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source: BOL/script_install/install_lmdz.sh @ 4427

Last change on this file since 4427 was 4427, checked in by Laurent Fairhead, 15 months ago
Adataption of script to r4426 and modified arch.path files
Property svn:executable set to ``*
File size: 56.7 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=20221201.trunk
75
76	getlmdzor=1
77	netcdf=1 # 1: for automatic installation;
78	# or 0: do not install NetCDF and look for it in standard locations;
79	# or absolute path: look for NetCDF there
80	check_linux=1
81	ioipsl=1
82	bench=1
83	pclinux=1
84	pcmac=0 # default: not on a Mac
85	compiler=gfortran
86	if [ `gfortran -dumpversion \| cut -d. -f1` -ge 11 ] ; then allow_arg_mismatch="-fallow-argument-mismatch" ; fi
87	SCM=0
88	# surface/vegetation scheme treatment
89	# controlled by the single variable veget which can have the following values
90	# - NONE: bucket scheme (default)
91	# - CMIP6: orchidee version used in CMIP exercise, rev 5661
92	# - number: orchidee version number
93	veget=NONE
94	# choose the resolution for the bench runs
95	# grid_resolution= 32x24x11 or 48x36x19 for tests (test without ORCHIDEE)
96	# 96x71x19 standard configuration
97	grid_resolution=144x142x79
98	grid_resolution=96x95x39
99	grid_resolution=48x36x19
100	grid_resolution=32x32x39
101	# choose the physiq version you want to test
102	#physiq=NPv6.0.14splith
103	physiq=
104
105	## parallel can take the values none/mpi/omp/mpi_omp
106	parallel=mpi_omp
107	parallel=none
108	idris_acct=lmd
109	trusting=testing
110	OPT_GPROF=""
111	OPT_MAKELMDZ=""
112	MODEL=""
113
114	## also compile XIOS? (and more recent NetCDF/HDF5 libraries) Default=no
115	with_xios="n"
116	opt_makelmdz_xios=""
117
118	## compile with oldrad/rrtm/ecrad radiatif code (Default=rrtm)
119	rad=rrtm
120
121	## compile_with_fcm=1 : use makelmdz_fcm (1) or makelmdz (0)
122	compile_with_fcm=1
123
124	#Compilation with Cosp (cosp=NONE/v1/v2 ; default=NONE)
125	cosp=NONE
126	opt_cosp=""
127
128	# Check if on a Mac
129	if [ `uname` = "Darwin" ]
130	then
131	pcmac=1
132	export MAKE=make
133	fi
134	#echo "pcmac="$pcmac
135
136	env_file=""
137
138	#########################################################################
139	# Options interactives
140	#########################################################################
141	while (($# > 0))
142	do
143	case $1 in
144	"-h") cat <<........fin
145	$0 [ -v version ] [ -r svn_release ]
146	[ -parallel PARA ] [ -d GRID_RESOLUTION ] [ -bench 0/1 ]
147	[-name LOCAL_MODEL_NAME] [-gprof] [-opt_makelmdz] [-rad RADIATIF]
148
149	-v "version" like 20150828.trunk
150	see http://www.lmd.jussieu.fr/~lmdz/Distrib/LISMOI.trunk
151
152	-r "svn_release" : either the svn release number or "last"
153
154	-compiler gfortran\|ifort\|pgf90 (default: gfortran)
155
156	-parallel PARA : can be mpi_omp (mpi with openMP) or none (for sequential)
157
158	-d GRID_RESOLUTION should be among the available benchs if -bench 1
159	among which : 48x36x19, 48x36x39
160	if wanting to run a bench simulation in addition to compilation
161	default : 48x36x19
162
163	-bench activating the bench or not (0/1). Default 1
164
165	-testing/unstable
166
167	-name LOCAL_MODEL_NAME : default = LMDZversion.release
168
169	-netcdf 0, 1 or PATH
170	0: do not download NetCDF, look for it in standard locations
171	1: download and compile NetCDF
172	PATH: full path to an existing installed NetCDF library
173
174	-xios also download and compile the XIOS library
175	(requires the NetCDF4-HDF5 library, also installed by default)
176	(requires to also have -parallel mpi_omp)
177
178	-gprof to compile with -pg to enable profiling with gprof
179
180	-cosp to run without our with cospv1 or cospv2 [none/v1/v2]
181
182	-rad RADIATIF can be oldrad, rrtm or ecrad radiatif code
183
184	-nofcm to compile without fcm
185
186	-SCM install 1D version automatically
187
188	-debug compile everything in debug mode
189
190	-opt_makelmdz to call makelmdz or makelmdz_fcm with additional options
191
192	-physiq to choose which physics package to use
193
194	-env_file specify an arch.env file to overwrite the existing one
195
196	-veget surface model to run [NONE/CMIP6/xxxx]
197
198	........fin
199	exit ;;
200	"-v") version=$2 ; shift ; shift ;;
201	"-r") svn=$2 ; shift ; shift ;;
202	"-compiler") compiler=$2
203	case $compiler in
204	"gfortran"\|"ifort"\|"pgf90") compiler=$2 ; shift
205	shift ;;
206	*) echo "Only gfortran , ifort or pgf90 for the " \
207	"compiler option"
208	exit
209	esac ;;
210	"-d") grid_resolution=$2 ; shift ; shift ;;
211	"-gprof") OPT_GPROF="-pg" ; shift ;;
212	"-unstable"\|"-testing") trusting=`echo $1 \| cut -c2-` ; shift ;;
213	"-cosp") cosp=$2
214	case $cosp in
215	"none"\|"v1"\|"v2") cosp=$2 ; shift ; shift ;;
216	*) echo Only none v1 v2 for cosp option ; exit
217	esac ;;
218	"-nofcm") compile_with_fcm=0 ; echo This option will be reactivated soon '(promesse du 8dec2022)' ; exit 1 ; shift ;;
219	"-SCM") SCM=1 ; shift ;;
220	"-opt_makelmdz") OPT_MAKELMDZ="$2" ; shift ; shift ;;
221	"-rrtm") rrtm="$2"
222	if [ "$2" = "false" ] ; then
223	rad="oldrad"
224	else
225	rad="rrtm"
226	fi
227	shift ; shift ;;
228	"-rad") rad=$2
229	case $rad in
230	"oldrad"\|"rrtm"\|"ecrad") rad=$2 ; shift ; shift ;;
231	*) echo Only oldrad rrtm ecrad for rad option ; exit
232	esac ;;
233	"-parallel") parallel=$2
234	case $parallel in
235	"none"\|"mpi"\|"omp"\|"mpi_omp") parallel=$2 ; shift
236	shift ;;
237	*) echo Only none mpi omp mpi_omp for the parallel \
238	option
239	exit
240	esac ;;
241	"-bench") bench=$2 ; shift ; shift ;;
242	"-debug") optim=-debug ; shift ;;
243	"-name") MODEL=$2 ; shift ; shift ;;
244	"-netcdf") case $2 in
245	0\|1) netcdf=$2 ;;
246	*) netcdf=`ls -d $2` ; if [ $? != 0 ] ; then echo No directory $2 ; exit 1 ; fi
247	esac
248	shift ; shift ;;
249	"-physiq") physiq=$2 ; shift ; shift ;;
250	"-xios") with_xios="y" ; shift ;;
251	"-env_file") env_file=$2 ; shift ; shift ;;
252	"-veget") veget=$2 ; shift ; shift ;;
253	*) ./install_lmdz.sh -h ; exit
254	esac
255	done
256
257	# Option de compilation du rayonnement : depend de $mysvn ><= r4185,
258	# sera donc definie plus bas
259
260	#opt_rad=""
261	#case $rad in
262	# rrtm) opt_rad="-rad rrtm" ;;
263	# ecrad) opt_rad="-rad ecrad" ;;
264	#esac
265
266
267	# Option de compilation pour Cosp
268	opt_cosp=""
269	case cosp in
270	v1) opt_cosp="-cosp true" ;;
271	v2) opt_cosp="-cospv2 true" ;;
272	esac
273
274	# Check on veget version
275	#if [ "$veget" != 'NONE' -a "$veget" != "CMIP6" -a "$veget" != +([0-9]) ] ; then
