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source: BOL/script_install/install_lmdz.sh @ 4738

Last change on this file since 4738 was 4731, checked in by asima, 13 months ago
Updating "version" to the new testing : LMDZ rev 4729, modipsl.20231022.trunk
Property svn:executable set to ``*
File size: 57.8 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 11 ] ; 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 intel-compilers/19.0.4 ;
321	#module load intel-mpi/19.0.4 ;
322	#module load intel-mkl/19.0.4 ;
323	module load hdf5/1.10.5-mpi ;
324	module load netcdf/4.7.2-mpi ;
325	module load netcdf-fortran/4.5.2-mpi ;
326	module load subversion/1.9.7 ;
327	module load cmake
328	export NETCDF_LIBDIR=./
329	export NETCDFFORTRAN_INCDIR=./
330	export NETCDFFORTRAN_LIBDIR=./
331	arch=X64_JEANZAY ;;
332
333	cicla\|camel) compiler="gfortran" ;
334	module purge
335	module load gnu/10.2.0
336	module load openmpi/4.0.5
337	module load hdf5/1.10.7-mpi
338	module load netcdf-c/4.7.4-mpi
339	module load netcdf-fortran/4.5.3-mpi
340	netcdf=/net/nfs/tools/PrgEnv/linux-scientific6-x86_64/gcc-10.2.0/netcdf-fortran-4.5.3-k3drgfqok3lip62hnm3tsyof4cjen5sk
341	module load svn/1.14.0
342
343	if [ $parallel != none ] ; then
344	root_mpi=/net/nfs/tools/meso-sl6/openmpi/4.0.5-gcc-10.2.0
345	path_mpi=$root_mpi/bin ;
346	par_comp=${path_mpi}/mpif90 ;
347	mpirun=${path_mpi}/mpirun ;
348	fi ;
349	arch=local ;
350	make=make ;
351	o_ins_make="-t g95" ;;
352
353	*) if [ $parallel = none -o -f /usr/bin/mpif90 ] ; then
354	path_mpi=`which mpif90 \| sed -e s:/mpif90::` ;
355	if [ -d /usr/lib64/openmpi ] ; then
356	root_mpi="/usr/lib64/openmpi"
357	else
358	root_mpi="/usr"
359	fi
360	else
361	echo "Cannot find mpif90" ;
362	if [ $parallel = none ] ; then exit ; fi ;
363	fi ;
364	if [ $parallel != none ] ; then
365	root_mpi=$(which mpif90 \| sed -e s:/bin/mpif90::)
366	path_mpi=$(which mpif90 \| sed -e s:/mpif90::)
367	export LD_LIBRARY_PATH=${root_mpi}/lib:$LD_LIBRARY_PATH
368	fi
369	par_comp=${path_mpi}/mpif90 ;
370	mpirun=${path_mpi}/mpirun ;
371	arch=local ;
372	make=make ;
373	o_ins_make="-t g95"
374	esac
375
376	# Flags for parallelism:
377	if [ $parallel != none ] ; then
378	# MPI_LD are the flags needed for linking with MPI
379	MPI_LD="-L${root_mpi}/lib -lmpi"
380	if [ "$compiler" = "gfortran" ] ; then
381	# MPI_FLAGS are the flags needed for compilation with MPI
382	MPI_FLAGS="-fcray-pointer"
383	# OMP_FLAGS are the flags needed for compilation with OpenMP
384	OMP_FLAGS="-fopenmp -fcray-pointer"
385	# OMP_LD are the flags needed for linking with OpenMP
386	OMP_LD="-fopenmp"
387	elif [ "$compiler" = "ifort" ] ; then
388	MPI_FLAGS=""
389	OMP_FLAGS="-openmp"
390	OMP_LD="-openmp"
391	else # pgf90
392	MPI_FLAGS=""
393	OMP_FLAGS="-mp"
394	OMP_LD="-mp"
395	fi
396	fi
397
398	#####################################################################
399	# Test for old gfortran compilers
400	# If the compiler is too old (older than 4.3.x) we test if the
401	# temporary gfortran44 patch is available on the computer in which
402	# case the compiler is changed from gfortran to gfortran44
403	# Must be aware than parallelism can not be activated in this case
404	#####################################################################
405
406	if [ "$compiler" = "gfortran" ] ; then
407	gfortran=gfortran
408	gfortranv=`gfortran --version \| \
409	head -1 \| awk ' { print $NF } ' \| awk -F. ' { print $1 * 10 + $2 } '`
410	if [ $gfortranv -le 43 ] ; then
411	echo ERROR : Your gfortran compiler is too old
412	echo 'Please choose a new one (ifort) and change the line'
413	echo compiler=xxx
414	echo in the install_lmdz.sh script and rerun it
415	if [ `which gfortran44 \| wc -w` -ne 0 ] ; then
416	gfortran=gfortran44
417	else
418	echo gfotran trop vieux ; exit
419	fi
420	fi
421	compiler=$gfortran
422	fi
423	#####################################################################
424
425	## if also compiling XIOS, parallel must be mpi_omp
426	if [ "$with_xios" = "y" -a "$parallel" != "mpi_omp" ] ; then
427	echo "Error, you must set -parallel mpi_omp if you want XIOS"
428	exit
429	fi
430
431	if [ "$with_xios" = "y" ] ; then
432	opt_makelmdz_xios="-io xios"
433	fi
434
435	if [ "$cosp" = "v2" -a "$with_xios" = "n" ] ; then
436	echo "Error, Cospv2 cannot run without Xios"
437	exit
438	fi
439
440	echo '################################################################'
441	echo Choix des options de compilation
442	echo '################################################################'
443
444	export FC=$compiler
445	export F90=$compiler
446	export F77=$compiler
447	export CPPFLAGS=
448	OPTIMNC=$OPTIM
449	BASE_LD="$OPT_GPROF"
450	OPTPREC="$OPT_GPROF"
451	ARFLAGS="rs"
452	if [ "`lsb_release -i -s`" = "Ubuntu" ] ; then
453	if [ "`lsb_release -r -s \| cut -d. -f1`" -ge 16 ] ; then
454	ARFLAGS="rU"
455	fi
456	fi
457
458	if [ "$compiler" = "$gfortran" ] ; then
459	OPTIM="-O3 $allow_arg_mismatch"
460	OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all -fbacktrace -finit-real=snan $allow_arg_mismatch"
461	OPTDEV="-Wall -fbounds-check $allow_arg_mismatch"
462	fmod='I '
463	OPTPREC="$OPTPREC -cpp -ffree-line-length-0"
464	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE" ; fi
465	export F90FLAGS=" -ffree-form $OPTIMNC"
466	export FFLAGS=" $OPTIMNC"
467	export CC=gcc
468	export CXX=g++
469	export fpp_flags="-P -C -traditional -ffreestanding"
470
471	elif [ $compiler = mpif90 ] ; then
472	OPTIM='-O3'
473	OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all"
474	OPTDEV="-Wall -fbounds-check"
475	BASE_LD="$BASE_LD -lblas"
476	fmod='I '
477	if [ $real = r8 ] ; then
478	OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE -fcray-pointer"
479	fi
480	export F90FLAGS=" -ffree-form $OPTIMNC"
481	export FFLAGS=" $OPTIMNC"
482	export CC=gcc
483	export CXX=g++
484
485	elif [ $compiler = pgf90 ] ; then
486	OPTIM='-O2 -Mipa -Munroll -Mnoframe -Mautoinline -Mcache_align'
487	OPTDEB='-g -Mdclchk -Mbounds -Mchkfpstk -Mchkptr -Minform=inform -Mstandard -Ktrap=fp -traceback'
488	OPTDEV='-g -Mbounds -Ktrap=fp -traceback'
489	fmod='module '
490	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -r8 -DNC_DOUBLE" ; fi
