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source: BOL/script_install_new

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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_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	if [[ $compiler = g95 ]]; then echo g95 is not supported anymore; exit 1; fi
298
299	################################################################
300	# Specificite des machines
301	################################################################
302
303	hostname=$(hostname)
304	if [[ $pclinux = 1 ]]; then o_ins_make="-t g95"; else o_ins_make=""; fi
305
306	case ${hostname:0:5} in
307
308	jean-) compiler="mpiifort";
309	par_comp="mpiifort";
310	o_ins_make="-t jeanzay";
311	make=gmake;
312	module purge
313	module load intel-compilers/19.0.4;
314	#module load intel-mpi/19.0.4;
315	#module load intel-mkl/19.0.4;
316	module load hdf5/1.10.5-mpi;
317	module load netcdf/4.7.2-mpi;
318	module load netcdf-fortran/4.5.2-mpi;
319	module load subversion/1.9.7;
320	module load cmake
321	export NETCDF_LIBDIR=./
322	export NETCDFFORTRAN_INCDIR=./
323	export NETCDFFORTRAN_LIBDIR=./
324	arch=X64_JEANZAY;;
325
326	cicla\|camel) compiler="gfortran";
327	module purge
328	module load gnu/10.2.0
329	module load openmpi/4.0.5
330	module load hdf5/1.10.7-mpi
331	module load netcdf-c/4.7.4-mpi
332	module load netcdf-fortran/4.5.3-mpi
333	netcdf=/net/nfs/tools/PrgEnv/linux-scientific6-x86_64/gcc-10.2.0/netcdf-fortran-4.5.3-k3drgfqok3lip62hnm3tsyof4cjen5sk
334	module load svn/1.14.0
335
336	if [[ $parallel != none ]]; then
337	root_mpi=/net/nfs/tools/meso-sl6/openmpi/4.0.5-gcc-10.2.0
338	path_mpi=$root_mpi/bin;
339	par_comp=${path_mpi}/mpif90;
340	mpirun=${path_mpi}/mpirun;
341	fi;
342	arch="local" ;
343	make="make";
344	o_ins_make="-t g95";;
345
346	*) if [[ $parallel = none \|\| -f /usr/bin/mpif90 ]]; then
347	path_mpi=$(which mpif90 \| sed -e s:/mpif90::);
348	if [[ -d /usr/lib64/openmpi ]]; then
349	root_mpi="/usr/lib64/openmpi"
350	else
351	root_mpi="/usr"
352	fi
353	else
354	echo "Cannot find mpif90";
355	if [[ $parallel = none ]]; then exit 1; fi;
356	fi;
357	if [[ $parallel != none ]]; then
358	root_mpi=$(which mpif90 \| sed -e s:/bin/mpif90::)
359	path_mpi=$(which mpif90 \| sed -e s:/mpif90::)
360	export LD_LIBRARY_PATH=${root_mpi}/lib:$LD_LIBRARY_PATH
361	fi
362	par_comp=${path_mpi}/mpif90;
363	mpirun=${path_mpi}/mpirun;
364	arch="local" ;
365	make="make";
366	o_ins_make="-t g95"
367	esac
368
369	# Flags for parallelism:
370	if [[ $parallel != none ]]; then
371	# MPI_LD are the flags needed for linking with MPI
372	MPI_LD="-L${root_mpi}/lib -lmpi"
373	if [[ "$compiler" = "gfortran" ]]; then
374	# MPI_FLAGS are the flags needed for compilation with MPI
375	MPI_FLAGS="-fcray-pointer"
376	# OMP_FLAGS are the flags needed for compilation with OpenMP
377	OMP_FLAGS="-fopenmp -fcray-pointer"
378	# OMP_LD are the flags needed for linking with OpenMP
379	OMP_LD="-fopenmp"
380	elif [[ "$compiler" = "ifort" ]]; then
381	MPI_FLAGS=""
382	OMP_FLAGS="-openmp"
383	OMP_LD="-openmp"
384	else # pgf90
385	MPI_FLAGS=""
386	OMP_FLAGS="-mp"
387	OMP_LD="-mp"
388	fi
389	fi
390
391	#####################################################################
392	# Test for old gfortran compilers
393	# If the compiler is too old (older than 4.3.x) we test if the
394	# temporary gfortran44 patch is available on the computer in which
395	# case the compiler is changed from gfortran to gfortran44
396	# Must be aware than parallelism can not be activated in this case
397	#####################################################################
398
399	if [[ "$compiler" = "gfortran" ]]; then
400	gfortran=gfortran
401	gfortranv=$(gfortran --version \| \
402	head -1 \| awk ' { print $NF } ' \| awk -F. ' { print $1 * 10 + $2 } ')
403	if [[ $gfortranv -le 43 ]]; then
404	\cat <<EOF
405	ERROR : Your gfortran compiler is too old
406	Please choose a new one (ifort) and change the line
407	compiler=xxx
408	in the install_lmdz.sh script and rerun it
409	EOF
410	if [[ $(which gfortran44 \| wc -w) -ne 0 ]]; then
411	gfortran=gfortran44
412	else
413	echo gfotran trop vieux; exit 1
414	fi
415	fi
416	compiler=$gfortran
417	fi
418	#####################################################################
419
420	## if also compiling XIOS, parallel must be mpi_omp
421	if [[ "$with_xios" = "y" && "$parallel" != "mpi_omp" ]]; then
422	echo "Error, you must set -parallel mpi_omp if you want XIOS"
423	exit 1
424	fi
425
426	if [[ "$with_xios" = "y" ]]; then
427	opt_makelmdz_xios="-io xios"
428	fi
429
430	if [[ "$cosp" = "v2" && "$with_xios" = "n" ]]; then
431	echo "Error, Cospv2 cannot run without Xios"
432	exit 1
433	fi
434
435	echo '################################################################'
436	echo Choix des options de compilation
437	echo '################################################################'
438
439	export FC=$compiler
440	export F90=$compiler
441	export F77=$compiler
442	export CPPFLAGS=
443	OPTIMNC=""
444	BASE_LD="$OPT_GPROF"
445	OPTPREC="$OPT_GPROF"
446	ARFLAGS="rs"
447	if [[ "$(lsb_release -i -s)" = "Ubuntu" ]]; then
448	if [[ "$(lsb_release -r -s \| cut -d. -f1)" -ge 16 ]]; then
449	ARFLAGS="rU"
450	fi
451	fi
452
453	if [[ "$compiler" = "$gfortran" ]]; then
454	OPTIM="-O3 $allow_arg_mismatch"
455	OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all -fbacktrace -finit-real=snan $allow_arg_mismatch"
456	OPTDEV="-Wall -fbounds-check $allow_arg_mismatch"
457	fmod='I '
458	OPTPREC="$OPTPREC -cpp -ffree-line-length-0"
459	if [[ $real = r8 ]]; then OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE"; fi
460	export F90FLAGS=" -ffree-form $OPTIMNC"
461	export FFLAGS=" $OPTIMNC"
462	export CC=gcc
463	export CXX=g++
464	export fpp_flags="-P -C -traditional -ffreestanding"
465
466	elif [[ $compiler = mpif90 ]]; then
467	OPTIM='-O3'
468	OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all"
469	OPTDEV="-Wall -fbounds-check"
470	BASE_LD="$BASE_LD -lblas"
471	fmod='I '
472	if [[ $real = r8 ]]; then
473	OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE -fcray-pointer"
474	fi
475	export F90FLAGS=" -ffree-form $OPTIMNC"
476	export FFLAGS=" $OPTIMNC"
477	export CC=gcc
478	export CXX=g++
479
480	elif [[ $compiler = pgf90 ]]; then
481	OPTIM='-O2 -Mipa -Munroll -Mnoframe -Mautoinline -Mcache_align'
482	OPTDEB='-g -Mdclchk -Mbounds -Mchkfpstk -Mchkptr -Minform=inform -Mstandard -Ktrap=fp -traceback'
