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install_lmdz.sh @ 4499

Last change on this file since 4499 was 4494, checked in by lguez, 20 months ago

Do not remove bin and lib for parallel compile

The lines that we remove in this commit appeared in
revision r3044. They do not seem useful since we run `makeorchidee_fcm
-clean afterwards. Now that lib also contains libnetcdf95.a`, we
would have to save libnetcdf95.a and put it back to lib, just as we
did for IOIPSL. It is simpler not to remove lib. (Note that bin is
empty at this point.) Then we do not create ioipsl.tar.

Property svn:executable set to *

File size: 56.6 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 [ $ioipsl = 1 ]
789	fi
790
791	#=========================================================================
792	if [ "$with_xios" = "y" ] ; then
793	echo '##########################################################'
794	echo 'Compiling XIOS'
795	echo '##########################################################'
796	cd $MODEL/modipsl/modeles
797	xioslog=`pwd`/xios.log
798	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/install_xios.bash
799	myget script_install/install_xios.bash
800	chmod u=rwx install_xios.bash
801	if [ ${hostname:0:5} = jean- ] ; then
802	svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5 \
803	XIOS
804	cd XIOS/arch
805	svn update
806	cd ..
807	echo "Compiling XIOS, start" `date` \
808	"(it takes about 20 min on Jean-Zay)"
809	echo "log file: $xioslog"
810	./make_xios --prod --arch $arch --job 4 > xios.log 2>&1
811	else
812	./install_xios.bash -prefix $MODEL/modipsl/modeles \
813	-netcdf ${ncdfdir} -hdf5 ${ncdfdir} \
814	-MPI $root_mpi -arch $arch > xios.log 2>&1
815	fi # of case Jean-Zay
816	if [ -f XIOS/lib/libxios.a ] ; then
817	echo "XIOS library successfully generated"
818	echo install_lmdz.sh XIOS_OK `date`
819	fi
820	fi
821
822	#============================================================================
823	veget_version=false
824	if [ "$veget" != 'NONE' ] ; then
825	cd $MODEL/modipsl/modeles/ORCHIDEE
826	set +e ; svn upgrade ; set -e
827	if [ "$veget" = "CMIP6" ] ; then
828	veget_version=orchidee2.0
829	orchidee_rev=6592
830	else # specific orchidee revision newer than CMIP6, on 2_1 or 2_2 branches
831	veget_version=orchidee2.1
832	orchidee_rev=$veget
833	if [ $veget -lt 4465 ] ; then
834	echo 'Stopping, ORCHIDEE version too old, script needs work on ' \
835	'the CPP flags to pass to makelmdz'
836	exit 1
837	fi
838	set +e
839	# which branch is my version on?
840	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}'`
841	# switch to that branch
842	echo IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at \
843	orchidee-help@listes.ipsl.fr
844	svn switch -r $veget --accept theirs-full \
845	svn://forge.ipsl.jussieu.fr/orchidee/$orcbranch
846	svn log -r $veget \| grep $veget
847	if [ $? -gt 0 ] ; then
848	echo 'Cannot update ORCHIDEE as not on the right branch for ' \
849	'ORCHIDEE'
850	exit
851	fi
852	set -e
853	set +e ; svn update -r $veget ; set -e
854	fi
855	# Correctif suite debug Jean-Zay
856	sed -i -e 's/9010 FORMAT(A52,F17.14)/9010 FORMAT(A52,F20.14)/' \
857	src_stomate/stomate.f90
858	opt_orc="-prod" ; if [ "$optim" = "-debug" ] ; then opt_orc="-debug" ; fi
859
860	orchideelog=`pwd`/orchidee.log
861	echo '########################################################'
862	echo 'Compiling ORCHIDEE, the continental surface model '
863	echo '########################################################'
864	echo Start of the first compilation of orchidee, in sequential mode: `date`
865	echo log file : $orchideelog
866
867	export ORCHPATH=`pwd`
868	xios_orchid="-noxios"
869	if [ "$with_xios" = "y" ] ; then
870	xios_orchid="-xios"
871	fi
872	if [ -d tools ] ; then
873	###################################################################
874	# Pour les experts qui voudraient changer de version d'orchidee.
