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source: BOL/script_install/install_lmdz_new.sh @ 4219

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1	#!/bin/bash
2
3	#set -vx
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	set -e
40
41	################################################################
42	# Choice of installation options
43	################################################################
44
45	################################################################
46	# A function to fetch files either locally or on the internet
47	################################################################
48	function myget { #1st and only argument should be file name
49	# Path on local computer where to look for the datafile
50	if [ -f /u/lmdz/WWW/LMDZ/pub/$1 ] ; then
51	\cp -f -p /u/lmdz/WWW/LMDZ/pub/$1 .
52	elif [ -f ~/LMDZ/pub/$1 ] ; then
53	\cp -f -p ~/LMDZ/pub/$1 .
54	else
55	wget --no-check-certificate -nv http://lmdz.lmd.jussieu.fr/pub/$1
56	save_pub_locally=0
57	if [ $save_pub_locally = 1 ] ; then # saving wget files on ~/LMDZ/pub
58	dir=~/LMDZ/pub/`dirname $1` ; mkdir -p $dir
59	cp -r `basename $1` $dir
60	fi
61	fi
62	}
63
64	# 04_2021 : tester si r4 marche encore !
65	#real=r4
66	real=r8
67
68
69	#########################################################################
70	# Valeur par défaut des parametres
71	#########################################################################
72	svn=""
73	#version=trunk
74	version=20220131.trunk
75
76	getlmdzor=1
77	netcdf=0 # 1: for automatic installation;
78	# or 0: do not install NetCDF and look for it in standard locations;
79	# or absolute path: look for NetCDF there
80	check_linux=1
81	ioipsl=1
82	bench=1
83	pclinux=1
84	pcmac=0 # default: not on a Mac
85	compiler=gfortran
86	SCM=0
87	# surface/vegetation scheme treatment
88	# controlled by the single variable veget which can have the following values
89	# - NONE: bucket scheme (default)
90	# - CMIP6: orchidee version used in CMIP exercise, rev 5661
91	# - number: orchidee version number
92	veget=NONE
93	# choose the resolution for the bench runs
94	# grid_resolution= 32x24x11 or 48x36x19 for tests (test without ORCHIDEE)
95	# 96x71x19 standard configuration
96	grid_resolution=144x142x79
97	grid_resolution=96x95x39
98	grid_resolution=48x36x19
99	grid_resolution=32x32x39
100	# choose the physiq version you want to test
101	#physiq=NPv6.0.14splith
102	physiq=
103
104	## parallel can take the values none/mpi/omp/mpi_omp
105	parallel=mpi_omp
106	parallel=none
107	idris_acct=lmd
108	OPT_GPROF=""
109	OPT_MAKELMDZ=""
110	MODEL=""
111
112	## also compile XIOS? (and more recent NetCDF/HDF5 libraries) Default=no
113	with_xios="n"
114	opt_makelmdz_xios=""
115
116	## compile with oldrad/rrtm/ecrad radiatif code (Default=rrtm)
117	rad=rrtm
118
119	## compile_with_fcm=1 : use makelmdz_fcm (1) or makelmdz (0)
120	compile_with_fcm=1
121
122	#Compilation with Cosp (cosp=NONE/v1/v2 ; default=NONE)
123	cosp=NONE
124	opt_cosp=""
125
126	# Check if on a Mac
127	if [ `uname` = "Darwin" ]
128	then
129	pcmac=1
130	export MAKE=make
131	fi
132	#echo "pcmac="$pcmac
133
134	env_file=""
135
136	#########################################################################
137	# Options interactives
138	#########################################################################
139	while (($# > 0))
140	do
141	case $1 in
142	"-h") cat <<........fin
143	$0 [ -v version ] [ -r svn_release ]
144	[ -parallel PARA ] [ -d GRID_RESOLUTION ] [ -bench 0/1 ]
145	[-name LOCAL_MODEL_NAME] [-gprof] [-opt_makelmdz] [-rad RADIATIF]
146
147	-v "version" like 20150828.trunk
148	see http://www.lmd.jussieu.fr/~lmdz/Distrib/LISMOI.trunk
149
150	-r "svn_release" : either the svn release number or "last"
151
152	-compiler gfortran\|ifort\|pgf90 (default: gfortran)
153
154	-parallel PARA : can be mpi_omp (mpi with openMP) or none (for sequential)
155
156	-d GRID_RESOLUTION should be among the available benchs if -bench 1
157	among which : 48x36x19, 48x36x39
158	if wanting to run a bench simulation in addition to compilation
159	default : 48x36x19
160
161	-bench activating the bench or not (0/1). Default 1
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 ;;
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
205	esac ;;
206	"-d") grid_resolution=$2 ; shift ; shift ;;
207	"-gprof") OPT_GPROF="-pg" ; shift ;;
208	"-cosp") cosp=$2
209	case $cosp in
210	"none"\|"v1"\|"v2") cosp=$2 ; shift ; shift ;;
211	*) echo Only none v1 v2 for cosp option ; exit
212	esac ;;
213	"-nofcm") compile_with_fcm=0 ; shift ;;
214	"-SCM") SCM=1 ; shift ;;
215	"-opt_makelmdz") OPT_MAKELMDZ="$2" ; shift ; shift ;;
216	"-rrtm") rrtm="$2"
217	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
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 \
233	option
234	exit
235	esac ;;
236	"-bench") bench=$2 ; shift ; shift ;;
237	"-debug") optim=-debug ; shift ;;
238	"-name") MODEL=$2 ; shift ; shift ;;
239	"-netcdf") netcdf=$2 ; shift ; shift ;;
240	"-physiq") physiq=$2 ; shift ; shift ;;
241	"-xios") with_xios="y" ; shift ;;
242	"-env_file") env_file=$2 ; shift ; shift ;;
243	"-veget") veget=$2 ; shift ; shift ;;
244	*) ./install_lmdz.sh -h ; exit
245	esac
246	done
247
248	# Option de compilation du rayonnement : depend de $mysvn ><= r4185,
249	# sera donc definie plus bas
250
251	#opt_rad=""
252	#case $rad in
253	# rrtm) opt_rad="-rad rrtm" ;;
254	# ecrad) opt_rad="-rad ecrad" ;;
255	#esac
256
257
258	# Option de compilation pour Cosp
259	opt_cosp=""
260	case cosp in
261	v1) opt_cosp="-cosp true" ;;
262	v2) opt_cosp="-cospv2 true" ;;
263	esac
264
265	# Check on veget version
266	#if [ "$veget" != 'NONE' -a "$veget" != "CMIP6" -a "$veget" != +([0-9]) ] ; then
267	if [ $veget != 'NONE' -a $veget != "CMIP6" ] ; then
268	re='^[0-9]+$'
269	if ! [[ $veget =~ $re ]] ; then
270	echo 'Valeur de l option veget non valable'
271	exit
272	fi
273	fi
274
275	#Define veget-related suffix for gcm name
276	if [ "$veget" = 'NONE' ] ; then
277	suff_orc=''
278	#For use with tutorial, orchidee_rev is also defined (will be
279	#written in surface_env at the end of the script)
280	orchidee_rev=''
281	else
282	suff_orc='_orch'
