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source: BOL/script_install/install_lmdz.sh @ 4248

Last change on this file since 4248 was 4239, checked in by lguez, 22 months ago
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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` $dir
60	fi
61	fi
62	}
63
64	# 04_2021 : tester si r4 marche encore !
65	#real=r4
66	real=r8
67
68
69	#########################################################################
70	# Valeur par défaut des parametres
71	#########################################################################
72	svn=""
73	#version=trunk
74	version=20220131.trunk
75
76	getlmdzor=1
77	netcdf=1 # 1: for automatic installation;
78	# or 0: do not install NetCDF and look for it in standard locations;
79	# or absolute path: look for NetCDF there
80	check_linux=1
81	ioipsl=1
82	bench=1
83	pclinux=1
84	pcmac=0 # default: not on a Mac
85	compiler=gfortran
86	SCM=0
87	# surface/vegetation scheme treatment
88	# controlled by the single variable veget which can have the following values
89	# - NONE: bucket scheme (default)
90	# - CMIP6: orchidee version used in CMIP exercise, rev 5661
91	# - number: orchidee version number
92	veget=NONE
93	# choose the resolution for the bench runs
94	# grid_resolution= 32x24x11 or 48x36x19 for tests (test without ORCHIDEE)
95	# 96x71x19 standard configuration
96	grid_resolution=144x142x79
97	grid_resolution=96x95x39
98	grid_resolution=48x36x19
99	grid_resolution=32x32x39
100	# choose the physiq version you want to test
101	#physiq=NPv6.0.14splith
102	physiq=
103
104	## parallel can take the values none/mpi/omp/mpi_omp
105	parallel=mpi_omp
106	parallel=none
107	idris_acct=lmd
108	OPT_GPROF=""
109	OPT_MAKELMDZ=""
110	MODEL=""
111
112	## also compile XIOS? (and more recent NetCDF/HDF5 libraries) Default=no
113	with_xios="n"
114	opt_makelmdz_xios=""
115
116	## compile with oldrad/rrtm/ecrad radiatif code (Default=rrtm)
117	rad=rrtm
118
119	## compile_with_fcm=1 : use makelmdz_fcm (1) or makelmdz (0)
120	compile_with_fcm=1
121
122	#Compilation with Cosp (cosp=NONE/v1/v2 ; default=NONE)
123	cosp=NONE
124	opt_cosp=""
125
126	# Check if on a Mac
127	if [ `uname` = "Darwin" ]
128	then
129	pcmac=1
130	export MAKE=make
131	fi
132	#echo "pcmac="$pcmac
133
134	env_file=""
135
136	#########################################################################
137	# Options interactives
138	#########################################################################
139	while (($# > 0))
140	do
141	case $1 in
142	"-h") cat <<........fin
143	$0 [ -v version ] [ -r svn_release ]
144	[ -parallel PARA ] [ -d GRID_RESOLUTION ] [ -bench 0/1 ]
145	[-name LOCAL_MODEL_NAME] [-gprof] [-opt_makelmdz] [-rad RADIATIF]
146
147	-v "version" like 20150828.trunk
148	see http://www.lmd.jussieu.fr/~lmdz/Distrib/LISMOI.trunk
149
150	-r "svn_release" : either the svn release number or "last"
151
152	-compiler gfortran\|ifort\|pgf90 (default: gfortran)
153
154	-parallel PARA : can be mpi_omp (mpi with openMP) or none (for sequential)
155
156	-d GRID_RESOLUTION should be among the available benchs if -bench 1
157	among which : 48x36x19, 48x36x39
158	if wanting to run a bench simulation in addition to compilation
159	default : 48x36x19
160
161	-bench activating the bench or not (0/1). Default 1
162
163	-name LOCAL_MODEL_NAME : default = LMDZversion.release
164
165	-netcdf 0, 1 or PATH
166	0: do not download NetCDF, look for it in standard locations
167	1: download and compile NetCDF
168	PATH: full path to an existing installed NetCDF library
169
170	-xios also download and compile the XIOS library
171	(requires the NetCDF4-HDF5 library, also installed by default)
172	(requires to also have -parallel mpi_omp)
173
174	-gprof to compile with -pg to enable profiling with gprof
175
176	-cosp to run without our with cospv1 or cospv2 [none/v1/v2]
177
178	-rad RADIATIF can be oldrad, rrtm or ecrad radiatif code
179
180	-nofcm to compile without fcm
181
182	-SCM install 1D version automatically
183
184	-debug compile everything in debug mode
185
186	-opt_makelmdz to call makelmdz or makelmdz_fcm with additional options
187
188	-physiq to choose which physics package to use
189
190	-env_file specify an arch.env file to overwrite the existing one
191
192	-veget surface model to run [NONE/CMIP6/xxxx]
193
194	........fin
195	exit ;;
196	"-v") version=$2 ; shift ; shift ;;
197	"-r") svn=$2 ; shift ; shift ;;
198	"-compiler") compiler=$2
199	case $compiler in
200	"gfortran"\|"ifort"\|"pgf90") compiler=$2 ; shift
201	shift ;;
202	*) echo "Only gfortran , ifort or pgf90 for the " \
203	"compiler option"
204	exit
205	esac ;;
206	"-d") grid_resolution=$2 ; shift ; shift ;;
207	"-gprof") OPT_GPROF="-pg" ; shift ;;
208	"-cosp") cosp=$2
209	case $cosp in
210	"none"\|"v1"\|"v2") cosp=$2 ; shift ; shift ;;
211	*) echo Only none v1 v2 for cosp option ; exit
212	esac ;;
213	"-nofcm") compile_with_fcm=0 ; shift ;;
214	"-SCM") SCM=1 ; shift ;;
215	"-opt_makelmdz") OPT_MAKELMDZ="$2" ; shift ; shift ;;
216	"-rrtm") rrtm="$2"
217	if [ "$2" = "false" ] ; then
218	rad="oldrad"
219	else
220	rad="rrtm"
221	fi
222	shift ; shift ;;
223	"-rad") rad=$2
224	case $rad in
225	"oldrad"\|"rrtm"\|"ecrad") rad=$2 ; shift ; shift ;;
226	*) echo Only oldrad rrtm ecrad for rad option ; exit
227	esac ;;
228	"-parallel") parallel=$2
229	case $parallel in
230	"none"\|"mpi"\|"omp"\|"mpi_omp") parallel=$2 ; shift
231	shift ;;
232	*) echo Only none mpi omp mpi_omp for the parallel \
233	option
234	exit
235	esac ;;
236	"-bench") bench=$2 ; shift ; shift ;;
237	"-debug") optim=-debug ; shift ;;
238	"-name") MODEL=$2 ; shift ; shift ;;
239	"-netcdf") netcdf=$2 ; shift ; shift ;;
240	"-physiq") physiq=$2 ; shift ; shift ;;
241	"-xios") with_xios="y" ; shift ;;
242	"-env_file") env_file=$2 ; shift ; shift ;;
243	"-veget") veget=$2 ; shift ; shift ;;
244	*) ./install_lmdz.sh -h ; exit
245	esac
246	done
247
248	# Option de compilation du rayonnement : depend de $mysvn ><= r4185,
249	# sera donc definie plus bas
250
251	#opt_rad=""
252	#case $rad in
253	# rrtm) opt_rad="-rad rrtm" ;;
254	# ecrad) opt_rad="-rad ecrad" ;;
255	#esac
256
257
258	# Option de compilation pour Cosp
259	opt_cosp=""
260	case cosp in
261	v1) opt_cosp="-cosp true" ;;
262	v2) opt_cosp="-cospv2 true" ;;
263	esac
264
265	# Check on veget version
266	#if [ "$veget" != 'NONE' -a "$veget" != "CMIP6" -a "$veget" != +([0-9]) ] ; then
267	if [ $veget != 'NONE' -a $veget != "CMIP6" ] ; then
268	re='^[0-9]+$'
269	if ! [[ $veget =~ $re ]] ; then
270	echo 'Valeur de l option veget non valable'
271	exit
272	fi
273	fi
274
275	#Define veget-related suffix for gcm name
276	if [ "$veget" = 'NONE' ] ; then
