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source: BOL/script_install/install_lmdz.sh @ 5137

Last change on this file since 5137 was 5021, checked in by asima, 5 months ago
Changes in order to be able to compile XIOS on Jean-Zay at Idris after the OS upgrade from Red Hat 8.6 to 9.2. (cf. A. Caubel and L. Fairhead)
Property svn:executable set to ``*
File size: 57.5 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
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=20231022.trunk
75
76	getlmdzor=1
77	netcdf=1 # 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	if [ `gfortran -dumpversion \| cut -d. -f1` -ge 10 ] ; then allow_arg_mismatch="-fallow-argument-mismatch" ; fi
87	SCM=0
88	# surface/vegetation scheme treatment
89	# controlled by the single variable veget which can have the following values
90	# - NONE: bucket scheme (default)
91	# - CMIP6: orchidee version used in CMIP exercise, rev 5661
92	# - number: orchidee version number
93	veget=NONE
94	# choose the resolution for the bench runs
95	# grid_resolution= 32x24x11 or 48x36x19 for tests (test without ORCHIDEE)
96	# 96x71x19 standard configuration
97	grid_resolution=144x142x79
98	grid_resolution=96x95x39
99	grid_resolution=48x36x19
100	grid_resolution=32x32x39
101	# choose the physiq version you want to test
102	#physiq=NPv6.0.14splith
103	physiq=
104
105	## parallel can take the values none/mpi/omp/mpi_omp
106	parallel=mpi_omp
107	parallel=none
108	idris_acct=lmd
109	trusting=testing
110	OPT_GPROF=""
111	OPT_MAKELMDZ=""
112	MODEL=""
113
114	## also compile XIOS? (and more recent NetCDF/HDF5 libraries) Default=no
115	with_xios="n"
116	opt_makelmdz_xios=""
117
118	## compile with oldrad/rrtm/ecrad radiatif code (Default=rrtm)
119	rad=rrtm
120
121	## compile_with_fcm=1 : use makelmdz_fcm (1) or makelmdz (0)
122	compile_with_fcm=1
123
124	#Compilation with Cosp (cosp=NONE/v1/v2 ; default=NONE)
125	cosp=NONE
126	opt_cosp=""
127
128	# Check if on a Mac
129	if [ `uname` = "Darwin" ]
130	then
131	pcmac=1
132	export MAKE=make
133	fi
134	#echo "pcmac="$pcmac
135
136	env_file=""
137
138	#########################################################################
139	# Options interactives
140	#########################################################################
141	while (($# > 0))
142	do
143	case $1 in
144	"-h") cat <<........fin
145	$0 [ -v version ] [ -r svn_release ]
146	[ -parallel PARA ] [ -d GRID_RESOLUTION ] [ -bench 0/1 ]
147	[-name LOCAL_MODEL_NAME] [-gprof] [-opt_makelmdz] [-rad RADIATIF]
148
149	-v "version" like 20150828.trunk
150	see http://www.lmd.jussieu.fr/~lmdz/Distrib/LISMOI.trunk
151
152	-r "svn_release" : either the svn release number or "last"
153
154	-compiler gfortran\|ifort\|pgf90 (default: gfortran)
155
156	-parallel PARA : can be mpi_omp (mpi with openMP) or none (for sequential)
157
158	-d GRID_RESOLUTION should be among the available benchs if -bench 1
159	among which : 48x36x19, 48x36x39
160	if wanting to run a bench simulation in addition to compilation
161	default : 48x36x19
162
163	-bench activating the bench or not (0/1). Default 1
164
165	-testing/unstable
166
167	-name LOCAL_MODEL_NAME : default = LMDZversion.release
168
169	-netcdf 0, 1 or PATH
170	0: do not download NetCDF, look for it in standard locations
171	1: download and compile NetCDF
172	PATH: full path to an existing installed NetCDF library
173
174	-xios also download and compile the XIOS library
175	(requires the NetCDF4-HDF5 library, also installed by default)
176	(requires to also have -parallel mpi_omp)
177
178	-gprof to compile with -pg to enable profiling with gprof
179
180	-cosp to run without our with cospv1 or cospv2 [none/v1/v2]
181
182	-rad RADIATIF can be oldrad, rrtm or ecrad radiatif code
183
184	-nofcm to compile without fcm
185
186	-SCM install 1D version automatically
187
188	-debug compile everything in debug mode
189
190	-opt_makelmdz to call makelmdz or makelmdz_fcm with additional options
191
192	-physiq to choose which physics package to use
193
194	-env_file specify an arch.env file to overwrite the existing one
195
196	-veget surface model to run [NONE/CMIP6/xxxx]
197
198	........fin
199	exit ;;
200	"-v") version=$2 ; shift ; shift ;;
201	"-r") svn=$2 ; shift ; shift ;;
202	"-compiler") compiler=$2
203	case $compiler in
204	"gfortran"\|"ifort"\|"pgf90") compiler=$2 ; shift
205	shift ;;
206	*) echo "Only gfortran , ifort or pgf90 for the " \
207	"compiler option"
208	exit
209	esac ;;
210	"-d") grid_resolution=$2 ; shift ; shift ;;
211	"-gprof") OPT_GPROF="-pg" ; shift ;;
212	"-unstable"\|"-testing") trusting=`echo $1 \| cut -c2-` ; shift ;;
213	"-cosp") cosp=$2
214	case $cosp in
215	"none"\|"v1"\|"v2") cosp=$2 ; shift ; shift ;;
216	*) echo Only none v1 v2 for cosp option ; exit
217	esac ;;
218	"-nofcm") compile_with_fcm=0 ; echo This option will be reactivated soon '(promesse du 8dec2022)' ; exit 1 ; shift ;;
219	"-SCM") SCM=1 ; shift ;;
220	"-opt_makelmdz") OPT_MAKELMDZ="$2" ; shift ; shift ;;
221	"-rrtm") rrtm="$2"
222	if [ "$2" = "false" ] ; then
223	rad="oldrad"
224	else
225	rad="rrtm"
226	fi
227	shift ; shift ;;
228	"-rad") rad=$2
229	case $rad in
230	"oldrad"\|"rrtm"\|"ecrad") rad=$2 ; shift ; shift ;;
231	*) echo Only oldrad rrtm ecrad for rad option ; exit
232	esac ;;
233	"-parallel") parallel=$2
234	case $parallel in
235	"none"\|"mpi"\|"omp"\|"mpi_omp") parallel=$2 ; shift
236	shift ;;
237	*) echo Only none mpi omp mpi_omp for the parallel \
238	option
239	exit
240	esac ;;
241	"-bench") bench=$2 ; shift ; shift ;;
242	"-debug") optim=-debug ; shift ;;
243	"-name") MODEL=$2 ; shift ; shift ;;
244	"-netcdf") netcdf=$2 ; shift ; shift ;;
245	"-physiq") physiq=$2 ; shift ; shift ;;
246	"-xios") with_xios="y" ; shift ;;
247	"-env_file") env_file=$2 ; shift ; shift ;;
248	"-veget") veget=$2 ; shift ; shift ;;
249	*) bash install_lmdz.sh -h ; exit
250	esac
251	done
252
253	# Option de compilation du rayonnement : depend de $mysvn ><= r4185,
254	# sera donc definie plus bas
255
256	#opt_rad=""
257	#case $rad in
258	# rrtm) opt_rad="-rad rrtm" ;;
259	# ecrad) opt_rad="-rad ecrad" ;;
260	#esac
261
262
263	# Option de compilation pour Cosp
264	opt_cosp=""
265	case $cosp in
266	v1) opt_cosp="-cosp true" ;;
267	v2) opt_cosp="-cospv2 true" ;;
268	esac
269
270	# Check on veget version
271	#if [ "$veget" != 'NONE' -a "$veget" != "CMIP6" -a "$veget" != +([0-9]) ] ; then
272	if [ $veget != 'NONE' -a $veget != "CMIP6" ] ; then
273	re='^[0-9]+$'
274	if ! [[ $veget =~ $re ]] ; then
275	echo 'Valeur de l option veget non valable'