276	if [ $veget != 'NONE' -a $veget != "CMIP6" ] ; then
277	re='^[0-9]+$'
278	if ! [[ $veget =~ $re ]] ; then
279	echo 'Valeur de l option veget non valable'
280	exit
281	fi
282	fi
283
284	#Define veget-related suffix for gcm name
285	if [ "$veget" = 'NONE' ] ; then
286	suff_orc=''
287	#For use with tutorial, orchidee_rev is also defined (will be
288	#written in surface_env at the end of the script)
289	orchidee_rev=''
290	else
291	suff_orc='_orch'
292	fi
293
294
295	if [ $parallel = none ] ; then
296	sequential=1; suff_exe='_seq'
297	else
298	sequential=0; suff_exe='_para_mem'
299	fi
300
301	#Chemin pour placer le modele
302	if [ "$MODEL" = "" ] ; then MODEL=./LMDZ$version$svn$optim ; fi
303
304
305	arch=local
306
307
308	if [ $compiler = g95 ] ; then echo g95 is not supported anymore ; exit ; fi
309
310	################################################################
311	# Specificite des machines
312	################################################################
313
314	hostname=`hostname`
315	if [ "$pclinux" = 1 ] ; then o_ins_make="-t g95" ; else o_ins_make="" ; fi
316
317	case ${hostname:0:5} in
318
319	jean-) compiler="mpiifort" ;
320	par_comp="mpiifort" ;
321	o_ins_make="-t jeanzay" ;
322	make=gmake ;
323	module purge
324	module load intel-compilers/19.0.4 ;
325	#module load intel-mpi/19.0.4 ;
326	#module load intel-mkl/19.0.4 ;
327	module load hdf5/1.10.5-mpi ;
328	module load netcdf/4.7.2-mpi ;
329	module load netcdf-fortran/4.5.2-mpi ;
330	module load subversion/1.9.7 ;
331	export NETCDF_LIBDIR=./
332	export NETCDFFORTRAN_INCDIR=./
333	export NETCDFFORTRAN_LIBDIR=./
334	arch=X64_JEANZAY ;;
335
336	cicla\|camel) compiler="gfortran" ;
337	module purge
338	module load gnu/10.2.0
339	module load openmpi/4.0.5
340	module load hdf5/1.10.7-mpi
341	module load netcdf-c/4.7.4-mpi
342	module load netcdf-fortran/4.5.3-mpi
343	netcdf=/net/nfs/tools/PrgEnv/linux-scientific6-x86_64/gcc-10.2.0/netcdf-fortran-4.5.3-k3drgfqok3lip62hnm3tsyof4cjen5sk
344	module load svn/1.14.0
345
346	if [ $parallel != none ] ; then
347	root_mpi=/net/nfs/tools/meso-sl6/openmpi/4.0.5-gcc-10.2.0
348	path_mpi=$root_mpi/bin ;
349	par_comp=${path_mpi}/mpif90 ;
350	mpirun=${path_mpi}/mpirun ;
351	fi ;
352	arch=local ;
353	make=make ;
354	o_ins_make="-t g95" ;;
355
356	*) if [ $parallel = none -o -f /usr/bin/mpif90 ] ; then
357	path_mpi=`which mpif90 \| sed -e s:/mpif90::` ;
358	if [ -d /usr/lib64/openmpi ] ; then
359	root_mpi="/usr/lib64/openmpi"
360	else
361	root_mpi="/usr"
362	fi
363	else
364	echo "Cannot find mpif90" ;
365	if [ $parallel = none ] ; then exit ; fi ;
366	fi ;
367	if [ $parallel != none ] ; then
368	root_mpi=$(which mpif90 \| sed -e s:/bin/mpif90::)
369	path_mpi=$(which mpif90 \| sed -e s:/mpif90::)
370	export LD_LIBRARY_PATH=${root_mpi}/lib:$LD_LIBRARY_PATH
371	fi
372	par_comp=${path_mpi}/mpif90 ;
373	mpirun=${path_mpi}/mpirun ;
374	arch=local ;
375	make=make ;
376	o_ins_make="-t g95"
377	esac
378
379	# Flags for parallelism:
380	if [ $parallel != none ] ; then
381	# MPI_LD are the flags needed for linking with MPI
382	MPI_LD="-L${root_mpi}/lib -lmpi"
383	if [ "$compiler" = "gfortran" ] ; then
384	# MPI_FLAGS are the flags needed for compilation with MPI
385	MPI_FLAGS="-fcray-pointer"
386	# OMP_FLAGS are the flags needed for compilation with OpenMP
387	OMP_FLAGS="-fopenmp -fcray-pointer"
388	# OMP_LD are the flags needed for linking with OpenMP
389	OMP_LD="-fopenmp"
390	elif [ "$compiler" = "ifort" ] ; then
391	MPI_FLAGS=""
392	OMP_FLAGS="-openmp"
393	OMP_LD="-openmp"
394	else # pgf90
395	MPI_FLAGS=""
396	OMP_FLAGS="-mp"
397	OMP_LD="-mp"
398	fi
399	fi
400
401	#####################################################################
402	# Test for old gfortran compilers
403	# If the compiler is too old (older than 4.3.x) we test if the
404	# temporary gfortran44 patch is available on the computer in which
405	# case the compiler is changed from gfortran to gfortran44
406	# Must be aware than parallelism can not be activated in this case
407	#####################################################################
408
409	if [ "$compiler" = "gfortran" ] ; then
410	gfortran=gfortran
411	gfortranv=`gfortran --version \| \
412	head -1 \| awk ' { print $NF } ' \| awk -F. ' { print $1 * 10 + $2 } '`
413	if [ $gfortranv -le 43 ] ; then
414	echo ERROR : Your gfortran compiler is too old
415	echo 'Please choose a new one (ifort) and change the line'
416	echo compiler=xxx
417	echo in the install_lmdz.sh script and rerun it
418	if [ `which gfortran44 \| wc -w` -ne 0 ] ; then
419	gfortran=gfortran44
420	else
421	echo gfotran trop vieux ; exit
422	fi
423	fi
424	compiler=$gfortran
425	fi
426	#####################################################################
427
428	## if also compiling XIOS, parallel must be mpi_omp
429	if [ "$with_xios" = "y" -a "$parallel" != "mpi_omp" ] ; then
430	echo "Error, you must set -parallel mpi_omp if you want XIOS"
431	exit
432	fi
433
434	if [ "$with_xios" = "y" ] ; then
435	opt_makelmdz_xios="-io xios"
436	fi
437
438	if [ "$cosp" = "v2" -a "$with_xios" = "n" ] ; then
439	echo "Error, Cospv2 cannot run without Xios"
440	exit
441	fi
442
443	echo '################################################################'
444	echo Choix des options de compilation
445	echo '################################################################'
446
447	export FC=$compiler
448	export F90=$compiler
449	export F77=$compiler
450	export CPPFLAGS=
451	OPTIMNC=$OPTIM
452	BASE_LD="$OPT_GPROF"
453	OPTPREC="$OPT_GPROF"
454	ARFLAGS="rs"
455	if [ "`lsb_release -i -s`" = "Ubuntu" ] ; then
456	if [ "`lsb_release -r -s \| cut -d. -f1`" -ge 16 ] ; then
457	ARFLAGS="rU"
458	fi
459	fi
460
461	if [ "$compiler" = "$gfortran" ] ; then
462	OPTIM="-O3 $allow_arg_mismatch"
463	OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all -fbacktrace -finit-real=snan $allow_arg_mismatch"
464	OPTDEV="-Wall -fbounds-check $allow_arg_mismatch"
465	fmod='I '
466	OPTPREC="$OPTPREC -cpp -ffree-line-length-0"
467	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE" ; fi
468	export F90FLAGS=" -ffree-form $OPTIMNC"
469	export FFLAGS=" $OPTIMNC"
470	export CC=gcc
471	export CXX=g++
472	export fpp_flags="-P -C -traditional -ffreestanding"
473
474	elif [ $compiler = mpif90 ] ; then
475	OPTIM='-O3'
476	OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all"
477	OPTDEV="-Wall -fbounds-check"
478	BASE_LD="$BASE_LD -lblas"
479	fmod='I '
480	if [ $real = r8 ] ; then
481	OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE -fcray-pointer"
482	fi
