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source: BOL/script_install/install_lmdz.sh @ 4503

Last change on this file since 4503 was 4503, checked in by asima, 15 months ago
Add "module load cmake" for Jean-Zay, needed after merging ECRad branch (LMDZ r4489 by L. Guez).
Property svn:executable set to ``*
File size: 56.7 KB

Line
1	#!/bin/bash
2
3	#set -vx
4
5	###########################################################################
6	# Author : Laurent Fairhead et Frédéric Hourdin
7	# Usage : install_lmdz.sh -help
8	#
9	# bash installation script of the LMDZ model on different computer types :
10	# Linux PC, "mesocentre" (IPSL-UPMC, IPSL-X), super-computer (IDRIS)
11	#
12	# The model is downloaded in the following directory tree
13	# $MODEL/modipsl/modeles/...
14	# using the "modipsl" infrastructure created by the "IPSL"
15	# for coupled (atmosphere/ocean/vegetation/chemistry) climate modeling
16	# activities.
17	# Here we only download atmospheric (LMDZ) and vegetation (ORCHIDEE)
18	# components.
19	#
20	# The sources of the models can be found in the "modeles" directory.
21	# In the present case, LMDZ, ORCHIDEE, and IOIPSL or XIOS (handling of
22	# input-outputs using the NetCDF library).
23	#
24	# The script downloads various source files (including a version of NetCDF)
25	# and utilities, compiles the model, and runs a test simulation in a
26	# minimal configuration.
27	#
28	# Prerequisites : pgf90/gfortran, bash or ksh, wget , gunzip, tar, ...
29	#
30	# Modif 18/11/2011
31	# changes for option real 8.
32	# We compile with -r8 (or equivalent) and -DNC_DOUBLE for the GCM
33	# but with -r4 for netcdf. Variable real must be set to
34	# r4 or r8 at the beginning of the script below.
35	#
36	###########################################################################
37
38	echo install_lmdz.sh DEBUT `date`
39	set -e
40
41	################################################################
42	# Choice of installation options
43	################################################################
44
45	################################################################
46	# A function to fetch files either locally or on the internet
47	################################################################
48	function myget { #1st and only argument should be file name
49	# Path on local computer where to look for the datafile
50	if [ -f /u/lmdz/WWW/LMDZ/pub/$1 ] ; then
51	\cp -f -p /u/lmdz/WWW/LMDZ/pub/$1 .
52	elif [ -f ~/LMDZ/pub/$1 ] ; then
53	\cp -f -p ~/LMDZ/pub/$1 .
54	else
55	wget --no-check-certificate -nv http://lmdz.lmd.jussieu.fr/pub/$1
56	save_pub_locally=0
57	if [ $save_pub_locally = 1 ] ; then # saving wget files on ~/LMDZ/pub
58	dir=~/LMDZ/pub/`dirname $1` ; mkdir -p $dir
59	cp -r `basename $1` $dir
60	fi
61	fi
62	}
63
64	# 04_2021 : tester si r4 marche encore !
65	#real=r4
66	real=r8
67
68
69	#########################################################################
70	# Valeur par défaut des parametres
71	#########################################################################
72	svn=""
73	#version=trunk
74	version=20221201.trunk
75
76	getlmdzor=1
77	netcdf=1 # 1: for automatic installation;
78	# or 0: do not install NetCDF and look for it in standard locations;
79	# or absolute path: look for NetCDF there
80	check_linux=1
81	ioipsl=1
82	bench=1
83	pclinux=1
84	pcmac=0 # default: not on a Mac
85	compiler=gfortran
86	if [ `gfortran -dumpversion \| cut -d. -f1` -ge 11 ] ; then allow_arg_mismatch="-fallow-argument-mismatch" ; fi
87	SCM=0
88	# surface/vegetation scheme treatment
89	# controlled by the single variable veget which can have the following values
90	# - NONE: bucket scheme (default)
91	# - CMIP6: orchidee version used in CMIP exercise, rev 5661
92	# - number: orchidee version number
93	veget=NONE
94	# choose the resolution for the bench runs
95	# grid_resolution= 32x24x11 or 48x36x19 for tests (test without ORCHIDEE)
96	# 96x71x19 standard configuration
97	grid_resolution=144x142x79
98	grid_resolution=96x95x39
99	grid_resolution=48x36x19
100	grid_resolution=32x32x39
101	# choose the physiq version you want to test
102	#physiq=NPv6.0.14splith
103	physiq=
104
105	## parallel can take the values none/mpi/omp/mpi_omp
106	parallel=mpi_omp
107	parallel=none
108	idris_acct=lmd
109	trusting=testing
110	OPT_GPROF=""
111	OPT_MAKELMDZ=""
112	MODEL=""
113
114	## also compile XIOS? (and more recent NetCDF/HDF5 libraries) Default=no
115	with_xios="n"
116	opt_makelmdz_xios=""
117
118	## compile with oldrad/rrtm/ecrad radiatif code (Default=rrtm)
119	rad=rrtm
120
121	## compile_with_fcm=1 : use makelmdz_fcm (1) or makelmdz (0)
122	compile_with_fcm=1
123
124	#Compilation with Cosp (cosp=NONE/v1/v2 ; default=NONE)
125	cosp=NONE
126	opt_cosp=""
127
128	# Check if on a Mac
129	if [ `uname` = "Darwin" ]
130	then
131	pcmac=1
132	export MAKE=make
133	fi
134	#echo "pcmac="$pcmac
135
136	env_file=""
137
138	#########################################################################
139	# Options interactives
140	#########################################################################
141	while (($# > 0))
142	do
143	case $1 in
144	"-h") cat <<........fin
145	$0 [ -v version ] [ -r svn_release ]
146	[ -parallel PARA ] [ -d GRID_RESOLUTION ] [ -bench 0/1 ]
147	[-name LOCAL_MODEL_NAME] [-gprof] [-opt_makelmdz] [-rad RADIATIF]
148
149	-v "version" like 20150828.trunk
150	see http://www.lmd.jussieu.fr/~lmdz/Distrib/LISMOI.trunk
151
152	-r "svn_release" : either the svn release number or "last"
153
154	-compiler gfortran\|ifort\|pgf90 (default: gfortran)
155
156	-parallel PARA : can be mpi_omp (mpi with openMP) or none (for sequential)
157
158	-d GRID_RESOLUTION should be among the available benchs if -bench 1
159	among which : 48x36x19, 48x36x39
160	if wanting to run a bench simulation in addition to compilation
161	default : 48x36x19
162
163	-bench activating the bench or not (0/1). Default 1
164
165	-testing/unstable
166
167	-name LOCAL_MODEL_NAME : default = LMDZversion.release
168
169	-netcdf 0, 1 or PATH
170	0: do not download NetCDF, look for it in standard locations
171	1: download and compile NetCDF
172	PATH: full path to an existing installed NetCDF library
173
174	-xios also download and compile the XIOS library
175	(requires the NetCDF4-HDF5 library, also installed by default)
176	(requires to also have -parallel mpi_omp)
177
178	-gprof to compile with -pg to enable profiling with gprof
179
180	-cosp to run without our with cospv1 or cospv2 [none/v1/v2]
181
182	-rad RADIATIF can be oldrad, rrtm or ecrad radiatif code
183
184	-nofcm to compile without fcm
185
186	-SCM install 1D version automatically
187
188	-debug compile everything in debug mode
189
190	-opt_makelmdz to call makelmdz or makelmdz_fcm with additional options
191
192	-physiq to choose which physics package to use
193
194	-env_file specify an arch.env file to overwrite the existing one
195
196	-veget surface model to run [NONE/CMIP6/xxxx]
197
198	........fin
199	exit ;;
200	"-v") version=$2 ; shift ; shift ;;
201	"-r") svn=$2 ; shift ; shift ;;
202	"-compiler") compiler=$2
203	case $compiler in
204	"gfortran"\|"ifort"\|"pgf90") compiler=$2 ; shift
205	shift ;;
206	*) echo "Only gfortran , ifort or pgf90 for the " \
207	"compiler option"
208	exit
209	esac ;;
210	"-d") grid_resolution=$2 ; shift ; shift ;;
211	"-gprof") OPT_GPROF="-pg" ; shift ;;
212	"-unstable"\|"-testing") trusting=`echo $1 \| cut -c2-` ; shift ;;
213	"-cosp") cosp=$2
214	case $cosp in
