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source: BOL/script_install/install_lmdz_new.sh @ 4221

Last change on this file since 4221 was 4221, checked in by lguez, 2 years ago

Define compiler variables for mpiifort

With mpiifort, we only need to add the definition of CC to compile
NetCDF95, but it is simpler to just merge the cases ifort and
mpiifort.

Property svn:executable set to *

File size: 49.4 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` $dir
60	fi
61	fi
62	}
63
64	# 04_2021 : tester si r4 marche encore !
65	#real=r4
66	real=r8
67
68
69	#########################################################################
70	# Valeur par défaut des parametres
71	#########################################################################
72	svn=""
73	#version=trunk
74	version=20220131.trunk
75
76	getlmdzor=1
77	netcdf=0 # 1: for automatic installation;
78	# or 0: do not install NetCDF and look for it in standard locations;
79	# or absolute path: look for NetCDF there
80	check_linux=1
81	ioipsl=1
82	bench=1
83	pclinux=1
84	pcmac=0 # default: not on a Mac
85	compiler=gfortran
86	SCM=0
87	# surface/vegetation scheme treatment
88	# controlled by the single variable veget which can have the following values
89	# - NONE: bucket scheme (default)
90	# - CMIP6: orchidee version used in CMIP exercise, rev 5661
91	# - number: orchidee version number
92	veget=NONE
93	# choose the resolution for the bench runs
94	# grid_resolution= 32x24x11 or 48x36x19 for tests (test without ORCHIDEE)
95	# 96x71x19 standard configuration
96	grid_resolution=144x142x79
97	grid_resolution=96x95x39
98	grid_resolution=48x36x19
99	grid_resolution=32x32x39
100	# choose the physiq version you want to test
101	#physiq=NPv6.0.14splith
102	physiq=
103
104	## parallel can take the values none/mpi/omp/mpi_omp
105	parallel=mpi_omp
106	parallel=none
107	idris_acct=lmd
108	OPT_GPROF=""
109	OPT_MAKELMDZ=""
110	MODEL=""
111
112	## also compile XIOS? (and more recent NetCDF/HDF5 libraries) Default=no
113	with_xios="n"
114	opt_makelmdz_xios=""
115
116	## compile with oldrad/rrtm/ecrad radiatif code (Default=rrtm)
117	rad=rrtm
118
119	## compile_with_fcm=1 : use makelmdz_fcm (1) or makelmdz (0)
120	compile_with_fcm=1
121
122	#Compilation with Cosp (cosp=NONE/v1/v2 ; default=NONE)
123	cosp=NONE
124	opt_cosp=""
125
126	# Check if on a Mac
127	if [ `uname` = "Darwin" ]
128	then
129	pcmac=1
130	export MAKE=make
131	fi
132	#echo "pcmac="$pcmac
133
134	env_file=""
135
136	#########################################################################
137	# Options interactives
138	#########################################################################
139	while (($# > 0))
140	do
141	case $1 in
142	"-h") cat <<........fin
143	$0 [ -v version ] [ -r svn_release ]
144	[ -parallel PARA ] [ -d GRID_RESOLUTION ] [ -bench 0/1 ]
145	[-name LOCAL_MODEL_NAME] [-gprof] [-opt_makelmdz] [-rad RADIATIF]
146
147	-v "version" like 20150828.trunk
148	see http://www.lmd.jussieu.fr/~lmdz/Distrib/LISMOI.trunk
149
150	-r "svn_release" : either the svn release number or "last"
151
152	-compiler gfortran\|ifort\|pgf90 (default: gfortran)
153
154	-parallel PARA : can be mpi_omp (mpi with openMP) or none (for sequential)