483	export F90FLAGS=" -ffree-form $OPTIMNC"
484	export FFLAGS=" $OPTIMNC"
485	export CC=gcc
486	export CXX=g++
487
488	elif [ $compiler = pgf90 ] ; then
489	OPTIM='-O2 -Mipa -Munroll -Mnoframe -Mautoinline -Mcache_align'
490	OPTDEB='-g -Mdclchk -Mbounds -Mchkfpstk -Mchkptr -Minform=inform -Mstandard -Ktrap=fp -traceback'
491	OPTDEV='-g -Mbounds -Ktrap=fp -traceback'
492	fmod='module '
493	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -r8 -DNC_DOUBLE" ; fi
494	export CPPFLAGS="-DpgiFortran"
495	export CC=pgcc
496	export CFLAGS="-O2 -Msignextend"
497	export CXX=pgCC
498	export CXXFLAGS="-O2 -Msignextend"
499	export FFLAGS="-O2 $OPTIMNC"
500	export F90FLAGS="-O2 $OPTIMNC"
501	compile_with_fcm=1
502
503	elif [[ $compiler = ifort \|\| $compiler = mpiifort ]] ; then
504	OPTIM="-O2 -fp-model strict -ip -align all "
505	OPTDEV="-p -g -O2 -traceback -fp-stack-check -ftrapuv -check"
506	OPTDEB="-g -no-ftz -traceback -ftrapuv -fp-stack-check -check"
507	fmod='module '
508	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -real-size 64 -DNC_DOUBLE" ; fi
509	export CPP="icc -E"
510	export FFLAGS="-O2 -ip -fpic -mcmodel=large"
511	export FCFLAGS="-O2 -ip -fpic -mcmodel=large"
512	export CC=icc
513	export CFLAGS="-O2 -ip -fpic -mcmodel=large"
514	export CXX=icpc
515	export CXXFLAGS="-O2 -ip -fpic -mcmodel=large"
516	export fpp_flags="-P -traditional"
517	# Pourquoi forcer la compilation fcm. Marche mieux sans
518	#compile_with_fcm=1
519	else
520	echo unexpected compiler $compiler ; exit
521	fi
522
523	OPTIMGCM="$OPTIM $OPTPREC"
524
525	hostname=`hostname`
526
527	##########################################################################
528	# If installing on known machines such as Jean-Zay at IDRIS,
529	# don't check for available software and don't install netcdf
530	if [ ${hostname:0:5} = jean- ] ; then
531	netcdf=0 # no need to recompile netcdf, alreday available
532	check_linux=0
533	pclinux=0
534	ioipsl=0 # no need to recompile ioipsl, already available
535	#netcdf="/smplocal/pub/NetCDF/4.1.3"
536	compiler="mpiifort"
537	fmod='module '
538	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -i4 -r8 -DNC_DOUBLE" ; fi
539	OPTIM="-auto -align all -O2 -fp-model strict -xHost "
540	OPTIMGCM="$OPTIM $OPTPREC"
541	fi
542	##########################################################################
543
544
545	mkdir -p $MODEL
546	echo $MODEL
547	MODEL=`( cd $MODEL ; pwd )` # to get absolute path, if necessary
548
549
550	if [ "$check_linux" = 1 ] ; then
551	echo '################################################################'
552	echo Check if required software is available
553	echo '################################################################'
554
555	#### Ehouarn: test if the required shell is available
556	#### Maj FH-LF-AS 2021-04 : default=bash ; if bash missing, use ksh
557	use_shell="bash" # default
558	if [ "`which bash`" = "" ] ; then
559	echo "no bash ; we will use ksh"
560	use_shell="ksh"
561	if [ "`which ksh`" = "" ] ; then
562	echo "bash (or ksh) needed!! Install it!"
563	exit
564	fi
565	fi
566
567	for logiciel in wget tar gzip make $compiler gcc cmake m4 c++ ; do
568	if [ "`which $logiciel`" = "" ] ; then
569	echo You must first install $logiciel on your system
570	exit
571	fi
572	done
573
574	if [ $pclinux = 1 ] ; then
575	cd $MODEL
576	cat <<eod > tt.f90
577	print*,'coucou'
578	end
579	eod
580	$compiler tt.f90 -o a.out
581	./a.out >\| tt
582	if [ "`cat tt \| sed -e 's/ //g' `" != "coucou" ] ; then
583	echo problem installing with compiler $compiler ; exit ; fi
584	\rm tt a.out tt.f90
585	fi
586	fi
587
588	###########################################################################
589	if [ $getlmdzor = 1 -a ! -d $MODEL/modipsl ] ; then
590	###########################################################################
591	echo '##########################################################'
592	echo Download a slightly modified version of LMDZ
593	echo '##########################################################'
594	cd $MODEL
595	getlog=`pwd`/get.log
596	echo logfile : $getlog
597	myget src_archives/$trusting/modipsl.$version.tar.gz >> get.log 2>&1
598	echo install_lmdz.sh wget_OK `date`
599	gunzip modipsl.$version.tar.gz >> get.log 2>&1
600	tar xf modipsl.$version.tar >> get.log 2>&1
601	\rm modipsl.$version.tar
602	fi
603
604	###########################################################################
605	if [ $netcdf = 1 ] ; then
606	###########################################################################
607	cd $MODEL
608	netcdflog=`pwd`/netcdf.log
609	echo '----------------------------------------------------------'
610	echo Compiling the Netcdf library
611	echo '----------------------------------------------------------'
612	echo log file : $netcdflog
613
614	case $compiler in
615	gfortran) opt1="-compiler gnu" ; opt2="-CC gcc -FC gfortran -CXX g++" ;;
616	ifort) opt1="-compiler intel" ; opt2="-CC icc -FC ifort -CXX icpc" ;;
617	pgf90) opt1="-compiler pgf90" ; opt2="-CC pgcc -FC pgf90 -CXX pgCC" ;;
618	*) echo "unexpected compiler $compiler" for netcdf ; exit 1
619	esac
620
621	case $with_xios in
622	n) script_install_netcdf=install_netcdf4_hdf5_seq.bash
623	ncdfdir=$MODEL/netcdf4_hdf5_seq
624	opt_=$opt1 ;;
625	y) script_install_netcdf=install_netcdf4_hdf5.bash
626	ncdfdir=$MODEL/netcdf4_hdf5
627	opt_="$opt2 -MPI $root_mpi" ;;
628	*) echo with_xios=$with_xios, should be n or y ; exit 1
629	esac
630
631	if [[ ! -d $ncdfdir ]] ; then
632	myget script_install/$script_install_netcdf >> $netcdflog 2>&1
633	chmod u=rwx $script_install_netcdf
634	./$script_install_netcdf -prefix $ncdfdir $opt_ >> $netcdflog 2>&1
635	fi
636
637	#----------------------------------------------------------------------------
638	# LF rajout d'une verrue, pour une raison non encore expliquee,
639	# la librairie est parfois rangée dans lib64 et non dans lib
640	# par certains compilateurs
641	if [ ! -e lib -a -d lib64 ] ; then ln -s lib64 lib; fi
642	#----------------------------------------------------------------------------
643
644	echo install_lmdz.sh netcdf_OK `date`
645
646	elif [ $netcdf = 0 ] ; then
647	ncdfdir=/usr
648	else
649	ncdfdir=$netcdf
650	fi
651
652	cat >test_netcdf90.f90 <<EOF
653	use netcdf
654	print *, "NetCDF library version: ", nf90_inq_libvers()
655	end
656	EOF
657
658	$compiler -I$ncdfdir/include test_netcdf90.f90 -L$ncdfdir/lib -lnetcdff \
659	-lnetcdf -Wl,-rpath=$ncdfdir/lib && ./a.out
660
661	if (($? == 0))
662	then
663	rm test_netcdf90.f90 a.out
664	else
665	echo "Failed test program using NetCDF-Fortran."