276	exit
277	fi
278	fi
279
280	#Define veget-related suffix for gcm name
281	if [ "$veget" = 'NONE' ] ; then
282	suff_orc=''
283	#For use with tutorial, orchidee_rev is also defined (will be
284	#written in surface_env at the end of the script)
285	orchidee_rev=''
286	else
287	suff_orc='_orch'
288	fi
289
290
291	if [ $parallel = none ] ; then
292	sequential=1; suff_exe='_seq'
293	else
294	sequential=0; suff_exe='_para_mem'
295	fi
296
297	#Chemin pour placer le modele
298	if [ "$MODEL" = "" ] ; then MODEL=./LMDZ$version$svn$optim ; fi
299
300
301	arch=local
302
303
304	if [ $compiler = g95 ] ; then echo g95 is not supported anymore ; exit ; fi
305
306	################################################################
307	# Specificite des machines
308	################################################################
309
310	hostname=`hostname`
311	if [ "$pclinux" = 1 ] ; then o_ins_make="-t g95" ; else o_ins_make="" ; fi
312
313	case ${hostname:0:5} in
314
315	jean-) compiler="mpiifort" ;
316	par_comp="mpiifort" ;
317	o_ins_make="-t jeanzay" ;
318	make=gmake ;
319	module purge
320	module load gcc/6.5.0
321	module load intel-compilers/19.0.4 ;
322	#module load intel-mpi/19.0.4 ;
323	#module load intel-mkl/19.0.4 ;
324	module load hdf5/1.10.5-mpi ;
325	module load netcdf/4.7.2-mpi ;
326	module load netcdf-fortran/4.5.2-mpi ;
327	module load subversion/1.9.7 ;
328	module load cmake
329	export NETCDF_LIBDIR=./
330	export NETCDFFORTRAN_INCDIR=./
331	export NETCDFFORTRAN_LIBDIR=./
332	arch=X64_JEANZAY ;;
333
334	cicla\|camel) compiler="gfortran" ;
335	module purge
336	module load gnu/10.2.0
337	module load openmpi/4.0.5
338	module load hdf5/1.10.7-mpi
339	module load netcdf-c/4.7.4-mpi
340	module load netcdf-fortran/4.5.3-mpi
341	netcdf=/net/nfs/tools/PrgEnv/linux-scientific6-x86_64/gcc-10.2.0/netcdf-fortran-4.5.3-k3drgfqok3lip62hnm3tsyof4cjen5sk
342	module load svn/1.14.0
343
344	if [ $parallel != none ] ; then
345	root_mpi=/net/nfs/tools/meso-sl6/openmpi/4.0.5-gcc-10.2.0
346	path_mpi=$root_mpi/bin ;
347	par_comp=${path_mpi}/mpif90 ;
348	mpirun=${path_mpi}/mpirun ;
349	fi ;
350	arch=local ;
351	make=make ;
352	o_ins_make="-t g95" ;;
353
354	*) if [ $parallel = none -o -f /usr/bin/mpif90 ] ; then
355	path_mpi=`which mpif90 \| sed -e s:/mpif90::` ;
356	if [ -d /usr/lib64/openmpi ] ; then
357	root_mpi="/usr/lib64/openmpi"
358	else
359	root_mpi="/usr"
360	fi
361	else
362	echo "Cannot find mpif90" ;
363	if [ $parallel = none ] ; then exit ; fi ;
364	fi ;
365	if [ $parallel != none ] ; then
366	root_mpi=$(which mpif90 \| sed -e s:/bin/mpif90::)
367	path_mpi=$(which mpif90 \| sed -e s:/mpif90::)
368	export LD_LIBRARY_PATH=${root_mpi}/lib:$LD_LIBRARY_PATH
369	fi
370	par_comp=${path_mpi}/mpif90 ;
371	mpirun=${path_mpi}/mpirun ;
372	arch=local ;
373	make=make ;
374	o_ins_make="-t g95"
375	esac
376
377	# Flags for parallelism:
378	if [ $parallel != none ] ; then
379	# MPI_LD are the flags needed for linking with MPI
380	MPI_LD="-L${root_mpi}/lib -lmpi"
381	if [ "$compiler" = "gfortran" ] ; then
382	# MPI_FLAGS are the flags needed for compilation with MPI
383	MPI_FLAGS="-fcray-pointer"
384	# OMP_FLAGS are the flags needed for compilation with OpenMP
385	OMP_FLAGS="-fopenmp -fcray-pointer"
386	# OMP_LD are the flags needed for linking with OpenMP
387	OMP_LD="-fopenmp"
388	elif [ "$compiler" = "ifort" ] ; then
389	MPI_FLAGS=""
390	OMP_FLAGS="-openmp"
391	OMP_LD="-openmp"
392	else # pgf90
393	MPI_FLAGS=""
394	OMP_FLAGS="-mp"
395	OMP_LD="-mp"
396	fi
397	fi
398
399	#####################################################################
400	# Test for old gfortran compilers
401	# If the compiler is too old (older than 4.3.x) we test if the
402	# temporary gfortran44 patch is available on the computer in which
403	# case the compiler is changed from gfortran to gfortran44
404	# Must be aware than parallelism can not be activated in this case
405	#####################################################################
406
407	if [ "$compiler" = "gfortran" ] ; then
408	gfortran=gfortran
409	gfortranv=`gfortran --version \| \
410	head -1 \| awk ' { print $NF } ' \| awk -F. ' { print $1 * 10 + $2 } '`
411	if [ $gfortranv -le 43 ] ; then
412	echo ERROR : Your gfortran compiler is too old
413	echo 'Please choose a new one (ifort) and change the line'
414	echo compiler=xxx
415	echo in the install_lmdz.sh script and rerun it
416	if [ `which gfortran44 \| wc -w` -ne 0 ] ; then
417	gfortran=gfortran44
418	else
419	echo gfotran trop vieux ; exit
420	fi
421	fi
422	compiler=$gfortran
423	fi
424	#####################################################################
425
426	## if also compiling XIOS, parallel must be mpi_omp
427	if [ "$with_xios" = "y" -a "$parallel" != "mpi_omp" ] ; then
428	echo "Error, you must set -parallel mpi_omp if you want XIOS"
429	exit
430	fi
431
432	if [ "$with_xios" = "y" ] ; then
433	opt_makelmdz_xios="-io xios"
434	fi
435
436	if [ "$cosp" = "v2" -a "$with_xios" = "n" ] ; then
437	echo "Error, Cospv2 cannot run without Xios"
438	exit
439	fi
440
441	echo '################################################################'
442	echo Choix des options de compilation
443	echo '################################################################'
444
445	export FC=$compiler
446	export F90=$compiler
447	export F77=$compiler
448	export CPPFLAGS=
449	OPTIMNC=$OPTIM
450	BASE_LD="$OPT_GPROF"
451	OPTPREC="$OPT_GPROF"
452	ARFLAGS="rs"
453	if [ "`lsb_release -i -s`" = "Ubuntu" ] ; then
454	if [ "`lsb_release -r -s \| cut -d. -f1`" -ge 16 ] ; then
455	ARFLAGS="rU"
456	fi
457	fi
458
459	if [ "$compiler" = "$gfortran" ] ; then
460	OPTIM="-O3 $allow_arg_mismatch"
461	OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all -fbacktrace -finit-real=snan $allow_arg_mismatch"
462	OPTDEV="-Wall -fbounds-check $allow_arg_mismatch"
463	fmod='I '
464	OPTPREC="$OPTPREC -cpp -ffree-line-length-0"
465	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE" ; fi
466	export F90FLAGS=" -ffree-form $OPTIMNC"
467	export FFLAGS=" $OPTIMNC"
468	export CC=gcc
469	export CXX=g++
470	export fpp_flags="-P -C -traditional -ffreestanding"
471
472	elif [ $compiler = mpif90 ] ; then
473	OPTIM='-O3'
474	OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all"
475	OPTDEV="-Wall -fbounds-check"
476	BASE_LD="$BASE_LD -lblas"
477	fmod='I '
478	if [ $real = r8 ] ; then
479	OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE -fcray-pointer"
480	fi
481	export F90FLAGS=" -ffree-form $OPTIMNC"
482	export FFLAGS=" $OPTIMNC"
483	export CC=gcc
484	export CXX=g++
485
