	# Below, we run a benchmark if bench=1 or tuto
1205	##################################################################
1206
1207	if [[ $bench = tuto ]]; then
1208	myget Training/tutorial.tar; tar xf tutorial.tar; cd TUTORIAL
1209	./init.sh
1210
1211	elif [[ $bench = 1 && ! -d BENCH${grid_resolution} ]]; then
1212	# TOUTE CETTE SECTION DEVRAIT DISPARAITRE POUR UNE COMMANDE
1213	# OU DES BENCHS PAR MOTS CLES COMME tuto
1214
1215	echo '##########################################################'
1216	echo ' Running a test run '
1217	echo '##########################################################'
1218
1219	\rm -rf "BENCH${grid_resolution}"
1220	bench=bench_lmdz_${grid_resolution}
1221	echo "install_lmdz.sh before bench download $(date)"
1222	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/$bench.tar.gz
1223	myget "3DBenchs/$bench.tar.gz"
1224	echo "install_lmdz.sh after bench download $(date)"
1225	tar xf "$bench.tar.gz"
1226
1227	if [[ "$cosp" = "v1" \|\| "$cosp" = "v2" ]]; then
1228	cd "BENCH${grid_resolution}"
1229	# copier les fichiers namelist input et output our COSP
1230	cp ../DefLists/cosp*_input_nl.txt .
1231	cp ../DefLists/cosp*_output_nl.txt .
1232	# Activer la cles ok_cosp pour tourner avec COSP
1233	sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp
1234	\mv -f tmp config.def
1235	cd ..
1236	fi
1237
1238	if [[ -n "$physiq" ]]; then
1239	cd "BENCH${grid_resolution}"
1240	if [[ -f "physiq.def_${physiq}" ]]; then
1241	cp "physiq.def_${physiq}" physiq.def
1242	echo using "physiq.def_${physiq}"
1243	else
1244	echo using standard physiq.def
1245	fi
1246	cd ..
1247	else
1248	echo using standard physiq.def
1249	fi
1250
1251	if [[ "$with_xios" = "y" ]]; then
1252	cd "BENCH${grid_resolution}"
1253	cp ../DefLists/iodef.xml .
1254	cp ../DefLists/context_lmdz.xml .
1255	cp ../DefLists/field_def_lmdz.xml .
1256	# A raffiner par la suite
1257	echo "A FAIRE : Copier les *xml en fonction de l option cosp"
1258	cp ../DefLists/field_def_cosp*.xml .
1259	cp ../DefLists/file_def_hist*xml .
1260	# adapt iodef.xml to use attached mode
1261	sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' \
1262	iodef.xml > tmp
1263	\mv -f tmp iodef.xml
1264
1265	# and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
1266	# except for histday
1267	for histfile in file_def_hist*xml
1268	do
1269	if [[ "$histfile" = "file_def_histday_lmdz.xml" ]]; then
1270	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' \
1271	"$histfile" > tmp
1272	\mv -f tmp "$histfile"
1273	sed -e 's@output_level="_AUTO_"@output_level="5"@' "$histfile" \
1274	> tmp
1275	\mv -f tmp "$histfile"
1276	sed -e 's@compression_level="2"@compression_level="0"@' \
1277	"$histfile" > tmp
1278	\mv -f tmp "$histfile"
1279	else
1280	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
1281	"$histfile" > tmp
1282	\mv -f tmp "$histfile"
1283	fi
1284	done
1285	# and add option "ok_all_xml=y" in config.def
1286	echo "### XIOS outputs" >> config.def
1287	echo 'ok_all_xml=.true.' >> config.def
1288
1289	#activer les sorties pour Cosp
1290	if [[ "$cosp" = "v1" ]]; then
1291	sed -i'' -e 's@enabled=".FALSE."@enabled=".TRUE."@' \
1292	-e 's@output_level="_AUTO_"@output_level="5"@' \
1293	-e 's@compression_level="2"@compression_level="0"@' \
1294	file_def_histdayCOSP_lmdz.xml
1295	fi
1296	if [[ "$cosp" = "v2" ]]; then
1297	sed -e 's@compression_level="2"@compression_level="0"@' file_def_histdayCOSPv2_lmdz.xml
1298	for type_ in hf day mth; do
1299	file=file_def_hist${type_}COSP
1300	sed -i'' -e 's@src="./'${file}'_lmdz.xml"@src="./'${file}'v2_lmdz.xml"@' context_lmdz.xml
1301	done
1302	sed -i '' -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' field_def_lmdz.xml
1303	fi
1304
1305	cd ..