491	export CPPFLAGS="-DpgiFortran"
492	export CC=pgcc
493	export CFLAGS="-O2 -Msignextend"
494	export CXX=pgCC
495	export CXXFLAGS="-O2 -Msignextend"
496	export FFLAGS="-O2 $OPTIMNC"
497	export F90FLAGS="-O2 $OPTIMNC"
498	compile_with_fcm=1
499
500	elif [[ $compiler = ifort \|\| $compiler = mpiifort ]] ; then
501	OPTIM="-O2 -fp-model strict -ip -align all "
502	OPTDEV="-p -g -O2 -traceback -fp-stack-check -ftrapuv -check"
503	OPTDEB="-g -no-ftz -traceback -ftrapuv -fp-stack-check -check"
504	fmod='module '
505	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -real-size 64 -DNC_DOUBLE" ; fi
506	export CPP="icc -E"
507	export FFLAGS="-O2 -ip -fpic -mcmodel=large"
508	export FCFLAGS="-O2 -ip -fpic -mcmodel=large"
509	export CC=icc
510	export CFLAGS="-O2 -ip -fpic -mcmodel=large"
511	export CXX=icpc
512	export CXXFLAGS="-O2 -ip -fpic -mcmodel=large"
513	export fpp_flags="-P -traditional"
514	# Pourquoi forcer la compilation fcm. Marche mieux sans
515	#compile_with_fcm=1
516	else
517	echo unexpected compiler $compiler ; exit
518	fi
519
520	OPTIMGCM="$OPTIM $OPTPREC"
521
522	hostname=`hostname`
523
524	##########################################################################
525	# If installing on known machines such as Jean-Zay at IDRIS,
526	# don't check for available software and don't install netcdf
527	if [ ${hostname:0:5} = jean- ] ; then
528	netcdf=0 # no need to recompile netcdf, alreday available
529	check_linux=0
530	pclinux=0
531	ioipsl=0 # no need to recompile ioipsl, already available
532	#netcdf="/smplocal/pub/NetCDF/4.1.3"
533	compiler="mpiifort"
534	fmod='module '
535	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -i4 -r8 -DNC_DOUBLE" ; fi
536	OPTIM="-auto -align all -O2 -fp-model strict -xHost "
537	OPTIMGCM="$OPTIM $OPTPREC"
538	fi
539	##########################################################################
540
541
542	mkdir -p $MODEL
543	echo $MODEL
544	MODEL=`( cd $MODEL ; pwd )` # to get absolute path, if necessary
545
546
547	if [ "$check_linux" = 1 ] ; then
548	echo '################################################################'
549	echo Check if required software is available
550	echo '################################################################'
551
552	#### Ehouarn: test if the required shell is available
553	#### Maj FH-LF-AS 2021-04 : default=bash ; if bash missing, use ksh
554	use_shell="bash" # default
555	if [ "`which bash`" = "" ] ; then
556	echo "no bash ; we will use ksh"
557	use_shell="ksh"
558	if [ "`which ksh`" = "" ] ; then
559	echo "bash (or ksh) needed!! Install it!"
560	exit
561	fi
562	fi
563
564	for logiciel in wget tar gzip make $compiler gcc cmake m4 c++ ; do
565	if [ "`which $logiciel`" = "" ] ; then
566	echo You must first install $logiciel on your system
567	exit
568	fi
569	done
570
571	if [ $pclinux = 1 ] ; then
572	cd $MODEL
573	cat <<eod > tt.f90
574	print*,'coucou'
575	end
576	eod
577	$compiler tt.f90 -o a.out
578	./a.out >\| tt
579	if [ "`cat tt \| sed -e 's/ //g' `" != "coucou" ] ; then
580	echo problem installing with compiler $compiler ; exit ; fi
581	\rm tt a.out tt.f90
582	fi
583	fi
584
585	###########################################################################
586	if [ $getlmdzor = 1 -a ! -d $MODEL/modipsl ] ; then
587	###########################################################################
588	echo '##########################################################'
589	echo Download a slightly modified version of LMDZ
590	echo '##########################################################'
591	cd $MODEL
592	getlog=`pwd`/get.log
593	echo logfile : $getlog
594	myget src_archives/$trusting/modipsl.$version.tar.gz >> get.log 2>&1
595	echo install_lmdz.sh wget_OK `date`
596	gunzip modipsl.$version.tar.gz >> get.log 2>&1
597	tar xf modipsl.$version.tar >> get.log 2>&1
598	\rm modipsl.$version.tar
599	fi
600
601	###########################################################################
602	echo Installing Netcdf
603	###########################################################################
604
605	if [ $netcdf = 0 ] ; then
606	ncdfdir=/usr
607
608	else
609	cd $MODEL
610
611	case $compiler in
612	gfortran) opt1="-compiler gnu" ; opt2="-CC gcc -FC gfortran -CXX g++" ;;
613	ifort) opt1="-compiler intel" ; opt2="-CC icc -FC ifort -CXX icpc" ;;
614	pgf90) opt1="-compiler pgf90" ; opt2="-CC pgcc -FC pgf90 -CXX pgCC" ;;
615	*) echo "unexpected compiler $compiler" for netcdf ; exit 1
616	esac
617
618	case $with_xios in
619	n) script_install_netcdf=install_netcdf4_hdf5_seq.bash
620	ncdfdir=netcdf4_hdf5_seq
621	opt_=$opt1 ;;
622	y) script_install_netcdf=install_netcdf4_hdf5.bash
623	ncdfdir=netcdf4_hdf5
624	opt_="$opt2 -MPI $root_mpi" ;;
625	*) echo with_xios=$with_xios, should be n or y ; exit 1
626	esac
627	if [ $netcdf = 1 ] ; then
628	ncdfdir=$MODEL/$ncdfdir
629	else
630	mkdir -p $netcdf ; ncdfdir=$netcdf/$ncdfdir
631	fi
632
633	echo Repertoire netcdf $ncdfdir
634	if [ ! -d $ncdfdir ] ; then
635	netcdflog=`pwd`/netcdf.log
636	echo '----------------------------------------------------------'
637	echo Compiling the Netcdf library
638	echo '----------------------------------------------------------'
639	echo log file : $netcdflog
640	myget script_install/$script_install_netcdf >> $netcdflog 2>&1
641	chmod u=rwx $script_install_netcdf
642	./$script_install_netcdf -prefix $ncdfdir $opt_ >> $netcdflog 2>&1
643	fi
644
645	#----------------------------------------------------------------------------
646	# LF rajout d'une verrue, pour une raison non encore expliquee,
647	# la librairie est parfois rangée dans lib64 et non dans lib
648	# par certains compilateurs
649	if [ ! -e lib -a -d lib64 ] ; then ln -s lib64 lib; fi
650	#----------------------------------------------------------------------------
651
652	echo install_lmdz.sh netcdf_OK `date`
653
654	fi
655
656	cat >test_netcdf90.f90 <<EOF
657	use netcdf
658	print *, "NetCDF library version: ", nf90_inq_libvers()
659	end
660	EOF
661
662	$compiler -I$ncdfdir/include test_netcdf90.f90 -L$ncdfdir/lib -lnetcdff \
663	-lnetcdf -Wl,-rpath=$ncdfdir/lib && ./a.out
664
665	if (($? == 0))
666	then
667	rm test_netcdf90.f90 a.out
668	else
669	echo "Failed test program using NetCDF-Fortran."