277	suff_orc=''
278	#For use with tutorial, orchidee_rev is also defined (will be
279	#written in surface_env at the end of the script)
280	orchidee_rev=''
281	else
282	suff_orc='_orch'
283	fi
284
285
286	if [ $parallel = none ] ; then
287	sequential=1; suff_exe='_seq'
288	else
289	sequential=0; suff_exe='_para_mem'
290	fi
291
292	#Chemin pour placer le modele
293	if [ "$MODEL" = "" ] ; then MODEL=./LMDZ$version$svn$optim ; fi
294
295
296	arch=local
297
298
299	if [ $compiler = g95 ] ; then echo g95 is not supported anymore ; exit ; fi
300
301	################################################################
302	# Specificite des machines
303	################################################################
304
305	hostname=`hostname`
306	if [ "$pclinux" = 1 ] ; then o_ins_make="-t g95" ; else o_ins_make="" ; fi
307
308	case ${hostname:0:5} in
309
310	jean-) compiler="mpiifort" ;
311	par_comp="mpiifort" ;
312	o_ins_make="-t jeanzay" ;
313	make=gmake ;
314	module purge
315	module load intel-compilers/19.0.4 ;
316	#module load intel-mpi/19.0.4 ;
317	#module load intel-mkl/19.0.4 ;
318	module load hdf5/1.10.5-mpi ;
319	module load netcdf/4.7.2-mpi ;
320	module load netcdf-fortran/4.5.2-mpi ;
321	module load subversion/1.9.7 ;
322	export NETCDF_LIBDIR=./
323	export NETCDFFORTRAN_INCDIR=./
324	export NETCDFFORTRAN_LIBDIR=./
325	arch=X64_JEANZAY ;;
326
327	cicla\|camel) compiler="gfortran" ;
328	module purge
329	module load gnu/10.2.0
330	module load openmpi/4.0.5
331	module load hdf5/1.10.7-mpi
332	module load netcdf-c/4.7.4-mpi
333	module load netcdf-fortran/4.5.3-mpi
334	netcdf=/net/nfs/tools/PrgEnv/linux-scientific6-x86_64/gcc-10.2.0/netcdf-fortran-4.5.3-k3drgfqok3lip62hnm3tsyof4cjen5sk
335	module load svn/1.14.0
336
337	if [ $parallel != none ] ; then
338	root_mpi=/net/nfs/tools/meso-sl6/openmpi/4.0.5-gcc-10.2.0
339	path_mpi=$root_mpi/bin ;
340	par_comp=${path_mpi}/mpif90 ;
341	mpirun=${path_mpi}/mpirun ;
342	fi ;
343	arch=local ;
344	make=make ;
345	o_ins_make="-t g95" ;;
346
347	*) if [ $parallel = none -o -f /usr/bin/mpif90 ] ; then
348	path_mpi=`which mpif90 \| sed -e s:/mpif90::` ;
349	if [ -d /usr/lib64/openmpi ] ; then
350	root_mpi="/usr/lib64/openmpi"
351	else
352	root_mpi="/usr"
353	fi
354	else
355	echo "Cannot find mpif90" ;
356	if [ $parallel = none ] ; then exit ; fi ;
357	fi ;
358	if [ $parallel != none ] ; then
359	root_mpi=$(which mpif90 \| sed -e s:/bin/mpif90::)
360	path_mpi=$(which mpif90 \| sed -e s:/mpif90::)
361	export LD_LIBRARY_PATH=${root_mpi}/lib:$LD_LIBRARY_PATH
362	fi
363	par_comp=${path_mpi}/mpif90 ;
364	mpirun=${path_mpi}/mpirun ;
365	arch=local ;
366	make=make ;
367	o_ins_make="-t g95"
368	esac
369
370	# Flags for parallelism:
371	if [ $parallel != none ] ; then
372	# MPI_LD are the flags needed for linking with MPI
373	MPI_LD="-L${root_mpi}/lib -lmpi"
374	if [ "$compiler" = "gfortran" ] ; then
375	# MPI_FLAGS are the flags needed for compilation with MPI
376	MPI_FLAGS="-fcray-pointer"
377	# OMP_FLAGS are the flags needed for compilation with OpenMP
378	OMP_FLAGS="-fopenmp -fcray-pointer"
379	# OMP_LD are the flags needed for linking with OpenMP
380	OMP_LD="-fopenmp"
381	elif [ "$compiler" = "ifort" ] ; then
382	MPI_FLAGS=""
383	OMP_FLAGS="-openmp"
384	OMP_LD="-openmp"
385	else # pgf90
386	MPI_FLAGS=""
387	OMP_FLAGS="-mp"
388	OMP_LD="-mp"
389	fi
390	fi
391
392	#####################################################################
393	# Test for old gfortran compilers
394	# If the compiler is too old (older than 4.3.x) we test if the
395	# temporary gfortran44 patch is available on the computer in which
396	# case the compiler is changed from gfortran to gfortran44
397	# Must be aware than parallelism can not be activated in this case
398	#####################################################################
399
400	if [ "$compiler" = "gfortran" ] ; then
401	gfortran=gfortran
402	gfortranv=`gfortran --version \| \
403	head -1 \| awk ' { print $NF } ' \| awk -F. ' { print $1 * 10 + $2 } '`
404	if [ $gfortranv -le 43 ] ; then
405	echo ERROR : Your gfortran compiler is too old
406	echo 'Please choose a new one (ifort) and change the line'
407	echo compiler=xxx
408	echo in the install_lmdz.sh script and rerun it
409	if [ `which gfortran44 \| wc -w` -ne 0 ] ; then
410	gfortran=gfortran44
411	else
412	echo gfotran trop vieux ; exit
413	fi
414	fi
415	compiler=$gfortran
416	fi
417	#####################################################################
418
419	## if also compiling XIOS, parallel must be mpi_omp
420	if [ "$with_xios" = "y" -a "$parallel" != "mpi_omp" ] ; then
421	echo "Error, you must set -parallel mpi_omp if you want XIOS"
422	exit
423	fi
424
425	if [ "$with_xios" = "y" ] ; then
426	opt_makelmdz_xios="-io xios"
427	fi
428
429	if [ "$cosp" = "v2" -a "$with_xios" = "n" ] ; then
430	echo "Error, Cospv2 cannot run without Xios"
431	exit
432	fi
433
434	echo '################################################################'
435	echo Choix des options de compilation
436	echo '################################################################'
437
438	export FC=$compiler
439	export F90=$compiler
440	export F77=$compiler
441	export CPPFLAGS=
442	OPTIMNC=$OPTIM
443	BASE_LD="$OPT_GPROF"
444	OPTPREC="$OPT_GPROF"
445	ARFLAGS="rs"
446	if [ -f /etc/issue ] ; then
447	if [ "`grep -i ubuntu /etc/issue`" != "" ] ; then
448	if [ "`grep -i ubuntu /etc/issue \| awk ' { print $2 } ' \| cut -d. -f1`" -ge 16 ]
449	then
450	ARFLAGS="rU"
451	fi
452	fi
453	fi
454
455
456
457	if [ "$compiler" = "$gfortran" ] ; then
458	OPTIM='-O3'
459	OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all -fbacktrace -finit-real=snan"
460	OPTDEV="-Wall -fbounds-check"
461	fmod='I '
462	OPTPREC="$OPTPREC -cpp -ffree-line-length-0"
463	if [ $real = r8 ] ; then
464	OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE"
465	fi
466	export F90FLAGS=" -ffree-form $OPTIMNC"
467	export FFLAGS=" $OPTIMNC"
468	export CC=gcc
469	export CXX=g++
470	export fpp_flags="-P -C -traditional -ffreestanding"
471
472	elif [ $compiler = mpif90 ] ; then
473	OPTIM='-O3'
474	OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all"
475	OPTDEV="-Wall -fbounds-check"
476	BASE_LD="$BASE_LD -lblas"
477	fmod='I '
478	if [ $real = r8 ] ; then
479	OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE -fcray-pointer"
480	fi
481	export F90FLAGS=" -ffree-form $OPTIMNC"
482	export FFLAGS=" $OPTIMNC"
483	export CC=gcc
484	export CXX=g++
485
486	elif [ $compiler = pgf90 ] ; then
487	OPTIM='-O2 -Mipa -Munroll -Mnoframe -Mautoinline -Mcache_align'
488	OPTDEB='-g -Mdclchk -Mbounds -Mchkfpstk -Mchkptr -Minform=inform -Mstandard -Ktrap=fp -traceback'