486	elif [ $compiler = pgf90 ] ; then
487	OPTIM='-O2 -Mipa -Munroll -Mnoframe -Mautoinline -Mcache_align'
488	OPTDEB='-g -Mdclchk -Mbounds -Mchkfpstk -Mchkptr -Minform=inform -Mstandard -Ktrap=fp -traceback'
489	OPTDEV='-g -Mbounds -Ktrap=fp -traceback'
490	fmod='module '
491	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -r8 -DNC_DOUBLE" ; fi
492	export CPPFLAGS="-DpgiFortran"
493	export CC=pgcc
494	export CFLAGS="-O2 -Msignextend"
495	export CXX=pgCC
496	export CXXFLAGS="-O2 -Msignextend"
497	export FFLAGS="-O2 $OPTIMNC"
498	export F90FLAGS="-O2 $OPTIMNC"
499	compile_with_fcm=1
500
501	elif [[ $compiler = ifort \|\| $compiler = mpiifort ]] ; then
502	OPTIM="-O2 -fp-model strict -ip -align all "
503	OPTDEV="-p -g -O2 -traceback -fp-stack-check -ftrapuv -check"
504	OPTDEB="-g -no-ftz -traceback -ftrapuv -fp-stack-check -check"
505	fmod='module '
506	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -real-size 64 -DNC_DOUBLE" ; fi
507	export CPP="icc -E"
508	export FFLAGS="-O2 -ip -fpic -mcmodel=large"
509	export FCFLAGS="-O2 -ip -fpic -mcmodel=large"
510	export CC=icc
511	export CFLAGS="-O2 -ip -fpic -mcmodel=large"
512	export CXX=icpc
513	export CXXFLAGS="-O2 -ip -fpic -mcmodel=large"
514	export fpp_flags="-P -traditional"
515	# Pourquoi forcer la compilation fcm. Marche mieux sans
516	#compile_with_fcm=1
517	else
518	echo unexpected compiler $compiler ; exit
519	fi
520
521	OPTIMGCM="$OPTIM $OPTPREC"
522
523	hostname=`hostname`
524
525	##########################################################################
526	# If installing on known machines such as Jean-Zay at IDRIS,
527	# don't check for available software and don't install netcdf
528	if [ ${hostname:0:5} = jean- ] ; then
529	netcdf=0 # no need to recompile netcdf, alreday available
530	check_linux=0
531	pclinux=0
532	ioipsl=0 # no need to recompile ioipsl, already available
533	#netcdf="/smplocal/pub/NetCDF/4.1.3"
534	compiler="mpiifort"
535	fmod='module '
536	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -i4 -r8 -DNC_DOUBLE" ; fi
537	OPTIM="-auto -align all -O2 -fp-model strict -xHost "
538	OPTIMGCM="$OPTIM $OPTPREC"
539	fi
540	##########################################################################
541
542
543	mkdir -p $MODEL
544	echo $MODEL
545	MODEL=`( cd $MODEL ; pwd )` # to get absolute path, if necessary
546
547
548	if [ "$check_linux" = 1 ] ; then
549	echo '################################################################'
550	echo Check if required software is available
551	echo '################################################################'
552
553	#### Ehouarn: test if the required shell is available
554	#### Maj FH-LF-AS 2021-04 : default=bash ; if bash missing, use ksh
555	use_shell="bash" # default
556	if [ "`which bash`" = "" ] ; then
557	echo "no bash ; we will use ksh"
558	use_shell="ksh"
559	if [ "`which ksh`" = "" ] ; then
560	echo "bash (or ksh) needed!! Install it!"
561	exit
562	fi
563	fi
564
565	for logiciel in wget tar gzip make $compiler gcc cmake m4 c++ ; do
566	if [ "`which $logiciel`" = "" ] ; then
567	echo You must first install $logiciel on your system
568	exit
569	fi
570	done
571
572	if [ $pclinux = 1 ] ; then
573	cd $MODEL
574	cat <<eod > tt.f90
575	print*,'coucou'
576	end
577	eod
578	$compiler tt.f90 -o a.out
579	./a.out >\| tt
580	if [ "`cat tt \| sed -e 's/ //g' `" != "coucou" ] ; then
581	echo problem installing with compiler $compiler ; exit ; fi
582	\rm tt a.out tt.f90
583	fi
584	fi
585
586	###########################################################################
587	if [ $getlmdzor = 1 -a ! -d $MODEL/modipsl ] ; then
588	###########################################################################
589	echo '##########################################################'
590	echo Download a slightly modified version of LMDZ
591	echo '##########################################################'
592	cd $MODEL
593	getlog=`pwd`/get.log
594	echo logfile : $getlog
595	myget src_archives/$trusting/modipsl.$version.tar.gz >> get.log 2>&1
596	echo install_lmdz.sh wget_OK `date`
597	gunzip modipsl.$version.tar.gz >> get.log 2>&1
598	tar xf modipsl.$version.tar >> get.log 2>&1
599	\rm modipsl.$version.tar
600	fi
601
602	###########################################################################
603	echo Installing Netcdf
604	###########################################################################
605
606	if [ $netcdf = 0 ] ; then
607	ncdfdir=/usr
608
609	else
610	cd $MODEL
611
612	case $compiler in
613	gfortran) opt1="-compiler gnu" ; opt2="-CC gcc -FC gfortran -CXX g++" ;;
614	ifort) opt1="-compiler intel" ; opt2="-CC icc -FC ifort -CXX icpc" ;;
615	pgf90) opt1="-compiler pgf90" ; opt2="-CC pgcc -FC pgf90 -CXX pgCC" ;;
616	*) echo "unexpected compiler $compiler" for netcdf ; exit 1
617	esac
618
619	case $with_xios in
620	n) script_install_netcdf=install_netcdf4_hdf5_seq.bash
621	ncdfdir=netcdf4_hdf5_seq
622	opt_=$opt1 ;;
623	y) script_install_netcdf=install_netcdf4_hdf5.bash
624	ncdfdir=netcdf4_hdf5
625	opt_="$opt2 -MPI $root_mpi" ;;
626	*) echo with_xios=$with_xios, should be n or y ; exit 1
627	esac
628	if [ $netcdf = 1 ] ; then
629	ncdfdir=$MODEL/$ncdfdir
630	else
631	mkdir -p $netcdf ; ncdfdir=$netcdf/$ncdfdir
632	fi
633
634	echo Repertoire netcdf $ncdfdir
635	if [ ! -d $ncdfdir ] ; then
636	netcdflog=`pwd`/netcdf.log
637	echo '----------------------------------------------------------'
638	echo Compiling the Netcdf library
639	echo '----------------------------------------------------------'
640	echo log file : $netcdflog
641	myget script_install/$script_install_netcdf >> $netcdflog 2>&1
642	chmod u=rwx $script_install_netcdf
643	./$script_install_netcdf -prefix $ncdfdir $opt_ >> $netcdflog 2>&1
644	fi
645
646	#----------------------------------------------------------------------------
647	# LF rajout d'une verrue, pour une raison non encore expliquee,
648	# la librairie est parfois rangée dans lib64 et non dans lib
649	# par certains compilateurs
650	if [ ! -e lib -a -d lib64 ] ; then ln -s lib64 lib; fi
651	#----------------------------------------------------------------------------
652
653	echo install_lmdz.sh netcdf_OK `date`
654
655	fi
656
657	cat >test_netcdf90.f90 <<EOF
658	use netcdf
659	print *, "NetCDF library version: ", nf90_inq_libvers()
660	end
661	EOF
662
663	$compiler -I$ncdfdir/include test_netcdf90.f90 -L$ncdfdir/lib -lnetcdff \
664	-lnetcdf -Wl,-rpath=$ncdfdir/lib && ./a.out
665
666	if (($? == 0))
667	then
668	rm test_netcdf90.f90 a.out
669	else
670	echo "Failed test program using NetCDF-Fortran."
