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source: BOL/script_install/install_lmdz.sh @ 4303

Last change on this file since 4303 was 4299, checked in by lguez, 2 years ago
Require m4 because it is needed for installation of NetCDF
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 m4; 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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