666	echo "You can:"
667	echo "- check that you have NetCDF-Fortran installed in your system"
668	echo "- or specify an installation directory with option -netcdf of" \
669	"install_lmdz.sh"
670	echo "- or download and compile NetCDF-Fortran with option -netcdf 1 of" \
671	"install_lmdz.sh"
672	exit 1
673	fi
674
675	#=========================================================================
676	if [[ ! -f $MODEL/modipsl/lib/libioipsl.a ]]
677	then
678	if [ $ioipsl = 1 ] ; then
679	#=====================================================================
680	echo OK ioipsl=$ioipsl
681	echo '##########################################################'
682	echo 'Installing MODIPSL, the installation package manager for the '
683	echo 'IPSL models and tools'
684	echo '##########################################################'
685	echo `date`
686
687	cd $MODEL/modipsl
688	\rm -rf lib/*
689	cd util
690	cp AA_make.gdef AA_make.orig
691	F_C="$compiler -c "
692	if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ]
693	then
694	F_C="$compiler -c -cpp "
695	fi
696	if [ "$compiler" = "pgf90" ] ; then F_C="$compiler -c -Mpreprocess" ; fi
697	sed -e 's/^\#..g95..\#.*.$/\#/' AA_make.gdef > tmp
698	sed -e "s:F_L = g95:F_L = $compiler:" \
699	-e "s:F_C = g95 -c -cpp:F_C = $F_C": \
700	-e 's/g95..w_w..(F_D)/g95 w_w = '"$OPTIMGCM"'/' \
701	-e 's:g95..NCDF_INC..$:g95 NCDF_INC= '"$ncdfdir"'/include:' \
702	-e 's:g95..NCDF_LIB..$:g95 NCDF_LIB= -L'"$ncdfdir"'/lib -lnetcdff -lnetcdf:' \
703	-e 's:g95 L_O =:g95 L_O = -Wl,-rpath='"$ncdfdir"'/lib:' \
704	-e "s:-fmod=:-$fmod:" -e 's/-fno-second-underscore//' \
705	-e 's:#-Q- g95 M_K = gmake:#-Q- g95 M_K = make:' \
706	tmp >\| AA_make.gdef
707
708	if [ $pcmac == 1 ]
709	then
710	cp AA_make.gdef tmp
711	sed -e 's/rpath=/rpath,/g' tmp > AA_make.gdef
712	fi
713
714
715	# We use lines for g95 even for the other compilers to run ins_make
716	if [ "$use_shell" = "ksh" ] ; then
717	./ins_make $o_ins_make
718	else # bash
719	sed -e s:/bin/ksh:/bin/bash:g ins_make > ins_make.bash
720	if [ "`grep jeanzay AA_make.gdef`" = "" ] ; then
721	# Bidouille pour compiler sur ada des vieux modipsl.tar
722	echo 'Warning jean-zay not in AA_make.gdef'
723	echo 'Think about updating'
724	exit 1
725	fi
726
727	chmod u=rwx ins_make.bash
728	./ins_make.bash $o_ins_make
729	fi # of if [ "$use_shell" = "ksh" ]
730
731	echo install_lmdz.sh MODIPSL_OK `date`
732
733	cd $MODEL/modipsl/modeles/IOIPSL/src
734	ioipsllog=`pwd`/ioipsl.log
735	echo '##########################################################'
736	echo 'Compiling IOIPSL, the interface library with Netcdf'
737	echo '##########################################################'
738	echo `date`
739	echo log file : $ioipsllog
740
741	if [ "$use_shell" = "bash" ] ; then
742	cp Makefile Makefile.ksh
743	sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile
744	fi
745	# if [ "$pclinux" = 1 ] ; then
746	# Build IOIPSL modules and library
747	$make clean
748	$make > $ioipsllog 2>&1
749	if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then
750	# copy module files to lib
751	cp -f *.mod ../../../lib
752	fi
753	# Build IOIPSL tools (ie: "rebuild", if present)
754	if [ -f $MODEL/modipsl/modeles/IOIPSL/tools/rebuild ] ; then
755	cd $MODEL/modipsl/modeles/IOIPSL/tools
756	# adapt Makefile & rebuild script if in bash
757	if [ "$use_shell" = "bash" ] ; then
758	cp Makefile Makefile.ksh
759	sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile
760	cp rebuild rebuild.ksh
761	sed -e 's:/bin/ksh:/bin/bash:g' \
762	-e 's:print -u2:echo:g' \
763	-e 's:print:echo:g' rebuild.ksh > rebuild
764	fi
765	$make clean
766	$make > $ioipsllog 2>&1
767	fi
768	# fi # of if [ "$pclinux" = 1 ]
769
770	else # of if [ $ioipsl = 1 ]
771	if [ ${hostname:0:5} = jean- ] ; then
772	cd $MODEL/modipsl
773	cd util
774	if [ "`grep jeanzay AA_make.gdef`" = "" ] ; then
775	echo 'Warning jean-zay not in AA_make.gdef'
776	echo 'Think about updating'
777	exit 1
778	fi
779	./ins_make $o_ins_make
780	# Compile IOIPSL on jean-zay
781	cd $MODEL/modipsl/modeles/IOIPSL/src
782	gmake > ioipsl.log
783	cd $MODEL/modipsl/modeles/IOIPSL/tools
784	gmake > ioipsl.log
785
786	fi
787	echo install_lmdz.sh ioipsl_OK `date`
788	fi # of if [ $ioipsl = 1 ]
789	fi
790	# Saving ioipsl lib for possible parallel compile
791	cd $MODEL/modipsl
792	tar cf ioipsl.tar lib/ bin/
793
794	#=========================================================================
795	if [ "$with_xios" = "y" ] ; then
796	echo '##########################################################'
797	echo 'Compiling XIOS'
798	echo '##########################################################'
799	cd $MODEL/modipsl/modeles
800	xioslog=`pwd`/xios.log
801	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/install_xios.bash
802	myget script_install/install_xios.bash
803	chmod u=rwx install_xios.bash
804	if [ ${hostname:0:5} = jean- ] ; then
805	svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5 \
806	XIOS
807	cd XIOS/arch
808	svn update
809	cd ..
810	echo "Compiling XIOS, start" `date` \
811	"(it takes about 20 min on Jean-Zay)"
812	echo "log file: $xioslog"
813	./make_xios --prod --arch $arch --job 4 > xios.log 2>&1
814	else
815	./install_xios.bash -prefix $MODEL/modipsl/modeles \
816	-netcdf ${ncdfdir} -hdf5 ${ncdfdir} \
817	-MPI $root_mpi -arch $arch > xios.log 2>&1
818	fi # of case Jean-Zay
819	if [ -f XIOS/lib/libxios.a ] ; then
820	echo "XIOS library successfully generated"
821	echo install_lmdz.sh XIOS_OK `date`
822	fi
823	fi
824
825	#============================================================================
826	veget_version=false
827	if [ "$veget" != 'NONE' ] ; then
828	cd $MODEL/modipsl/modeles/ORCHIDEE
829	set +e ; svn upgrade ; set -e
830	if [ "$veget" = "CMIP6" ] ; then
831	veget_version=orchidee2.0
832	orchidee_rev=6592
833	else # specific orchidee revision newer than CMIP6, on 2_1 or 2_2 branches
834	veget_version=orchidee2.1
835	orchidee_rev=$veget
836	if [ $veget -lt 4465 ] ; then
837	echo 'Stopping, ORCHIDEE version too old, script needs work on ' \
838	'the CPP flags to pass to makelmdz'
839	exit 1
840	fi
841	set +e
842	# which branch is my version on?
843	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}'`
844	# switch to that branch
845	echo IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at \
846	orchidee-help@listes.ipsl.fr
847	svn switch -r $veget --accept theirs-full \
848	svn://forge.ipsl.jussieu.fr/orchidee/$orcbranch
849	svn log -r $veget \| grep $veget
850	if [ $? -gt 0 ] ; then
851	echo 'Cannot update ORCHIDEE as not on the right branch for ' \
852	'ORCHIDEE'
853	exit
854	fi
855	set -e
856	set +e ; svn update -r $veget ; set -e
857	fi
858	# Correctif suite debug Jean-Zay
859	sed -i -e 's/9010 FORMAT(A52,F17.14)/9010 FORMAT(A52,F20.14)/' \
860	src_stomate/stomate.f90
861	opt_orc="-prod" ; if [ "$optim" = "-debug" ] ; then opt_orc="-debug" ; fi
862
863	orchideelog=`pwd`/orchidee.log
864	echo '########################################################'
865	echo 'Compiling ORCHIDEE, the continental surface model '
866	echo '########################################################'
867	echo Start of the first compilation of orchidee, in sequential mode: `date`
868	echo log file : $orchideelog
869
870	export ORCHPATH=`pwd`
871	xios_orchid="-noxios"
872	if [ "$with_xios" = "y" ] ; then
873	xios_orchid="-xios"
874	fi
875	if [ -d tools ] ; then
876	###################################################################
877	# Pour les experts qui voudraient changer de version d'orchidee.