155
156	-d GRID_RESOLUTION should be among the available benchs if -bench 1
157	among which : 48x36x19, 48x36x39
158	if wanting to run a bench simulation in addition to compilation
159	default : 48x36x19
160
161	-bench activating the bench or not (0/1). Default 1
162
163	-name LOCAL_MODEL_NAME : default = LMDZversion.release
164
165	-netcdf 0, 1 or PATH
166	0: do not download NetCDF, look for it in standard locations
167	1: download and compile NetCDF
168	PATH: full path to an existing installed NetCDF library
169
170	-xios also download and compile the XIOS library
171	(requires the NetCDF4-HDF5 library, also installed by default)
172	(requires to also have -parallel mpi_omp)
173
174	-gprof to compile with -pg to enable profiling with gprof
175
176	-cosp to run without our with cospv1 or cospv2 [none/v1/v2]
177
178	-rad RADIATIF can be oldrad, rrtm or ecrad radiatif code
179
180	-nofcm to compile without fcm
181
182	-SCM install 1D version automatically
183
184	-debug compile everything in debug mode
185
186	-opt_makelmdz to call makelmdz or makelmdz_fcm with additional options
187
188	-physiq to choose which physics package to use
189
190	-env_file specify an arch.env file to overwrite the existing one
191
192	-veget surface model to run [NONE/CMIP6/xxxx]
193
194	........fin
195	exit ;;
196	"-v") version=$2 ; shift ; shift ;;
197	"-r") svn=$2 ; shift ; shift ;;
198	"-compiler") compiler=$2
199	case $compiler in
200	"gfortran"\|"ifort"\|"pgf90") compiler=$2 ; shift
201	shift ;;
202	*) echo "Only gfortran , ifort or pgf90 for the " \
203	"compiler option"
204	exit
205	esac ;;
206	"-d") grid_resolution=$2 ; shift ; shift ;;
207	"-gprof") OPT_GPROF="-pg" ; shift ;;
208	"-cosp") cosp=$2
209	case $cosp in
210	"none"\|"v1"\|"v2") cosp=$2 ; shift ; shift ;;
211	*) echo Only none v1 v2 for cosp option ; exit
212	esac ;;
213	"-nofcm") compile_with_fcm=0 ; shift ;;
214	"-SCM") SCM=1 ; shift ;;
215	"-opt_makelmdz") OPT_MAKELMDZ="$2" ; shift ; shift ;;
216	"-rrtm") rrtm="$2"
217	if [ "$2" = "false" ] ; then
218	rad="oldrad"
219	else
220	rad="rrtm"
221	fi
222	shift ; shift ;;
223	"-rad") rad=$2
224	case $rad in
225	"oldrad"\|"rrtm"\|"ecrad") rad=$2 ; shift ; shift ;;
226	*) echo Only oldrad rrtm ecrad for rad option ; exit
227	esac ;;
228	"-parallel") parallel=$2
229	case $parallel in
230	"none"\|"mpi"\|"omp"\|"mpi_omp") parallel=$2 ; shift
231	shift ;;
232	*) echo Only none mpi omp mpi_omp for the parallel \
233	option
234	exit
235	esac ;;
236	"-bench") bench=$2 ; shift ; shift ;;
237	"-debug") optim=-debug ; shift ;;
238	"-name") MODEL=$2 ; shift ; shift ;;
239	"-netcdf") netcdf=$2 ; shift ; shift ;;
240	"-physiq") physiq=$2 ; shift ; shift ;;
241	"-xios") with_xios="y" ; shift ;;
242	"-env_file") env_file=$2 ; shift ; shift ;;
243	"-veget") veget=$2 ; shift ; shift ;;
244	*) ./install_lmdz.sh -h ; exit
245	esac
246	done
247
248	# Option de compilation du rayonnement : depend de $mysvn ><= r4185,
249	# sera donc definie plus bas
250
251	#opt_rad=""
252	#case $rad in
253	# rrtm) opt_rad="-rad rrtm" ;;
254	# ecrad) opt_rad="-rad ecrad" ;;
255	#esac
256
257
258	# Option de compilation pour Cosp
259	opt_cosp=""