215	"none"\|"v1"\|"v2") cosp=$2 ; shift ; shift ;;
216	*) echo Only none v1 v2 for cosp option ; exit
217	esac ;;
218	"-nofcm") compile_with_fcm=0 ; echo This option will be reactivated soon '(promesse du 8dec2022)' ; exit 1 ; shift ;;
219	"-SCM") SCM=1 ; shift ;;
220	"-opt_makelmdz") OPT_MAKELMDZ="$2" ; shift ; shift ;;
221	"-rrtm") rrtm="$2"
222	if [ "$2" = "false" ] ; then
223	rad="oldrad"
224	else
225	rad="rrtm"
226	fi
227	shift ; shift ;;
228	"-rad") rad=$2
229	case $rad in
230	"oldrad"\|"rrtm"\|"ecrad") rad=$2 ; shift ; shift ;;
231	*) echo Only oldrad rrtm ecrad for rad option ; exit
232	esac ;;
233	"-parallel") parallel=$2
234	case $parallel in
235	"none"\|"mpi"\|"omp"\|"mpi_omp") parallel=$2 ; shift
236	shift ;;
237	*) echo Only none mpi omp mpi_omp for the parallel \
238	option
239	exit
240	esac ;;
241	"-bench") bench=$2 ; shift ; shift ;;
242	"-debug") optim=-debug ; shift ;;
243	"-name") MODEL=$2 ; shift ; shift ;;
244	"-netcdf") case $2 in
245	0\|1) netcdf=$2 ;;
246	*) netcdf=`ls -d $2` ; if [ $? != 0 ] ; then echo No directory $2 ; exit 1 ; fi
247	esac
248	shift ; shift ;;
249	"-physiq") physiq=$2 ; shift ; shift ;;
250	"-xios") with_xios="y" ; shift ;;
251	"-env_file") env_file=$2 ; shift ; shift ;;
252	"-veget") veget=$2 ; shift ; shift ;;
253	*) ./install_lmdz.sh -h ; exit
254	esac
255	done
256
257	# Option de compilation du rayonnement : depend de $mysvn ><= r4185,
258	# sera donc definie plus bas
259
260	#opt_rad=""
261	#case $rad in
262	# rrtm) opt_rad="-rad rrtm" ;;
263	# ecrad) opt_rad="-rad ecrad" ;;
264	#esac
265
266
267	# Option de compilation pour Cosp
268	opt_cosp=""
269	case cosp in
270	v1) opt_cosp="-cosp true" ;;
271	v2) opt_cosp="-cospv2 true" ;;
272	esac
273
274	# Check on veget version
275	#if [ "$veget" != 'NONE' -a "$veget" != "CMIP6" -a "$veget" != +([0-9]) ] ; then
276	if [ $veget != 'NONE' -a $veget != "CMIP6" ] ; then
277	re='^[0-9]+$'
278	if ! [[ $veget =~ $re ]] ; then
279	echo 'Valeur de l option veget non valable'
280	exit
281	fi
282	fi
283
284	#Define veget-related suffix for gcm name
285	if [ "$veget" = 'NONE' ] ; then
286	suff_orc=''
287	#For use with tutorial, orchidee_rev is also defined (will be
288	#written in surface_env at the end of the script)
289	orchidee_rev=''
290	else
291	suff_orc='_orch'
292	fi
293
294
295	if [ $parallel = none ] ; then
296	sequential=1; suff_exe='_seq'
297	else
298	sequential=0; suff_exe='_para_mem'
299	fi
300
301	#Chemin pour placer le modele
302	if [ "$MODEL" = "" ] ; then MODEL=./LMDZ$version$svn$optim ; fi
303
304
305	arch=local
306
307
308	if [ $compiler = g95 ] ; then echo g95 is not supported anymore ; exit ; fi
309
310	################################################################
311	# Specificite des machines
312	################################################################
313
314	hostname=`hostname`
315	if [ "$pclinux" = 1 ] ; then o_ins_make="-t g95" ; else o_ins_make="" ; fi
316
317	case ${hostname:0:5} in
318
319	jean-) compiler="mpiifort" ;
320	par_comp="mpiifort" ;
321	o_ins_make="-t jeanzay" ;
322	make=gmake ;
323	module purge
324	module load intel-compilers/19.0.4 ;
325	#module load intel-mpi/19.0.4 ;
326	#module load intel-mkl/19.0.4 ;
327	module load hdf5/1.10.5-mpi ;
328	module load netcdf/4.7.2-mpi ;
329	module load netcdf-fortran/4.5.2-mpi ;
330	module load subversion/1.9.7 ;
331	module load cmake
332	export NETCDF_LIBDIR=./
333	export NETCDFFORTRAN_INCDIR=./
334	export NETCDFFORTRAN_LIBDIR=./
335	arch=X64_JEANZAY ;;
336
337	cicla\|camel) compiler="gfortran" ;
338	module purge
339	module load gnu/10.2.0
340	module load openmpi/4.0.5
341	module load hdf5/1.10.7-mpi
342	module load netcdf-c/4.7.4-mpi
343	module load netcdf-fortran/4.5.3-mpi
344	netcdf=/net/nfs/tools/PrgEnv/linux-scientific6-x86_64/gcc-10.2.0/netcdf-fortran-4.5.3-k3drgfqok3lip62hnm3tsyof4cjen5sk
345	module load svn/1.14.0
346
347	if [ $parallel != none ] ; then
348	root_mpi=/net/nfs/tools/meso-sl6/openmpi/4.0.5-gcc-10.2.0
349	path_mpi=$root_mpi/bin ;
350	par_comp=${path_mpi}/mpif90 ;
351	mpirun=${path_mpi}/mpirun ;
352	fi ;
353	arch=local ;
354	make=make ;
355	o_ins_make="-t g95" ;;
356
357	*) if [ $parallel = none -o -f /usr/bin/mpif90 ] ; then
358	path_mpi=`which mpif90 \| sed -e s:/mpif90::` ;
359	if [ -d /usr/lib64/openmpi ] ; then
360	root_mpi="/usr/lib64/openmpi"
361	else
362	root_mpi="/usr"
363	fi
364	else
365	echo "Cannot find mpif90" ;
366	if [ $parallel = none ] ; then exit ; fi ;
367	fi ;
368	if [ $parallel != none ] ; then
369	root_mpi=$(which mpif90 \| sed -e s:/bin/mpif90::)
370	path_mpi=$(which mpif90 \| sed -e s:/mpif90::)
371	export LD_LIBRARY_PATH=${root_mpi}/lib:$LD_LIBRARY_PATH
372	fi
373	par_comp=${path_mpi}/mpif90 ;
374	mpirun=${path_mpi}/mpirun ;
375	arch=local ;
376	make=make ;
377	o_ins_make="-t g95"
378	esac
379
380	# Flags for parallelism:
381	if [ $parallel != none ] ; then
382	# MPI_LD are the flags needed for linking with MPI
383	MPI_LD="-L${root_mpi}/lib -lmpi"
384	if [ "$compiler" = "gfortran" ] ; then
385	# MPI_FLAGS are the flags needed for compilation with MPI
386	MPI_FLAGS="-fcray-pointer"
387	# OMP_FLAGS are the flags needed for compilation with OpenMP
388	OMP_FLAGS="-fopenmp -fcray-pointer"
389	# OMP_LD are the flags needed for linking with OpenMP
390	OMP_LD="-fopenmp"
391	elif [ "$compiler" = "ifort" ] ; then
392	MPI_FLAGS=""
393	OMP_FLAGS="-openmp"
394	OMP_LD="-openmp"
395	else # pgf90
396	MPI_FLAGS=""
397	OMP_FLAGS="-mp"
398	OMP_LD="-mp"
399	fi
400	fi
401
402	#####################################################################
403	# Test for old gfortran compilers
404	# If the compiler is too old (older than 4.3.x) we test if the
405	# temporary gfortran44 patch is available on the computer in which
406	# case the compiler is changed from gfortran to gfortran44
407	# Must be aware than parallelism can not be activated in this case
408	#####################################################################
409
410	if [ "$compiler" = "gfortran" ] ; then
411	gfortran=gfortran
412	gfortranv=`gfortran --version \| \
413	head -1 \| awk ' { print $NF } ' \| awk -F. ' { print $1 * 10 + $2 } '`
414	if [ $gfortranv -le 43 ] ; then
415	echo ERROR : Your gfortran compiler is too old
416	echo 'Please choose a new one (ifort) and change the line'
417	echo compiler=xxx
418	echo in the install_lmdz.sh script and rerun it
419	if [ `which gfortran44 \| wc -w` -ne 0 ] ; then
420	gfortran=gfortran44
421	else
422	echo gfotran trop vieux ; exit
423	fi
424	fi
425	compiler=$gfortran
426	fi
427	#####################################################################
428
429	## if also compiling XIOS, parallel must be mpi_omp
430	if [ "$with_xios" = "y" -a "$parallel" != "mpi_omp" ] ; then
431	echo "Error, you must set -parallel mpi_omp if you want XIOS"
432	exit
433	fi
434
435	if [ "$with_xios" = "y" ] ; then
436	opt_makelmdz_xios="-io xios"
437	fi
438
439	if [ "$cosp" = "v2" -a "$with_xios" = "n" ] ; then
440	echo "Error, Cospv2 cannot run without Xios"
441	exit
442	fi
443
444	echo '################################################################'
445	echo Choix des options de compilation
446	echo '################################################################'
447
448	export FC=$compiler
449	export F90=$compiler
450	export F77=$compiler
451	export CPPFLAGS=
452	OPTIMNC=$OPTIM
453	BASE_LD="$OPT_GPROF"
454	OPTPREC="$OPT_GPROF"
455	ARFLAGS="rs"
456	if [ "`lsb_release -i -s`" = "Ubuntu" ] ; then
457	if [ "`lsb_release -r -s \| cut -d. -f1`" -ge 16 ] ; then