878	# Attention : necessite d'avoir le password pour orchidee
879
880	# Correctif suite debug Jean-Zay
881	if [ -f src_global/time.f90 ] ; then
882	sed -i -e 's/CALL tlen2itau/\!CALL tlen2itau/' src_global/time.f90
883	fi
884	###################################################################
885	if [ "$veget_version" == "false" ] ; then
886	veget_version=orchidee2.0
887	fi
888	cd arch
889	sed -e s:"%COMPILER .*.$":"%COMPILER $compiler":1 \
890	-e s:"%LINK .*.$":"%LINK $compiler":1 \
891	-e s:"%FPP_FLAGS .*.$":"%FPP_FLAGS $fpp_flags":1 \
892	-e s:"%PROD_FFLAGS .*.$":"%PROD_FFLAGS $OPTIM":1 \
893	-e s:"%DEV_FFLAGS .*.$":"%DEV_FFLAGS $OPTDEV":1 \
894	-e s:"%DEBUG_FFLAGS .*.$":"%DEBUG_FFLAGS $OPTDEB":1 \
895	-e s:"%BASE_FFLAGS .*.$":"%BASE_FFLAGS $OPTPREC":1 \
896	-e s:"%BASE_LD .*.$":"%BASE_LD $BASE_LD":1 \
897	-e s:"%ARFLAGS .*.$":"%ARFLAGS $ARFLAGS":1 \
898	arch-gfortran.fcm > arch-local.fcm
899	echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib -lnetcdff -lnetcdf\"" \
900	> arch-local.path
901	echo "NETCDF_INCDIR=${ncdfdir}/include" >> arch-local.path
902	echo "IOIPSL_INCDIR=$ORCHPATH/../../lib" >> arch-local.path
903	echo "IOIPSL_LIBDIR=$ORCHPATH/../../lib" >> arch-local.path
904	echo 'XIOS_INCDIR=${ORCHDIR}/../XIOS/inc' >> arch-local.path
905	echo 'XIOS_LIBDIR="${ORCHDIR}/../XIOS/lib -lxios"' >> arch-local.path
906	cd ../
907
908	echo ./makeorchidee_fcm -j $xios_orchid $opt_orc -parallel none \
909	-arch $arch
910	./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel none \
911	-arch $arch > $orchideelog 2>&1
912	pwd
913	else # of "if [ -d tools ]"
914	if [ -d src_parallel ] ; then
915	liste_src="parallel parameters global stomate sechiba driver"
916	if [ "$veget_version" == "false" ] ; then
917	veget_version=orchidee2.0
918	fi
919	fi
920	for d in $liste_src ; do
921	src_d=src_$d
922	echo src_d $src_d
923	echo ls ; ls
924	if [ ! -d $src_d ] ; then
925	echo Problem orchidee : no $src_d ; exit
926	fi
927	cd $src_d ; \rm -f *.mod make ; $make clean
928	$make > $orchideelog 2>&1
929	if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then
930	cp -f *.mod ../../../lib
931	fi
932	cd ..
933	done
934	fi # of "if [ -d tools ]"
935	echo install_lmdz.sh orchidee_compil_seq_OK `date`
936	fi # of if [ "$veget" != 'NONE' ]
937
938
939	#============================================================================
940	# Ehouarn: the directory name LMDZ* depends on version/tar file...
941	if [ -d $MODEL/modipsl/modeles/LMD* ] ; then
942	echo '###############################################################'
943	echo 'Preparing LMDZ compilation : arch file, svn switch if needed...'
944	echo '###############################################################'
945	cd $MODEL/modipsl/modeles/LMD*
946	LMDZPATH=`pwd`
947	else
948	echo "ERROR: No LMD* directory !!!"
949	exit
950	fi
951
952	###########################################################
953	# For those who want to use fcm to compile via :
954	# makelmdz_fcm -arch local .....
955	############################################################
956
957
958
959	cd $MODEL/modipsl/modeles/LMDZ*
960	lmdzlog=`pwd`/lmdz.log
961
962	##################################################################
963	# Possibly update LMDZ if a specific svn release is requested
964	##################################################################
965
966	set +e ; svn upgrade ; set -e
967
968	if [ "$svn" = "last" ] ; then svnopt="" ; else svnopt="-r $svn" ; fi
969	if [ "$svn" != "" ] ; then
970	set +e ; svn info \| grep -q 'http:'
971	if [ $? = 0 ] ; then
972	svn switch --relocate http://svn.lmd.jussieu.fr/LMDZ \
973	https://svn.lmd.jussieu.fr/LMDZ
974	fi
975	svn update $svnopt
976	set -e
977	fi
978
979	#---------------------------------------------------------------------
980	# Retrieve the final svn release number, and adjust compilation
981	# options accordingly
982	# If svn not available, will use the svn writen in $MODEL/Readm*md
983	# For old version it assumes that it is before 4185 (the version
984	# for which the test was introduced
985	#---------------------------------------------------------------------
986
987	set +e ; mysvn=`svnversion . \| egrep -o "[0-9]+" 2>/dev/null` ; set -e
988	if [ "$mysvn" = "" ] ; then mysvn=`grep 'Revision: [0-9]' $MODEL/Read*.md \| awk ' { print $2 } ' 2>/dev/null` ; fi
989	if [ "$mysvn" = "" ] ; then mysvn=4190 ; fi
990
991	if [[ "$pclinux" = "1" && ! -f arch/arch-local.path ]] ; then
992
993	# create local 'arch' files (if on Linux PC):
994	cd arch
995	# arch-local.path file
996	# test for version as arch.pth file changed format with rev 4426
997	if [ "$mysvn" -gt 4425 ] ; then
998	echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib \"" > arch-local.path
999	echo "NETCDF_LIB=\"-lnetcdff -lnetcdf\"" >> arch-local.path
1000	echo "NETCDF_INCDIR=-I${ncdfdir}/include" >> arch-local.path
1001	echo 'NETCDF95_INCDIR=-I$LMDGCM/../../include' >> arch-local.path
1002	echo 'NETCDF95_LIBDIR=-L$LMDGCM/../../lib' >> arch-local.path
1003	echo 'NETCDF95_LIB=-lnetcdf95' >> arch-local.path
1004	echo 'IOIPSL_INCDIR=-I$LMDGCM/../../lib' >> arch-local.path
1005	echo 'IOIPSL_LIBDIR=-L$LMDGCM/../../lib' >> arch-local.path
1006	echo 'IOIPSL_LIB=-lioipsl' >> arch-local.path
1007	echo 'XIOS_INCDIR=-I$LMDGCM/../XIOS/inc' >> arch-local.path
1008	echo 'XIOS_LIBDIR=-L$LMDGCM/../XIOS/lib' >> arch-local.path
1009	echo "XIOS_LIB=\"-lxios -lstdc++\"" >> arch-local.path
1010	echo 'ORCH_INCDIR=-I$LMDGCM/../../lib' >> arch-local.path
1011	echo 'ORCH_LIBDIR=-L$LMDGCM/../../lib' >> arch-local.path
1012	else
1013	echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib -lnetcdff -lnetcdf\"" \
1014	> arch-local.path
1015	echo "NETCDF_INCDIR=-I${ncdfdir}/include" >> arch-local.path
1016	echo 'NETCDF95_INCDIR=$LMDGCM/../../include' >> arch-local.path
1017	echo 'NETCDF95_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
1018	echo 'IOIPSL_INCDIR=$LMDGCM/../../lib' >> arch-local.path
1019	echo 'IOIPSL_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
1020	echo 'XIOS_INCDIR=$LMDGCM/../XIOS/inc' >> arch-local.path
1021	echo 'XIOS_LIBDIR=$LMDGCM/../XIOS/lib' >> arch-local.path
1022	echo 'ORCH_INCDIR=$LMDGCM/../../lib' >> arch-local.path
1023	echo 'ORCH_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
1024	fi
1025
1026	if [ $pcmac == 1 ] ; then
1027	BASE_LD="$BASE_LD -Wl,-rpath,${ncdfdir}/lib"
1028	else
1029	BASE_LD="$BASE_LD -Wl,-rpath=${ncdfdir}/lib"
1030	fi
1031	# Arch-local.fcm file (adapted from arch-linux-32bit.fcm)
1032
1033	if [ $real = r8 ] ; then FPP_DEF=NC_DOUBLE ; else FPP_DEF="" ; fi
1034	sed -e s:"%COMPILER .*.$":"%COMPILER $compiler":1 \
1035	-e s:"%LINK .*.$":"%LINK $compiler":1 \
1036	-e s:"%PROD_FFLAGS .*.$":"%PROD_FFLAGS $OPTIM":1 \
1037	-e s:"%DEV_FFLAGS .*.$":"%DEV_FFLAGS $OPTDEV":1 \
1038	-e s:"%DEBUG_FFLAGS .*.$":"%DEBUG_FFLAGS $OPTDEB":1 \
1039	-e s:"%BASE_FFLAGS .*.$":"%BASE_FFLAGS $OPTPREC":1 \
1040	-e s:"%FPP_DEF .*.$":"%FPP_DEF $FPP_DEF":1 \
1041	-e s:"%BASE_LD .*.$":"%BASE_LD $BASE_LD":1 \
1042	-e s:"%ARFLAGS .*.$":"%ARFLAGS $ARFLAGS":1 \
1043	arch-linux-32bit.fcm > arch-local.fcm
1044
1045	cd ..