671	echo "You can:"
672	echo "- check that you have NetCDF-Fortran installed in your system"
673	echo "- or specify an installation directory with option -netcdf of" \
674	"install_lmdz.sh"
675	echo "- or download and compile NetCDF-Fortran with option -netcdf 1 of" \
676	"install_lmdz.sh"
677	exit 1
678	fi
679
680	#=========================================================================
681	if [[ ! -f $MODEL/modipsl/lib/libioipsl.a ]]
682	then
683	if [ $ioipsl = 1 ] ; then
684	#=====================================================================
685	echo OK ioipsl=$ioipsl
686	echo '##########################################################'
687	echo 'Installing MODIPSL, the installation package manager for the '
688	echo 'IPSL models and tools'
689	echo '##########################################################'
690	echo `date`
691
692	cd $MODEL/modipsl
693	\rm -rf lib/*
694	cd util
695	cp AA_make.gdef AA_make.orig
696	F_C="$compiler -c "
697	if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ]
698	then
699	F_C="$compiler -c -cpp "
700	fi
701	if [ "$compiler" = "pgf90" ] ; then F_C="$compiler -c -Mpreprocess" ; fi
702	sed -e 's/^\#..g95..\#.*.$/\#/' AA_make.gdef > tmp
703	sed -e "s:F_L = g95:F_L = $compiler:" \
704	-e "s:F_C = g95 -c -cpp:F_C = $F_C": \
705	-e 's/g95..w_w..(F_D)/g95 w_w = '"$OPTIMGCM"'/' \
706	-e 's:g95..NCDF_INC..$:g95 NCDF_INC= '"$ncdfdir"'/include:' \
707	-e 's:g95..NCDF_LIB..$:g95 NCDF_LIB= -L'"$ncdfdir"'/lib -lnetcdff -lnetcdf:' \
708	-e 's:g95 L_O =:g95 L_O = -Wl,-rpath='"$ncdfdir"'/lib:' \
709	-e "s:-fmod=:-$fmod:" -e 's/-fno-second-underscore//' \
710	-e 's:#-Q- g95 M_K = gmake:#-Q- g95 M_K = make:' \
711	tmp >\| AA_make.gdef
712
713	if [ $pcmac == 1 ]
714	then
715	cp AA_make.gdef tmp
716	sed -e 's/rpath=/rpath,/g' tmp > AA_make.gdef
717	fi
718
719
720	# We use lines for g95 even for the other compilers to run ins_make
721	if [ "$use_shell" = "ksh" ] ; then
722	./ins_make $o_ins_make
723	else # bash
724	sed -e s:/bin/ksh:/bin/bash:g ins_make > ins_make.bash
725	if [ "`grep jeanzay AA_make.gdef`" = "" ] ; then
726	# Bidouille pour compiler sur ada des vieux modipsl.tar
727	echo 'Warning jean-zay not in AA_make.gdef'
728	echo 'Think about updating'
729	exit 1
730	fi
731
732	chmod u=rwx ins_make.bash
733	./ins_make.bash $o_ins_make
734	fi # of if [ "$use_shell" = "ksh" ]
735
736	echo install_lmdz.sh MODIPSL_OK `date`
737
738	cd $MODEL/modipsl/modeles/IOIPSL/src
739	ioipsllog=`pwd`/ioipsl.log
740	echo '##########################################################'
741	echo 'Compiling IOIPSL, the interface library with Netcdf'
742	echo '##########################################################'
743	echo `date`
744	echo log file : $ioipsllog
745
746	if [ "$use_shell" = "bash" ] ; then
747	cp Makefile Makefile.ksh
748	sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile
749	fi
750	### if [ "$pclinux" = 1 ] ; then
751	# Build IOIPSL modules and library
752	$make clean
753	$make > $ioipsllog 2>&1
754	if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then
755	# copy module files to lib
756	cp -f *.mod ../../../lib
757	fi
758	# Build IOIPSL tools (ie: "rebuild", if present)
759	# For IOIPSLv_2_2_2, "rebuild" files are in IOIPSL/tools
760	rebuild_dir=""
761	if [ -f $MODEL/modipsl/modeles/IOIPSL/tools/rebuild ] ; then
762	rebuild_dir=$MODEL/modipsl/modeles/IOIPSL/tools
763	elif [ -d $MODEL/modipsl/modeles/IOIPSL/rebuild ] ; then
764	rebuild_dir=$MODEL/modipsl/modeles/IOIPSL/rebuild
765	fi
766	if [ $rebuild_dir != "" ] ; then
767	cd $rebuild_dir
768	# adapt Makefile & rebuild script if in bash
769	if [ "$use_shell" = "bash" ] ; then
770	cp Makefile Makefile.ksh
771	sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile
772	cp rebuild rebuild.ksh
773	sed -e 's:/bin/ksh:/bin/bash:g' \
774	-e 's:print -u2:echo:g' \
775	-e 's:print:echo:g' rebuild.ksh > rebuild
776	fi
777	$make clean
778	$make > $ioipsllog 2>&1
779	fi
780	### fi # of if [ "$pclinux" = 1 ] which is commented out
781
782	else # of if [ $ioipsl = 1 ]
783	if [ ${hostname:0:5} = jean- ] ; then
784	cd $MODEL/modipsl
785	cd util
786	if [ "`grep jeanzay AA_make.gdef`" = "" ] ; then
787	echo 'Warning jean-zay not in AA_make.gdef'
788	echo 'Think about updating'
789	exit 1
790	fi
791	./ins_make $o_ins_make
792	# Compile IOIPSL on jean-zay
793	cd $MODEL/modipsl/modeles/IOIPSL/src
794	gmake > ioipsl.log
795	# For IOIPSLv_2_2_2, "rebuild" files are in IOIPSL/tools, so "gmake" in IOIPSL/tools is enough
796	# For IOIPSLv_2_2_5, "rebuild" files are in a separate IOIPSL/rebuild folder , while "tools" only contains "FCM"
797	if [ -f $MODEL/modipsl/modeles/IOIPSL/tools/Makefile ] ; then
798	cd $MODEL/modipsl/modeles/IOIPSL/tools
799	gmake > ioipsl.log
800	fi
801	if [ -d $MODEL/modipsl/modeles/IOIPSL/rebuild ] ; then
802	cd $MODEL/modipsl/modeles/IOIPSL/rebuild
803	gmake > ioipsl.log
804	fi
805
806	fi
807	echo install_lmdz.sh ioipsl_OK `date`
808	fi # of if [ $ioipsl = 1 ]
809	fi # of if [[ ! -f $MODEL/modipsl/lib/libioipsl.a ]]
810
811	#=========================================================================
812	if [ "$with_xios" = "y" ] ; then
813	echo '##########################################################'
814	echo 'Compiling XIOS'
815	echo '##########################################################'
816	cd $MODEL/modipsl/modeles
817	xioslog=`pwd`/XIOS/xios.log
818	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/install_xios.bash
819	myget script_install/install_xios.bash
820	chmod u=rwx install_xios.bash
821	# following will be recalculated later on once LMDZ is updated
822	# mysvn=`svnversion LMDZ \| egrep -o "[0-9]+" 2>/dev/null`
823	mysvn=`grep 'Revision: [0-9]' $MODEL/Read*.md \| awk ' { print $2 } ' 2>/dev/null`
824	if [ "$svn" != "" ] ; then mysvn=$svn ; fi
825	echo mysvn $mysvn
826
827	if [ ${hostname:0:5} = jean- ] ; then
828	if [ $mysvn -ge 4619 ] ; then
829	svn co http://forge.ipsl.fr/ioserver/svn/XIOS2/branches/xios-2.6 \
830	XIOS
831	else
832	svn co http://forge.ipsl.fr/ioserver/svn/XIOS2/branches/xios-2.5 \
833	XIOS
834	fi
835	cd XIOS/arch
836	svn update
837	cd ..
838	echo "Compiling XIOS, start" `date` \
839	echo "log file: $xioslog"
840	#./make_xios --prod --arch $arch --job 4 > xios.log 2>&1
841	cat > compile_xios.sh <<EOD
842	./make_xios --prod --arch X64_JEANZAY --full --job 4 > xios.log 2>&1
843	EOD
844	srun --pty --ntasks=1 --cpus-per-task=20 --hint=nomultithread -t 00:30:00 \
845	--account=gzi@cpu --qos=qos_cpu-dev bash ./compile_xios.sh
846
847	else
848	./install_xios.bash -prefix $MODEL/modipsl/modeles \
849	-netcdf ${ncdfdir} -hdf5 ${ncdfdir} \
850	-MPI $root_mpi -arch $arch > xios.log 2>&1
851	fi # of case Jean-Zay
852	if [ -f XIOS/lib/libxios.a ] ; then
853	echo "XIOS library successfully generated"
854	echo install_lmdz.sh XIOS_OK `date`
855	fi
856	fi
857
858	#============================================================================
859	veget_version=false
860	if [ "$veget" != 'NONE' ] ; then
861	cd $MODEL/modipsl/modeles/ORCHIDEE
862	set +e ; svn upgrade ; set -e
863	if [ "$veget" = "CMIP6" ] ; then
864	veget_version=orchidee2.0
865	orchidee_rev=6592
866	else # specific orchidee revision newer than CMIP6, on 2_1 or 2_2 branches
867	veget_version=orchidee2.1
868	orchidee_rev=$veget
869	if [ $veget -lt 4465 ] ; then
870	echo 'Stopping, ORCHIDEE version too old, script needs work on ' \
871	'the CPP flags to pass to makelmdz'
872	exit 1
873	fi
874	set +e
875	# which branch is my version on?