283	fi
284
285
286	if [ $parallel = none ] ; then
287	sequential=1; suff_exe='_seq'
288	else
289	sequential=0; suff_exe='_para_mem'
290	fi
291
292	#Chemin pour placer le modele
293	if [ "$MODEL" = "" ] ; then MODEL=./LMDZ$version$svn$optim ; fi
294
295
296	arch=local
297
298
299	if [ $compiler = g95 ] ; then echo g95 is not supported anymore ; exit ; fi
300
301	################################################################
302	# Specificite des machines
303	################################################################
304
305	hostname=`hostname`
306	if [ "$pclinux" = 1 ] ; then o_ins_make="-t g95" ; else o_ins_make="" ; fi
307
308	case ${hostname:0:5} in
309
310	jean-) compiler="mpiifort" ;
311	par_comp="mpiifort" ;
312	o_ins_make="-t jeanzay" ;
313	make=gmake ;
314	module purge
315	module load intel-compilers/19.0.4 ;
316	#module load intel-mpi/19.0.4 ;
317	#module load intel-mkl/19.0.4 ;
318	module load hdf5/1.10.5-mpi ;
319	module load netcdf/4.7.2-mpi ;
320	module load netcdf-fortran/4.5.2-mpi ;
321	module load subversion/1.9.7 ;
322	export NETCDF_LIBDIR=./
323	export NETCDFFORTRAN_INCDIR=./
324	export NETCDFFORTRAN_LIBDIR=./
325	arch=X64_JEANZAY ;;
326
327	cicla\|camel) compiler="gfortran" ;
328	module load netcdf4/4.3.3.1-gfortran;
329	netcdf=/opt/netcdf43/gfortran
330
331	if [ $parallel != none ] ; then
332	module load openmpi/1.6.5-gfortran ;
333	root_mpi=$MPI_HOME ;
334	path_mpi=$root_mpi/bin ;
335	par_comp=${path_mpi}/mpif90 ;
336	mpirun=${path_mpi}/mpirun ;
337	fi ;
338	arch=local ;
339	make=make ;
340	o_ins_make="-t g95" ;;
341
342	*) if [ $parallel = none -o -f /usr/bin/mpif90 ] ; then
343	path_mpi=`which mpif90 \| sed -e s:/mpif90::` ;
344	if [ -d /usr/lib64/openmpi ] ; then
345	root_mpi="/usr/lib64/openmpi"
346	else
347	root_mpi="/usr"
348	fi
349	else
350	echo "Cannot find mpif90" ;
351	if [ $parallel = none ] ; then exit ; fi ;
352	fi ;
353	if [ $parallel != none ] ; then
354	root_mpi=$(which mpif90 \| sed -e s:/bin/mpif90::)
355	path_mpi=$(which mpif90 \| sed -e s:/mpif90::)
356	export LD_LIBRARY_PATH=${root_mpi}/lib:$LD_LIBRARY_PATH
357	fi
358	par_comp=${path_mpi}/mpif90 ;
359	mpirun=${path_mpi}/mpirun ;
360	arch=local ;
361	make=make ;
362	o_ins_make="-t g95"
363	esac
364
365	# Flags for parallelism:
366	if [ $parallel != none ] ; then
367	# MPI_LD are the flags needed for linking with MPI
368	MPI_LD="-L${root_mpi}/lib -lmpi"
369	if [ "$compiler" = "gfortran" ] ; then
370	# MPI_FLAGS are the flags needed for compilation with MPI
371	MPI_FLAGS="-fcray-pointer"
372	# OMP_FLAGS are the flags needed for compilation with OpenMP
373	OMP_FLAGS="-fopenmp -fcray-pointer"
374	# OMP_LD are the flags needed for linking with OpenMP
375	OMP_LD="-fopenmp"
376	elif [ "$compiler" = "ifort" ] ; then
377	MPI_FLAGS=""
378	OMP_FLAGS="-openmp"
379	OMP_LD="-openmp"
380	else # pgf90
381	MPI_FLAGS=""
382	OMP_FLAGS="-mp"
383	OMP_LD="-mp"
384	fi
385	fi
386
387	#####################################################################
388	# Test for old gfortran compilers
389	# If the compiler is too old (older than 4.3.x) we test if the
390	# temporary gfortran44 patch is available on the computer in which
391	# case the compiler is changed from gfortran to gfortran44
392	# Must be aware than parallelism can not be activated in this case
393	#####################################################################
394
395	if [ "$compiler" = "gfortran" ] ; then
396	gfortran=gfortran
397	gfortranv=`gfortran --version \| \
398	head -1 \| awk ' { print $NF } ' \| awk -F. ' { print $1 * 10 + $2 } '`
399	if [ $gfortranv -le 43 ] ; then
400	echo ERROR : Your gfortran compiler is too old
401	echo 'Please choose a new one (ifort) and change the line'
402	echo compiler=xxx
403	echo in the install_lmdz.sh script and rerun it
404	if [ `which gfortran44 \| wc -w` -ne 0 ] ; then
405	gfortran=gfortran44
406	else
407	echo gfotran trop vieux ; exit
408	fi
409	fi
410	compiler=$gfortran
411	fi
412	#####################################################################
413
414	## if also compiling XIOS, parallel must be mpi_omp
415	if [ "$with_xios" = "y" -a "$parallel" != "mpi_omp" ] ; then
416	echo "Error, you must set -parallel mpi_omp if you want XIOS"
417	exit
418	fi
419
420	if [ "$with_xios" = "y" ] ; then
421	opt_makelmdz_xios="-io xios"
422	fi
423
424	if [ "$cosp" = "v2" -a "$with_xios" = "n" ] ; then
425	echo "Error, Cospv2 cannot run without Xios"
426	exit
427	fi
428
429	echo '################################################################'
430	echo Choix des options de compilation
431	echo '################################################################'
432
433	export FC=$compiler
434	export F90=$compiler
435	export F77=$compiler
436	export CPPFLAGS=
437	OPTIMNC=$OPTIM
438	BASE_LD="$OPT_GPROF"
439	OPTPREC="$OPT_GPROF"
440	ARFLAGS="rs"
441	if [ -f /etc/issue ] ; then
442	if [ "`grep -i ubuntu /etc/issue`" != "" ] ; then
443	if [ "`grep -i ubuntu /etc/issue \| awk ' { print $2 } ' \| cut -d. -f1`" -ge 16 ]
444	then
445	ARFLAGS="rU"
446	fi
447	fi
448	fi
449
450
451
452	if [ "$compiler" = "$gfortran" ] ; then
453	OPTIM='-O3'
454	OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all -fbacktrace -finit-real=snan"
455	OPTDEV="-Wall -fbounds-check"
456	fmod='I '
457	OPTPREC="$OPTPREC -cpp -ffree-line-length-0"
458	if [ $real = r8 ] ; then
459	OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE"
460	fi
461	export F90FLAGS=" -ffree-form $OPTIMNC"
462	export FFLAGS=" $OPTIMNC"
463	export CC=gcc
464	export CXX=g++
465	export fpp_flags="-P -C -traditional -ffreestanding"
466
467	elif [ $compiler = mpif90 ] ; then
468	OPTIM='-O3'
469	OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all"
470	OPTDEV="-Wall -fbounds-check"
471	BASE_LD="$BASE_LD -lblas"
472	fmod='I '
473	if [ $real = r8 ] ; then
474	OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE -fcray-pointer"
475	fi
476	export F90FLAGS=" -ffree-form $OPTIMNC"
477	export FFLAGS=" $OPTIMNC"
478	export CC=gcc
479	export CXX=g++
480
481	elif [ $compiler = pgf90 ] ; then
482	OPTIM='-O2 -Mipa -Munroll -Mnoframe -Mautoinline -Mcache_align'
483	OPTDEB='-g -Mdclchk -Mbounds -Mchkfpstk -Mchkptr -Minform=inform -Mstandard -Ktrap=fp -traceback'