458	ARFLAGS="rU"
459	fi
460	fi
461
462	if [ "$compiler" = "$gfortran" ] ; then
463	OPTIM="-O3 $allow_arg_mismatch"
464	OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all -fbacktrace -finit-real=snan $allow_arg_mismatch"
465	OPTDEV="-Wall -fbounds-check $allow_arg_mismatch"
466	fmod='I '
467	OPTPREC="$OPTPREC -cpp -ffree-line-length-0"
468	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE" ; fi
469	export F90FLAGS=" -ffree-form $OPTIMNC"
470	export FFLAGS=" $OPTIMNC"
471	export CC=gcc
472	export CXX=g++
473	export fpp_flags="-P -C -traditional -ffreestanding"
474
475	elif [ $compiler = mpif90 ] ; then
476	OPTIM='-O3'
477	OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all"
478	OPTDEV="-Wall -fbounds-check"
479	BASE_LD="$BASE_LD -lblas"
480	fmod='I '
481	if [ $real = r8 ] ; then
482	OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE -fcray-pointer"
483	fi
484	export F90FLAGS=" -ffree-form $OPTIMNC"
485	export FFLAGS=" $OPTIMNC"
486	export CC=gcc
487	export CXX=g++
488
489	elif [ $compiler = pgf90 ] ; then
490	OPTIM='-O2 -Mipa -Munroll -Mnoframe -Mautoinline -Mcache_align'
491	OPTDEB='-g -Mdclchk -Mbounds -Mchkfpstk -Mchkptr -Minform=inform -Mstandard -Ktrap=fp -traceback'
492	OPTDEV='-g -Mbounds -Ktrap=fp -traceback'
493	fmod='module '
494	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -r8 -DNC_DOUBLE" ; fi
495	export CPPFLAGS="-DpgiFortran"
496	export CC=pgcc
497	export CFLAGS="-O2 -Msignextend"
498	export CXX=pgCC
499	export CXXFLAGS="-O2 -Msignextend"
500	export FFLAGS="-O2 $OPTIMNC"
501	export F90FLAGS="-O2 $OPTIMNC"
502	compile_with_fcm=1
503
504	elif [[ $compiler = ifort \|\| $compiler = mpiifort ]] ; then
505	OPTIM="-O2 -fp-model strict -ip -align all "
506	OPTDEV="-p -g -O2 -traceback -fp-stack-check -ftrapuv -check"
507	OPTDEB="-g -no-ftz -traceback -ftrapuv -fp-stack-check -check"
508	fmod='module '
509	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -real-size 64 -DNC_DOUBLE" ; fi
510	export CPP="icc -E"
511	export FFLAGS="-O2 -ip -fpic -mcmodel=large"
512	export FCFLAGS="-O2 -ip -fpic -mcmodel=large"
513	export CC=icc
514	export CFLAGS="-O2 -ip -fpic -mcmodel=large"
515	export CXX=icpc
516	export CXXFLAGS="-O2 -ip -fpic -mcmodel=large"
517	export fpp_flags="-P -traditional"
518	# Pourquoi forcer la compilation fcm. Marche mieux sans
519	#compile_with_fcm=1
520	else
521	echo unexpected compiler $compiler ; exit
522	fi
523
524	OPTIMGCM="$OPTIM $OPTPREC"
525
526	hostname=`hostname`
527
528	##########################################################################
529	# If installing on known machines such as Jean-Zay at IDRIS,
530	# don't check for available software and don't install netcdf
531	if [ ${hostname:0:5} = jean- ] ; then
532	netcdf=0 # no need to recompile netcdf, alreday available
533	check_linux=0
534	pclinux=0
535	ioipsl=0 # no need to recompile ioipsl, already available
536	#netcdf="/smplocal/pub/NetCDF/4.1.3"
537	compiler="mpiifort"
538	fmod='module '
539	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -i4 -r8 -DNC_DOUBLE" ; fi
540	OPTIM="-auto -align all -O2 -fp-model strict -xHost "
541	OPTIMGCM="$OPTIM $OPTPREC"
542	fi
543	##########################################################################
544
545
546	mkdir -p $MODEL
547	echo $MODEL
548	MODEL=`( cd $MODEL ; pwd )` # to get absolute path, if necessary
549
550
551	if [ "$check_linux" = 1 ] ; then
552	echo '################################################################'
553	echo Check if required software is available
554	echo '################################################################'
555
556	#### Ehouarn: test if the required shell is available
557	#### Maj FH-LF-AS 2021-04 : default=bash ; if bash missing, use ksh
558	use_shell="bash" # default
559	if [ "`which bash`" = "" ] ; then
560	echo "no bash ; we will use ksh"
561	use_shell="ksh"
562	if [ "`which ksh`" = "" ] ; then
563	echo "bash (or ksh) needed!! Install it!"
564	exit
565	fi
566	fi
567
568	for logiciel in wget tar gzip make $compiler gcc cmake m4 c++ ; do
569	if [ "`which $logiciel`" = "" ] ; then
570	echo You must first install $logiciel on your system
571	exit
572	fi
573	done
574
575	if [ $pclinux = 1 ] ; then
576	cd $MODEL
577	cat <<eod > tt.f90
578	print*,'coucou'
579	end
580	eod
581	$compiler tt.f90 -o a.out
582	./a.out >\| tt
583	if [ "`cat tt \| sed -e 's/ //g' `" != "coucou" ] ; then
584	echo problem installing with compiler $compiler ; exit ; fi
585	\rm tt a.out tt.f90
586	fi
587	fi
588
589	###########################################################################
590	if [ $getlmdzor = 1 -a ! -d $MODEL/modipsl ] ; then
591	###########################################################################
592	echo '##########################################################'
593	echo Download a slightly modified version of LMDZ
594	echo '##########################################################'
595	cd $MODEL
596	getlog=`pwd`/get.log
597	echo logfile : $getlog
598	myget src_archives/$trusting/modipsl.$version.tar.gz >> get.log 2>&1
599	echo install_lmdz.sh wget_OK `date`
600	gunzip modipsl.$version.tar.gz >> get.log 2>&1
601	tar xf modipsl.$version.tar >> get.log 2>&1
602	\rm modipsl.$version.tar
603	fi
604
605	###########################################################################
606	if [ $netcdf = 1 ] ; then
607	###########################################################################
608	cd $MODEL
609	netcdflog=`pwd`/netcdf.log
610	echo '----------------------------------------------------------'
611	echo Compiling the Netcdf library
612	echo '----------------------------------------------------------'
613	echo log file : $netcdflog
614
615	case $compiler in
616	gfortran) opt1="-compiler gnu" ; opt2="-CC gcc -FC gfortran -CXX g++" ;;
617	ifort) opt1="-compiler intel" ; opt2="-CC icc -FC ifort -CXX icpc" ;;
618	pgf90) opt1="-compiler pgf90" ; opt2="-CC pgcc -FC pgf90 -CXX pgCC" ;;
619	*) echo "unexpected compiler $compiler" for netcdf ; exit 1
620	esac
621
622	case $with_xios in
623	n) script_install_netcdf=install_netcdf4_hdf5_seq.bash
624	ncdfdir=$MODEL/netcdf4_hdf5_seq
625	opt_=$opt1 ;;
626	y) script_install_netcdf=install_netcdf4_hdf5.bash
627	ncdfdir=$MODEL/netcdf4_hdf5
628	opt_="$opt2 -MPI $root_mpi" ;;
629	*) echo with_xios=$with_xios, should be n or y ; exit 1
630	esac
631
632	if [[ ! -d $ncdfdir ]] ; then
633	myget script_install/$script_install_netcdf >> $netcdflog 2>&1
634	chmod u=rwx $script_install_netcdf
635	./$script_install_netcdf -prefix $ncdfdir $opt_ >> $netcdflog 2>&1
636	fi
637
638	#----------------------------------------------------------------------------
639	# LF rajout d'une verrue, pour une raison non encore expliquee,
640	# la librairie est parfois rangée dans lib64 et non dans lib
641	# par certains compilateurs
642	if [ ! -e lib -a -d lib64 ] ; then ln -s lib64 lib; fi
643	#----------------------------------------------------------------------------
644
645	echo install_lmdz.sh netcdf_OK `date`
646
647	elif [ $netcdf = 0 ] ; then
648	ncdfdir=/usr
649	else
650	ncdfdir=$netcdf
651	fi
652
653	cat >test_netcdf90.f90 <<EOF
654	use netcdf
655	print *, "NetCDF library version: ", nf90_inq_libvers()
656	end
657	EOF
658
659	$compiler -I$ncdfdir/include test_netcdf90.f90 -L$ncdfdir/lib -lnetcdff \
660	-lnetcdf -Wl,-rpath=$ncdfdir/lib && ./a.out
661
662	if (($? == 0))
663	then
664	rm test_netcdf90.f90 a.out
665	else
666	echo "Failed test program using NetCDF-Fortran."