876	orcbranch=`svn log -v -q svn://forge.ipsl.fr/orchidee/ -r $veget \|grep ORCHIDEE \|head -1\| sed -e 's:ORCHIDEE/.*$:ORCHIDEE:' \| awk '{print $2}'`
877	# switch to that branch
878	echo IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at \
879	orchidee-help@listes.ipsl.fr
880	svn switch -r $veget --accept theirs-full \
881	svn://forge.ipsl.fr/orchidee/$orcbranch
882	svn log -r $veget \| grep $veget
883	if [ $? -gt 0 ] ; then
884	echo 'Cannot update ORCHIDEE as not on the right branch for ' \
885	'ORCHIDEE'
886	exit
887	fi
888	set -e
889	set +e ; svn update -r $veget ; set -e
890	fi
891	# Correctif suite debug Jean-Zay
892	sed -i -e 's/9010 FORMAT(A52,F17.14)/9010 FORMAT(A52,F20.14)/' \
893	src_stomate/stomate.f90
894	opt_orc="-prod" ; if [ "$optim" = "-debug" ] ; then opt_orc="-debug" ; fi
895
896	orchideelog=`pwd`/orchidee.log
897	echo '########################################################'
898	echo 'Compiling ORCHIDEE, the continental surface model '
899	echo '########################################################'
900	echo Start of the first compilation of orchidee, in sequential mode: `date`
901	echo log file : $orchideelog
902
903	export ORCHPATH=`pwd`
904	xios_orchid="-noxios"
905	if [ "$with_xios" = "y" ] ; then
906	xios_orchid="-xios"
907	fi
908	if [ -d tools ] ; then
909	###################################################################
910	# Pour les experts qui voudraient changer de version d'orchidee.
911	# Attention : necessite d'avoir le password pour orchidee
912
913	# Correctif suite debug Jean-Zay
914	if [ -f src_global/time.f90 ] ; then
915	sed -i -e 's/CALL tlen2itau/\!CALL tlen2itau/' src_global/time.f90
916	fi
917	###################################################################
918	if [ "$veget_version" == "false" ] ; then
919	veget_version=orchidee2.0
920	fi
921	cd arch
922	sed -e s:"%COMPILER .*.$":"%COMPILER $compiler":1 \
923	-e s:"%LINK .*.$":"%LINK $compiler":1 \
924	-e s:"%FPP_FLAGS .*.$":"%FPP_FLAGS $fpp_flags":1 \
925	-e s:"%PROD_FFLAGS .*.$":"%PROD_FFLAGS $OPTIM":1 \
926	-e s:"%DEV_FFLAGS .*.$":"%DEV_FFLAGS $OPTDEV":1 \
927	-e s:"%DEBUG_FFLAGS .*.$":"%DEBUG_FFLAGS $OPTDEB":1 \
928	-e s:"%BASE_FFLAGS .*.$":"%BASE_FFLAGS $OPTPREC":1 \
929	-e s:"%BASE_LD .*.$":"%BASE_LD $BASE_LD":1 \
930	-e s:"%ARFLAGS .*.$":"%ARFLAGS $ARFLAGS":1 \
931	arch-gfortran.fcm > arch-local.fcm
932	echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib -lnetcdff -lnetcdf\"" \
933	> arch-local.path
934	echo "NETCDF_INCDIR=${ncdfdir}/include" >> arch-local.path
935	echo "IOIPSL_INCDIR=$ORCHPATH/../../lib" >> arch-local.path
936	echo "IOIPSL_LIBDIR=$ORCHPATH/../../lib" >> arch-local.path
937	echo 'XIOS_INCDIR=${ORCHDIR}/../XIOS/inc' >> arch-local.path
938	echo 'XIOS_LIBDIR="${ORCHDIR}/../XIOS/lib -lxios"' >> arch-local.path
939	cd ../
940
941	echo ./makeorchidee_fcm -j $xios_orchid $opt_orc -parallel none \
942	-arch $arch
943	./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel none \
944	-arch $arch > $orchideelog 2>&1
945	pwd
946	else # of "if [ -d tools ]"
947	if [ -d src_parallel ] ; then
948	liste_src="parallel parameters global stomate sechiba driver"
949	if [ "$veget_version" == "false" ] ; then
950	veget_version=orchidee2.0
951	fi
952	fi
953	for d in $liste_src ; do
954	src_d=src_$d
955	echo src_d $src_d
956	echo ls ; ls
957	if [ ! -d $src_d ] ; then
958	echo Problem orchidee : no $src_d ; exit
959	fi
960	cd $src_d ; \rm -f *.mod make ; $make clean
961	$make > $orchideelog 2>&1
962	if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then
963	cp -f *.mod ../../../lib
964	fi
965	cd ..
966	done
967	fi # of "if [ -d tools ]"
968	echo install_lmdz.sh orchidee_compil_seq_OK `date`
969	fi # of if [ "$veget" != 'NONE' ]
970
971
972	#============================================================================
973	# Ehouarn: the directory name LMDZ* depends on version/tar file...
974	if [ -d $MODEL/modipsl/modeles/LMD* ] ; then
975	echo '###############################################################'
976	echo 'Preparing LMDZ compilation : arch file, svn switch if needed...'
977	echo '###############################################################'
978	cd $MODEL/modipsl/modeles/LMD*
979	LMDZPATH=`pwd`
980	else
981	echo "ERROR: No LMD* directory !!!"
982	exit
983	fi
984
985	###########################################################
986	# For those who want to use fcm to compile via :
987	# makelmdz_fcm -arch local .....