483	OPTDEV='-g -Mbounds -Ktrap=fp -traceback'
484	fmod='module '
485	if [[ $real = r8 ]]; then OPTPREC="$OPTPREC -r8 -DNC_DOUBLE"; fi
486	export CPPFLAGS="-DpgiFortran"
487	export CC=pgcc
488	export CFLAGS="-O2 -Msignextend"
489	export CXX=pgCC
490	export CXXFLAGS="-O2 -Msignextend"
491	export FFLAGS="-O2 $OPTIMNC"
492	export F90FLAGS="-O2 $OPTIMNC"
493	compile_with_fcm=1
494
495	elif [[ $compiler = ifort \|\| $compiler = mpiifort ]]; then
496	OPTIM="-O2 -fp-model strict -ip -align all "
497	OPTDEV="-p -g -O2 -traceback -fp-stack-check -ftrapuv -check"
498	OPTDEB="-g -no-ftz -traceback -ftrapuv -fp-stack-check -check"
499	fmod='module '
500	if [[ $real = r8 ]]; then OPTPREC="$OPTPREC -real-size 64 -DNC_DOUBLE"; fi
501	export CPP="icc -E"
502	export FFLAGS="-O2 -ip -fpic -mcmodel=large"
503	export FCFLAGS="-O2 -ip -fpic -mcmodel=large"
504	export CC=icc
505	export CFLAGS="-O2 -ip -fpic -mcmodel=large"
506	export CXX=icpc
507	export CXXFLAGS="-O2 -ip -fpic -mcmodel=large"
508	export fpp_flags="-P -traditional"
509	# Pourquoi forcer la compilation fcm. Marche mieux sans
510	#compile_with_fcm=1
511	else
512	echo "unexpected compiler $compiler"; exit 1
513	fi
514
515	OPTIMGCM="$OPTIM $OPTPREC"
516
517	hostname=$(hostname)
518
519	##########################################################################
520	# If installing on known machines such as Jean-Zay at IDRIS,
521	# don't check for available software and don't install netcdf
522	if [[ ${hostname:0:5} = jean- ]]; then
523	netcdf=0 # no need to recompile netcdf, alreday available
524	check_linux=0
525	pclinux=0
526	ioipsl=0 # no need to recompile ioipsl, already available
527	#netcdf="/smplocal/pub/NetCDF/4.1.3"
528	compiler="mpiifort"
529	fmod='module '
530	if [[ $real = r8 ]]; then OPTPREC="$OPTPREC -i4 -r8 -DNC_DOUBLE"; fi
531	OPTIM="-auto -align all -O2 -fp-model strict -xHost "
532	OPTIMGCM="$OPTIM $OPTPREC"
533	fi
534	##########################################################################
535
536
537	mkdir -p "$MODEL"
538	echo "$MODEL"
539	MODEL=$( cd "$MODEL"; pwd ) # to get absolute path, if necessary
540
541
542	if [[ "$check_linux" = 1 ]]; then
543	echo "################################################################"
544	echo "Check if required software is available"
545	echo "################################################################"
546
547	#### Ehouarn: test if the required shell is available
548	#### Maj FH-LF-AS 2021-04 : default=bash; if bash missing, use ksh
549	use_shell="bash" # default
550	if [[ $(which bash) = "" ]]; then
551	echo "no bash; we will use ksh"
552	use_shell="ksh"
553	if [[ $(which ksh) = "" ]]; then
554	echo "bash (or ksh) needed!! Install it!"
555	exit 1
556	fi
557	fi
558
559	for logiciel in wget tar gzip make $compiler gcc cmake m4 c++; do
560	if [[ $(which $logiciel) = "" ]]; then
561	echo "You must first install $logiciel on your system"
562	exit 1
563	fi
564	done
565
566	if [[ $pclinux = 1 ]]; then
567	cd "$MODEL"
568	cat <<eod > tt.f90
569	print*,'coucou'
570	end
571	eod
572	$compiler tt.f90 \|\| a.out
573	./a.out >\| tt
574	if [[ $(< tt sed -e 's/ //g' ) != "coucou" ]]; then
575	echo "problem installing with compiler $compiler"; exit 1; fi
576	\rm tt a.out tt.f90
577	fi
578	fi
579
580	###########################################################################
581	if [[ $getlmdzor = 1 && ! -d $MODEL/modipsl ]]; then
582	###########################################################################
583	echo "##########################################################"
584	echo "Download a slightly modified version of LMDZ"
585	echo "##########################################################"
586	cd "$MODEL"
587	getlog=$(pwd)/get.log
588	echo logfile : "$getlog"
589	myget "src_archives/$trusting/modipsl.$version.tar.gz" >> get.log 2>&1
590	echo install_lmdz.sh wget_OK "$(date)"
591	gunzip "modipsl.$version.tar.gz" >> get.log 2>&1
592	tar xf "modipsl.$version.tar" >> get.log 2>&1
593	\rm "modipsl.$version.tar"
594	fi
595
596	###########################################################################
597	echo Installing Netcdf
598	###########################################################################
599
600	if [[ $netcdf = 0 ]]; then
601	ncdfdir=/usr
602
603	else
604	cd "$MODEL"
605
606	case $compiler in
607	gfortran) opt1="-compiler gnu"; opt2="-CC gcc -FC gfortran -CXX g++";;
608	ifort) opt1="-compiler intel"; opt2="-CC icc -FC ifort -CXX icpc";;
609	pgf90) opt1="-compiler pgf90"; opt2="-CC pgcc -FC pgf90 -CXX pgCC";;
610	*) echo "unexpected compiler $compiler" for netcdf; exit 1
611	esac
612
613	case $with_xios in
614	n) script_install_netcdf=install_netcdf4_hdf5_seq.bash
615	ncdfdir=netcdf4_hdf5_seq
616	opt_=$opt1;;
617	y) script_install_netcdf=install_netcdf4_hdf5.bash
618	ncdfdir=netcdf4_hdf5
619	opt_="$opt2 -MPI $root_mpi";;
620	*) echo with_xios=$with_xios, should be n or y; exit 1
621	esac
622	if [[ $netcdf = 1 ]]; then
623	ncdfdir=$MODEL/$ncdfdir
624	else
625	mkdir -p $netcdf; ncdfdir=$netcdf/$ncdfdir
626	fi
627
628	echo "Repertoire netcdf $ncdfdir"
629	if [[ ! -d $ncdfdir ]]; then
630	netcdflog=$(pwd)/netcdf.log
631	echo "----------------------------------------------------------"
632	echo "Compiling the Netcdf library"
633	echo "----------------------------------------------------------"
634	echo "log file : $netcdflog"
635	myget script_install/$script_install_netcdf >> "$netcdflog" 2>&1
636	chmod u=rwx $script_install_netcdf
637	# shellcheck disable=SC2086
638	./$script_install_netcdf -prefix "$ncdfdir" $opt_ >> "$netcdflog" 2>&1
639	fi
640
641	#----------------------------------------------------------------------------
642	# LF rajout d'une verrue, pour une raison non encore expliquee,
643	# la librairie est parfois rang�e dans lib64 et non dans lib
644	# par certains compilateurs
645	if [[ ! -e lib && -d lib64 ]]; then ln -s lib64 lib; fi
646	#----------------------------------------------------------------------------
647
648	echo install_lmdz.sh netcdf_OK "$(date)"
649
650	fi
651
652	cat >test_netcdf90.f90 <<EOF
653	use netcdf
654	print *, "NetCDF library version: ", nf90_inq_libvers()
655	end
656	EOF
657
658	if $compiler -I"$ncdfdir"/include test_netcdf90.f90 -L"$ncdfdir"/lib -lnetcdff \
659	-lnetcdf -Wl,-rpath="$ncdfdir"/lib && ./a.out
660	then
661	rm test_netcdf90.f90 a.out
662	else
663	echo "Failed test program using NetCDF-Fortran."