489	OPTDEV='-g -Mbounds -Ktrap=fp -traceback'
490	fmod='module '
491	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -r8 -DNC_DOUBLE" ; fi
492	export CPPFLAGS="-DpgiFortran"
493	export CC=pgcc
494	export CFLAGS="-O2 -Msignextend"
495	export CXX=pgCC
496	export CXXFLAGS="-O2 -Msignextend"
497	export FFLAGS="-O2 $OPTIMNC"
498	export F90FLAGS="-O2 $OPTIMNC"
499	compile_with_fcm=1
500
501	elif [[ $compiler = ifort \|\| $compiler = mpiifort ]] ; then
502	OPTIM="-O2 -fp-model strict -ip -align all "
503	OPTDEV="-p -g -O2 -traceback -fp-stack-check -ftrapuv -check"
504	OPTDEB="-g -no-ftz -traceback -ftrapuv -fp-stack-check -check"
505	fmod='module '
506	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -real-size 64 -DNC_DOUBLE" ; fi
507	export CPP="icc -E"
508	export FFLAGS="-O2 -ip -fpic -mcmodel=large"
509	export FCFLAGS="-O2 -ip -fpic -mcmodel=large"
510	export CC=icc
511	export CFLAGS="-O2 -ip -fpic -mcmodel=large"
512	export CXX=icpc
513	export CXXFLAGS="-O2 -ip -fpic -mcmodel=large"
514	export fpp_flags="-P -traditional"
515	# Pourquoi forcer la compilation fcm. Marche mieux sans
516	#compile_with_fcm=1
517	else
518	echo unexpected compiler $compiler ; exit
519	fi
520
521	OPTIMGCM="$OPTIM $OPTPREC"
522
523	hostname=`hostname`
524
525	##########################################################################
526	# If installing on known machines such as Jean-Zay at IDRIS,
527	# don't check for available software and don't install netcdf
528	if [ ${hostname:0:5} = jean- ] ; then
529	netcdf=0 # no need to recompile netcdf, alreday available
530	check_linux=0
531	pclinux=0
532	ioipsl=0 # no need to recompile ioipsl, already available
533	#netcdf="/smplocal/pub/NetCDF/4.1.3"
534	compiler="mpiifort"
535	fmod='module '
536	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -i4 -r8 -DNC_DOUBLE" ; fi
537	OPTIM="-auto -align all -O2 -fp-model strict -xHost "
538	OPTIMGCM="$OPTIM $OPTPREC"
539	fi
540	##########################################################################
541
542
543	mkdir -p $MODEL
544	echo $MODEL
545	MODEL=`( cd $MODEL ; pwd )` # to get absolute path, if necessary
546
547
548	echo '################################################################'
549	if [ "$check_linux" = 1 ] ; then
550	echo Check if required software is available
551	echo '################################################################'
552
553	#### Ehouarn: test if the required shell is available
554	#### Maj FH-LF-AS 2021-04 : default=bash ; if bash missing, use ksh
555	use_shell="bash" # default
556	if [ "`which bash`" = "" ] ; then
557	echo "no bash ; we will use ksh"
558	use_shell="ksh"
559	if [ "`which ksh`" = "" ] ; then
560	echo "bash (or ksh) needed!! Install it!"
561	exit
562	fi
563	fi
564
565	for logiciel in wget tar gzip make $compiler gcc cmake ; do
566	if [ "`which $logiciel`" = "" ] ; then
567	echo You must first install $logiciel on your system
568	exit
569	fi
570	done
571
572	if [ $pclinux = 1 ] ; then
573	cd $MODEL
574	cat <<eod > tt.f90
575	print*,'coucou'
576	end
577	eod
578	$compiler tt.f90 -o a.out
579	./a.out >\| tt
580	if [ "`cat tt \| sed -e 's/ //g' `" != "coucou" ] ; then
581	echo problem installing with compiler $compiler ; exit ; fi
582	\rm tt a.out tt.f90
583	fi
584	fi
585
586	###########################################################################
587	if [ $getlmdzor = 1 -a ! -d $MODEL/modipsl ] ; then
588	###########################################################################
589	echo '##########################################################'
590	echo Download a slightly modified version of LMDZ
591	echo '##########################################################'
592	cd $MODEL
593	myget src/modipsl.$version.tar.gz
594	echo install_lmdz.sh wget_OK `date`
595	gunzip modipsl.$version.tar.gz
596	tar xf modipsl.$version.tar
597	\rm modipsl.$version.tar
598	fi
599
600	###########################################################################
601	if [ $netcdf = 1 ] ; then
602	###########################################################################
603	cd $MODEL
604	netcdflog=`pwd`/netcdf.log
605	echo '##########################################################'
606	echo Compiling the Netcdf library
607	echo '##########################################################'
608	echo log file : $netcdflog
609	if [[ "$with_xios" = "n" && ! -d $MODEL/netcdf4_hdf5_seq ]] ; then
610	myget import/install_netcdf4_hdf5_seq.bash
611	chmod +x install_netcdf4_hdf5_seq.bash
612
613	if [ "$compiler" = "gfortran" ]
614	then
615	./install_netcdf4_hdf5_seq.bash -prefix $MODEL/netcdf4_hdf5_seq \
616	-compiler gnu > $netcdflog 2>&1
617	elif [ "$compiler" = "ifort" ]
618	then
619	./install_netcdf4_hdf5_seq.bash -prefix $MODEL/netcdf4_hdf5_seq \
620	-compiler intel > $netcdflog 2>&1
621	else
622	echo "unexpected compiler $compiler" ; exit
623	fi
624
625	# LF rajout d'une verrue, pour une raison non encore expliquee,
626	# la librairie est parfois rangée dans lib64 et non dans lib
627	# par certains compilateurs
628	if [ ! -e lib -a -d lib64 ] ; then ln -s lib64 lib; fi
629	elif [[ "$with_xios" = "y" && ! -d $MODEL/netcdf4_hdf5 ]]
630	then
631	# download and compile hdf5 and netcdf, etc. using the
632	# install_netcdf4_hdf5.bash script
633	myget import/install_netcdf4_hdf5.bash
634	chmod u=rwx install_netcdf4_hdf5.bash
635	if [ "$compiler" = "gfortran" ] ; then
636	./install_netcdf4_hdf5.bash -prefix $MODEL/netcdf4_hdf5 -CC gcc \
637	-FC gfortran -CXX g++ -MPI $root_mpi > $netcdflog 2>&1
638	elif [ "$compiler" = "ifort" ] ; then
639	./install_netcdf4_hdf5.bash -prefix $MODEL/netcdf4_hdf5 -CC icc \
640	-FC ifort -CXX icpc -MPI $root_mpi > $netcdflog 2>&1
641	elif [ "$compiler" = "pgf90" ] ; then
642	./install_netcdf4_hdf5.bash -prefix $MODEL/netcdf4_hdf5 -CC pgcc \
643	-FC pgf90 -CXX pgCC -MPI $root_mpi > $netcdflog 2>&1
644	else
645	echo "unexpected compiler $compiler" ; exit
646	fi
647	fi # of if [ "$with_xios" = "n" ]
648	echo install_lmdz.sh netcdf_OK `date`
649	fi # of if [ $netcdf = 1 ]
650
651	# ncdfdir contains the directory where netcdf is installed
652	if [ $netcdf = 1 ] ; then
653	if [ "$with_xios" = "y" ] ; then
654	ncdfdir=$MODEL/netcdf4_hdf5
655	else
656	ncdfdir=$MODEL/netcdf4_hdf5_seq
657	fi
658	elif [ $netcdf = 0 ]
659	then
660	ncdfdir=/usr
661	else
662	ncdfdir=$netcdf
663	fi
664
665	cat >test_netcdf90.f90 <<EOF
666	use netcdf
667	print *, "NetCDF library version: ", nf90_inq_libvers()
668	end
669	EOF
670
671	$compiler -I$ncdfdir/include test_netcdf90.f90 -L$ncdfdir/lib -l netcdff \
672	-lnetcdf && ./a.out
673
674	if (($? == 0))
675	then
676	rm test_netcdf90.f90 a.out
677	else
678	echo "Failed test program using NetCDF-Fortran."
