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source: BOL/script_install/install_lmdz.sh @ 4298

Last change on this file since 4298 was 4286, checked in by lguez, 2 years ago

Remove verbose option of tar

This printed thousands of not very interesting lines. The option on
one of the tar commands was already removed in revision 4205 and
unvoluntarily put back in revision 4267.

Property svn:executable set to *

File size: 50.5 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=20220131.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	OPT_GPROF=""
110	OPT_MAKELMDZ=""
111	MODEL=""
112
113	## also compile XIOS? (and more recent NetCDF/HDF5 libraries) Default=no
114	with_xios="n"
115	opt_makelmdz_xios=""
116
117	## compile with oldrad/rrtm/ecrad radiatif code (Default=rrtm)
118	rad=rrtm
119
120	## compile_with_fcm=1 : use makelmdz_fcm (1) or makelmdz (0)
121	compile_with_fcm=1
122
123	#Compilation with Cosp (cosp=NONE/v1/v2 ; default=NONE)
124	cosp=NONE
125	opt_cosp=""
126
127	# Check if on a Mac
128	if [ `uname` = "Darwin" ]
129	then
130	pcmac=1
131	export MAKE=make
132	fi
133	#echo "pcmac="$pcmac
134
135	env_file=""
136
137	#########################################################################
138	# Options interactives
139	#########################################################################
140	while (($# > 0))
141	do
142	case $1 in
143	"-h") cat <<........fin
144	$0 [ -v version ] [ -r svn_release ]
145	[ -parallel PARA ] [ -d GRID_RESOLUTION ] [ -bench 0/1 ]
146	[-name LOCAL_MODEL_NAME] [-gprof] [-opt_makelmdz] [-rad RADIATIF]
147
148	-v "version" like 20150828.trunk
149	see http://www.lmd.jussieu.fr/~lmdz/Distrib/LISMOI.trunk
150
151	-r "svn_release" : either the svn release number or "last"
152
153	-compiler gfortran\|ifort\|pgf90 (default: gfortran)
154
155	-parallel PARA : can be mpi_omp (mpi with openMP) or none (for sequential)
156
157	-d GRID_RESOLUTION should be among the available benchs if -bench 1
158	among which : 48x36x19, 48x36x39
159	if wanting to run a bench simulation in addition to compilation
160	default : 48x36x19
161
162	-bench activating the bench or not (0/1). Default 1
163
164	-name LOCAL_MODEL_NAME : default = LMDZversion.release
165
166	-netcdf 0, 1 or PATH
167	0: do not download NetCDF, look for it in standard locations
168	1: download and compile NetCDF
169	PATH: full path to an existing installed NetCDF library
170
171	-xios also download and compile the XIOS library
172	(requires the NetCDF4-HDF5 library, also installed by default)
173	(requires to also have -parallel mpi_omp)
174
175	-gprof to compile with -pg to enable profiling with gprof
176
177	-cosp to run without our with cospv1 or cospv2 [none/v1/v2]
178
179	-rad RADIATIF can be oldrad, rrtm or ecrad radiatif code
180
181	-nofcm to compile without fcm
182
183	-SCM install 1D version automatically
184
185	-debug compile everything in debug mode
186
187	-opt_makelmdz to call makelmdz or makelmdz_fcm with additional options
188
189	-physiq to choose which physics package to use
190
191	-env_file specify an arch.env file to overwrite the existing one
192
193	-veget surface model to run [NONE/CMIP6/xxxx]
194
195	........fin
196	exit ;;
197	"-v") version=$2 ; shift ; shift ;;
198	"-r") svn=$2 ; shift ; shift ;;
199	"-compiler") compiler=$2
200	case $compiler in
201	"gfortran"\|"ifort"\|"pgf90") compiler=$2 ; shift
202	shift ;;
203	*) echo "Only gfortran , ifort or pgf90 for the " \
204	"compiler option"
205	exit
206	esac ;;
207	"-d") grid_resolution=$2 ; shift ; shift ;;
208	"-gprof") OPT_GPROF="-pg" ; shift ;;
209	"-cosp") cosp=$2
210	case $cosp in
211	"none"\|"v1"\|"v2") cosp=$2 ; shift ; shift ;;
212	*) echo Only none v1 v2 for cosp option ; exit
213	esac ;;
214	"-nofcm") compile_with_fcm=0 ; shift ;;
215	"-SCM") SCM=1 ; shift ;;
216	"-opt_makelmdz") OPT_MAKELMDZ="$2" ; shift ; shift ;;
217	"-rrtm") rrtm="$2"
218	if [ "$2" = "false" ] ; then
219	rad="oldrad"
220	else
221	rad="rrtm"
222	fi
223	shift ; shift ;;
224	"-rad") rad=$2
225	case $rad in
226	"oldrad"\|"rrtm"\|"ecrad") rad=$2 ; shift ; shift ;;
227	*) echo Only oldrad rrtm ecrad for rad option ; exit
228	esac ;;
229	"-parallel") parallel=$2
230	case $parallel in
231	"none"\|"mpi"\|"omp"\|"mpi_omp") parallel=$2 ; shift
232	shift ;;
233	*) echo Only none mpi omp mpi_omp for the parallel \
234	option
235	exit
236	esac ;;
237	"-bench") bench=$2 ; shift ; shift ;;
238	"-debug") optim=-debug ; shift ;;
239	"-name") MODEL=$2 ; shift ; shift ;;
240	"-netcdf") netcdf=$2 ; shift ; shift ;;
241	"-physiq") physiq=$2 ; shift ; shift ;;
242	"-xios") with_xios="y" ; shift ;;
243	"-env_file") env_file=$2 ; shift ; shift ;;
244	"-veget") veget=$2 ; shift ; shift ;;
245	*) ./install_lmdz.sh -h ; exit
246	esac
247	done
248
249	# Option de compilation du rayonnement : depend de $mysvn ><= r4185,
250	# sera donc definie plus bas
251
252	#opt_rad=""
253	#case $rad in
254	# rrtm) opt_rad="-rad rrtm" ;;
255	# ecrad) opt_rad="-rad ecrad" ;;
256	#esac
257
258
259	# Option de compilation pour Cosp
260	opt_cosp=""
261	case cosp in
262	v1) opt_cosp="-cosp true" ;;
263	v2) opt_cosp="-cospv2 true" ;;
264	esac
265
266	# Check on veget version
267	#if [ "$veget" != 'NONE' -a "$veget" != "CMIP6" -a "$veget" != +([0-9]) ] ; then
268	if [ $veget != 'NONE' -a $veget != "CMIP6" ] ; then
269	re='^[0-9]+$'
270	if ! [[ $veget =~ $re ]] ; then
271	echo 'Valeur de l option veget non valable'
272	exit
273	fi