1046	### Adapt "bld.cfg" (add the shell):
1047	#whereisthatshell=$(which ${use_shell})
1048	#echo "bld::tool::SHELL $whereisthatshell" >> bld.cfg
1049
1050	fi # of if [ "$pclinux" = 1 ]
1051	#---------------------------------------------------------------------
1052	# Option de compilation du rayonnement : depend de $mysvn ><= r4185
1053	#---------------------------------------------------------------------
1054	opt_rad=""
1055
1056	case $rad in
1057	oldrad) iflag_rrtm=0 ; NSW=2 ; opt_rad="" ;;
1058	rrtm) iflag_rrtm=1 ; NSW=6
1059	if [ $mysvn -le 4185 ] ; then
1060	opt_rad="-rrtm true"
1061	else
1062	opt_rad="-rad rrtm"
1063	fi ;;
1064	ecrad) iflag_rrtm=2 ; NSW=6 ; opt_rad="-rad ecrad" ;;
1065	*) echo Only oldrad rrtm ecrad for rad option ; exit
1066	esac
1067
1068	if [ $mysvn -le 4185 -a $rad = "ecrad" ] ; then
1069	echo "ecrad only available for LMDZ rev starting with 4186 " ; exit
1070	fi
1071
1072	##################################################################
1073
1074
1075	if [[ ! -f libf/misc/netcdf95.F90 && ! -d $MODEL/NetCDF95-0.2 ]]
1076	then
1077	cd $MODEL
1078	myget src_archives/netcdf/NetCDF95-0.2.tar.gz
1079	tar -xf NetCDF95-0.2.tar.gz
1080	rm NetCDF95-0.2.tar.gz
1081	cd NetCDF95-0.2
1082	mkdir build
1083	cd build
1084	cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=$ncdfdir \
1085	-DCMAKE_INSTALL_PREFIX=$MODEL/modipsl
1086	make install
1087	cd $MODEL/modipsl/modeles/LMDZ*
1088	fi
1089
1090	echo '##################################################################'
1091	echo "Preparing script compile.sh for LMDZ compilation"
1092	echo "It will only be run automatically if bench=1/tuto"
1093	echo Here bench=$bench
1094	echo '##################################################################'
1095
1096	if [ "$env_file" != "" ] ; then
1097	mv arch/arch-${arch}.env arch/arch-${arch}.orig
1098	\cp -f $env_file arch/arch-${arch}.env
1099	fi
1100
1101	if [ $compile_with_fcm = 1 ] ; then
1102	makelmdz="makelmdz_fcm $optim -arch $arch -j 8 "
1103	else
1104	makelmdz="makelmdz $optim -arch $arch"
1105	fi
1106
1107	# sequential compilation
1108	if [ "$sequential" = 1 ] ; then
1109	echo Sequential compilation command, saved in compile.sh:
1110	echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp " \
1111	"-d ${grid_resolution} -v $veget_version gcm "
1112	echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp " \
1113	"-d ${grid_resolution} -v $veget_version gcm " > compile.sh
1114	chmod +x ./compile.sh
1115	if [ $bench = 1 ] ; then
1116	echo install_lmdz.sh start_lmdz_seq_compilation `date`
1117	echo log file: $lmdzlog
1118	./compile.sh > $lmdzlog 2>&1
1119	echo install_lmdz.sh end_lmdz_seq_compilation `date`
1120	fi
1121	fi # fin sequential
1122
1123	# compiling in parallel mode
1124	if [ $parallel != "none" ] ; then
1125	echo '##########################################################'
1126	echo ' Parallel compile '
1127	echo '##########################################################'
1128	echo "(after saving the sequential libs and binaries)"
1129	cd $MODEL/modipsl
1130	tar cf sequential.tar bin/ lib/
1131	\rm -rf bin/ lib/
1132	tar xf ioipsl.tar
1133	#
1134	# Orchidee
1135	#
1136	cd $ORCHPATH
1137	if [ -d src_parallel -a $veget != 'NONE' ] ; then
1138	cd arch
1139	sed \
1140	-e s:"%COMPILER.*.$":"%COMPILER $par_comp":1 \
1141	-e s:"%LINK.*.$":"%LINK $par_comp":1 \
1142	-e s:"%MPI_FFLAG.*.$":"%MPI_FFLAGS $MPI_FLAGS":1 \
1143	-e s:"%OMP_FFLAG.*.$":"%OMP_FFLAGS $OMP_FLAGS":1 \
1144	-e s:"%MPI_LD.*.$":"%MPI_LD $MPI_LD":1 \
1145	-e s:"%OMP_LD.*.$":"%OMP_LD $OMP_LD":1 \
1146	arch-local.fcm > tmp.fcm
1147
1148	mv tmp.fcm arch-local.fcm
1149	cd ../
1150	echo Compiling ORCHIDEE in parallel mode `date`
1151	echo logfile $orchideelog
1152	echo "NOTE : to recompile it when necessary, use ./compile_orc.sh " \
1153	"in modipsl/modeles/ORCHIDEE"
1154	echo ./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc \
1155	-parallel $parallel -arch $arch > compile_orc.sh
1156	echo ./makeorchidee_fcm -j 8 $xios_orchid $opt_orc \
1157	-parallel $parallel -arch $arch >> compile_orc.sh
1158	echo echo Now you must also recompile LMDZ, by running ./compile.sh \
1159	in modeles/LMDZ >> compile_orc.sh
1160	chmod u+x compile_orc.sh
1161	./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc \
1162	-parallel $parallel -arch $arch > $orchideelog 2>&1
1163	./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel $parallel \
1164	-arch $arch >> $orchideelog 2>&1
1165	echo End of ORCHIDEE compilation in parallel mode `date`
1166	elif [ $veget != 'NONE' ] ; then
1167	echo '##########################################################'
1168	echo ' Orchidee version too old '
1169	echo ' Please update to new version '
1170	echo '##########################################################'
1171	exit
1172	fi # of [ -d src_parallel -a $veget != 'NONE' ]
1173
1174	# LMDZ
1175	cd $LMDZPATH
1176	if [ $arch = local ] ; then
1177	cd arch
1178	sed -e s:"%COMPILER.*.$":"%COMPILER $par_comp":1 \
1179	-e s:"%LINK.*.$":"%LINK $par_comp":1 \
1180	-e s:"%MPI_FFLAG.*.$":"%MPI_FFLAGS $MPI_FLAGS":1 \
1181	-e s:"%OMP_FFLAG.*.$":"%OMP_FFLAGS $OMP_FLAGS":1 \
1182	-e s:"%ARFLAGS.*.$":"%ARFLAGS $ARFLAGS":1 \
1183	-e s@"%BASE_LD.*.$"@"%BASE_LD -Wl,-rpath=${root_mpi}/lib:${ncdfdir}/lib"@1 \
1184	-e s:"%MPI_LD.*.$":"%MPI_LD $MPI_LD":1 \
1185	-e s:"%OMP_LD.*.$":"%OMP_LD $OMP_LD":1 \
1186	arch-local.fcm > tmp.fcm
1187	mv tmp.fcm arch-local.fcm
1188	cd ../
1189	fi
1190	rm -f compile.sh
1191	echo resol=${grid_resolution} >> compile.sh
1192	if [ ${hostname:0:5} = jean- -a "$cosp" = "v2" ] ; then
1193
1194	echo LMDZ compilation command in parallel mode, saved in compile.sh, \
1195	is :
1196	echo "(ATTENTION le probleme de cospv2 sur jean-zay en mode prod " \
1197	"n est pas corrige ! )"
1198	# ATTENTION le probleme de cospv2 sur jean-zay en mode prod n
1199	# est pas corrige
1200	echo ./$makelmdz -dev $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
1201	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
1202	-parallel $parallel gcm >> compile.sh
1203	echo ./$makelmdz -dev $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
1204	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
1205	-parallel $parallel gcm
1206	else
1207	echo ./$makelmdz $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
1208	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
1209	-parallel $parallel gcm >> compile.sh
1210	echo ./$makelmdz $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
1211	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
1212	-parallel $parallel gcm
1213	fi
1214	chmod +x ./compile.sh
1215
1216	if [ $bench = 1 ] ; then
1217	echo Compiling LMDZ in parallel mode `date`, LMDZ log file: $lmdzlog
1218	./compile.sh > $lmdzlog 2>&1
1219	fi
1220
1221	fi # of if [ $parallel != "none" ]
1222
1223
1224	##################################################################
1225	# Verification du succes de la compilation
1226	##################################################################
1227
1228	# Recherche de l'executable dont le nom a change au fil du temps ...