484	OPTDEV='-g -Mbounds -Ktrap=fp -traceback'
485	fmod='module '
486	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -r8 -DNC_DOUBLE" ; fi
487	export CPPFLAGS="-DpgiFortran"
488	export CC=pgcc
489	export CFLAGS="-O2 -Msignextend"
490	export CXX=pgCC
491	export CXXFLAGS="-O2 -Msignextend"
492	export FFLAGS="-O2 $OPTIMNC"
493	export F90FLAGS="-O2 $OPTIMNC"
494	compile_with_fcm=1
495
496	elif [ $compiler = ifort ] ; then
497	OPTIM="-O2 -fp-model strict -ip -align all "
498	OPTDEV="-p -g -O2 -traceback -fp-stack-check -ftrapuv -check"
499	OPTDEB="-g -no-ftz -traceback -ftrapuv -fp-stack-check -check"
500	fmod='module '
501	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -real-size 64 -DNC_DOUBLE" ; fi
502	export CPP="icc -E"
503	export FFLAGS="-O2 -ip -fpic -mcmodel=large"
504	export FCFLAGS="-O2 -ip -fpic -mcmodel=large"
505	export CC=icc
506	export CFLAGS="-O2 -ip -fpic -mcmodel=large"
507	export CXX=icpc
508	export CXXFLAGS="-O2 -ip -fpic -mcmodel=large"
509	export fpp_flags="-P -traditional"
510	# Pourquoi forcer la compilation fcm. Marche mieux sans
511	#compile_with_fcm=1
512
513	elif [ $compiler = mpiifort ] ; then
514	echo on ne fait rien la
515	# Pourquoi forcer la compilation fcm. Marche mieux sans
516	#compile_with_fcm=1
517
518	else
519	echo unexpected compiler $compiler ; exit
520	fi
521
522	OPTIMGCM="$OPTIM $OPTPREC"
523
524	hostname=`hostname`
525
526	##########################################################################
527	# If installing on known machines such as Jean-Zay at IDRIS,
528	# don't check for available software and don't install netcdf
529	if [ ${hostname:0:5} = jean- ] ; then
530	netcdf=0 # no need to recompile netcdf, alreday available
531	check_linux=0
532	pclinux=0
533	ioipsl=0 # no need to recompile ioipsl, already available
534	#netcdf="/smplocal/pub/NetCDF/4.1.3"
535	compiler="mpiifort"
536	fmod='module '
537	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -i4 -r8 -DNC_DOUBLE" ; fi
538	OPTIM="-auto -align all -O2 -fp-model strict -xHost "
539	OPTIMGCM="$OPTIM $OPTPREC"
540	fi
541	##########################################################################
542
543
544	mkdir -p $MODEL
545	echo $MODEL
546	MODEL=`( cd $MODEL ; pwd )` # to get absolute path, if necessary
547
548
549	echo '################################################################'
550	if [ "$check_linux" = 1 ] ; then
551	echo Check if required software is available
552	echo '################################################################'
553
554	#### Ehouarn: test if the required shell is available
555	#### Maj FH-LF-AS 2021-04 : default=bash ; if bash missing, use ksh
556	use_shell="bash" # default
557	if [ "`which bash`" = "" ] ; then
558	echo "no bash ; we will use ksh"
559	use_shell="ksh"
560	if [ "`which ksh`" = "" ] ; then
561	echo "bash (or ksh) needed!! Install it!"
562	exit
563	fi
564	fi
565
566	for logiciel in wget tar gzip make $compiler gcc cmake ; do
567	if [ "`which $logiciel`" = "" ] ; then
568	echo You must first install $logiciel on your system
569	exit
570	fi
571	done
572
573	if [ $pclinux = 1 ] ; then
574	cd $MODEL
575	cat <<eod > tt.f90
576	print*,'coucou'
577	end
578	eod
579	$compiler tt.f90 -o a.out
580	./a.out >\| tt
581	if [ "`cat tt \| sed -e 's/ //g' `" != "coucou" ] ; then
582	echo problem installing with compiler $compiler ; exit ; fi
583	\rm tt a.out tt.f90
584	fi
585	fi
586
587	###########################################################################
588	if [ $getlmdzor = 1 -a ! -d $MODEL/modipsl ] ; then
589	###########################################################################
590	echo '##########################################################'
591	echo Download a slightly modified version of LMDZ
592	echo '##########################################################'
593	cd $MODEL
594	myget src/modipsl.$version.tar.gz
595	echo install_lmdz.sh wget_OK `date`
596	gunzip modipsl.$version.tar.gz
597	tar xf modipsl.$version.tar
598	\rm modipsl.$version.tar
599	fi
600
601	###########################################################################
602	if [ $netcdf = 1 ] ; then
603	###########################################################################
604	cd $MODEL
605	netcdflog=`pwd`/netcdf.log
606	echo '##########################################################'
607	echo Compiling the Netcdf library
608	echo '##########################################################'
609	echo log file : $netcdflog
610	if [[ "$with_xios" = "n" && ! -d $MODEL/netcdf4_hdf5_seq ]] ; then
611	myget import/install_netcdf4_hdf5_seq.bash
612	chmod +x install_netcdf4_hdf5_seq.bash
613
614	if [ "$compiler" = "gfortran" ]
615	then
616	./install_netcdf4_hdf5_seq.bash -prefix $MODEL/netcdf4_hdf5_seq \
617	-compiler gnu > $netcdflog 2>&1
618	elif [ "$compiler" = "ifort" ]
619	then
620	./install_netcdf4_hdf5_seq.bash -prefix $MODEL/netcdf4_hdf5_seq \
621	-compiler intel > $netcdflog 2>&1
622	else
623	echo "unexpected compiler $compiler" ; exit
624	fi
625
626	# LF rajout d'une verrue, pour une raison non encore expliquee,
627	# la librairie est parfois rangée dans lib64 et non dans lib
628	# par certains compilateurs
629	if [ ! -e lib -a -d lib64 ] ; then ln -s lib64 lib; fi
630	elif [[ "$with_xios" = "y" && ! -d $MODEL/netcdf4_hdf5 ]]
631	then
632	# download and compile hdf5 and netcdf, etc. using the
633	# install_netcdf4_hdf5.bash script
634	myget import/install_netcdf4_hdf5.bash
635	chmod u=rwx install_netcdf4_hdf5.bash
636	if [ "$compiler" = "gfortran" ] ; then
637	./install_netcdf4_hdf5.bash -prefix $MODEL/netcdf4_hdf5 -CC gcc \
638	-FC gfortran -CXX g++ -MPI $root_mpi > $netcdflog 2>&1
639	elif [ "$compiler" = "ifort" ] ; then
640	./install_netcdf4_hdf5.bash -prefix $MODEL/netcdf4_hdf5 -CC icc \
641	-FC ifort -CXX icpc -MPI $root_mpi > $netcdflog 2>&1
642	elif [ "$compiler" = "pgf90" ] ; then
643	./install_netcdf4_hdf5.bash -prefix $MODEL/netcdf4_hdf5 -CC pgcc \
644	-FC pgf90 -CXX pgCC -MPI $root_mpi > $netcdflog 2>&1
645	else
646	echo "unexpected compiler $compiler" ; exit
647	fi
648	fi # of if [ "$with_xios" = "n" ]
649	echo install_lmdz.sh netcdf_OK `date`