988	############################################################
989
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 'https:'
1004	if [ $? = 0 ] ; then
1005	svn switch --relocate https://svn.lmd.jussieu.fr/LMDZ \
1006	http://svn.lmd.jussieu.fr/LMDZ
1007	fi
1008	svn update $svnopt
1009	set -e
1010	fi
1011
1012	#---------------------------------------------------------------------
1013	# Retrieve the final svn release number, and adjust compilation
1014	# options accordingly
1015	# If svn not available, will use the svn writen in $MODEL/Readm*md
1016	# For old version it assumes that it is before 4185 (the version
1017	# for which the test was introduced
1018	#---------------------------------------------------------------------
1019
1020	set +e ; mysvn=`svnversion . \| egrep -o "[0-9]+" 2>/dev/null` ; set -e
1021	if [ "$mysvn" = "" ] ; then mysvn=`grep 'Revision: [0-9]' $MODEL/Read*.md \| awk ' { print $2 } ' 2>/dev/null` ; fi
1022	if [ "$mysvn" = "" ] ; then mysvn=4190 ; fi
1023
1024	if [[ "$pclinux" = "1" && ! -f arch/arch-local.path ]] ; then
1025
1026	# create local 'arch' files (if on Linux PC):
1027	cd arch
1028	# arch-local.path file
1029	# test for version as arch.pth file changed format with rev 4426
1030	if [ "$mysvn" -gt 4425 ] ; then
1031	echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib \"" > arch-local.path
1032	echo "NETCDF_LIB=\"-lnetcdff -lnetcdf\"" >> arch-local.path
1033	echo "NETCDF_INCDIR=-I${ncdfdir}/include" >> arch-local.path
1034	echo 'NETCDF95_INCDIR=-I$LMDGCM/../../include' >> arch-local.path
1035	echo 'NETCDF95_LIBDIR=-L$LMDGCM/../../lib' >> arch-local.path
1036	echo 'NETCDF95_LIB=-lnetcdf95' >> arch-local.path
1037	echo 'IOIPSL_INCDIR=-I$LMDGCM/../../lib' >> arch-local.path
1038	echo 'IOIPSL_LIBDIR=-L$LMDGCM/../../lib' >> arch-local.path
1039	echo 'IOIPSL_LIB=-lioipsl' >> arch-local.path
1040	echo 'XIOS_INCDIR=-I$LMDGCM/../XIOS/inc' >> arch-local.path
1041	echo 'XIOS_LIBDIR=-L$LMDGCM/../XIOS/lib' >> arch-local.path
1042	echo "XIOS_LIB=\"-lxios -lstdc++\"" >> arch-local.path
1043	echo 'ORCH_INCDIR=-I$LMDGCM/../../lib' >> arch-local.path
1044	echo 'ORCH_LIBDIR=-L$LMDGCM/../../lib' >> arch-local.path
1045	else
1046	echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib -lnetcdff -lnetcdf\"" \
1047	> arch-local.path
1048	echo "NETCDF_INCDIR=-I${ncdfdir}/include" >> arch-local.path
1049	echo 'NETCDF95_INCDIR=$LMDGCM/../../include' >> arch-local.path
1050	echo 'NETCDF95_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
1051	echo 'IOIPSL_INCDIR=$LMDGCM/../../lib' >> arch-local.path
1052	echo 'IOIPSL_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
1053	echo 'XIOS_INCDIR=$LMDGCM/../XIOS/inc' >> arch-local.path
1054	echo 'XIOS_LIBDIR=$LMDGCM/../XIOS/lib' >> arch-local.path
1055	echo 'ORCH_INCDIR=$LMDGCM/../../lib' >> arch-local.path
1056	echo 'ORCH_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
1057	fi
1058
1059	if [ $pcmac == 1 ] ; then
1060	BASE_LD="$BASE_LD -Wl,-rpath,${ncdfdir}/lib"
1061	else
1062	BASE_LD="$BASE_LD -Wl,-rpath=${ncdfdir}/lib"
1063	fi
1064	# Arch-local.fcm file (adapted from arch-linux-32bit.fcm)
1065
1066	if [ $real = r8 ] ; then FPP_DEF=NC_DOUBLE ; else FPP_DEF="" ; fi
1067	sed -e s:"%COMPILER .*.$":"%COMPILER $compiler":1 \
1068	-e s:"%LINK .*.$":"%LINK $compiler":1 \
1069	-e s:"%PROD_FFLAGS .*.$":"%PROD_FFLAGS $OPTIM":1 \
1070	-e s:"%DEV_FFLAGS .*.$":"%DEV_FFLAGS $OPTDEV":1 \
1071	-e s:"%DEBUG_FFLAGS .*.$":"%DEBUG_FFLAGS $OPTDEB":1 \
1072	-e s:"%BASE_FFLAGS .*.$":"%BASE_FFLAGS $OPTPREC":1 \
1073	-e s:"%FPP_DEF .*.$":"%FPP_DEF $FPP_DEF":1 \
1074	-e s:"%BASE_LD .*.$":"%BASE_LD $BASE_LD":1 \
1075	-e s:"%ARFLAGS .*.$":"%ARFLAGS $ARFLAGS":1 \
1076	arch-linux-32bit.fcm > arch-local.fcm
1077
1078	cd ..
1079	### Adapt "bld.cfg" (add the shell):
1080	#whereisthatshell=$(which ${use_shell})
1081	#echo "bld::tool::SHELL $whereisthatshell" >> bld.cfg
1082
1083	fi # of if [ "$pclinux" = 1 ]
1084	#---------------------------------------------------------------------
1085	# Option de compilation du rayonnement : depend de $mysvn ><= r4185
1086	#---------------------------------------------------------------------
1087	opt_rad=""
1088
1089	case $rad in
1090	oldrad) iflag_rrtm=0 ; NSW=2 ; opt_rad="" ;;
1091	rrtm) iflag_rrtm=1 ; NSW=6
1092	if [ $mysvn -le 4185 ] ; then
1093	opt_rad="-rrtm true"
1094	else
1095	opt_rad="-rad rrtm"
1096	fi ;;
1097	ecrad) iflag_rrtm=2 ; NSW=6 ; opt_rad="-rad ecrad" ;;
1098	*) echo Only oldrad rrtm ecrad for rad option ; exit
1099	esac
1100
1101	if [ $mysvn -le 4185 -a $rad = "ecrad" ] ; then
1102	echo "ecrad only available for LMDZ rev starting with 4186 " ; exit
1103	fi
1104
1105	##################################################################
1106
1107
1108	if [[ ! -f libf/misc/netcdf95.F90 && ! -d $MODEL/NetCDF95-0.3 ]]
1109	then
1110	cd $MODEL
1111	myget src_archives/netcdf/NetCDF95-0.3.tar.gz
1112	tar -xf NetCDF95-0.3.tar.gz
1113	rm NetCDF95-0.3.tar.gz
1114	cd NetCDF95-0.3
1115	mkdir build
1116	cd build
1117	cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=$ncdfdir \
1118	-DCMAKE_INSTALL_PREFIX=$MODEL/modipsl
1119	make install
1120	cd $MODEL/modipsl/modeles/LMDZ*
1121	fi
1122
1123	echo '##################################################################'
1124	echo "Preparing script compile.sh for LMDZ compilation"
1125	echo "It will only be run automatically if bench=1/tuto"
1126	echo Here bench=$bench
1127	echo '##################################################################'
1128
1129	if [ "$env_file" != "" ] ; then
1130	mv arch/arch-${arch}.env arch/arch-${arch}.orig
1131	\cp -f $env_file arch/arch-${arch}.env
1132	fi
1133
1134	if [ $compile_with_fcm = 1 ] ; then
1135	makelmdz="makelmdz_fcm $optim -arch $arch -j 8 "
1136	else
1137	makelmdz="makelmdz $optim -arch $arch"
1138	fi
1139
1140	# sequential compilation
1141	if [ "$sequential" = 1 ] ; then
1142	echo Sequential compilation command, saved in compile.sh:
1143	echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp " \
1144	"-d ${grid_resolution} -v $veget_version gcm "
1145	echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp " \
1146	"-d ${grid_resolution} -v $veget_version gcm " > compile.sh
1147	chmod +x ./compile.sh
1148	if [ $bench = 1 ] ; then
1149	echo install_lmdz.sh start_lmdz_seq_compilation `date`
1150	echo log file: $lmdzlog
1151	./compile.sh > $lmdzlog 2>&1
1152	echo install_lmdz.sh end_lmdz_seq_compilation `date`
1153	fi
1154	fi # fin sequential
1155
1156	# compiling in parallel mode
1157	if [ $parallel != "none" ] ; then
1158	echo '##########################################################'
1159	echo ' Parallel compile '
1160	echo '##########################################################'
1161	echo "(after saving the sequential libs and binaries)"
1162	cd $MODEL/modipsl
1163	tar cf sequential.tar bin/ lib/
1164	#
1165	# Orchidee
1166	#
1167	cd $ORCHPATH
1168	if [ -d src_parallel -a $veget != 'NONE' ] ; then
1169	cd arch
1170	sed \
1171	-e s:"%COMPILER.*.$":"%COMPILER $par_comp":1 \
1172	-e s:"%LINK.*.$":"%LINK $par_comp":1 \
1173	-e s:"%MPI_FFLAG.*.$":"%MPI_FFLAGS $MPI_FLAGS":1 \
1174	-e s:"%OMP_FFLAG.*.$":"%OMP_FFLAGS $OMP_FLAGS":1 \
1175	-e s:"%MPI_LD.*.$":"%MPI_LD $MPI_LD":1 \
1176	-e s:"%OMP_LD.*.$":"%OMP_LD $OMP_LD":1 \
1177	arch-local.fcm > tmp.fcm
1178
1179	mv tmp.fcm arch-local.fcm
1180	cd ../
1181	echo Compiling ORCHIDEE in parallel mode `date`
1182	echo logfile $orchideelog
1183	echo "NOTE : to recompile it when necessary, use ./compile_orc.sh " \
1184	"in modipsl/modeles/ORCHIDEE"
1185	echo ./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc \
1186	-parallel $parallel -arch $arch > compile_orc.sh