679	echo "You can:"
680	echo "- check that you have NetCDF-Fortran installed in your system"
681	echo "- or specify an installation directory with option -netcdf of" \
682	"install_lmdz.sh"
683	echo "- or download and compile NetCDF-Fortran with option -netcdf 1 of" \
684	"install_lmdz.sh"
685	exit 1
686	fi
687
688	#=========================================================================
689	if [[ ! -f $MODEL/modipsl/lib/libioipsl.a ]]
690	then
691	if [ $ioipsl = 1 ] ; then
692	#=====================================================================
693	echo OK ioipsl=$ioipsl
694	echo '##########################################################'
695	echo 'Installing MODIPSL, the installation package manager for the '
696	echo 'IPSL models and tools'
697	echo '##########################################################'
698	echo `date`
699
700	cd $MODEL/modipsl
701	\rm -rf lib/*
702	cd util
703	cp AA_make.gdef AA_make.orig
704	F_C="$compiler -c "
705	if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ]
706	then
707	F_C="$compiler -c -cpp "
708	fi
709	if [ "$compiler" = "pgf90" ] ; then F_C="$compiler -c -Mpreprocess" ; fi
710	sed -e 's/^\#..g95..\#.*.$/\#/' AA_make.gdef > tmp
711	sed -e "s:F_L = g95:F_L = $compiler:" \
712	-e "s:F_C = g95 -c -cpp:F_C = $F_C": \
713	-e 's/g95..w_w..(F_D)/g95 w_w = '"$OPTIMGCM"'/' \
714	-e 's:g95..NCDF_INC..$:g95 NCDF_INC= '"$ncdfdir"'/include:' \
715	-e 's:g95..NCDF_LIB..$:g95 NCDF_LIB= -L'"$ncdfdir"'/lib -lnetcdff -lnetcdf:' \
716	-e 's:g95 L_O =:g95 L_O = -Wl,-rpath='"$ncdfdir"'/lib:' \
717	-e "s:-fmod=:-$fmod:" -e 's/-fno-second-underscore//' \
718	-e 's:#-Q- g95 M_K = gmake:#-Q- g95 M_K = make:' \
719	tmp >\| AA_make.gdef
720
721	if [ $pcmac == 1 ]
722	then
723	cp AA_make.gdef tmp
724	sed -e 's/rpath=/rpath,/g' tmp > AA_make.gdef
725	fi
726
727
728	# We use lines for g95 even for the other compilers to run ins_make
729	if [ "$use_shell" = "ksh" ] ; then
730	./ins_make $o_ins_make
731	else # bash
732	sed -e s:/bin/ksh:/bin/bash:g ins_make > ins_make.bash
733	if [ "`grep jeanzay AA_make.gdef`" = "" ] ; then
734	# Bidouille pour compiler sur ada des vieux modipsl.tar
735	echo 'Warning jean-zay not in AA_make.gdef'
736	echo 'Think about updating'
737	exit 1
738	fi
739
740	chmod u=rwx ins_make.bash
741	./ins_make.bash $o_ins_make
742	fi # of if [ "$use_shell" = "ksh" ]
743
744	echo install_lmdz.sh MODIPSL_OK `date`
745
746	cd $MODEL/modipsl/modeles/IOIPSL/src
747	ioipsllog=`pwd`/ioipsl.log
748	echo '##########################################################'
749	echo 'Compiling IOIPSL, the interface library with Netcdf'
750	echo '##########################################################'
751	echo `date`
752	echo log file : $ioipsllog
753
754	if [ "$use_shell" = "bash" ] ; then
755	cp Makefile Makefile.ksh
756	sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile
757	fi
758	# if [ "$pclinux" = 1 ] ; then
759	# Build IOIPSL modules and library
760	$make clean
761	$make > $ioipsllog 2>&1
762	if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then
763	# copy module files to lib
764	cp -f *.mod ../../../lib
765	fi
766	# Build IOIPSL tools (ie: "rebuild", if present)
767	if [ -f $MODEL/modipsl/modeles/IOIPSL/tools/rebuild ] ; then
768	cd $MODEL/modipsl/modeles/IOIPSL/tools
769	# adapt Makefile & rebuild script if in bash
770	if [ "$use_shell" = "bash" ] ; then
771	cp Makefile Makefile.ksh
772	sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile
773	cp rebuild rebuild.ksh
774	sed -e 's:/bin/ksh:/bin/bash:g' \
775	-e 's:print -u2:echo:g' \
776	-e 's:print:echo:g' rebuild.ksh > rebuild
777	fi
778	$make clean
779	$make > $ioipsllog 2>&1
780	fi
781	# fi # of if [ "$pclinux" = 1 ]
782
783	else # of if [ $ioipsl = 1 ]
784	if [ ${hostname:0:5} = jean- ] ; then
785	cd $MODEL/modipsl
786	cd util
787	if [ "`grep jeanzay AA_make.gdef`" = "" ] ; then
788	echo 'Warning jean-zay not in AA_make.gdef'
789	echo 'Think about updating'
790	exit 1
791	fi
792	./ins_make $o_ins_make
793	# Compile IOIPSL on jean-zay
794	cd $MODEL/modipsl/modeles/IOIPSL/src
795	gmake > ioipsl.log
796	cd $MODEL/modipsl/modeles/IOIPSL/tools
797	gmake > ioipsl.log
798
799	fi
800	echo install_lmdz.sh ioipsl_OK `date`
801	fi # of if [ $ioipsl = 1 ]
802	fi
803	# Saving ioipsl lib for possible parallel compile
804	cd $MODEL/modipsl
805	tar cf ioipsl.tar lib/ bin/
806
807	#=========================================================================
808	if [ "$with_xios" = "y" ] ; then
809	echo '##########################################################'
810	echo 'Compiling XIOS'
811	echo '##########################################################'
812	cd $MODEL/modipsl/modeles
813	xioslog=`pwd`/xios.log
814	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/install_xios.bash
815	myget import/install_xios.bash
816	chmod u=rwx install_xios.bash
817	if [ ${hostname:0:5} = jean- ] ; then
818	svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5 \
819	XIOS
820	cd XIOS/arch
821	svn update
822	cd ..
823	echo "Compiling XIOS, start" `date` \
824	"(it takes about 20 min on Jean-Zay)"
825	echo "log file: $xioslog"
826	./make_xios --prod --arch $arch --job 4 > xios.log 2>&1
827	else
828	./install_xios.bash -prefix $MODEL/modipsl/modeles \
829	-netcdf ${ncdfdir} -hdf5 ${ncdfdir} \
830	-MPI $root_mpi -arch $arch > xios.log 2>&1
831	fi # of case Jean-Zay
832	if [ -f XIOS/lib/libxios.a ] ; then
833	echo "XIOS library successfully generated"
834	echo install_lmdz.sh XIOS_OK `date`
835	fi
836	fi
837
838	#============================================================================
839	veget_version=false
840	if [ "$veget" != 'NONE' ] ; then
841	cd $MODEL/modipsl/modeles/ORCHIDEE
842	set +e ; svn upgrade ; set -e
843	if [ "$veget" = "CMIP6" ] ; then
844	veget_version=orchidee2.0
845	orchidee_rev=6592
846	else # specific orchidee revision newer than CMIP6, on 2_1 or 2_2 branches
847	veget_version=orchidee2.1
848	orchidee_rev=$veget
849	if [ $veget -lt 4465 ] ; then
850	echo 'Stopping, ORCHIDEE version too old, script needs work on ' \
851	'the CPP flags to pass to makelmdz'
852	exit 1
853	fi
854	set +e
855	# which branch is my version on?