650	fi # of if [ $netcdf = 1 ]
651
652	# ncdfdir contains the directory where netcdf is installed
653	if [ $netcdf = 1 ] ; then
654	if [ "$with_xios" = "y" ] ; then
655	ncdfdir=$MODEL/netcdf4_hdf5
656	else
657	ncdfdir=$MODEL/netcdf4_hdf5_seq
658	fi
659	elif [ $netcdf = 0 ]
660	then
661	ncdfdir=/usr
662	else
663	ncdfdir=$netcdf
664	fi
665
666	#=========================================================================
667	if [[ ! -f $MODEL/modipsl/lib/libioipsl.a ]]
668	then
669	if [ $ioipsl = 1 ] ; then
670	#=====================================================================
671	echo OK ioipsl=$ioipsl
672	echo '##########################################################'
673	echo 'Installing MODIPSL, the installation package manager for the '
674	echo 'IPSL models and tools'
675	echo '##########################################################'
676	echo `date`
677
678	cd $MODEL/modipsl
679	\rm -rf lib/*
680	cd util
681	cp AA_make.gdef AA_make.orig
682	F_C="$compiler -c "
683	if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ]
684	then
685	F_C="$compiler -c -cpp "
686	fi
687	if [ "$compiler" = "pgf90" ] ; then F_C="$compiler -c -Mpreprocess" ; fi
688	sed -e 's/^\#..g95..\#.*.$/\#/' AA_make.gdef > tmp
689	sed -e "s:F_L = g95:F_L = $compiler:" \
690	-e "s:F_C = g95 -c -cpp:F_C = $F_C": \
691	-e 's/g95..w_w..(F_D)/g95 w_w = '"$OPTIMGCM"'/' \
692	-e 's:g95..NCDF_INC..$:g95 NCDF_INC= '"$ncdfdir"'/include:' \
693	-e 's:g95..NCDF_LIB..$:g95 NCDF_LIB= -L'"$ncdfdir"'/lib -lnetcdff -lnetcdf:' \
694	-e 's:g95 L_O =:g95 L_O = -Wl,-rpath='"$ncdfdir"'/lib:' \
695	-e "s:-fmod=:-$fmod:" -e 's/-fno-second-underscore//' \
696	-e 's:#-Q- g95 M_K = gmake:#-Q- g95 M_K = make:' \
697	tmp >\| AA_make.gdef
698
699	if [ $pcmac == 1 ]
700	then
701	cp AA_make.gdef tmp
702	sed -e 's/rpath=/rpath,/g' tmp > AA_make.gdef
703	fi
704
705
706	# We use lines for g95 even for the other compilers to run ins_make
707	if [ "$use_shell" = "ksh" ] ; then
708	./ins_make $o_ins_make
709	else # bash
710	sed -e s:/bin/ksh:/bin/bash:g ins_make > ins_make.bash
711	if [ "`grep jeanzay AA_make.gdef`" = "" ] ; then
712	# Bidouille pour compiler sur ada des vieux modipsl.tar
713	echo 'Warning jean-zay not in AA_make.gdef'
714	echo 'Think about updating'
715	exit 1
716	fi
717
718	chmod u=rwx ins_make.bash
719	./ins_make.bash $o_ins_make
720	fi # of if [ "$use_shell" = "ksh" ]
721
722	echo install_lmdz.sh MODIPSL_OK `date`
723
724	cd $MODEL/modipsl/modeles/IOIPSL/src
725	ioipsllog=`pwd`/ioipsl.log
726	echo '##########################################################'
727	echo 'Compiling IOIPSL, the interface library with Netcdf'
728	echo '##########################################################'
729	echo `date`
730	echo log file : $ioipsllog
731
732	if [ "$use_shell" = "bash" ] ; then
733	cp Makefile Makefile.ksh
734	sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile
735	fi
736	# if [ "$pclinux" = 1 ] ; then
737	# Build IOIPSL modules and library
738	$make clean
739	$make > $ioipsllog 2>&1
740	if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then
741	# copy module files to lib
742	cp -f *.mod ../../../lib
743	fi
744	# Build IOIPSL tools (ie: "rebuild", if present)
745	if [ -f $MODEL/modipsl/modeles/IOIPSL/tools/rebuild ] ; then
746	cd $MODEL/modipsl/modeles/IOIPSL/tools
747	# adapt Makefile & rebuild script if in bash
748	if [ "$use_shell" = "bash" ] ; then
749	cp Makefile Makefile.ksh
750	sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile
751	cp rebuild rebuild.ksh
752	sed -e 's:/bin/ksh:/bin/bash:g' \
753	-e 's:print -u2:echo:g' \
754	-e 's:print:echo:g' rebuild.ksh > rebuild
755	fi
756	$make clean
757	$make > $ioipsllog 2>&1
758	fi
759	# fi # of if [ "$pclinux" = 1 ]
760
761	else # of if [ $ioipsl = 1 ]
762	if [ ${hostname:0:5} = jean- ] ; then
763	cd $MODEL/modipsl
764	cd util
765	if [ "`grep jeanzay AA_make.gdef`" = "" ] ; then
766	echo 'Warning jean-zay not in AA_make.gdef'
767	echo 'Think about updating'
768	exit 1
769	fi
770	./ins_make $o_ins_make
771	# Compile IOIPSL on jean-zay
772	cd $MODEL/modipsl/modeles/IOIPSL/src
773	gmake > ioipsl.log
774	cd $MODEL/modipsl/modeles/IOIPSL/tools
775	gmake > ioipsl.log
776
777	fi
778	echo install_lmdz.sh ioipsl_OK `date`
779	fi # of if [ $ioipsl = 1 ]
780	fi
781	# Saving ioipsl lib for possible parallel compile
782	cd $MODEL/modipsl
783	tar cf ioipsl.tar lib/ bin/
784
785	#=========================================================================
786	if [ "$with_xios" = "y" ] ; then
787	echo '##########################################################'
788	echo 'Compiling XIOS'
789	echo '##########################################################'
790	cd $MODEL/modipsl/modeles
791	xioslog=`pwd`/xios.log
792	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/install_xios.bash
793	myget import/install_xios.bash
794	chmod u=rwx install_xios.bash
795	if [ ${hostname:0:5} = jean- ] ; then
796	svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5 \
797	XIOS
798	cd XIOS/arch
799	svn update
800	cd ..
801	echo "Compiling XIOS, start" `date` \
802	"(it takes about 20 min on Jean-Zay)"
803	echo "log file: $xioslog"
804	./make_xios --prod --arch $arch --job 4 > xios.log 2>&1
805	else
806	./install_xios.bash -prefix $MODEL/modipsl/modeles \
807	-netcdf ${ncdfdir} -hdf5 ${ncdfdir} \
808	-MPI $root_mpi -arch $arch > xios.log 2>&1
809	fi # of case Jean-Zay
810	if [ -f XIOS/lib/libxios.a ] ; then
811	echo "XIOS library successfully generated"
812	echo install_lmdz.sh XIOS_OK `date`
813	fi
814	fi
815
816	#============================================================================
817	veget_version=false
818	if [ "$veget" != 'NONE' ] ; then
819	cd $MODEL/modipsl/modeles/ORCHIDEE
820	set +e ; svn upgrade ; set -e
821	if [ "$veget" = "CMIP6" ] ; then
822	veget_version=orchidee2.0
823	orchidee_rev=6592
824	else # specific orchidee revision newer than CMIP6, on 2_1 or 2_2 branches
825	veget_version=orchidee2.1
826	orchidee_rev=$veget
827	if [ $veget -lt 4465 ] ; then
828	echo 'Stopping, ORCHIDEE version too old, script needs work on ' \
829	'the CPP flags to pass to makelmdz'
830	exit 1
831	fi
832	set +e
833	# which branch is my version on?
