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source: BOL/script_install/install_lmdz.sh @ 4372

Last change on this file since 4372 was 4372, checked in by fhourdin, 18 months ago

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1	#!/bin/bash
2
3	#set -vx
4
5	###########################################################################
6	# Author : Laurent Fairhead et Frédéric Hourdin
7	# Usage : install_lmdz.sh -help
8	#
9	# bash installation script of the LMDZ model on different computer types :
10	# Linux PC, "mesocentre" (IPSL-UPMC, IPSL-X), super-computer (IDRIS)
11	#
12	# The model is downloaded in the following directory tree
13	# $MODEL/modipsl/modeles/...
14	# using the "modipsl" infrastructure created by the "IPSL"
15	# for coupled (atmosphere/ocean/vegetation/chemistry) climate modeling
16	# activities.
17	# Here we only download atmospheric (LMDZ) and vegetation (ORCHIDEE)
18	# components.
19	#
20	# The sources of the models can be found in the "modeles" directory.
21	# In the present case, LMDZ, ORCHIDEE, and IOIPSL or XIOS (handling of
22	# input-outputs using the NetCDF library).
23	#
24	# The script downloads various source files (including a version of NetCDF)
25	# and utilities, compiles the model, and runs a test simulation in a
26	# minimal configuration.
27	#
28	# Prerequisites : pgf90/gfortran, bash or ksh, wget , gunzip, tar, ...
29	#
30	# Modif 18/11/2011
31	# changes for option real 8.
32	# We compile with -r8 (or equivalent) and -DNC_DOUBLE for the GCM
33	# but with -r4 for netcdf. Variable real must be set to
34	# r4 or r8 at the beginning of the script below.
35	#
36	###########################################################################
37
38	echo install_lmdz.sh DEBUT `date`
39	set -e
40
41	################################################################
42	# Choice of installation options
43	################################################################
44
45	################################################################
46	# A function to fetch files either locally or on the internet
47	################################################################
48	function myget { #1st and only argument should be file name
49	# Path on local computer where to look for the datafile
50	if [ -f /u/lmdz/WWW/LMDZ/pub/$1 ] ; then
51	\cp -f -p /u/lmdz/WWW/LMDZ/pub/$1 .
52	elif [ -f ~/LMDZ/pub/$1 ] ; then
53	\cp -f -p ~/LMDZ/pub/$1 .
54	else
55	wget --no-check-certificate -nv http://lmdz.lmd.jussieu.fr/pub/$1
56	save_pub_locally=0
57	if [ $save_pub_locally = 1 ] ; then # saving wget files on ~/LMDZ/pub
58	dir=~/LMDZ/pub/`dirname $1` ; mkdir -p $dir
59	cp -r `basename $1` $dir
60	fi
61	fi
62	}
63
64	# 04_2021 : tester si r4 marche encore !
65	#real=r4
66	real=r8
67
68
69	#########################################################################
70	# Valeur par défaut des parametres
71	#########################################################################
72	svn=""
73	#version=trunk
74	version=20221028.trunk
75
76	getlmdzor=1
77	netcdf=1 # 1: for automatic installation;
78	# or 0: do not install NetCDF and look for it in standard locations;
79	# or absolute path: look for NetCDF there
80	check_linux=1
81	ioipsl=1
82	bench=1
83	pclinux=1
84	pcmac=0 # default: not on a Mac
85	compiler=gfortran
86	if [ `gfortran -dumpversion \| cut -d. -f1` -ge 11 ] ; then allow_arg_mismatch="-fallow-argument-mismatch" ; fi
87	SCM=0
88	# surface/vegetation scheme treatment
89	# controlled by the single variable veget which can have the following values
90	# - NONE: bucket scheme (default)
91	# - CMIP6: orchidee version used in CMIP exercise, rev 5661
92	# - number: orchidee version number
93	veget=NONE
94	# choose the resolution for the bench runs
95	# grid_resolution= 32x24x11 or 48x36x19 for tests (test without ORCHIDEE)
96	# 96x71x19 standard configuration
97	grid_resolution=144x142x79
98	grid_resolution=96x95x39
99	grid_resolution=48x36x19
100	grid_resolution=32x32x39
101	# choose the physiq version you want to test
102	#physiq=NPv6.0.14splith
103	physiq=
104
105	## parallel can take the values none/mpi/omp/mpi_omp
106	parallel=mpi_omp
107	parallel=none
108	idris_acct=lmd
109	OPT_GPROF=""
110	OPT_MAKELMDZ=""
111	MODEL=""
112
113	## also compile XIOS? (and more recent NetCDF/HDF5 libraries) Default=no
114	with_xios="n"
115	opt_makelmdz_xios=""
116
117	## compile with oldrad/rrtm/ecrad radiatif code (Default=rrtm)
118	rad=rrtm
119
120	## compile_with_fcm=1 : use makelmdz_fcm (1) or makelmdz (0)
121	compile_with_fcm=1
122
123	#Compilation with Cosp (cosp=NONE/v1/v2 ; default=NONE)
124	cosp=NONE
125	opt_cosp=""
126
127	# Check if on a Mac
128	if [ `uname` = "Darwin" ]
129	then
130	pcmac=1
131	export MAKE=make
132	fi
133	#echo "pcmac="$pcmac
134
135	env_file=""
136
137	#########################################################################
138	# Options interactives
139	#########################################################################
140	while (($# > 0))
141	do
142	case $1 in
143	"-h") cat <<........fin
144	$0 [ -v version ] [ -r svn_release ]
145	[ -parallel PARA ] [ -d GRID_RESOLUTION ] [ -bench 0/1 ]
146	[-name LOCAL_MODEL_NAME] [-gprof] [-opt_makelmdz] [-rad RADIATIF]
147
148	-v "version" like 20150828.trunk
149	see http://www.lmd.jussieu.fr/~lmdz/Distrib/LISMOI.trunk
150
151	-r "svn_release" : either the svn release number or "last"
152
153	-compiler gfortran\|ifort\|pgf90 (default: gfortran)
154
155	-parallel PARA : can be mpi_omp (mpi with openMP) or none (for sequential)
156
157	-d GRID_RESOLUTION should be among the available benchs if -bench 1
158	among which : 48x36x19, 48x36x39
159	if wanting to run a bench simulation in addition to compilation
160	default : 48x36x19
161
162	-bench activating the bench or not (0/1). Default 1
163
164	-name LOCAL_MODEL_NAME : default = LMDZversion.release
165
166	-netcdf 0, 1 or PATH
167	0: do not download NetCDF, look for it in standard locations
168	1: download and compile NetCDF
169	PATH: full path to an existing installed NetCDF library
170
171	-xios also download and compile the XIOS library
172	(requires the NetCDF4-HDF5 library, also installed by default)
173	(requires to also have -parallel mpi_omp)
174
175	-gprof to compile with -pg to enable profiling with gprof
176
177	-cosp to run without our with cospv1 or cospv2 [none/v1/v2]
178
179	-rad RADIATIF can be oldrad, rrtm or ecrad radiatif code
180
181	-nofcm to compile without fcm
182
183	-SCM install 1D version automatically
184
185	-debug compile everything in debug mode
186
187	-opt_makelmdz to call makelmdz or makelmdz_fcm with additional options
188
189	-physiq to choose which physics package to use
190
191	-env_file specify an arch.env file to overwrite the existing one
192
193	-veget surface model to run [NONE/CMIP6/xxxx]
194
195	........fin
196	exit ;;
197	"-v") version=$2 ; shift ; shift ;;
198	"-r") svn=$2 ; shift ; shift ;;
199	"-compiler") compiler=$2
200	case $compiler in
201	"gfortran"\|"ifort"\|"pgf90") compiler=$2 ; shift
202	shift ;;
203	*) echo "Only gfortran , ifort or pgf90 for the " \
204	"compiler option"
205	exit
206	esac ;;
207	"-d") grid_resolution=$2 ; shift ; shift ;;
208	"-gprof") OPT_GPROF="-pg" ; shift ;;
209	"-cosp") cosp=$2
210	case $cosp in
211	"none"\|"v1"\|"v2") cosp=$2 ; shift ; shift ;;
212	*) echo Only none v1 v2 for cosp option ; exit
213	esac ;;
214	"-nofcm") compile_with_fcm=0 ; echo This option will be reactivated soon '(promesse du 8dec2022)' ; exit 1 ; shift ;;
215	"-SCM") SCM=1 ; shift ;;
216	"-opt_makelmdz") OPT_MAKELMDZ="$2" ; shift ; shift ;;
217	"-rrtm") rrtm="$2"