664	echo "You can:"
665	echo "- check that you have NetCDF-Fortran installed in your system"
666	echo "- or specify an installation directory with option -netcdf of" \
667	"install_lmdz.sh"
668	echo "- or download and compile NetCDF-Fortran with option -netcdf 1 of" \
669	"install_lmdz.sh"
670	exit 1
671	fi
672
673	if [[ ! -f $MODEL/modipsl/lib/libioipsl.a ]]
674	then
675	if [[ $ioipsl = 1 ]]; then
676	cat <<EOF
677	OK ioipsl=$ioipsl
678	##########################################################
679	Installing MODIPSL, the installation package manager for the
680	IPSL models and tools
681	##########################################################
682	$(date)
683	EOF
684	cd "$MODEL/modipsl"
685	\rm -rf lib/*
686	cd util
687	cp AA_make.gdef AA_make.orig
688	F_C="$compiler -c "
689	if [[ $compiler = "$gfortran" \|\| $compiler = "mpif90" ]]
690	then
691	F_C="$compiler -c -cpp "
692	fi
693	if [[ "$compiler" = "pgf90" ]]; then F_C="$compiler -c -Mpreprocess"; fi
694	sed -e 's/^\#..g95..\#.*.$/\#/' AA_make.gdef > tmp
695	sed -e "s:F_L = g95:F_L = $compiler:" \
696	-e "s:F_C = g95 -c -cpp:F_C = $F_C": \
697	-e 's/g95..w_w..(F_D)/g95 w_w = '"$OPTIMGCM"'/' \
698	-e 's:g95..NCDF_INC..$:g95 NCDF_INC= '"$ncdfdir"'/include:' \
699	-e 's:g95..NCDF_LIB..$:g95 NCDF_LIB= -L'"$ncdfdir"'/lib -lnetcdff -lnetcdf:' \
700	-e 's:g95 L_O =:g95 L_O = -Wl,-rpath='"$ncdfdir"'/lib:' \
701	-e "s:-fmod=:-$fmod:" -e 's/-fno-second-underscore//' \
702	-e 's:#-Q- g95 M_K = gmake:#-Q- g95 M_K = make:' \
703	tmp >\| AA_make.gdef
704
705	if [[ $pcmac == 1 ]]
706	then
707	cp AA_make.gdef tmp
708	sed -e 's/rpath=/rpath,/g' tmp > AA_make.gdef
709	fi
710
711
712	# We use lines for g95 even for the other compilers to run ins_make
713	if [[ "$use_shell" = "ksh" ]]; then
714	./ins_make "$o_ins_make"
715	else # bash
716	sed -e s:/bin/ksh:/bin/bash:g ins_make > ins_make.bash
717	if [[ $(grep jeanzay AA_make.gdef) = "" ]]; then
718	# Bidouille pour compiler sur ada des vieux modipsl.tar
719	echo 'Warning jean-zay not in AA_make.gdef'
720	echo 'Think about updating'
721	exit 1
722	fi
723
724	chmod u=rwx ins_make.bash
725	./ins_make.bash "$o_ins_make"
726	fi # of if [[ "$use_shell" = "ksh" ]]
727
728	echo "install_lmdz.sh MODIPSL_OK $(date)"
729
730	cd "$MODEL/modipsl/modeles/IOIPSL/src"
731	ioipsllog=$(pwd)/ioipsl.log
732	echo '##########################################################'
733	echo 'Compiling IOIPSL, the interface library with Netcdf'
734	echo '##########################################################'
735	echo "log file : $ioipsllog $(date)"
736
737	if [[ "$use_shell" = "bash" ]]; then
738	cp Makefile Makefile.ksh
739	sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile
740	fi
741	### if [[ "$pclinux" = 1 ]]; then
742	# Build IOIPSL modules and library
743	$make clean
744	$make > "$ioipsllog" 2>&1
745	if [[ $compiler = "$gfortran" \|\| $compiler = "mpif90" ]]; then
746	# copy module files to lib
747	cp -f -- *.mod ../../../lib
748	fi
749	# Build IOIPSL tools (ie: "rebuild", if present)
750	# For IOIPSLv_2_2_2, "rebuild" files are in IOIPSL/tools
751	rebuild_dir=""
752	if [[ -f $MODEL/modipsl/modeles/IOIPSL/tools/rebuild ]]; then
753	rebuild_dir=$MODEL/modipsl/modeles/IOIPSL/tools
754	elif [[ -d $MODEL/modipsl/modeles/IOIPSL/rebuild ]]; then
755	rebuild_dir=$MODEL/modipsl/modeles/IOIPSL/rebuild
756	fi
757	if [[ $rebuild_dir != "" ]]; then
758	cd "$rebuild_dir"
759	# adapt Makefile & rebuild script if in bash
760	if [[ "$use_shell" = "bash" ]]; then
761	cp Makefile Makefile.ksh
762	sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile
763	cp rebuild rebuild.ksh
764	sed -e 's:/bin/ksh:/bin/bash:g' \
765	-e 's:print -u2:echo:g' \
766	-e 's:print:echo:g' rebuild.ksh > rebuild
767	fi
768	$make clean
769	$make > "$ioipsllog" 2>&1
770	fi
771	### fi # of if [[ "$pclinux" = 1 ]] which is commented out
772
773	else # of if [[ $ioipsl = 1 ]]
774	if [[ ${hostname:0:5} = jean- ]]; then
775	cd "$MODEL/modipsl"
776	cd util
777	if [[ $(grep jeanzay AA_make.gdef) = "" ]]; then
778	echo 'Warning jean-zay not in AA_make.gdef'
779	echo 'Think about updating'
780	exit 1
781	fi
782	./ins_make "$o_ins_make"
783	# Compile IOIPSL on jean-zay
784	cd "$MODEL/modipsl/modeles/IOIPSL/src"
785	gmake > ioipsl.log
786	# For IOIPSLv_2_2_2, "rebuild" files are in IOIPSL/tools, so "gmake" in IOIPSL/tools is enough
787	# For IOIPSLv_2_2_5, "rebuild" files are in a separate IOIPSL/rebuild folder , while "tools" only contains "FCM"
788	if [[ -f $MODEL/modipsl/modeles/IOIPSL/tools/Makefile ]]; then
789	cd "$MODEL/modipsl/modeles/IOIPSL/tools"
790	gmake > ioipsl.log
791	fi
792	if [[ -d $MODEL/modipsl/modeles/IOIPSL/rebuild ]]; then
793	cd "$MODEL/modipsl/modeles/IOIPSL/rebuild"
794	gmake > ioipsl.log
795	fi
796
797	fi
798	echo "install_lmdz.sh ioipsl_OK $(date)"
799	fi # of if [[ $ioipsl = 1 ]]
800	fi # of if [[ ! -f $MODEL/modipsl/lib/libioipsl.a ]]
801
802	#=========================================================================
803	if [[ "$with_xios" = "y" ]]; then
804	echo '##########################################################'
805	echo 'Compiling XIOS'
806	echo '##########################################################'
807	cd "$MODEL/modipsl/modeles"
808	xioslog="$(pwd)/xios.log"
809	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/install_xios.bash
810	myget script_install/install_xios.bash
811	chmod u=rwx install_xios.bash
812	# following will be recalculated later on once LMDZ is updated
813	# mysvn=`svnversion LMDZ \| egrep \|\| "[0-9]+" 2>/dev/null`
814	mysvn=$(grep 'Revision: [0-9]' "$MODEL"/Read*.md \| awk ' { print $2 } ' 2>/dev/null)
815	if [[ $svn != "" ]]; then mysvn=$svn; fi
816	echo "mysvn $mysvn"
817
818	if [[ ${hostname:0:5} = jean- ]]; then
819	if [[ $mysvn -ge 4619 ]]; then
820	svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS2/branches/xios-2.6 \
821	XIOS
822	else
823	svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS2/branches/xios-2.5 \
824	XIOS
825	fi
826	cd XIOS/arch
827	svn update
828	cd ..