834	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}'`
835	# switch to that branch
836	echo IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at \
837	orchidee-help@listes.ipsl.fr
838	svn switch -r $veget --accept theirs-full \
839	svn://forge.ipsl.jussieu.fr/orchidee/$orcbranch
840	svn log -r $veget \| grep $veget
841	if [ $? -gt 0 ] ; then
842	echo 'Cannot update ORCHIDEE as not on the right branch for ' \
843	'ORCHIDEE'
844	exit
845	fi
846	set -e
847	set +e ; svn update -r $veget ; set -e
848	fi
849	# Correctif suite debug Jean-Zay
850	sed -i -e 's/9010 FORMAT(A52,F17.14)/9010 FORMAT(A52,F20.14)/' \
851	src_stomate/stomate.f90
852	opt_orc="-prod" ; if [ "$optim" = "-debug" ] ; then opt_orc="-debug" ; fi
853
854	orchideelog=`pwd`/orchidee.log
855	echo '########################################################'
856	echo 'Compiling ORCHIDEE, the continental surface model '
857	echo '########################################################'
858	echo Start of the first compilation of orchidee, in sequential mode: `date`
859	echo log file : $orchideelog
860
861	export ORCHPATH=`pwd`
862	xios_orchid="-noxios"
863	if [ "$with_xios" = "y" ] ; then
864	xios_orchid="-xios"
865	fi
866	if [ -d tools ] ; then
867	###################################################################
868	# Pour les experts qui voudraient changer de version d'orchidee.
869	# Attention : necessite d'avoir le password pour orchidee
870
871	# Correctif suite debug Jean-Zay
872	if [ -f src_global/time.f90 ] ; then
873	sed -i -e 's/CALL tlen2itau/\!CALL tlen2itau/' src_global/time.f90
874	fi
875	###################################################################
876	if [ "$veget_version" == "false" ] ; then
877	veget_version=orchidee2.0
878	fi
879	cd arch
880	sed -e s:"%COMPILER .*.$":"%COMPILER $compiler":1 \
881	-e s:"%LINK .*.$":"%LINK $compiler":1 \
882	-e s:"%FPP_FLAGS .*.$":"%FPP_FLAGS $fpp_flags":1 \
883	-e s:"%PROD_FFLAGS .*.$":"%PROD_FFLAGS $OPTIM":1 \
884	-e s:"%DEV_FFLAGS .*.$":"%DEV_FFLAGS $OPTDEV":1 \
885	-e s:"%DEBUG_FFLAGS .*.$":"%DEBUG_FFLAGS $OPTDEB":1 \
886	-e s:"%BASE_FFLAGS .*.$":"%BASE_FFLAGS $OPTPREC":1 \
887	-e s:"%BASE_LD .*.$":"%BASE_LD $BASE_LD":1 \
888	-e s:"%ARFLAGS .*.$":"%ARFLAGS $ARFLAGS":1 \
889	arch-gfortran.fcm > arch-local.fcm
890	echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib -lnetcdff -lnetcdf\"" \
891	> arch-local.path
892	echo "NETCDF_INCDIR=${ncdfdir}/include" >> arch-local.path
893	echo "IOIPSL_INCDIR=$ORCHPATH/../../lib" >> arch-local.path
894	echo "IOIPSL_LIBDIR=$ORCHPATH/../../lib" >> arch-local.path
895	echo 'XIOS_INCDIR=${ORCHDIR}/../XIOS/inc' >> arch-local.path
896	echo 'XIOS_LIBDIR="${ORCHDIR}/../XIOS/lib -lxios"' >> arch-local.path
897	cd ../
898
899	echo ./makeorchidee_fcm -j $xios_orchid $opt_orc -parallel none \
900	-arch $arch
901	./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel none \
902	-arch $arch > $orchideelog 2>&1
903	pwd
904	else # of "if [ -d tools ]"
905	if [ -d src_parallel ] ; then
906	liste_src="parallel parameters global stomate sechiba driver"
907	if [ "$veget_version" == "false" ] ; then
908	veget_version=orchidee2.0
909	fi
910	fi
911	for d in $liste_src ; do
912	src_d=src_$d
913	echo src_d $src_d
914	echo ls ; ls
915	if [ ! -d $src_d ] ; then
916	echo Problem orchidee : no $src_d ; exit
917	fi
918	cd $src_d ; \rm -f *.mod make ; $make clean
919	$make > $orchideelog 2>&1
920	if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then
921	cp -f *.mod ../../../lib
922	fi
923	cd ..
924	done
925	fi # of "if [ -d tools ]"
926	echo install_lmdz.sh orchidee_compil_seq_OK `date`
927	fi # of if [ "$veget" != 'NONE' ]
928
929
930	#============================================================================
931	# Ehouarn: the directory name LMDZ* depends on version/tar file...
932	if [ -d $MODEL/modipsl/modeles/LMD* ] ; then
933	echo '###############################################################'
934	echo 'Preparing LMDZ compilation : arch file, svn switch if needed...'
935	echo '###############################################################'
936	cd $MODEL/modipsl/modeles/LMD*
937	LMDZPATH=`pwd`
938	else
939	echo "ERROR: No LMD* directory !!!"
940	exit
941	fi
942
943	###########################################################
944	# For those who want to use fcm to compile via :
945	# makelmdz_fcm -arch local .....
946	############################################################
947
948	if [[ "$pclinux" = "1" && ! -f arch/arch-local.path ]] ; then
949
950	# create local 'arch' files (if on Linux PC):
951	cd arch
952	# arch-local.path file
953	echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib -lnetcdff -lnetcdf\"" \
954	> arch-local.path
955	echo "NETCDF_INCDIR=-I${ncdfdir}/include" >> arch-local.path
956	echo 'NETCDF95_INCDIR=$LMDGCM/../../include' >> arch-local.path
957	echo 'NETCDF95_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
958	echo 'IOIPSL_INCDIR=$LMDGCM/../../lib' >> arch-local.path
959	echo 'IOIPSL_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
960	echo 'XIOS_INCDIR=$LMDGCM/../XIOS/inc' >> arch-local.path
961	echo 'XIOS_LIBDIR=$LMDGCM/../XIOS/lib' >> arch-local.path
962	echo 'ORCH_INCDIR=$LMDGCM/../../lib' >> arch-local.path
963	echo 'ORCH_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
964
965	if [ $pcmac == 1 ] ; then
966	BASE_LD="$BASE_LD -Wl,-rpath,${ncdfdir}/lib"
967	else
968	BASE_LD="$BASE_LD -Wl,-rpath=${ncdfdir}/lib"
969	fi
970	# Arch-local.fcm file (adapted from arch-linux-32bit.fcm)
971
972	if [ $real = r8 ] ; then FPP_DEF=NC_DOUBLE ; else FPP_DEF="" ; fi
973	sed -e s:"%COMPILER .*.$":"%COMPILER $compiler":1 \
974	-e s:"%LINK .*.$":"%LINK $compiler":1 \
975	-e s:"%PROD_FFLAGS .*.$":"%PROD_FFLAGS $OPTIM":1 \
976	-e s:"%DEV_FFLAGS .*.$":"%DEV_FFLAGS $OPTDEV":1 \
977	-e s:"%DEBUG_FFLAGS .*.$":"%DEBUG_FFLAGS $OPTDEB":1 \
978	-e s:"%BASE_FFLAGS .*.$":"%BASE_FFLAGS $OPTPREC":1 \
979	-e s:"%FPP_DEF .*.$":"%FPP_DEF $FPP_DEF":1 \
980	-e s:"%BASE_LD .*.$":"%BASE_LD $BASE_LD":1 \
981	-e s:"%ARFLAGS .*.$":"%ARFLAGS $ARFLAGS":1 \
982	arch-linux-32bit.fcm > arch-local.fcm
983
984	cd ..