856	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}'`
857	# switch to that branch
858	echo IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at \
859	orchidee-help@listes.ipsl.fr
860	svn switch -r $veget --accept theirs-full \
861	svn://forge.ipsl.jussieu.fr/orchidee/$orcbranch
862	svn log -r $veget \| grep $veget
863	if [ $? -gt 0 ] ; then
864	echo 'Cannot update ORCHIDEE as not on the right branch for ' \
865	'ORCHIDEE'
866	exit
867	fi
868	set -e
869	set +e ; svn update -r $veget ; set -e
870	fi
871	# Correctif suite debug Jean-Zay
872	sed -i -e 's/9010 FORMAT(A52,F17.14)/9010 FORMAT(A52,F20.14)/' \
873	src_stomate/stomate.f90
874	opt_orc="-prod" ; if [ "$optim" = "-debug" ] ; then opt_orc="-debug" ; fi
875
876	orchideelog=`pwd`/orchidee.log
877	echo '########################################################'
878	echo 'Compiling ORCHIDEE, the continental surface model '
879	echo '########################################################'
880	echo Start of the first compilation of orchidee, in sequential mode: `date`
881	echo log file : $orchideelog
882
883	export ORCHPATH=`pwd`
884	xios_orchid="-noxios"
885	if [ "$with_xios" = "y" ] ; then
886	xios_orchid="-xios"
887	fi
888	if [ -d tools ] ; then
889	###################################################################
890	# Pour les experts qui voudraient changer de version d'orchidee.
891	# Attention : necessite d'avoir le password pour orchidee
892
893	# Correctif suite debug Jean-Zay
894	if [ -f src_global/time.f90 ] ; then
895	sed -i -e 's/CALL tlen2itau/\!CALL tlen2itau/' src_global/time.f90
896	fi
897	###################################################################
898	if [ "$veget_version" == "false" ] ; then
899	veget_version=orchidee2.0
900	fi
901	cd arch
902	sed -e s:"%COMPILER .*.$":"%COMPILER $compiler":1 \
903	-e s:"%LINK .*.$":"%LINK $compiler":1 \
904	-e s:"%FPP_FLAGS .*.$":"%FPP_FLAGS $fpp_flags":1 \
905	-e s:"%PROD_FFLAGS .*.$":"%PROD_FFLAGS $OPTIM":1 \
906	-e s:"%DEV_FFLAGS .*.$":"%DEV_FFLAGS $OPTDEV":1 \
907	-e s:"%DEBUG_FFLAGS .*.$":"%DEBUG_FFLAGS $OPTDEB":1 \
908	-e s:"%BASE_FFLAGS .*.$":"%BASE_FFLAGS $OPTPREC":1 \
909	-e s:"%BASE_LD .*.$":"%BASE_LD $BASE_LD":1 \
910	-e s:"%ARFLAGS .*.$":"%ARFLAGS $ARFLAGS":1 \
911	arch-gfortran.fcm > arch-local.fcm
912	echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib -lnetcdff -lnetcdf\"" \
913	> arch-local.path
914	echo "NETCDF_INCDIR=${ncdfdir}/include" >> arch-local.path
915	echo "IOIPSL_INCDIR=$ORCHPATH/../../lib" >> arch-local.path
916	echo "IOIPSL_LIBDIR=$ORCHPATH/../../lib" >> arch-local.path
917	echo 'XIOS_INCDIR=${ORCHDIR}/../XIOS/inc' >> arch-local.path
918	echo 'XIOS_LIBDIR="${ORCHDIR}/../XIOS/lib -lxios"' >> arch-local.path
919	cd ../
920
921	echo ./makeorchidee_fcm -j $xios_orchid $opt_orc -parallel none \
922	-arch $arch
923	./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel none \
924	-arch $arch > $orchideelog 2>&1
925	pwd
926	else # of "if [ -d tools ]"
927	if [ -d src_parallel ] ; then
928	liste_src="parallel parameters global stomate sechiba driver"
929	if [ "$veget_version" == "false" ] ; then
930	veget_version=orchidee2.0
931	fi
932	fi
933	for d in $liste_src ; do
934	src_d=src_$d
935	echo src_d $src_d
936	echo ls ; ls
937	if [ ! -d $src_d ] ; then
938	echo Problem orchidee : no $src_d ; exit
939	fi
940	cd $src_d ; \rm -f *.mod make ; $make clean
941	$make > $orchideelog 2>&1
942	if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then
943	cp -f *.mod ../../../lib
944	fi
945	cd ..
946	done
947	fi # of "if [ -d tools ]"
948	echo install_lmdz.sh orchidee_compil_seq_OK `date`
949	fi # of if [ "$veget" != 'NONE' ]
950
951
952	#============================================================================
953	# Ehouarn: the directory name LMDZ* depends on version/tar file...
954	if [ -d $MODEL/modipsl/modeles/LMD* ] ; then
955	echo '###############################################################'
956	echo 'Preparing LMDZ compilation : arch file, svn switch if needed...'
957	echo '###############################################################'
958	cd $MODEL/modipsl/modeles/LMD*
959	LMDZPATH=`pwd`
960	else
961	echo "ERROR: No LMD* directory !!!"
962	exit
963	fi
964
965	###########################################################
966	# For those who want to use fcm to compile via :
967	# makelmdz_fcm -arch local .....
968	############################################################
969
970	if [[ "$pclinux" = "1" && ! -f arch/arch-local.path ]] ; then
971
972	# create local 'arch' files (if on Linux PC):
973	cd arch
974	# arch-local.path file
975	echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib -lnetcdff -lnetcdf\"" \
976	> arch-local.path
977	echo "NETCDF_INCDIR=-I${ncdfdir}/include" >> arch-local.path
978	echo 'NETCDF95_INCDIR=$LMDGCM/../../include' >> arch-local.path
979	echo 'NETCDF95_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
980	echo 'IOIPSL_INCDIR=$LMDGCM/../../lib' >> arch-local.path
981	echo 'IOIPSL_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
982	echo 'XIOS_INCDIR=$LMDGCM/../XIOS/inc' >> arch-local.path
983	echo 'XIOS_LIBDIR=$LMDGCM/../XIOS/lib' >> arch-local.path
984	echo 'ORCH_INCDIR=$LMDGCM/../../lib' >> arch-local.path
985	echo 'ORCH_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
986
987	if [ $pcmac == 1 ] ; then
988	BASE_LD="$BASE_LD -Wl,-rpath,${ncdfdir}/lib"
989	else
990	BASE_LD="$BASE_LD -Wl,-rpath=${ncdfdir}/lib"
991	fi
992	# Arch-local.fcm file (adapted from arch-linux-32bit.fcm)
993
994	if [ $real = r8 ] ; then FPP_DEF=NC_DOUBLE ; else FPP_DEF="" ; fi
995	sed -e s:"%COMPILER .*.$":"%COMPILER $compiler":1 \
996	-e s:"%LINK .*.$":"%LINK $compiler":1 \
997	-e s:"%PROD_FFLAGS .*.$":"%PROD_FFLAGS $OPTIM":1 \
998	-e s:"%DEV_FFLAGS .*.$":"%DEV_FFLAGS $OPTDEV":1 \
999	-e s:"%DEBUG_FFLAGS .*.$":"%DEBUG_FFLAGS $OPTDEB":1 \
1000	-e s:"%BASE_FFLAGS .*.$":"%BASE_FFLAGS $OPTPREC":1 \
1001	-e s:"%FPP_DEF .*.$":"%FPP_DEF $FPP_DEF":1 \
1002	-e s:"%BASE_LD .*.$":"%BASE_LD $BASE_LD":1 \
1003	-e s:"%ARFLAGS .*.$":"%ARFLAGS $ARFLAGS":1 \
1004	arch-linux-32bit.fcm > arch-local.fcm
1005
1006	cd ..
