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source: BOL/script_install/install_lmdz_new.sh @ 4217

Last change on this file since 4217 was 4217, checked in by lguez, 2 years ago
Bug fix: correct the name of NetCDF directory
Property svn:executable set to ``*
File size: 49.0 KB

Line
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 input-outputs
22	# 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 ; cp -r `basename $1` $dir
59	fi
60	fi
61	}
62
63	# 04_2021 : tester si r4 marche encore !
64	#real=r4
65	real=r8
66
67
68	#########################################################################
69	# Valeur par défaut des parametres
70	#########################################################################
71	svn=""
72	#version=trunk
73	version=20220131.trunk
74
75	getlmdzor=1
76	netcdf=0 # 1: for automatic installation;
77	# or 0: do not install NetCDF and look for it in standard locations;
78	# or absolute path: look for NetCDF there
79	check_linux=1
80	ioipsl=1
81	bench=1
82	pclinux=1
83	pcmac=0 # default: not on a Mac
84	compiler=gfortran
85	SCM=0
86	# surface/vegetation scheme treatment
87	# controlled by the single variable veget which can have the following values
88	# - NONE: bucket scheme (default)
89	# - CMIP6: orchidee version used in CMIP exercise, rev 5661
90	# - number: orchidee version number
91	veget=NONE
92	# choose the resolution for the bench runs
93	# grid_resolution= 32x24x11 or 48x36x19 for tests (test without ORCHIDEE)
94	# 96x71x19 standard configuration
95	grid_resolution=144x142x79
96	grid_resolution=96x95x39
97	grid_resolution=48x36x19
98	grid_resolution=32x32x39
99	# choose the physiq version you want to test
100	#physiq=NPv6.0.14splith
101	physiq=
102
103	## parallel can take the values none/mpi/omp/mpi_omp
104	parallel=mpi_omp
105	parallel=none
106	idris_acct=lmd
107	OPT_GPROF=""
108	OPT_MAKELMDZ=""
109	MODEL=""
110
111	## also compile XIOS? (and more recent NetCDF/HDF5 libraries) Default=no
112	with_xios="n"
113	opt_makelmdz_xios=""
114
115	## compile with oldrad/rrtm/ecrad radiatif code (Default=rrtm)
116	rad=rrtm
117
118	## compile_with_fcm=1 : use makelmdz_fcm (1) or makelmdz (0)
119	compile_with_fcm=1
120
121	#Compilation with Cosp (cosp=NONE/v1/v2 ; default=NONE)
122	cosp=NONE
123	opt_cosp=""
124
125	# Check if on a Mac
126	if [ `uname` = "Darwin" ]
127	then
128	pcmac=1
129	export MAKE=make
130	fi
131	#echo "pcmac="$pcmac
132
133	env_file=""
134
135	#########################################################################
136	# Options interactives
137	#########################################################################
138	while (($# > 0))
139	do
140	case $1 in
141	"-h") cat <<........fin
142	$0 [ -v version ] [ -r svn_release ]
143	[ -parallel PARA ] [ -d GRID_RESOLUTION ] [ -bench 0/1 ]
144	[-name LOCAL_MODEL_NAME] [-gprof] [-opt_makelmdz] [-rad RADIATIF]
145
146	-v "version" like 20150828.trunk
147	see http://www.lmd.jussieu.fr/~lmdz/Distrib/LISMOI.trunk
148
149	-r "svn_release" : either the svn release number or "last"
150
151	-compiler gfortran\|ifort\|pgf90 (default: gfortran)
152
153	-parallel PARA : can be mpi_omp (mpi with openMP) or none (for sequential)
154
155	-d GRID_RESOLUTION should be among the available benchs if -bench 1
156	among which : 48x36x19, 48x36x39
157	if wanting to run a bench simulation in addition to compilation
158	default : 48x36x19
159
160	-bench activating the bench or not (0/1). Default 1
161
162	-name LOCAL_MODEL_NAME : default = LMDZversion.release
163
164	-netcdf 0, 1 or PATH
165	0: do not download NetCDF, look for it in standard locations
166	1: download and compile NetCDF
167	PATH: full path to an existing installed NetCDF library
168
169	-xios also download and compile the XIOS library
170	(requires the NetCDF4-HDF5 library, also installed by default)
171	(requires to also have -parallel mpi_omp)
172
173	-gprof to compile with -pg to enable profiling with gprof
174
175	-cosp to run without our with cospv1 or cospv2 [none/v1/v2]
176
177	-rad RADIATIF can be oldrad, rrtm or ecrad radiatif code
178
179	-nofcm to compile without fcm
180
181	-SCM install 1D version automatically
182
183	-debug compile everything in debug mode
184
185	-opt_makelmdz to call makelmdz or makelmdz_fcm with additional options
186
187	-physiq to choose which physics package to use
188
189	-env_file specify an arch.env file to overwrite the existing one
190
191	-veget surface model to run [NONE/CMIP6/xxxx]
192
193	........fin
194	exit ;;
195	"-v") version=$2 ; shift ; shift ;;
196	"-r") svn=$2 ; shift ; shift ;;
197	"-compiler") compiler=$2
198	case $compiler in
199	"gfortran"\|"ifort"\|"pgf90") compiler=$2 ; shift ; shift ;;
200	*) echo "Only gfortran , ifort or pgf90 for the compiler option" ; exit
201	esac ;;
202	"-d") grid_resolution=$2 ; shift ; shift ;;
203	"-gprof") OPT_GPROF="-pg" ; shift ;;
204	"-cosp") cosp=$2
205	case $cosp in
206	"none"\|"v1"\|"v2") cosp=$2 ; shift ; shift ;;
207	*) echo Only none v1 v2 for cosp option ; exit
208	esac ;;
209	"-nofcm") compile_with_fcm=0 ; shift ;;
210	"-SCM") SCM=1 ; shift ;;
211	"-opt_makelmdz") OPT_MAKELMDZ="$2" ; shift ; shift ;;
212	"-rrtm") rrtm="$2" ; if [ "$2" = "false" ] ; then rad="oldrad" ; else rad="rrtm" ; fi ; shift ; shift ;;
213	"-rad") rad=$2
214	case $rad in
215	"oldrad"\|"rrtm"\|"ecrad") rad=$2 ; shift ; shift ;;
216	*) echo Only oldrad rrtm ecrad for rad option ; exit
217	esac ;;
218	"-parallel") parallel=$2
219	case $parallel in
220	"none"\|"mpi"\|"omp"\|"mpi_omp") parallel=$2 ; shift ; shift ;;
221	*) echo Only none mpi omp mpi_omp for the parallel option ; exit
222	esac ;;
223	"-bench") bench=$2 ; shift ; shift ;;
224	"-debug") optim=-debug ; shift ;;
225	"-name") MODEL=$2 ; shift ; shift ;;
226	"-netcdf") netcdf=$2 ; shift ; shift ;;
227	"-physiq") physiq=$2 ; shift ; shift ;;
228	"-xios") with_xios="y" ; shift ;;
229	"-env_file") env_file=$2 ; shift ; shift ;;
230	"-veget") veget=$2 ; shift ; shift ;;
231	*) ./install_lmdz.sh -h ; exit
232	esac
233	done
234
235	# Option de compilation du rayonnement : depend de $mysvn ><= r4185, sera donc definie plus bas
236	#opt_rad=""
237	#case $rad in
238	# rrtm) opt_rad="-rad rrtm" ;;
239	# ecrad) opt_rad="-rad ecrad" ;;
240	#esac
241
242
243	# Option de compilation pour Cosp
244	opt_cosp=""
245	case cosp in