985	### Adapt "bld.cfg" (add the shell):
986	#whereisthatshell=$(which ${use_shell})
987	#echo "bld::tool::SHELL $whereisthatshell" >> bld.cfg
988
989	fi # of if [ "$pclinux" = 1 ]
990
991
992	cd $MODEL/modipsl/modeles/LMDZ*
993	lmdzlog=`pwd`/lmdz.log
994
995	##################################################################
996	# Possibly update LMDZ if a specific svn release is requested
997	##################################################################
998
999	set +e ; svn upgrade ; set -e
1000
1001	if [ "$svn" = "last" ] ; then svnopt="" ; else svnopt="-r $svn" ; fi
1002	if [ "$svn" != "" ] ; then
1003	set +e ; svn info \| grep -q 'http:'
1004	if [ $? = 0 ] ; then
1005	svn switch --relocate http://svn.lmd.jussieu.fr/LMDZ \
1006	https://svn.lmd.jussieu.fr/LMDZ
1007	fi
1008	svn update $svnopt
1009	fi
1010	set -e
1011
1012	##################################################################
1013	# Retrieve the final svn release number, and adjust compilation
1014	# options accordingly
1015	mysvn=`svnversion . \| egrep -o "[0-9]+"`
1016
1017	# Option de compilation du rayonnement : depend de $mysvn ><= r4185
1018	opt_rad=""
1019
1020	case $rad in
1021	oldrad) iflag_rrtm=0 ; NSW=2 ; opt_rad="" ;;
1022	rrtm) iflag_rrtm=1 ; NSW=6
1023	if [ $mysvn -le 4185 ] ; then
1024	opt_rad="-rrtm true"
1025	else
1026	opt_rad="-rad rrtm"
1027	fi ;;
1028	ecrad) iflag_rrtm=2 ; NSW=6 ; opt_rad="-rad ecrad" ;;
1029	*) echo Only oldrad rrtm ecrad for rad option ; exit
1030	esac
1031
1032	if [ $mysvn -le 4185 -a $rad = "ecrad" ] ; then
1033	echo "ecrad only available for LMDZ rev starting with 4186 " ; exit
1034	fi
1035
1036	##################################################################
1037
1038
1039	if [[ ! -f libf/misc/netcdf95.F90 && ! -d $MODEL/NetCDF95-0.2 ]]
1040	then
1041	cd $MODEL
1042	myget import/NetCDF95-0.2.tar.gz
1043	tar -xf NetCDF95-0.2.tar.gz
1044	rm NetCDF95-0.2.tar.gz
1045	cd NetCDF95-0.2
1046	mkdir build
1047	cd build
1048	cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=$ncdfdir \
1049	-DCMAKE_INSTALL_PREFIX=$MODEL/modipsl
1050	make install
1051	cd $MODEL/modipsl/modeles/LMDZ*
1052	fi
1053
1054	echo '##################################################################'
1055	echo "Preparing script compile.sh for LMDZ compilation"
1056	echo "It will only be run automatically if bench=1/tuto"
1057	echo Here bench=$bench
1058	echo '##################################################################'
1059
1060	if [ "$env_file" != "" ] ; then
1061	mv arch/arch-${arch}.env arch/arch-${arch}.orig
1062	\cp -f $env_file arch/arch-${arch}.env
1063	fi
1064
1065	if [ $compile_with_fcm = 1 ] ; then
1066	makelmdz="makelmdz_fcm $optim -arch $arch -j 8 "
1067	else
1068	makelmdz="makelmdz $optim -arch $arch"
1069	fi
1070
1071	# sequential compilation
1072	if [ "$sequential" = 1 ] ; then
1073	echo Sequential compilation command, saved in compile.sh:
1074	echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp " \
1075	"-d ${grid_resolution} -v $veget_version gcm "
1076	echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp " \
1077	"-d ${grid_resolution} -v $veget_version gcm " > compile.sh
1078	chmod +x ./compile.sh
1079	if [ $bench = 1 ] ; then
1080	echo install_lmdz.sh start_lmdz_seq_compilation `date`
1081	echo log file: $lmdzlog
1082	./compile.sh > $lmdzlog 2>&1
1083	echo install_lmdz.sh end_lmdz_seq_compilation `date`
1084	fi
1085	fi # fin sequential
1086
1087	# compiling in parallel mode
1088	if [ $parallel != "none" ] ; then
1089	echo '##########################################################'
1090	echo ' Parallel compile '
1091	echo '##########################################################'
1092	echo "(after saving the sequential libs and binaries)"
1093	cd $MODEL/modipsl
1094	tar cf sequential.tar bin/ lib/
1095	\rm -rf bin/ lib/
1096	tar xf ioipsl.tar
1097	#
1098	# Orchidee
1099	#
1100	cd $ORCHPATH
1101	if [ -d src_parallel -a $veget != 'NONE' ] ; then
1102	cd arch
1103	sed \
1104	-e s:"%COMPILER.*.$":"%COMPILER $par_comp":1 \
1105	-e s:"%LINK.*.$":"%LINK $par_comp":1 \
1106	-e s:"%MPI_FFLAG.*.$":"%MPI_FFLAGS $MPI_FLAGS":1 \
1107	-e s:"%OMP_FFLAG.*.$":"%OMP_FFLAGS $OMP_FLAGS":1 \
1108	-e s:"%MPI_LD.*.$":"%MPI_LD $MPI_LD":1 \
1109	-e s:"%OMP_LD.*.$":"%OMP_LD $OMP_LD":1 \
1110	arch-local.fcm > tmp.fcm
1111
1112	mv tmp.fcm arch-local.fcm
1113	cd ../
1114	echo Compiling ORCHIDEE in parallel mode `date`
1115	echo logfile $orchideelog
1116	echo "NOTE : to recompile it when necessary, use ./compile_orc.sh " \
1117	"in modipsl/modeles/ORCHIDEE"
1118	echo ./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc \
1119	-parallel $parallel -arch $arch > compile_orc.sh
1120	echo ./makeorchidee_fcm -j 8 $xios_orchid $opt_orc \
1121	-parallel $parallel -arch $arch >> compile_orc.sh
1122	echo echo Now you must also recompile LMDZ, by running ./compile.sh \
1123	in modeles/LMDZ >> compile_orc.sh
1124	chmod u+x compile_orc.sh
1125	./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc \
1126	-parallel $parallel -arch $arch > $orchideelog 2>&1
1127	./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel $parallel \
1128	-arch $arch >> $orchideelog 2>&1
1129	echo End of ORCHIDEE compilation in parallel mode `date`
1130	elif [ $veget != 'NONE' ] ; then
1131	echo '##########################################################'
1132	echo ' Orchidee version too old '
1133	echo ' Please update to new version '
1134	echo '##########################################################'
1135	exit
1136	fi # of [ -d src_parallel -a $veget != 'NONE' ]
1137
1138	# LMDZ
1139	cd $LMDZPATH
1140	if [ $arch = local ] ; then
1141	cd arch
1142	sed -e s:"%COMPILER.*.$":"%COMPILER $par_comp":1 \
1143	-e s:"%LINK.*.$":"%LINK $par_comp":1 \
1144	-e s:"%MPI_FFLAG.*.$":"%MPI_FFLAGS $MPI_FLAGS":1 \
1145	-e s:"%OMP_FFLAG.*.$":"%OMP_FFLAGS $OMP_FLAGS":1 \
1146	-e s:"%ARFLAGS.*.$":"%ARFLAGS $ARFLAGS":1 \
1147	-e s@"%BASE_LD.*.$"@"%BASE_LD -Wl,-rpath=${root_mpi}/lib:${ncdfdir}/lib"@1 \
1148	-e s:"%MPI_LD.*.$":"%MPI_LD $MPI_LD":1 \
1149	-e s:"%OMP_LD.*.$":"%OMP_LD $OMP_LD":1 \
1150	arch-local.fcm > tmp.fcm
1151	mv tmp.fcm arch-local.fcm
1152	cd ../
1153	fi
1154	rm -f compile.sh
1155	echo resol=${grid_resolution} >> compile.sh
1156	if [ ${hostname:0:5} = jean- -a "$cosp" = "v2" ] ; then
1157
1158	echo LMDZ compilation command in parallel mode, saved in compile.sh, \
1159	is :
1160	echo "(ATTENTION le probleme de cospv2 sur jean-zay en mode prod " \
1161	"n est pas corrige ! )"
1162	# ATTENTION le probleme de cospv2 sur jean-zay en mode prod n
1163	# est pas corrige
1164	echo ./$makelmdz -dev $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
1165	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
1166	-parallel $parallel gcm >> compile.sh
1167	echo ./$makelmdz -dev $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
1168	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
1169	-parallel $parallel gcm
1170	else
1171	echo ./$makelmdz $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
1172	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
1173	-parallel $parallel gcm >> compile.sh
1174	echo ./$makelmdz $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
1175	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
1176	-parallel $parallel gcm
1177	fi
1178	chmod +x ./compile.sh
1179
1180	if [ $bench = 1 ] ; then
1181	echo Compiling LMDZ in parallel mode `date`, LMDZ log file: $lmdzlog
1182	./compile.sh > $lmdzlog 2>&1
1183	fi
1184
1185	fi # of if [ $parallel != "none" ]
1186
1187
1188	##################################################################
1189	# Verification du succes de la compilation
1190	##################################################################
1191
1192	# Recherche de l'executable dont le nom a change au fil du temps ...