1007	### Adapt "bld.cfg" (add the shell):
1008	#whereisthatshell=$(which ${use_shell})
1009	#echo "bld::tool::SHELL $whereisthatshell" >> bld.cfg
1010
1011	fi # of if [ "$pclinux" = 1 ]
1012
1013
1014	cd $MODEL/modipsl/modeles/LMDZ*
1015	lmdzlog=`pwd`/lmdz.log
1016
1017	##################################################################
1018	# Possibly update LMDZ if a specific svn release is requested
1019	##################################################################
1020
1021	set +e ; svn upgrade ; set -e
1022
1023	if [ "$svn" = "last" ] ; then svnopt="" ; else svnopt="-r $svn" ; fi
1024	if [ "$svn" != "" ] ; then
1025	set +e ; svn info \| grep -q 'http:'
1026	if [ $? = 0 ] ; then
1027	svn switch --relocate http://svn.lmd.jussieu.fr/LMDZ \
1028	https://svn.lmd.jussieu.fr/LMDZ
1029	fi
1030	svn update $svnopt
1031	fi
1032	set -e
1033
1034	##################################################################
1035	# Retrieve the final svn release number, and adjust compilation
1036	# options accordingly
1037	mysvn=`svnversion . \| egrep -o "[0-9]+"`
1038
1039	# Option de compilation du rayonnement : depend de $mysvn ><= r4185
1040	opt_rad=""
1041
1042	case $rad in
1043	oldrad) iflag_rrtm=0 ; NSW=2 ; opt_rad="" ;;
1044	rrtm) iflag_rrtm=1 ; NSW=6
1045	if [ $mysvn -le 4185 ] ; then
1046	opt_rad="-rrtm true"
1047	else
1048	opt_rad="-rad rrtm"
1049	fi ;;
1050	ecrad) iflag_rrtm=2 ; NSW=6 ; opt_rad="-rad ecrad" ;;
1051	*) echo Only oldrad rrtm ecrad for rad option ; exit
1052	esac
1053
1054	if [ $mysvn -le 4185 -a $rad = "ecrad" ] ; then
1055	echo "ecrad only available for LMDZ rev starting with 4186 " ; exit
1056	fi
1057
1058	##################################################################
1059
1060
1061	if [[ ! -f libf/misc/netcdf95.F90 && ! -d $MODEL/NetCDF95-0.2 ]]
1062	then
1063	cd $MODEL
1064	myget import/NetCDF95-0.2.tar.gz
1065	tar -xf NetCDF95-0.2.tar.gz
1066	rm NetCDF95-0.2.tar.gz
1067	cd NetCDF95-0.2
1068	mkdir build
1069	cd build
1070	cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=$ncdfdir \
1071	-DCMAKE_INSTALL_PREFIX=$MODEL/modipsl
1072	make install
1073	cd $MODEL/modipsl/modeles/LMDZ*
1074	fi
1075
1076	echo '##################################################################'
1077	echo "Preparing script compile.sh for LMDZ compilation"
1078	echo "It will only be run automatically if bench=1/tuto"
1079	echo Here bench=$bench
1080	echo '##################################################################'
1081
1082	if [ "$env_file" != "" ] ; then
1083	mv arch/arch-${arch}.env arch/arch-${arch}.orig
1084	\cp -f $env_file arch/arch-${arch}.env
1085	fi
1086
1087	if [ $compile_with_fcm = 1 ] ; then
1088	makelmdz="makelmdz_fcm $optim -arch $arch -j 8 "
1089	else
1090	makelmdz="makelmdz $optim -arch $arch"
1091	fi
1092
1093	# sequential compilation
1094	if [ "$sequential" = 1 ] ; then
1095	echo Sequential compilation command, saved in compile.sh:
1096	echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp " \
1097	"-d ${grid_resolution} -v $veget_version gcm "
1098	echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp " \
1099	"-d ${grid_resolution} -v $veget_version gcm " > compile.sh
1100	chmod +x ./compile.sh
1101	if [ $bench = 1 ] ; then
1102	echo install_lmdz.sh start_lmdz_seq_compilation `date`
1103	echo log file: $lmdzlog
1104	./compile.sh > $lmdzlog 2>&1
1105	echo install_lmdz.sh end_lmdz_seq_compilation `date`
1106	fi
1107	fi # fin sequential
1108
1109	# compiling in parallel mode
1110	if [ $parallel != "none" ] ; then
1111	echo '##########################################################'
1112	echo ' Parallel compile '
1113	echo '##########################################################'
1114	echo "(after saving the sequential libs and binaries)"
1115	cd $MODEL/modipsl
1116	tar cf sequential.tar bin/ lib/
1117	\rm -rf bin/ lib/
1118	tar xf ioipsl.tar
1119	#
1120	# Orchidee
1121	#
1122	cd $ORCHPATH
1123	if [ -d src_parallel -a $veget != 'NONE' ] ; then
1124	cd arch
1125	sed \
1126	-e s:"%COMPILER.*.$":"%COMPILER $par_comp":1 \
1127	-e s:"%LINK.*.$":"%LINK $par_comp":1 \
1128	-e s:"%MPI_FFLAG.*.$":"%MPI_FFLAGS $MPI_FLAGS":1 \
1129	-e s:"%OMP_FFLAG.*.$":"%OMP_FFLAGS $OMP_FLAGS":1 \
1130	-e s:"%MPI_LD.*.$":"%MPI_LD $MPI_LD":1 \
1131	-e s:"%OMP_LD.*.$":"%OMP_LD $OMP_LD":1 \
1132	arch-local.fcm > tmp.fcm
1133
1134	mv tmp.fcm arch-local.fcm
1135	cd ../
1136	echo Compiling ORCHIDEE in parallel mode `date`
1137	echo logfile $orchideelog
1138	echo "NOTE : to recompile it when necessary, use ./compile_orc.sh " \
1139	"in modipsl/modeles/ORCHIDEE"
1140	echo ./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc \
1141	-parallel $parallel -arch $arch > compile_orc.sh
1142	echo ./makeorchidee_fcm -j 8 $xios_orchid $opt_orc \
1143	-parallel $parallel -arch $arch >> compile_orc.sh
1144	echo echo Now you must also recompile LMDZ, by running ./compile.sh \
1145	in modeles/LMDZ >> compile_orc.sh
1146	chmod u+x compile_orc.sh
1147	./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc \
1148	-parallel $parallel -arch $arch > $orchideelog 2>&1
1149	./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel $parallel \
1150	-arch $arch >> $orchideelog 2>&1
1151	echo End of ORCHIDEE compilation in parallel mode `date`
1152	elif [ $veget != 'NONE' ] ; then
1153	echo '##########################################################'
1154	echo ' Orchidee version too old '
1155	echo ' Please update to new version '
1156	echo '##########################################################'
1157	exit
1158	fi # of [ -d src_parallel -a $veget != 'NONE' ]
1159
1160	# LMDZ
1161	cd $LMDZPATH
1162	if [ $arch = local ] ; then
1163	cd arch
1164	sed -e s:"%COMPILER.*.$":"%COMPILER $par_comp":1 \
1165	-e s:"%LINK.*.$":"%LINK $par_comp":1 \
1166	-e s:"%MPI_FFLAG.*.$":"%MPI_FFLAGS $MPI_FLAGS":1 \
1167	-e s:"%OMP_FFLAG.*.$":"%OMP_FFLAGS $OMP_FLAGS":1 \
1168	-e s:"%ARFLAGS.*.$":"%ARFLAGS $ARFLAGS":1 \
1169	-e s@"%BASE_LD.*.$"@"%BASE_LD -Wl,-rpath=${root_mpi}/lib:${ncdfdir}/lib"@1 \
1170	-e s:"%MPI_LD.*.$":"%MPI_LD $MPI_LD":1 \
1171	-e s:"%OMP_LD.*.$":"%OMP_LD $OMP_LD":1 \
1172	arch-local.fcm > tmp.fcm
1173	mv tmp.fcm arch-local.fcm
1174	cd ../
1175	fi
1176	rm -f compile.sh
1177	echo resol=${grid_resolution} >> compile.sh
1178	if [ ${hostname:0:5} = jean- -a "$cosp" = "v2" ] ; then
1179
1180	echo LMDZ compilation command in parallel mode, saved in compile.sh, \
1181	is :
1182	echo "(ATTENTION le probleme de cospv2 sur jean-zay en mode prod " \
1183	"n est pas corrige ! )"
1184	# ATTENTION le probleme de cospv2 sur jean-zay en mode prod n
1185	# est pas corrige
1186	echo ./$makelmdz -dev $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
1187	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
1188	-parallel $parallel gcm >> compile.sh
1189	echo ./$makelmdz -dev $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
1190	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
1191	-parallel $parallel gcm
1192	else
1193	echo ./$makelmdz $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
1194	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
1195	-parallel $parallel gcm >> compile.sh
1196	echo ./$makelmdz $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
1197	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
1198	-parallel $parallel gcm
1199	fi
1200	chmod +x ./compile.sh
1201
1202	if [ $bench = 1 ] ; then
1203	echo Compiling LMDZ in parallel mode `date`, LMDZ log file: $lmdzlog
1204	./compile.sh > $lmdzlog 2>&1
1205	fi
1206
1207	fi # of if [ $parallel != "none" ]
1208
1209
1210	##################################################################
1211	# Verification du succes de la compilation
1212	##################################################################
1213
1214	# Recherche de l'executable dont le nom a change au fil du temps ...