875	# Attention : necessite d'avoir le password pour orchidee
876
877	# Correctif suite debug Jean-Zay
878	if [ -f src_global/time.f90 ] ; then
879	sed -i -e 's/CALL tlen2itau/\!CALL tlen2itau/' src_global/time.f90
880	fi
881	###################################################################
882	if [ "$veget_version" == "false" ] ; then
883	veget_version=orchidee2.0
884	fi
885	cd arch
886	sed -e s:"%COMPILER .*.$":"%COMPILER $compiler":1 \
887	-e s:"%LINK .*.$":"%LINK $compiler":1 \
888	-e s:"%FPP_FLAGS .*.$":"%FPP_FLAGS $fpp_flags":1 \
889	-e s:"%PROD_FFLAGS .*.$":"%PROD_FFLAGS $OPTIM":1 \
890	-e s:"%DEV_FFLAGS .*.$":"%DEV_FFLAGS $OPTDEV":1 \
891	-e s:"%DEBUG_FFLAGS .*.$":"%DEBUG_FFLAGS $OPTDEB":1 \
892	-e s:"%BASE_FFLAGS .*.$":"%BASE_FFLAGS $OPTPREC":1 \
893	-e s:"%BASE_LD .*.$":"%BASE_LD $BASE_LD":1 \
894	-e s:"%ARFLAGS .*.$":"%ARFLAGS $ARFLAGS":1 \
895	arch-gfortran.fcm > arch-local.fcm
896	echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib -lnetcdff -lnetcdf\"" \
897	> arch-local.path
898	echo "NETCDF_INCDIR=${ncdfdir}/include" >> arch-local.path
899	echo "IOIPSL_INCDIR=$ORCHPATH/../../lib" >> arch-local.path
900	echo "IOIPSL_LIBDIR=$ORCHPATH/../../lib" >> arch-local.path
901	echo 'XIOS_INCDIR=${ORCHDIR}/../XIOS/inc' >> arch-local.path
902	echo 'XIOS_LIBDIR="${ORCHDIR}/../XIOS/lib -lxios"' >> arch-local.path
903	cd ../
904
905	echo ./makeorchidee_fcm -j $xios_orchid $opt_orc -parallel none \
906	-arch $arch
907	./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel none \
908	-arch $arch > $orchideelog 2>&1
909	pwd
910	else # of "if [ -d tools ]"
911	if [ -d src_parallel ] ; then
912	liste_src="parallel parameters global stomate sechiba driver"
913	if [ "$veget_version" == "false" ] ; then
914	veget_version=orchidee2.0
915	fi
916	fi
917	for d in $liste_src ; do
918	src_d=src_$d
919	echo src_d $src_d
920	echo ls ; ls
921	if [ ! -d $src_d ] ; then
922	echo Problem orchidee : no $src_d ; exit
923	fi
924	cd $src_d ; \rm -f *.mod make ; $make clean
925	$make > $orchideelog 2>&1
926	if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then
927	cp -f *.mod ../../../lib
928	fi
929	cd ..
930	done
931	fi # of "if [ -d tools ]"
932	echo install_lmdz.sh orchidee_compil_seq_OK `date`
933	fi # of if [ "$veget" != 'NONE' ]
934
935
936	#============================================================================
937	# Ehouarn: the directory name LMDZ* depends on version/tar file...
938	if [ -d $MODEL/modipsl/modeles/LMD* ] ; then
939	echo '###############################################################'
940	echo 'Preparing LMDZ compilation : arch file, svn switch if needed...'
941	echo '###############################################################'
942	cd $MODEL/modipsl/modeles/LMD*
943	LMDZPATH=`pwd`
944	else
945	echo "ERROR: No LMD* directory !!!"
946	exit
947	fi
948
949	###########################################################
950	# For those who want to use fcm to compile via :
951	# makelmdz_fcm -arch local .....