260	case cosp in
261	v1) opt_cosp="-cosp true" ;;
262	v2) opt_cosp="-cospv2 true" ;;
263	esac
264
265	# Check on veget version
266	#if [ "$veget" != 'NONE' -a "$veget" != "CMIP6" -a "$veget" != +([0-9]) ] ; then
267	if [ $veget != 'NONE' -a $veget != "CMIP6" ] ; then
268	re='^[0-9]+$'
269	if ! [[ $veget =~ $re ]] ; then
270	echo 'Valeur de l option veget non valable'
271	exit
272	fi
273	fi
274
275	#Define veget-related suffix for gcm name
276	if [ "$veget" = 'NONE' ] ; then
277	suff_orc=''
278	#For use with tutorial, orchidee_rev is also defined (will be
279	#written in surface_env at the end of the script)
280	orchidee_rev=''
281	else
282	suff_orc='_orch'
283	fi
284
285
286	if [ $parallel = none ] ; then
287	sequential=1; suff_exe='_seq'
288	else
289	sequential=0; suff_exe='_para_mem'
290	fi
291
292	#Chemin pour placer le modele
293	if [ "$MODEL" = "" ] ; then MODEL=./LMDZ$version$svn$optim ; fi
294
295
296	arch=local
297
298
299	if [ $compiler = g95 ] ; then echo g95 is not supported anymore ; exit ; fi
300
301	################################################################
302	# Specificite des machines
303	################################################################
304
305	hostname=`hostname`
306	if [ "$pclinux" = 1 ] ; then o_ins_make="-t g95" ; else o_ins_make="" ; fi
307
308	case ${hostname:0:5} in
309
310	jean-) compiler="mpiifort" ;
311	par_comp="mpiifort" ;
312	o_ins_make="-t jeanzay" ;
313	make=gmake ;
314	module purge
315	module load intel-compilers/19.0.4 ;
316	#module load intel-mpi/19.0.4 ;
317	#module load intel-mkl/19.0.4 ;
318	module load hdf5/1.10.5-mpi ;
319	module load netcdf/4.7.2-mpi ;
320	module load netcdf-fortran/4.5.2-mpi ;
321	module load subversion/1.9.7 ;
322	export NETCDF_LIBDIR=./
323	export NETCDFFORTRAN_INCDIR=./
324	export NETCDFFORTRAN_LIBDIR=./
325	arch=X64_JEANZAY ;;
326
327	cicla\|camel) compiler="gfortran" ;
328	module load netcdf4/4.3.3.1-gfortran;
329	netcdf=/opt/netcdf43/gfortran
330
331	if [ $parallel != none ] ; then
332	module load openmpi/1.6.5-gfortran ;
333	root_mpi=$MPI_HOME ;
334	path_mpi=$root_mpi/bin ;
335	par_comp=${path_mpi}/mpif90 ;
336	mpirun=${path_mpi}/mpirun ;
337	fi ;
338	arch=local ;
339	make=make ;
340	o_ins_make="-t g95" ;;
341
342	*) if [ $parallel = none -o -f /usr/bin/mpif90 ] ; then
343	path_mpi=`which mpif90 \| sed -e s:/mpif90::` ;
344	if [ -d /usr/lib64/openmpi ] ; then
345	root_mpi="/usr/lib64/openmpi"
346	else
347	root_mpi="/usr"
348	fi
349	else
350	echo "Cannot find mpif90" ;
351	if [ $parallel = none ] ; then exit ; fi ;
352	fi ;
353	if [ $parallel != none ] ; then
354	root_mpi=$(which mpif90 \| sed -e s:/bin/mpif90::)
355	path_mpi=$(which mpif90 \| sed -e s:/mpif90::)
356	export LD_LIBRARY_PATH=${root_mpi}/lib:$LD_LIBRARY_PATH
357	fi
358	par_comp=${path_mpi}/mpif90 ;
359	mpirun=${path_mpi}/mpirun ;
360	arch=local ;
361	make=make ;
362	o_ins_make="-t g95"
363	esac
364
365	# Flags for parallelism:
366	if [ $parallel != none ] ; then
367	# MPI_LD are the flags needed for linking with MPI
368	MPI_LD="-L${root_mpi}/lib -lmpi"
369	if [ "$compiler" = "gfortran" ] ; then
370	# MPI_FLAGS are the flags needed for compilation with MPI
371	MPI_FLAGS="-fcray-pointer"