218	if [ "$2" = "false" ] ; then
219	rad="oldrad"
220	else
221	rad="rrtm"
222	fi
223	shift ; shift ;;
224	"-rad") rad=$2
225	case $rad in
226	"oldrad"\|"rrtm"\|"ecrad") rad=$2 ; shift ; shift ;;
227	*) echo Only oldrad rrtm ecrad for rad option ; exit
228	esac ;;
229	"-parallel") parallel=$2
230	case $parallel in
231	"none"\|"mpi"\|"omp"\|"mpi_omp") parallel=$2 ; shift
232	shift ;;
233	*) echo Only none mpi omp mpi_omp for the parallel \
234	option
235	exit
236	esac ;;
237	"-bench") bench=$2 ; shift ; shift ;;
238	"-debug") optim=-debug ; shift ;;
239	"-name") MODEL=$2 ; shift ; shift ;;
240	"-netcdf") netcdf=$2 ; shift ; shift ;;
241	"-physiq") physiq=$2 ; shift ; shift ;;
242	"-xios") with_xios="y" ; shift ;;
243	"-env_file") env_file=$2 ; shift ; shift ;;
244	"-veget") veget=$2 ; shift ; shift ;;
245	*) ./install_lmdz.sh -h ; exit
246	esac
247	done
248
249	# Option de compilation du rayonnement : depend de $mysvn ><= r4185,
250	# sera donc definie plus bas
251
252	#opt_rad=""
253	#case $rad in
254	# rrtm) opt_rad="-rad rrtm" ;;
255	# ecrad) opt_rad="-rad ecrad" ;;
256	#esac
257
258
259	# Option de compilation pour Cosp
260	opt_cosp=""
261	case cosp in
262	v1) opt_cosp="-cosp true" ;;
263	v2) opt_cosp="-cospv2 true" ;;
264	esac
265
266	# Check on veget version
267	#if [ "$veget" != 'NONE' -a "$veget" != "CMIP6" -a "$veget" != +([0-9]) ] ; then
268	if [ $veget != 'NONE' -a $veget != "CMIP6" ] ; then
269	re='^[0-9]+$'
270	if ! [[ $veget =~ $re ]] ; then
271	echo 'Valeur de l option veget non valable'
272	exit
273	fi
274	fi
275
276	#Define veget-related suffix for gcm name
277	if [ "$veget" = 'NONE' ] ; then
278	suff_orc=''
279	#For use with tutorial, orchidee_rev is also defined (will be
280	#written in surface_env at the end of the script)
281	orchidee_rev=''
282	else
283	suff_orc='_orch'
284	fi
285
286
287	if [ $parallel = none ] ; then
288	sequential=1; suff_exe='_seq'
289	else
290	sequential=0; suff_exe='_para_mem'
291	fi
292
293	#Chemin pour placer le modele
294	if [ "$MODEL" = "" ] ; then MODEL=./LMDZ$version$svn$optim ; fi
295
296
297	arch=local
298
299
300	if [ $compiler = g95 ] ; then echo g95 is not supported anymore ; exit ; fi
301
302	################################################################
303	# Specificite des machines
304	################################################################
305
306	hostname=`hostname`
307	if [ "$pclinux" = 1 ] ; then o_ins_make="-t g95" ; else o_ins_make="" ; fi
308
309	case ${hostname:0:5} in
310
311	jean-) compiler="mpiifort" ;
312	par_comp="mpiifort" ;
313	o_ins_make="-t jeanzay" ;
314	make=gmake ;
315	module purge
316	module load intel-compilers/19.0.4 ;
317	#module load intel-mpi/19.0.4 ;
318	#module load intel-mkl/19.0.4 ;
319	module load hdf5/1.10.5-mpi ;
320	module load netcdf/4.7.2-mpi ;
321	module load netcdf-fortran/4.5.2-mpi ;
322	module load subversion/1.9.7 ;
323	export NETCDF_LIBDIR=./
324	export NETCDFFORTRAN_INCDIR=./
325	export NETCDFFORTRAN_LIBDIR=./
326	arch=X64_JEANZAY ;;
327
328	cicla\|camel) compiler="gfortran" ;
329	module purge
330	module load gnu/10.2.0
331	module load openmpi/4.0.5
332	module load hdf5/1.10.7-mpi
333	module load netcdf-c/4.7.4-mpi
334	module load netcdf-fortran/4.5.3-mpi
335	netcdf=/net/nfs/tools/PrgEnv/linux-scientific6-x86_64/gcc-10.2.0/netcdf-fortran-4.5.3-k3drgfqok3lip62hnm3tsyof4cjen5sk
336	module load svn/1.14.0
337
338	if [ $parallel != none ] ; then
339	root_mpi=/net/nfs/tools/meso-sl6/openmpi/4.0.5-gcc-10.2.0
340	path_mpi=$root_mpi/bin ;
341	par_comp=${path_mpi}/mpif90 ;
342	mpirun=${path_mpi}/mpirun ;
343	fi ;
344	arch=local ;
345	make=make ;
346	o_ins_make="-t g95" ;;
347
348	*) if [ $parallel = none -o -f /usr/bin/mpif90 ] ; then
349	path_mpi=`which mpif90 \| sed -e s:/mpif90::` ;
350	if [ -d /usr/lib64/openmpi ] ; then
351	root_mpi="/usr/lib64/openmpi"
352	else
353	root_mpi="/usr"
354	fi
355	else
356	echo "Cannot find mpif90" ;
357	if [ $parallel = none ] ; then exit ; fi ;
358	fi ;
359	if [ $parallel != none ] ; then
360	root_mpi=$(which mpif90 \| sed -e s:/bin/mpif90::)
361	path_mpi=$(which mpif90 \| sed -e s:/mpif90::)
362	export LD_LIBRARY_PATH=${root_mpi}/lib:$LD_LIBRARY_PATH
363	fi
364	par_comp=${path_mpi}/mpif90 ;
365	mpirun=${path_mpi}/mpirun ;
366	arch=local ;
367	make=make ;
368	o_ins_make="-t g95"
369	esac
370
371	# Flags for parallelism:
372	if [ $parallel != none ] ; then
373	# MPI_LD are the flags needed for linking with MPI
374	MPI_LD="-L${root_mpi}/lib -lmpi"
375	if [ "$compiler" = "gfortran" ] ; then
376	# MPI_FLAGS are the flags needed for compilation with MPI
377	MPI_FLAGS="-fcray-pointer"
378	# OMP_FLAGS are the flags needed for compilation with OpenMP
379	OMP_FLAGS="-fopenmp -fcray-pointer"
380	# OMP_LD are the flags needed for linking with OpenMP
381	OMP_LD="-fopenmp"
382	elif [ "$compiler" = "ifort" ] ; then
383	MPI_FLAGS=""
384	OMP_FLAGS="-openmp"
385	OMP_LD="-openmp"
386	else # pgf90
387	MPI_FLAGS=""
388	OMP_FLAGS="-mp"
389	OMP_LD="-mp"
390	fi
391	fi
392
393	#####################################################################
394	# Test for old gfortran compilers
395	# If the compiler is too old (older than 4.3.x) we test if the
396	# temporary gfortran44 patch is available on the computer in which
397	# case the compiler is changed from gfortran to gfortran44
398	# Must be aware than parallelism can not be activated in this case
399	#####################################################################
400
401	if [ "$compiler" = "gfortran" ] ; then
402	gfortran=gfortran
403	gfortranv=`gfortran --version \| \
404	head -1 \| awk ' { print $NF } ' \| awk -F. ' { print $1 * 10 + $2 } '`
405	if [ $gfortranv -le 43 ] ; then
406	echo ERROR : Your gfortran compiler is too old
407	echo 'Please choose a new one (ifort) and change the line'
408	echo compiler=xxx
409	echo in the install_lmdz.sh script and rerun it
410	if [ `which gfortran44 \| wc -w` -ne 0 ] ; then
411	gfortran=gfortran44
412	else
413	echo gfotran trop vieux ; exit
414	fi
415	fi
416	compiler=$gfortran
417	fi
418	#####################################################################
419
420	## if also compiling XIOS, parallel must be mpi_omp
421	if [ "$with_xios" = "y" -a "$parallel" != "mpi_omp" ] ; then
422	echo "Error, you must set -parallel mpi_omp if you want XIOS"
423	exit
424	fi
425
426	if [ "$with_xios" = "y" ] ; then
427	opt_makelmdz_xios="-io xios"
428	fi
429
430	if [ "$cosp" = "v2" -a "$with_xios" = "n" ] ; then
431	echo "Error, Cospv2 cannot run without Xios"
432	exit
433	fi
434
435	echo '################################################################'
436	echo Choix des options de compilation
437	echo '################################################################'
438
439	export FC=$compiler
440	export F90=$compiler
441	export F77=$compiler
442	export CPPFLAGS=
443	OPTIMNC=$OPTIM
444	BASE_LD="$OPT_GPROF"
445	OPTPREC="$OPT_GPROF"
446	ARFLAGS="rs"
447	if [ -f /etc/issue ] ; then
448	if [ "`grep -i ubuntu /etc/issue`" != "" ] ; then
449	if [ "`grep -i ubuntu /etc/issue \| awk ' { print $2 } ' \| cut -d. -f1`" -ge 16 ]
450	then
451	ARFLAGS="rU"
452	fi
453	fi
454	fi
455
456
457
458	if [ "$compiler" = "$gfortran" ] ; then
459	OPTIM="-O3 $allow_arg_mismatch"
460	OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all -fbacktrace -finit-real=snan $allow_arg_mismatch"
461	OPTDEV="-Wall -fbounds-check $allow_arg_mismatch"
462	fmod='I '
463	OPTPREC="$OPTPREC -cpp -ffree-line-length-0"
464	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE" ; fi
465	export F90FLAGS=" -ffree-form $OPTIMNC"
466	export FFLAGS=" $OPTIMNC"