952	############################################################
953
954
955
956	cd $MODEL/modipsl/modeles/LMDZ*
957	lmdzlog=`pwd`/lmdz.log
958
959	##################################################################
960	# Possibly update LMDZ if a specific svn release is requested
961	##################################################################
962
963	set +e ; svn upgrade ; set -e
964
965	if [ "$svn" = "last" ] ; then svnopt="" ; else svnopt="-r $svn" ; fi
966	if [ "$svn" != "" ] ; then
967	set +e ; svn info \| grep -q 'http:'
968	if [ $? = 0 ] ; then
969	svn switch --relocate http://svn.lmd.jussieu.fr/LMDZ \
970	https://svn.lmd.jussieu.fr/LMDZ
971	fi
972	svn update $svnopt
973	set -e
974	fi
975
976	#---------------------------------------------------------------------
977	# Retrieve the final svn release number, and adjust compilation
978	# options accordingly
979	# If svn not available, will use the svn writen in $MODEL/Readm*md
980	# For old version it assumes that it is before 4185 (the version
981	# for which the test was introduced
982	#---------------------------------------------------------------------
983
984	set +e ; mysvn=`svnversion . \| egrep -o "[0-9]+" 2>/dev/null` ; set -e
985	if [ "$mysvn" = "" ] ; then mysvn=`grep 'Revision: [0-9]' $MODEL/Read*.md \| awk ' { print $2 } ' 2>/dev/null` ; fi
986	if [ "$mysvn" = "" ] ; then mysvn=4190 ; fi
987
988	if [[ "$pclinux" = "1" && ! -f arch/arch-local.path ]] ; then
989
990	# create local 'arch' files (if on Linux PC):
991	cd arch
992	# arch-local.path file
993	# test for version as arch.pth file changed format with rev 4426
994	if [ "$mysvn" -gt 4425 ] ; then
995	echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib \"" > arch-local.path
996	echo "NETCDF_LIB=\"-lnetcdff -lnetcdf\"" >> arch-local.path
997	echo "NETCDF_INCDIR=-I${ncdfdir}/include" >> arch-local.path
998	echo 'NETCDF95_INCDIR=-I$LMDGCM/../../include' >> arch-local.path
999	echo 'NETCDF95_LIBDIR=-L$LMDGCM/../../lib' >> arch-local.path
1000	echo 'NETCDF95_LIB=-lnetcdf95' >> arch-local.path
1001	echo 'IOIPSL_INCDIR=-I$LMDGCM/../../lib' >> arch-local.path
1002	echo 'IOIPSL_LIBDIR=-L$LMDGCM/../../lib' >> arch-local.path
1003	echo 'IOIPSL_LIB=-lioipsl' >> arch-local.path
1004	echo 'XIOS_INCDIR=-I$LMDGCM/../XIOS/inc' >> arch-local.path
1005	echo 'XIOS_LIBDIR=-L$LMDGCM/../XIOS/lib' >> arch-local.path
1006	echo "XIOS_LIB=\"-lxios -lstdc++\"" >> arch-local.path
1007	echo 'ORCH_INCDIR=-I$LMDGCM/../../lib' >> arch-local.path
1008	echo 'ORCH_LIBDIR=-L$LMDGCM/../../lib' >> arch-local.path
1009	else
1010	echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib -lnetcdff -lnetcdf\"" \
1011	> arch-local.path
1012	echo "NETCDF_INCDIR=-I${ncdfdir}/include" >> arch-local.path
1013	echo 'NETCDF95_INCDIR=$LMDGCM/../../include' >> arch-local.path
1014	echo 'NETCDF95_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
1015	echo 'IOIPSL_INCDIR=$LMDGCM/../../lib' >> arch-local.path
1016	echo 'IOIPSL_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
1017	echo 'XIOS_INCDIR=$LMDGCM/../XIOS/inc' >> arch-local.path
1018	echo 'XIOS_LIBDIR=$LMDGCM/../XIOS/lib' >> arch-local.path
1019	echo 'ORCH_INCDIR=$LMDGCM/../../lib' >> arch-local.path
1020	echo 'ORCH_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
1021	fi
1022
1023	if [ $pcmac == 1 ] ; then
1024	BASE_LD="$BASE_LD -Wl,-rpath,${ncdfdir}/lib"
1025	else
1026	BASE_LD="$BASE_LD -Wl,-rpath=${ncdfdir}/lib"
1027	fi
1028	# Arch-local.fcm file (adapted from arch-linux-32bit.fcm)
1029
1030	if [ $real = r8 ] ; then FPP_DEF=NC_DOUBLE ; else FPP_DEF="" ; fi
1031	sed -e s:"%COMPILER .*.$":"%COMPILER $compiler":1 \
1032	-e s:"%LINK .*.$":"%LINK $compiler":1 \
1033	-e s:"%PROD_FFLAGS .*.$":"%PROD_FFLAGS $OPTIM":1 \
1034	-e s:"%DEV_FFLAGS .*.$":"%DEV_FFLAGS $OPTDEV":1 \
1035	-e s:"%DEBUG_FFLAGS .*.$":"%DEBUG_FFLAGS $OPTDEB":1 \
1036	-e s:"%BASE_FFLAGS .*.$":"%BASE_FFLAGS $OPTPREC":1 \
1037	-e s:"%FPP_DEF .*.$":"%FPP_DEF $FPP_DEF":1 \
1038	-e s:"%BASE_LD .*.$":"%BASE_LD $BASE_LD":1 \
1039	-e s:"%ARFLAGS .*.$":"%ARFLAGS $ARFLAGS":1 \
1040	arch-linux-32bit.fcm > arch-local.fcm
1041
1042	cd ..