372	# OMP_FLAGS are the flags needed for compilation with OpenMP
373	OMP_FLAGS="-fopenmp -fcray-pointer"
374	# OMP_LD are the flags needed for linking with OpenMP
375	OMP_LD="-fopenmp"
376	elif [ "$compiler" = "ifort" ] ; then
377	MPI_FLAGS=""
378	OMP_FLAGS="-openmp"
379	OMP_LD="-openmp"
380	else # pgf90
381	MPI_FLAGS=""
382	OMP_FLAGS="-mp"
383	OMP_LD="-mp"
384	fi
385	fi
386
387	#####################################################################
388	# Test for old gfortran compilers
389	# If the compiler is too old (older than 4.3.x) we test if the
390	# temporary gfortran44 patch is available on the computer in which
391	# case the compiler is changed from gfortran to gfortran44
392	# Must be aware than parallelism can not be activated in this case
393	#####################################################################
394
395	if [ "$compiler" = "gfortran" ] ; then
396	gfortran=gfortran
397	gfortranv=`gfortran --version \| \
398	head -1 \| awk ' { print $NF } ' \| awk -F. ' { print $1 * 10 + $2 } '`
399	if [ $gfortranv -le 43 ] ; then
400	echo ERROR : Your gfortran compiler is too old
401	echo 'Please choose a new one (ifort) and change the line'
402	echo compiler=xxx
403	echo in the install_lmdz.sh script and rerun it
404	if [ `which gfortran44 \| wc -w` -ne 0 ] ; then
405	gfortran=gfortran44
406	else
407	echo gfotran trop vieux ; exit
408	fi
409	fi
410	compiler=$gfortran
411	fi
412	#####################################################################
413
414	## if also compiling XIOS, parallel must be mpi_omp
415	if [ "$with_xios" = "y" -a "$parallel" != "mpi_omp" ] ; then
416	echo "Error, you must set -parallel mpi_omp if you want XIOS"
417	exit
418	fi
419
420	if [ "$with_xios" = "y" ] ; then
421	opt_makelmdz_xios="-io xios"
422	fi
423
424	if [ "$cosp" = "v2" -a "$with_xios" = "n" ] ; then
425	echo "Error, Cospv2 cannot run without Xios"
426	exit
427	fi
428
429	echo '################################################################'
430	echo Choix des options de compilation
431	echo '################################################################'
432
433	export FC=$compiler
434	export F90=$compiler
435	export F77=$compiler
436	export CPPFLAGS=
437	OPTIMNC=$OPTIM
438	BASE_LD="$OPT_GPROF"
439	OPTPREC="$OPT_GPROF"
440	ARFLAGS="rs"
441	if [ -f /etc/issue ] ; then
442	if [ "`grep -i ubuntu /etc/issue`" != "" ] ; then
443	if [ "`grep -i ubuntu /etc/issue \| awk ' { print $2 } ' \| cut -d. -f1`" -ge 16 ]
444	then
445	ARFLAGS="rU"
446	fi
447	fi
448	fi
449
450
451
452	if [ "$compiler" = "$gfortran" ] ; then
453	OPTIM='-O3'
454	OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all -fbacktrace -finit-real=snan"
455	OPTDEV="-Wall -fbounds-check"
456	fmod='I '
457	OPTPREC="$OPTPREC -cpp -ffree-line-length-0"
458	if [ $real = r8 ] ; then
459	OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE"
460	fi
461	export F90FLAGS=" -ffree-form $OPTIMNC"
462	export FFLAGS=" $OPTIMNC"
463	export CC=gcc
464	export CXX=g++
465	export fpp_flags="-P -C -traditional -ffreestanding"
466
467	elif [ $compiler = mpif90 ] ; then
468	OPTIM='-O3'
469	OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all"
470	OPTDEV="-Wall -fbounds-check"