246	v1) opt_cosp="-cosp true" ;;
247	v2) opt_cosp="-cospv2 true" ;;
248	esac
249
250	# Check on veget version
251	#if [ "$veget" != 'NONE' -a "$veget" != "CMIP6" -a "$veget" != +([0-9]) ] ; then
252	if [ $veget != 'NONE' -a $veget != "CMIP6" ] ; then
253	re='^[0-9]+$'
254	if ! [[ $veget =~ $re ]] ; then
255	echo 'Valeur de l option veget non valable'
256	exit
257	fi
258	fi
259
260	#Define veget-related suffix for gcm name
261	if [ "$veget" = 'NONE' ] ; then
262	suff_orc=''
263	#For use with tutorial, orchidee_rev is also defined (will be written in surface_env at the end of the script)
264	orchidee_rev=''
265	else
266	suff_orc='_orch'
267	fi
268
269
270	if [ $parallel = none ] ; then sequential=1; suff_exe='_seq' ; else sequential=0; suff_exe='_para_mem' ; fi
271
272	#Chemin pour placer le modele
273	if [ "$MODEL" = "" ] ; then MODEL=./LMDZ$version$svn$optim ; fi
274
275
276	arch=local
277
278
279	if [ $compiler = g95 ] ; then echo g95 is not supported anymore ; exit ; fi
280
281	################################################################
282	# Specificite des machines
283	################################################################
284
285	hostname=`hostname`
286	if [ "$pclinux" = 1 ] ; then o_ins_make="-t g95" ; else o_ins_make="" ; fi
287
288	case ${hostname:0:5} in
289
290	jean-) compiler="mpiifort" ;
291	par_comp="mpiifort" ;
292	o_ins_make="-t jeanzay" ;
293	make=gmake ;
294	module purge
295	module load intel-compilers/19.0.4 ;
296	#module load intel-mpi/19.0.4 ;
297	#module load intel-mkl/19.0.4 ;
298	module load hdf5/1.10.5-mpi ;
299	module load netcdf/4.7.2-mpi ;
300	module load netcdf-fortran/4.5.2-mpi ;
301	module load subversion/1.9.7 ;
302	export NETCDF_LIBDIR=./
303	export NETCDFFORTRAN_INCDIR=./
304	export NETCDFFORTRAN_LIBDIR=./
305	arch=X64_JEANZAY ;;
306
307	cicla\|camel) compiler="gfortran" ;
308	module load netcdf4/4.3.3.1-gfortran;
309	netcdf=/opt/netcdf43/gfortran
310
311	if [ $parallel != none ] ; then
312	module load openmpi/1.6.5-gfortran ;
313	root_mpi=$MPI_HOME ;
314	path_mpi=$root_mpi/bin ;
315	par_comp=${path_mpi}/mpif90 ;
316	mpirun=${path_mpi}/mpirun ;
317	fi ;
318	arch=local ;
319	make=make ;
320	o_ins_make="-t g95" ;;
321
322	*) if [ $parallel = none -o -f /usr/bin/mpif90 ] ; then
323	path_mpi=`which mpif90 \| sed -e s:/mpif90::` ;
324	if [ -d /usr/lib64/openmpi ] ; then
325	root_mpi="/usr/lib64/openmpi"
326	else
327	root_mpi="/usr"
328	fi
329	else
330	echo "Cannot find mpif90" ;
331	if [ $parallel = none ] ; then exit ; fi ;
332	fi ;
333	if [ $parallel != none ] ; then
334	root_mpi=$(which mpif90 \| sed -e s:/bin/mpif90::)
335	path_mpi=$(which mpif90 \| sed -e s:/mpif90::)
336	export LD_LIBRARY_PATH=${root_mpi}/lib:$LD_LIBRARY_PATH
337	fi
338	par_comp=${path_mpi}/mpif90 ;
339	mpirun=${path_mpi}/mpirun ;
340	arch=local ;
341	make=make ;
342	o_ins_make="-t g95"
343	esac
344
345	# Flags for parallelism:
346	if [ $parallel != none ] ; then
347	# MPI_LD are the flags needed for linking with MPI
348	MPI_LD="-L${root_mpi}/lib -lmpi"
349	if [ "$compiler" = "gfortran" ] ; then
350	# MPI_FLAGS are the flags needed for compilation with MPI
351	MPI_FLAGS="-fcray-pointer"
352	# OMP_FLAGS are the flags needed for compilation with OpenMP
353	OMP_FLAGS="-fopenmp -fcray-pointer"
354	# OMP_LD are the flags needed for linking with OpenMP
355	OMP_LD="-fopenmp"
356	elif [ "$compiler" = "ifort" ] ; then
357	MPI_FLAGS=""
358	OMP_FLAGS="-openmp"
359	OMP_LD="-openmp"
360	else # pgf90
361	MPI_FLAGS=""
362	OMP_FLAGS="-mp"
363	OMP_LD="-mp"
364	fi
365	fi
366
367	#####################################################################
368	# Test for old gfortran compilers
369	# If the compiler is too old (older than 4.3.x) we test if the
370	# temporary gfortran44 patch is available on the computer in which
371	# case the compiler is changed from gfortran to gfortran44
372	# Must be aware than parallelism can not be activated in this case
373	#####################################################################
374
375	if [ "$compiler" = "gfortran" ] ; then
376	gfortran=gfortran
377	gfortranv=`gfortran --version \| \
378	head -1 \| awk ' { print $NF } ' \| awk -F. ' { print $1 * 10 + $2 } '`
379	if [ $gfortranv -le 43 ] ; then
380	echo ERROR : Your gfortran compiler is too old
381	echo 'Please choose a new one (ifort) and change the line'
382	echo compiler=xxx
383	echo in the install_lmdz.sh script and rerun it
384	if [ `which gfortran44 \| wc -w` -ne 0 ] ; then
385	gfortran=gfortran44
386	else
387	echo gfotran trop vieux ; exit
388	fi
389	fi
390	compiler=$gfortran
391	fi
392	#####################################################################
393
394	## if also compiling XIOS, parallel must be mpi_omp
395	if [ "$with_xios" = "y" -a "$parallel" != "mpi_omp" ] ; then
396	echo "Error, you must set -parallel mpi_omp if you want XIOS"
397	exit
398	fi
399
400	if [ "$with_xios" = "y" ] ; then
401	opt_makelmdz_xios="-io xios"
402	fi
403
404	if [ "$cosp" = "v2" -a "$with_xios" = "n" ] ; then
405	echo "Error, Cospv2 cannot run without Xios"
406	exit
407	fi
408
409	echo '################################################################'
410	echo Choix des options de compilation
411	echo '################################################################'
412
413	export FC=$compiler
414	export F90=$compiler
415	export F77=$compiler
416	export CPPFLAGS=
417	OPTIMNC=$OPTIM
418	BASE_LD="$OPT_GPROF"
419	OPTPREC="$OPT_GPROF"
420	ARFLAGS="rs" ; if [ -f /etc/issue ] ; then if [ "`grep -i ubuntu /etc/issue`" != "" ] ; then if [ "`grep -i ubuntu /etc/issue \| awk ' { print $2 } ' \| cut -d. -f1`" -ge 16 ] ; then ARFLAGS="rU" ; fi ; fi ; fi
421
422
423
424	if [ "$compiler" = "$gfortran" ] ; then
425	OPTIM='-O3'
426	OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all -fbacktrace -finit-real=snan"
427	OPTDEV="-Wall -fbounds-check"
428	fmod='I '
429	OPTPREC="$OPTPREC -cpp -ffree-line-length-0"
430	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE" ; fi
431	export F90FLAGS=" -ffree-form $OPTIMNC"
432	export FFLAGS=" $OPTIMNC"
433	export CC=gcc
434	export CXX=g++
435	export fpp_flags="-P -C -traditional -ffreestanding"
436
437	elif [ $compiler = mpif90 ] ; then
438	OPTIM='-O3'
439	OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all"
440	OPTDEV="-Wall -fbounds-check"
441	BASE_LD="$BASE_LD -lblas"