274	fi
275
276	#Define veget-related suffix for gcm name
277	if [ "$veget" = 'NONE' ] ; then
278	suff_orc=''
279	#For use with tutorial, orchidee_rev is also defined (will be
280	#written in surface_env at the end of the script)
281	orchidee_rev=''
282	else
283	suff_orc='_orch'
284	fi
285
286
287	if [ $parallel = none ] ; then
288	sequential=1; suff_exe='_seq'
289	else
290	sequential=0; suff_exe='_para_mem'
291	fi
292
293	#Chemin pour placer le modele
294	if [ "$MODEL" = "" ] ; then MODEL=./LMDZ$version$svn$optim ; fi
295
296
297	arch=local
298
299
300	if [ $compiler = g95 ] ; then echo g95 is not supported anymore ; exit ; fi
301
302	################################################################
303	# Specificite des machines
304	################################################################
305
306	hostname=`hostname`
307	if [ "$pclinux" = 1 ] ; then o_ins_make="-t g95" ; else o_ins_make="" ; fi
308
309	case ${hostname:0:5} in
310
311	jean-) compiler="mpiifort" ;
312	par_comp="mpiifort" ;
313	o_ins_make="-t jeanzay" ;
314	make=gmake ;
315	module purge
316	module load intel-compilers/19.0.4 ;
317	#module load intel-mpi/19.0.4 ;
318	#module load intel-mkl/19.0.4 ;
319	module load hdf5/1.10.5-mpi ;
320	module load netcdf/4.7.2-mpi ;
321	module load netcdf-fortran/4.5.2-mpi ;
322	module load subversion/1.9.7 ;
323	export NETCDF_LIBDIR=./
324	export NETCDFFORTRAN_INCDIR=./
325	export NETCDFFORTRAN_LIBDIR=./
326	arch=X64_JEANZAY ;;
327
328	cicla\|camel) compiler="gfortran" ;
329	module purge
330	module load gnu/10.2.0
331	module load openmpi/4.0.5
332	module load hdf5/1.10.7-mpi
333	module load netcdf-c/4.7.4-mpi
334	module load netcdf-fortran/4.5.3-mpi
335	netcdf=/net/nfs/tools/PrgEnv/linux-scientific6-x86_64/gcc-10.2.0/netcdf-fortran-4.5.3-k3drgfqok3lip62hnm3tsyof4cjen5sk
336	module load svn/1.14.0
337
338	if [ $parallel != none ] ; then
339	root_mpi=/net/nfs/tools/meso-sl6/openmpi/4.0.5-gcc-10.2.0
340	path_mpi=$root_mpi/bin ;
341	par_comp=${path_mpi}/mpif90 ;
342	mpirun=${path_mpi}/mpirun ;
343	fi ;
344	arch=local ;
345	make=make ;
346	o_ins_make="-t g95" ;;
347
348	*) if [ $parallel = none -o -f /usr/bin/mpif90 ] ; then
349	path_mpi=`which mpif90 \| sed -e s:/mpif90::` ;
350	if [ -d /usr/lib64/openmpi ] ; then
351	root_mpi="/usr/lib64/openmpi"
352	else
353	root_mpi="/usr"
354	fi
355	else
356	echo "Cannot find mpif90" ;
357	if [ $parallel = none ] ; then exit ; fi ;
358	fi ;
359	if [ $parallel != none ] ; then
360	root_mpi=$(which mpif90 \| sed -e s:/bin/mpif90::)
361	path_mpi=$(which mpif90 \| sed -e s:/mpif90::)
362	export LD_LIBRARY_PATH=${root_mpi}/lib:$LD_LIBRARY_PATH
363	fi
364	par_comp=${path_mpi}/mpif90 ;
365	mpirun=${path_mpi}/mpirun ;
366	arch=local ;
367	make=make ;
368	o_ins_make="-t g95"
369	esac
370
371	# Flags for parallelism:
372	if [ $parallel != none ] ; then
373	# MPI_LD are the flags needed for linking with MPI
374	MPI_LD="-L${root_mpi}/lib -lmpi"
375	if [ "$compiler" = "gfortran" ] ; then
376	# MPI_FLAGS are the flags needed for compilation with MPI
377	MPI_FLAGS="-fcray-pointer"
378	# OMP_FLAGS are the flags needed for compilation with OpenMP
379	OMP_FLAGS="-fopenmp -fcray-pointer"
380	# OMP_LD are the flags needed for linking with OpenMP
381	OMP_LD="-fopenmp"
382	elif [ "$compiler" = "ifort" ] ; then
383	MPI_FLAGS=""
384	OMP_FLAGS="-openmp"
385	OMP_LD="-openmp"
386	else # pgf90
387	MPI_FLAGS=""
388	OMP_FLAGS="-mp"
389	OMP_LD="-mp"
390	fi
391	fi
392
393	#####################################################################
394	# Test for old gfortran compilers
395	# If the compiler is too old (older than 4.3.x) we test if the
396	# temporary gfortran44 patch is available on the computer in which
397	# case the compiler is changed from gfortran to gfortran44
398	# Must be aware than parallelism can not be activated in this case
399	#####################################################################
400
401	if [ "$compiler" = "gfortran" ] ; then
402	gfortran=gfortran
403	gfortranv=`gfortran --version \| \
404	head -1 \| awk ' { print $NF } ' \| awk -F. ' { print $1 * 10 + $2 } '`
405	if [ $gfortranv -le 43 ] ; then
406	echo ERROR : Your gfortran compiler is too old
407	echo 'Please choose a new one (ifort) and change the line'
408	echo compiler=xxx
409	echo in the install_lmdz.sh script and rerun it
410	if [ `which gfortran44 \| wc -w` -ne 0 ] ; then
411	gfortran=gfortran44
412	else
413	echo gfotran trop vieux ; exit
414	fi
415	fi
416	compiler=$gfortran
417	fi
418	#####################################################################
419
420	## if also compiling XIOS, parallel must be mpi_omp
421	if [ "$with_xios" = "y" -a "$parallel" != "mpi_omp" ] ; then
422	echo "Error, you must set -parallel mpi_omp if you want XIOS"
423	exit
424	fi
425
426	if [ "$with_xios" = "y" ] ; then
427	opt_makelmdz_xios="-io xios"
428	fi
429
430	if [ "$cosp" = "v2" -a "$with_xios" = "n" ] ; then
431	echo "Error, Cospv2 cannot run without Xios"
432	exit
433	fi
434
435	echo '################################################################'
436	echo Choix des options de compilation
437	echo '################################################################'
438
439	export FC=$compiler
440	export F90=$compiler
441	export F77=$compiler
442	export CPPFLAGS=
443	OPTIMNC=$OPTIM
444	BASE_LD="$OPT_GPROF"
445	OPTPREC="$OPT_GPROF"
446	ARFLAGS="rs"
447	if [ -f /etc/issue ] ; then
448	if [ "`grep -i ubuntu /etc/issue`" != "" ] ; then