471	BASE_LD="$BASE_LD -lblas"
472	fmod='I '
473	if [ $real = r8 ] ; then
474	OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE -fcray-pointer"
475	fi
476	export F90FLAGS=" -ffree-form $OPTIMNC"
477	export FFLAGS=" $OPTIMNC"
478	export CC=gcc
479	export CXX=g++
480
481	elif [ $compiler = pgf90 ] ; then
482	OPTIM='-O2 -Mipa -Munroll -Mnoframe -Mautoinline -Mcache_align'
483	OPTDEB='-g -Mdclchk -Mbounds -Mchkfpstk -Mchkptr -Minform=inform -Mstandard -Ktrap=fp -traceback'
484	OPTDEV='-g -Mbounds -Ktrap=fp -traceback'
485	fmod='module '
486	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -r8 -DNC_DOUBLE" ; fi
487	export CPPFLAGS="-DpgiFortran"
488	export CC=pgcc
489	export CFLAGS="-O2 -Msignextend"
490	export CXX=pgCC
491	export CXXFLAGS="-O2 -Msignextend"
492	export FFLAGS="-O2 $OPTIMNC"
493	export F90FLAGS="-O2 $OPTIMNC"
494	compile_with_fcm=1
495
496	elif [[ $compiler = ifort \|\| $compiler = mpiifort ]] ; then
497	OPTIM="-O2 -fp-model strict -ip -align all "
498	OPTDEV="-p -g -O2 -traceback -fp-stack-check -ftrapuv -check"
499	OPTDEB="-g -no-ftz -traceback -ftrapuv -fp-stack-check -check"
500	fmod='module '
501	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -real-size 64 -DNC_DOUBLE" ; fi
502	export CPP="icc -E"
503	export FFLAGS="-O2 -ip -fpic -mcmodel=large"
504	export FCFLAGS="-O2 -ip -fpic -mcmodel=large"
505	export CC=icc
506	export CFLAGS="-O2 -ip -fpic -mcmodel=large"
507	export CXX=icpc
508	export CXXFLAGS="-O2 -ip -fpic -mcmodel=large"
509	export fpp_flags="-P -traditional"
510	# Pourquoi forcer la compilation fcm. Marche mieux sans
511	#compile_with_fcm=1
512	else
513	echo unexpected compiler $compiler ; exit
514	fi
515
516	OPTIMGCM="$OPTIM $OPTPREC"
517
518	hostname=`hostname`
519
520	##########################################################################
521	# If installing on known machines such as Jean-Zay at IDRIS,
522	# don't check for available software and don't install netcdf
523	if [ ${hostname:0:5} = jean- ] ; then
524	netcdf=0 # no need to recompile netcdf, alreday available
525	check_linux=0
526	pclinux=0
527	ioipsl=0 # no need to recompile ioipsl, already available
528	#netcdf="/smplocal/pub/NetCDF/4.1.3"
529	compiler="mpiifort"
530	fmod='module '
531	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -i4 -r8 -DNC_DOUBLE" ; fi
532	OPTIM="-auto -align all -O2 -fp-model strict -xHost "
533	OPTIMGCM="$OPTIM $OPTPREC"
534	fi
535	##########################################################################
536
537
538	mkdir -p $MODEL
539	echo $MODEL
540	MODEL=`( cd $MODEL ; pwd )` # to get absolute path, if necessary
541
542
543	echo '################################################################'
544	if [ "$check_linux" = 1 ] ; then
545	echo Check if required software is available
546	echo '################################################################'
547
548	#### Ehouarn: test if the required shell is available
549	#### Maj FH-LF-AS 2021-04 : default=bash ; if bash missing, use ksh
550	use_shell="bash" # default
551	if [ "`which bash`" = "" ] ; then
552	echo "no bash ; we will use ksh"
553	use_shell="ksh"
554	if [ "`which ksh`" = "" ] ; then
555	echo "bash (or ksh) needed!! Install it!"