442	fmod='I '
443	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE -fcray-pointer" ; fi
444	export F90FLAGS=" -ffree-form $OPTIMNC"
445	export FFLAGS=" $OPTIMNC"
446	export CC=gcc
447	export CXX=g++
448
449	elif [ $compiler = pgf90 ] ; then
450	OPTIM='-O2 -Mipa -Munroll -Mnoframe -Mautoinline -Mcache_align'
451	OPTDEB='-g -Mdclchk -Mbounds -Mchkfpstk -Mchkptr -Minform=inform -Mstandard -Ktrap=fp -traceback'
452	OPTDEV='-g -Mbounds -Ktrap=fp -traceback'
453	fmod='module '
454	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -r8 -DNC_DOUBLE" ; fi
455	export CPPFLAGS="-DpgiFortran"
456	export CC=pgcc
457	export CFLAGS="-O2 -Msignextend"
458	export CXX=pgCC
459	export CXXFLAGS="-O2 -Msignextend"
460	export FFLAGS="-O2 $OPTIMNC"
461	export F90FLAGS="-O2 $OPTIMNC"
462	compile_with_fcm=1
463
464	elif [ $compiler = ifort ] ; then
465	OPTIM="-O2 -fp-model strict -ip -align all "
466	OPTDEV="-p -g -O2 -traceback -fp-stack-check -ftrapuv -check"
467	OPTDEB="-g -no-ftz -traceback -ftrapuv -fp-stack-check -check"
468	fmod='module '
469	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -real-size 64 -DNC_DOUBLE" ; fi
470	export CPP="icc -E"
471	export FFLAGS="-O2 -ip -fpic -mcmodel=large"
472	export FCFLAGS="-O2 -ip -fpic -mcmodel=large"
473	export CC=icc
474	export CFLAGS="-O2 -ip -fpic -mcmodel=large"
475	export CXX=icpc
476	export CXXFLAGS="-O2 -ip -fpic -mcmodel=large"
477	export fpp_flags="-P -traditional"
478	# Pourquoi forcer la compilation fcm. Marche mieux sans
479	#compile_with_fcm=1
480
481	elif [ $compiler = mpiifort ] ; then
482	echo on ne fait rien la
483	# Pourquoi forcer la compilation fcm. Marche mieux sans
484	#compile_with_fcm=1
485
486	else
487	echo unexpected compiler $compiler ; exit
488	fi
489
490	OPTIMGCM="$OPTIM $OPTPREC"
491
492	hostname=`hostname`
493
494	##########################################################################
495	# If installing on known machines such as Jean-Zay at IDRIS,
496	# don't check for available software and don't install netcdf
497	if [ ${hostname:0:5} = jean- ] ; then
498	netcdf=0 # no need to recompile netcdf, alreday available
499	check_linux=0
500	pclinux=0
501	ioipsl=0 # no need to recompile ioipsl, already available
502	#netcdf="/smplocal/pub/NetCDF/4.1.3"
503	compiler="mpiifort"
504	fmod='module '
505	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -i4 -r8 -DNC_DOUBLE" ; fi
506	OPTIM="-auto -align all -O2 -fp-model strict -xHost "
507	OPTIMGCM="$OPTIM $OPTPREC"
508	fi
509	##########################################################################
510
511
512	mkdir -p $MODEL
513	echo $MODEL
514	MODEL=`( cd $MODEL ; pwd )` # to get absolute path, if necessary
515
516
517	echo '################################################################'
518	if [ "$check_linux" = 1 ] ; then
519	echo Check if required software is available
520	echo '################################################################'
521
522	#### Ehouarn: test if the required shell is available
523	#### Maj FH-LF-AS 2021-04 : default=bash ; if bash missing, use ksh
524	use_shell="bash" # default
525	if [ "`which bash`" = "" ] ; then
526	echo "no bash ; we will use ksh"
527	use_shell="ksh"
528	if [ "`which ksh`" = "" ] ; then
529	echo "bash (or ksh) needed!! Install it!"
530	exit
531	fi
532	fi
533
534	for logiciel in wget tar gzip make $compiler gcc cmake ; do
535	if [ "`which $logiciel`" = "" ] ; then
536	echo You must first install $logiciel on your system
537	exit
538	fi
539	done
540
541	if [ $pclinux = 1 ] ; then
542	cd $MODEL
543	cat <<eod > tt.f90
544	print*,'coucou'
545	end
546	eod
547	$compiler tt.f90 -o a.out
548	./a.out >\| tt
549	if [ "`cat tt \| sed -e 's/ //g' `" != "coucou" ] ; then
550	echo problem installing with compiler $compiler ; exit ; fi
551	\rm tt a.out tt.f90
552	fi
553	fi
554
555	###########################################################################
556	if [ $getlmdzor = 1 -a ! -d $MODEL/modipsl ] ; then
557	###########################################################################
558	echo '##########################################################'
559	echo Download a slightly modified version of LMDZ
560	echo '##########################################################'
561	cd $MODEL
562	myget src/modipsl.$version.tar.gz
563	echo install_lmdz.sh wget_OK `date`
564	gunzip modipsl.$version.tar.gz
565	tar xf modipsl.$version.tar
566	\rm modipsl.$version.tar
567	fi
568
569	###########################################################################
570	if [ $netcdf = 1 ] ; then
571	###########################################################################
572	cd $MODEL
573	netcdflog=`pwd`/netcdf.log
574	echo '##########################################################'
575	echo Compiling the Netcdf library
576	echo '##########################################################'
577	echo log file : $netcdflog
578	if [[ "$with_xios" = "n" && ! -d $MODEL/netcdf4_hdf5_seq ]] ; then
579	myget import/install_netcdf4_hdf5_seq.bash
580	chmod +x install_netcdf4_hdf5_seq.bash
581
582	if [ "$compiler" = "gfortran" ]
583	then
584	./install_netcdf4_hdf5_seq.bash -prefix $MODEL/netcdf4_hdf5_seq \
585	-compiler gnu > $netcdflog 2>&1
586	elif [ "$compiler" = "ifort" ]
587	then
588	./install_netcdf4_hdf5_seq.bash -prefix $MODEL/netcdf4_hdf5_seq \
589	-compiler intel > $netcdflog 2>&1
590	else
591	echo "unexpected compiler $compiler" ; exit
592	fi
593
594	# LF rajout d'une verrue, pour une raison non encore expliquee,
595	# la librairie est parfois rangée dans lib64 et non dans lib
596	# par certains compilateurs
597	if [ ! -e lib -a -d lib64 ] ; then ln -s lib64 lib; fi
598	elif [[ "$with_xios" = "y" && ! -d $MODEL/netcdf4_hdf5 ]]
599	then
600	# download and compile hdf5 and netcdf, etc. using the
601	# install_netcdf4_hdf5.bash script
602	myget import/install_netcdf4_hdf5.bash
603	chmod u=rwx install_netcdf4_hdf5.bash
604	if [ "$compiler" = "gfortran" ] ; then
605	./install_netcdf4_hdf5.bash -prefix $MODEL/netcdf4_hdf5 -CC gcc -FC gfortran -CXX g++ -MPI $root_mpi > $netcdflog 2>&1
606	elif [ "$compiler" = "ifort" ] ; then
607	./install_netcdf4_hdf5.bash -prefix $MODEL/netcdf4_hdf5 -CC icc -FC ifort -CXX icpc -MPI $root_mpi > $netcdflog 2>&1
608	elif [ "$compiler" = "pgf90" ] ; then
609	./install_netcdf4_hdf5.bash -prefix $MODEL/netcdf4_hdf5 -CC pgcc -FC pgf90 -CXX pgCC -MPI $root_mpi > $netcdflog 2>&1