829	echo "Compiling XIOS, start $(date) (it takes about 20 min on Jean-Zay)"
830	echo "log file: $xioslog"
831	./make_xios --prod --arch $arch --job 4 > xios.log 2>&1
832	else
833	./install_xios.bash -prefix "$MODEL/modipsl/modeles" \
834	-netcdf "$ncdfdir" -hdf5 "$ncdfdir" \
835	-MPI "$root_mpi" -arch $arch > xios.log 2>&1
836	fi # of case Jean-Zay
837	if [[ -f XIOS/lib/libxios.a ]]; then
838	echo "XIOS library successfully generated"
839	echo install_lmdz.sh XIOS_OK "$(date)"
840	fi
841	fi
842
843	#============================================================================
844	veget_version=false
845	if [[ "$veget" != 'NONE' ]]; then
846	cd "$MODEL/modipsl/modeles/ORCHIDEE"
847	set +e; svn upgrade; set -e
848	if [[ "$veget" = "CMIP6" ]]; then
849	veget_version=orchidee2.0
850	orchidee_rev=6592
851	else # specific orchidee revision newer than CMIP6, on 2_1 or 2_2 branches
852	veget_version=orchidee2.1
853	orchidee_rev=$veget
854	if [[ $veget -lt 4465 ]]; then
855	echo 'Stopping, ORCHIDEE version too old, script needs work on ' \
856	'the CPP flags to pass to makelmdz'
857	exit 1
858	fi
859	set +e
860	# which branch is my version on?
861	orcbranch=$(svn log -v -q svn://forge.ipsl.jussieu.fr/orchidee/ -r "$veget" \|grep ORCHIDEE \|head -1\| sed -e 's:ORCHIDEE/.*$:ORCHIDEE:' \| awk '{print $2}')
862	# switch to that branch
863	echo IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at \
864	orchidee-help@listes.ipsl.fr
865	svn switch -r "$veget" --accept theirs-full "svn://forge.ipsl.jussieu.fr/orchidee/$orcbranch"
866	if ! (svn log -r "$veget" \| grep "$veget"); then
867	echo 'Cannot update ORCHIDEE as not on the right branch for ORCHIDEE'
868	exit 1
869	fi
870	set -e
871	set +e; svn update -r "$veget"; set -e
872	fi
873	# Correctif suite debug Jean-Zay
874	sed -i -e 's/9010 FORMAT(A52,F17.14)/9010 FORMAT(A52,F20.14)/' \
875	src_stomate/stomate.f90
876	opt_orc="-prod"; if [[ "$optim" = "-debug" ]]; then opt_orc="-debug"; fi
877
878	orchideelog=$(pwd)/orchidee.log
879	echo '########################################################'
880	echo 'Compiling ORCHIDEE, the continental surface model '
881	echo '########################################################'
882	echo "Start of the first compilation of orchidee, in sequential mode: $(date)"
883	echo "log file : $orchideelog"
884
885	ORCHPATH=$(pwd)
886	export ORCHPATH=$ORCHPATH
887	xios_orchid="-noxios"
888	if [[ "$with_xios" = "y" ]]; then
889	xios_orchid="-xios"
890	fi
891	if [[ -d tools ]]; then
892	###################################################################
893	# Pour les experts qui voudraient changer de version d'orchidee.
894	# Attention : necessite d'avoir le password pour orchidee
895
896	# Correctif suite debug Jean-Zay
897	if [[ -f src_global/time.f90 ]]; then
898	sed -i -e 's/CALL tlen2itau/\!CALL tlen2itau/' src_global/time.f90
899	fi
900	###################################################################
901	if [[ "$veget_version" == "false" ]]; then
902	veget_version=orchidee2.0
903	fi
904	cd arch
905	sed -e s:"%COMPILER .*.$:%COMPILER $compiler":1 \
906	-e s:"%LINK .*.$:%LINK $compiler":1 \
907	-e s:"%FPP_FLAGS .*.$:%FPP_FLAGS $fpp_flags":1 \
908	-e s:"%PROD_FFLAGS .*.$:%PROD_FFLAGS $OPTIM":1 \
909	-e s:"%DEV_FFLAGS .*.$:%DEV_FFLAGS $OPTDEV":1 \
910	-e s:"%DEBUG_FFLAGS .*.$:%DEBUG_FFLAGS $OPTDEB":1 \
911	-e s:"%BASE_FFLAGS .*.$:%BASE_FFLAGS $OPTPREC":1 \
912	-e s:"%BASE_LD .*.$:%BASE_LD $BASE_LD":1 \
913	-e s:"%ARFLAGS .*.$:%ARFLAGS $ARFLAGS":1 \
914	arch-gfortran.fcm > arch-local.fcm
915	cat <<EOF > arch-local.path
916	NETCDF_LIBDIR="-L$ncdfdir/lib -lnetcdff -lnetcdf"
917	NETCDF_INCDIR="$ncdfdir/include"
918	IOIPSL_INCDIR="$ORCHPATH/../../lib"
919	IOIPSL_LIBDIR="$ORCHPATH/../../lib"
920	XIOS_INCDIR="\$ORCHDIR/../XIOS/inc"
921	XIOS_LIBDIR="\$ORCHDIR/../XIOS/lib -lxios"
922	EOF
923	cd ../
924
925	echo ./makeorchidee_fcm -j $xios_orchid $opt_orc -parallel none \
926	-arch $arch
927	./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel none \
928	-arch $arch > "$orchideelog" 2>&1
929	pwd
930	else # of "if [[ -d tools ]]"
931	if [[ -d src_parallel ]]; then
932	liste_src="parallel parameters global stomate sechiba driver"
933	if [[ "$veget_version" == "false" ]]; then
934	veget_version=orchidee2.0
935	fi
936	fi
937	for d in $liste_src; do
938	src_d=src_$d
939	echo src_d "$src_d"
940	echo ls; ls
941	if [[ ! -d $src_d ]]; then
942	echo "Problem orchidee : no $src_d"; exit 1
943	fi
944	cd "$src_d"; \rm -f -- *.mod make; $make clean
945	$make > "$orchideelog" 2>&1
946	if [[ "$compiler" = "$gfortran" \|\| "$compiler" = "mpif90" ]]; then
947	cp -f -- *.mod ../../../lib
948	fi
949	cd ..