1193	# suffix contains radiative option starting with revision 4186
1194	if [ $mysvn -ge 4186 ] ; then suff_exe=_${rad}${suff_exe} ; fi
1195	gcm=""
1196
1197	for exe in gcm.e bin/gcm_${grid_resolution}_phylmd${suff_exe}${suff_orc}.e
1198	do
1199	if [ -f $exe ] ; then gcm=$exe ; fi
1200	done
1201
1202	if [ "$gcm" = "" ] ; then
1203	if [ $bench = 1 ] ; then
1204	echo 'Compilation failed !! Cannot run the benchmark;'
1205	exit
1206	else
1207	echo 'Compilation not done (only done when bench=1)'
1208	fi
1209	else
1210	echo '##########################################################'
1211	echo 'Compilation successfull !! ' `date`
1212	echo '##########################################################'
1213	echo The executable is $gcm
1214	fi
1215
1216	##################################################################
1217	# Below, we run a benchmark if bench=1 or tuto
1218	##################################################################
1219
1220	if [ $bench = tuto ] ; then
1221	myget Training/tutorial.tar ; tar xvf tutorial.tar ; cd TUTORIAL
1222	./init.sh
1223
1224	elif [[ $bench = 1 && ! -d BENCH${grid_resolution} ]] ; then
1225	# TOUTE CETTE SECTION DEVRAIT DISPARAITRE POUR UNE COMMANDE
1226	# OU DES BENCHS PAR MOTS CLES COMME tuto
1227
1228	echo '##########################################################'
1229	echo ' Running a test run '
1230	echo '##########################################################'
1231
1232	\rm -rf BENCH${grid_resolution}
1233	bench=bench_lmdz_${grid_resolution}
1234	echo install_lmdz.sh before bench download `date`
1235	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/$bench.tar.gz
1236	myget 3DBenchs/$bench.tar.gz
1237	echo install_lmdz.sh after bench download `date`
1238	tar xvf $bench.tar.gz
1239
1240	if [ "$cosp" = "v1" -o "$cosp" = "v2" ] ; then
1241	cd BENCH${grid_resolution}
1242	# copier les fichiers namelist input et output our COSP
1243	cp ../DefLists/cosp*_input_nl.txt .
1244	cp ../DefLists/cosp*_output_nl.txt .
1245	# Activer la cles ok_cosp pour tourner avec COSP
1246	sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp
1247	\mv -f tmp config.def
1248	cd ..
1249	fi
1250
1251	if [ -n "$physiq" ]; then
1252	cd BENCH${grid_resolution}
1253	if [ -f physiq.def_${physiq} ]; then
1254	cp physiq.def_${physiq} physiq.def
1255	echo using physiq.def_${physiq}
1256	else
1257	echo using standard physiq.def
1258	fi
1259	cd ..
1260	else
1261	echo using standard physiq.def
1262	fi
1263
1264	if [ "$with_xios" = "y" ] ; then
1265	cd BENCH${grid_resolution}
1266	cp ../DefLists/iodef.xml .
1267	cp ../DefLists/context_lmdz.xml .
1268	cp ../DefLists/field_def_lmdz.xml .
1269	# A raffiner par la suite
1270	echo A FAIRE : Copier les *xml en fonction de l option cosp
1271	cp ../DefLists/field_def_cosp*.xml .
1272	cp ../DefLists/file_def_hist*xml .
1273	# adapt iodef.xml to use attached mode
1274	sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' \
1275	iodef.xml > tmp
1276	\mv -f tmp iodef.xml
1277
1278	# and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
1279	# except for histday
1280	for histfile in file_def_hist*xml
1281	do
1282	if [ "$histfile" = "file_def_histday_lmdz.xml" ] ; then
1283	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' \
1284	$histfile > tmp
1285	\mv -f tmp $histfile
1286	sed -e 's@output_level="_AUTO_"@output_level="5"@' $histfile \
1287	> tmp
1288	\mv -f tmp $histfile
1289	sed -e 's@compression_level="2"@compression_level="0"@' \
1290	$histfile > tmp
1291	\mv -f tmp $histfile
1292	else
1293	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
1294	$histfile > tmp
1295	\mv -f tmp $histfile
1296	fi
1297	done
1298	# and add option "ok_all_xml=y" in config.def
1299	echo "### XIOS outputs" >> config.def
1300	echo 'ok_all_xml=.true.' >> config.def
1301
1302	#activer les sorties pour Cosp
1303	if [ "$cosp" = "v1" ] ; then
1304	histfile=file_def_histdayCOSP_lmdz.xml
1305	sed -e 's@enabled=".FALSE."@enabled=".TRUE."@' $histfile > tmp
1306	\mv -f tmp $histfile
1307	sed -e 's@output_level="_AUTO_"@output_level="5"@' $histfile > tmp
1308	\mv -f tmp $histfile
1309	sed -e 's@compression_level="2"@compression_level="0"@' \
1310	$histfile > tmp
1311	\mv -f tmp $histfile
1312	fi
1313	if [ "$cosp" = "v2" ] ; then
1314	histfile=file_def_histdayCOSPv2_lmdz.xml
1315	sed -e 's@compression_level="2"@compression_level="0"@' \
1316	$histfile > tmp
1317	\mv -f tmp $histfile
1318	contextfile=context_lmdz.xml
1319	sed -e 's@src="./file_def_histdayCOSP_lmdz.xml"@src="./file_def_histdayCOSPv2_lmdz.xml"@' \
1320	$contextfile > tmp
1321	\mv -f tmp $contextfile
1322	sed -e 's@src="./file_def_histmthCOSP_lmdz.xml"@src="./file_def_histmthCOSPv2_lmdz.xml"@' \
1323	$contextfile > tmp
1324	\mv -f tmp $contextfile
1325	sed -e 's@src="./file_def_histhfCOSP_lmdz.xml"@src="./file_def_histhfCOSPv2_lmdz.xml"@' \
1326	$contextfile > tmp
1327	\mv -f tmp $contextfile
1328	fieldfile=field_def_lmdz.xml
1329	sed -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' $fieldfile \
1330	> tmp
1331	\mv -f tmp $fieldfile
1332	fi
1333
1334	cd ..
1335	fi
1336
1337	# Cas Bensh avec ecrad
1338	if [ "$rad" = "ecrad" ] ; then
1339	cd BENCH${grid_resolution}
1340	cp ../DefLists/namelist_ecrad .