610	else
611	echo "unexpected compiler $compiler" ; exit
612	fi
613	fi # of if [ "$with_xios" = "n" ]
614	echo install_lmdz.sh netcdf_OK `date`
615	fi # of if [ $netcdf = 1 ]
616
617	# ncdfdir contains the directory where netcdf is installed
618	if [ $netcdf = 1 ] ; then
619	if [ "$with_xios" = "y" ] ; then
620	ncdfdir=$MODEL/netcdf4_hdf5
621	else
622	ncdfdir=$MODEL/netcdf4_hdf5_seq
623	fi
624	elif [ $netcdf = 0 ]
625	then
626	ncdfdir=/usr
627	else
628	ncdfdir=$netcdf
629	fi
630
631	#=========================================================================
632	if [[ ! -f $MODEL/modipsl/lib/libioipsl.a ]]
633	then
634	if [ $ioipsl = 1 ] ; then
635	#=========================================================================
636	echo OK ioipsl=$ioipsl
637	echo '##########################################################'
638	echo 'Installing MODIPSL, the installation package manager for the '
639	echo 'IPSL models and tools'
640	echo '##########################################################'
641	echo `date`
642
643	cd $MODEL/modipsl
644	\rm -rf lib/*
645	cd util
646	cp AA_make.gdef AA_make.orig
647	F_C="$compiler -c " ; if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then F_C="$compiler -c -cpp " ; fi
648	if [ "$compiler" = "pgf90" ] ; then F_C="$compiler -c -Mpreprocess" ; fi
649	sed -e 's/^\#..g95..\#.*.$/\#/' AA_make.gdef > tmp
650	sed -e "s:F_L = g95:F_L = $compiler:" -e "s:F_C = g95 -c -cpp:F_C = $F_C": \
651	-e 's/g95..w_w..(F_D)/g95 w_w = '"$OPTIMGCM"'/' \
652	-e 's:g95..NCDF_INC..$:g95 NCDF_INC= '"$ncdfdir"'/include:' \
653	-e 's:g95..NCDF_LIB..$:g95 NCDF_LIB= -L'"$ncdfdir"'/lib -lnetcdff -lnetcdf:' \
654	-e 's:g95 L_O =:g95 L_O = -Wl,-rpath='"$ncdfdir"'/lib:' \
655	-e "s:-fmod=:-$fmod:" -e 's/-fno-second-underscore//' \
656	-e 's:#-Q- g95 M_K = gmake:#-Q- g95 M_K = make:' \
657	tmp >\| AA_make.gdef
658
659	if [ $pcmac == 1 ]
660	then
661	cp AA_make.gdef tmp
662	sed -e 's/rpath=/rpath,/g' tmp > AA_make.gdef
663	fi
664
665
666	# We use lines for g95 even for the other compilers to run ins_make
667	if [ "$use_shell" = "ksh" ] ; then
668	./ins_make $o_ins_make
669	else # bash
670	sed -e s:/bin/ksh:/bin/bash:g ins_make > ins_make.bash
671	if [ "`grep jeanzay AA_make.gdef`" = "" ] ; then # Bidouille pour compiler sur ada des vieux modipsl.tar
672	echo 'Warning jean-zay not in AA_make.gdef'
673	echo 'Think about updating'
674	exit 1
675	fi
676
677	chmod u=rwx ins_make.bash
678	./ins_make.bash $o_ins_make
679	fi # of if [ "$use_shell" = "ksh" ]
680
681	echo install_lmdz.sh MODIPSL_OK `date`
682
683	cd $MODEL/modipsl/modeles/IOIPSL/src
684	ioipsllog=`pwd`/ioipsl.log
685	echo '##########################################################'
686	echo 'Compiling IOIPSL, the interface library with Netcdf'
687	echo '##########################################################'
688	echo `date`
689	echo log file : $ioipsllog
690
691	if [ "$use_shell" = "bash" ] ; then
692	cp Makefile Makefile.ksh
693	sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile
694	fi
695	# if [ "$pclinux" = 1 ] ; then
696	# Build IOIPSL modules and library
697	$make clean
698	$make > $ioipsllog 2>&1
699	if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then # copy module files to lib
700	cp -f *.mod ../../../lib
701	fi
702	# Build IOIPSL tools (ie: "rebuild", if present)
703	if [ -f $MODEL/modipsl/modeles/IOIPSL/tools/rebuild ] ; then
704	cd $MODEL/modipsl/modeles/IOIPSL/tools
705	# adapt Makefile & rebuild script if in bash
706	if [ "$use_shell" = "bash" ] ; then
707	cp Makefile Makefile.ksh
708	sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile
709	cp rebuild rebuild.ksh
710	sed -e 's:/bin/ksh:/bin/bash:g' \
711	-e 's:print -u2:echo:g' \
712	-e 's:print:echo:g' rebuild.ksh > rebuild
713	fi
714	$make clean
715	$make > $ioipsllog 2>&1
716	fi
717	# fi # of if [ "$pclinux" = 1 ]
718
719	else # of if [ $ioipsl = 1 ]
720	if [ ${hostname:0:5} = jean- ] ; then
721	cd $MODEL/modipsl
722	cd util
723	if [ "`grep jeanzay AA_make.gdef`" = "" ] ; then
724	echo 'Warning jean-zay not in AA_make.gdef'
725	echo 'Think about updating'
726	exit 1
727	fi
728	./ins_make $o_ins_make
729	# Compile IOIPSL on jean-zay
730	cd $MODEL/modipsl/modeles/IOIPSL/src
731	gmake > ioipsl.log
732	cd $MODEL/modipsl/modeles/IOIPSL/tools
733	gmake > ioipsl.log
734
735	fi
736	echo install_lmdz.sh ioipsl_OK `date`
737	fi # of if [ $ioipsl = 1 ]
738	fi
739	# Saving ioipsl lib for possible parallel compile
740	cd $MODEL/modipsl
741	tar cf ioipsl.tar lib/ bin/
742
743	#=========================================================================
744	if [ "$with_xios" = "y" ] ; then
745	echo '##########################################################'
746	echo 'Compiling XIOS'
747	echo '##########################################################'
748	cd $MODEL/modipsl/modeles
749	xioslog=`pwd`/xios.log
750	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/install_xios.bash
751	myget import/install_xios.bash
752	chmod u=rwx install_xios.bash
753	if [ ${hostname:0:5} = jean- ] ; then
754	svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5 XIOS
755	cd XIOS/arch
756	svn update
757	cd ..
758	echo "Compiling XIOS, start" `date` "(it takes about 20 min on Jean-Zay)"
759	echo "log file: $xioslog"
760	./make_xios --prod --arch $arch --job 4 > xios.log 2>&1
761	else
762	./install_xios.bash -prefix $MODEL/modipsl/modeles \
763	-netcdf ${ncdfdir} -hdf5 ${ncdfdir} \
764	-MPI $root_mpi -arch $arch > xios.log 2>&1
765	fi # of case Jean-Zay
766	if [ -f XIOS/lib/libxios.a ] ; then
767	echo "XIOS library successfully generated"
768	echo install_lmdz.sh XIOS_OK `date`
769	fi
770	fi
771
772	#============================================================================
773	veget_version=false
774	if [ "$veget" != 'NONE' ] ; then
775	cd $MODEL/modipsl/modeles/ORCHIDEE
776	set +e ; svn upgrade ; set -e
777	if [ "$veget" = "CMIP6" ] ; then
778	veget_version=orchidee2.0
779	orchidee_rev=6592
780	else # specific orchidee revision newer than CMIP6, on 2_1 or 2_2 branches
781	veget_version=orchidee2.1
782	orchidee_rev=$veget
783	if [ $veget -lt 4465 ] ; then
784	echo 'Stopping, ORCHIDEE version too old, script needs work on the CPP flags to pass to makelmdz'
785	exit 1
786	fi
787	set +e
788	# which branch is my version on?