1043	### Adapt "bld.cfg" (add the shell):
1044	#whereisthatshell=$(which ${use_shell})
1045	#echo "bld::tool::SHELL $whereisthatshell" >> bld.cfg
1046
1047	fi # of if [ "$pclinux" = 1 ]
1048	#---------------------------------------------------------------------
1049	# Option de compilation du rayonnement : depend de $mysvn ><= r4185
1050	#---------------------------------------------------------------------
1051	opt_rad=""
1052
1053	case $rad in
1054	oldrad) iflag_rrtm=0 ; NSW=2 ; opt_rad="" ;;
1055	rrtm) iflag_rrtm=1 ; NSW=6
1056	if [ $mysvn -le 4185 ] ; then
1057	opt_rad="-rrtm true"
1058	else
1059	opt_rad="-rad rrtm"
1060	fi ;;
1061	ecrad) iflag_rrtm=2 ; NSW=6 ; opt_rad="-rad ecrad" ;;
1062	*) echo Only oldrad rrtm ecrad for rad option ; exit
1063	esac
1064
1065	if [ $mysvn -le 4185 -a $rad = "ecrad" ] ; then
1066	echo "ecrad only available for LMDZ rev starting with 4186 " ; exit
1067	fi
1068
1069	##################################################################
1070
1071
1072	if [[ ! -f libf/misc/netcdf95.F90 && ! -d $MODEL/NetCDF95-0.2 ]]
1073	then
1074	cd $MODEL
1075	myget src_archives/netcdf/NetCDF95-0.2.tar.gz
1076	tar -xf NetCDF95-0.2.tar.gz
1077	rm NetCDF95-0.2.tar.gz
1078	cd NetCDF95-0.2
1079	mkdir build
1080	cd build
1081	cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=$ncdfdir \
1082	-DCMAKE_INSTALL_PREFIX=$MODEL/modipsl
1083	make install
1084	cd $MODEL/modipsl/modeles/LMDZ*
1085	fi
1086
1087	echo '##################################################################'
1088	echo "Preparing script compile.sh for LMDZ compilation"
1089	echo "It will only be run automatically if bench=1/tuto"
1090	echo Here bench=$bench
1091	echo '##################################################################'
1092
1093	if [ "$env_file" != "" ] ; then
1094	mv arch/arch-${arch}.env arch/arch-${arch}.orig
1095	\cp -f $env_file arch/arch-${arch}.env
1096	fi
1097
1098	if [ $compile_with_fcm = 1 ] ; then
1099	makelmdz="makelmdz_fcm $optim -arch $arch -j 8 "
1100	else
1101	makelmdz="makelmdz $optim -arch $arch"
1102	fi
1103
1104	# sequential compilation
1105	if [ "$sequential" = 1 ] ; then
1106	echo Sequential compilation command, saved in compile.sh:
1107	echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp " \
1108	"-d ${grid_resolution} -v $veget_version gcm "
1109	echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp " \
1110	"-d ${grid_resolution} -v $veget_version gcm " > compile.sh
1111	chmod +x ./compile.sh
1112	if [ $bench = 1 ] ; then
1113	echo install_lmdz.sh start_lmdz_seq_compilation `date`
1114	echo log file: $lmdzlog
1115	./compile.sh > $lmdzlog 2>&1
1116	echo install_lmdz.sh end_lmdz_seq_compilation `date`
1117	fi
1118	fi # fin sequential
1119
1120	# compiling in parallel mode
1121	if [ $parallel != "none" ] ; then
1122	echo '##########################################################'
1123	echo ' Parallel compile '
1124	echo '##########################################################'
1125	echo "(after saving the sequential libs and binaries)"
1126	cd $MODEL/modipsl
1127	tar cf sequential.tar bin/ lib/
1128	#
1129	# Orchidee
1130	#
1131	cd $ORCHPATH
1132	if [ -d src_parallel -a $veget != 'NONE' ] ; then
1133	cd arch
1134	sed \
1135	-e s:"%COMPILER.*.$":"%COMPILER $par_comp":1 \
1136	-e s:"%LINK.*.$":"%LINK $par_comp":1 \
1137	-e s:"%MPI_FFLAG.*.$":"%MPI_FFLAGS $MPI_FLAGS":1 \
1138	-e s:"%OMP_FFLAG.*.$":"%OMP_FFLAGS $OMP_FLAGS":1 \
1139	-e s:"%MPI_LD.*.$":"%MPI_LD $MPI_LD":1 \
1140	-e s:"%OMP_LD.*.$":"%OMP_LD $OMP_LD":1 \