556	exit
557	fi
558	fi
559
560	for logiciel in wget tar gzip make $compiler gcc cmake ; do
561	if [ "`which $logiciel`" = "" ] ; then
562	echo You must first install $logiciel on your system
563	exit
564	fi
565	done
566
567	if [ $pclinux = 1 ] ; then
568	cd $MODEL
569	cat <<eod > tt.f90
570	print*,'coucou'
571	end
572	eod
573	$compiler tt.f90 -o a.out
574	./a.out >\| tt
575	if [ "`cat tt \| sed -e 's/ //g' `" != "coucou" ] ; then
576	echo problem installing with compiler $compiler ; exit ; fi
577	\rm tt a.out tt.f90
578	fi
579	fi
580
581	###########################################################################
582	if [ $getlmdzor = 1 -a ! -d $MODEL/modipsl ] ; then
583	###########################################################################
584	echo '##########################################################'
585	echo Download a slightly modified version of LMDZ
586	echo '##########################################################'
587	cd $MODEL
588	myget src/modipsl.$version.tar.gz
589	echo install_lmdz.sh wget_OK `date`
590	gunzip modipsl.$version.tar.gz
591	tar xf modipsl.$version.tar
592	\rm modipsl.$version.tar
593	fi
594
595	###########################################################################
596	if [ $netcdf = 1 ] ; then
597	###########################################################################
598	cd $MODEL
599	netcdflog=`pwd`/netcdf.log
600	echo '##########################################################'
601	echo Compiling the Netcdf library
602	echo '##########################################################'
603	echo log file : $netcdflog
604	if [[ "$with_xios" = "n" && ! -d $MODEL/netcdf4_hdf5_seq ]] ; then
605	myget import/install_netcdf4_hdf5_seq.bash
606	chmod +x install_netcdf4_hdf5_seq.bash
607
608	if [ "$compiler" = "gfortran" ]
609	then
610	./install_netcdf4_hdf5_seq.bash -prefix $MODEL/netcdf4_hdf5_seq \
611	-compiler gnu > $netcdflog 2>&1
612	elif [ "$compiler" = "ifort" ]
613	then
614	./install_netcdf4_hdf5_seq.bash -prefix $MODEL/netcdf4_hdf5_seq \
615	-compiler intel > $netcdflog 2>&1
616	else
617	echo "unexpected compiler $compiler" ; exit
618	fi
619
620	# LF rajout d'une verrue, pour une raison non encore expliquee,
621	# la librairie est parfois rangée dans lib64 et non dans lib
622	# par certains compilateurs
623	if [ ! -e lib -a -d lib64 ] ; then ln -s lib64 lib; fi
624	elif [[ "$with_xios" = "y" && ! -d $MODEL/netcdf4_hdf5 ]]
625	then
626	# download and compile hdf5 and netcdf, etc. using the
627	# install_netcdf4_hdf5.bash script
628	myget import/install_netcdf4_hdf5.bash
629	chmod u=rwx install_netcdf4_hdf5.bash
630	if [ "$compiler" = "gfortran" ] ; then
631	./install_netcdf4_hdf5.bash -prefix $MODEL/netcdf4_hdf5 -CC gcc \
632	-FC gfortran -CXX g++ -MPI $root_mpi > $netcdflog 2>&1
633	elif [ "$compiler" = "ifort" ] ; then
634	./install_netcdf4_hdf5.bash -prefix $MODEL/netcdf4_hdf5 -CC icc \
635	-FC ifort -CXX icpc -MPI $root_mpi > $netcdflog 2>&1
636	elif [ "$compiler" = "pgf90" ] ; then
637	./install_netcdf4_hdf5.bash -prefix $MODEL/netcdf4_hdf5 -CC pgcc \
638	-FC pgf90 -CXX pgCC -MPI $root_mpi > $netcdflog 2>&1
639	else
640	echo "unexpected compiler $compiler" ; exit
641	fi
642	fi # of if [ "$with_xios" = "n" ]
643	echo install_lmdz.sh netcdf_OK `date`
644	fi # of if [ $netcdf = 1 ]
645
646	# ncdfdir contains the directory where netcdf is installed
647	if [ $netcdf = 1 ] ; then
648	if [ "$with_xios" = "y" ] ; then
649	ncdfdir=$MODEL/netcdf4_hdf5
650	else
651	ncdfdir=$MODEL/netcdf4_hdf5_seq
652	fi
653	elif [ $netcdf = 0 ]
654	then
655	ncdfdir=/usr
656	else
657	ncdfdir=$netcdf
658	fi
659
660	#=========================================================================
661	if [[ ! -f $MODEL/modipsl/lib/libioipsl.a ]]
662	then
663	if [ $ioipsl = 1 ] ; then
664	#=====================================================================
665	echo OK ioipsl=$ioipsl
666	echo '##########################################################'
667	echo 'Installing MODIPSL, the installation package manager for the '
668	echo 'IPSL models and tools'
669	echo '##########################################################'
670	echo `date`