449	if [ "`grep -i ubuntu /etc/issue \| awk ' { print $2 } ' \| cut -d. -f1`" -ge 16 ]
450	then
451	ARFLAGS="rU"
452	fi
453	fi
454	fi
455
456
457
458	if [ "$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 $MODEL ; pwd )` # to get absolute path, if necessary
545
546
547	echo '################################################################'
548	if [ "$check_linux" = 1 ] ; then
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 ; 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 : $getlog
594	myget src/modipsl.$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	if [ $netcdf = 1 ] ; then
603	###########################################################################
604	cd $MODEL
605	netcdflog=`pwd`/netcdf.log
606	echo '##########################################################'
607	echo Compiling the Netcdf library
608	echo '##########################################################'
609	echo log file : $netcdflog
610	if [[ "$with_xios" = "n" && ! -d $MODEL/netcdf4_hdf5_seq ]] ; then
611	myget import/install_netcdf4_hdf5_seq.bash >> $netcdflog 2>&1
612	chmod +x install_netcdf4_hdf5_seq.bash
613
614	if [ "$compiler" = "gfortran" ]
615	then
616	./install_netcdf4_hdf5_seq.bash -prefix $MODEL/netcdf4_hdf5_seq \
617	-compiler gnu >> $netcdflog 2>&1
618	elif [ "$compiler" = "ifort" ]
619	then
620	./install_netcdf4_hdf5_seq.bash -prefix $MODEL/netcdf4_hdf5_seq \
621	-compiler intel >> $netcdflog 2>&1
622	else
623	echo "unexpected compiler $compiler" ; exit
624	fi
625
626	# LF rajout d'une verrue, pour une raison non encore expliquee,
627	# la librairie est parfois rangée dans lib64 et non dans lib
628	# par certains compilateurs
629	if [ ! -e lib -a -d lib64 ] ; then ln -s lib64 lib; fi
630	elif [[ "$with_xios" = "y" && ! -d $MODEL/netcdf4_hdf5 ]]
631	then
632	# download and compile hdf5 and netcdf, etc. using the
633	# install_netcdf4_hdf5.bash script
634	myget import/install_netcdf4_hdf5.bash >> $netcdflog 2>&1
635	chmod u=rwx install_netcdf4_hdf5.bash
636	if [ "$compiler" = "gfortran" ] ; then
637	./install_netcdf4_hdf5.bash -prefix $MODEL/netcdf4_hdf5 -CC gcc \
638	-FC gfortran -CXX g++ -MPI $root_mpi >> $netcdflog 2>&1
639	elif [ "$compiler" = "ifort" ] ; then
640	./install_netcdf4_hdf5.bash -prefix $MODEL/netcdf4_hdf5 -CC icc \
641	-FC ifort -CXX icpc -MPI $root_mpi >> $netcdflog 2>&1
642	elif [ "$compiler" = "pgf90" ] ; then
643	./install_netcdf4_hdf5.bash -prefix $MODEL/netcdf4_hdf5 -CC pgcc \
644	-FC pgf90 -CXX pgCC -MPI $root_mpi >> $netcdflog 2>&1
645	else
646	echo "unexpected compiler $compiler" ; exit
647	fi
648	fi # of if [ "$with_xios" = "n" ]
649	echo install_lmdz.sh netcdf_OK `date`
650	fi # of if [ $netcdf = 1 ]
651
652	# ncdfdir contains the directory where netcdf is installed
653	if [ $netcdf = 1 ] ; then
654	if [ "$with_xios" = "y" ] ; then
655	ncdfdir=$MODEL/netcdf4_hdf5
656	else
657	ncdfdir=$MODEL/netcdf4_hdf5_seq
658	fi
659	elif [ $netcdf = 0 ]
660	then
661	ncdfdir=/usr
662	else
663	ncdfdir=$netcdf
664	fi
665
666	cat >test_netcdf90.f90 <<EOF
667	use netcdf
668	print *, "NetCDF library version: ", nf90_inq_libvers()
669	end
670	EOF
671
672	$compiler -I$ncdfdir/include test_netcdf90.f90 -L$ncdfdir/lib -l netcdff \
673	-lnetcdf -Wl,-rpath=$ncdfdir/lib && ./a.out
674
675	if (($? == 0))
676	then
677	rm test_netcdf90.f90 a.out
678	else
679	echo "Failed test program using NetCDF-Fortran."
680	echo "You can:"
681	echo "- check that you have NetCDF-Fortran installed in your system"
682	echo "- or specify an installation directory with option -netcdf of" \
683	"install_lmdz.sh"
684	echo "- or download and compile NetCDF-Fortran with option -netcdf 1 of" \
685	"install_lmdz.sh"
686	exit 1
687	fi
688
689	#=========================================================================
690	if [[ ! -f $MODEL/modipsl/lib/libioipsl.a ]]
691	then
692	if [ $ioipsl = 1 ] ; then
693	#=====================================================================
694	echo OK ioipsl=$ioipsl
695	echo '##########################################################'
696	echo 'Installing MODIPSL, the installation package manager for the '
697	echo 'IPSL models and tools'
698	echo '##########################################################'
699	echo `date`
700
701	cd $MODEL/modipsl
702	\rm -rf lib/*
703	cd util
704	cp AA_make.gdef AA_make.orig
705	F_C="$compiler -c "
706	if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ]
707	then
708	F_C="$compiler -c -cpp "
709	fi
710	if [ "$compiler" = "pgf90" ] ; then F_C="$compiler -c -Mpreprocess" ; fi
711	sed -e 's/^\#..g95..\#.*.$/\#/' AA_make.gdef > tmp
712	sed -e "s:F_L = g95:F_L = $compiler:" \
713	-e "s:F_C = g95 -c -cpp:F_C = $F_C": \
714	-e 's/g95..w_w..(F_D)/g95 w_w = '"$OPTIMGCM"'/' \
715	-e 's:g95..NCDF_INC..$:g95 NCDF_INC= '"$ncdfdir"'/include:' \
716	-e 's:g95..NCDF_LIB..$:g95 NCDF_LIB= -L'"$ncdfdir"'/lib -lnetcdff -lnetcdf:' \
717	-e 's:g95 L_O =:g95 L_O = -Wl,-rpath='"$ncdfdir"'/lib:' \
718	-e "s:-fmod=:-$fmod:" -e 's/-fno-second-underscore//' \
719	-e 's:#-Q- g95 M_K = gmake:#-Q- g95 M_K = make:' \
720	tmp >\| AA_make.gdef
721
722	if [ $pcmac == 1 ]
723	then
724	cp AA_make.gdef tmp
725	sed -e 's/rpath=/rpath,/g' tmp > AA_make.gdef
726	fi
727
728
729	# We use lines for g95 even for the other compilers to run ins_make
730	if [ "$use_shell" = "ksh" ] ; then
731	./ins_make $o_ins_make
732	else # bash
733	sed -e s:/bin/ksh:/bin/bash:g ins_make > ins_make.bash
734	if [ "`grep jeanzay AA_make.gdef`" = "" ] ; then