667	echo "You can:"
668	echo "- check that you have NetCDF-Fortran installed in your system"
669	echo "- or specify an installation directory with option -netcdf of" \
670	"install_lmdz.sh"
671	echo "- or download and compile NetCDF-Fortran with option -netcdf 1 of" \
672	"install_lmdz.sh"
673	exit 1
674	fi
675
676	#=========================================================================
677	if [[ ! -f $MODEL/modipsl/lib/libioipsl.a ]]
678	then
679	if [ $ioipsl = 1 ] ; then
680	#=====================================================================
681	echo OK ioipsl=$ioipsl
682	echo '##########################################################'
683	echo 'Installing MODIPSL, the installation package manager for the '
684	echo 'IPSL models and tools'
685	echo '##########################################################'
686	echo `date`
687
688	cd $MODEL/modipsl
689	\rm -rf lib/*
690	cd util
691	cp AA_make.gdef AA_make.orig
692	F_C="$compiler -c "
693	if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ]
694	then
695	F_C="$compiler -c -cpp "
696	fi
697	if [ "$compiler" = "pgf90" ] ; then F_C="$compiler -c -Mpreprocess" ; fi
698	sed -e 's/^\#..g95..\#.*.$/\#/' AA_make.gdef > tmp
699	sed -e "s:F_L = g95:F_L = $compiler:" \
700	-e "s:F_C = g95 -c -cpp:F_C = $F_C": \
701	-e 's/g95..w_w..(F_D)/g95 w_w = '"$OPTIMGCM"'/' \
702	-e 's:g95..NCDF_INC..$:g95 NCDF_INC= '"$ncdfdir"'/include:' \
703	-e 's:g95..NCDF_LIB..$:g95 NCDF_LIB= -L'"$ncdfdir"'/lib -lnetcdff -lnetcdf:' \
704	-e 's:g95 L_O =:g95 L_O = -Wl,-rpath='"$ncdfdir"'/lib:' \
705	-e "s:-fmod=:-$fmod:" -e 's/-fno-second-underscore//' \
706	-e 's:#-Q- g95 M_K = gmake:#-Q- g95 M_K = make:' \
707	tmp >\| AA_make.gdef
708
709	if [ $pcmac == 1 ]
710	then
711	cp AA_make.gdef tmp
712	sed -e 's/rpath=/rpath,/g' tmp > AA_make.gdef
713	fi
714
715
716	# We use lines for g95 even for the other compilers to run ins_make
717	if [ "$use_shell" = "ksh" ] ; then
718	./ins_make $o_ins_make
719	else # bash
720	sed -e s:/bin/ksh:/bin/bash:g ins_make > ins_make.bash
721	if [ "`grep jeanzay AA_make.gdef`" = "" ] ; then
722	# Bidouille pour compiler sur ada des vieux modipsl.tar
723	echo 'Warning jean-zay not in AA_make.gdef'
724	echo 'Think about updating'
725	exit 1
726	fi
727
728	chmod u=rwx ins_make.bash
729	./ins_make.bash $o_ins_make
730	fi # of if [ "$use_shell" = "ksh" ]
731
732	echo install_lmdz.sh MODIPSL_OK `date`
733
734	cd $MODEL/modipsl/modeles/IOIPSL/src
735	ioipsllog=`pwd`/ioipsl.log
736	echo '##########################################################'
737	echo 'Compiling IOIPSL, the interface library with Netcdf'
738	echo '##########################################################'
739	echo `date`
740	echo log file : $ioipsllog
741
742	if [ "$use_shell" = "bash" ] ; then
743	cp Makefile Makefile.ksh
744	sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile
745	fi
746	# if [ "$pclinux" = 1 ] ; then
747	# Build IOIPSL modules and library
748	$make clean
749	$make > $ioipsllog 2>&1
750	if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then
751	# copy module files to lib
752	cp -f *.mod ../../../lib
753	fi
754	# Build IOIPSL tools (ie: "rebuild", if present)
755	if [ -f $MODEL/modipsl/modeles/IOIPSL/tools/rebuild ] ; then
756	cd $MODEL/modipsl/modeles/IOIPSL/tools
757	# adapt Makefile & rebuild script if in bash
758	if [ "$use_shell" = "bash" ] ; then
759	cp Makefile Makefile.ksh
760	sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile
761	cp rebuild rebuild.ksh
762	sed -e 's:/bin/ksh:/bin/bash:g' \
763	-e 's:print -u2:echo:g' \
764	-e 's:print:echo:g' rebuild.ksh > rebuild
765	fi
766	$make clean
767	$make > $ioipsllog 2>&1
768	fi
769	# fi # of if [ "$pclinux" = 1 ]
770
771	else # of if [ "$pclinux" = 1 ]
772	if [ ${hostname:0:5} = jean- ] ; then
773	cd $MODEL/modipsl
774	cd util
775	if [ "`grep jeanzay AA_make.gdef`" = "" ] ; then
776	echo 'Warning jean-zay not in AA_make.gdef'
777	echo 'Think about updating'
778	exit 1
779	fi
780	./ins_make $o_ins_make
781	# Compile IOIPSL on jean-zay
782	cd $MODEL/modipsl/modeles/IOIPSL/src
783	gmake > ioipsl.log
784	if [ -f $MODEL/modipsl/modeles/IOIPSL/tools/rebuild ] ; then
785	cd $MODEL/modipsl/modeles/IOIPSL/tools
786	gmake > ioipsl.log
787	fi
788	fi
789	echo install_lmdz.sh ioipsl_OK `date`
790	fi # of if [ $ioipsl = 1 ]
791	fi
792
793	#=========================================================================
794	if [ "$with_xios" = "y" ] ; then
795	echo '##########################################################'
796	echo 'Compiling XIOS'
797	echo '##########################################################'
798	cd $MODEL/modipsl/modeles
799	xioslog=`pwd`/xios.log
800	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/install_xios.bash
801	myget script_install/install_xios.bash
802	chmod u=rwx install_xios.bash
803	if [ ${hostname:0:5} = jean- ] ; then
804	svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5 \
805	XIOS
806	cd XIOS/arch
807	svn update
808	cd ..
809	echo "Compiling XIOS, start" `date` \
810	"(it takes about 20 min on Jean-Zay)"
811	echo "log file: $xioslog"
812	./make_xios --prod --arch $arch --job 4 > xios.log 2>&1
813	else
814	./install_xios.bash -prefix $MODEL/modipsl/modeles \
815	-netcdf ${ncdfdir} -hdf5 ${ncdfdir} \
816	-MPI $root_mpi -arch $arch > xios.log 2>&1
817	fi # of case Jean-Zay
818	if [ -f XIOS/lib/libxios.a ] ; then
819	echo "XIOS library successfully generated"
820	echo install_lmdz.sh XIOS_OK `date`
821	fi
822	fi
823
824	#============================================================================
825	veget_version=false
826	if [ "$veget" != 'NONE' ] ; then
827	cd $MODEL/modipsl/modeles/ORCHIDEE
828	set +e ; svn upgrade ; set -e
829	if [ "$veget" = "CMIP6" ] ; then
830	veget_version=orchidee2.0
831	orchidee_rev=6592
832	else # specific orchidee revision newer than CMIP6, on 2_1 or 2_2 branches
833	veget_version=orchidee2.1
834	orchidee_rev=$veget
835	if [ $veget -lt 4465 ] ; then
836	echo 'Stopping, ORCHIDEE version too old, script needs work on ' \
837	'the CPP flags to pass to makelmdz'
838	exit 1
839	fi
840	set +e
841	# which branch is my version on?