467	export CC=gcc
468	export CXX=g++
469	export fpp_flags="-P -C -traditional -ffreestanding"
470
471	elif [ $compiler = mpif90 ] ; then
472	OPTIM='-O3'
473	OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all"
474	OPTDEV="-Wall -fbounds-check"
475	BASE_LD="$BASE_LD -lblas"
476	fmod='I '
477	if [ $real = r8 ] ; then
478	OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE -fcray-pointer"
479	fi
480	export F90FLAGS=" -ffree-form $OPTIMNC"
481	export FFLAGS=" $OPTIMNC"
482	export CC=gcc
483	export CXX=g++
484
485	elif [ $compiler = pgf90 ] ; then
486	OPTIM='-O2 -Mipa -Munroll -Mnoframe -Mautoinline -Mcache_align'
487	OPTDEB='-g -Mdclchk -Mbounds -Mchkfpstk -Mchkptr -Minform=inform -Mstandard -Ktrap=fp -traceback'
488	OPTDEV='-g -Mbounds -Ktrap=fp -traceback'
489	fmod='module '
490	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -r8 -DNC_DOUBLE" ; fi
491	export CPPFLAGS="-DpgiFortran"
492	export CC=pgcc
493	export CFLAGS="-O2 -Msignextend"
494	export CXX=pgCC
495	export CXXFLAGS="-O2 -Msignextend"
496	export FFLAGS="-O2 $OPTIMNC"
497	export F90FLAGS="-O2 $OPTIMNC"
498	compile_with_fcm=1
499
500	elif [[ $compiler = ifort \|\| $compiler = mpiifort ]] ; then
501	OPTIM="-O2 -fp-model strict -ip -align all "
502	OPTDEV="-p -g -O2 -traceback -fp-stack-check -ftrapuv -check"
503	OPTDEB="-g -no-ftz -traceback -ftrapuv -fp-stack-check -check"
504	fmod='module '
505	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -real-size 64 -DNC_DOUBLE" ; fi
506	export CPP="icc -E"
507	export FFLAGS="-O2 -ip -fpic -mcmodel=large"
508	export FCFLAGS="-O2 -ip -fpic -mcmodel=large"
509	export CC=icc
510	export CFLAGS="-O2 -ip -fpic -mcmodel=large"
511	export CXX=icpc
512	export CXXFLAGS="-O2 -ip -fpic -mcmodel=large"
513	export fpp_flags="-P -traditional"
514	# Pourquoi forcer la compilation fcm. Marche mieux sans
515	#compile_with_fcm=1
516	else
517	echo unexpected compiler $compiler ; exit
518	fi
519
520	OPTIMGCM="$OPTIM $OPTPREC"
521
522	hostname=`hostname`
523
524	##########################################################################
525	# If installing on known machines such as Jean-Zay at IDRIS,
526	# don't check for available software and don't install netcdf
527	if [ ${hostname:0:5} = jean- ] ; then
528	netcdf=0 # no need to recompile netcdf, alreday available
529	check_linux=0
530	pclinux=0
531	ioipsl=0 # no need to recompile ioipsl, already available
532	#netcdf="/smplocal/pub/NetCDF/4.1.3"
533	compiler="mpiifort"
534	fmod='module '
535	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -i4 -r8 -DNC_DOUBLE" ; fi
536	OPTIM="-auto -align all -O2 -fp-model strict -xHost "
537	OPTIMGCM="$OPTIM $OPTPREC"
538	fi
539	##########################################################################
540
541
542	mkdir -p $MODEL
543	echo $MODEL
544	MODEL=`( cd $MODEL ; pwd )` # to get absolute path, if necessary
545
546
547	if [ "$check_linux" = 1 ] ; then
548	echo '################################################################'
549	echo Check if required software is available
550	echo '################################################################'
551
552	#### Ehouarn: test if the required shell is available
553	#### Maj FH-LF-AS 2021-04 : default=bash ; if bash missing, use ksh
554	use_shell="bash" # default
555	if [ "`which bash`" = "" ] ; then
556	echo "no bash ; we will use ksh"
557	use_shell="ksh"
558	if [ "`which ksh`" = "" ] ; then
559	echo "bash (or ksh) needed!! Install it!"
560	exit
561	fi
562	fi
563
564	for logiciel in wget tar gzip make $compiler gcc cmake m4 c++ ; do
565	if [ "`which $logiciel`" = "" ] ; then
566	echo You must first install $logiciel on your system
567	exit
568	fi
569	done
570
571	if [ $pclinux = 1 ] ; then
572	cd $MODEL
573	cat <<eod > tt.f90
574	print*,'coucou'
575	end
576	eod
577	$compiler tt.f90 -o a.out
578	./a.out >\| tt
579	if [ "`cat tt \| sed -e 's/ //g' `" != "coucou" ] ; then
580	echo problem installing with compiler $compiler ; exit ; fi
581	\rm tt a.out tt.f90
582	fi
583	fi
584
585	###########################################################################
586	if [ $getlmdzor = 1 -a ! -d $MODEL/modipsl ] ; then
587	###########################################################################
588	echo '##########################################################'
589	echo Download a slightly modified version of LMDZ
590	echo '##########################################################'
591	cd $MODEL
592	getlog=`pwd`/get.log
593	echo logfile : $getlog
594	myget src/modipsl.$version.tar.gz >> get.log 2>&1
595	echo install_lmdz.sh wget_OK `date`
596	gunzip modipsl.$version.tar.gz >> get.log 2>&1
597	tar xf modipsl.$version.tar >> get.log 2>&1
598	\rm modipsl.$version.tar
599	fi
600
601	###########################################################################
602	if [ $netcdf = 1 ] ; then
603	###########################################################################
604	cd $MODEL
605	netcdflog=`pwd`/netcdf.log
606	echo '##########################################################'
607	echo Compiling the Netcdf library
608	echo '##########################################################'
609	echo log file : $netcdflog
610	if [[ "$with_xios" = "n" && ! -d $MODEL/netcdf4_hdf5_seq ]] ; then
611	myget import/install_netcdf4_hdf5_seq.bash >> $netcdflog 2>&1
612	chmod +x install_netcdf4_hdf5_seq.bash
613
614	if [ "$compiler" = "gfortran" ]
615	then
616	./install_netcdf4_hdf5_seq.bash -prefix $MODEL/netcdf4_hdf5_seq \
617	-compiler gnu >> $netcdflog 2>&1
618	elif [ "$compiler" = "ifort" ]
619	then
620	./install_netcdf4_hdf5_seq.bash -prefix $MODEL/netcdf4_hdf5_seq \
621	-compiler intel >> $netcdflog 2>&1
622	else
623	echo "unexpected compiler $compiler" ; exit
624	fi
625
626	# LF rajout d'une verrue, pour une raison non encore expliquee,
627	# la librairie est parfois rangée dans lib64 et non dans lib
628	# par certains compilateurs
629	if [ ! -e lib -a -d lib64 ] ; then ln -s lib64 lib; fi
630	elif [[ "$with_xios" = "y" && ! -d $MODEL/netcdf4_hdf5 ]]
631	then
632	# download and compile hdf5 and netcdf, etc. using the
633	# install_netcdf4_hdf5.bash script
634	myget import/install_netcdf4_hdf5.bash >> $netcdflog 2>&1
635	chmod u=rwx install_netcdf4_hdf5.bash
636	if [ "$compiler" = "gfortran" ] ; then
637	./install_netcdf4_hdf5.bash -prefix $MODEL/netcdf4_hdf5 -CC gcc \
638	-FC gfortran -CXX g++ -MPI $root_mpi >> $netcdflog 2>&1
639	elif [ "$compiler" = "ifort" ] ; then
640	./install_netcdf4_hdf5.bash -prefix $MODEL/netcdf4_hdf5 -CC icc \
641	-FC ifort -CXX icpc -MPI $root_mpi >> $netcdflog 2>&1
642	elif [ "$compiler" = "pgf90" ] ; then
643	./install_netcdf4_hdf5.bash -prefix $MODEL/netcdf4_hdf5 -CC pgcc \
644	-FC pgf90 -CXX pgCC -MPI $root_mpi >> $netcdflog 2>&1
645	else
646	echo "unexpected compiler $compiler" ; exit
647	fi
648	fi # of if [ "$with_xios" = "n" ]
649	echo install_lmdz.sh netcdf_OK `date`
650	fi # of if [ $netcdf = 1 ]
651
652	# ncdfdir contains the directory where netcdf is installed
653	if [ $netcdf = 1 ] ; then
654	if [ "$with_xios" = "y" ] ; then
655	ncdfdir=$MODEL/netcdf4_hdf5
656	else
657	ncdfdir=$MODEL/netcdf4_hdf5_seq
658	fi
659	elif [ $netcdf = 0 ]
660	then
661	ncdfdir=/usr
662	else
663	ncdfdir=$netcdf
664	fi
665
666	cat >test_netcdf90.f90 <<EOF
667	use netcdf
668	print *, "NetCDF library version: ", nf90_inq_libvers()
669	end
670	EOF
671
672	$compiler -I$ncdfdir/include test_netcdf90.f90 -L$ncdfdir/lib -l netcdff \
673	-lnetcdf -Wl,-rpath=$ncdfdir/lib && ./a.out
674
675	if (($? == 0))
676	then
677	rm test_netcdf90.f90 a.out
678	else
679	echo "Failed test program using NetCDF-Fortran."