1141	arch-local.fcm > tmp.fcm
1142
1143	mv tmp.fcm arch-local.fcm
1144	cd ../
1145	echo Compiling ORCHIDEE in parallel mode `date`
1146	echo logfile $orchideelog
1147	echo "NOTE : to recompile it when necessary, use ./compile_orc.sh " \
1148	"in modipsl/modeles/ORCHIDEE"
1149	echo ./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc \
1150	-parallel $parallel -arch $arch > compile_orc.sh
1151	echo ./makeorchidee_fcm -j 8 $xios_orchid $opt_orc \
1152	-parallel $parallel -arch $arch >> compile_orc.sh
1153	echo echo Now you must also recompile LMDZ, by running ./compile.sh \
1154	in modeles/LMDZ >> compile_orc.sh
1155	chmod u+x compile_orc.sh
1156	./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc \
1157	-parallel $parallel -arch $arch > $orchideelog 2>&1
1158	./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel $parallel \
1159	-arch $arch >> $orchideelog 2>&1
1160	echo End of ORCHIDEE compilation in parallel mode `date`
1161	elif [ $veget != 'NONE' ] ; then
1162	echo '##########################################################'
1163	echo ' Orchidee version too old '
1164	echo ' Please update to new version '
1165	echo '##########################################################'
1166	exit
1167	fi # of [ -d src_parallel -a $veget != 'NONE' ]
1168
1169	# LMDZ
1170	cd $LMDZPATH
1171	if [ $arch = local ] ; then
1172	cd arch
1173	sed -e s:"%COMPILER.*.$":"%COMPILER $par_comp":1 \
1174	-e s:"%LINK.*.$":"%LINK $par_comp":1 \
1175	-e s:"%MPI_FFLAG.*.$":"%MPI_FFLAGS $MPI_FLAGS":1 \
1176	-e s:"%OMP_FFLAG.*.$":"%OMP_FFLAGS $OMP_FLAGS":1 \
1177	-e s:"%ARFLAGS.*.$":"%ARFLAGS $ARFLAGS":1 \
1178	-e s@"%BASE_LD.*.$"@"%BASE_LD -Wl,-rpath=${root_mpi}/lib:${ncdfdir}/lib"@1 \
1179	-e s:"%MPI_LD.*.$":"%MPI_LD $MPI_LD":1 \
1180	-e s:"%OMP_LD.*.$":"%OMP_LD $OMP_LD":1 \
1181	arch-local.fcm > tmp.fcm
1182	mv tmp.fcm arch-local.fcm
1183	cd ../
1184	fi
1185	rm -f compile.sh
1186	echo resol=${grid_resolution} >> compile.sh
1187	if [ ${hostname:0:5} = jean- -a "$cosp" = "v2" ] ; then
1188
1189	echo LMDZ compilation command in parallel mode, saved in compile.sh, \
1190	is :
1191	echo "(ATTENTION le probleme de cospv2 sur jean-zay en mode prod " \
1192	"n est pas corrige ! )"
1193	# ATTENTION le probleme de cospv2 sur jean-zay en mode prod n
1194	# est pas corrige
1195	echo ./$makelmdz -dev $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
1196	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
1197	-parallel $parallel gcm >> compile.sh
1198	echo ./$makelmdz -dev $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
1199	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
1200	-parallel $parallel gcm
1201	else
1202	echo ./$makelmdz $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
1203	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
1204	-parallel $parallel gcm >> compile.sh
1205	echo ./$makelmdz $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
1206	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
1207	-parallel $parallel gcm
1208	fi
1209	chmod +x ./compile.sh
1210
1211	if [ $bench = 1 ] ; then
1212	echo Compiling LMDZ in parallel mode `date`, LMDZ log file: $lmdzlog
1213	./compile.sh > $lmdzlog 2>&1
1214	fi
1215
1216	fi # of if [ $parallel != "none" ]
1217
1218
1219	##################################################################
1220	# Verification du succes de la compilation
1221	##################################################################
1222
1223	# Recherche de l'executable dont le nom a change au fil du temps ...