1187	echo ./makeorchidee_fcm -j 8 $xios_orchid $opt_orc \
1188	-parallel $parallel -arch $arch >> compile_orc.sh
1189	echo echo Now you must also recompile LMDZ, by running ./compile.sh \
1190	in modeles/LMDZ >> compile_orc.sh
1191	chmod u+x compile_orc.sh
1192	./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc \
1193	-parallel $parallel -arch $arch > $orchideelog 2>&1
1194	./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel $parallel \
1195	-arch $arch >> $orchideelog 2>&1
1196	echo End of ORCHIDEE compilation in parallel mode `date`
1197	elif [ $veget != 'NONE' ] ; then
1198	echo '##########################################################'
1199	echo ' Orchidee version too old '
1200	echo ' Please update to new version '
1201	echo '##########################################################'
1202	exit
1203	fi # of [ -d src_parallel -a $veget != 'NONE' ]
1204
1205	# LMDZ
1206	cd $LMDZPATH
1207	if [ $arch = local ] ; then
1208	cd arch
1209	sed -e s:"%COMPILER.*.$":"%COMPILER $par_comp":1 \
1210	-e s:"%LINK.*.$":"%LINK $par_comp":1 \
1211	-e s:"%MPI_FFLAG.*.$":"%MPI_FFLAGS $MPI_FLAGS":1 \
1212	-e s:"%OMP_FFLAG.*.$":"%OMP_FFLAGS $OMP_FLAGS":1 \
1213	-e s:"%ARFLAGS.*.$":"%ARFLAGS $ARFLAGS":1 \
1214	-e s@"%BASE_LD.*.$"@"%BASE_LD -Wl,-rpath=${root_mpi}/lib:${ncdfdir}/lib"@1 \
1215	-e s:"%MPI_LD.*.$":"%MPI_LD $MPI_LD":1 \
1216	-e s:"%OMP_LD.*.$":"%OMP_LD $OMP_LD":1 \
1217	arch-local.fcm > tmp.fcm
1218	mv tmp.fcm arch-local.fcm
1219	cd ../
1220	fi
1221	rm -f compile.sh
1222	echo resol=${grid_resolution} >> compile.sh
1223	if [ ${hostname:0:5} = jean- -a "$cosp" = "v2" ] ; then
1224
1225	echo LMDZ compilation command in parallel mode, saved in compile.sh, \
1226	is :
1227	echo "(ATTENTION le probleme de cospv2 sur jean-zay en mode prod " \
1228	"n est pas corrige ! )"
1229	# ATTENTION le probleme de cospv2 sur jean-zay en mode prod n
1230	# est pas corrige
1231	echo ./$makelmdz -dev $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
1232	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
1233	-parallel $parallel gcm >> compile.sh
1234	echo ./$makelmdz -dev $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
1235	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
1236	-parallel $parallel gcm
1237	else
1238	echo ./$makelmdz $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
1239	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
1240	-parallel $parallel gcm >> compile.sh
1241	echo ./$makelmdz $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
1242	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
1243	-parallel $parallel gcm
1244	fi
1245	chmod +x ./compile.sh
1246
1247	if [ $bench = 1 ] ; then
1248	echo Compiling LMDZ in parallel mode `date`, LMDZ log file: $lmdzlog
1249	./compile.sh > $lmdzlog 2>&1
1250	fi
1251
1252	fi # of if [ $parallel != "none" ]
1253
1254
1255	##################################################################
1256	# Verification du succes de la compilation
1257	##################################################################
1258
1259	# Recherche de l'executable dont le nom a change au fil du temps ...
1260	# suffix contains radiative option starting with revision 4186
1261	if [ $mysvn -ge 4186 ] ; then suff_exe=_${rad}${suff_exe} ; fi
1262	gcm=""
1263
1264	for exe in gcm.e bin/gcm_${grid_resolution}_phylmd${suff_exe}${suff_orc}.e
1265	do
1266	if [ -f $exe ] ; then gcm=$exe ; fi
1267	done
1268
1269	if [ "$gcm" = "" ] ; then
1270	if [ $bench = 1 ] ; then
1271	echo 'Compilation failed !! Cannot run the benchmark;'
1272	exit
1273	else
1274	echo 'Compilation not done (only done when bench=1)'
1275	fi
1276	else
1277	echo '##########################################################'
1278	echo 'Compilation successfull !! ' `date`
1279	echo '##########################################################'
1280	echo The executable is $gcm
1281	fi
1282
1283	##################################################################
1284	# Below, we run a benchmark if bench=1 or tuto
1285	##################################################################
1286
1287	if [ $bench = tuto ] ; then
1288	myget Training/tutorial.tar ; tar xf tutorial.tar ; cd TUTORIAL
1289	./init.sh
1290
1291	elif [[ $bench = 1 && ! -d BENCH${grid_resolution} ]] ; then
1292	# TOUTE CETTE SECTION DEVRAIT DISPARAITRE POUR UNE COMMANDE
1293	# OU DES BENCHS PAR MOTS CLES COMME tuto
1294
1295	echo '##########################################################'
1296	echo ' Running a test run '
1297	echo '##########################################################'
1298
1299	\rm -rf BENCH${grid_resolution}
1300	bench=bench_lmdz_${grid_resolution}
1301	echo install_lmdz.sh before bench download `date`
1302	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/$bench.tar.gz
1303	myget 3DBenchs/$bench.tar.gz
1304	echo install_lmdz.sh after bench download `date`
1305	tar xf $bench.tar.gz
1306
1307	if [ "$cosp" = "v1" -o "$cosp" = "v2" ] ; then
1308	cd BENCH${grid_resolution}
1309	# copier les fichiers namelist input et output our COSP
1310	cp ../DefLists/cosp*_input_nl.txt .
1311	cp ../DefLists/cosp*_output_nl.txt .
1312	# Activer la cles ok_cosp pour tourner avec COSP
1313	sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp
1314	\mv -f tmp config.def
1315	cd ..
1316	fi
1317
1318	if [ -n "$physiq" ]; then
1319	cd BENCH${grid_resolution}
1320	if [ -f physiq.def_${physiq} ]; then
1321	cp physiq.def_${physiq} physiq.def
1322	echo using physiq.def_${physiq}
1323	else
1324	echo using standard physiq.def
1325	fi
1326	cd ..
1327	else
1328	echo using standard physiq.def
1329	fi
1330
1331	if [ "$with_xios" = "y" ] ; then
1332	cd BENCH${grid_resolution}
1333	cp ../DefLists/iodef.xml .
1334	cp ../DefLists/context_lmdz.xml .
1335	cp ../DefLists/field_def_lmdz.xml .
1336	# A raffiner par la suite
1337	echo A FAIRE : Copier les *xml en fonction de l option cosp
1338	cp ../DefLists/field_def_cosp*.xml .
1339	cp ../DefLists/file_def_hist*xml .
1340	# adapt iodef.xml to use attached mode
1341	sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' \
1342	iodef.xml > tmp
1343	\mv -f tmp iodef.xml
1344
1345	# and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
1346	# except for histday
1347	for histfile in file_def_hist*xml
1348	do
1349	if [ "$histfile" = "file_def_histday_lmdz.xml" ] ; then
1350	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' \
1351	$histfile > tmp
1352	\mv -f tmp $histfile
1353	sed -e 's@output_level="_AUTO_"@output_level="5"@' $histfile \
1354	> tmp
1355	\mv -f tmp $histfile
1356	sed -e 's@compression_level="2"@compression_level="0"@' \
1357	$histfile > tmp
1358	\mv -f tmp $histfile
1359	else
1360	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
1361	$histfile > tmp
1362	\mv -f tmp $histfile
1363	fi
1364	done
1365	# and add option "ok_all_xml=y" in config.def
1366	echo "### XIOS outputs" >> config.def
1367	echo 'ok_all_xml=.true.' >> config.def
1368
1369	#activer les sorties pour Cosp
1370	if [ "$cosp" = "v1" ] ; then
1371	sed -i'' -e 's@enabled=".FALSE."@enabled=".TRUE."@' \
1372	-e 's@output_level="_AUTO_"@output_level="5"@' \
1373	-e 's@compression_level="2"@compression_level="0"@' \
1374	file_def_histdayCOSP_lmdz.xml
1375	fi
1376	if [ "$cosp" = "v2" ] ; then
1377	sed -e 's@compression_level="2"@compression_level="0"@' file_def_histdayCOSPv2_lmdz.xml
1378	for type_ in hf day mth ; do
1379	file=file_def_hist${type_}COSP
1380	sed -i'' -e 's@src="./'${file}'_lmdz.xml"@src="./'${file}'v2_lmdz.xml"@' context_lmdz.xml
1381	done
1382	sed -i '' -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' field_def_lmdz.xml
1383	fi
1384
1385	cd ..