1306	fi
1307
1308	# Cas Bensh avec ecrad
1309	if [[ "$rad" = "ecrad" ]]; then
1310	cd "BENCH${grid_resolution}"
1311	cp ../DefLists/namelist_ecrad .
1312	cp -r ../libf/phylmd/ecrad/data .
1313	cd ..
1314	fi
1315
1316	# Adjusting bench physiq.def to radiative code chosen
1317	cd "BENCH${grid_resolution}"
1318	sed -e 's/iflag_rrtm=.*.$/iflag_rrtm='$iflag_rrtm'/' \
1319	-e 's/NSW=.*.$/NSW='$NSW'/' physiq.def > tmpdef
1320	\mv tmpdef physiq.def
1321	cd ..
1322
1323	cp "$gcm" "BENCH${grid_resolution}/gcm.e"
1324
1325	cd "BENCH${grid_resolution}"
1326	# On cree le fichier bench.sh au besoin
1327	# Dans le cas 48x36x39 le bench.sh existe deja en parallele
1328
1329	if [[ "$grid_resolution" = "48x36x39" ]]; then
1330	echo On ne touche pas au bench.sh
1331	# But we have to adapt "run_local.sh" for $mpirun
1332	sed -e "s@mpirun@$mpirun@g" run_local.sh > tmp
1333	mv -f tmp run_local.sh
1334	chmod u=rwx run_local.sh
1335	elif [[ "${parallel:0:3}" = "mpi" ]]; then
1336	# Lancement avec deux procs mpi et 2 openMP
1337	echo "export OMP_STACKSIZE=800M" > bench.sh
1338	if [[ "${parallel:4:3}" = "omp" ]]; then
1339	echo "export OMP_NUM_THREADS=2" >> bench.sh
1340	fi
1341	if [[ "$cosp" = "v1" \|\| "$cosp" = "v2" ]]; then
1342	if [[ ${hostname:0:5} = jean- ]]; then
1343	chmod +x ../arch.env
1344	../arch.env
1345	echo "ulimit -s 2000000" >> bench.sh
1346	else
1347	echo "ulimit -s 200000" >> bench.sh
1348	fi
1349	else
1350	echo "ulimit -s unlimited" >> bench.sh
1351	fi
1352	if [[ ${hostname:0:5} = jean- ]]; then
1353	. ../arch/arch-${arch}.env
1354	echo "srun -n 2 && $idris_acct@cpu gcm.e > listing 2>&1" \
1355	>> bench.sh
1356	else
1357	echo "$mpirun -np 2 gcm.e > listing 2>&1" >> bench.sh
1358	fi
1359	# Add rebuild, using reb.sh if it is there
1360	cat <<EOF >> bench.sh
1361	if [[ -f reb.sh ]]; then
1362	./reb.sh histday; ./reb.sh histmth; ./reb.sh histhf;
1363	./reb.sh histins; ./reb.sh stomate_history;
1364	./reb.sh sechiba_history; ./reb.sh sechiba_out_2
1365	fi
1366	EOF
1367	else
1368	echo "./gcm.e > listing 2>&1" > bench.sh
1369	fi
1370	# Getting orchidee stuff
1371	if [[ $veget == 'CMIP6' ]]; then
1372	#echo 'myget 3DBenchs/BENCHorch11.tar.gz'
1373	#myget 3DBenchs/BENCHorch11.tar.gz
1374	#tar xvzf BENCHorch11.tar.gz
1375	echo 'myget 3DBenchs/BENCHCMIP6.tar.gz'
1376	myget 3DBenchs/BENCHCMIP6.tar.gz
1377	tar xvzf BENCHCMIP6.tar.gz
1378	sed -e "s:VEGET=n:VEGET=y:" config.def > tmp
1379	mv -f tmp config.def
1380	if [[ "$with_xios" = "y" ]]; then
1381	cp ../../ORCHIDEE/src_xml/context_orchidee.xml .