671
672	cd $MODEL/modipsl
673	\rm -rf lib/*
674	cd util
675	cp AA_make.gdef AA_make.orig
676	F_C="$compiler -c "
677	if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ]
678	then
679	F_C="$compiler -c -cpp "
680	fi
681	if [ "$compiler" = "pgf90" ] ; then F_C="$compiler -c -Mpreprocess" ; fi
682	sed -e 's/^\#..g95..\#.*.$/\#/' AA_make.gdef > tmp
683	sed -e "s:F_L = g95:F_L = $compiler:" \
684	-e "s:F_C = g95 -c -cpp:F_C = $F_C": \
685	-e 's/g95..w_w..(F_D)/g95 w_w = '"$OPTIMGCM"'/' \
686	-e 's:g95..NCDF_INC..$:g95 NCDF_INC= '"$ncdfdir"'/include:' \
687	-e 's:g95..NCDF_LIB..$:g95 NCDF_LIB= -L'"$ncdfdir"'/lib -lnetcdff -lnetcdf:' \
688	-e 's:g95 L_O =:g95 L_O = -Wl,-rpath='"$ncdfdir"'/lib:' \
689	-e "s:-fmod=:-$fmod:" -e 's/-fno-second-underscore//' \
690	-e 's:#-Q- g95 M_K = gmake:#-Q- g95 M_K = make:' \
691	tmp >\| AA_make.gdef
692
693	if [ $pcmac == 1 ]
694	then
695	cp AA_make.gdef tmp
696	sed -e 's/rpath=/rpath,/g' tmp > AA_make.gdef
697	fi
698
699
700	# We use lines for g95 even for the other compilers to run ins_make
701	if [ "$use_shell" = "ksh" ] ; then
702	./ins_make $o_ins_make
703	else # bash
704	sed -e s:/bin/ksh:/bin/bash:g ins_make > ins_make.bash
705	if [ "`grep jeanzay AA_make.gdef`" = "" ] ; then
706	# Bidouille pour compiler sur ada des vieux modipsl.tar
707	echo 'Warning jean-zay not in AA_make.gdef'
708	echo 'Think about updating'
709	exit 1
710	fi
711
712	chmod u=rwx ins_make.bash
713	./ins_make.bash $o_ins_make
714	fi # of if [ "$use_shell" = "ksh" ]
715
716	echo install_lmdz.sh MODIPSL_OK `date`
717
718	cd $MODEL/modipsl/modeles/IOIPSL/src
719	ioipsllog=`pwd`/ioipsl.log
720	echo '##########################################################'
721	echo 'Compiling IOIPSL, the interface library with Netcdf'
722	echo '##########################################################'
723	echo `date`
724	echo log file : $ioipsllog
725
726	if [ "$use_shell" = "bash" ] ; then
727	cp Makefile Makefile.ksh
728	sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile
729	fi
730	# if [ "$pclinux" = 1 ] ; then
731	# Build IOIPSL modules and library
732	$make clean
733	$make > $ioipsllog 2>&1
734	if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then
735	# copy module files to lib
736	cp -f *.mod ../../../lib
737	fi
738	# Build IOIPSL tools (ie: "rebuild", if present)
739	if [ -f $MODEL/modipsl/modeles/IOIPSL/tools/rebuild ] ; then
740	cd $MODEL/modipsl/modeles/IOIPSL/tools
741	# adapt Makefile & rebuild script if in bash
742	if [ "$use_shell" = "bash" ] ; then
743	cp Makefile Makefile.ksh
744	sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile
745	cp rebuild rebuild.ksh
746	sed -e 's:/bin/ksh:/bin/bash:g' \
747	-e 's:print -u2:echo:g' \
748	-e 's:print:echo:g' rebuild.ksh > rebuild
749	fi
750	$make clean
751	$make > $ioipsllog 2>&1
752	fi
753	# fi # of if [ "$pclinux" = 1 ]
754
755	else # of if [ $ioipsl = 1 ]
756	if [ ${hostname:0:5} = jean- ] ; then
757	cd $MODEL/modipsl
758	cd util
759	if [ "`grep jeanzay AA_make.gdef`" = "" ] ; then
760	echo 'Warning jean-zay not in AA_make.gdef'
761	echo 'Think about updating'
762	exit 1
763	fi
764	./ins_make $o_ins_make
765	# Compile IOIPSL on jean-zay
766	cd $MODEL/modipsl/modeles/IOIPSL/src
767	gmake > ioipsl.log
768	cd $MODEL/modipsl/modeles/IOIPSL/tools
769	gmake > ioipsl.log
770
771	fi
772	echo install_lmdz.sh ioipsl_OK `date`
773	fi # of if [ $ioipsl = 1 ]
774	fi
775	# Saving ioipsl lib for possible parallel compile
776	cd $MODEL/modipsl
777	tar cf ioipsl.tar lib/ bin/
778
779	#=========================================================================
780	if [ "$with_xios" = "y" ] ; then
781	echo '##########################################################'
782	echo 'Compiling XIOS'
783	echo '##########################################################'
784	cd $MODEL/modipsl/modeles
785	xioslog=`pwd`/xios.log
786	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/install_xios.bash
787	myget import/install_xios.bash
788	chmod u=rwx install_xios.bash
789	if [ ${hostname:0:5} = jean- ] ; then
790	svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5 \
791	XIOS
792	cd XIOS/arch
793	svn update
794	cd ..