789	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}'`
790	# switch to that branch
791	echo IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at orchidee-help@listes.ipsl.fr
792	svn switch -r $veget --accept theirs-full svn://forge.ipsl.jussieu.fr/orchidee/$orcbranch
793	svn log -r $veget \| grep $veget
794	if [ $? -gt 0 ] ; then
795	echo 'Cannot update ORCHIDEE as not on the right branch for ORCHIDEE'
796	exit
797	fi
798	set -e
799	set +e ; svn update -r $veget ; set -e
800	fi
801	# Correctif suite debug Jean-Zay
802	sed -i -e 's/9010 FORMAT(A52,F17.14)/9010 FORMAT(A52,F20.14)/' src_stomate/stomate.f90
803	opt_orc="-prod" ; if [ "$optim" = "-debug" ] ; then opt_orc="-debug" ; fi
804
805	orchideelog=`pwd`/orchidee.log
806	echo '########################################################'
807	echo 'Compiling ORCHIDEE, the continental surface model '
808	echo '########################################################'
809	echo Start of the first compilation of orchidee, in sequential mode: `date`
810	echo log file : $orchideelog
811
812	export ORCHPATH=`pwd`
813	xios_orchid="-noxios"
814	if [ "$with_xios" = "y" ] ; then
815	xios_orchid="-xios"
816	fi
817	if [ -d tools ] ; then
818	###################################################################
819	# Pour les experts qui voudraient changer de version d'orchidee.
820	# Attention : necessite d'avoir le password pour orchidee
821
822	# Correctif suite debug Jean-Zay
823	if [ -f src_global/time.f90 ] ; then sed -i -e 's/CALL tlen2itau/\!CALL tlen2itau/' src_global/time.f90 ; fi
824	###################################################################
825	if [ "$veget_version" == "false" ] ; then veget_version=orchidee2.0 ; fi
826	cd arch
827	sed -e s:"%COMPILER .*.$":"%COMPILER $compiler":1 \
828	-e s:"%LINK .*.$":"%LINK $compiler":1 \
829	-e s:"%FPP_FLAGS .*.$":"%FPP_FLAGS $fpp_flags":1 \
830	-e s:"%PROD_FFLAGS .*.$":"%PROD_FFLAGS $OPTIM":1 \
831	-e s:"%DEV_FFLAGS .*.$":"%DEV_FFLAGS $OPTDEV":1 \
832	-e s:"%DEBUG_FFLAGS .*.$":"%DEBUG_FFLAGS $OPTDEB":1 \
833	-e s:"%BASE_FFLAGS .*.$":"%BASE_FFLAGS $OPTPREC":1 \
834	-e s:"%BASE_LD .*.$":"%BASE_LD $BASE_LD":1 \
835	-e s:"%ARFLAGS .*.$":"%ARFLAGS $ARFLAGS":1 \
836	arch-gfortran.fcm > arch-local.fcm
837	echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib -lnetcdff -lnetcdf\"" > arch-local.path
838	echo "NETCDF_INCDIR=${ncdfdir}/include" >> arch-local.path
839	echo "IOIPSL_INCDIR=$ORCHPATH/../../lib" >> arch-local.path
840	echo "IOIPSL_LIBDIR=$ORCHPATH/../../lib" >> arch-local.path
841	echo 'XIOS_INCDIR=${ORCHDIR}/../XIOS/inc' >> arch-local.path
842	echo 'XIOS_LIBDIR="${ORCHDIR}/../XIOS/lib -lxios"' >> arch-local.path
843	cd ../
844
845	echo ./makeorchidee_fcm -j $xios_orchid $opt_orc -parallel none -arch $arch
846	./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel none -arch $arch > $orchideelog 2>&1
847	pwd
848	else # of "if [ -d tools ]"
849	if [ -d src_parallel ] ; then
850	liste_src="parallel parameters global stomate sechiba driver"
851	if [ "$veget_version" == "false" ] ; then veget_version=orchidee2.0 ; fi
852	fi
853	for d in $liste_src ; do src_d=src_$d
854	echo src_d $src_d
855	echo ls ; ls
856	if [ ! -d $src_d ] ; then echo Problem orchidee : no $src_d ; exit ; fi
857	cd $src_d ; \rm -f *.mod make ; $make clean
858	$make > $orchideelog 2>&1 ; if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then cp -f *.mod ../../../lib ; fi
859	cd ..
860	done
861	fi # of "if [ -d tools ]"
862	echo install_lmdz.sh orchidee_compil_seq_OK `date`
863	fi # of if [ "$veget" != 'NONE' ]
864
865
866	#============================================================================
867	# Ehouarn: the directory name LMDZ* depends on version/tar file...
868	if [ -d $MODEL/modipsl/modeles/LMD* ] ; then
869	echo '###############################################################'
870	echo 'Preparing LMDZ compilation : arch file, svn switch if needed...'
871	echo '###############################################################'
872	cd $MODEL/modipsl/modeles/LMD*
873	LMDZPATH=`pwd`
874	else
875	echo "ERROR: No LMD* directory !!!"
876	exit
877	fi
878
879	###########################################################
880	# For those who want to use fcm to compile via :
881	# makelmdz_fcm -arch local .....
882	############################################################
883
884	if [[ "$pclinux" = "1" && ! -f arch/arch-local.path ]] ; then
885
886	# create local 'arch' files (if on Linux PC):
887	cd arch
888	# arch-local.path file
889	echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib -lnetcdff -lnetcdf\"" > arch-local.path
890	echo "NETCDF_INCDIR=-I${ncdfdir}/include" >> arch-local.path
891	echo 'NETCDF95_INCDIR=$LMDGCM/../../include' >> arch-local.path
892	echo 'NETCDF95_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
893	echo 'IOIPSL_INCDIR=$LMDGCM/../../lib' >> arch-local.path
894	echo 'IOIPSL_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
895	echo 'XIOS_INCDIR=$LMDGCM/../XIOS/inc' >> arch-local.path
896	echo 'XIOS_LIBDIR=$LMDGCM/../XIOS/lib' >> arch-local.path
897	echo 'ORCH_INCDIR=$LMDGCM/../../lib' >> arch-local.path
898	echo 'ORCH_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
899
900	if [ $pcmac == 1 ] ; then
901	BASE_LD="$BASE_LD -Wl,-rpath,${ncdfdir}/lib"
902	else
903	BASE_LD="$BASE_LD -Wl,-rpath=${ncdfdir}/lib"
904	fi
905	# Arch-local.fcm file (adapted from arch-linux-32bit.fcm)
906
907	if [ $real = r8 ] ; then FPP_DEF=NC_DOUBLE ; else FPP_DEF="" ; fi
908	sed -e s:"%COMPILER .*.$":"%COMPILER $compiler":1 \
909	-e s:"%LINK .*.$":"%LINK $compiler":1 \
910	-e s:"%PROD_FFLAGS .*.$":"%PROD_FFLAGS $OPTIM":1 \
911	-e s:"%DEV_FFLAGS .*.$":"%DEV_FFLAGS $OPTDEV":1 \
912	-e s:"%DEBUG_FFLAGS .*.$":"%DEBUG_FFLAGS $OPTDEB":1 \
913	-e s:"%BASE_FFLAGS .*.$":"%BASE_FFLAGS $OPTPREC":1 \
914	-e s:"%FPP_DEF .*.$":"%FPP_DEF $FPP_DEF":1 \
915	-e s:"%BASE_LD .*.$":"%BASE_LD $BASE_LD":1 \
916	-e s:"%ARFLAGS .*.$":"%ARFLAGS $ARFLAGS":1 \
917	arch-linux-32bit.fcm > arch-local.fcm
918
919	cd ..