1386	fi
1387
1388	# Cas Bensh avec ecrad
1389	if [ "$rad" = "ecrad" ] ; then
1390	cd BENCH${grid_resolution}
1391	cp ../DefLists/namelist_ecrad .
1392	cp -r ../libf/phylmd/ecrad/data .
1393	cd ..
1394	fi
1395
1396	# Adjusting bench physiq.def to radiative code chosen
1397	cd BENCH${grid_resolution}
1398	sed -e 's/iflag_rrtm=.*.$/iflag_rrtm='$iflag_rrtm'/' \
1399	-e 's/NSW=.*.$/NSW='$NSW'/' physiq.def > tmpdef
1400	\mv tmpdef physiq.def
1401	cd ..
1402
1403	cp $gcm BENCH${grid_resolution}/gcm.e
1404
1405	cd BENCH${grid_resolution}
1406	# On cree le fichier bench.sh au besoin
1407	# Dans le cas 48x36x39 le bench.sh existe deja en parallele
1408
1409	if [ "$grid_resolution" = "48x36x39" ] ; then
1410	echo On ne touche pas au bench.sh
1411	# But we have to adapt "run_local.sh" for $mpirun
1412	sed -e "s@mpirun@$mpirun@g" run_local.sh > tmp
1413	mv -f tmp run_local.sh
1414	chmod u=rwx run_local.sh
1415	elif [ "${parallel:0:3}" = "mpi" ] ; then
1416	# Lancement avec deux procs mpi et 2 openMP
1417	echo "export OMP_STACKSIZE=800M" > bench.sh
1418	if [ "${parallel:4:3}" = "omp" ] ; then
1419	echo "export OMP_NUM_THREADS=2" >> bench.sh
1420	fi
1421	if [ "$cosp" = "v1" -o "$cosp" = "v2" ] ; then
1422	if [ ${hostname:0:5} = jean- ] ; then
1423	chmod +x ../arch.env
1424	../arch.env
1425	echo "ulimit -s 2000000" >> bench.sh
1426	else
1427	echo "ulimit -s 200000" >> bench.sh
1428	fi
1429	else
1430	echo "ulimit -s unlimited" >> bench.sh
1431	fi
1432	if [ ${hostname:0:5} = jean- ] ; then
1433	. ../arch/arch-${arch}.env
1434	echo "srun -n 2 -A $idris_acct@cpu gcm.e > listing 2>&1" \
1435	>> bench.sh
1436	else
1437	echo "$mpirun -np 2 gcm.e > listing 2>&1" >> bench.sh
1438	fi
1439	# Add rebuild, using reb.sh if it is there
1440	echo 'if [ -f reb.sh ] ; then' >> bench.sh
1441	echo ' ./reb.sh histday ; ./reb.sh histmth ; ./reb.sh histhf ; ' \
1442	'./reb.sh histins ; ./reb.sh stomate_history ; ' \
1443	'./reb.sh sechiba_history ; ./reb.sh sechiba_out_2 ' >> bench.sh
1444	echo 'fi' >> bench.sh
1445	else
1446	echo "./gcm.e > listing 2>&1" > bench.sh
1447	fi
1448	# Getting orchidee stuff
1449	if [ $veget == 'CMIP6' ] ; then
1450	#echo 'myget 3DBenchs/BENCHorch11.tar.gz'
1451	#myget 3DBenchs/BENCHorch11.tar.gz
1452	#tar xvzf BENCHorch11.tar.gz
1453	echo 'myget 3DBenchs/BENCHCMIP6.tar.gz'
1454	myget 3DBenchs/BENCHCMIP6.tar.gz
1455	tar xvzf BENCHCMIP6.tar.gz
1456	sed -e "s:VEGET=n:VEGET=y:" config.def > tmp
1457	mv -f tmp config.def
1458	if [ "$with_xios" = "y" ] ; then
1459	cp ../../ORCHIDEE/src_xml/context_orchidee.xml .
1460	echo '<context id="orchidee" src="./context_orchidee.xml"/>' \
1461	> add.tmp
1462	cp ../../ORCHIDEE/src_xml/field_def_orchidee.xml .
1463	cp ../../ORCHIDEE/src_xml/file_def_orchidee.xml .
1464	cp ../../ORCHIDEE/src_xml/file_def_input_orchidee.xml .
1465	if [ -f ../../ORCHIDEE/src_xml/context_input_orchidee.xml ] ; then
1466	cp ../../ORCHIDEE/src_xml/context_input_orchidee.xml .
1467	echo '<context id="orchidee" ' \
1468	'src="./context_input_orchidee.xml"/>' >> add.tmp
1469	fi
1470	sed -e '/id="LMDZ"/r add.tmp' iodef.xml > tmp
1471	mv tmp iodef.xml
1472	sed -e'{/sechiba1/ s/enabled="_AUTO_"/type="one_file" enabled=".TRUE."/}' \
1473	file_def_orchidee.xml > tmp
1474	\mv -f tmp file_def_orchidee.xml
1475	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
1476	file_def_orchidee.xml > tmp
1477	\mv -f tmp file_def_orchidee.xml
1478	sed -e 's@output_level="_AUTO_"@output_level="1"@' \
1479	file_def_orchidee.xml > tmp
1480	\mv -f tmp file_def_orchidee.xml
1481	sed -e 's@output_freq="_AUTO_"@output_freq="1d"@' \
1482	file_def_orchidee.xml > tmp
1483	\mv -f tmp file_def_orchidee.xml
1484	sed -e 's@compression_level="4"@compression_level="0"@' \
1485	file_def_orchidee.xml > tmp
1486	\mv -f tmp file_def_orchidee.xml
1487	sed -e 's@XIOS_ORCHIDEE_OK = n@XIOS_ORCHIDEE_OK = y@' \
1488	orchidee.def > tmp
1489	\mv -f tmp orchidee.def
1490	fi
1491	fi
1492
1493	if [[ -f ../arch.env ]]
1494	then
1495	source ../arch.env
1496	fi
1497
1498	echo EXECUTION DU BENCH
1499	set +e
1500	date ; ./bench.sh > out.bench 2>&1 ; date
1501	set -e
1502	tail listing
1503
1504
1505	echo '##########################################################'
1506	echo 'Simulation finished in' `pwd`
1507	echo 'You have compiled with:'
1508	cat ../compile.sh
1509	if [ $parallel = "none" ] ; then
1510	echo 'You may re-run it with : cd ' `pwd` ' ; gcm.e'
1511	echo 'or ./bench.sh'
1512	else
1513	echo 'You may re-run it with : '
1514	echo 'cd ' `pwd` '; ./bench.sh'
1515	# echo 'ulimit -s unlimited'
1516	# echo 'export OMP_NUM_THREADS=2'
1517	# echo 'export OMP_STACKSIZE=800M'
1518	# echo "$mpirun -np 2 gcm.e "
1519	fi
1520	echo '##########################################################'
1521
1522	fi # bench
1523
1524
1525	#################################################################
1526	# Installation eventuelle du 1D
1527	#################################################################
1528
1529	if [ $SCM = 1 ] ; then
1530	cd $MODEL
1531	myget 1D/1D.tar.gz
1532	tar xf 1D.tar.gz
1533	cd 1D
1534	if [ $rad = oldrad ] ; then
1535	sed -i'' -e 's/^rad=.*$/rad=oldrad/' run.sh
1536	sed -i'' -e 's/^rad=.*$/rad=oldrad/' bin/compile
1537	fi
1538	if [ $rad = ecrad ] ; then
1539	sed -i'' -e 's/^rad=.*$/rad=ecrad/' run.sh
1540	sed -i'' -e 's/^rad=.*$/rad=ecrad/' bin/compile
1541	fi
1542	echo Running 1D/run.sh, log in `pwd`/run1d.log
1543	./run.sh > `pwd`/run1d.log 2>&1
1544	fi
1545
1546
1547	#################################################################
1548	# sauvegarde des options veget pour utilisation eventuelle tutorial_prod
1549	#################################################################
1550	cd $MODEL/modipsl/modeles
1551	#echo surface_env file created in $MODEL
1552	echo 'veget='$veget > surface_env
1553	#opt_veget="-v $veget_version"
1554	#echo 'opt_veget="'$opt_veget\" >> surface_env
1555	echo 'opt_veget="'-v $veget_version\" >> surface_env
1556	echo 'orchidee_rev='$orchidee_rev >> surface_env
1557	echo 'suforch='$suff_orc >> surface_env

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