735	# Bidouille pour compiler sur ada des vieux modipsl.tar
736	echo 'Warning jean-zay not in AA_make.gdef'
737	echo 'Think about updating'
738	exit 1
739	fi
740
741	chmod u=rwx ins_make.bash
742	./ins_make.bash $o_ins_make
743	fi # of if [ "$use_shell" = "ksh" ]
744
745	echo install_lmdz.sh MODIPSL_OK `date`
746
747	cd $MODEL/modipsl/modeles/IOIPSL/src
748	ioipsllog=`pwd`/ioipsl.log
749	echo '##########################################################'
750	echo 'Compiling IOIPSL, the interface library with Netcdf'
751	echo '##########################################################'
752	echo `date`
753	echo log file : $ioipsllog
754
755	if [ "$use_shell" = "bash" ] ; then
756	cp Makefile Makefile.ksh
757	sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile
758	fi
759	# if [ "$pclinux" = 1 ] ; then
760	# Build IOIPSL modules and library
761	$make clean
762	$make > $ioipsllog 2>&1
763	if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then
764	# copy module files to lib
765	cp -f *.mod ../../../lib
766	fi
767	# Build IOIPSL tools (ie: "rebuild", if present)
768	if [ -f $MODEL/modipsl/modeles/IOIPSL/tools/rebuild ] ; then
769	cd $MODEL/modipsl/modeles/IOIPSL/tools
770	# adapt Makefile & rebuild script if in bash
771	if [ "$use_shell" = "bash" ] ; then
772	cp Makefile Makefile.ksh
773	sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile
774	cp rebuild rebuild.ksh
775	sed -e 's:/bin/ksh:/bin/bash:g' \
776	-e 's:print -u2:echo:g' \
777	-e 's:print:echo:g' rebuild.ksh > rebuild
778	fi
779	$make clean
780	$make > $ioipsllog 2>&1
781	fi
782	# fi # of if [ "$pclinux" = 1 ]
783
784	else # of if [ $ioipsl = 1 ]
785	if [ ${hostname:0:5} = jean- ] ; then
786	cd $MODEL/modipsl
787	cd util
788	if [ "`grep jeanzay AA_make.gdef`" = "" ] ; then
789	echo 'Warning jean-zay not in AA_make.gdef'
790	echo 'Think about updating'
791	exit 1
792	fi
793	./ins_make $o_ins_make
794	# Compile IOIPSL on jean-zay
795	cd $MODEL/modipsl/modeles/IOIPSL/src
796	gmake > ioipsl.log
797	cd $MODEL/modipsl/modeles/IOIPSL/tools
798	gmake > ioipsl.log
799
800	fi
801	echo install_lmdz.sh ioipsl_OK `date`
802	fi # of if [ $ioipsl = 1 ]
803	fi
804	# Saving ioipsl lib for possible parallel compile
805	cd $MODEL/modipsl
806	tar cf ioipsl.tar lib/ bin/
807
808	#=========================================================================
809	if [ "$with_xios" = "y" ] ; then
810	echo '##########################################################'
811	echo 'Compiling XIOS'
812	echo '##########################################################'
813	cd $MODEL/modipsl/modeles
814	xioslog=`pwd`/xios.log
815	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/install_xios.bash
816	myget import/install_xios.bash
817	chmod u=rwx install_xios.bash
818	if [ ${hostname:0:5} = jean- ] ; then
819	svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5 \
820	XIOS
821	cd XIOS/arch
822	svn update
823	cd ..
824	echo "Compiling XIOS, start" `date` \
825	"(it takes about 20 min on Jean-Zay)"
826	echo "log file: $xioslog"
827	./make_xios --prod --arch $arch --job 4 > xios.log 2>&1
828	else
829	./install_xios.bash -prefix $MODEL/modipsl/modeles \
830	-netcdf ${ncdfdir} -hdf5 ${ncdfdir} \
831	-MPI $root_mpi -arch $arch > xios.log 2>&1
832	fi # of case Jean-Zay
833	if [ -f XIOS/lib/libxios.a ] ; then
834	echo "XIOS library successfully generated"
835	echo install_lmdz.sh XIOS_OK `date`
836	fi
837	fi
838
839	#============================================================================
840	veget_version=false
841	if [ "$veget" != 'NONE' ] ; then
842	cd $MODEL/modipsl/modeles/ORCHIDEE
843	set +e ; svn upgrade ; set -e
844	if [ "$veget" = "CMIP6" ] ; then
845	veget_version=orchidee2.0
846	orchidee_rev=6592
847	else # specific orchidee revision newer than CMIP6, on 2_1 or 2_2 branches
848	veget_version=orchidee2.1
849	orchidee_rev=$veget
850	if [ $veget -lt 4465 ] ; then
851	echo 'Stopping, ORCHIDEE version too old, script needs work on ' \
852	'the CPP flags to pass to makelmdz'
853	exit 1
854	fi
855	set +e
856	# which branch is my version on?
857	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}'`
858	# switch to that branch
859	echo IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at \
860	orchidee-help@listes.ipsl.fr
861	svn switch -r $veget --accept theirs-full \
862	svn://forge.ipsl.jussieu.fr/orchidee/$orcbranch
863	svn log -r $veget \| grep $veget
864	if [ $? -gt 0 ] ; then
865	echo 'Cannot update ORCHIDEE as not on the right branch for ' \
866	'ORCHIDEE'
867	exit
868	fi
869	set -e
870	set +e ; svn update -r $veget ; set -e
871	fi
872	# Correctif suite debug Jean-Zay
873	sed -i -e 's/9010 FORMAT(A52,F17.14)/9010 FORMAT(A52,F20.14)/' \
874	src_stomate/stomate.f90
875	opt_orc="-prod" ; if [ "$optim" = "-debug" ] ; then opt_orc="-debug" ; fi
876
877	orchideelog=`pwd`/orchidee.log
878	echo '########################################################'
879	echo 'Compiling ORCHIDEE, the continental surface model '
880	echo '########################################################'
881	echo Start of the first compilation of orchidee, in sequential mode: `date`
882	echo log file : $orchideelog
883
884	export ORCHPATH=`pwd`
885	xios_orchid="-noxios"
886	if [ "$with_xios" = "y" ] ; then
887	xios_orchid="-xios"
888	fi
889	if [ -d tools ] ; then
890	###################################################################
891	# Pour les experts qui voudraient changer de version d'orchidee.