842	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}'`
843	# switch to that branch
844	echo IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at \
845	orchidee-help@listes.ipsl.fr
846	svn switch -r $veget --accept theirs-full \
847	svn://forge.ipsl.jussieu.fr/orchidee/$orcbranch
848	svn log -r $veget \| grep $veget
849	if [ $? -gt 0 ] ; then
850	echo 'Cannot update ORCHIDEE as not on the right branch for ' \
851	'ORCHIDEE'
852	exit
853	fi
854	set -e
855	set +e ; svn update -r $veget ; set -e
856	fi
857	# Correctif suite debug Jean-Zay
858	sed -i -e 's/9010 FORMAT(A52,F17.14)/9010 FORMAT(A52,F20.14)/' \
859	src_stomate/stomate.f90
860	opt_orc="-prod" ; if [ "$optim" = "-debug" ] ; then opt_orc="-debug" ; fi
861
862	orchideelog=`pwd`/orchidee.log
863	echo '########################################################'
864	echo 'Compiling ORCHIDEE, the continental surface model '
865	echo '########################################################'
866	echo Start of the first compilation of orchidee, in sequential mode: `date`
867	echo log file : $orchideelog
868
869	export ORCHPATH=`pwd`
870	xios_orchid="-noxios"
871	if [ "$with_xios" = "y" ] ; then
872	xios_orchid="-xios"
873	fi
874	if [ -d tools ] ; then
875	###################################################################
876	# Pour les experts qui voudraient changer de version d'orchidee.
877	# Attention : necessite d'avoir le password pour orchidee
878
879	# Correctif suite debug Jean-Zay
880	if [ -f src_global/time.f90 ] ; then
881	sed -i -e 's/CALL tlen2itau/\!CALL tlen2itau/' src_global/time.f90
882	fi
883	###################################################################
884	if [ "$veget_version" == "false" ] ; then
885	veget_version=orchidee2.0
886	fi
887	cd arch
888	sed -e s:"%COMPILER .*.$":"%COMPILER $compiler":1 \
889	-e s:"%LINK .*.$":"%LINK $compiler":1 \
890	-e s:"%FPP_FLAGS .*.$":"%FPP_FLAGS $fpp_flags":1 \
891	-e s:"%PROD_FFLAGS .*.$":"%PROD_FFLAGS $OPTIM":1 \
892	-e s:"%DEV_FFLAGS .*.$":"%DEV_FFLAGS $OPTDEV":1 \
893	-e s:"%DEBUG_FFLAGS .*.$":"%DEBUG_FFLAGS $OPTDEB":1 \
894	-e s:"%BASE_FFLAGS .*.$":"%BASE_FFLAGS $OPTPREC":1 \
895	-e s:"%BASE_LD .*.$":"%BASE_LD $BASE_LD":1 \
896	-e s:"%ARFLAGS .*.$":"%ARFLAGS $ARFLAGS":1 \
897	arch-gfortran.fcm > arch-local.fcm
898	echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib -lnetcdff -lnetcdf\"" \
899	> arch-local.path
900	echo "NETCDF_INCDIR=${ncdfdir}/include" >> arch-local.path
901	echo "IOIPSL_INCDIR=$ORCHPATH/../../lib" >> arch-local.path
902	echo "IOIPSL_LIBDIR=$ORCHPATH/../../lib" >> arch-local.path
903	echo 'XIOS_INCDIR=${ORCHDIR}/../XIOS/inc' >> arch-local.path
904	echo 'XIOS_LIBDIR="${ORCHDIR}/../XIOS/lib -lxios"' >> arch-local.path
905	cd ../
906
907	echo ./makeorchidee_fcm -j $xios_orchid $opt_orc -parallel none \
908	-arch $arch
909	./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel none \
910	-arch $arch > $orchideelog 2>&1
911	pwd
912	else # of "if [ -d tools ]"
913	if [ -d src_parallel ] ; then
914	liste_src="parallel parameters global stomate sechiba driver"
915	if [ "$veget_version" == "false" ] ; then
916	veget_version=orchidee2.0
917	fi
918	fi
919	for d in $liste_src ; do
920	src_d=src_$d
921	echo src_d $src_d
922	echo ls ; ls
923	if [ ! -d $src_d ] ; then
924	echo Problem orchidee : no $src_d ; exit
925	fi
926	cd $src_d ; \rm -f *.mod make ; $make clean
927	$make > $orchideelog 2>&1
928	if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then
929	cp -f *.mod ../../../lib
930	fi
931	cd ..
932	done
933	fi # of "if [ -d tools ]"
934	echo install_lmdz.sh orchidee_compil_seq_OK `date`
935	fi # of if [ "$veget" != 'NONE' ]
936
937
938	#============================================================================
939	# Ehouarn: the directory name LMDZ* depends on version/tar file...
940	if [ -d $MODEL/modipsl/modeles/LMD* ] ; then
941	echo '###############################################################'
942	echo 'Preparing LMDZ compilation : arch file, svn switch if needed...'
943	echo '###############################################################'
944	cd $MODEL/modipsl/modeles/LMD*
945	LMDZPATH=`pwd`
946	else
947	echo "ERROR: No LMD* directory !!!"
948	exit
949	fi
950
951	###########################################################
952	# For those who want to use fcm to compile via :
953	# makelmdz_fcm -arch local .....
954	############################################################
955
956
957
958	cd $MODEL/modipsl/modeles/LMDZ*
959	lmdzlog=`pwd`/lmdz.log
960
961	##################################################################
962	# Possibly update LMDZ if a specific svn release is requested
963	##################################################################
964
965	set +e ; svn upgrade ; set -e
966
967	if [ "$svn" = "last" ] ; then svnopt="" ; else svnopt="-r $svn" ; fi
968	if [ "$svn" != "" ] ; then
969	set +e ; svn info \| grep -q 'http:'
970	if [ $? = 0 ] ; then
971	svn switch --relocate http://svn.lmd.jussieu.fr/LMDZ \
972	https://svn.lmd.jussieu.fr/LMDZ
973	fi
974	svn update $svnopt
975	set -e
976	fi
977
978	#---------------------------------------------------------------------
979	# Retrieve the final svn release number, and adjust compilation
980	# options accordingly
981	# If svn not available, will use the svn writen in $MODEL/Readm*md
982	# For old version it assumes that it is before 4185 (the version
983	# for which the test was introduced
984	#---------------------------------------------------------------------
985
986	set +e ; mysvn=`svnversion . \| egrep -o "[0-9]+" 2>/dev/null` ; set -e
987	if [ "$mysvn" = "" ] ; then mysvn=`grep 'Revision: [0-9]' $MODEL/Read*.md \| awk ' { print $2 } ' 2>/dev/null` ; fi
988	if [ "$mysvn" = "" ] ; then mysvn=4190 ; fi
989
990	if [[ "$pclinux" = "1" && ! -f arch/arch-local.path ]] ; then
991
992	# create local 'arch' files (if on Linux PC):
993	cd arch
994	# arch-local.path file
995	# test for version as arch.pth file changed format with rev 4426
996	if [ "$mysvn" -gt 4425 ] ; then
997	echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib \"" > arch-local.path
998	echo "NETCDF_LIB=\"-lnetcdff -lnetcdf\"" >> arch-local.path
999	echo "NETCDF_INCDIR=-I${ncdfdir}/include" >> arch-local.path
1000	echo 'NETCDF95_INCDIR=-I$LMDGCM/../../include' >> arch-local.path
1001	echo 'NETCDF95_LIBDIR=-L$LMDGCM/../../lib' >> arch-local.path
1002	echo 'NETCDF95_LIB=-lnetcdf95' >> arch-local.path
1003	echo 'IOIPSL_INCDIR=-I$LMDGCM/../../lib' >> arch-local.path
1004	echo 'IOIPSL_LIBDIR=-L$LMDGCM/../../lib' >> arch-local.path
1005	echo 'IOIPSL_LIB=-lioipsl' >> arch-local.path
1006	echo 'XIOS_INCDIR=-I$LMDGCM/../XIOS/inc' >> arch-local.path
1007	echo 'XIOS_LIBDIR=-L$LMDGCM/../XIOS/lib' >> arch-local.path
1008	echo "XIOS_LIB=\"-lxios -lstdc++\"" >> arch-local.path
1009	echo 'ORCH_INCDIR=-I$LMDGCM/../../lib' >> arch-local.path