1382	echo '<context id="orchidee" src="./context_orchidee.xml"/>' \
1383	> add.tmp
1384	cp ../../ORCHIDEE/src_xml/field_def_orchidee.xml .
1385	cp ../../ORCHIDEE/src_xml/file_def_orchidee.xml .
1386	cp ../../ORCHIDEE/src_xml/file_def_input_orchidee.xml .
1387	if [[ -f ../../ORCHIDEE/src_xml/context_input_orchidee.xml ]]; then
1388	cp ../../ORCHIDEE/src_xml/context_input_orchidee.xml .
1389	echo '<context id="orchidee" ' \
1390	'src="./context_input_orchidee.xml"/>' >> add.tmp
1391	fi
1392	sed -e '/id="LMDZ"/r add.tmp' iodef.xml > tmp
1393	mv tmp iodef.xml
1394	sed -e'{/sechiba1/ s/enabled="_AUTO_"/type="one_file" enabled=".TRUE."/}' \
1395	file_def_orchidee.xml > tmp
1396	\mv -f tmp file_def_orchidee.xml
1397	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
1398	file_def_orchidee.xml > tmp
1399	\mv -f tmp file_def_orchidee.xml
1400	sed -e 's@output_level="_AUTO_"@output_level="1"@' \
1401	file_def_orchidee.xml > tmp
1402	\mv -f tmp file_def_orchidee.xml
1403	sed -e 's@output_freq="_AUTO_"@output_freq="1d"@' \
1404	file_def_orchidee.xml > tmp
1405	\mv -f tmp file_def_orchidee.xml
1406	sed -e 's@compression_level="4"@compression_level="0"@' \
1407	file_def_orchidee.xml > tmp
1408	\mv -f tmp file_def_orchidee.xml
1409	sed -e 's@XIOS_ORCHIDEE_OK = n@XIOS_ORCHIDEE_OK = y@' \
1410	orchidee.def > tmp
1411	\mv -f tmp orchidee.def
1412	fi
1413	fi
1414
1415	if [[ -f ../arch.env ]]
1416	then
1417	source ../arch.env
1418	fi
1419
1420	echo EXECUTION DU BENCH
1421	set +e
1422	date; ./bench.sh > out.bench 2>&1; date
1423	set -e
1424	tail listing
1425
1426
1427	echo "##########################################################"
1428	echo "Simulation finished in $(pwd)"
1429	echo "You have compiled with:"
1430	cat ../compile.sh
1431	if [[ $parallel = "none" ]]; then
1432	echo "You may re-run it with : cd $(pwd) ; gcm.e"
1433	echo "or ./bench.sh"
1434	else
1435	echo "You may re-run it with : "
1436	echo "cd $(pwd) ; ./bench.sh"
1437	# echo 'ulimit -s unlimited'
1438	# echo 'export OMP_NUM_THREADS=2'
1439	# echo 'export OMP_STACKSIZE=800M'
1440	# echo "$mpirun -np 2 gcm.e "
1441	fi
1442	echo '##########################################################'
1443
1444	fi # bench
1445
1446
1447	#################################################################
1448	# Installation eventuelle du 1D
1449	#################################################################
1450
1451	if [[ $SCM = 1 ]]; then
1452	cd "$MODEL"
1453	myget 1D/1D.tar.gz
1454	tar xf 1D.tar.gz
1455	cd 1D
1456	if [[ $rad = oldrad ]]; then
1457	sed -i'' -e 's/^rad=.*$/rad=oldrad/' run.sh
1458	sed -i'' -e 's/^rad=.*$/rad=oldrad/' bin/compile
1459	fi
1460	echo "Running 1D/run.sh, log in $(pwd)/run1d.log"
1461	./run.sh > "$(pwd)/run1d.log" 2>&1
1462	fi
1463
1464
1465	#################################################################
1466	# sauvegarde des options veget pour utilisation eventuelle tutorial_prod
1467	#################################################################
1468	cd "$MODEL/modipsl/modeles"
1469	#echo surface_env file created in $MODEL
1470	cat <<EOF >surface_env
1471	veget=$veget
1472	opt_veget="-v $veget_version"
1473	orchidee_rev=$orchidee_rev
1474	suforch=$suff_orc
1475	EOF

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