892	# Attention : necessite d'avoir le password pour orchidee
893
894	# Correctif suite debug Jean-Zay
895	if [ -f src_global/time.f90 ] ; then
896	sed -i -e 's/CALL tlen2itau/\!CALL tlen2itau/' src_global/time.f90
897	fi
898	###################################################################
899	if [ "$veget_version" == "false" ] ; then
900	veget_version=orchidee2.0
901	fi
902	cd arch
903	sed -e s:"%COMPILER .*.$":"%COMPILER $compiler":1 \
904	-e s:"%LINK .*.$":"%LINK $compiler":1 \
905	-e s:"%FPP_FLAGS .*.$":"%FPP_FLAGS $fpp_flags":1 \
906	-e s:"%PROD_FFLAGS .*.$":"%PROD_FFLAGS $OPTIM":1 \
907	-e s:"%DEV_FFLAGS .*.$":"%DEV_FFLAGS $OPTDEV":1 \
908	-e s:"%DEBUG_FFLAGS .*.$":"%DEBUG_FFLAGS $OPTDEB":1 \
909	-e s:"%BASE_FFLAGS .*.$":"%BASE_FFLAGS $OPTPREC":1 \
910	-e s:"%BASE_LD .*.$":"%BASE_LD $BASE_LD":1 \
911	-e s:"%ARFLAGS .*.$":"%ARFLAGS $ARFLAGS":1 \
912	arch-gfortran.fcm > arch-local.fcm
913	echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib -lnetcdff -lnetcdf\"" \
914	> arch-local.path
915	echo "NETCDF_INCDIR=${ncdfdir}/include" >> arch-local.path
916	echo "IOIPSL_INCDIR=$ORCHPATH/../../lib" >> arch-local.path
917	echo "IOIPSL_LIBDIR=$ORCHPATH/../../lib" >> arch-local.path
918	echo 'XIOS_INCDIR=${ORCHDIR}/../XIOS/inc' >> arch-local.path
919	echo 'XIOS_LIBDIR="${ORCHDIR}/../XIOS/lib -lxios"' >> arch-local.path
920	cd ../
921
922	echo ./makeorchidee_fcm -j $xios_orchid $opt_orc -parallel none \
923	-arch $arch
924	./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel none \
925	-arch $arch > $orchideelog 2>&1
926	pwd
927	else # of "if [ -d tools ]"
928	if [ -d src_parallel ] ; then
929	liste_src="parallel parameters global stomate sechiba driver"
930	if [ "$veget_version" == "false" ] ; then
931	veget_version=orchidee2.0
932	fi
933	fi
934	for d in $liste_src ; do
935	src_d=src_$d
936	echo src_d $src_d
937	echo ls ; ls
938	if [ ! -d $src_d ] ; then
939	echo Problem orchidee : no $src_d ; exit
940	fi
941	cd $src_d ; \rm -f *.mod make ; $make clean
942	$make > $orchideelog 2>&1
943	if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then
944	cp -f *.mod ../../../lib
945	fi
946	cd ..
947	done
948	fi # of "if [ -d tools ]"
949	echo install_lmdz.sh orchidee_compil_seq_OK `date`
950	fi # of if [ "$veget" != 'NONE' ]
951
952
953	#============================================================================
954	# Ehouarn: the directory name LMDZ* depends on version/tar file...
955	if [ -d $MODEL/modipsl/modeles/LMD* ] ; then
956	echo '###############################################################'
957	echo 'Preparing LMDZ compilation : arch file, svn switch if needed...'
958	echo '###############################################################'
959	cd $MODEL/modipsl/modeles/LMD*
960	LMDZPATH=`pwd`
961	else
962	echo "ERROR: No LMD* directory !!!"
963	exit
964	fi
965
966	###########################################################
967	# For those who want to use fcm to compile via :
968	# makelmdz_fcm -arch local .....
969	############################################################
970
971	if [[ "$pclinux" = "1" && ! -f arch/arch-local.path ]] ; then
972
973	# create local 'arch' files (if on Linux PC):
974	cd arch
975	# arch-local.path file
976	echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib -lnetcdff -lnetcdf\"" \
977	> arch-local.path
978	echo "NETCDF_INCDIR=-I${ncdfdir}/include" >> arch-local.path
979	echo 'NETCDF95_INCDIR=$LMDGCM/../../include' >> arch-local.path
980	echo 'NETCDF95_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
981	echo 'IOIPSL_INCDIR=$LMDGCM/../../lib' >> arch-local.path
982	echo 'IOIPSL_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
983	echo 'XIOS_INCDIR=$LMDGCM/../XIOS/inc' >> arch-local.path
984	echo 'XIOS_LIBDIR=$LMDGCM/../XIOS/lib' >> arch-local.path
985	echo 'ORCH_INCDIR=$LMDGCM/../../lib' >> arch-local.path
986	echo 'ORCH_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
987
988	if [ $pcmac == 1 ] ; then
989	BASE_LD="$BASE_LD -Wl,-rpath,${ncdfdir}/lib"
990	else
991	BASE_LD="$BASE_LD -Wl,-rpath=${ncdfdir}/lib"
992	fi
993	# Arch-local.fcm file (adapted from arch-linux-32bit.fcm)
994
995	if [ $real = r8 ] ; then FPP_DEF=NC_DOUBLE ; else FPP_DEF="" ; fi
996	sed -e s:"%COMPILER .*.$":"%COMPILER $compiler":1 \
997	-e s:"%LINK .*.$":"%LINK $compiler":1 \
998	-e s:"%PROD_FFLAGS .*.$":"%PROD_FFLAGS $OPTIM":1 \
999	-e s:"%DEV_FFLAGS .*.$":"%DEV_FFLAGS $OPTDEV":1 \
1000	-e s:"%DEBUG_FFLAGS .*.$":"%DEBUG_FFLAGS $OPTDEB":1 \
1001	-e s:"%BASE_FFLAGS .*.$":"%BASE_FFLAGS $OPTPREC":1 \
1002	-e s:"%FPP_DEF .*.$":"%FPP_DEF $FPP_DEF":1 \
1003	-e s:"%BASE_LD .*.$":"%BASE_LD $BASE_LD":1 \
1004	-e s:"%ARFLAGS .*.$":"%ARFLAGS $ARFLAGS":1 \
1005	arch-linux-32bit.fcm > arch-local.fcm
1006
1007	cd ..