680	echo "You can:"
681	echo "- check that you have NetCDF-Fortran installed in your system"
682	echo "- or specify an installation directory with option -netcdf of" \
683	"install_lmdz.sh"
684	echo "- or download and compile NetCDF-Fortran with option -netcdf 1 of" \
685	"install_lmdz.sh"
686	exit 1
687	fi
688
689	#=========================================================================
690	if [[ ! -f $MODEL/modipsl/lib/libioipsl.a ]]
691	then
692	if [ $ioipsl = 1 ] ; then
693	#=====================================================================
694	echo OK ioipsl=$ioipsl
695	echo '##########################################################'
696	echo 'Installing MODIPSL, the installation package manager for the '
697	echo 'IPSL models and tools'
698	echo '##########################################################'
699	echo `date`
700
701	cd $MODEL/modipsl
702	\rm -rf lib/*
703	cd util
704	cp AA_make.gdef AA_make.orig
705	F_C="$compiler -c "
706	if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ]
707	then
708	F_C="$compiler -c -cpp "
709	fi
710	if [ "$compiler" = "pgf90" ] ; then F_C="$compiler -c -Mpreprocess" ; fi
711	sed -e 's/^\#..g95..\#.*.$/\#/' AA_make.gdef > tmp
712	sed -e "s:F_L = g95:F_L = $compiler:" \
713	-e "s:F_C = g95 -c -cpp:F_C = $F_C": \
714	-e 's/g95..w_w..(F_D)/g95 w_w = '"$OPTIMGCM"'/' \
715	-e 's:g95..NCDF_INC..$:g95 NCDF_INC= '"$ncdfdir"'/include:' \
716	-e 's:g95..NCDF_LIB..$:g95 NCDF_LIB= -L'"$ncdfdir"'/lib -lnetcdff -lnetcdf:' \
717	-e 's:g95 L_O =:g95 L_O = -Wl,-rpath='"$ncdfdir"'/lib:' \
718	-e "s:-fmod=:-$fmod:" -e 's/-fno-second-underscore//' \
719	-e 's:#-Q- g95 M_K = gmake:#-Q- g95 M_K = make:' \
720	tmp >\| AA_make.gdef
721
722	if [ $pcmac == 1 ]
723	then
724	cp AA_make.gdef tmp
725	sed -e 's/rpath=/rpath,/g' tmp > AA_make.gdef
726	fi
727
728
729	# We use lines for g95 even for the other compilers to run ins_make
730	if [ "$use_shell" = "ksh" ] ; then
731	./ins_make $o_ins_make
732	else # bash
733	sed -e s:/bin/ksh:/bin/bash:g ins_make > ins_make.bash
734	if [ "`grep jeanzay AA_make.gdef`" = "" ] ; then
735	# Bidouille pour compiler sur ada des vieux modipsl.tar
736	echo 'Warning jean-zay not in AA_make.gdef'
737	echo 'Think about updating'
738	exit 1
739	fi
740
741	chmod u=rwx ins_make.bash
742	./ins_make.bash $o_ins_make
743	fi # of if [ "$use_shell" = "ksh" ]
744
745	echo install_lmdz.sh MODIPSL_OK `date`
746
747	cd $MODEL/modipsl/modeles/IOIPSL/src
748	ioipsllog=`pwd`/ioipsl.log
749	echo '##########################################################'
750	echo 'Compiling IOIPSL, the interface library with Netcdf'
751	echo '##########################################################'
752	echo `date`
753	echo log file : $ioipsllog
754
755	if [ "$use_shell" = "bash" ] ; then
756	cp Makefile Makefile.ksh
757	sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile
758	fi
759	# if [ "$pclinux" = 1 ] ; then
760	# Build IOIPSL modules and library
761	$make clean
762	$make > $ioipsllog 2>&1
763	if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then
764	# copy module files to lib
765	cp -f *.mod ../../../lib
766	fi
767	# Build IOIPSL tools (ie: "rebuild", if present)
768	if [ -f $MODEL/modipsl/modeles/IOIPSL/tools/rebuild ] ; then
769	cd $MODEL/modipsl/modeles/IOIPSL/tools
770	# adapt Makefile & rebuild script if in bash
771	if [ "$use_shell" = "bash" ] ; then
772	cp Makefile Makefile.ksh
773	sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile
774	cp rebuild rebuild.ksh
775	sed -e 's:/bin/ksh:/bin/bash:g' \
776	-e 's:print -u2:echo:g' \
777	-e 's:print:echo:g' rebuild.ksh > rebuild
778	fi
779	$make clean
780	$make > $ioipsllog 2>&1
781	fi
782	# fi # of if [ "$pclinux" = 1 ]
783
784	else # of if [ $ioipsl = 1 ]
785	if [ ${hostname:0:5} = jean- ] ; then
786	cd $MODEL/modipsl
787	cd util
788	if [ "`grep jeanzay AA_make.gdef`" = "" ] ; then
789	echo 'Warning jean-zay not in AA_make.gdef'
790	echo 'Think about updating'
791	exit 1
792	fi
793	./ins_make $o_ins_make
794	# Compile IOIPSL on jean-zay
795	cd $MODEL/modipsl/modeles/IOIPSL/src
796	gmake > ioipsl.log
797	cd $MODEL/modipsl/modeles/IOIPSL/tools
798	gmake > ioipsl.log
799
800	fi
801	echo install_lmdz.sh ioipsl_OK `date`
802	fi # of if [ $ioipsl = 1 ]
803	fi
804	# Saving ioipsl lib for possible parallel compile
805	cd $MODEL/modipsl
806	tar cf ioipsl.tar lib/ bin/
807
808	#=========================================================================
809	if [ "$with_xios" = "y" ] ; then
810	echo '##########################################################'
811	echo 'Compiling XIOS'
812	echo '##########################################################'
813	cd $MODEL/modipsl/modeles
814	xioslog=`pwd`/xios.log
815	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/install_xios.bash
816	myget import/install_xios.bash
817	chmod u=rwx install_xios.bash
818	if [ ${hostname:0:5} = jean- ] ; then
819	svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5 \
820	XIOS
821	cd XIOS/arch
822	svn update
823	cd ..