1224	# suffix contains radiative option starting with revision 4186
1225	if [ $mysvn -ge 4186 ] ; then suff_exe=_${rad}${suff_exe} ; fi
1226	gcm=""
1227
1228	for exe in gcm.e bin/gcm_${grid_resolution}_phylmd${suff_exe}${suff_orc}.e
1229	do
1230	if [ -f $exe ] ; then gcm=$exe ; fi
1231	done
1232
1233	if [ "$gcm" = "" ] ; then
1234	if [ $bench = 1 ] ; then
1235	echo 'Compilation failed !! Cannot run the benchmark;'
1236	exit
1237	else
1238	echo 'Compilation not done (only done when bench=1)'
1239	fi
1240	else
1241	echo '##########################################################'
1242	echo 'Compilation successfull !! ' `date`
1243	echo '##########################################################'
1244	echo The executable is $gcm
1245	fi
1246
1247	##################################################################
1248	# Below, we run a benchmark if bench=1 or tuto
1249	##################################################################
1250
1251	if [ $bench = tuto ] ; then
1252	myget Training/tutorial.tar ; tar xf tutorial.tar ; cd TUTORIAL
1253	./init.sh
1254
1255	elif [[ $bench = 1 && ! -d BENCH${grid_resolution} ]] ; then
1256	# TOUTE CETTE SECTION DEVRAIT DISPARAITRE POUR UNE COMMANDE
1257	# OU DES BENCHS PAR MOTS CLES COMME tuto
1258
1259	echo '##########################################################'
1260	echo ' Running a test run '
1261	echo '##########################################################'
1262
1263	\rm -rf BENCH${grid_resolution}
1264	bench=bench_lmdz_${grid_resolution}
1265	echo install_lmdz.sh before bench download `date`
1266	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/$bench.tar.gz
1267	myget 3DBenchs/$bench.tar.gz
1268	echo install_lmdz.sh after bench download `date`
1269	tar xf $bench.tar.gz
1270
1271	if [ "$cosp" = "v1" -o "$cosp" = "v2" ] ; then
1272	cd BENCH${grid_resolution}
1273	# copier les fichiers namelist input et output our COSP
1274	cp ../DefLists/cosp*_input_nl.txt .
1275	cp ../DefLists/cosp*_output_nl.txt .
1276	# Activer la cles ok_cosp pour tourner avec COSP
1277	sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp
1278	\mv -f tmp config.def
1279	cd ..
1280	fi
1281
1282	if [ -n "$physiq" ]; then
1283	cd BENCH${grid_resolution}
1284	if [ -f physiq.def_${physiq} ]; then
1285	cp physiq.def_${physiq} physiq.def
1286	echo using physiq.def_${physiq}
1287	else
1288	echo using standard physiq.def
1289	fi
1290	cd ..
1291	else
1292	echo using standard physiq.def
1293	fi
1294
1295	if [ "$with_xios" = "y" ] ; then
1296	cd BENCH${grid_resolution}
1297	cp ../DefLists/iodef.xml .
1298	cp ../DefLists/context_lmdz.xml .
1299	cp ../DefLists/field_def_lmdz.xml .
1300	# A raffiner par la suite
1301	echo A FAIRE : Copier les *xml en fonction de l option cosp
1302	cp ../DefLists/field_def_cosp*.xml .
1303	cp ../DefLists/file_def_hist*xml .
1304	# adapt iodef.xml to use attached mode
1305	sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' \
1306	iodef.xml > tmp
1307	\mv -f tmp iodef.xml
1308
1309	# and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
1310	# except for histday
1311	for histfile in file_def_hist*xml
1312	do
1313	if [ "$histfile" = "file_def_histday_lmdz.xml" ] ; then
1314	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' \
1315	$histfile > tmp
1316	\mv -f tmp $histfile
1317	sed -e 's@output_level="_AUTO_"@output_level="5"@' $histfile \
1318	> tmp
1319	\mv -f tmp $histfile
1320	sed -e 's@compression_level="2"@compression_level="0"@' \
1321	$histfile > tmp
1322	\mv -f tmp $histfile
1323	else
1324	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
1325	$histfile > tmp
1326	\mv -f tmp $histfile
1327	fi
1328	done
1329	# and add option "ok_all_xml=y" in config.def
1330	echo "### XIOS outputs" >> config.def
1331	echo 'ok_all_xml=.true.' >> config.def
1332
1333	#activer les sorties pour Cosp
1334	if [ "$cosp" = "v1" ] ; then
1335	histfile=file_def_histdayCOSP_lmdz.xml
1336	sed -e 's@enabled=".FALSE."@enabled=".TRUE."@' $histfile > tmp
1337	\mv -f tmp $histfile
1338	sed -e 's@output_level="_AUTO_"@output_level="5"@' $histfile > tmp
1339	\mv -f tmp $histfile
1340	sed -e 's@compression_level="2"@compression_level="0"@' \
1341	$histfile > tmp
1342	\mv -f tmp $histfile
1343	fi
1344	if [ "$cosp" = "v2" ] ; then
1345	histfile=file_def_histdayCOSPv2_lmdz.xml
1346	sed -e 's@compression_level="2"@compression_level="0"@' \
1347	$histfile > tmp
1348	\mv -f tmp $histfile
1349	contextfile=context_lmdz.xml
1350	sed -e 's@src="./file_def_histdayCOSP_lmdz.xml"@src="./file_def_histdayCOSPv2_lmdz.xml"@' \
1351	$contextfile > tmp
1352	\mv -f tmp $contextfile
1353	sed -e 's@src="./file_def_histmthCOSP_lmdz.xml"@src="./file_def_histmthCOSPv2_lmdz.xml"@' \
1354	$contextfile > tmp
1355	\mv -f tmp $contextfile
1356	sed -e 's@src="./file_def_histhfCOSP_lmdz.xml"@src="./file_def_histhfCOSPv2_lmdz.xml"@' \
1357	$contextfile > tmp
1358	\mv -f tmp $contextfile
1359	fieldfile=field_def_lmdz.xml
1360	sed -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' $fieldfile \
1361	> tmp
1362	\mv -f tmp $fieldfile
1363	fi
1364
1365	cd ..