1008	### Adapt "bld.cfg" (add the shell):
1009	#whereisthatshell=$(which ${use_shell})
1010	#echo "bld::tool::SHELL $whereisthatshell" >> bld.cfg
1011
1012	fi # of if [ "$pclinux" = 1 ]
1013
1014
1015	cd $MODEL/modipsl/modeles/LMDZ*
1016	lmdzlog=`pwd`/lmdz.log
1017
1018	##################################################################
1019	# Possibly update LMDZ if a specific svn release is requested
1020	##################################################################
1021
1022	set +e ; svn upgrade ; set -e
1023
1024	if [ "$svn" = "last" ] ; then svnopt="" ; else svnopt="-r $svn" ; fi
1025	if [ "$svn" != "" ] ; then
1026	set +e ; svn info \| grep -q 'http:'
1027	if [ $? = 0 ] ; then
1028	svn switch --relocate http://svn.lmd.jussieu.fr/LMDZ \
1029	https://svn.lmd.jussieu.fr/LMDZ
1030	fi
1031	svn update $svnopt
1032	fi
1033	set -e
1034
1035	##################################################################
1036	# Retrieve the final svn release number, and adjust compilation
1037	# options accordingly
1038	mysvn=`svnversion . \| egrep -o "[0-9]+"`
1039
1040	# Option de compilation du rayonnement : depend de $mysvn ><= r4185
1041	opt_rad=""
1042
1043	case $rad in
1044	oldrad) iflag_rrtm=0 ; NSW=2 ; opt_rad="" ;;
1045	rrtm) iflag_rrtm=1 ; NSW=6
1046	if [ $mysvn -le 4185 ] ; then
1047	opt_rad="-rrtm true"
1048	else
1049	opt_rad="-rad rrtm"
1050	fi ;;
1051	ecrad) iflag_rrtm=2 ; NSW=6 ; opt_rad="-rad ecrad" ;;
1052	*) echo Only oldrad rrtm ecrad for rad option ; exit
1053	esac
1054
1055	if [ $mysvn -le 4185 -a $rad = "ecrad" ] ; then
1056	echo "ecrad only available for LMDZ rev starting with 4186 " ; exit
1057	fi
1058
1059	##################################################################
1060
1061
1062	if [[ ! -f libf/misc/netcdf95.F90 && ! -d $MODEL/NetCDF95-0.2 ]]
1063	then
1064	cd $MODEL
1065	myget import/NetCDF95-0.2.tar.gz
1066	tar -xf NetCDF95-0.2.tar.gz
1067	rm NetCDF95-0.2.tar.gz
1068	cd NetCDF95-0.2
1069	mkdir build
1070	cd build
1071	cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=$ncdfdir \
1072	-DCMAKE_INSTALL_PREFIX=$MODEL/modipsl
1073	make install
1074	cd $MODEL/modipsl/modeles/LMDZ*
1075	fi
1076
1077	echo '##################################################################'
1078	echo "Preparing script compile.sh for LMDZ compilation"
1079	echo "It will only be run automatically if bench=1/tuto"
1080	echo Here bench=$bench
1081	echo '##################################################################'
1082
1083	if [ "$env_file" != "" ] ; then
1084	mv arch/arch-${arch}.env arch/arch-${arch}.orig
1085	\cp -f $env_file arch/arch-${arch}.env
1086	fi
1087
1088	if [ $compile_with_fcm = 1 ] ; then
1089	makelmdz="makelmdz_fcm $optim -arch $arch -j 8 "
1090	else
1091	makelmdz="makelmdz $optim -arch $arch"
1092	fi
1093
1094	# sequential compilation
1095	if [ "$sequential" = 1 ] ; then
1096	echo Sequential compilation command, saved in compile.sh:
1097	echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp " \
1098	"-d ${grid_resolution} -v $veget_version gcm "
1099	echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp " \
1100	"-d ${grid_resolution} -v $veget_version gcm " > compile.sh
1101	chmod +x ./compile.sh
1102	if [ $bench = 1 ] ; then
1103	echo install_lmdz.sh start_lmdz_seq_compilation `date`
1104	echo log file: $lmdzlog
1105	./compile.sh > $lmdzlog 2>&1
1106	echo install_lmdz.sh end_lmdz_seq_compilation `date`
1107	fi
1108	fi # fin sequential
1109
1110	# compiling in parallel mode
1111	if [ $parallel != "none" ] ; then
1112	echo '##########################################################'
1113	echo ' Parallel compile '
1114	echo '##########################################################'
1115	echo "(after saving the sequential libs and binaries)"
1116	cd $MODEL/modipsl
1117	tar cf sequential.tar bin/ lib/
1118	\rm -rf bin/ lib/
1119	tar xf ioipsl.tar
1120	#
1121	# Orchidee
1122	#
1123	cd $ORCHPATH
1124	if [ -d src_parallel -a $veget != 'NONE' ] ; then
1125	cd arch
1126	sed \
1127	-e s:"%COMPILER.*.$":"%COMPILER $par_comp":1 \
1128	-e s:"%LINK.*.$":"%LINK $par_comp":1 \
1129	-e s:"%MPI_FFLAG.*.$":"%MPI_FFLAGS $MPI_FLAGS":1 \
1130	-e s:"%OMP_FFLAG.*.$":"%OMP_FFLAGS $OMP_FLAGS":1 \
1131	-e s:"%MPI_LD.*.$":"%MPI_LD $MPI_LD":1 \
1132	-e s:"%OMP_LD.*.$":"%OMP_LD $OMP_LD":1 \
1133	arch-local.fcm > tmp.fcm
1134
1135	mv tmp.fcm arch-local.fcm
1136	cd ../
1137	echo Compiling ORCHIDEE in parallel mode `date`
1138	echo logfile $orchideelog
1139	echo "NOTE : to recompile it when necessary, use ./compile_orc.sh " \
1140	"in modipsl/modeles/ORCHIDEE"
1141	echo ./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc \
1142	-parallel $parallel -arch $arch > compile_orc.sh
1143	echo ./makeorchidee_fcm -j 8 $xios_orchid $opt_orc \
1144	-parallel $parallel -arch $arch >> compile_orc.sh
1145	echo echo Now you must also recompile LMDZ, by running ./compile.sh \
1146	in modeles/LMDZ >> compile_orc.sh
1147	chmod u+x compile_orc.sh
1148	./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc \
1149	-parallel $parallel -arch $arch > $orchideelog 2>&1
1150	./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel $parallel \
1151	-arch $arch >> $orchideelog 2>&1
1152	echo End of ORCHIDEE compilation in parallel mode `date`
1153	elif [ $veget != 'NONE' ] ; then
1154	echo '##########################################################'
1155	echo ' Orchidee version too old '
1156	echo ' Please update to new version '
1157	echo '##########################################################'
1158	exit
1159	fi # of [ -d src_parallel -a $veget != 'NONE' ]
1160
1161	# LMDZ
1162	cd $LMDZPATH
1163	if [ $arch = local ] ; then
1164	cd arch
1165	sed -e s:"%COMPILER.*.$":"%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 $OMP_FLAGS":1 \
1169	-e s:"%ARFLAGS.*.$":"%ARFLAGS $ARFLAGS":1 \
1170	-e s@"%BASE_LD.*.$"@"%BASE_LD -Wl,-rpath=${root_mpi}/lib:${ncdfdir}/lib"@1 \
1171	-e s:"%MPI_LD.*.$":"%MPI_LD $MPI_LD":1 \
1172	-e s:"%OMP_LD.*.$":"%OMP_LD $OMP_LD":1 \
1173	arch-local.fcm > tmp.fcm
1174	mv tmp.fcm arch-local.fcm
1175	cd ../
1176	fi
1177	rm -f compile.sh
1178	echo resol=${grid_resolution} >> compile.sh
1179	if [ ${hostname:0:5} = jean- -a "$cosp" = "v2" ] ; then
1180
1181	echo LMDZ compilation command in parallel mode, saved in compile.sh, \
1182	is :
1183	echo "(ATTENTION le probleme de cospv2 sur jean-zay en mode prod " \
1184	"n est pas corrige ! )"
1185	# ATTENTION le probleme de cospv2 sur jean-zay en mode prod n
1186	# est pas corrige
1187	echo ./$makelmdz -dev $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
1188	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
1189	-parallel $parallel gcm >> compile.sh
1190	echo ./$makelmdz -dev $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
1191	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
1192	-parallel $parallel gcm
1193	else
1194	echo ./$makelmdz $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
1195	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
1196	-parallel $parallel gcm >> compile.sh
1197	echo ./$makelmdz $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
1198	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
1199	-parallel $parallel gcm
1200	fi
1201	chmod +x ./compile.sh
1202
1203	if [ $bench = 1 ] ; then
1204	echo Compiling LMDZ in parallel mode `date`, LMDZ log file: $lmdzlog
1205	./compile.sh > $lmdzlog 2>&1
1206	fi
1207
1208	fi # of if [ $parallel != "none" ]
1209
1210
1211	##################################################################
1212	# Verification du succes de la compilation
1213	##################################################################
1214
1215	# Recherche de l'executable dont le nom a change au fil du temps ...