670	echo "You can:"
671	echo "- check that you have NetCDF-Fortran installed in your system"
672	echo "- or specify an installation directory with option -netcdf of" \
673	"install_lmdz.sh"
674	echo "- or download and compile NetCDF-Fortran with option -netcdf 1 of" \
675	"install_lmdz.sh"
676	exit 1
677	fi
678
679	#=========================================================================
680	if [[ ! -f $MODEL/modipsl/lib/libioipsl.a ]]
681	then
682	if [ $ioipsl = 1 ] ; then
683	#=====================================================================
684	echo OK ioipsl=$ioipsl
685	echo '##########################################################'
686	echo 'Installing MODIPSL, the installation package manager for the '
687	echo 'IPSL models and tools'
688	echo '##########################################################'
689	echo `date`
690
691	cd $MODEL/modipsl
692	\rm -rf lib/*
693	cd util
694	cp AA_make.gdef AA_make.orig
695	F_C="$compiler -c "
696	if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ]
697	then
698	F_C="$compiler -c -cpp "
699	fi
700	if [ "$compiler" = "pgf90" ] ; then F_C="$compiler -c -Mpreprocess" ; fi
701	sed -e 's/^\#..g95..\#.*.$/\#/' AA_make.gdef > tmp
702	sed -e "s:F_L = g95:F_L = $compiler:" \
703	-e "s:F_C = g95 -c -cpp:F_C = $F_C": \
704	-e 's/g95..w_w..(F_D)/g95 w_w = '"$OPTIMGCM"'/' \
705	-e 's:g95..NCDF_INC..$:g95 NCDF_INC= '"$ncdfdir"'/include:' \
706	-e 's:g95..NCDF_LIB..$:g95 NCDF_LIB= -L'"$ncdfdir"'/lib -lnetcdff -lnetcdf:' \
707	-e 's:g95 L_O =:g95 L_O = -Wl,-rpath='"$ncdfdir"'/lib:' \
708	-e "s:-fmod=:-$fmod:" -e 's/-fno-second-underscore//' \
709	-e 's:#-Q- g95 M_K = gmake:#-Q- g95 M_K = make:' \
710	tmp >\| AA_make.gdef
711
712	if [ $pcmac == 1 ]
713	then
714	cp AA_make.gdef tmp
715	sed -e 's/rpath=/rpath,/g' tmp > AA_make.gdef
716	fi
717
718
719	# We use lines for g95 even for the other compilers to run ins_make
720	if [ "$use_shell" = "ksh" ] ; then
721	./ins_make $o_ins_make
722	else # bash
723	sed -e s:/bin/ksh:/bin/bash:g ins_make > ins_make.bash
724	if [ "`grep jeanzay AA_make.gdef`" = "" ] ; then
725	# Bidouille pour compiler sur ada des vieux modipsl.tar
726	echo 'Warning jean-zay not in AA_make.gdef'
727	echo 'Think about updating'
728	exit 1
729	fi
730
731	chmod u=rwx ins_make.bash
732	./ins_make.bash $o_ins_make
733	fi # of if [ "$use_shell" = "ksh" ]
734
735	echo install_lmdz.sh MODIPSL_OK `date`
736
737	cd $MODEL/modipsl/modeles/IOIPSL/src
738	ioipsllog=`pwd`/ioipsl.log
739	echo '##########################################################'
740	echo 'Compiling IOIPSL, the interface library with Netcdf'
741	echo '##########################################################'
742	echo `date`
743	echo log file : $ioipsllog
744
745	if [ "$use_shell" = "bash" ] ; then
746	cp Makefile Makefile.ksh
747	sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile
748	fi
749	### if [ "$pclinux" = 1 ] ; then
750	# Build IOIPSL modules and library
751	$make clean
752	$make > $ioipsllog 2>&1
753	if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then
754	# copy module files to lib
755	cp -f *.mod ../../../lib
756	fi
757	# Build IOIPSL tools (ie: "rebuild", if present)
758	# For IOIPSLv_2_2_2, "rebuild" files are in IOIPSL/tools
759	rebuild_dir=""
760	if [ -f $MODEL/modipsl/modeles/IOIPSL/tools/rebuild ] ; then
761	rebuild_dir=$MODEL/modipsl/modeles/IOIPSL/tools
762	elif [ -d $MODEL/modipsl/modeles/IOIPSL/rebuild ] ; then
763	rebuild_dir=$MODEL/modipsl/modeles/IOIPSL/rebuild
764	fi
765	if [ $rebuild_dir != "" ] ; then
766	cd $rebuild_dir
767	# adapt Makefile & rebuild script if in bash
768	if [ "$use_shell" = "bash" ] ; then
769	cp Makefile Makefile.ksh
770	sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile
771	cp rebuild rebuild.ksh
772	sed -e 's:/bin/ksh:/bin/bash:g' \
773	-e 's:print -u2:echo:g' \
774	-e 's:print:echo:g' rebuild.ksh > rebuild
775	fi
776	$make clean
777	$make > $ioipsllog 2>&1
778	fi
779	### fi # of if [ "$pclinux" = 1 ] which is commented out
780
781	else # of if [ $ioipsl = 1 ]
782	if [ ${hostname:0:5} = jean- ] ; then
783	cd $MODEL/modipsl
784	cd util
785	if [ "`grep jeanzay AA_make.gdef`" = "" ] ; then
786	echo 'Warning jean-zay not in AA_make.gdef'
787	echo 'Think about updating'
788	exit 1
789	fi
790	./ins_make $o_ins_make
791	# Compile IOIPSL on jean-zay
792	cd $MODEL/modipsl/modeles/IOIPSL/src
793	gmake > ioipsl.log
794	# For IOIPSLv_2_2_2, "rebuild" files are in IOIPSL/tools, so "gmake" in IOIPSL/tools is enough
795	# For IOIPSLv_2_2_5, "rebuild" files are in a separate IOIPSL/rebuild folder , while "tools" only contains "FCM"
796	if [ -f $MODEL/modipsl/modeles/IOIPSL/tools/Makefile ] ; then
797	cd $MODEL/modipsl/modeles/IOIPSL/tools
798	gmake > ioipsl.log
799	fi
800	if [ -d $MODEL/modipsl/modeles/IOIPSL/rebuild ] ; then
801	cd $MODEL/modipsl/modeles/IOIPSL/rebuild
802	gmake > ioipsl.log
803	fi
804
805	fi
806	echo install_lmdz.sh ioipsl_OK `date`
807	fi # of if [ $ioipsl = 1 ]
808	fi # of if [[ ! -f $MODEL/modipsl/lib/libioipsl.a ]]
809
810	#=========================================================================
811	if [ "$with_xios" = "y" ] ; then
812	echo '##########################################################'
813	echo 'Compiling XIOS'
814	echo '##########################################################'
815	cd $MODEL/modipsl/modeles
816	xioslog=`pwd`/xios.log
817	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/install_xios.bash
818	myget script_install/install_xios.bash
819	chmod u=rwx install_xios.bash
820	# following will be recalculated later on once LMDZ is updated
821	# mysvn=`svnversion LMDZ \| egrep -o "[0-9]+" 2>/dev/null`
822	mysvn=`grep 'Revision: [0-9]' $MODEL/Read*.md \| awk ' { print $2 } ' 2>/dev/null`
823	if [ "$svn" != "" ] ; then mysvn=$svn ; fi
824	echo mysvn $mysvn
825
826	if [ ${hostname:0:5} = jean- ] ; then
827	if [ $mysvn -ge 4619 ] ; then
828	svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS2/branches/xios-2.6 \
829	XIOS
830	else
831	svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS2/branches/xios-2.5 \
832	XIOS
833	fi
834	cd XIOS/arch
835	svn update
836	cd ..