1010	echo 'ORCH_LIBDIR=-L$LMDGCM/../../lib' >> arch-local.path
1011	else
1012	echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib -lnetcdff -lnetcdf\"" \
1013	> arch-local.path
1014	echo "NETCDF_INCDIR=-I${ncdfdir}/include" >> arch-local.path
1015	echo 'NETCDF95_INCDIR=$LMDGCM/../../include' >> arch-local.path
1016	echo 'NETCDF95_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
1017	echo 'IOIPSL_INCDIR=$LMDGCM/../../lib' >> arch-local.path
1018	echo 'IOIPSL_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
1019	echo 'XIOS_INCDIR=$LMDGCM/../XIOS/inc' >> arch-local.path
1020	echo 'XIOS_LIBDIR=$LMDGCM/../XIOS/lib' >> arch-local.path
1021	echo 'ORCH_INCDIR=$LMDGCM/../../lib' >> arch-local.path
1022	echo 'ORCH_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
1023	fi
1024
1025	if [ $pcmac == 1 ] ; then
1026	BASE_LD="$BASE_LD -Wl,-rpath,${ncdfdir}/lib"
1027	else
1028	BASE_LD="$BASE_LD -Wl,-rpath=${ncdfdir}/lib"
1029	fi
1030	# Arch-local.fcm file (adapted from arch-linux-32bit.fcm)
1031
1032	if [ $real = r8 ] ; then FPP_DEF=NC_DOUBLE ; else FPP_DEF="" ; fi
1033	sed -e s:"%COMPILER .*.$":"%COMPILER $compiler":1 \
1034	-e s:"%LINK .*.$":"%LINK $compiler":1 \
1035	-e s:"%PROD_FFLAGS .*.$":"%PROD_FFLAGS $OPTIM":1 \
1036	-e s:"%DEV_FFLAGS .*.$":"%DEV_FFLAGS $OPTDEV":1 \
1037	-e s:"%DEBUG_FFLAGS .*.$":"%DEBUG_FFLAGS $OPTDEB":1 \
1038	-e s:"%BASE_FFLAGS .*.$":"%BASE_FFLAGS $OPTPREC":1 \
1039	-e s:"%FPP_DEF .*.$":"%FPP_DEF $FPP_DEF":1 \
1040	-e s:"%BASE_LD .*.$":"%BASE_LD $BASE_LD":1 \
1041	-e s:"%ARFLAGS .*.$":"%ARFLAGS $ARFLAGS":1 \
1042	arch-linux-32bit.fcm > arch-local.fcm
1043
1044	cd ..
1045	### Adapt "bld.cfg" (add the shell):
1046	#whereisthatshell=$(which ${use_shell})
1047	#echo "bld::tool::SHELL $whereisthatshell" >> bld.cfg
1048
1049	fi # of if [ "$pclinux" = 1 ]
1050	#---------------------------------------------------------------------
1051	# Option de compilation du rayonnement : depend de $mysvn ><= r4185
1052	#---------------------------------------------------------------------
1053	opt_rad=""
1054
1055	case $rad in
1056	oldrad) iflag_rrtm=0 ; NSW=2 ; opt_rad="" ;;
1057	rrtm) iflag_rrtm=1 ; NSW=6
1058	if [ $mysvn -le 4185 ] ; then
1059	opt_rad="-rrtm true"
1060	else
1061	opt_rad="-rad rrtm"
1062	fi ;;
1063	ecrad) iflag_rrtm=2 ; NSW=6 ; opt_rad="-rad ecrad" ;;
1064	*) echo Only oldrad rrtm ecrad for rad option ; exit
1065	esac
1066
1067	if [ $mysvn -le 4185 -a $rad = "ecrad" ] ; then
1068	echo "ecrad only available for LMDZ rev starting with 4186 " ; exit
1069	fi
1070
1071	##################################################################
1072
1073
1074	if [[ ! -f libf/misc/netcdf95.F90 && ! -d $MODEL/NetCDF95-0.2 ]]
1075	then
1076	cd $MODEL
1077	myget src_archives/netcdf/NetCDF95-0.2.tar.gz
1078	tar -xf NetCDF95-0.2.tar.gz
1079	rm NetCDF95-0.2.tar.gz
1080	cd NetCDF95-0.2
1081	mkdir build
1082	cd build
1083	cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=$ncdfdir \
1084	-DCMAKE_INSTALL_PREFIX=$MODEL/modipsl
1085	make install
1086	cd $MODEL/modipsl/modeles/LMDZ*
1087	fi
1088
1089	echo '##################################################################'
1090	echo "Preparing script compile.sh for LMDZ compilation"
1091	echo "It will only be run automatically if bench=1/tuto"
1092	echo Here bench=$bench
1093	echo '##################################################################'
1094
1095	if [ "$env_file" != "" ] ; then
1096	mv arch/arch-${arch}.env arch/arch-${arch}.orig
1097	\cp -f $env_file arch/arch-${arch}.env
1098	fi
1099
1100	if [ $compile_with_fcm = 1 ] ; then
1101	makelmdz="makelmdz_fcm $optim -arch $arch -j 8 "
1102	else
1103	makelmdz="makelmdz $optim -arch $arch"
1104	fi
1105
1106	# sequential compilation
1107	if [ "$sequential" = 1 ] ; then
1108	echo Sequential compilation command, saved in compile.sh:
1109	echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp " \
1110	"-d ${grid_resolution} -v $veget_version gcm "
1111	echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp " \
1112	"-d ${grid_resolution} -v $veget_version gcm " > compile.sh
1113	chmod +x ./compile.sh
1114	if [ $bench = 1 ] ; then
1115	echo install_lmdz.sh start_lmdz_seq_compilation `date`
1116	echo log file: $lmdzlog
1117	./compile.sh > $lmdzlog 2>&1
1118	echo install_lmdz.sh end_lmdz_seq_compilation `date`
1119	fi
1120	fi # fin sequential
1121
1122	# compiling in parallel mode
1123	if [ $parallel != "none" ] ; then
1124	echo '##########################################################'
1125	echo ' Parallel compile '
1126	echo '##########################################################'
1127	echo "(after saving the sequential libs and binaries)"
1128	cd $MODEL/modipsl
1129	tar cf sequential.tar bin/ lib/
1130	#
1131	# Orchidee
1132	#
1133	cd $ORCHPATH
1134	if [ -d src_parallel -a $veget != 'NONE' ] ; then
1135	cd arch
1136	sed \
1137	-e s:"%COMPILER.*.$":"%COMPILER $par_comp":1 \
1138	-e s:"%LINK.*.$":"%LINK $par_comp":1 \
1139	-e s:"%MPI_FFLAG.*.$":"%MPI_FFLAGS $MPI_FLAGS":1 \
1140	-e s:"%OMP_FFLAG.*.$":"%OMP_FFLAGS $OMP_FLAGS":1 \
1141	-e s:"%MPI_LD.*.$":"%MPI_LD $MPI_LD":1 \
1142	-e s:"%OMP_LD.*.$":"%OMP_LD $OMP_LD":1 \
1143	arch-local.fcm > tmp.fcm
1144
1145	mv tmp.fcm arch-local.fcm
1146	cd ../
1147	echo Compiling ORCHIDEE in parallel mode `date`
1148	echo logfile $orchideelog
1149	echo "NOTE : to recompile it when necessary, use ./compile_orc.sh " \
1150	"in modipsl/modeles/ORCHIDEE"
1151	echo ./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc \
1152	-parallel $parallel -arch $arch > compile_orc.sh
1153	echo ./makeorchidee_fcm -j 8 $xios_orchid $opt_orc \
1154	-parallel $parallel -arch $arch >> compile_orc.sh
1155	echo echo Now you must also recompile LMDZ, by running ./compile.sh \
1156	in modeles/LMDZ >> compile_orc.sh
1157	chmod u+x compile_orc.sh
1158	./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc \
1159	-parallel $parallel -arch $arch > $orchideelog 2>&1
1160	./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel $parallel \
1161	-arch $arch >> $orchideelog 2>&1
1162	echo End of ORCHIDEE compilation in parallel mode `date`
1163	elif [ $veget != 'NONE' ] ; then
1164	echo '##########################################################'
1165	echo ' Orchidee version too old '
1166	echo ' Please update to new version '
1167	echo '##########################################################'
1168	exit
1169	fi # of [ -d src_parallel -a $veget != 'NONE' ]
1170
1171	# LMDZ
1172	cd $LMDZPATH
1173	if [ $arch = local ] ; then
1174	cd arch
1175	sed -e s:"%COMPILER.*.$":"%COMPILER $par_comp":1 \
1176	-e s:"%LINK.*.$":"%LINK $par_comp":1 \
1177	-e s:"%MPI_FFLAG.*.$":"%MPI_FFLAGS $MPI_FLAGS":1 \
1178	-e s:"%OMP_FFLAG.*.$":"%OMP_FFLAGS $OMP_FLAGS":1 \
1179	-e s:"%ARFLAGS.*.$":"%ARFLAGS $ARFLAGS":1 \
1180	-e s@"%BASE_LD.*.$"@"%BASE_LD -Wl,-rpath=${root_mpi}/lib:${ncdfdir}/lib"@1 \