1215	# suffix contains radiative option starting with revision 4186
1216	if [ $mysvn -ge 4186 ] ; then suff_exe=_${rad}${suff_exe} ; fi
1217	gcm=""
1218
1219	for exe in gcm.e bin/gcm_${grid_resolution}_phylmd${suff_exe}${suff_orc}.e
1220	do
1221	if [ -f $exe ] ; then gcm=$exe ; fi
1222	done
1223
1224	if [ "$gcm" = "" ] ; then
1225	if [ $bench = 1 ] ; then
1226	echo 'Compilation failed !! Cannot run the benchmark;'
1227	exit
1228	else
1229	echo 'Compilation not done (only done when bench=1)'
1230	fi
1231	else
1232	echo '##########################################################'
1233	echo 'Compilation successfull !! ' `date`
1234	echo '##########################################################'
1235	echo The executable is $gcm
1236	fi
1237
1238	##################################################################
1239	# Below, we run a benchmark if bench=1 or tuto
1240	##################################################################
1241
1242	if [ $bench = tuto ] ; then
1243	myget Training/tutorial.tar ; tar xvf tutorial.tar ; cd TUTORIAL
1244	./init.sh
1245
1246	elif [[ $bench = 1 && ! -d BENCH${grid_resolution} ]] ; then
1247	# TOUTE CETTE SECTION DEVRAIT DISPARAITRE POUR UNE COMMANDE
1248	# OU DES BENCHS PAR MOTS CLES COMME tuto
1249
1250	echo '##########################################################'
1251	echo ' Running a test run '
1252	echo '##########################################################'
1253
1254	\rm -rf BENCH${grid_resolution}
1255	bench=bench_lmdz_${grid_resolution}
1256	echo install_lmdz.sh before bench download `date`
1257	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/$bench.tar.gz
1258	myget 3DBenchs/$bench.tar.gz
1259	echo install_lmdz.sh after bench download `date`
1260	tar xvf $bench.tar.gz
1261
1262	if [ "$cosp" = "v1" -o "$cosp" = "v2" ] ; then
1263	cd BENCH${grid_resolution}
1264	# copier les fichiers namelist input et output our COSP
1265	cp ../DefLists/cosp*_input_nl.txt .
1266	cp ../DefLists/cosp*_output_nl.txt .
1267	# Activer la cles ok_cosp pour tourner avec COSP
1268	sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp
1269	\mv -f tmp config.def
1270	cd ..
1271	fi
1272
1273	if [ -n "$physiq" ]; then
1274	cd BENCH${grid_resolution}
1275	if [ -f physiq.def_${physiq} ]; then
1276	cp physiq.def_${physiq} physiq.def
1277	echo using physiq.def_${physiq}
1278	else
1279	echo using standard physiq.def
1280	fi
1281	cd ..
1282	else
1283	echo using standard physiq.def
1284	fi
1285
1286	if [ "$with_xios" = "y" ] ; then
1287	cd BENCH${grid_resolution}
1288	cp ../DefLists/iodef.xml .
1289	cp ../DefLists/context_lmdz.xml .
1290	cp ../DefLists/field_def_lmdz.xml .
1291	# A raffiner par la suite
1292	echo A FAIRE : Copier les *xml en fonction de l option cosp
1293	cp ../DefLists/field_def_cosp*.xml .
1294	cp ../DefLists/file_def_hist*xml .
1295	# adapt iodef.xml to use attached mode
1296	sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' \
1297	iodef.xml > tmp
1298	\mv -f tmp iodef.xml
1299
1300	# and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
1301	# except for histday
1302	for histfile in file_def_hist*xml
1303	do
1304	if [ "$histfile" = "file_def_histday_lmdz.xml" ] ; then
1305	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' \
1306	$histfile > tmp
1307	\mv -f tmp $histfile
1308	sed -e 's@output_level="_AUTO_"@output_level="5"@' $histfile \
1309	> tmp
1310	\mv -f tmp $histfile
1311	sed -e 's@compression_level="2"@compression_level="0"@' \
1312	$histfile > tmp
1313	\mv -f tmp $histfile
1314	else
1315	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
1316	$histfile > tmp
1317	\mv -f tmp $histfile
1318	fi
1319	done
1320	# and add option "ok_all_xml=y" in config.def
1321	echo "### XIOS outputs" >> config.def
1322	echo 'ok_all_xml=.true.' >> config.def
1323
1324	#activer les sorties pour Cosp
1325	if [ "$cosp" = "v1" ] ; then
1326	histfile=file_def_histdayCOSP_lmdz.xml
1327	sed -e 's@enabled=".FALSE."@enabled=".TRUE."@' $histfile > tmp
1328	\mv -f tmp $histfile
1329	sed -e 's@output_level="_AUTO_"@output_level="5"@' $histfile > tmp
1330	\mv -f tmp $histfile
1331	sed -e 's@compression_level="2"@compression_level="0"@' \
1332	$histfile > tmp
1333	\mv -f tmp $histfile
1334	fi
1335	if [ "$cosp" = "v2" ] ; then
1336	histfile=file_def_histdayCOSPv2_lmdz.xml
1337	sed -e 's@compression_level="2"@compression_level="0"@' \
1338	$histfile > tmp
1339	\mv -f tmp $histfile
1340	contextfile=context_lmdz.xml
1341	sed -e 's@src="./file_def_histdayCOSP_lmdz.xml"@src="./file_def_histdayCOSPv2_lmdz.xml"@' \
1342	$contextfile > tmp
1343	\mv -f tmp $contextfile
1344	sed -e 's@src="./file_def_histmthCOSP_lmdz.xml"@src="./file_def_histmthCOSPv2_lmdz.xml"@' \
1345	$contextfile > tmp
1346	\mv -f tmp $contextfile
1347	sed -e 's@src="./file_def_histhfCOSP_lmdz.xml"@src="./file_def_histhfCOSPv2_lmdz.xml"@' \
1348	$contextfile > tmp
1349	\mv -f tmp $contextfile
1350	fieldfile=field_def_lmdz.xml
1351	sed -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' $fieldfile \
1352	> tmp
1353	\mv -f tmp $fieldfile
1354	fi
1355
1356	cd ..