837	echo "Compiling XIOS, start" `date` \
838	"(it takes about 20 min on Jean-Zay)"
839	echo "log file: $xioslog"
840	./make_xios --prod --arch $arch --job 4 > xios.log 2>&1
841	else
842	./install_xios.bash -prefix $MODEL/modipsl/modeles \
843	-netcdf ${ncdfdir} -hdf5 ${ncdfdir} \
844	-MPI $root_mpi -arch $arch > xios.log 2>&1
845	fi # of case Jean-Zay
846	if [ -f XIOS/lib/libxios.a ] ; then
847	echo "XIOS library successfully generated"
848	echo install_lmdz.sh XIOS_OK `date`
849	fi
850	fi
851
852	#============================================================================
853	veget_version=false
854	if [ "$veget" != 'NONE' ] ; then
855	cd $MODEL/modipsl/modeles/ORCHIDEE
856	set +e ; svn upgrade ; set -e
857	if [ "$veget" = "CMIP6" ] ; then
858	veget_version=orchidee2.0
859	orchidee_rev=6592
860	else # specific orchidee revision newer than CMIP6, on 2_1 or 2_2 branches
861	veget_version=orchidee2.1
862	orchidee_rev=$veget
863	if [ $veget -lt 4465 ] ; then
864	echo 'Stopping, ORCHIDEE version too old, script needs work on ' \
865	'the CPP flags to pass to makelmdz'
866	exit 1
867	fi
868	set +e
869	# which branch is my version on?
870	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}'`
871	# switch to that branch
872	echo IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at \
873	orchidee-help@listes.ipsl.fr
874	svn switch -r $veget --accept theirs-full \
875	svn://forge.ipsl.jussieu.fr/orchidee/$orcbranch
876	svn log -r $veget \| grep $veget
877	if [ $? -gt 0 ] ; then
878	echo 'Cannot update ORCHIDEE as not on the right branch for ' \
879	'ORCHIDEE'
880	exit
881	fi
882	set -e
883	set +e ; svn update -r $veget ; set -e
884	fi
885	# Correctif suite debug Jean-Zay
886	sed -i -e 's/9010 FORMAT(A52,F17.14)/9010 FORMAT(A52,F20.14)/' \
887	src_stomate/stomate.f90
888	opt_orc="-prod" ; if [ "$optim" = "-debug" ] ; then opt_orc="-debug" ; fi
889
890	orchideelog=`pwd`/orchidee.log
891	echo '########################################################'
892	echo 'Compiling ORCHIDEE, the continental surface model '
893	echo '########################################################'
894	echo Start of the first compilation of orchidee, in sequential mode: `date`
895	echo log file : $orchideelog
896
897	export ORCHPATH=`pwd`
898	xios_orchid="-noxios"
899	if [ "$with_xios" = "y" ] ; then
900	xios_orchid="-xios"
901	fi
902	if [ -d tools ] ; then
903	###################################################################
904	# Pour les experts qui voudraient changer de version d'orchidee.
905	# Attention : necessite d'avoir le password pour orchidee
906
907	# Correctif suite debug Jean-Zay
908	if [ -f src_global/time.f90 ] ; then
909	sed -i -e 's/CALL tlen2itau/\!CALL tlen2itau/' src_global/time.f90
910	fi
911	###################################################################
912	if [ "$veget_version" == "false" ] ; then
913	veget_version=orchidee2.0
914	fi
915	cd arch
916	sed -e s:"%COMPILER .*.$":"%COMPILER $compiler":1 \
917	-e s:"%LINK .*.$":"%LINK $compiler":1 \
918	-e s:"%FPP_FLAGS .*.$":"%FPP_FLAGS $fpp_flags":1 \
919	-e s:"%PROD_FFLAGS .*.$":"%PROD_FFLAGS $OPTIM":1 \
920	-e s:"%DEV_FFLAGS .*.$":"%DEV_FFLAGS $OPTDEV":1 \
921	-e s:"%DEBUG_FFLAGS .*.$":"%DEBUG_FFLAGS $OPTDEB":1 \
922	-e s:"%BASE_FFLAGS .*.$":"%BASE_FFLAGS $OPTPREC":1 \
923	-e s:"%BASE_LD .*.$":"%BASE_LD $BASE_LD":1 \
924	-e s:"%ARFLAGS .*.$":"%ARFLAGS $ARFLAGS":1 \
925	arch-gfortran.fcm > arch-local.fcm
926	echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib -lnetcdff -lnetcdf\"" \
927	> arch-local.path
928	echo "NETCDF_INCDIR=${ncdfdir}/include" >> arch-local.path
929	echo "IOIPSL_INCDIR=$ORCHPATH/../../lib" >> arch-local.path
930	echo "IOIPSL_LIBDIR=$ORCHPATH/../../lib" >> arch-local.path
931	echo 'XIOS_INCDIR=${ORCHDIR}/../XIOS/inc' >> arch-local.path
932	echo 'XIOS_LIBDIR="${ORCHDIR}/../XIOS/lib -lxios"' >> arch-local.path
933	cd ../
934
935	echo ./makeorchidee_fcm -j $xios_orchid $opt_orc -parallel none \
936	-arch $arch
937	./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel none \
938	-arch $arch > $orchideelog 2>&1
939	pwd
940	else # of "if [ -d tools ]"
941	if [ -d src_parallel ] ; then
942	liste_src="parallel parameters global stomate sechiba driver"
943	if [ "$veget_version" == "false" ] ; then
944	veget_version=orchidee2.0
945	fi
946	fi
947	for d in $liste_src ; do
948	src_d=src_$d
949	echo src_d $src_d
950	echo ls ; ls
951	if [ ! -d $src_d ] ; then
952	echo Problem orchidee : no $src_d ; exit
953	fi
954	cd $src_d ; \rm -f *.mod make ; $make clean
955	$make > $orchideelog 2>&1
956	if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then
957	cp -f *.mod ../../../lib
958	fi
959	cd ..
960	done
961	fi # of "if [ -d tools ]"
962	echo install_lmdz.sh orchidee_compil_seq_OK `date`
963	fi # of if [ "$veget" != 'NONE' ]
964
965
966	#============================================================================
967	# Ehouarn: the directory name LMDZ* depends on version/tar file...