920	### Adapt "bld.cfg" (add the shell):
921	#whereisthatshell=$(which ${use_shell})
922	#echo "bld::tool::SHELL $whereisthatshell" >> bld.cfg
923
924	fi # of if [ "$pclinux" = 1 ]
925
926
927	cd $MODEL/modipsl/modeles/LMDZ*
928	lmdzlog=`pwd`/lmdz.log
929
930	##################################################################
931	# Possibly update LMDZ if a specific svn release is requested
932	##################################################################
933
934	set +e ; svn upgrade ; set -e
935
936	if [ "$svn" = "last" ] ; then svnopt="" ; else svnopt="-r $svn" ; fi
937	if [ "$svn" != "" ] ; then
938	set +e ; svn info \| grep -q 'http:'
939	if [ $? = 0 ] ; then
940	svn switch --relocate http://svn.lmd.jussieu.fr/LMDZ https://svn.lmd.jussieu.fr/LMDZ
941	fi
942	svn update $svnopt
943	fi
944	set -e
945
946	##################################################################
947	# Retrieve the final svn release number, and adjust compilation options accordingly
948	mysvn=`svnversion . \| egrep -o "[0-9]+"`
949
950	# Option de compilation du rayonnement : depend de $mysvn ><= r4185
951	opt_rad=""
952
953	case $rad in
954	oldrad) iflag_rrtm=0 ; NSW=2 ; opt_rad="" ;;
955	rrtm) iflag_rrtm=1 ; NSW=6 ; if [ $mysvn -le 4185 ] ; then opt_rad="-rrtm true" ; else opt_rad="-rad rrtm" ; fi ;;
956	ecrad) iflag_rrtm=2 ; NSW=6 ; opt_rad="-rad ecrad" ;;
957	*) echo Only oldrad rrtm ecrad for rad option ; exit
958	esac
959
960	if [ $mysvn -le 4185 -a $rad = "ecrad" ] ; then echo "ecrad only available for LMDZ rev starting with 4186 " ; exit ; fi
961
962	##################################################################
963
964
965	if [[ ! -f libf/misc/netcdf95.F90 && ! -d $MODEL/NetCDF95-0.2 ]]
966	then
967	cd $MODEL
968	myget import/NetCDF95-0.2.tar.gz
969	tar -xf NetCDF95-0.2.tar.gz
970	rm NetCDF95-0.2.tar.gz
971	cd NetCDF95-0.2
972	mkdir build
973	cd build
974	cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=$ncdfdir \
975	-DCMAKE_INSTALL_PREFIX=$MODEL/modipsl
976	make install
977	cd $MODEL/modipsl/modeles/LMDZ*
978	fi
979
980	echo '##################################################################'
981	echo "Preparing script compile.sh for LMDZ compilation"
982	echo "It will only be run automatically if bench=1/tuto"
983	echo Here bench=$bench
984	echo '##################################################################'
985
986	if [ "$env_file" != "" ] ; then mv arch/arch-${arch}.env arch/arch-${arch}.orig ; \cp -f $env_file arch/arch-${arch}.env ; fi
987
988	if [ $compile_with_fcm = 1 ] ; then makelmdz="makelmdz_fcm $optim -arch $arch -j 8 " ; else makelmdz="makelmdz $optim -arch $arch" ; fi
989
990	# sequential compilation
991	if [ "$sequential" = 1 ] ; then
992	echo Sequential compilation command, saved in compile.sh:
993	echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp -d ${grid_resolution} -v $veget_version gcm "
994	echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp -d ${grid_resolution} -v $veget_version gcm " > compile.sh
995	chmod +x ./compile.sh
996	if [ $bench = 1 ] ; then
997	echo install_lmdz.sh start_lmdz_seq_compilation `date`
998	echo log file: $lmdzlog
999	./compile.sh > $lmdzlog 2>&1
1000	echo install_lmdz.sh end_lmdz_seq_compilation `date`
1001	fi
1002	fi # fin sequential
1003
1004	# compiling in parallel mode
1005	if [ $parallel != "none" ] ; then
1006	echo '##########################################################'
1007	echo ' Parallel compile '
1008	echo '##########################################################'
1009	echo "(after saving the sequential libs and binaries)"
1010	cd $MODEL/modipsl
1011	tar cf sequential.tar bin/ lib/
1012	\rm -rf bin/ lib/
1013	tar xf ioipsl.tar
1014	#
1015	# Orchidee
1016	#
1017	cd $ORCHPATH
1018	if [ -d src_parallel -a $veget != 'NONE' ] ; then
1019	cd arch
1020	sed \
1021	-e s:"%COMPILER.*.$":"%COMPILER $par_comp":1 \
1022	-e s:"%LINK.*.$":"%LINK $par_comp":1 \
1023	-e s:"%MPI_FFLAG.*.$":"%MPI_FFLAGS $MPI_FLAGS":1 \
1024	-e s:"%OMP_FFLAG.*.$":"%OMP_FFLAGS $OMP_FLAGS":1 \
1025	-e s:"%MPI_LD.*.$":"%MPI_LD $MPI_LD":1 \
1026	-e s:"%OMP_LD.*.$":"%OMP_LD $OMP_LD":1 \
1027	arch-local.fcm > tmp.fcm
1028
1029	mv tmp.fcm arch-local.fcm
1030	cd ../
1031	echo Compiling ORCHIDEE in parallel mode `date`
1032	echo logfile $orchideelog
1033	echo "NOTE : to recompile it when necessary, use ./compile_orc.sh in modipsl/modeles/ORCHIDEE"
1034	echo ./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc -parallel $parallel -arch $arch > compile_orc.sh
1035	echo ./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel $parallel -arch $arch >> compile_orc.sh
1036	echo echo Now you must also recompile LMDZ, by running ./compile.sh in modeles/LMDZ >> compile_orc.sh
1037	chmod u+x compile_orc.sh
1038	./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc -parallel $parallel -arch $arch > $orchideelog 2>&1
1039	./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel $parallel -arch $arch >> $orchideelog 2>&1
1040	echo End of ORCHIDEE compilation in parallel mode `date`
1041	elif [ $veget != 'NONE' ] ; then
1042	echo '##########################################################'
1043	echo ' Orchidee version too old '
1044	echo ' Please update to new version '
1045	echo '##########################################################'
1046	exit
1047	fi # of [ -d src_parallel -a $veget != 'NONE' ]
1048
1049	# LMDZ
1050	cd $LMDZPATH
1051	if [ $arch = local ] ; then
1052	cd arch
1053	sed -e s:"%COMPILER.*.$":"%COMPILER $par_comp":1 \
1054	-e s:"%LINK.*.$":"%LINK $par_comp":1 \
1055	-e s:"%MPI_FFLAG.*.$":"%MPI_FFLAGS $MPI_FLAGS":1 \
1056	-e s:"%OMP_FFLAG.*.$":"%OMP_FFLAGS $OMP_FLAGS":1 \
1057	-e s:"%ARFLAGS.*.$":"%ARFLAGS $ARFLAGS":1 \
1058	-e s@"%BASE_LD.*.$"@"%BASE_LD -Wl,-rpath=${root_mpi}/lib:${ncdfdir}/lib"@1 \
1059	-e s:"%MPI_LD.*.$":"%MPI_LD $MPI_LD":1 \
1060	-e s:"%OMP_LD.*.$":"%OMP_LD $OMP_LD":1 \
1061	arch-local.fcm > tmp.fcm
1062	mv tmp.fcm arch-local.fcm
1063	cd ../
1064	fi
1065	rm -f compile.sh
1066	echo resol=${grid_resolution} >> compile.sh
1067	if [ ${hostname:0:5} = jean- -a "$cosp" = "v2" ] ; then
1068
1069	echo LMDZ compilation command in parallel mode, saved in compile.sh, is :
1070	echo "(ATTENTION le probleme de cospv2 sur jean-zay en mode prod n est pas corrige ! )"
1071	# ATTENTION le probleme de cospv2 sur jean-zay en mode prod n est pas corrige
1072	echo ./$makelmdz -dev $optim $OPT_MAKELMDZ $opt_rad $opt_cosp $opt_makelmdz_xios -d \$resol -v $veget_version -mem -parallel $parallel gcm >> compile.sh
1073	echo ./$makelmdz -dev $optim $OPT_MAKELMDZ $opt_rad $opt_cosp $opt_makelmdz_xios -d \$resol -v $veget_version -mem -parallel $parallel gcm
1074	else
1075	echo ./$makelmdz $optim $OPT_MAKELMDZ $opt_rad $opt_cosp $opt_makelmdz_xios -d \$resol -v $veget_version -mem -parallel $parallel gcm >> compile.sh
1076	echo ./$makelmdz $optim $OPT_MAKELMDZ $opt_rad $opt_cosp $opt_makelmdz_xios -d \$resol -v $veget_version -mem -parallel $parallel gcm
1077	fi
1078	chmod +x ./compile.sh
1079
1080	if [ $bench = 1 ] ; then
1081	echo Compiling LMDZ in parallel mode `date`, LMDZ log file: $lmdzlog ; ./compile.sh > $lmdzlog 2>&1
1082	fi
1083
1084	fi # of if [ $parallel != "none" ]
1085
1086
1087	##################################################################
1088	# Verification du succes de la compilation
1089	##################################################################
1090
1091	# Recherche de l'executable dont le nom a change au fil du temps ...