1366	fi
1367
1368	# Cas Bensh avec ecrad
1369	if [ "$rad" = "ecrad" ] ; then
1370	cd BENCH${grid_resolution}
1371	cp ../DefLists/namelist_ecrad .
1372	cp -r ../libf/phylmd/ecrad/data .
1373	cd ..
1374	fi
1375
1376	# Adjusting bench physiq.def to radiative code chosen
1377	cd BENCH${grid_resolution}
1378	sed -e 's/iflag_rrtm=.*.$/iflag_rrtm='$iflag_rrtm'/' \
1379	-e 's/NSW=.*.$/NSW='$NSW'/' physiq.def > tmpdef
1380	\mv tmpdef physiq.def
1381	cd ..
1382
1383	cp $gcm BENCH${grid_resolution}/gcm.e
1384
1385	cd BENCH${grid_resolution}
1386	# On cree le fichier bench.sh au besoin
1387	# Dans le cas 48x36x39 le bench.sh existe deja en parallele
1388
1389	if [ "$grid_resolution" = "48x36x39" ] ; then
1390	echo On ne touche pas au bench.sh
1391	# But we have to adapt "run_local.sh" for $mpirun
1392	sed -e "s@mpirun@$mpirun@g" run_local.sh > tmp
1393	mv -f tmp run_local.sh
1394	chmod u=rwx run_local.sh
1395	elif [ "${parallel:0:3}" = "mpi" ] ; then
1396	# Lancement avec deux procs mpi et 2 openMP
1397	echo "export OMP_STACKSIZE=800M" > bench.sh
1398	if [ "${parallel:4:3}" = "omp" ] ; then
1399	echo "export OMP_NUM_THREADS=2" >> bench.sh
1400	fi
1401	if [ "$cosp" = "v1" -o "$cosp" = "v2" ] ; then
1402	if [ ${hostname:0:5} = jean- ] ; then
1403	chmod +x ../arch.env
1404	../arch.env
1405	echo "ulimit -s 2000000" >> bench.sh
1406	else
1407	echo "ulimit -s 200000" >> bench.sh
1408	fi
1409	else
1410	echo "ulimit -s unlimited" >> bench.sh
1411	fi
1412	if [ ${hostname:0:5} = jean- ] ; then
1413	. ../arch/arch-${arch}.env
1414	echo "srun -n 2 -A $idris_acct@cpu gcm.e > listing 2>&1" \
1415	>> bench.sh
1416	else
1417	echo "$mpirun -np 2 gcm.e > listing 2>&1" >> bench.sh
1418	fi
1419	# Add rebuild, using reb.sh if it is there
1420	echo 'if [ -f reb.sh ] ; then' >> bench.sh
1421	echo ' ./reb.sh histday ; ./reb.sh histmth ; ./reb.sh histhf ; ' \
1422	'./reb.sh histins ; ./reb.sh stomate_history ; ' \
1423	'./reb.sh sechiba_history ; ./reb.sh sechiba_out_2 ' >> bench.sh
1424	echo 'fi' >> bench.sh
1425	else
1426	echo "./gcm.e > listing 2>&1" > bench.sh
1427	fi
1428	# Getting orchidee stuff
1429	if [ $veget == 'CMIP6' ] ; then
1430	#echo 'myget 3DBenchs/BENCHorch11.tar.gz'
1431	#myget 3DBenchs/BENCHorch11.tar.gz
1432	#tar xvzf BENCHorch11.tar.gz
1433	echo 'myget 3DBenchs/BENCHCMIP6.tar.gz'
1434	myget 3DBenchs/BENCHCMIP6.tar.gz
1435	tar xvzf BENCHCMIP6.tar.gz
1436	sed -e "s:VEGET=n:VEGET=y:" config.def > tmp
1437	mv -f tmp config.def
1438	if [ "$with_xios" = "y" ] ; then
1439	cp ../../ORCHIDEE/src_xml/context_orchidee.xml .