1216	# suffix contains radiative option starting with revision 4186
1217	if [ $mysvn -ge 4186 ] ; then suff_exe=_${rad}${suff_exe} ; fi
1218	gcm=""
1219
1220	for exe in gcm.e bin/gcm_${grid_resolution}_phylmd${suff_exe}${suff_orc}.e
1221	do
1222	if [ -f $exe ] ; then gcm=$exe ; fi
1223	done
1224
1225	if [ "$gcm" = "" ] ; then
1226	if [ $bench = 1 ] ; then
1227	echo 'Compilation failed !! Cannot run the benchmark;'
1228	exit
1229	else
1230	echo 'Compilation not done (only done when bench=1)'
1231	fi
1232	else
1233	echo '##########################################################'
1234	echo 'Compilation successfull !! ' `date`
1235	echo '##########################################################'
1236	echo The executable is $gcm
1237	fi
1238
1239	##################################################################
1240	# Below, we run a benchmark if bench=1 or tuto
1241	##################################################################
1242
1243	if [ $bench = tuto ] ; then
1244	myget Training/tutorial.tar ; tar xf tutorial.tar ; cd TUTORIAL
1245	./init.sh
1246
1247	elif [[ $bench = 1 && ! -d BENCH${grid_resolution} ]] ; then
1248	# TOUTE CETTE SECTION DEVRAIT DISPARAITRE POUR UNE COMMANDE
1249	# OU DES BENCHS PAR MOTS CLES COMME tuto
1250
1251	echo '##########################################################'
1252	echo ' Running a test run '
1253	echo '##########################################################'
1254
1255	\rm -rf BENCH${grid_resolution}
1256	bench=bench_lmdz_${grid_resolution}
1257	echo install_lmdz.sh before bench download `date`
1258	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/$bench.tar.gz
1259	myget 3DBenchs/$bench.tar.gz
1260	echo install_lmdz.sh after bench download `date`
1261	tar xf $bench.tar.gz
1262
1263	if [ "$cosp" = "v1" -o "$cosp" = "v2" ] ; then
1264	cd BENCH${grid_resolution}
1265	# copier les fichiers namelist input et output our COSP
1266	cp ../DefLists/cosp*_input_nl.txt .
1267	cp ../DefLists/cosp*_output_nl.txt .
1268	# Activer la cles ok_cosp pour tourner avec COSP
1269	sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp
1270	\mv -f tmp config.def
1271	cd ..
1272	fi
1273
1274	if [ -n "$physiq" ]; then
1275	cd BENCH${grid_resolution}
1276	if [ -f physiq.def_${physiq} ]; then
1277	cp physiq.def_${physiq} physiq.def
1278	echo using physiq.def_${physiq}
1279	else
1280	echo using standard physiq.def
1281	fi
1282	cd ..
1283	else
1284	echo using standard physiq.def
1285	fi
1286
1287	if [ "$with_xios" = "y" ] ; then
1288	cd BENCH${grid_resolution}
1289	cp ../DefLists/iodef.xml .
1290	cp ../DefLists/context_lmdz.xml .
1291	cp ../DefLists/field_def_lmdz.xml .
1292	# A raffiner par la suite
1293	echo A FAIRE : Copier les *xml en fonction de l option cosp
1294	cp ../DefLists/field_def_cosp*.xml .
1295	cp ../DefLists/file_def_hist*xml .
1296	# adapt iodef.xml to use attached mode
1297	sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' \
1298	iodef.xml > tmp
1299	\mv -f tmp iodef.xml
1300
1301	# and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
1302	# except for histday
1303	for histfile in file_def_hist*xml
1304	do
1305	if [ "$histfile" = "file_def_histday_lmdz.xml" ] ; then
1306	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' \
1307	$histfile > tmp
1308	\mv -f tmp $histfile
1309	sed -e 's@output_level="_AUTO_"@output_level="5"@' $histfile \
1310	> tmp
1311	\mv -f tmp $histfile
1312	sed -e 's@compression_level="2"@compression_level="0"@' \
1313	$histfile > tmp
1314	\mv -f tmp $histfile
1315	else
1316	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
1317	$histfile > tmp
1318	\mv -f tmp $histfile
1319	fi
1320	done
1321	# and add option "ok_all_xml=y" in config.def
1322	echo "### XIOS outputs" >> config.def
1323	echo 'ok_all_xml=.true.' >> config.def
1324
1325	#activer les sorties pour Cosp
1326	if [ "$cosp" = "v1" ] ; then
1327	histfile=file_def_histdayCOSP_lmdz.xml
1328	sed -e 's@enabled=".FALSE."@enabled=".TRUE."@' $histfile > tmp
1329	\mv -f tmp $histfile
1330	sed -e 's@output_level="_AUTO_"@output_level="5"@' $histfile > tmp
1331	\mv -f tmp $histfile
1332	sed -e 's@compression_level="2"@compression_level="0"@' \
1333	$histfile > tmp
1334	\mv -f tmp $histfile
1335	fi
1336	if [ "$cosp" = "v2" ] ; then
1337	histfile=file_def_histdayCOSPv2_lmdz.xml
1338	sed -e 's@compression_level="2"@compression_level="0"@' \
1339	$histfile > tmp
1340	\mv -f tmp $histfile
1341	contextfile=context_lmdz.xml
1342	sed -e 's@src="./file_def_histdayCOSP_lmdz.xml"@src="./file_def_histdayCOSPv2_lmdz.xml"@' \
1343	$contextfile > tmp
1344	\mv -f tmp $contextfile
1345	sed -e 's@src="./file_def_histmthCOSP_lmdz.xml"@src="./file_def_histmthCOSPv2_lmdz.xml"@' \
1346	$contextfile > tmp
1347	\mv -f tmp $contextfile
1348	sed -e 's@src="./file_def_histhfCOSP_lmdz.xml"@src="./file_def_histhfCOSPv2_lmdz.xml"@' \
1349	$contextfile > tmp
1350	\mv -f tmp $contextfile
1351	fieldfile=field_def_lmdz.xml
1352	sed -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' $fieldfile \
1353	> tmp
1354	\mv -f tmp $fieldfile
1355	fi
1356
1357	cd ..
1358	fi
1359
1360	# Cas Bensh avec ecrad
1361	if [ "$rad" = "ecrad" ] ; then
1362	cd BENCH${grid_resolution}
1363	cp ../DefLists/namelist_ecrad .
1364	cp -r ../libf/phylmd/ecrad/data .
1365	cd ..
1366	fi
1367
1368	# Adjusting bench physiq.def to radiative code chosen
1369	cd BENCH${grid_resolution}
1370	sed -e 's/iflag_rrtm=.*.$/iflag_rrtm='$iflag_rrtm'/' \
1371	-e 's/NSW=.*.$/NSW='$NSW'/' physiq.def > tmpdef
1372	\mv tmpdef physiq.def
1373	cd ..