1181	-e s:"%MPI_LD.*.$":"%MPI_LD $MPI_LD":1 \
1182	-e s:"%OMP_LD.*.$":"%OMP_LD $OMP_LD":1 \
1183	arch-local.fcm > tmp.fcm
1184	mv tmp.fcm arch-local.fcm
1185	cd ../
1186	fi
1187	rm -f compile.sh
1188	echo resol=${grid_resolution} >> compile.sh
1189	if [ ${hostname:0:5} = jean- -a "$cosp" = "v2" ] ; then
1190
1191	echo LMDZ compilation command in parallel mode, saved in compile.sh, \
1192	is :
1193	echo "(ATTENTION le probleme de cospv2 sur jean-zay en mode prod " \
1194	"n est pas corrige ! )"
1195	# ATTENTION le probleme de cospv2 sur jean-zay en mode prod n
1196	# est pas corrige
1197	echo ./$makelmdz -dev $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
1198	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
1199	-parallel $parallel gcm >> compile.sh
1200	echo ./$makelmdz -dev $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
1201	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
1202	-parallel $parallel gcm
1203	else
1204	echo ./$makelmdz $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
1205	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
1206	-parallel $parallel gcm >> compile.sh
1207	echo ./$makelmdz $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
1208	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
1209	-parallel $parallel gcm
1210	fi
1211	chmod +x ./compile.sh
1212
1213	if [ $bench = 1 ] ; then
1214	echo Compiling LMDZ in parallel mode `date`, LMDZ log file: $lmdzlog
1215	./compile.sh > $lmdzlog 2>&1
1216	fi
1217
1218	fi # of if [ $parallel != "none" ]
1219
1220
1221	##################################################################
1222	# Verification du succes de la compilation
1223	##################################################################
1224
1225	# Recherche de l'executable dont le nom a change au fil du temps ...
1226	# suffix contains radiative option starting with revision 4186
1227	if [ $mysvn -ge 4186 ] ; then suff_exe=_${rad}${suff_exe} ; fi
1228	gcm=""
1229
1230	for exe in gcm.e bin/gcm_${grid_resolution}_phylmd${suff_exe}${suff_orc}.e
1231	do
1232	if [ -f $exe ] ; then gcm=$exe ; fi
1233	done
1234
1235	if [ "$gcm" = "" ] ; then
1236	if [ $bench = 1 ] ; then
1237	echo 'Compilation failed !! Cannot run the benchmark;'
1238	exit
1239	else
1240	echo 'Compilation not done (only done when bench=1)'
1241	fi
1242	else
1243	echo '##########################################################'
1244	echo 'Compilation successfull !! ' `date`
1245	echo '##########################################################'
1246	echo The executable is $gcm
1247	fi
1248
1249	##################################################################
1250	# Below, we run a benchmark if bench=1 or tuto
1251	##################################################################
1252
1253	if [ $bench = tuto ] ; then
1254	myget Training/tutorial.tar ; tar xf tutorial.tar ; cd TUTORIAL
1255	./init.sh
1256
1257	elif [[ $bench = 1 && ! -d BENCH${grid_resolution} ]] ; then
1258	# TOUTE CETTE SECTION DEVRAIT DISPARAITRE POUR UNE COMMANDE
1259	# OU DES BENCHS PAR MOTS CLES COMME tuto
1260
1261	echo '##########################################################'
1262	echo ' Running a test run '
1263	echo '##########################################################'
1264
1265	\rm -rf BENCH${grid_resolution}
1266	bench=bench_lmdz_${grid_resolution}
1267	echo install_lmdz.sh before bench download `date`
1268	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/$bench.tar.gz
1269	myget 3DBenchs/$bench.tar.gz
1270	echo install_lmdz.sh after bench download `date`
1271	tar xf $bench.tar.gz
1272
1273	if [ "$cosp" = "v1" -o "$cosp" = "v2" ] ; then
1274	cd BENCH${grid_resolution}
1275	# copier les fichiers namelist input et output our COSP
1276	cp ../DefLists/cosp*_input_nl.txt .
1277	cp ../DefLists/cosp*_output_nl.txt .
1278	# Activer la cles ok_cosp pour tourner avec COSP
1279	sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp
1280	\mv -f tmp config.def
1281	cd ..
1282	fi
1283
1284	if [ -n "$physiq" ]; then
1285	cd BENCH${grid_resolution}
1286	if [ -f physiq.def_${physiq} ]; then
1287	cp physiq.def_${physiq} physiq.def
1288	echo using physiq.def_${physiq}
1289	else
1290	echo using standard physiq.def
1291	fi
1292	cd ..
1293	else
1294	echo using standard physiq.def
1295	fi
1296
1297	if [ "$with_xios" = "y" ] ; then
1298	cd BENCH${grid_resolution}
1299	cp ../DefLists/iodef.xml .
1300	cp ../DefLists/context_lmdz.xml .
1301	cp ../DefLists/field_def_lmdz.xml .
1302	# A raffiner par la suite
1303	echo A FAIRE : Copier les *xml en fonction de l option cosp
1304	cp ../DefLists/field_def_cosp*.xml .
1305	cp ../DefLists/file_def_hist*xml .
1306	# adapt iodef.xml to use attached mode
1307	sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' \
1308	iodef.xml > tmp
1309	\mv -f tmp iodef.xml
1310
1311	# and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
1312	# except for histday
1313	for histfile in file_def_hist*xml
1314	do
1315	if [ "$histfile" = "file_def_histday_lmdz.xml" ] ; then
1316	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' \
1317	$histfile > tmp
1318	\mv -f tmp $histfile
1319	sed -e 's@output_level="_AUTO_"@output_level="5"@' $histfile \
1320	> tmp
1321	\mv -f tmp $histfile
1322	sed -e 's@compression_level="2"@compression_level="0"@' \
1323	$histfile > tmp
1324	\mv -f tmp $histfile
1325	else
1326	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
1327	$histfile > tmp
1328	\mv -f tmp $histfile
1329	fi
1330	done
1331	# and add option "ok_all_xml=y" in config.def
1332	echo "### XIOS outputs" >> config.def
1333	echo 'ok_all_xml=.true.' >> config.def
1334
1335	#activer les sorties pour Cosp
1336	if [ "$cosp" = "v1" ] ; then
1337	histfile=file_def_histdayCOSP_lmdz.xml
1338	sed -e 's@enabled=".FALSE."@enabled=".TRUE."@' $histfile > tmp
1339	\mv -f tmp $histfile
1340	sed -e 's@output_level="_AUTO_"@output_level="5"@' $histfile > tmp
1341	\mv -f tmp $histfile
1342	sed -e 's@compression_level="2"@compression_level="0"@' \
1343	$histfile > tmp
1344	\mv -f tmp $histfile
1345	fi
1346	if [ "$cosp" = "v2" ] ; then
1347	histfile=file_def_histdayCOSPv2_lmdz.xml
1348	sed -e 's@compression_level="2"@compression_level="0"@' \
1349	$histfile > tmp
1350	\mv -f tmp $histfile
1351	contextfile=context_lmdz.xml
1352	sed -e 's@src="./file_def_histdayCOSP_lmdz.xml"@src="./file_def_histdayCOSPv2_lmdz.xml"@' \
1353	$contextfile > tmp
1354	\mv -f tmp $contextfile
1355	sed -e 's@src="./file_def_histmthCOSP_lmdz.xml"@src="./file_def_histmthCOSPv2_lmdz.xml"@' \
1356	$contextfile > tmp
1357	\mv -f tmp $contextfile
1358	sed -e 's@src="./file_def_histhfCOSP_lmdz.xml"@src="./file_def_histhfCOSPv2_lmdz.xml"@' \
1359	$contextfile > tmp
1360	\mv -f tmp $contextfile
1361	fieldfile=field_def_lmdz.xml
1362	sed -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' $fieldfile \
1363	> tmp
1364	\mv -f tmp $fieldfile
1365	fi
1366
1367	cd ..