824	echo "Compiling XIOS, start" `date` \
825	"(it takes about 20 min on Jean-Zay)"
826	echo "log file: $xioslog"
827	./make_xios --prod --arch $arch --job 4 > xios.log 2>&1
828	else
829	./install_xios.bash -prefix $MODEL/modipsl/modeles \
830	-netcdf ${ncdfdir} -hdf5 ${ncdfdir} \
831	-MPI $root_mpi -arch $arch > xios.log 2>&1
832	fi # of case Jean-Zay
833	if [ -f XIOS/lib/libxios.a ] ; then
834	echo "XIOS library successfully generated"
835	echo install_lmdz.sh XIOS_OK `date`
836	fi
837	fi
838
839	#============================================================================
840	veget_version=false
841	if [ "$veget" != 'NONE' ] ; then
842	cd $MODEL/modipsl/modeles/ORCHIDEE
843	set +e ; svn upgrade ; set -e
844	if [ "$veget" = "CMIP6" ] ; then
845	veget_version=orchidee2.0
846	orchidee_rev=6592
847	else # specific orchidee revision newer than CMIP6, on 2_1 or 2_2 branches
848	veget_version=orchidee2.1
849	orchidee_rev=$veget
850	if [ $veget -lt 4465 ] ; then
851	echo 'Stopping, ORCHIDEE version too old, script needs work on ' \
852	'the CPP flags to pass to makelmdz'
853	exit 1
854	fi
855	set +e
856	# which branch is my version on?
857	orcbranch=`svn log -v -q svn://forge.ipsl.jussieu.fr/orchidee/ -r $veget \|grep ORCHIDEE \|head -1\| sed -e 's:ORCHIDEE/.*$:ORCHIDEE:' \| awk '{print $2}'`
858	# switch to that branch
859	echo IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at \
860	orchidee-help@listes.ipsl.fr
861	svn switch -r $veget --accept theirs-full \
862	svn://forge.ipsl.jussieu.fr/orchidee/$orcbranch
863	svn log -r $veget \| grep $veget
864	if [ $? -gt 0 ] ; then
865	echo 'Cannot update ORCHIDEE as not on the right branch for ' \
866	'ORCHIDEE'
867	exit
868	fi
869	set -e
870	set +e ; svn update -r $veget ; set -e
871	fi
872	# Correctif suite debug Jean-Zay
873	sed -i -e 's/9010 FORMAT(A52,F17.14)/9010 FORMAT(A52,F20.14)/' \
874	src_stomate/stomate.f90
875	opt_orc="-prod" ; if [ "$optim" = "-debug" ] ; then opt_orc="-debug" ; fi
876
877	orchideelog=`pwd`/orchidee.log
878	echo '########################################################'
879	echo 'Compiling ORCHIDEE, the continental surface model '
880	echo '########################################################'
881	echo Start of the first compilation of orchidee, in sequential mode: `date`
882	echo log file : $orchideelog
883
884	export ORCHPATH=`pwd`
885	xios_orchid="-noxios"
886	if [ "$with_xios" = "y" ] ; then
887	xios_orchid="-xios"
888	fi
889	if [ -d tools ] ; then
890	###################################################################
891	# Pour les experts qui voudraient changer de version d'orchidee.
892	# Attention : necessite d'avoir le password pour orchidee
893
894	# Correctif suite debug Jean-Zay
895	if [ -f src_global/time.f90 ] ; then
896	sed -i -e 's/CALL tlen2itau/\!CALL tlen2itau/' src_global/time.f90
897	fi
898	###################################################################
899	if [ "$veget_version" == "false" ] ; then
900	veget_version=orchidee2.0
901	fi
902	cd arch
903	sed -e s:"%COMPILER .*.$":"%COMPILER $compiler":1 \
904	-e s:"%LINK .*.$":"%LINK $compiler":1 \
905	-e s:"%FPP_FLAGS .*.$":"%FPP_FLAGS $fpp_flags":1 \
906	-e s:"%PROD_FFLAGS .*.$":"%PROD_FFLAGS $OPTIM":1 \
907	-e s:"%DEV_FFLAGS .*.$":"%DEV_FFLAGS $OPTDEV":1 \
908	-e s:"%DEBUG_FFLAGS .*.$":"%DEBUG_FFLAGS $OPTDEB":1 \
909	-e s:"%BASE_FFLAGS .*.$":"%BASE_FFLAGS $OPTPREC":1 \
910	-e s:"%BASE_LD .*.$":"%BASE_LD $BASE_LD":1 \
911	-e s:"%ARFLAGS .*.$":"%ARFLAGS $ARFLAGS":1 \
912	arch-gfortran.fcm > arch-local.fcm
913	echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib -lnetcdff -lnetcdf\"" \
914	> arch-local.path
915	echo "NETCDF_INCDIR=${ncdfdir}/include" >> arch-local.path
916	echo "IOIPSL_INCDIR=$ORCHPATH/../../lib" >> arch-local.path
917	echo "IOIPSL_LIBDIR=$ORCHPATH/../../lib" >> arch-local.path
918	echo 'XIOS_INCDIR=${ORCHDIR}/../XIOS/inc' >> arch-local.path
919	echo 'XIOS_LIBDIR="${ORCHDIR}/../XIOS/lib -lxios"' >> arch-local.path
920	cd ../
921
922	echo ./makeorchidee_fcm -j $xios_orchid $opt_orc -parallel none \
923	-arch $arch
924	./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel none \
925	-arch $arch > $orchideelog 2>&1
926	pwd
927	else # of "if [ -d tools ]"
928	if [ -d src_parallel ] ; then
929	liste_src="parallel parameters global stomate sechiba driver"
930	if [ "$veget_version" == "false" ] ; then
931	veget_version=orchidee2.0
932	fi
933	fi
934	for d in $liste_src ; do
935	src_d=src_$d
936	echo src_d $src_d
937	echo ls ; ls
938	if [ ! -d $src_d ] ; then
939	echo Problem orchidee : no $src_d ; exit
940	fi
941	cd $src_d ; \rm -f *.mod make ; $make clean
942	$make > $orchideelog 2>&1
943	if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then
944	cp -f *.mod ../../../lib
945	fi
946	cd ..
947	done
948	fi # of "if [ -d tools ]"
949	echo install_lmdz.sh orchidee_compil_seq_OK `date`
950	fi # of if [ "$veget" != 'NONE' ]
951
952
953	#============================================================================
954	# Ehouarn: the directory name LMDZ* depends on version/tar file...
955	if [ -d $MODEL/modipsl/modeles/LMD* ] ; then
956	echo '###############################################################'
957	echo 'Preparing LMDZ compilation : arch file, svn switch if needed...'
958	echo '###############################################################'
959	cd $MODEL/modipsl/modeles/LMD*
960	LMDZPATH=`pwd`
961	else
962	echo "ERROR: No LMD* directory !!!"
963	exit
964	fi
965
966	###########################################################
967	# For those who want to use fcm to compile via :
968	# makelmdz_fcm -arch local .....
969	############################################################
970
971	if [[ "$pclinux" = "1" && ! -f arch/arch-local.path ]] ; then
972
973	# create local 'arch' files (if on Linux PC):
974	cd arch
975	# arch-local.path file
976	echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib -lnetcdff -lnetcdf\"" \
977	> arch-local.path
978	echo "NETCDF_INCDIR=-I${ncdfdir}/include" >> arch-local.path
979	echo 'NETCDF95_INCDIR=$LMDGCM/../../include' >> arch-local.path
980	echo 'NETCDF95_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
981	echo 'IOIPSL_INCDIR=$LMDGCM/../../lib' >> arch-local.path
982	echo 'IOIPSL_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
983	echo 'XIOS_INCDIR=$LMDGCM/../XIOS/inc' >> arch-local.path
984	echo 'XIOS_LIBDIR=$LMDGCM/../XIOS/lib' >> arch-local.path
985	echo 'ORCH_INCDIR=$LMDGCM/../../lib' >> arch-local.path
986	echo 'ORCH_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
987
988	if [ $pcmac == 1 ] ; then
989	BASE_LD="$BASE_LD -Wl,-rpath,${ncdfdir}/lib"
990	else
991	BASE_LD="$BASE_LD -Wl,-rpath=${ncdfdir}/lib"
992	fi
993	# Arch-local.fcm file (adapted from arch-linux-32bit.fcm)
994
995	if [ $real = r8 ] ; then FPP_DEF=NC_DOUBLE ; else FPP_DEF="" ; fi
996	sed -e s:"%COMPILER .*.$":"%COMPILER $compiler":1 \
997	-e s:"%LINK .*.$":"%LINK $compiler":1 \
998	-e s:"%PROD_FFLAGS .*.$":"%PROD_FFLAGS $OPTIM":1 \
999	-e s:"%DEV_FFLAGS .*.$":"%DEV_FFLAGS $OPTDEV":1 \
1000	-e s:"%DEBUG_FFLAGS .*.$":"%DEBUG_FFLAGS $OPTDEB":1 \
1001	-e s:"%BASE_FFLAGS .*.$":"%BASE_FFLAGS $OPTPREC":1 \
1002	-e s:"%FPP_DEF .*.$":"%FPP_DEF $FPP_DEF":1 \
1003	-e s:"%BASE_LD .*.$":"%BASE_LD $BASE_LD":1 \
1004	-e s:"%ARFLAGS .*.$":"%ARFLAGS $ARFLAGS":1 \
1005	arch-linux-32bit.fcm > arch-local.fcm
1006
1007	cd ..