950	done
951	fi # of "if [[ -d tools ]]"
952	echo "install_lmdz.sh orchidee_compil_seq_OK $(date)"
953	fi # of if [[ "$veget" != 'NONE' ]]
954
955
956	#============================================================================
957	# Ehouarn: the directory name LMDZ* depends on version/tar file...
958	if [[ -d $MODEL/modipsl/modeles/LMD* ]]; then
959	echo '###############################################################'
960	echo 'Preparing LMDZ compilation : arch file, svn switch if needed...'
961	echo '###############################################################'
962	cd "$MODEL/modipsl/modeles/"LMD*
963	LMDZPATH=$(pwd)
964	else
965	echo "ERROR: No LMD* directory !!!"
966	exit 1
967	fi
968
969	###########################################################
970	# For those who want to use fcm to compile via :
971	# makelmdz_fcm -arch local .....
972	############################################################
973
974
975
976	cd "$MODEL/modipsl/modeles"/LMDZ*
977	lmdzlog=$(pwd)/lmdz.log
978
979	##################################################################
980	# Possibly update LMDZ if a specific svn release is requested
981	##################################################################
982
983	set +e; svn upgrade; set -e
984
985	if [[ $svn = "last" ]]; then svnopt=""; else svnopt="-r $svn"; fi
986	if [[ $svn != "" ]]; then
987	if set +e; svn info \| grep -q 'https:'; then
988	svn switch --relocate https://svn.lmd.jussieu.fr/LMDZ \
989	http://svn.lmd.jussieu.fr/LMDZ
990	fi
991	svn update "$svnopt"
992	set -e
993	fi
994
995	#---------------------------------------------------------------------
996	# Retrieve the final svn release number, and adjust compilation
997	# options accordingly
998	# If svn not available, will use the svn writen in $MODEL/Readm*md
999	# For old version it assumes that it is before 4185 (the version
1000	# for which the test was introduced
1001	#---------------------------------------------------------------------
1002
1003	set +e; mysvn=$(svnversion . \| grep -E \|\| "[0-9]+" 2>/dev/null); set -e
1004	if [[ "$mysvn" = "" ]]; then mysvn=$(grep 'Revision: [0-9]' "$MODEL"/Read*.md \| awk ' { print $2 } ' 2>/dev/null); fi
1005	if [[ "$mysvn" = "" ]]; then mysvn=4190; fi
1006
1007	if [[ "$pclinux" = "1" && ! -f arch/arch-local.path ]]; then
1008
1009	# create local 'arch' files (if on Linux PC):
1010	cd arch
1011	# arch-local.path file
1012	# test for version as arch.pth file changed format with rev 4426
1013	if [[ "$mysvn" -gt 4425 ]]; then
1014	cat <<EOF > arch-local.path
1015	NETCDF_LIBDIR="-L$ncdfdir/lib"
1016	NETCDF_LIB="-lnetcdff -lnetcdf\"
1017	NETCDF_INCDIR=-I$ncdfdir/include
1018	NETCDF95_INCDIR=-I\$LMDGCM/../../include
1019	NETCDF95_LIBDIR=-L\$LMDGCM/../../lib
1020	NETCDF95_LIB=-lnetcdf95
1021	IOIPSL_INCDIR=-I\$LMDGCM/../../lib
1022	IOIPSL_LIBDIR=-L\$LMDGCM/../../lib
1023	IOIPSL_LIB=-lioipsl
1024	XIOS_INCDIR=-I\$LMDGCM/../XIOS/inc
1025	XIOS_LIBDIR=-L\$LMDGCM/../XIOS/lib
1026	XIOS_LIB="-lxios -lstdc++"
1027	ORCH_INCDIR=-I\$LMDGCM/../../lib
1028	ORCH_LIBDIR=-L\$LMDGCM/../../lib
1029	EOF
1030	else
1031	cat <<EOF > arch-local.path
1032	NETCDF_LIBDIR="-L$ncdfdir/lib -lnetcdff -lnetcdf"
1033	NETCDF_INCDIR=-I$ncdfdir/include
1034	NETCDF95_INCDIR=\$LMDGCM/../../include
1035	NETCDF95_LIBDIR=\$LMDGCM/../../lib
1036	IOIPSL_INCDIR=\$LMDGCM/../../lib
1037	IOIPSL_LIBDIR=\$LMDGCM/../../lib
1038	XIOS_INCDIR=\$LMDGCM/../XIOS/inc
1039	XIOS_LIBDIR=\$LMDGCM/../XIOS/lib
1040	ORCH_INCDIR=\$LMDGCM/../../lib
1041	ORCH_LIBDIR=\$LMDGCM/../../lib
1042	EOF
1043	fi
1044
1045	if [[ $pcmac == 1 ]]; then
1046	BASE_LD="$BASE_LD -Wl,-rpath,${ncdfdir}/lib"
1047	else
1048	BASE_LD="$BASE_LD -Wl,-rpath=${ncdfdir}/lib"
1049	fi
1050	# Arch-local.fcm file (adapted from arch-linux-32bit.fcm)
1051
1052	if [[ $real = r8 ]]; then FPP_DEF=NC_DOUBLE; else FPP_DEF=""; fi
1053	sed -e s:"%COMPILER .*.$:%COMPILER $compiler":1 \
1054	-e s:"%LINK .*.$:%LINK $compiler":1 \
1055	-e s:"%PROD_FFLAGS .*.$:%PROD_FFLAGS $OPTIM":1 \
1056	-e s:"%DEV_FFLAGS .*.$:%DEV_FFLAGS $OPTDEV":1 \
1057	-e s:"%DEBUG_FFLAGS .*.$:%DEBUG_FFLAGS $OPTDEB":1 \
1058	-e s:"%BASE_FFLAGS .*.$:%BASE_FFLAGS $OPTPREC":1 \
1059	-e s:"%FPP_DEF .*.$:%FPP_DEF $FPP_DEF":1 \
1060	-e s:"%BASE_LD .*.$:%BASE_LD $BASE_LD":1 \
1061	-e s:"%ARFLAGS .*.$:%ARFLAGS $ARFLAGS":1 \
1062	arch-linux-32bit.fcm > arch-local.fcm
1063
1064	cd ..