968	if [ -d $MODEL/modipsl/modeles/LMD* ] ; then
969	echo '###############################################################'
970	echo 'Preparing LMDZ compilation : arch file, svn switch if needed...'
971	echo '###############################################################'
972	cd $MODEL/modipsl/modeles/LMD*
973	LMDZPATH=`pwd`
974	else
975	echo "ERROR: No LMD* directory !!!"
976	exit
977	fi
978
979	###########################################################
980	# For those who want to use fcm to compile via :
981	# makelmdz_fcm -arch local .....
982	############################################################
983
984
985
986	cd $MODEL/modipsl/modeles/LMDZ*
987	lmdzlog=`pwd`/lmdz.log
988
989	##################################################################
990	# Possibly update LMDZ if a specific svn release is requested
991	##################################################################
992
993	set +e ; svn upgrade ; set -e
994
995	if [ "$svn" = "last" ] ; then svnopt="" ; else svnopt="-r $svn" ; fi
996	if [ "$svn" != "" ] ; then
997	set +e ; svn info \| grep -q 'https:'
998	if [ $? = 0 ] ; then
999	svn switch --relocate https://svn.lmd.jussieu.fr/LMDZ \
1000	http://svn.lmd.jussieu.fr/LMDZ
1001	fi
1002	svn update $svnopt
1003	set -e
1004	fi
1005
1006	#---------------------------------------------------------------------
1007	# Retrieve the final svn release number, and adjust compilation
1008	# options accordingly
1009	# If svn not available, will use the svn writen in $MODEL/Readm*md
1010	# For old version it assumes that it is before 4185 (the version
1011	# for which the test was introduced
1012	#---------------------------------------------------------------------
1013
1014	set +e ; mysvn=`svnversion . \| egrep -o "[0-9]+" 2>/dev/null` ; set -e
1015	if [ "$mysvn" = "" ] ; then mysvn=`grep 'Revision: [0-9]' $MODEL/Read*.md \| awk ' { print $2 } ' 2>/dev/null` ; fi
1016	if [ "$mysvn" = "" ] ; then mysvn=4190 ; fi
1017
1018	if [[ "$pclinux" = "1" && ! -f arch/arch-local.path ]] ; then
1019
1020	# create local 'arch' files (if on Linux PC):
1021	cd arch
1022	# arch-local.path file
1023	# test for version as arch.pth file changed format with rev 4426
1024	if [ "$mysvn" -gt 4425 ] ; then
1025	echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib \"" > arch-local.path
1026	echo "NETCDF_LIB=\"-lnetcdff -lnetcdf\"" >> arch-local.path
1027	echo "NETCDF_INCDIR=-I${ncdfdir}/include" >> arch-local.path
1028	echo 'NETCDF95_INCDIR=-I$LMDGCM/../../include' >> arch-local.path
1029	echo 'NETCDF95_LIBDIR=-L$LMDGCM/../../lib' >> arch-local.path
1030	echo 'NETCDF95_LIB=-lnetcdf95' >> arch-local.path
1031	echo 'IOIPSL_INCDIR=-I$LMDGCM/../../lib' >> arch-local.path
1032	echo 'IOIPSL_LIBDIR=-L$LMDGCM/../../lib' >> arch-local.path
1033	echo 'IOIPSL_LIB=-lioipsl' >> arch-local.path
1034	echo 'XIOS_INCDIR=-I$LMDGCM/../XIOS/inc' >> arch-local.path
1035	echo 'XIOS_LIBDIR=-L$LMDGCM/../XIOS/lib' >> arch-local.path
1036	echo "XIOS_LIB=\"-lxios -lstdc++\"" >> arch-local.path
1037	echo 'ORCH_INCDIR=-I$LMDGCM/../../lib' >> arch-local.path
1038	echo 'ORCH_LIBDIR=-L$LMDGCM/../../lib' >> arch-local.path
1039	else
1040	echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib -lnetcdff -lnetcdf\"" \
1041	> arch-local.path
1042	echo "NETCDF_INCDIR=-I${ncdfdir}/include" >> arch-local.path
1043	echo 'NETCDF95_INCDIR=$LMDGCM/../../include' >> arch-local.path
1044	echo 'NETCDF95_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
1045	echo 'IOIPSL_INCDIR=$LMDGCM/../../lib' >> arch-local.path
1046	echo 'IOIPSL_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
1047	echo 'XIOS_INCDIR=$LMDGCM/../XIOS/inc' >> arch-local.path
1048	echo 'XIOS_LIBDIR=$LMDGCM/../XIOS/lib' >> arch-local.path
1049	echo 'ORCH_INCDIR=$LMDGCM/../../lib' >> arch-local.path
1050	echo 'ORCH_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
1051	fi
1052
1053	if [ $pcmac == 1 ] ; then
1054	BASE_LD="$BASE_LD -Wl,-rpath,${ncdfdir}/lib"
1055	else
1056	BASE_LD="$BASE_LD -Wl,-rpath=${ncdfdir}/lib"
1057	fi
1058	# Arch-local.fcm file (adapted from arch-linux-32bit.fcm)
1059
1060	if [ $real = r8 ] ; then FPP_DEF=NC_DOUBLE ; else FPP_DEF="" ; fi
1061	sed -e s:"%COMPILER .*.$":"%COMPILER $compiler":1 \
1062	-e s:"%LINK .*.$":"%LINK $compiler":1 \
1063	-e s:"%PROD_FFLAGS .*.$":"%PROD_FFLAGS $OPTIM":1 \
1064	-e s:"%DEV_FFLAGS .*.$":"%DEV_FFLAGS $OPTDEV":1 \
1065	-e s:"%DEBUG_FFLAGS .*.$":"%DEBUG_FFLAGS $OPTDEB":1 \
1066	-e s:"%BASE_FFLAGS .*.$":"%BASE_FFLAGS $OPTPREC":1 \
1067	-e s:"%FPP_DEF .*.$":"%FPP_DEF $FPP_DEF":1 \
1068	-e s:"%BASE_LD .*.$":"%BASE_LD $BASE_LD":1 \
1069	-e s:"%ARFLAGS .*.$":"%ARFLAGS $ARFLAGS":1 \
1070	arch-linux-32bit.fcm > arch-local.fcm
1071
1072	cd ..