1008	### Adapt "bld.cfg" (add the shell):
1009	#whereisthatshell=$(which ${use_shell})
1010	#echo "bld::tool::SHELL $whereisthatshell" >> bld.cfg
1011
1012	fi # of if [ "$pclinux" = 1 ]
1013
1014
1015	cd $MODEL/modipsl/modeles/LMDZ*
1016	lmdzlog=`pwd`/lmdz.log
1017
1018	##################################################################
1019	# Possibly update LMDZ if a specific svn release is requested
1020	##################################################################
1021
1022	set +e ; svn upgrade ; set -e
1023
1024	if [ "$svn" = "last" ] ; then svnopt="" ; else svnopt="-r $svn" ; fi
1025	if [ "$svn" != "" ] ; then
1026	set +e ; svn info \| grep -q 'http:'
1027	if [ $? = 0 ] ; then
1028	svn switch --relocate http://svn.lmd.jussieu.fr/LMDZ \
1029	https://svn.lmd.jussieu.fr/LMDZ
1030	fi
1031	svn update $svnopt
1032	set -e
1033	fi
1034
1035	#---------------------------------------------------------------------
1036	# Retrieve the final svn release number, and adjust compilation
1037	# options accordingly
1038	# If svn not available, will use the svn writen in $MODEL/Readm*md
1039	# For old version it assumes that it is before 4185 (the version
1040	# for which the test was introduced
1041	#---------------------------------------------------------------------
1042
1043	set +e ; mysvn=`svnversion . \| egrep -o "[0-9]+" 2>/dev/null` ; set -e
1044	if [ "$mysvn" = "" ] ; then mysvn=`grep 'Revision: [0-9]' $MODEL/Read*.md \| awk ' { print $2 } ' 2>/dev/null` ; fi
1045	if [ "$mysvn" = "" ] ; then mysvn=4190 ; fi
1046
1047	#---------------------------------------------------------------------
1048	# Option de compilation du rayonnement : depend de $mysvn ><= r4185
1049	#---------------------------------------------------------------------
1050	opt_rad=""
1051
1052	case $rad in
1053	oldrad) iflag_rrtm=0 ; NSW=2 ; opt_rad="" ;;
1054	rrtm) iflag_rrtm=1 ; NSW=6
1055	if [ $mysvn -le 4185 ] ; then
1056	opt_rad="-rrtm true"
1057	else
1058	opt_rad="-rad rrtm"
1059	fi ;;
1060	ecrad) iflag_rrtm=2 ; NSW=6 ; opt_rad="-rad ecrad" ;;
1061	*) echo Only oldrad rrtm ecrad for rad option ; exit
1062	esac
1063
1064	if [ $mysvn -le 4185 -a $rad = "ecrad" ] ; then
1065	echo "ecrad only available for LMDZ rev starting with 4186 " ; exit
1066	fi
1067
1068	##################################################################
1069
1070
1071	if [[ ! -f libf/misc/netcdf95.F90 && ! -d $MODEL/NetCDF95-0.2 ]]
1072	then
1073	cd $MODEL
1074	myget import/NetCDF95-0.2.tar.gz
1075	tar -xf NetCDF95-0.2.tar.gz
1076	rm NetCDF95-0.2.tar.gz
1077	cd NetCDF95-0.2
1078	mkdir build
1079	cd build
1080	cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=$ncdfdir \
1081	-DCMAKE_INSTALL_PREFIX=$MODEL/modipsl
1082	make install
1083	cd $MODEL/modipsl/modeles/LMDZ*
1084	fi
1085
1086	echo '##################################################################'
1087	echo "Preparing script compile.sh for LMDZ compilation"
1088	echo "It will only be run automatically if bench=1/tuto"
1089	echo Here bench=$bench
1090	echo '##################################################################'
1091
1092	if [ "$env_file" != "" ] ; then
1093	mv arch/arch-${arch}.env arch/arch-${arch}.orig
1094	\cp -f $env_file arch/arch-${arch}.env
1095	fi
1096
1097	if [ $compile_with_fcm = 1 ] ; then
1098	makelmdz="makelmdz_fcm $optim -arch $arch -j 8 "
1099	else
1100	makelmdz="makelmdz $optim -arch $arch"
1101	fi
1102
1103	# sequential compilation
1104	if [ "$sequential" = 1 ] ; then
1105	echo Sequential compilation command, saved in compile.sh:
1106	echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp " \
1107	"-d ${grid_resolution} -v $veget_version gcm "
1108	echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp " \
1109	"-d ${grid_resolution} -v $veget_version gcm " > compile.sh
1110	chmod +x ./compile.sh
1111	if [ $bench = 1 ] ; then
1112	echo install_lmdz.sh start_lmdz_seq_compilation `date`
1113	echo log file: $lmdzlog
1114	./compile.sh > $lmdzlog 2>&1
1115	echo install_lmdz.sh end_lmdz_seq_compilation `date`
1116	fi
1117	fi # fin sequential
1118
1119	# compiling in parallel mode
1120	if [ $parallel != "none" ] ; then
1121	echo '##########################################################'
1122	echo ' Parallel compile '
1123	echo '##########################################################'
1124	echo "(after saving the sequential libs and binaries)"
1125	cd $MODEL/modipsl
1126	tar cf sequential.tar bin/ lib/
1127	\rm -rf bin/ lib/
1128	tar xf ioipsl.tar
1129	#
1130	# Orchidee
1131	#
1132	cd $ORCHPATH
1133	if [ -d src_parallel -a $veget != 'NONE' ] ; then
1134	cd arch
1135	sed \
1136	-e s:"%COMPILER.*.$":"%COMPILER $par_comp":1 \
1137	-e s:"%LINK.*.$":"%LINK $par_comp":1 \
1138	-e s:"%MPI_FFLAG.*.$":"%MPI_FFLAGS $MPI_FLAGS":1 \
1139	-e s:"%OMP_FFLAG.*.$":"%OMP_FFLAGS $OMP_FLAGS":1 \
1140	-e s:"%MPI_LD.*.$":"%MPI_LD $MPI_LD":1 \
1141	-e s:"%OMP_LD.*.$":"%OMP_LD $OMP_LD":1 \
1142	arch-local.fcm > tmp.fcm
1143
1144	mv tmp.fcm arch-local.fcm
1145	cd ../
1146	echo Compiling ORCHIDEE in parallel mode `date`
1147	echo logfile $orchideelog
1148	echo "NOTE : to recompile it when necessary, use ./compile_orc.sh " \
1149	"in modipsl/modeles/ORCHIDEE"
1150	echo ./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc \
1151	-parallel $parallel -arch $arch > compile_orc.sh
1152	echo ./makeorchidee_fcm -j 8 $xios_orchid $opt_orc \
1153	-parallel $parallel -arch $arch >> compile_orc.sh
1154	echo echo Now you must also recompile LMDZ, by running ./compile.sh \
1155	in modeles/LMDZ >> compile_orc.sh
1156	chmod u+x compile_orc.sh
1157	./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc \
1158	-parallel $parallel -arch $arch > $orchideelog 2>&1
1159	./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel $parallel \
1160	-arch $arch >> $orchideelog 2>&1
1161	echo End of ORCHIDEE compilation in parallel mode `date`
1162	elif [ $veget != 'NONE' ] ; then
1163	echo '##########################################################'
1164	echo ' Orchidee version too old '
1165	echo ' Please update to new version '
1166	echo '##########################################################'
1167	exit
1168	fi # of [ -d src_parallel -a $veget != 'NONE' ]
1169
1170	# LMDZ
1171	cd $LMDZPATH
1172	if [ $arch = local ] ; then
1173	cd arch
1174	sed -e s:"%COMPILER.*.$":"%COMPILER $par_comp":1 \
1175	-e s:"%LINK.*.$":"%LINK $par_comp":1 \
1176	-e s:"%MPI_FFLAG.*.$":"%MPI_FFLAGS $MPI_FLAGS":1 \
1177	-e s:"%OMP_FFLAG.*.$":"%OMP_FFLAGS $OMP_FLAGS":1 \
1178	-e s:"%ARFLAGS.*.$":"%ARFLAGS $ARFLAGS":1 \
1179	-e s@"%BASE_LD.*.$"@"%BASE_LD -Wl,-rpath=${root_mpi}/lib:${ncdfdir}/lib"@1 \
1180	-e s:"%MPI_LD.*.$":"%MPI_LD $MPI_LD":1 \
1181	-e s:"%OMP_LD.*.$":"%OMP_LD $OMP_LD":1 \
1182	arch-local.fcm > tmp.fcm