1065	### Adapt "bld.cfg" (add the shell):
1066	#whereisthatshell=$(which ${use_shell})
1067	#echo "bld::tool::SHELL $whereisthatshell" >> bld.cfg
1068
1069	fi # of if [[ "$pclinux" = 1 ]]
1070	#---------------------------------------------------------------------
1071	# Option de compilation du rayonnement : depend de $mysvn ><= r4185
1072	#---------------------------------------------------------------------
1073	opt_rad=""
1074
1075	case $rad in
1076	oldrad) iflag_rrtm=0; NSW=2; opt_rad="";;
1077	rrtm) iflag_rrtm=1; NSW=6
1078	if [[ $mysvn -le 4185 ]]; then
1079	opt_rad="-rrtm true"
1080	else
1081	opt_rad="-rad rrtm"
1082	fi;;
1083	ecrad) iflag_rrtm=2; NSW=6; opt_rad="-rad ecrad";;
1084	*) echo "Only oldrad rrtm ecrad for rad option"; exit 1
1085	esac
1086
1087	if [[ $mysvn -le 4185 && $rad = "ecrad" ]]; then
1088	echo "ecrad only available for LMDZ rev starting with 4186 "; exit 1
1089	fi
1090
1091	##################################################################
1092
1093
1094	if [[ ! -f libf/misc/netcdf95.F90 && ! -d $MODEL/NetCDF95-0.3 ]]; then
1095	cd "$MODEL"
1096	myget src_archives/netcdf/NetCDF95-0.3.tar.gz
1097	tar -xf NetCDF95-0.3.tar.gz
1098	rm NetCDF95-0.3.tar.gz
1099	cd NetCDF95-0.3
1100	mkdir build
1101	cd build
1102	cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH="$ncdfdir" \
1103	-DCMAKE_INSTALL_PREFIX="$MODEL/modipsl"
1104	make install
1105	cd "$MODEL/modipsl/modeles/"LMDZ*
1106	fi
1107
1108	echo '##################################################################'
1109	echo "Preparing script compile.sh for LMDZ compilation"
1110	echo "It will only be run automatically if bench=1/tuto"
1111	echo "Here bench=$bench"
1112	echo '##################################################################'
1113
1114	if [[ $env_file != "" ]]; then
1115	mv arch/arch-${arch}.env arch/arch-${arch}.orig
1116	\cp -f "$env_file" arch/arch-${arch}.env
1117	fi
1118
1119	if [[ $compile_with_fcm = 1 ]]; then
1120	makelmdz="makelmdz_fcm $optim -arch $arch -j 8 "
1121	else
1122	makelmdz="makelmdz $optim -arch $arch"
1123	fi
1124
1125	# sequential compilation
1126	if [[ "$sequential" = 1 ]]; then
1127	echo Sequential compilation command, saved in compile.sh:
1128	echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp " \
1129	"-d ${grid_resolution} -v $veget_version gcm "
1130	echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp " \
1131	"-d ${grid_resolution} -v $veget_version gcm " > compile.sh
1132	chmod +x ./compile.sh
1133	if [[ $bench = 1 ]]; then
1134	echo "install_lmdz.sh start_lmdz_seq_compilation $(date)"
1135	echo "log file: $lmdzlog"
1136	./compile.sh > "$lmdzlog" 2>&1
1137	echo "install_lmdz.sh end_lmdz_seq_compilation $(date)"
1138	fi
1139	fi # fin sequential
1140
1141	# compiling in parallel mode
1142	if [[ $parallel != "none" ]]; then
1143	echo '##########################################################'
1144	echo ' Parallel compile '
1145	echo '##########################################################'
1146	echo "(after saving the sequential libs and binaries)"
1147	cd "$MODEL/modipsl"
1148	tar cf sequential.tar bin/ lib/
1149	#
1150	# Orchidee
1151	#
1152	cd "$ORCHPATH"
1153	if [[ -d src_parallel && $veget != 'NONE' ]]; then
1154	cd arch
1155	sed \
1156	-e s:"%COMPILER.*.$:%COMPILER $par_comp":1 \
1157	-e s:"%LINK.*.$:%LINK $par_comp":1 \
1158	-e s:"%MPI_FFLAG.*.$:%MPI_FFLAGS $MPI_FLAGS":1 \
1159	-e s:"%OMP_FFLAG.*.$:%OMP_FFLAGS $OMP_FLAGS":1 \
1160	-e s:"%MPI_LD.*.$:%MPI_LD $MPI_LD":1 \
1161	-e s:"%OMP_LD.*.$:%OMP_LD $OMP_LD":1 \
1162	arch-local.fcm > tmp.fcm
1163
1164	mv tmp.fcm arch-local.fcm
1165	cd ../
1166	echo "Compiling ORCHIDEE in parallel mode $(date)"
1167	echo "logfile $orchideelog"
1168	echo "NOTE : to recompile it when necessary, use ./compile_orc.sh " \
1169	"in modipsl/modeles/ORCHIDEE"
1170	echo ./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc \
1171	-parallel "$parallel" -arch $arch > compile_orc.sh
1172	echo ./makeorchidee_fcm -j 8 $xios_orchid $opt_orc \
1173	-parallel "$parallel" -arch $arch >> compile_orc.sh
1174	echo echo Now you must also recompile LMDZ, by running ./compile.sh \
1175	in modeles/LMDZ >> compile_orc.sh
1176	chmod u+x compile_orc.sh
1177	./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc \
1178	-parallel "$parallel" -arch $arch > "$orchideelog" 2>&1
1179	./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel "$parallel" \
1180	-arch $arch >> "$orchideelog" 2>&1
1181	echo "End of ORCHIDEE compilation in parallel mode $(date)"
1182	elif [[ $veget != 'NONE' ]]; then
1183	echo '##########################################################'
1184	echo ' Orchidee version too old '
1185	echo ' Please update to new version '
1186	echo '##########################################################'
1187	exit 1
1188	fi #�of [ -d src_parallel && $veget != 'NONE' ]
1189
1190	# LMDZ
1191	cd "$LMDZPATH"
1192	if [[ $arch = local ]]; then
1193	cd arch
1194	sed -e s:"%COMPILER.*.$:%COMPILER $par_comp":1 \
1195	-e s:"%LINK.*.$:%LINK $par_comp":1 \
1196	-e s:"%MPI_FFLAG.*.$:%MPI_FFLAGS $MPI_FLAGS":1 \
1197	-e s:"%OMP_FFLAG.*.$:%OMP_FFLAGS $OMP_FLAGS":1 \
1198	-e s:"%ARFLAGS.*.$:%ARFLAGS $ARFLAGS":1 \
1199	-e "s§%BASE_LD.*.$§%BASE_LD -Wl,-rpath=${root_mpi}/lib:${ncdfdir}/lib§1" \
1200	-e s:"%MPI_LD.*.$:%MPI_LD $MPI_LD":1 \
1201	-e s:"%OMP_LD.*.$:%OMP_LD $OMP_LD":1 \
1202	arch-local.fcm > tmp.fcm
1203	mv tmp.fcm arch-local.fcm
1204	cd ../
1205	fi
1206	rm -f compile.sh
1207	echo resol="$grid_resolution" >> compile.sh
1208	if [[ ${hostname:0:5} = jean- && "$cosp" = "v2" ]]; then
1209
1210	echo "LMDZ compilation command in parallel mode, saved in compile.sh, is :"
1211	echo "(ATTENTION le probleme de cospv2 sur jean-zay en mode prod " \
1212	"n est pas corrige ! )"
1213	# ATTENTION le probleme de cospv2 sur jean-zay en mode prod n
1214	# est pas corrige
1215	echo ./"$makelmdz" -dev $optim "$OPT_MAKELMDZ" "$opt_rad" "$opt_cosp" \
1216	"$opt_makelmdz_xios" -d \$resol -v $veget_version -mem \
1217	-parallel "$parallel" gcm >> compile.sh
1218	echo ./"$makelmdz" -dev $optim "$OPT_MAKELMDZ" "$opt_rad" "$opt_cosp" \
1219	"$opt_makelmdz_xios" -d \$resol -v $veget_version -mem \
1220	-parallel "$parallel" gcm
1221	else
1222	echo ./"$makelmdz" $optim "$OPT_MAKELMDZ" "$opt_rad" "$opt_cosp" \
1223	"$opt_makelmdz_xios" -d \$resol -v $veget_version -mem \
1224	-parallel "$parallel" gcm >> compile.sh
1225	echo ./"$makelmdz" $optim "$OPT_MAKELMDZ" "$opt_rad" "$opt_cosp" \
1226	"$opt_makelmdz_xios" -d \$resol -v $veget_version -mem \
1227	-parallel "$parallel" gcm
1228	fi
1229	chmod +x ./compile.sh
1230
1231	if [[ $bench = 1 ]]; then
1232	echo "Compiling LMDZ in parallel mode $(date), LMDZ log file: $lmdzlog"
1233	./compile.sh > "$lmdzlog" 2>&1
1234	fi
1235
1236	fi # of if [[ $parallel != "none" ]]
1237
1238
1239	##################################################################
1240	# Verification du succes de la compilation
1241	##################################################################
1242
1243	# Recherche de l'executable dont le nom a change au fil du temps ...