1092	# suffix contains radiative option starting with revision 4186
1093	if [ $mysvn -ge 4186 ] ; then suff_exe=_${rad}${suff_exe} ; fi
1094	gcm=""
1095	#for exe in gcm.e bin/gcm_${grid_resolution}_phylmd_seq_orch.e bin/gcm_${grid_resolution}_phylmd_seq.e bin/gcm_${grid_resolution}_phylmd_para_mem_orch.e bin/gcm_${grid_resolution}_phylmd_para_mem.e ; do
1096	for exe in gcm.e bin/gcm_${grid_resolution}_phylmd${suff_exe}${suff_orc}.e ; do if [ -f $exe ] ; then gcm=$exe ; fi
1097	done
1098
1099	if [ "$gcm" = "" ] ; then
1100	if [ $bench = 1 ] ; then
1101	echo 'Compilation failed !! Cannot run the benchmark;'
1102	exit
1103	else
1104	echo 'Compilation not done (only done when bench=1)'
1105	fi
1106	else
1107	echo '##########################################################'
1108	echo 'Compilation successfull !! ' `date`
1109	echo '##########################################################'
1110	echo The executable is $gcm
1111	fi
1112
1113	##################################################################
1114	# Below, we run a benchmark if bench=1 or tuto
1115	##################################################################
1116
1117	if [ $bench = tuto ] ; then
1118	myget Training/tutorial.tar ; tar xvf tutorial.tar ; cd TUTORIAL ; ./init.sh
1119
1120	elif [[ $bench = 1 && ! -d BENCH${grid_resolution} ]] ; then
1121	# TOUTE CETTE SECTION DEVRAIT DISPARAITRE POUR UNE COMMANDE
1122	# OU DES BENCHS PAR MOTS CLES COMME tuto
1123
1124	echo '##########################################################'
1125	echo ' Running a test run '
1126	echo '##########################################################'
1127
1128	\rm -rf BENCH${grid_resolution}
1129	bench=bench_lmdz_${grid_resolution}
1130	echo install_lmdz.sh before bench download `date`
1131	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/$bench.tar.gz
1132	myget 3DBenchs/$bench.tar.gz
1133	echo install_lmdz.sh after bench download `date`
1134	tar xvf $bench.tar.gz
1135
1136	if [ "$cosp" = "v1" -o "$cosp" = "v2" ] ; then
1137	cd BENCH${grid_resolution}
1138	# copier les fichiers namelist input et output our COSP
1139	cp ../DefLists/cosp*_input_nl.txt .
1140	cp ../DefLists/cosp*_output_nl.txt .
1141	# Activer la cles ok_cosp pour tourner avec COSP
1142	sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp
1143	\mv -f tmp config.def
1144	cd ..
1145	fi
1146
1147	if [ -n "$physiq" ]; then
1148	cd BENCH${grid_resolution}
1149	if [ -f physiq.def_${physiq} ]; then
1150	cp physiq.def_${physiq} physiq.def
1151	echo using physiq.def_${physiq}
1152	else
1153	echo using standard physiq.def
1154	fi
1155	cd ..
1156	else
1157	echo using standard physiq.def
1158	fi
1159
1160	if [ "$with_xios" = "y" ] ; then
1161	cd BENCH${grid_resolution}
1162	cp ../DefLists/iodef.xml .
1163	cp ../DefLists/context_lmdz.xml .
1164	cp ../DefLists/field_def_lmdz.xml .
1165	# A raffiner par la suite
1166	echo A FAIRE : Copier les *xml en fonction de l option cosp
1167	cp ../DefLists/field_def_cosp*.xml .
1168	cp ../DefLists/file_def_hist*xml .
1169	# adapt iodef.xml to use attached mode
1170	sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' iodef.xml > tmp
1171	\mv -f tmp iodef.xml
1172
1173	# and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
1174	# except for histday
1175	for histfile in file_def_hist*xml
1176	do
1177	if [ "$histfile" = "file_def_histday_lmdz.xml" ] ; then
1178	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' $histfile > tmp ; \mv -f tmp $histfile
1179	sed -e 's@output_level="_AUTO_"@output_level="5"@' $histfile > tmp ; \mv -f tmp $histfile
1180	sed -e 's@compression_level="2"@compression_level="0"@' $histfile > tmp ; \mv -f tmp $histfile
1181	else
1182	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' $histfile > tmp ; \mv -f tmp $histfile
1183	fi
1184	done
1185	# and add option "ok_all_xml=y" in config.def
1186	echo "### XIOS outputs" >> config.def
1187	echo 'ok_all_xml=.true.' >> config.def
1188
1189	#activer les sorties pour Cosp
1190	if [ "$cosp" = "v1" ] ; then
1191	histfile=file_def_histdayCOSP_lmdz.xml
1192	sed -e 's@enabled=".FALSE."@enabled=".TRUE."@' $histfile > tmp ; \mv -f tmp $histfile
1193	sed -e 's@output_level="_AUTO_"@output_level="5"@' $histfile > tmp ; \mv -f tmp $histfile
1194	sed -e 's@compression_level="2"@compression_level="0"@' $histfile > tmp ; \mv -f tmp $histfile
1195	fi
1196	if [ "$cosp" = "v2" ] ; then
1197	histfile=file_def_histdayCOSPv2_lmdz.xml
1198	sed -e 's@compression_level="2"@compression_level="0"@' $histfile > tmp ; \mv -f tmp $histfile
1199	contextfile=context_lmdz.xml
1200	sed -e 's@src="./file_def_histdayCOSP_lmdz.xml"@src="./file_def_histdayCOSPv2_lmdz.xml"@' $contextfile > tmp ; \mv -f tmp $contextfile
1201	sed -e 's@src="./file_def_histmthCOSP_lmdz.xml"@src="./file_def_histmthCOSPv2_lmdz.xml"@' $contextfile > tmp ; \mv -f tmp $contextfile
1202	sed -e 's@src="./file_def_histhfCOSP_lmdz.xml"@src="./file_def_histhfCOSPv2_lmdz.xml"@' $contextfile > tmp ; \mv -f tmp $contextfile
1203	fieldfile=field_def_lmdz.xml
1204	sed -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' $fieldfile > tmp ; \mv -f tmp $fieldfile
1205	fi
1206
1207	cd ..