1183	mv tmp.fcm arch-local.fcm
1184	cd ../
1185	fi
1186	rm -f compile.sh
1187	echo resol=${grid_resolution} >> compile.sh
1188	if [ ${hostname:0:5} = jean- -a "$cosp" = "v2" ] ; then
1189
1190	echo LMDZ compilation command in parallel mode, saved in compile.sh, \
1191	is :
1192	echo "(ATTENTION le probleme de cospv2 sur jean-zay en mode prod " \
1193	"n est pas corrige ! )"
1194	# ATTENTION le probleme de cospv2 sur jean-zay en mode prod n
1195	# est pas corrige
1196	echo ./$makelmdz -dev $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
1197	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
1198	-parallel $parallel gcm >> compile.sh
1199	echo ./$makelmdz -dev $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
1200	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
1201	-parallel $parallel gcm
1202	else
1203	echo ./$makelmdz $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
1204	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
1205	-parallel $parallel gcm >> compile.sh
1206	echo ./$makelmdz $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
1207	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
1208	-parallel $parallel gcm
1209	fi
1210	chmod +x ./compile.sh
1211
1212	if [ $bench = 1 ] ; then
1213	echo Compiling LMDZ in parallel mode `date`, LMDZ log file: $lmdzlog
1214	./compile.sh > $lmdzlog 2>&1
1215	fi
1216
1217	fi # of if [ $parallel != "none" ]
1218
1219
1220	##################################################################
1221	# Verification du succes de la compilation
1222	##################################################################
1223
1224	# Recherche de l'executable dont le nom a change au fil du temps ...
1225	# suffix contains radiative option starting with revision 4186
1226	if [ $mysvn -ge 4186 ] ; then suff_exe=_${rad}${suff_exe} ; fi
1227	gcm=""
1228
1229	for exe in gcm.e bin/gcm_${grid_resolution}_phylmd${suff_exe}${suff_orc}.e
1230	do
1231	if [ -f $exe ] ; then gcm=$exe ; fi
1232	done
1233
1234	if [ "$gcm" = "" ] ; then
1235	if [ $bench = 1 ] ; then
1236	echo 'Compilation failed !! Cannot run the benchmark;'
1237	exit
1238	else
1239	echo 'Compilation not done (only done when bench=1)'
1240	fi
1241	else
1242	echo '##########################################################'
1243	echo 'Compilation successfull !! ' `date`
1244	echo '##########################################################'
1245	echo The executable is $gcm
1246	fi
1247
1248	##################################################################
1249	# Below, we run a benchmark if bench=1 or tuto
1250	##################################################################
1251
1252	if [ $bench = tuto ] ; then
1253	myget Training/tutorial.tar ; tar xf tutorial.tar ; cd TUTORIAL
1254	./init.sh
1255
1256	elif [[ $bench = 1 && ! -d BENCH${grid_resolution} ]] ; then
1257	# TOUTE CETTE SECTION DEVRAIT DISPARAITRE POUR UNE COMMANDE
1258	# OU DES BENCHS PAR MOTS CLES COMME tuto
1259
1260	echo '##########################################################'
1261	echo ' Running a test run '
1262	echo '##########################################################'
1263
1264	\rm -rf BENCH${grid_resolution}
1265	bench=bench_lmdz_${grid_resolution}
1266	echo install_lmdz.sh before bench download `date`
1267	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/$bench.tar.gz
1268	myget 3DBenchs/$bench.tar.gz
1269	echo install_lmdz.sh after bench download `date`
1270	tar xf $bench.tar.gz
1271
1272	if [ "$cosp" = "v1" -o "$cosp" = "v2" ] ; then
1273	cd BENCH${grid_resolution}
1274	# copier les fichiers namelist input et output our COSP
1275	cp ../DefLists/cosp*_input_nl.txt .
1276	cp ../DefLists/cosp*_output_nl.txt .
1277	# Activer la cles ok_cosp pour tourner avec COSP
1278	sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp
1279	\mv -f tmp config.def
1280	cd ..
1281	fi
1282
1283	if [ -n "$physiq" ]; then
1284	cd BENCH${grid_resolution}
1285	if [ -f physiq.def_${physiq} ]; then
1286	cp physiq.def_${physiq} physiq.def
1287	echo using physiq.def_${physiq}
1288	else
1289	echo using standard physiq.def
1290	fi
1291	cd ..
1292	else
1293	echo using standard physiq.def
1294	fi
1295
1296	if [ "$with_xios" = "y" ] ; then
1297	cd BENCH${grid_resolution}
1298	cp ../DefLists/iodef.xml .
1299	cp ../DefLists/context_lmdz.xml .
1300	cp ../DefLists/field_def_lmdz.xml .
1301	# A raffiner par la suite
1302	echo A FAIRE : Copier les *xml en fonction de l option cosp
1303	cp ../DefLists/field_def_cosp*.xml .
1304	cp ../DefLists/file_def_hist*xml .
1305	# adapt iodef.xml to use attached mode
1306	sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' \
1307	iodef.xml > tmp
1308	\mv -f tmp iodef.xml
1309
1310	# and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
1311	# except for histday
1312	for histfile in file_def_hist*xml
1313	do
1314	if [ "$histfile" = "file_def_histday_lmdz.xml" ] ; then
1315	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' \
1316	$histfile > tmp
1317	\mv -f tmp $histfile
1318	sed -e 's@output_level="_AUTO_"@output_level="5"@' $histfile \
1319	> tmp
1320	\mv -f tmp $histfile
1321	sed -e 's@compression_level="2"@compression_level="0"@' \
1322	$histfile > tmp
1323	\mv -f tmp $histfile
1324	else
1325	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
1326	$histfile > tmp
1327	\mv -f tmp $histfile
1328	fi
1329	done
1330	# and add option "ok_all_xml=y" in config.def
1331	echo "### XIOS outputs" >> config.def
1332	echo 'ok_all_xml=.true.' >> config.def
1333
1334	#activer les sorties pour Cosp
1335	if [ "$cosp" = "v1" ] ; then
1336	histfile=file_def_histdayCOSP_lmdz.xml
1337	sed -e 's@enabled=".FALSE."@enabled=".TRUE."@' $histfile > tmp
1338	\mv -f tmp $histfile
1339	sed -e 's@output_level="_AUTO_"@output_level="5"@' $histfile > tmp
1340	\mv -f tmp $histfile
1341	sed -e 's@compression_level="2"@compression_level="0"@' \
1342	$histfile > tmp
1343	\mv -f tmp $histfile
1344	fi
1345	if [ "$cosp" = "v2" ] ; then
1346	histfile=file_def_histdayCOSPv2_lmdz.xml
1347	sed -e 's@compression_level="2"@compression_level="0"@' \
1348	$histfile > tmp
1349	\mv -f tmp $histfile
1350	contextfile=context_lmdz.xml
1351	sed -e 's@src="./file_def_histdayCOSP_lmdz.xml"@src="./file_def_histdayCOSPv2_lmdz.xml"@' \
1352	$contextfile > tmp
1353	\mv -f tmp $contextfile
1354	sed -e 's@src="./file_def_histmthCOSP_lmdz.xml"@src="./file_def_histmthCOSPv2_lmdz.xml"@' \
1355	$contextfile > tmp
1356	\mv -f tmp $contextfile
1357	sed -e 's@src="./file_def_histhfCOSP_lmdz.xml"@src="./file_def_histhfCOSPv2_lmdz.xml"@' \
1358	$contextfile > tmp
1359	\mv -f tmp $contextfile
1360	fieldfile=field_def_lmdz.xml
1361	sed -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' $fieldfile \
1362	> tmp
1363	\mv -f tmp $fieldfile
1364	fi
1365
1366	cd ..