1244	# suffix contains radiative option starting with revision 4186
1245	if [[ $mysvn -ge 4186 ]]; then suff_exe=_${rad}${suff_exe}; fi
1246	gcm=""
1247
1248	for exe in gcm.e bin/gcm_${grid_resolution}_phylmd${suff_exe}${suff_orc}.e
1249	do
1250	if [[ -f $exe ]]; then gcm=$exe; fi
1251	done
1252
1253	if [[ "$gcm" = "" ]]; then
1254	if [[ $bench = 1 ]]; then
1255	echo 'Compilation failed !! Cannot run the benchmark;'
1256	exit 1
1257	else
1258	echo 'Compilation not done (only done when bench=1)'
1259	fi
1260	else
1261	echo '##########################################################'
1262	echo "Compilation successfull !! $(date)"
1263	echo '##########################################################'
1264	echo "The executable is $gcm"
1265	fi
1266
1267	##################################################################
1268	# Below, we run a benchmark if bench=1 or tuto
1269	##################################################################
1270
1271	if [[ $bench = tuto ]]; then
1272	myget Training/tutorial.tar; tar xf tutorial.tar; cd TUTORIAL
1273	./init.sh
1274
1275	elif [[ $bench = 1 && ! -d BENCH${grid_resolution} ]]; then
1276	# TOUTE CETTE SECTION DEVRAIT DISPARAITRE POUR UNE COMMANDE
1277	# OU DES BENCHS PAR MOTS CLES COMME tuto
1278
1279	echo '##########################################################'
1280	echo ' Running a test run '
1281	echo '##########################################################'
1282
1283	\rm -rf "BENCH${grid_resolution}"
1284	bench=bench_lmdz_${grid_resolution}
1285	echo "install_lmdz.sh before bench download $(date)"
1286	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/$bench.tar.gz
1287	myget "3DBenchs/$bench.tar.gz"
1288	echo "install_lmdz.sh after bench download $(date)"
1289	tar xf "$bench.tar.gz"
1290
1291	if [[ "$cosp" = "v1" \|\| "$cosp" = "v2" ]]; then
1292	cd "BENCH${grid_resolution}"
1293	# copier les fichiers namelist input et output our COSP
1294	cp ../DefLists/cosp*_input_nl.txt .
1295	cp ../DefLists/cosp*_output_nl.txt .
1296	# Activer la cles ok_cosp pour tourner avec COSP
1297	sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp
1298	\mv -f tmp config.def
1299	cd ..
1300	fi
1301
1302	if [[ -n "$physiq" ]]; then
1303	cd "BENCH${grid_resolution}"
1304	if [[ -f "physiq.def_${physiq}" ]]; then
1305	cp "physiq.def_${physiq}" physiq.def
1306	echo using "physiq.def_${physiq}"
1307	else
1308	echo using standard physiq.def
1309	fi
1310	cd ..
1311	else
1312	echo using standard physiq.def
1313	fi
1314
1315	if [[ "$with_xios" = "y" ]]; then
1316	cd "BENCH${grid_resolution}"
1317	cp ../DefLists/iodef.xml .
1318	cp ../DefLists/context_lmdz.xml .
1319	cp ../DefLists/field_def_lmdz.xml .
1320	# A raffiner par la suite
1321	echo "A FAIRE : Copier les *xml en fonction de l option cosp"
1322	cp ../DefLists/field_def_cosp*.xml .
1323	cp ../DefLists/file_def_hist*xml .
1324	# adapt iodef.xml to use attached mode
1325	sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' \
1326	iodef.xml > tmp
1327	\mv -f tmp iodef.xml
1328
1329	# and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
1330	# except for histday
1331	for histfile in file_def_hist*xml
1332	do
1333	if [[ "$histfile" = "file_def_histday_lmdz.xml" ]]; then
1334	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' \
1335	"$histfile" > tmp
1336	\mv -f tmp "$histfile"
1337	sed -e 's@output_level="_AUTO_"@output_level="5"@' "$histfile" \
1338	> tmp
1339	\mv -f tmp "$histfile"
1340	sed -e 's@compression_level="2"@compression_level="0"@' \
1341	"$histfile" > tmp
1342	\mv -f tmp "$histfile"
1343	else
1344	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
1345	"$histfile" > tmp
1346	\mv -f tmp "$histfile"
1347	fi
1348	done
1349	# and add option "ok_all_xml=y" in config.def
1350	echo "### XIOS outputs" >> config.def
1351	echo 'ok_all_xml=.true.' >> config.def
1352
1353	#activer les sorties pour Cosp
1354	if [[ "$cosp" = "v1" ]]; then
1355	sed -i'' -e 's@enabled=".FALSE."@enabled=".TRUE."@' \
1356	-e 's@output_level="_AUTO_"@output_level="5"@' \
1357	-e 's@compression_level="2"@compression_level="0"@' \
1358	file_def_histdayCOSP_lmdz.xml
1359	fi
1360	if [[ "$cosp" = "v2" ]]; then
1361	sed -e 's@compression_level="2"@compression_level="0"@' file_def_histdayCOSPv2_lmdz.xml
1362	for type_ in hf day mth; do
1363	file=file_def_hist${type_}COSP
1364	sed -i'' -e 's@src="./'${file}'_lmdz.xml"@src="./'${file}'v2_lmdz.xml"@' context_lmdz.xml
1365	done
1366	sed -i '' -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' field_def_lmdz.xml
1367	fi
1368
1369	cd ..
1370	fi
1371
1372	# Cas Bensh avec ecrad
1373	if [[ "$rad" = "ecrad" ]]; then
1374	cd "BENCH${grid_resolution}"
1375	cp ../DefLists/namelist_ecrad .
1376	cp -r ../libf/phylmd/ecrad/data .
1377	cd ..
1378	fi
1379
1380	# Adjusting bench physiq.def to radiative code chosen
1381	cd "BENCH${grid_resolution}"
1382	sed -e 's/iflag_rrtm=.*.$/iflag_rrtm='$iflag_rrtm'/' \
1383	-e 's/NSW=.*.$/NSW='$NSW'/' physiq.def > tmpdef
1384	\mv tmpdef physiq.def
1385	cd ..