1341	cp -r ../libf/phylmd/ecrad/data .
1342	cd ..
1343	fi
1344
1345	# Adjusting bench physiq.def to radiative code chosen
1346	cd BENCH${grid_resolution}
1347	sed -e 's/iflag_rrtm=.*.$/iflag_rrtm='$iflag_rrtm'/' \
1348	-e 's/NSW=.*.$/NSW='$NSW'/' physiq.def > tmpdef
1349	\mv tmpdef physiq.def
1350	cd ..
1351
1352	cp $gcm BENCH${grid_resolution}/gcm.e
1353
1354	cd BENCH${grid_resolution}
1355	# On cree le fichier bench.sh au besoin
1356	# Dans le cas 48x36x39 le bench.sh existe deja en parallele
1357
1358	if [ "$grid_resolution" = "48x36x39" ] ; then
1359	echo On ne touche pas au bench.sh
1360	# But we have to adapt "run_local.sh" for $mpirun
1361	sed -e "s@mpirun@$mpirun@g" run_local.sh > tmp
1362	mv -f tmp run_local.sh
1363	chmod u=rwx run_local.sh
1364	elif [ "${parallel:0:3}" = "mpi" ] ; then
1365	# Lancement avec deux procs mpi et 2 openMP
1366	echo "export OMP_STACKSIZE=800M" > bench.sh
1367	if [ "${parallel:4:3}" = "omp" ] ; then
1368	echo "export OMP_NUM_THREADS=2" >> bench.sh
1369	fi
1370	if [ "$cosp" = "v1" -o "$cosp" = "v2" ] ; then
1371	if [ ${hostname:0:5} = jean- ] ; then
1372	chmod +x ../arch.env
1373	../arch.env
1374	echo "ulimit -s 2000000" >> bench.sh
1375	else
1376	echo "ulimit -s 200000" >> bench.sh
1377	fi
1378	else
1379	echo "ulimit -s unlimited" >> bench.sh
1380	fi
1381	if [ ${hostname:0:5} = jean- ] ; then
1382	. ../arch/arch-${arch}.env
1383	echo "srun -n 2 -A $idris_acct@cpu gcm.e > listing 2>&1" \
1384	>> bench.sh
1385	else
1386	echo "$mpirun -np 2 gcm.e > listing 2>&1" >> bench.sh
1387	fi
1388	# Add rebuild, using reb.sh if it is there
1389	echo 'if [ -f reb.sh ] ; then' >> bench.sh
1390	echo ' ./reb.sh histday ; ./reb.sh histmth ; ./reb.sh histhf ; ' \
1391	'./reb.sh histins ; ./reb.sh stomate_history ; ' \
1392	'./reb.sh sechiba_history ; ./reb.sh sechiba_out_2 ' >> bench.sh
1393	echo 'fi' >> bench.sh
1394	else
1395	echo "./gcm.e > listing 2>&1" > bench.sh
1396	fi
1397	# Getting orchidee stuff
1398	if [ $veget == 'CMIP6' ] ; then
1399	#echo 'myget 3DBenchs/BENCHorch11.tar.gz'
1400	#myget 3DBenchs/BENCHorch11.tar.gz
1401	#tar xvzf BENCHorch11.tar.gz
1402	echo 'myget 3DBenchs/BENCHCMIP6.tar.gz'
1403	myget 3DBenchs/BENCHCMIP6.tar.gz
1404	tar xvzf BENCHCMIP6.tar.gz
1405	sed -e "s:VEGET=n:VEGET=y:" config.def > tmp
1406	mv -f tmp config.def
1407	if [ "$with_xios" = "y" ] ; then
1408	cp ../../ORCHIDEE/src_xml/context_orchidee.xml .
1409	echo '<context id="orchidee" src="./context_orchidee.xml"/>' \
1410	> add.tmp
1411	cp ../../ORCHIDEE/src_xml/field_def_orchidee.xml .
1412	cp ../../ORCHIDEE/src_xml/file_def_orchidee.xml .
1413	cp ../../ORCHIDEE/src_xml/file_def_input_orchidee.xml .
1414	if [ -f ../../ORCHIDEE/src_xml/context_input_orchidee.xml ] ; then
1415	cp ../../ORCHIDEE/src_xml/context_input_orchidee.xml .
1416	echo '<context id="orchidee" ' \
1417	'src="./context_input_orchidee.xml"/>' >> add.tmp
1418	fi
1419	sed -e '/id="LMDZ"/r add.tmp' iodef.xml > tmp
1420	mv tmp iodef.xml
1421	sed -e'{/sechiba1/ s/enabled="_AUTO_"/type="one_file" enabled=".TRUE."/}' \
1422	file_def_orchidee.xml > tmp
1423	\mv -f tmp file_def_orchidee.xml
1424	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
1425	file_def_orchidee.xml > tmp
1426	\mv -f tmp file_def_orchidee.xml
1427	sed -e 's@output_level="_AUTO_"@output_level="1"@' \
1428	file_def_orchidee.xml > tmp
1429	\mv -f tmp file_def_orchidee.xml
1430	sed -e 's@output_freq="_AUTO_"@output_freq="1d"@' \
1431	file_def_orchidee.xml > tmp
1432	\mv -f tmp file_def_orchidee.xml
1433	sed -e 's@compression_level="4"@compression_level="0"@' \
1434	file_def_orchidee.xml > tmp
1435	\mv -f tmp file_def_orchidee.xml
1436	sed -e 's@XIOS_ORCHIDEE_OK = n@XIOS_ORCHIDEE_OK = y@' \
1437	orchidee.def > tmp
1438	\mv -f tmp orchidee.def
1439	fi
1440	fi
1441	echo EXECUTION DU BENCH
1442	set +e
1443	date ; ./bench.sh > out.bench 2>&1 ; date
1444	set -e
1445	tail listing
1446
1447
1448	echo '##########################################################'
1449	echo 'Simulation finished in' `pwd`
1450	echo 'You have compiled with:'
1451	cat ../compile.sh
1452	if [ $parallel = "none" ] ; then
1453	echo 'You may re-run it with : cd ' `pwd` ' ; gcm.e'
1454	echo 'or ./bench.sh'
1455	else
1456	echo 'You may re-run it with : '
1457	echo 'cd ' `pwd` '; ./bench.sh'
1458	# echo 'ulimit -s unlimited'
1459	# echo 'export OMP_NUM_THREADS=2'
1460	# echo 'export OMP_STACKSIZE=800M'
1461	# echo "$mpirun -np 2 gcm.e "
1462	fi
1463	echo '##########################################################'
1464
1465	fi # bench
1466
1467
1468	#################################################################
1469	# Installation eventuelle du 1D
1470	#################################################################
1471
1472	if [ $SCM = 1 ] ; then
1473	cd $MODEL
1474	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/1D.tar.gz
1475	myget 1D/1D.tar.gz
1476	tar xvf 1D.tar.gz
1477	cd 1D
1478	./run.sh -rad $rad
1479	fi
1480	#set -vx
1481
1482	#################################################################
1483	# sauvegarde des options veget pour utilisation eventuelle tutorial_prod
1484	#################################################################
1485	cd $MODEL/modipsl/modeles
1486	#echo surface_env file created in $MODEL
1487	echo 'veget='$veget > surface_env
1488	#opt_veget="-v $veget_version"
1489	#echo 'opt_veget="'$opt_veget\" >> surface_env
1490	echo 'opt_veget="'-v $veget_version\" >> surface_env
1491	echo 'orchidee_rev='$orchidee_rev >> surface_env
1492	echo 'suforch='$suff_orc >> surface_env

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