1367	fi
1368
1369	# Cas Bensh avec ecrad
1370	if [ "$rad" = "ecrad" ] ; then
1371	cd BENCH${grid_resolution}
1372	cp ../DefLists/namelist_ecrad .
1373	cp -r ../libf/phylmd/ecrad/data .
1374	cd ..
1375	fi
1376
1377	# Adjusting bench physiq.def to radiative code chosen
1378	cd BENCH${grid_resolution}
1379	sed -e 's/iflag_rrtm=.*.$/iflag_rrtm='$iflag_rrtm'/' \
1380	-e 's/NSW=.*.$/NSW='$NSW'/' physiq.def > tmpdef
1381	\mv tmpdef physiq.def
1382	cd ..
1383
1384	cp $gcm BENCH${grid_resolution}/gcm.e
1385
1386	cd BENCH${grid_resolution}
1387	# On cree le fichier bench.sh au besoin
1388	# Dans le cas 48x36x39 le bench.sh existe deja en parallele
1389
1390	if [ "$grid_resolution" = "48x36x39" ] ; then
1391	echo On ne touche pas au bench.sh
1392	# But we have to adapt "run_local.sh" for $mpirun
1393	sed -e "s@mpirun@$mpirun@g" run_local.sh > tmp
1394	mv -f tmp run_local.sh
1395	chmod u=rwx run_local.sh
1396	elif [ "${parallel:0:3}" = "mpi" ] ; then
1397	# Lancement avec deux procs mpi et 2 openMP
1398	echo "export OMP_STACKSIZE=800M" > bench.sh
1399	if [ "${parallel:4:3}" = "omp" ] ; then
1400	echo "export OMP_NUM_THREADS=2" >> bench.sh
1401	fi
1402	if [ "$cosp" = "v1" -o "$cosp" = "v2" ] ; then
1403	if [ ${hostname:0:5} = jean- ] ; then
1404	chmod +x ../arch.env
1405	../arch.env
1406	echo "ulimit -s 2000000" >> bench.sh
1407	else
1408	echo "ulimit -s 200000" >> bench.sh
1409	fi
1410	else
1411	echo "ulimit -s unlimited" >> bench.sh
1412	fi
1413	if [ ${hostname:0:5} = jean- ] ; then
1414	. ../arch/arch-${arch}.env
1415	echo "srun -n 2 -A $idris_acct@cpu gcm.e > listing 2>&1" \
1416	>> bench.sh
1417	else
1418	echo "$mpirun -np 2 gcm.e > listing 2>&1" >> bench.sh
1419	fi
1420	# Add rebuild, using reb.sh if it is there
1421	echo 'if [ -f reb.sh ] ; then' >> bench.sh
1422	echo ' ./reb.sh histday ; ./reb.sh histmth ; ./reb.sh histhf ; ' \
1423	'./reb.sh histins ; ./reb.sh stomate_history ; ' \
1424	'./reb.sh sechiba_history ; ./reb.sh sechiba_out_2 ' >> bench.sh
1425	echo 'fi' >> bench.sh
1426	else
1427	echo "./gcm.e > listing 2>&1" > bench.sh
1428	fi
1429	# Getting orchidee stuff
1430	if [ $veget == 'CMIP6' ] ; then
1431	#echo 'myget 3DBenchs/BENCHorch11.tar.gz'
1432	#myget 3DBenchs/BENCHorch11.tar.gz
1433	#tar xvzf BENCHorch11.tar.gz
1434	echo 'myget 3DBenchs/BENCHCMIP6.tar.gz'
1435	myget 3DBenchs/BENCHCMIP6.tar.gz
1436	tar xvzf BENCHCMIP6.tar.gz
1437	sed -e "s:VEGET=n:VEGET=y:" config.def > tmp
1438	mv -f tmp config.def
1439	if [ "$with_xios" = "y" ] ; then
1440	cp ../../ORCHIDEE/src_xml/context_orchidee.xml .
1441	echo '<context id="orchidee" src="./context_orchidee.xml"/>' \
1442	> add.tmp
1443	cp ../../ORCHIDEE/src_xml/field_def_orchidee.xml .
1444	cp ../../ORCHIDEE/src_xml/file_def_orchidee.xml .
1445	cp ../../ORCHIDEE/src_xml/file_def_input_orchidee.xml .
1446	if [ -f ../../ORCHIDEE/src_xml/context_input_orchidee.xml ] ; then
1447	cp ../../ORCHIDEE/src_xml/context_input_orchidee.xml .
1448	echo '<context id="orchidee" ' \
1449	'src="./context_input_orchidee.xml"/>' >> add.tmp
1450	fi
1451	sed -e '/id="LMDZ"/r add.tmp' iodef.xml > tmp
1452	mv tmp iodef.xml
1453	sed -e'{/sechiba1/ s/enabled="_AUTO_"/type="one_file" enabled=".TRUE."/}' \
1454	file_def_orchidee.xml > tmp
1455	\mv -f tmp file_def_orchidee.xml
1456	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
1457	file_def_orchidee.xml > tmp
1458	\mv -f tmp file_def_orchidee.xml
1459	sed -e 's@output_level="_AUTO_"@output_level="1"@' \
1460	file_def_orchidee.xml > tmp
1461	\mv -f tmp file_def_orchidee.xml
1462	sed -e 's@output_freq="_AUTO_"@output_freq="1d"@' \
1463	file_def_orchidee.xml > tmp
1464	\mv -f tmp file_def_orchidee.xml
1465	sed -e 's@compression_level="4"@compression_level="0"@' \
1466	file_def_orchidee.xml > tmp
1467	\mv -f tmp file_def_orchidee.xml
1468	sed -e 's@XIOS_ORCHIDEE_OK = n@XIOS_ORCHIDEE_OK = y@' \
1469	orchidee.def > tmp
1470	\mv -f tmp orchidee.def
1471	fi
1472	fi
1473
1474	if [[ -f ../arch.env ]]
1475	then
1476	source ../arch.env
1477	fi
1478
1479	echo EXECUTION DU BENCH
1480	set +e
1481	date ; ./bench.sh > out.bench 2>&1 ; date
1482	set -e
1483	tail listing
1484
1485
1486	echo '##########################################################'
1487	echo 'Simulation finished in' `pwd`
1488	echo 'You have compiled with:'
1489	cat ../compile.sh
1490	if [ $parallel = "none" ] ; then
1491	echo 'You may re-run it with : cd ' `pwd` ' ; gcm.e'
1492	echo 'or ./bench.sh'
1493	else
1494	echo 'You may re-run it with : '
1495	echo 'cd ' `pwd` '; ./bench.sh'
1496	# echo 'ulimit -s unlimited'
1497	# echo 'export OMP_NUM_THREADS=2'
1498	# echo 'export OMP_STACKSIZE=800M'
1499	# echo "$mpirun -np 2 gcm.e "
1500	fi
1501	echo '##########################################################'
1502
1503	fi # bench
1504
1505
1506	#################################################################
1507	# Installation eventuelle du 1D
1508	#################################################################
1509
1510	if [ $SCM = 1 ] ; then
1511	cd $MODEL
1512	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/1D.tar.gz
1513	myget 1D/1D.tar.gz
1514	tar xf 1D.tar.gz
1515	cd 1D
1516	./run.sh -rad $rad
1517	fi
1518	#set -vx
1519
1520	#################################################################
1521	# sauvegarde des options veget pour utilisation eventuelle tutorial_prod
1522	#################################################################
1523	cd $MODEL/modipsl/modeles
1524	#echo surface_env file created in $MODEL
1525	echo 'veget='$veget > surface_env
1526	#opt_veget="-v $veget_version"
1527	#echo 'opt_veget="'$opt_veget\" >> surface_env
1528	echo 'opt_veget="'-v $veget_version\" >> surface_env
1529	echo 'orchidee_rev='$orchidee_rev >> surface_env
1530	echo 'suforch='$suff_orc >> surface_env

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