1229	# suffix contains radiative option starting with revision 4186
1230	if [ $mysvn -ge 4186 ] ; then suff_exe=_${rad}${suff_exe} ; fi
1231	gcm=""
1232
1233	for exe in gcm.e bin/gcm_${grid_resolution}_phylmd${suff_exe}${suff_orc}.e
1234	do
1235	if [ -f $exe ] ; then gcm=$exe ; fi
1236	done
1237
1238	if [ "$gcm" = "" ] ; then
1239	if [ $bench = 1 ] ; then
1240	echo 'Compilation failed !! Cannot run the benchmark;'
1241	exit
1242	else
1243	echo 'Compilation not done (only done when bench=1)'
1244	fi
1245	else
1246	echo '##########################################################'
1247	echo 'Compilation successfull !! ' `date`
1248	echo '##########################################################'
1249	echo The executable is $gcm
1250	fi
1251
1252	##################################################################
1253	# Below, we run a benchmark if bench=1 or tuto
1254	##################################################################
1255
1256	if [ $bench = tuto ] ; then
1257	myget Training/tutorial.tar ; tar xf tutorial.tar ; cd TUTORIAL
1258	./init.sh
1259
1260	elif [[ $bench = 1 && ! -d BENCH${grid_resolution} ]] ; then
1261	# TOUTE CETTE SECTION DEVRAIT DISPARAITRE POUR UNE COMMANDE
1262	# OU DES BENCHS PAR MOTS CLES COMME tuto
1263
1264	echo '##########################################################'
1265	echo ' Running a test run '
1266	echo '##########################################################'
1267
1268	\rm -rf BENCH${grid_resolution}
1269	bench=bench_lmdz_${grid_resolution}
1270	echo install_lmdz.sh before bench download `date`
1271	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/$bench.tar.gz
1272	myget 3DBenchs/$bench.tar.gz
1273	echo install_lmdz.sh after bench download `date`
1274	tar xf $bench.tar.gz
1275
1276	if [ "$cosp" = "v1" -o "$cosp" = "v2" ] ; then
1277	cd BENCH${grid_resolution}
1278	# copier les fichiers namelist input et output our COSP
1279	cp ../DefLists/cosp*_input_nl.txt .
1280	cp ../DefLists/cosp*_output_nl.txt .
1281	# Activer la cles ok_cosp pour tourner avec COSP
1282	sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp
1283	\mv -f tmp config.def
1284	cd ..
1285	fi
1286
1287	if [ -n "$physiq" ]; then
1288	cd BENCH${grid_resolution}
1289	if [ -f physiq.def_${physiq} ]; then
1290	cp physiq.def_${physiq} physiq.def
1291	echo using physiq.def_${physiq}
1292	else
1293	echo using standard physiq.def
1294	fi
1295	cd ..
1296	else
1297	echo using standard physiq.def
1298	fi
1299
1300	if [ "$with_xios" = "y" ] ; then
1301	cd BENCH${grid_resolution}
1302	cp ../DefLists/iodef.xml .
1303	cp ../DefLists/context_lmdz.xml .
1304	cp ../DefLists/field_def_lmdz.xml .
1305	# A raffiner par la suite
1306	echo A FAIRE : Copier les *xml en fonction de l option cosp
1307	cp ../DefLists/field_def_cosp*.xml .
1308	cp ../DefLists/file_def_hist*xml .
1309	# adapt iodef.xml to use attached mode
1310	sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' \
1311	iodef.xml > tmp
1312	\mv -f tmp iodef.xml
1313
1314	# and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
1315	# except for histday
1316	for histfile in file_def_hist*xml
1317	do
1318	if [ "$histfile" = "file_def_histday_lmdz.xml" ] ; then
1319	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' \
1320	$histfile > tmp
1321	\mv -f tmp $histfile
1322	sed -e 's@output_level="_AUTO_"@output_level="5"@' $histfile \
1323	> tmp
1324	\mv -f tmp $histfile
1325	sed -e 's@compression_level="2"@compression_level="0"@' \
1326	$histfile > tmp
1327	\mv -f tmp $histfile
1328	else
1329	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
1330	$histfile > tmp
1331	\mv -f tmp $histfile
1332	fi
1333	done
1334	# and add option "ok_all_xml=y" in config.def
1335	echo "### XIOS outputs" >> config.def
1336	echo 'ok_all_xml=.true.' >> config.def
1337
1338	#activer les sorties pour Cosp
1339	if [ "$cosp" = "v1" ] ; then
1340	histfile=file_def_histdayCOSP_lmdz.xml
1341	sed -e 's@enabled=".FALSE."@enabled=".TRUE."@' $histfile > tmp
1342	\mv -f tmp $histfile
1343	sed -e 's@output_level="_AUTO_"@output_level="5"@' $histfile > tmp
1344	\mv -f tmp $histfile
1345	sed -e 's@compression_level="2"@compression_level="0"@' \
1346	$histfile > tmp
1347	\mv -f tmp $histfile
1348	fi
1349	if [ "$cosp" = "v2" ] ; then
1350	histfile=file_def_histdayCOSPv2_lmdz.xml
1351	sed -e 's@compression_level="2"@compression_level="0"@' \
1352	$histfile > tmp
1353	\mv -f tmp $histfile
1354	contextfile=context_lmdz.xml
1355	sed -e 's@src="./file_def_histdayCOSP_lmdz.xml"@src="./file_def_histdayCOSPv2_lmdz.xml"@' \
1356	$contextfile > tmp
1357	\mv -f tmp $contextfile
1358	sed -e 's@src="./file_def_histmthCOSP_lmdz.xml"@src="./file_def_histmthCOSPv2_lmdz.xml"@' \
1359	$contextfile > tmp
1360	\mv -f tmp $contextfile
1361	sed -e 's@src="./file_def_histhfCOSP_lmdz.xml"@src="./file_def_histhfCOSPv2_lmdz.xml"@' \
1362	$contextfile > tmp
1363	\mv -f tmp $contextfile
1364	fieldfile=field_def_lmdz.xml
1365	sed -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' $fieldfile \
1366	> tmp
1367	\mv -f tmp $fieldfile
1368	fi
1369
1370	cd ..