1073	### Adapt "bld.cfg" (add the shell):
1074	#whereisthatshell=$(which ${use_shell})
1075	#echo "bld::tool::SHELL $whereisthatshell" >> bld.cfg
1076
1077	fi # of if [ "$pclinux" = 1 ]
1078	#---------------------------------------------------------------------
1079	# Option de compilation du rayonnement : depend de $mysvn ><= r4185
1080	#---------------------------------------------------------------------
1081	opt_rad=""
1082
1083	case $rad in
1084	oldrad) iflag_rrtm=0 ; NSW=2 ; opt_rad="" ;;
1085	rrtm) iflag_rrtm=1 ; NSW=6
1086	if [ $mysvn -le 4185 ] ; then
1087	opt_rad="-rrtm true"
1088	else
1089	opt_rad="-rad rrtm"
1090	fi ;;
1091	ecrad) iflag_rrtm=2 ; NSW=6 ; opt_rad="-rad ecrad" ;;
1092	*) echo Only oldrad rrtm ecrad for rad option ; exit
1093	esac
1094
1095	if [ $mysvn -le 4185 -a $rad = "ecrad" ] ; then
1096	echo "ecrad only available for LMDZ rev starting with 4186 " ; exit
1097	fi
1098
1099	##################################################################
1100
1101
1102	if [[ ! -f libf/misc/netcdf95.F90 && ! -d $MODEL/NetCDF95-0.3 ]]
1103	then
1104	cd $MODEL
1105	myget src_archives/netcdf/NetCDF95-0.3.tar.gz
1106	tar -xf NetCDF95-0.3.tar.gz
1107	rm NetCDF95-0.3.tar.gz
1108	cd NetCDF95-0.3
1109	mkdir build
1110	cd build
1111	cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=$ncdfdir \
1112	-DCMAKE_INSTALL_PREFIX=$MODEL/modipsl
1113	make install
1114	cd $MODEL/modipsl/modeles/LMDZ*
1115	fi
1116
1117	echo '##################################################################'
1118	echo "Preparing script compile.sh for LMDZ compilation"
1119	echo "It will only be run automatically if bench=1/tuto"
1120	echo Here bench=$bench
1121	echo '##################################################################'
1122
1123	if [ "$env_file" != "" ] ; then
1124	mv arch/arch-${arch}.env arch/arch-${arch}.orig
1125	\cp -f $env_file arch/arch-${arch}.env
1126	fi
1127
1128	if [ $compile_with_fcm = 1 ] ; then
1129	makelmdz="makelmdz_fcm $optim -arch $arch -j 8 "
1130	else
1131	makelmdz="makelmdz $optim -arch $arch"
1132	fi
1133
1134	# sequential compilation
1135	if [ "$sequential" = 1 ] ; then
1136	echo Sequential compilation command, saved in compile.sh:
1137	echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp " \
1138	"-d ${grid_resolution} -v $veget_version gcm "
1139	echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp " \
1140	"-d ${grid_resolution} -v $veget_version gcm " > compile.sh
1141	chmod +x ./compile.sh
1142	if [ $bench = 1 ] ; then
1143	echo install_lmdz.sh start_lmdz_seq_compilation `date`
1144	echo log file: $lmdzlog
1145	./compile.sh > $lmdzlog 2>&1
1146	echo install_lmdz.sh end_lmdz_seq_compilation `date`
1147	fi
1148	fi # fin sequential
1149
1150	# compiling in parallel mode
1151	if [ $parallel != "none" ] ; then
1152	echo '##########################################################'
1153	echo ' Parallel compile '
1154	echo '##########################################################'
1155	echo "(after saving the sequential libs and binaries)"
1156	cd $MODEL/modipsl
1157	tar cf sequential.tar bin/ lib/
1158	#
1159	# Orchidee
1160	#
1161	cd $ORCHPATH
1162	if [ -d src_parallel -a $veget != 'NONE' ] ; then
1163	cd arch
1164	sed \
1165	-e s:"%COMPILER.*.$":"%COMPILER $par_comp":1 \
1166	-e s:"%LINK.*.$":"%LINK $par_comp":1 \
1167	-e s:"%MPI_FFLAG.*.$":"%MPI_FFLAGS $MPI_FLAGS":1 \
1168	-e s:"%OMP_FFLAG.*.$":"%OMP_FFLAGS $OMP_FLAGS":1 \
1169	-e s:"%MPI_LD.*.$":"%MPI_LD $MPI_LD":1 \
1170	-e s:"%OMP_LD.*.$":"%OMP_LD $OMP_LD":1 \
1171	arch-local.fcm > tmp.fcm
1172
1173	mv tmp.fcm arch-local.fcm
1174	cd ../
1175	echo Compiling ORCHIDEE in parallel mode `date`
1176	echo logfile $orchideelog
1177	echo "NOTE : to recompile it when necessary, use ./compile_orc.sh " \
1178	"in modipsl/modeles/ORCHIDEE"
1179	echo ./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc \
1180	-parallel $parallel -arch $arch > compile_orc.sh
1181	echo ./makeorchidee_fcm -j 8 $xios_orchid $opt_orc \
1182	-parallel $parallel -arch $arch >> compile_orc.sh
1183	echo echo Now you must also recompile LMDZ, by running ./compile.sh \
1184	in modeles/LMDZ >> compile_orc.sh
1185	chmod u+x compile_orc.sh
1186	./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc \
1187	-parallel $parallel -arch $arch > $orchideelog 2>&1
1188	./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel $parallel \
1189	-arch $arch >> $orchideelog 2>&1
1190	echo End of ORCHIDEE compilation in parallel mode `date`
1191	elif [ $veget != 'NONE' ] ; then
1192	echo '##########################################################'
1193	echo ' Orchidee version too old '
1194	echo ' Please update to new version '
1195	echo '##########################################################'
1196	exit
1197	fi # of [ -d src_parallel -a $veget != 'NONE' ]
1198
1199	# LMDZ
1200	cd $LMDZPATH
1201	if [ $arch = local ] ; then
1202	cd arch
1203	sed -e s:"%COMPILER.*.$":"%COMPILER $par_comp":1 \
1204	-e s:"%LINK.*.$":"%LINK $par_comp":1 \
1205	-e s:"%MPI_FFLAG.*.$":"%MPI_FFLAGS $MPI_FLAGS":1 \
1206	-e s:"%OMP_FFLAG.*.$":"%OMP_FFLAGS $OMP_FLAGS":1 \
1207	-e s:"%ARFLAGS.*.$":"%ARFLAGS $ARFLAGS":1 \
1208	-e s@"%BASE_LD.*.$"@"%BASE_LD -Wl,-rpath=${root_mpi}/lib:${ncdfdir}/lib"@1 \
1209	-e s:"%MPI_LD.*.$":"%MPI_LD $MPI_LD":1 \
1210	-e s:"%OMP_LD.*.$":"%OMP_LD $OMP_LD":1 \
1211	arch-local.fcm > tmp.fcm
1212	mv tmp.fcm arch-local.fcm
1213	cd ../
1214	fi
1215	rm -f compile.sh
1216	echo resol=${grid_resolution} >> compile.sh
1217	if [ ${hostname:0:5} = jean- -a "$cosp" = "v2" ] ; then
1218
1219	echo LMDZ compilation command in parallel mode, saved in compile.sh, \
1220	is :
1221	echo "(ATTENTION le probleme de cospv2 sur jean-zay en mode prod " \
1222	"n est pas corrige ! )"
1223	# ATTENTION le probleme de cospv2 sur jean-zay en mode prod n
1224	# est pas corrige
1225	echo ./$makelmdz -dev $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
1226	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
1227	-parallel $parallel gcm >> compile.sh
1228	echo ./$makelmdz -dev $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
1229	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
1230	-parallel $parallel gcm
1231	else
1232	echo ./$makelmdz $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
1233	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
1234	-parallel $parallel gcm >> compile.sh
1235	echo ./$makelmdz $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
1236	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
1237	-parallel $parallel gcm
1238	fi
1239	chmod +x ./compile.sh
1240
1241	if [ $bench = 1 ] ; then
1242	echo Compiling LMDZ in parallel mode `date`, LMDZ log file: $lmdzlog
1243	./compile.sh > $lmdzlog 2>&1
1244	fi
1245
1246	fi # of if [ $parallel != "none" ]
1247
1248
1249	##################################################################
1250	# Verification du succes de la compilation
1251	##################################################################
1252
1253	# Recherche de l'executable dont le nom a change au fil du temps ...