1374
1375	cp $gcm BENCH${grid_resolution}/gcm.e
1376
1377	cd BENCH${grid_resolution}
1378	# On cree le fichier bench.sh au besoin
1379	# Dans le cas 48x36x39 le bench.sh existe deja en parallele
1380
1381	if [ "$grid_resolution" = "48x36x39" ] ; then
1382	echo On ne touche pas au bench.sh
1383	# But we have to adapt "run_local.sh" for $mpirun
1384	sed -e "s@mpirun@$mpirun@g" run_local.sh > tmp
1385	mv -f tmp run_local.sh
1386	chmod u=rwx run_local.sh
1387	elif [ "${parallel:0:3}" = "mpi" ] ; then
1388	# Lancement avec deux procs mpi et 2 openMP
1389	echo "export OMP_STACKSIZE=800M" > bench.sh
1390	if [ "${parallel:4:3}" = "omp" ] ; then
1391	echo "export OMP_NUM_THREADS=2" >> bench.sh
1392	fi
1393	if [ "$cosp" = "v1" -o "$cosp" = "v2" ] ; then
1394	if [ ${hostname:0:5} = jean- ] ; then
1395	chmod +x ../arch.env
1396	../arch.env
1397	echo "ulimit -s 2000000" >> bench.sh
1398	else
1399	echo "ulimit -s 200000" >> bench.sh
1400	fi
1401	else
1402	echo "ulimit -s unlimited" >> bench.sh
1403	fi
1404	if [ ${hostname:0:5} = jean- ] ; then
1405	. ../arch/arch-${arch}.env
1406	echo "srun -n 2 -A $idris_acct@cpu gcm.e > listing 2>&1" \
1407	>> bench.sh
1408	else
1409	echo "$mpirun -np 2 gcm.e > listing 2>&1" >> bench.sh
1410	fi
1411	# Add rebuild, using reb.sh if it is there
1412	echo 'if [ -f reb.sh ] ; then' >> bench.sh
1413	echo ' ./reb.sh histday ; ./reb.sh histmth ; ./reb.sh histhf ; ' \
1414	'./reb.sh histins ; ./reb.sh stomate_history ; ' \
1415	'./reb.sh sechiba_history ; ./reb.sh sechiba_out_2 ' >> bench.sh
1416	echo 'fi' >> bench.sh
1417	else
1418	echo "./gcm.e > listing 2>&1" > bench.sh
1419	fi
1420	# Getting orchidee stuff
1421	if [ $veget == 'CMIP6' ] ; then
1422	#echo 'myget 3DBenchs/BENCHorch11.tar.gz'
1423	#myget 3DBenchs/BENCHorch11.tar.gz
1424	#tar xvzf BENCHorch11.tar.gz
1425	echo 'myget 3DBenchs/BENCHCMIP6.tar.gz'
1426	myget 3DBenchs/BENCHCMIP6.tar.gz
1427	tar xvzf BENCHCMIP6.tar.gz
1428	sed -e "s:VEGET=n:VEGET=y:" config.def > tmp
1429	mv -f tmp config.def
1430	if [ "$with_xios" = "y" ] ; then
1431	cp ../../ORCHIDEE/src_xml/context_orchidee.xml .
1432	echo '<context id="orchidee" src="./context_orchidee.xml"/>' \
1433	> add.tmp
1434	cp ../../ORCHIDEE/src_xml/field_def_orchidee.xml .
1435	cp ../../ORCHIDEE/src_xml/file_def_orchidee.xml .
1436	cp ../../ORCHIDEE/src_xml/file_def_input_orchidee.xml .
1437	if [ -f ../../ORCHIDEE/src_xml/context_input_orchidee.xml ] ; then
1438	cp ../../ORCHIDEE/src_xml/context_input_orchidee.xml .
1439	echo '<context id="orchidee" ' \
1440	'src="./context_input_orchidee.xml"/>' >> add.tmp
1441	fi
1442	sed -e '/id="LMDZ"/r add.tmp' iodef.xml > tmp
1443	mv tmp iodef.xml
1444	sed -e'{/sechiba1/ s/enabled="_AUTO_"/type="one_file" enabled=".TRUE."/}' \
1445	file_def_orchidee.xml > tmp
1446	\mv -f tmp file_def_orchidee.xml
1447	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
1448	file_def_orchidee.xml > tmp
1449	\mv -f tmp file_def_orchidee.xml
1450	sed -e 's@output_level="_AUTO_"@output_level="1"@' \
1451	file_def_orchidee.xml > tmp
1452	\mv -f tmp file_def_orchidee.xml
1453	sed -e 's@output_freq="_AUTO_"@output_freq="1d"@' \
1454	file_def_orchidee.xml > tmp
1455	\mv -f tmp file_def_orchidee.xml
1456	sed -e 's@compression_level="4"@compression_level="0"@' \
1457	file_def_orchidee.xml > tmp
1458	\mv -f tmp file_def_orchidee.xml
1459	sed -e 's@XIOS_ORCHIDEE_OK = n@XIOS_ORCHIDEE_OK = y@' \
1460	orchidee.def > tmp
1461	\mv -f tmp orchidee.def
1462	fi
1463	fi
1464
1465	if [[ -f ../arch.env ]]
1466	then
1467	source ../arch.env
1468	fi
1469
1470	echo EXECUTION DU BENCH
1471	set +e
1472	date ; ./bench.sh > out.bench 2>&1 ; date
1473	set -e
1474	tail listing
1475
1476
1477	echo '##########################################################'
1478	echo 'Simulation finished in' `pwd`
1479	echo 'You have compiled with:'
1480	cat ../compile.sh
1481	if [ $parallel = "none" ] ; then
1482	echo 'You may re-run it with : cd ' `pwd` ' ; gcm.e'
1483	echo 'or ./bench.sh'
1484	else
1485	echo 'You may re-run it with : '
1486	echo 'cd ' `pwd` '; ./bench.sh'
1487	# echo 'ulimit -s unlimited'
1488	# echo 'export OMP_NUM_THREADS=2'
1489	# echo 'export OMP_STACKSIZE=800M'
1490	# echo "$mpirun -np 2 gcm.e "
1491	fi
1492	echo '##########################################################'
1493
1494	fi # bench
1495
1496
1497	#################################################################
1498	# Installation eventuelle du 1D
1499	#################################################################
1500
1501	if [ $SCM = 1 ] ; then
1502	cd $MODEL
1503	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/1D.tar.gz
1504	myget 1D/1D.tar.gz
1505	tar xf 1D.tar.gz
1506	cd 1D
1507	./run.sh -rad $rad
1508	fi
1509	#set -vx
1510
1511	#################################################################
1512	# sauvegarde des options veget pour utilisation eventuelle tutorial_prod
1513	#################################################################
1514	cd $MODEL/modipsl/modeles
1515	#echo surface_env file created in $MODEL
1516	echo 'veget='$veget > surface_env
1517	#opt_veget="-v $veget_version"
1518	#echo 'opt_veget="'$opt_veget\" >> surface_env
1519	echo 'opt_veget="'-v $veget_version\" >> surface_env
1520	echo 'orchidee_rev='$orchidee_rev >> surface_env
1521	echo 'suforch='$suff_orc >> surface_env

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