1386
1387	cp "$gcm" "BENCH${grid_resolution}/gcm.e"
1388
1389	cd "BENCH${grid_resolution}"
1390	# On cree le fichier bench.sh au besoin
1391	# Dans le cas 48x36x39 le bench.sh existe deja en parallele
1392
1393	if [[ "$grid_resolution" = "48x36x39" ]]; then
1394	echo On ne touche pas au bench.sh
1395	# But we have to adapt "run_local.sh" for $mpirun
1396	sed -e "s@mpirun@$mpirun@g" run_local.sh > tmp
1397	mv -f tmp run_local.sh
1398	chmod u=rwx run_local.sh
1399	elif [[ "${parallel:0:3}" = "mpi" ]]; then
1400	# Lancement avec deux procs mpi et 2 openMP
1401	echo "export OMP_STACKSIZE=800M" > bench.sh
1402	if [[ "${parallel:4:3}" = "omp" ]]; then
1403	echo "export OMP_NUM_THREADS=2" >> bench.sh
1404	fi
1405	if [[ "$cosp" = "v1" \|\| "$cosp" = "v2" ]]; then
1406	if [[ ${hostname:0:5} = jean- ]]; then
1407	chmod +x ../arch.env
1408	../arch.env
1409	echo "ulimit -s 2000000" >> bench.sh
1410	else
1411	echo "ulimit -s 200000" >> bench.sh
1412	fi
1413	else
1414	echo "ulimit -s unlimited" >> bench.sh
1415	fi
1416	if [[ ${hostname:0:5} = jean- ]]; then
1417	. ../arch/arch-${arch}.env
1418	echo "srun -n 2 && $idris_acct@cpu gcm.e > listing 2>&1" \
1419	>> bench.sh
1420	else
1421	echo "$mpirun -np 2 gcm.e > listing 2>&1" >> bench.sh
1422	fi
1423	# Add rebuild, using reb.sh if it is there
1424	cat <<EOF >> bench.sh
1425	if [[ -f reb.sh ]]; then
1426	./reb.sh histday; ./reb.sh histmth; ./reb.sh histhf;
1427	./reb.sh histins; ./reb.sh stomate_history;
1428	./reb.sh sechiba_history; ./reb.sh sechiba_out_2
1429	fi
1430	EOF
1431	else
1432	echo "./gcm.e > listing 2>&1" > bench.sh
1433	fi
1434	# Getting orchidee stuff
1435	if [[ $veget == 'CMIP6' ]]; then
1436	#echo 'myget 3DBenchs/BENCHorch11.tar.gz'
1437	#myget 3DBenchs/BENCHorch11.tar.gz
1438	#tar xvzf BENCHorch11.tar.gz
1439	echo 'myget 3DBenchs/BENCHCMIP6.tar.gz'
1440	myget 3DBenchs/BENCHCMIP6.tar.gz
1441	tar xvzf BENCHCMIP6.tar.gz
1442	sed -e "s:VEGET=n:VEGET=y:" config.def > tmp
1443	mv -f tmp config.def
1444	if [[ "$with_xios" = "y" ]]; then
1445	cp ../../ORCHIDEE/src_xml/context_orchidee.xml .
1446	echo '<context id="orchidee" src="./context_orchidee.xml"/>' \
1447	> add.tmp
1448	cp ../../ORCHIDEE/src_xml/field_def_orchidee.xml .
1449	cp ../../ORCHIDEE/src_xml/file_def_orchidee.xml .
1450	cp ../../ORCHIDEE/src_xml/file_def_input_orchidee.xml .
1451	if [[ -f ../../ORCHIDEE/src_xml/context_input_orchidee.xml ]]; then
1452	cp ../../ORCHIDEE/src_xml/context_input_orchidee.xml .
1453	echo '<context id="orchidee" ' \
1454	'src="./context_input_orchidee.xml"/>' >> add.tmp
1455	fi
1456	sed -e '/id="LMDZ"/r add.tmp' iodef.xml > tmp
1457	mv tmp iodef.xml
1458	sed -e'{/sechiba1/ s/enabled="_AUTO_"/type="one_file" enabled=".TRUE."/}' \
1459	file_def_orchidee.xml > tmp
1460	\mv -f tmp file_def_orchidee.xml
1461	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
1462	file_def_orchidee.xml > tmp
1463	\mv -f tmp file_def_orchidee.xml
1464	sed -e 's@output_level="_AUTO_"@output_level="1"@' \
1465	file_def_orchidee.xml > tmp
1466	\mv -f tmp file_def_orchidee.xml
1467	sed -e 's@output_freq="_AUTO_"@output_freq="1d"@' \
1468	file_def_orchidee.xml > tmp
1469	\mv -f tmp file_def_orchidee.xml
1470	sed -e 's@compression_level="4"@compression_level="0"@' \
1471	file_def_orchidee.xml > tmp
1472	\mv -f tmp file_def_orchidee.xml
1473	sed -e 's@XIOS_ORCHIDEE_OK = n@XIOS_ORCHIDEE_OK = y@' \
1474	orchidee.def > tmp
1475	\mv -f tmp orchidee.def
1476	fi
1477	fi
1478
1479	if [[ -f ../arch.env ]]
1480	then
1481	source ../arch.env
1482	fi
1483
1484	echo EXECUTION DU BENCH
1485	set +e
1486	date; ./bench.sh > out.bench 2>&1; date
1487	set -e
1488	tail listing
1489
1490
1491	echo "##########################################################"
1492	echo "Simulation finished in $(pwd)"
1493	echo "You have compiled with:"
1494	cat ../compile.sh
1495	if [[ $parallel = "none" ]]; then
1496	echo "You may re-run it with : cd $(pwd) ; gcm.e"
1497	echo "or ./bench.sh"
1498	else
1499	echo "You may re-run it with : "
1500	echo "cd $(pwd) ; ./bench.sh"
1501	# echo 'ulimit -s unlimited'
1502	# echo 'export OMP_NUM_THREADS=2'
1503	# echo 'export OMP_STACKSIZE=800M'
1504	# echo "$mpirun -np 2 gcm.e "
1505	fi
1506	echo '##########################################################'
1507
1508	fi # bench
1509
1510
1511	#################################################################
1512	# Installation eventuelle du 1D
1513	#################################################################
1514
1515	if [[ $SCM = 1 ]]; then
1516	cd "$MODEL"
1517	myget 1D/1D.tar.gz
1518	tar xf 1D.tar.gz
1519	cd 1D
1520	if [[ $rad = oldrad ]]; then
1521	sed -i'' -e 's/^rad=.*$/rad=oldrad/' run.sh
1522	sed -i'' -e 's/^rad=.*$/rad=oldrad/' bin/compile
1523	fi
1524	echo "Running 1D/run.sh, log in $(pwd)/run1d.log"
1525	./run.sh > "$(pwd)/run1d.log" 2>&1
1526	fi
1527
1528
1529	#################################################################
1530	# sauvegarde des options veget pour utilisation eventuelle tutorial_prod
1531	#################################################################
1532	cd "$MODEL/modipsl/modeles"
1533	#echo surface_env file created in $MODEL
1534	cat <<EOF >surface_env
1535	veget=$veget
1536	opt_veget="-v $veget_version"
1537	orchidee_rev=$orchidee_rev
1538	suforch=$suff_orc
1539	EOF

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