1254	# suffix contains radiative option starting with revision 4186
1255	if [ $mysvn -ge 4186 ] ; then suff_exe=_${rad}${suff_exe} ; fi
1256	gcm=""
1257
1258	for exe in gcm.e bin/gcm_${grid_resolution}_phylmd${suff_exe}${suff_orc}.e
1259	do
1260	if [ -f $exe ] ; then gcm=$exe ; fi
1261	done
1262
1263	if [ "$gcm" = "" ] ; then
1264	if [ $bench = 1 ] ; then
1265	echo 'Compilation failed !! Cannot run the benchmark;'
1266	exit
1267	else
1268	echo 'Compilation not done (only done when bench=1)'
1269	fi
1270	else
1271	echo '##########################################################'
1272	echo 'Compilation successfull !! ' `date`
1273	echo '##########################################################'
1274	echo The executable is $gcm
1275	fi
1276
1277	##################################################################
1278	# Below, we run a benchmark if bench=1 or tuto
1279	##################################################################
1280
1281	if [ $bench = tuto ] ; then
1282	myget Training/tutorial.tar ; tar xf tutorial.tar ; cd TUTORIAL
1283	./init.sh
1284
1285	elif [[ $bench = 1 && ! -d BENCH${grid_resolution} ]] ; then
1286	# TOUTE CETTE SECTION DEVRAIT DISPARAITRE POUR UNE COMMANDE
1287	# OU DES BENCHS PAR MOTS CLES COMME tuto
1288
1289	echo '##########################################################'
1290	echo ' Running a test run '
1291	echo '##########################################################'
1292
1293	\rm -rf BENCH${grid_resolution}
1294	bench=bench_lmdz_${grid_resolution}
1295	echo install_lmdz.sh before bench download `date`
1296	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/$bench.tar.gz
1297	myget 3DBenchs/$bench.tar.gz
1298	echo install_lmdz.sh after bench download `date`
1299	tar xf $bench.tar.gz
1300
1301	if [ "$cosp" = "v1" -o "$cosp" = "v2" ] ; then
1302	cd BENCH${grid_resolution}
1303	# copier les fichiers namelist input et output our COSP
1304	cp ../DefLists/cosp*_input_nl.txt .
1305	cp ../DefLists/cosp*_output_nl.txt .
1306	# Activer la cles ok_cosp pour tourner avec COSP
1307	sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp
1308	\mv -f tmp config.def
1309	cd ..
1310	fi
1311
1312	if [ -n "$physiq" ]; then
1313	cd BENCH${grid_resolution}
1314	if [ -f physiq.def_${physiq} ]; then
1315	cp physiq.def_${physiq} physiq.def
1316	echo using physiq.def_${physiq}
1317	else
1318	echo using standard physiq.def
1319	fi
1320	cd ..
1321	else
1322	echo using standard physiq.def
1323	fi
1324
1325	if [ "$with_xios" = "y" ] ; then
1326	cd BENCH${grid_resolution}
1327	cp ../DefLists/iodef.xml .
1328	cp ../DefLists/context_lmdz.xml .
1329	cp ../DefLists/field_def_lmdz.xml .
1330	# A raffiner par la suite
1331	echo A FAIRE : Copier les *xml en fonction de l option cosp
1332	cp ../DefLists/field_def_cosp*.xml .
1333	cp ../DefLists/file_def_hist*xml .
1334	# adapt iodef.xml to use attached mode
1335	sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' \
1336	iodef.xml > tmp
1337	\mv -f tmp iodef.xml
1338
1339	# and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
1340	# except for histday
1341	for histfile in file_def_hist*xml
1342	do
1343	if [ "$histfile" = "file_def_histday_lmdz.xml" ] ; then
1344	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' \
1345	$histfile > tmp
1346	\mv -f tmp $histfile
1347	sed -e 's@output_level="_AUTO_"@output_level="5"@' $histfile \
1348	> tmp
1349	\mv -f tmp $histfile
1350	sed -e 's@compression_level="2"@compression_level="0"@' \
1351	$histfile > tmp
1352	\mv -f tmp $histfile
1353	else
1354	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
1355	$histfile > tmp
1356	\mv -f tmp $histfile
1357	fi
1358	done
1359	# and add option "ok_all_xml=y" in config.def
1360	echo "### XIOS outputs" >> config.def
1361	echo 'ok_all_xml=.true.' >> config.def
1362
1363	#activer les sorties pour Cosp
1364	if [ "$cosp" = "v1" ] ; then
1365	histfile=file_def_histdayCOSP_lmdz.xml
1366	sed -e 's@enabled=".FALSE."@enabled=".TRUE."@' $histfile > tmp
1367	\mv -f tmp $histfile
1368	sed -e 's@output_level="_AUTO_"@output_level="5"@' $histfile > tmp
1369	\mv -f tmp $histfile
1370	sed -e 's@compression_level="2"@compression_level="0"@' \
1371	$histfile > tmp
1372	\mv -f tmp $histfile
1373	fi
1374	if [ "$cosp" = "v2" ] ; then
1375	histfile=file_def_histdayCOSPv2_lmdz.xml
1376	sed -e 's@compression_level="2"@compression_level="0"@' \
1377	$histfile > tmp
1378	\mv -f tmp $histfile
1379	contextfile=context_lmdz.xml
1380	sed -e 's@src="./file_def_histdayCOSP_lmdz.xml"@src="./file_def_histdayCOSPv2_lmdz.xml"@' \
1381	$contextfile > tmp
1382	\mv -f tmp $contextfile
1383	sed -e 's@src="./file_def_histmthCOSP_lmdz.xml"@src="./file_def_histmthCOSPv2_lmdz.xml"@' \
1384	$contextfile > tmp
1385	\mv -f tmp $contextfile
1386	sed -e 's@src="./file_def_histhfCOSP_lmdz.xml"@src="./file_def_histhfCOSPv2_lmdz.xml"@' \
1387	$contextfile > tmp
1388	\mv -f tmp $contextfile
1389	fieldfile=field_def_lmdz.xml
1390	sed -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' $fieldfile \
1391	> tmp
1392	\mv -f tmp $fieldfile
1393	fi
1394
1395	cd ..
1396	fi
1397
1398	# Cas Bensh avec ecrad
1399	if [ "$rad" = "ecrad" ] ; then
1400	cd BENCH${grid_resolution}
1401	cp ../DefLists/namelist_ecrad .
1402	cp -r ../libf/phylmd/ecrad/data .
1403	cd ..
1404	fi
1405
1406	# Adjusting bench physiq.def to radiative code chosen
1407	cd BENCH${grid_resolution}
1408	sed -e 's/iflag_rrtm=.*.$/iflag_rrtm='$iflag_rrtm'/' \
1409	-e 's/NSW=.*.$/NSW='$NSW'/' physiq.def > tmpdef
1410	\mv tmpdef physiq.def
1411	cd ..