1208	fi
1209
1210	# Cas Bensh avec ecrad
1211	if [ "$rad" = "ecrad" ] ; then
1212	cd BENCH${grid_resolution}
1213	cp ../DefLists/namelist_ecrad .
1214	cp -r ../libf/phylmd/ecrad/data .
1215	cd ..
1216	fi
1217
1218	# Adjusting bench physiq.def to radiative code chosen
1219	cd BENCH${grid_resolution}
1220	sed -e 's/iflag_rrtm=..$/iflag_rrtm='$iflag_rrtm'/' -e 's/NSW=..$/NSW='$NSW'/' physiq.def > tmpdef
1221	\mv tmpdef physiq.def
1222	cd ..
1223
1224	cp $gcm BENCH${grid_resolution}/gcm.e
1225
1226	cd BENCH${grid_resolution}
1227	# On cree le fichier bench.sh au besoin
1228	# Dans le cas 48x36x39 le bench.sh existe deja en parallele
1229
1230	if [ "$grid_resolution" = "48x36x39" ] ; then
1231	echo On ne touche pas au bench.sh
1232	# But we have to adapt "run_local.sh" for $mpirun
1233	sed -e "s@mpirun@$mpirun@g" run_local.sh > tmp
1234	mv -f tmp run_local.sh
1235	chmod u=rwx run_local.sh
1236	elif [ "${parallel:0:3}" = "mpi" ] ; then
1237	# Lancement avec deux procs mpi et 2 openMP
1238	echo "export OMP_STACKSIZE=800M" > bench.sh
1239	if [ "${parallel:4:3}" = "omp" ] ; then
1240	echo "export OMP_NUM_THREADS=2" >> bench.sh
1241	fi
1242	if [ "$cosp" = "v1" -o "$cosp" = "v2" ] ; then
1243	if [ ${hostname:0:5} = jean- ] ; then
1244	chmod +x ../arch.env
1245	../arch.env
1246	echo "ulimit -s 2000000" >> bench.sh
1247	else
1248	echo "ulimit -s 200000" >> bench.sh
1249	fi
1250	else
1251	echo "ulimit -s unlimited" >> bench.sh
1252	fi
1253	if [ ${hostname:0:5} = jean- ] ; then
1254	. ../arch/arch-${arch}.env
1255	echo "srun -n 2 -A $idris_acct@cpu gcm.e > listing 2>&1" >> bench.sh
1256	else
1257	echo "$mpirun -np 2 gcm.e > listing 2>&1" >> bench.sh
1258	fi
1259	# Add rebuild, using reb.sh if it is there
1260	echo 'if [ -f reb.sh ] ; then' >> bench.sh
1261	echo ' ./reb.sh histday ; ./reb.sh histmth ; ./reb.sh histhf ; ./reb.sh histins ; ./reb.sh stomate_history ; ./reb.sh sechiba_history ; ./reb.sh sechiba_out_2 ' >> bench.sh
1262	echo 'fi' >> bench.sh
1263	else
1264	echo "./gcm.e > listing 2>&1" > bench.sh
1265	fi
1266	# Getting orchidee stuff
1267	if [ $veget == 'CMIP6' ] ; then
1268	#echo 'myget 3DBenchs/BENCHorch11.tar.gz'
1269	#myget 3DBenchs/BENCHorch11.tar.gz
1270	#tar xvzf BENCHorch11.tar.gz
1271	echo 'myget 3DBenchs/BENCHCMIP6.tar.gz'
1272	myget 3DBenchs/BENCHCMIP6.tar.gz
1273	tar xvzf BENCHCMIP6.tar.gz
1274	sed -e "s:VEGET=n:VEGET=y:" config.def > tmp
1275	mv -f tmp config.def
1276	if [ "$with_xios" = "y" ] ; then
1277	cp ../../ORCHIDEE/src_xml/context_orchidee.xml .
1278	echo '<context id="orchidee" src="./context_orchidee.xml"/>' > add.tmp
1279	cp ../../ORCHIDEE/src_xml/field_def_orchidee.xml .
1280	cp ../../ORCHIDEE/src_xml/file_def_orchidee.xml .
1281	cp ../../ORCHIDEE/src_xml/file_def_input_orchidee.xml .
1282	if [ -f ../../ORCHIDEE/src_xml/context_input_orchidee.xml ] ; then
1283	cp ../../ORCHIDEE/src_xml/context_input_orchidee.xml .
1284	echo '<context id="orchidee" src="./context_input_orchidee.xml"/>' >> add.tmp
1285	fi
1286	sed -e '/id="LMDZ"/r add.tmp' iodef.xml > tmp
1287	mv tmp iodef.xml
1288	sed -e'{/sechiba1/ s/enabled="_AUTO_"/type="one_file" enabled=".TRUE."/}' file_def_orchidee.xml > tmp ; \mv -f tmp file_def_orchidee.xml
1289	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' file_def_orchidee.xml > tmp ; \mv -f tmp file_def_orchidee.xml
1290	sed -e 's@output_level="_AUTO_"@output_level="1"@' file_def_orchidee.xml > tmp ; \mv -f tmp file_def_orchidee.xml
1291	sed -e 's@output_freq="_AUTO_"@output_freq="1d"@' file_def_orchidee.xml > tmp ; \mv -f tmp file_def_orchidee.xml
1292	sed -e 's@compression_level="4"@compression_level="0"@' file_def_orchidee.xml > tmp ; \mv -f tmp file_def_orchidee.xml
1293	sed -e 's@XIOS_ORCHIDEE_OK = n@XIOS_ORCHIDEE_OK = y@' orchidee.def > tmp ; \mv -f tmp orchidee.def
1294	fi
1295	fi
1296	echo EXECUTION DU BENCH
1297	set +e
1298	date ; ./bench.sh > out.bench 2>&1 ; date
1299	set -e
1300	tail listing
1301
1302
1303	echo '##########################################################'
1304	echo 'Simulation finished in' `pwd`
1305	echo 'You have compiled with:'
1306	cat ../compile.sh
1307	if [ $parallel = "none" ] ; then
1308	echo 'You may re-run it with : cd ' `pwd` ' ; gcm.e'
1309	echo 'or ./bench.sh'
1310	else
1311	echo 'You may re-run it with : '
1312	echo 'cd ' `pwd` '; ./bench.sh'
1313	# echo 'ulimit -s unlimited'
1314	# echo 'export OMP_NUM_THREADS=2'
1315	# echo 'export OMP_STACKSIZE=800M'
1316	# echo "$mpirun -np 2 gcm.e "
1317	fi
1318	echo '##########################################################'
1319
1320	fi # bench
1321
1322
1323	#################################################################
1324	# Installation eventuelle du 1D
1325	#################################################################
1326
1327	if [ $SCM = 1 ] ; then
1328	cd $MODEL
1329	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/1D.tar.gz
1330	myget 1D/1D.tar.gz
1331	tar xvf 1D.tar.gz
1332	cd 1D
1333	./run.sh -rad $rad
1334	fi
1335	#set -vx
1336
1337	#################################################################
1338	# sauvegarde des options veget pour utilisation eventuelle tutorial_prod
1339	#################################################################
1340	cd $MODEL/modipsl/modeles
1341	#echo surface_env file created in $MODEL
1342	echo 'veget='$veget > surface_env
1343	#opt_veget="-v $veget_version"
1344	#echo 'opt_veget="'$opt_veget\" >> surface_env
1345	echo 'opt_veget="'-v $veget_version\" >> surface_env
1346	echo 'orchidee_rev='$orchidee_rev >> surface_env
1347	echo 'suforch='$suff_orc >> surface_env

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