1357	fi
1358
1359	# Cas Bensh avec ecrad
1360	if [ "$rad" = "ecrad" ] ; then
1361	cd BENCH${grid_resolution}
1362	cp ../DefLists/namelist_ecrad .
1363	cp -r ../libf/phylmd/ecrad/data .
1364	cd ..
1365	fi
1366
1367	# Adjusting bench physiq.def to radiative code chosen
1368	cd BENCH${grid_resolution}
1369	sed -e 's/iflag_rrtm=.*.$/iflag_rrtm='$iflag_rrtm'/' \
1370	-e 's/NSW=.*.$/NSW='$NSW'/' physiq.def > tmpdef
1371	\mv tmpdef physiq.def
1372	cd ..
1373
1374	cp $gcm BENCH${grid_resolution}/gcm.e
1375
1376	cd BENCH${grid_resolution}
1377	# On cree le fichier bench.sh au besoin
1378	# Dans le cas 48x36x39 le bench.sh existe deja en parallele
1379
1380	if [ "$grid_resolution" = "48x36x39" ] ; then
1381	echo On ne touche pas au bench.sh
1382	# But we have to adapt "run_local.sh" for $mpirun
1383	sed -e "s@mpirun@$mpirun@g" run_local.sh > tmp
1384	mv -f tmp run_local.sh
1385	chmod u=rwx run_local.sh
1386	elif [ "${parallel:0:3}" = "mpi" ] ; then
1387	# Lancement avec deux procs mpi et 2 openMP
1388	echo "export OMP_STACKSIZE=800M" > bench.sh
1389	if [ "${parallel:4:3}" = "omp" ] ; then
1390	echo "export OMP_NUM_THREADS=2" >> bench.sh
1391	fi
1392	if [ "$cosp" = "v1" -o "$cosp" = "v2" ] ; then
1393	if [ ${hostname:0:5} = jean- ] ; then
1394	chmod +x ../arch.env
1395	../arch.env
1396	echo "ulimit -s 2000000" >> bench.sh
1397	else
1398	echo "ulimit -s 200000" >> bench.sh
1399	fi
1400	else
1401	echo "ulimit -s unlimited" >> bench.sh
1402	fi
1403	if [ ${hostname:0:5} = jean- ] ; then
1404	. ../arch/arch-${arch}.env
1405	echo "srun -n 2 -A $idris_acct@cpu gcm.e > listing 2>&1" \
1406	>> bench.sh
1407	else
1408	echo "$mpirun -np 2 gcm.e > listing 2>&1" >> bench.sh
1409	fi
1410	# Add rebuild, using reb.sh if it is there
1411	echo 'if [ -f reb.sh ] ; then' >> bench.sh
1412	echo ' ./reb.sh histday ; ./reb.sh histmth ; ./reb.sh histhf ; ' \
1413	'./reb.sh histins ; ./reb.sh stomate_history ; ' \
1414	'./reb.sh sechiba_history ; ./reb.sh sechiba_out_2 ' >> bench.sh
1415	echo 'fi' >> bench.sh
1416	else
1417	echo "./gcm.e > listing 2>&1" > bench.sh
1418	fi
1419	# Getting orchidee stuff
1420	if [ $veget == 'CMIP6' ] ; then
1421	#echo 'myget 3DBenchs/BENCHorch11.tar.gz'
1422	#myget 3DBenchs/BENCHorch11.tar.gz
1423	#tar xvzf BENCHorch11.tar.gz
1424	echo 'myget 3DBenchs/BENCHCMIP6.tar.gz'
1425	myget 3DBenchs/BENCHCMIP6.tar.gz
1426	tar xvzf BENCHCMIP6.tar.gz
1427	sed -e "s:VEGET=n:VEGET=y:" config.def > tmp
1428	mv -f tmp config.def
1429	if [ "$with_xios" = "y" ] ; then
1430	cp ../../ORCHIDEE/src_xml/context_orchidee.xml .
1431	echo '<context id="orchidee" src="./context_orchidee.xml"/>' \
1432	> add.tmp
1433	cp ../../ORCHIDEE/src_xml/field_def_orchidee.xml .
1434	cp ../../ORCHIDEE/src_xml/file_def_orchidee.xml .
1435	cp ../../ORCHIDEE/src_xml/file_def_input_orchidee.xml .
1436	if [ -f ../../ORCHIDEE/src_xml/context_input_orchidee.xml ] ; then
1437	cp ../../ORCHIDEE/src_xml/context_input_orchidee.xml .
1438	echo '<context id="orchidee" ' \
1439	'src="./context_input_orchidee.xml"/>' >> add.tmp
1440	fi
1441	sed -e '/id="LMDZ"/r add.tmp' iodef.xml > tmp
1442	mv tmp iodef.xml
1443	sed -e'{/sechiba1/ s/enabled="_AUTO_"/type="one_file" enabled=".TRUE."/}' \
1444	file_def_orchidee.xml > tmp
1445	\mv -f tmp file_def_orchidee.xml
1446	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
1447	file_def_orchidee.xml > tmp
1448	\mv -f tmp file_def_orchidee.xml
1449	sed -e 's@output_level="_AUTO_"@output_level="1"@' \
1450	file_def_orchidee.xml > tmp
1451	\mv -f tmp file_def_orchidee.xml
1452	sed -e 's@output_freq="_AUTO_"@output_freq="1d"@' \
1453	file_def_orchidee.xml > tmp
1454	\mv -f tmp file_def_orchidee.xml
1455	sed -e 's@compression_level="4"@compression_level="0"@' \
1456	file_def_orchidee.xml > tmp
1457	\mv -f tmp file_def_orchidee.xml
1458	sed -e 's@XIOS_ORCHIDEE_OK = n@XIOS_ORCHIDEE_OK = y@' \
1459	orchidee.def > tmp
1460	\mv -f tmp orchidee.def
1461	fi
1462	fi
1463
1464	if [[ -f ../arch.env ]]
1465	then
1466	source ../arch.env
1467	fi
1468
1469	echo EXECUTION DU BENCH
1470	set +e
1471	date ; ./bench.sh > out.bench 2>&1 ; date
1472	set -e
1473	tail listing
1474
1475
1476	echo '##########################################################'
1477	echo 'Simulation finished in' `pwd`
1478	echo 'You have compiled with:'
1479	cat ../compile.sh
1480	if [ $parallel = "none" ] ; then
1481	echo 'You may re-run it with : cd ' `pwd` ' ; gcm.e'
1482	echo 'or ./bench.sh'
1483	else
1484	echo 'You may re-run it with : '
1485	echo 'cd ' `pwd` '; ./bench.sh'
1486	# echo 'ulimit -s unlimited'
1487	# echo 'export OMP_NUM_THREADS=2'
1488	# echo 'export OMP_STACKSIZE=800M'
1489	# echo "$mpirun -np 2 gcm.e "
1490	fi
1491	echo '##########################################################'
1492
1493	fi # bench
1494
1495
1496	#################################################################
1497	# Installation eventuelle du 1D
1498	#################################################################
1499
1500	if [ $SCM = 1 ] ; then
1501	cd $MODEL
1502	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/1D.tar.gz
1503	myget 1D/1D.tar.gz
1504	tar xvf 1D.tar.gz
1505	cd 1D
1506	./run.sh -rad $rad
1507	fi
1508	#set -vx
1509
1510	#################################################################
1511	# sauvegarde des options veget pour utilisation eventuelle tutorial_prod
1512	#################################################################
1513	cd $MODEL/modipsl/modeles
1514	#echo surface_env file created in $MODEL
1515	echo 'veget='$veget > surface_env
1516	#opt_veget="-v $veget_version"
1517	#echo 'opt_veget="'$opt_veget\" >> surface_env
1518	echo 'opt_veget="'-v $veget_version\" >> surface_env
1519	echo 'orchidee_rev='$orchidee_rev >> surface_env
1520	echo 'suforch='$suff_orc >> surface_env

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