1412
1413	cp $gcm BENCH${grid_resolution}/gcm.e
1414
1415	cd BENCH${grid_resolution}
1416	# On cree le fichier bench.sh au besoin
1417	# Dans le cas 48x36x39 le bench.sh existe deja en parallele
1418
1419	if [ "$grid_resolution" = "48x36x39" ] ; then
1420	echo On ne touche pas au bench.sh
1421	# But we have to adapt "run_local.sh" for $mpirun
1422	sed -e "s@mpirun@$mpirun@g" run_local.sh > tmp
1423	mv -f tmp run_local.sh
1424	chmod u=rwx run_local.sh
1425	elif [ "${parallel:0:3}" = "mpi" ] ; then
1426	# Lancement avec deux procs mpi et 2 openMP
1427	echo "export OMP_STACKSIZE=800M" > bench.sh
1428	if [ "${parallel:4:3}" = "omp" ] ; then
1429	echo "export OMP_NUM_THREADS=2" >> bench.sh
1430	fi
1431	if [ "$cosp" = "v1" -o "$cosp" = "v2" ] ; then
1432	if [ ${hostname:0:5} = jean- ] ; then
1433	chmod +x ../arch.env
1434	../arch.env
1435	echo "ulimit -s 2000000" >> bench.sh
1436	else
1437	echo "ulimit -s 200000" >> bench.sh
1438	fi
1439	else
1440	echo "ulimit -s unlimited" >> bench.sh
1441	fi
1442	if [ ${hostname:0:5} = jean- ] ; then
1443	. ../arch/arch-${arch}.env
1444	echo "srun -n 2 -A $idris_acct@cpu gcm.e > listing 2>&1" \
1445	>> bench.sh
1446	else
1447	echo "$mpirun -np 2 gcm.e > listing 2>&1" >> bench.sh
1448	fi
1449	# Add rebuild, using reb.sh if it is there
1450	echo 'if [ -f reb.sh ] ; then' >> bench.sh
1451	echo ' ./reb.sh histday ; ./reb.sh histmth ; ./reb.sh histhf ; ' \
1452	'./reb.sh histins ; ./reb.sh stomate_history ; ' \
1453	'./reb.sh sechiba_history ; ./reb.sh sechiba_out_2 ' >> bench.sh
1454	echo 'fi' >> bench.sh
1455	else
1456	echo "./gcm.e > listing 2>&1" > bench.sh
1457	fi
1458	# Getting orchidee stuff
1459	if [ $veget == 'CMIP6' ] ; then
1460	#echo 'myget 3DBenchs/BENCHorch11.tar.gz'
1461	#myget 3DBenchs/BENCHorch11.tar.gz
1462	#tar xvzf BENCHorch11.tar.gz
1463	echo 'myget 3DBenchs/BENCHCMIP6.tar.gz'
1464	myget 3DBenchs/BENCHCMIP6.tar.gz
1465	tar xvzf BENCHCMIP6.tar.gz
1466	sed -e "s:VEGET=n:VEGET=y:" config.def > tmp
1467	mv -f tmp config.def
1468	if [ "$with_xios" = "y" ] ; then
1469	cp ../../ORCHIDEE/src_xml/context_orchidee.xml .
1470	echo '<context id="orchidee" src="./context_orchidee.xml"/>' \
1471	> add.tmp
1472	cp ../../ORCHIDEE/src_xml/field_def_orchidee.xml .
1473	cp ../../ORCHIDEE/src_xml/file_def_orchidee.xml .
1474	cp ../../ORCHIDEE/src_xml/file_def_input_orchidee.xml .
1475	if [ -f ../../ORCHIDEE/src_xml/context_input_orchidee.xml ] ; then
1476	cp ../../ORCHIDEE/src_xml/context_input_orchidee.xml .
1477	echo '<context id="orchidee" ' \
1478	'src="./context_input_orchidee.xml"/>' >> add.tmp
1479	fi
1480	sed -e '/id="LMDZ"/r add.tmp' iodef.xml > tmp
1481	mv tmp iodef.xml
1482	sed -e'{/sechiba1/ s/enabled="_AUTO_"/type="one_file" enabled=".TRUE."/}' \
1483	file_def_orchidee.xml > tmp
1484	\mv -f tmp file_def_orchidee.xml
1485	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
1486	file_def_orchidee.xml > tmp
1487	\mv -f tmp file_def_orchidee.xml
1488	sed -e 's@output_level="_AUTO_"@output_level="1"@' \
1489	file_def_orchidee.xml > tmp
1490	\mv -f tmp file_def_orchidee.xml
1491	sed -e 's@output_freq="_AUTO_"@output_freq="1d"@' \
1492	file_def_orchidee.xml > tmp
1493	\mv -f tmp file_def_orchidee.xml
1494	sed -e 's@compression_level="4"@compression_level="0"@' \
1495	file_def_orchidee.xml > tmp
1496	\mv -f tmp file_def_orchidee.xml
1497	sed -e 's@XIOS_ORCHIDEE_OK = n@XIOS_ORCHIDEE_OK = y@' \
1498	orchidee.def > tmp
1499	\mv -f tmp orchidee.def
1500	fi
1501	fi
1502
1503	if [[ -f ../arch.env ]]
1504	then
1505	source ../arch.env
1506	fi
1507
1508	echo EXECUTION DU BENCH
1509	set +e
1510	date ; ./bench.sh > out.bench 2>&1 ; date
1511	set -e
1512	tail listing
1513
1514
1515	echo '##########################################################'
1516	echo 'Simulation finished in' `pwd`
1517	echo 'You have compiled with:'
1518	cat ../compile.sh
1519	if [ $parallel = "none" ] ; then
1520	echo 'You may re-run it with : cd ' `pwd` ' ; gcm.e'
1521	echo 'or ./bench.sh'
1522	else
1523	echo 'You may re-run it with : '
1524	echo 'cd ' `pwd` '; ./bench.sh'
1525	# echo 'ulimit -s unlimited'
1526	# echo 'export OMP_NUM_THREADS=2'
1527	# echo 'export OMP_STACKSIZE=800M'
1528	# echo "$mpirun -np 2 gcm.e "
1529	fi
1530	echo '##########################################################'
1531
1532	fi # bench
1533
1534
1535	#################################################################
1536	# Installation eventuelle du 1D
1537	#################################################################
1538
1539	if [ $SCM = 1 ] ; then
1540	cd $MODEL
1541	myget 1D/1D.tar.gz
1542	tar xf 1D.tar.gz
1543	cd 1D
1544	if [ $rad = oldrad ] ; then
1545	sed -i'' -e 's/^rad=.*$/rad=oldrad/' run.sh
1546	sed -i'' -e 's/^rad=.*$/rad=oldrad/' bin/compile
1547	fi
1548	echo Running 1D/run.sh, log in `pwd`/run1d.log
1549	./run.sh > `pwd`/run1d.log 2>&1
1550	fi
1551
1552
1553	#################################################################
1554	# sauvegarde des options veget pour utilisation eventuelle tutorial_prod
1555	#################################################################
1556	cd $MODEL/modipsl/modeles
1557	#echo surface_env file created in $MODEL
1558	echo 'veget='$veget > surface_env
1559	#opt_veget="-v $veget_version"
1560	#echo 'opt_veget="'$opt_veget\" >> surface_env
1561	echo 'opt_veget="'-v $veget_version\" >> surface_env
1562	echo 'orchidee_rev='$orchidee_rev >> surface_env
1563	echo 'suforch='$suff_orc >> surface_env

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