1368	fi
1369
1370	# Cas Bensh avec ecrad
1371	if [ "$rad" = "ecrad" ] ; then
1372	cd BENCH${grid_resolution}
1373	cp ../DefLists/namelist_ecrad .
1374	cp -r ../libf/phylmd/ecrad/data .
1375	cd ..
1376	fi
1377
1378	# Adjusting bench physiq.def to radiative code chosen
1379	cd BENCH${grid_resolution}
1380	sed -e 's/iflag_rrtm=.*.$/iflag_rrtm='$iflag_rrtm'/' \
1381	-e 's/NSW=.*.$/NSW='$NSW'/' physiq.def > tmpdef
1382	\mv tmpdef physiq.def
1383	cd ..
1384
1385	cp $gcm BENCH${grid_resolution}/gcm.e
1386
1387	cd BENCH${grid_resolution}
1388	# On cree le fichier bench.sh au besoin
1389	# Dans le cas 48x36x39 le bench.sh existe deja en parallele
1390
1391	if [ "$grid_resolution" = "48x36x39" ] ; then
1392	echo On ne touche pas au bench.sh
1393	# But we have to adapt "run_local.sh" for $mpirun
1394	sed -e "s@mpirun@$mpirun@g" run_local.sh > tmp
1395	mv -f tmp run_local.sh
1396	chmod u=rwx run_local.sh
1397	elif [ "${parallel:0:3}" = "mpi" ] ; then
1398	# Lancement avec deux procs mpi et 2 openMP
1399	echo "export OMP_STACKSIZE=800M" > bench.sh
1400	if [ "${parallel:4:3}" = "omp" ] ; then
1401	echo "export OMP_NUM_THREADS=2" >> bench.sh
1402	fi
1403	if [ "$cosp" = "v1" -o "$cosp" = "v2" ] ; then
1404	if [ ${hostname:0:5} = jean- ] ; then
1405	chmod +x ../arch.env
1406	../arch.env
1407	echo "ulimit -s 2000000" >> bench.sh
1408	else
1409	echo "ulimit -s 200000" >> bench.sh
1410	fi
1411	else
1412	echo "ulimit -s unlimited" >> bench.sh
1413	fi
1414	if [ ${hostname:0:5} = jean- ] ; then
1415	. ../arch/arch-${arch}.env
1416	echo "srun -n 2 -A $idris_acct@cpu gcm.e > listing 2>&1" \
1417	>> bench.sh
1418	else
1419	echo "$mpirun -np 2 gcm.e > listing 2>&1" >> bench.sh
1420	fi
1421	# Add rebuild, using reb.sh if it is there
1422	echo 'if [ -f reb.sh ] ; then' >> bench.sh
1423	echo ' ./reb.sh histday ; ./reb.sh histmth ; ./reb.sh histhf ; ' \
1424	'./reb.sh histins ; ./reb.sh stomate_history ; ' \
1425	'./reb.sh sechiba_history ; ./reb.sh sechiba_out_2 ' >> bench.sh
1426	echo 'fi' >> bench.sh
1427	else
1428	echo "./gcm.e > listing 2>&1" > bench.sh
1429	fi
1430	# Getting orchidee stuff
1431	if [ $veget == 'CMIP6' ] ; then
1432	#echo 'myget 3DBenchs/BENCHorch11.tar.gz'
1433	#myget 3DBenchs/BENCHorch11.tar.gz
1434	#tar xvzf BENCHorch11.tar.gz
1435	echo 'myget 3DBenchs/BENCHCMIP6.tar.gz'
1436	myget 3DBenchs/BENCHCMIP6.tar.gz
1437	tar xvzf BENCHCMIP6.tar.gz
1438	sed -e "s:VEGET=n:VEGET=y:" config.def > tmp
1439	mv -f tmp config.def
1440	if [ "$with_xios" = "y" ] ; then
1441	cp ../../ORCHIDEE/src_xml/context_orchidee.xml .
1442	echo '<context id="orchidee" src="./context_orchidee.xml"/>' \
1443	> add.tmp
1444	cp ../../ORCHIDEE/src_xml/field_def_orchidee.xml .
1445	cp ../../ORCHIDEE/src_xml/file_def_orchidee.xml .
1446	cp ../../ORCHIDEE/src_xml/file_def_input_orchidee.xml .
1447	if [ -f ../../ORCHIDEE/src_xml/context_input_orchidee.xml ] ; then
1448	cp ../../ORCHIDEE/src_xml/context_input_orchidee.xml .
1449	echo '<context id="orchidee" ' \
1450	'src="./context_input_orchidee.xml"/>' >> add.tmp
1451	fi
1452	sed -e '/id="LMDZ"/r add.tmp' iodef.xml > tmp
1453	mv tmp iodef.xml
1454	sed -e'{/sechiba1/ s/enabled="_AUTO_"/type="one_file" enabled=".TRUE."/}' \
1455	file_def_orchidee.xml > tmp
1456	\mv -f tmp file_def_orchidee.xml
1457	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
1458	file_def_orchidee.xml > tmp
1459	\mv -f tmp file_def_orchidee.xml
1460	sed -e 's@output_level="_AUTO_"@output_level="1"@' \
1461	file_def_orchidee.xml > tmp
1462	\mv -f tmp file_def_orchidee.xml
1463	sed -e 's@output_freq="_AUTO_"@output_freq="1d"@' \
1464	file_def_orchidee.xml > tmp
1465	\mv -f tmp file_def_orchidee.xml
1466	sed -e 's@compression_level="4"@compression_level="0"@' \
1467	file_def_orchidee.xml > tmp
1468	\mv -f tmp file_def_orchidee.xml
1469	sed -e 's@XIOS_ORCHIDEE_OK = n@XIOS_ORCHIDEE_OK = y@' \
1470	orchidee.def > tmp
1471	\mv -f tmp orchidee.def
1472	fi
1473	fi
1474
1475	if [[ -f ../arch.env ]]
1476	then
1477	source ../arch.env
1478	fi
1479
1480	echo EXECUTION DU BENCH
1481	set +e
1482	date ; ./bench.sh > out.bench 2>&1 ; date
1483	set -e
1484	tail listing
1485
1486
1487	echo '##########################################################'
1488	echo 'Simulation finished in' `pwd`
1489	echo 'You have compiled with:'
1490	cat ../compile.sh
1491	if [ $parallel = "none" ] ; then
1492	echo 'You may re-run it with : cd ' `pwd` ' ; gcm.e'
1493	echo 'or ./bench.sh'
1494	else
1495	echo 'You may re-run it with : '
1496	echo 'cd ' `pwd` '; ./bench.sh'
1497	# echo 'ulimit -s unlimited'
1498	# echo 'export OMP_NUM_THREADS=2'
1499	# echo 'export OMP_STACKSIZE=800M'
1500	# echo "$mpirun -np 2 gcm.e "
1501	fi
1502	echo '##########################################################'
1503
1504	fi # bench
1505
1506
1507	#################################################################
1508	# Installation eventuelle du 1D
1509	#################################################################
1510
1511	if [ $SCM = 1 ] ; then
1512	cd $MODEL
1513	myget 1D/1D.tar.gz
1514	tar xf 1D.tar.gz
1515	cd 1D
1516	if [ $rad = oldrad ] ; then
1517	sed -i'' -e 's/^rad=.*$/rad=oldrad/' run.sh
1518	sed -i'' -e 's/^rad=.*$/rad=oldrad/' bin/compile
1519	fi
1520	echo Running 1D/run.sh, log in `pwd`/run1d.log
1521	./run.sh > `pwd`/run1d.log 2>&1
1522	fi
1523
1524
1525	#################################################################
1526	# sauvegarde des options veget pour utilisation eventuelle tutorial_prod
1527	#################################################################
1528	cd $MODEL/modipsl/modeles
1529	#echo surface_env file created in $MODEL
1530	echo 'veget='$veget > surface_env
1531	#opt_veget="-v $veget_version"
1532	#echo 'opt_veget="'$opt_veget\" >> surface_env
1533	echo 'opt_veget="'-v $veget_version\" >> surface_env
1534	echo 'orchidee_rev='$orchidee_rev >> surface_env
1535	echo 'suforch='$suff_orc >> surface_env

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