1440	echo '<context id="orchidee" src="./context_orchidee.xml"/>' \
1441	> add.tmp
1442	cp ../../ORCHIDEE/src_xml/field_def_orchidee.xml .
1443	cp ../../ORCHIDEE/src_xml/file_def_orchidee.xml .
1444	cp ../../ORCHIDEE/src_xml/file_def_input_orchidee.xml .
1445	if [ -f ../../ORCHIDEE/src_xml/context_input_orchidee.xml ] ; then
1446	cp ../../ORCHIDEE/src_xml/context_input_orchidee.xml .
1447	echo '<context id="orchidee" ' \
1448	'src="./context_input_orchidee.xml"/>' >> add.tmp
1449	fi
1450	sed -e '/id="LMDZ"/r add.tmp' iodef.xml > tmp
1451	mv tmp iodef.xml
1452	sed -e'{/sechiba1/ s/enabled="_AUTO_"/type="one_file" enabled=".TRUE."/}' \
1453	file_def_orchidee.xml > tmp
1454	\mv -f tmp file_def_orchidee.xml
1455	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
1456	file_def_orchidee.xml > tmp
1457	\mv -f tmp file_def_orchidee.xml
1458	sed -e 's@output_level="_AUTO_"@output_level="1"@' \
1459	file_def_orchidee.xml > tmp
1460	\mv -f tmp file_def_orchidee.xml
1461	sed -e 's@output_freq="_AUTO_"@output_freq="1d"@' \
1462	file_def_orchidee.xml > tmp
1463	\mv -f tmp file_def_orchidee.xml
1464	sed -e 's@compression_level="4"@compression_level="0"@' \
1465	file_def_orchidee.xml > tmp
1466	\mv -f tmp file_def_orchidee.xml
1467	sed -e 's@XIOS_ORCHIDEE_OK = n@XIOS_ORCHIDEE_OK = y@' \
1468	orchidee.def > tmp
1469	\mv -f tmp orchidee.def
1470	fi
1471	fi
1472
1473	if [[ -f ../arch.env ]]
1474	then
1475	source ../arch.env
1476	fi
1477
1478	echo EXECUTION DU BENCH
1479	set +e
1480	date ; ./bench.sh > out.bench 2>&1 ; date
1481	set -e
1482	tail listing
1483
1484
1485	echo '##########################################################'
1486	echo 'Simulation finished in' `pwd`
1487	echo 'You have compiled with:'
1488	cat ../compile.sh
1489	if [ $parallel = "none" ] ; then
1490	echo 'You may re-run it with : cd ' `pwd` ' ; gcm.e'
1491	echo 'or ./bench.sh'
1492	else
1493	echo 'You may re-run it with : '
1494	echo 'cd ' `pwd` '; ./bench.sh'
1495	# echo 'ulimit -s unlimited'
1496	# echo 'export OMP_NUM_THREADS=2'
1497	# echo 'export OMP_STACKSIZE=800M'
1498	# echo "$mpirun -np 2 gcm.e "
1499	fi
1500	echo '##########################################################'
1501
1502	fi # bench
1503
1504
1505	#################################################################
1506	# Installation eventuelle du 1D
1507	#################################################################
1508
1509	if [ $SCM = 1 ] ; then
1510	cd $MODEL
1511	myget 1D/1D.tar.gz
1512	tar xf 1D.tar.gz
1513	cd 1D
1514	if [ $rad = oldrad ] ; then
1515	sed -i'' -e 's/^rad=.*$/rad=oldrad/' run.sh
1516	sed -i'' -e 's/^rad=.*$/rad=oldrad/' bin/compile
1517	fi
1518	echo Running 1D/run.sh, log in `pwd`/run1d.log
1519	./run.sh > `pwd`/run1d.log 2>&1
1520	fi
1521
1522
1523	#################################################################
1524	# sauvegarde des options veget pour utilisation eventuelle tutorial_prod
1525	#################################################################
1526	cd $MODEL/modipsl/modeles
1527	#echo surface_env file created in $MODEL
1528	echo 'veget='$veget > surface_env
1529	#opt_veget="-v $veget_version"
1530	#echo 'opt_veget="'$opt_veget\" >> surface_env
1531	echo 'opt_veget="'-v $veget_version\" >> surface_env
1532	echo 'orchidee_rev='$orchidee_rev >> surface_env
1533	echo 'suforch='$suff_orc >> surface_env

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