1371	fi
1372
1373	# Cas Bensh avec ecrad
1374	if [ "$rad" = "ecrad" ] ; then
1375	cd BENCH${grid_resolution}
1376	cp ../DefLists/namelist_ecrad .
1377	cp -r ../libf/phylmd/ecrad/data .
1378	cd ..
1379	fi
1380
1381	# Adjusting bench physiq.def to radiative code chosen
1382	cd BENCH${grid_resolution}
1383	sed -e 's/iflag_rrtm=.*.$/iflag_rrtm='$iflag_rrtm'/' \
1384	-e 's/NSW=.*.$/NSW='$NSW'/' physiq.def > tmpdef
1385	\mv tmpdef physiq.def
1386	cd ..
1387
1388	cp $gcm BENCH${grid_resolution}/gcm.e
1389
1390	cd BENCH${grid_resolution}
1391	# On cree le fichier bench.sh au besoin
1392	# Dans le cas 48x36x39 le bench.sh existe deja en parallele
1393
1394	if [ "$grid_resolution" = "48x36x39" ] ; then
1395	echo On ne touche pas au bench.sh
1396	# But we have to adapt "run_local.sh" for $mpirun
1397	sed -e "s@mpirun@$mpirun@g" run_local.sh > tmp
1398	mv -f tmp run_local.sh
1399	chmod u=rwx run_local.sh
1400	elif [ "${parallel:0:3}" = "mpi" ] ; then
1401	# Lancement avec deux procs mpi et 2 openMP
1402	echo "export OMP_STACKSIZE=800M" > bench.sh
1403	if [ "${parallel:4:3}" = "omp" ] ; then
1404	echo "export OMP_NUM_THREADS=2" >> bench.sh
1405	fi
1406	if [ "$cosp" = "v1" -o "$cosp" = "v2" ] ; then
1407	if [ ${hostname:0:5} = jean- ] ; then
1408	chmod +x ../arch.env
1409	../arch.env
1410	echo "ulimit -s 2000000" >> bench.sh
1411	else
1412	echo "ulimit -s 200000" >> bench.sh
1413	fi
1414	else
1415	echo "ulimit -s unlimited" >> bench.sh
1416	fi
1417	if [ ${hostname:0:5} = jean- ] ; then
1418	. ../arch/arch-${arch}.env
1419	echo "srun -n 2 -A $idris_acct@cpu gcm.e > listing 2>&1" \
1420	>> bench.sh
1421	else
1422	echo "$mpirun -np 2 gcm.e > listing 2>&1" >> bench.sh
1423	fi
1424	# Add rebuild, using reb.sh if it is there
1425	echo 'if [ -f reb.sh ] ; then' >> bench.sh
1426	echo ' ./reb.sh histday ; ./reb.sh histmth ; ./reb.sh histhf ; ' \
1427	'./reb.sh histins ; ./reb.sh stomate_history ; ' \
1428	'./reb.sh sechiba_history ; ./reb.sh sechiba_out_2 ' >> bench.sh
1429	echo 'fi' >> bench.sh
1430	else
1431	echo "./gcm.e > listing 2>&1" > bench.sh
1432	fi
1433	# Getting orchidee stuff
1434	if [ $veget == 'CMIP6' ] ; then
1435	#echo 'myget 3DBenchs/BENCHorch11.tar.gz'
1436	#myget 3DBenchs/BENCHorch11.tar.gz
1437	#tar xvzf BENCHorch11.tar.gz
1438	echo 'myget 3DBenchs/BENCHCMIP6.tar.gz'
1439	myget 3DBenchs/BENCHCMIP6.tar.gz
1440	tar xvzf BENCHCMIP6.tar.gz
1441	sed -e "s:VEGET=n:VEGET=y:" config.def > tmp
1442	mv -f tmp config.def
1443	if [ "$with_xios" = "y" ] ; then
1444	cp ../../ORCHIDEE/src_xml/context_orchidee.xml .
1445	echo '<context id="orchidee" src="./context_orchidee.xml"/>' \
1446	> add.tmp
1447	cp ../../ORCHIDEE/src_xml/field_def_orchidee.xml .
1448	cp ../../ORCHIDEE/src_xml/file_def_orchidee.xml .
1449	cp ../../ORCHIDEE/src_xml/file_def_input_orchidee.xml .
1450	if [ -f ../../ORCHIDEE/src_xml/context_input_orchidee.xml ] ; then
1451	cp ../../ORCHIDEE/src_xml/context_input_orchidee.xml .
1452	echo '<context id="orchidee" ' \
1453	'src="./context_input_orchidee.xml"/>' >> add.tmp
1454	fi
1455	sed -e '/id="LMDZ"/r add.tmp' iodef.xml > tmp
1456	mv tmp iodef.xml
1457	sed -e'{/sechiba1/ s/enabled="_AUTO_"/type="one_file" enabled=".TRUE."/}' \
1458	file_def_orchidee.xml > tmp
1459	\mv -f tmp file_def_orchidee.xml
1460	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
1461	file_def_orchidee.xml > tmp
1462	\mv -f tmp file_def_orchidee.xml
1463	sed -e 's@output_level="_AUTO_"@output_level="1"@' \
1464	file_def_orchidee.xml > tmp
1465	\mv -f tmp file_def_orchidee.xml
1466	sed -e 's@output_freq="_AUTO_"@output_freq="1d"@' \
1467	file_def_orchidee.xml > tmp
1468	\mv -f tmp file_def_orchidee.xml
1469	sed -e 's@compression_level="4"@compression_level="0"@' \
1470	file_def_orchidee.xml > tmp
1471	\mv -f tmp file_def_orchidee.xml
1472	sed -e 's@XIOS_ORCHIDEE_OK = n@XIOS_ORCHIDEE_OK = y@' \
1473	orchidee.def > tmp
1474	\mv -f tmp orchidee.def
1475	fi
1476	fi
1477
1478	if [[ -f ../arch.env ]]
1479	then
1480	source ../arch.env
1481	fi
1482
1483	echo EXECUTION DU BENCH
1484	set +e
1485	date ; ./bench.sh > out.bench 2>&1 ; date
1486	set -e
1487	tail listing
1488
1489
1490	echo '##########################################################'
1491	echo 'Simulation finished in' `pwd`
1492	echo 'You have compiled with:'
1493	cat ../compile.sh
1494	if [ $parallel = "none" ] ; then
1495	echo 'You may re-run it with : cd ' `pwd` ' ; gcm.e'
1496	echo 'or ./bench.sh'
1497	else
1498	echo 'You may re-run it with : '
1499	echo 'cd ' `pwd` '; ./bench.sh'
1500	# echo 'ulimit -s unlimited'
1501	# echo 'export OMP_NUM_THREADS=2'
1502	# echo 'export OMP_STACKSIZE=800M'
1503	# echo "$mpirun -np 2 gcm.e "
1504	fi
1505	echo '##########################################################'
1506
1507	fi # bench
1508
1509
1510	#################################################################
1511	# Installation eventuelle du 1D
1512	#################################################################
1513
1514	if [ $SCM = 1 ] ; then
1515	cd $MODEL
1516	myget 1D/1D.tar.gz
1517	tar xf 1D.tar.gz
1518	cd 1D
1519	if [ $rad = oldrad ] ; then
1520	sed -i'' -e 's/^rad=.*$/rad=oldrad/' run.sh
1521	sed -i'' -e 's/^rad=.*$/rad=oldrad/' bin/compile
1522	fi
1523	echo Running 1D/run.sh, log in `pwd`/run1d.log
1524	./run.sh > `pwd`/run1d.log 2>&1 &
1525	fi
1526
1527
1528	#################################################################
1529	# sauvegarde des options veget pour utilisation eventuelle tutorial_prod
1530	#################################################################
1531	cd $MODEL/modipsl/modeles
1532	#echo surface_env file created in $MODEL
1533	echo 'veget='$veget > surface_env
1534	#opt_veget="-v $veget_version"
1535	#echo 'opt_veget="'$opt_veget\" >> surface_env
1536	echo 'opt_veget="'-v $veget_version\" >> surface_env
1537	echo 'orchidee_rev='$orchidee_rev >> surface_env
1538	echo 'suforch='$suff_orc >> surface_env

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