795	echo "Compiling XIOS, start" `date` \
796	"(it takes about 20 min on Jean-Zay)"
797	echo "log file: $xioslog"
798	./make_xios --prod --arch $arch --job 4 > xios.log 2>&1
799	else
800	./install_xios.bash -prefix $MODEL/modipsl/modeles \
801	-netcdf ${ncdfdir} -hdf5 ${ncdfdir} \
802	-MPI $root_mpi -arch $arch > xios.log 2>&1
803	fi # of case Jean-Zay
804	if [ -f XIOS/lib/libxios.a ] ; then
805	echo "XIOS library successfully generated"
806	echo install_lmdz.sh XIOS_OK `date`
807	fi
808	fi
809
810	#============================================================================
811	veget_version=false
812	if [ "$veget" != 'NONE' ] ; then
813	cd $MODEL/modipsl/modeles/ORCHIDEE
814	set +e ; svn upgrade ; set -e
815	if [ "$veget" = "CMIP6" ] ; then
816	veget_version=orchidee2.0
817	orchidee_rev=6592
818	else # specific orchidee revision newer than CMIP6, on 2_1 or 2_2 branches
819	veget_version=orchidee2.1
820	orchidee_rev=$veget
821	if [ $veget -lt 4465 ] ; then
822	echo 'Stopping, ORCHIDEE version too old, script needs work on ' \
823	'the CPP flags to pass to makelmdz'
824	exit 1
825	fi
826	set +e
827	# which branch is my version on?
828	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}'`
829	# switch to that branch
830	echo IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at \
831	orchidee-help@listes.ipsl.fr
832	svn switch -r $veget --accept theirs-full \
833	svn://forge.ipsl.jussieu.fr/orchidee/$orcbranch
834	svn log -r $veget \| grep $veget
835	if [ $? -gt 0 ] ; then
836	echo 'Cannot update ORCHIDEE as not on the right branch for ' \
837	'ORCHIDEE'
838	exit
839	fi
840	set -e
841	set +e ; svn update -r $veget ; set -e
842	fi
843	# Correctif suite debug Jean-Zay
844	sed -i -e 's/9010 FORMAT(A52,F17.14)/9010 FORMAT(A52,F20.14)/' \
845	src_stomate/stomate.f90
846	opt_orc="-prod" ; if [ "$optim" = "-debug" ] ; then opt_orc="-debug" ; fi
847
848	orchideelog=`pwd`/orchidee.log
849	echo '########################################################'
850	echo 'Compiling ORCHIDEE, the continental surface model '
851	echo '########################################################'
852	echo Start of the first compilation of orchidee, in sequential mode: `date`
853	echo log file : $orchideelog
854
855	export ORCHPATH=`pwd`
856	xios_orchid="-noxios"
857	if [ "$with_xios" = "y" ] ; then
858	xios_orchid="-xios"
859	fi
860	if [ -d tools ] ; then
861	###################################################################
862	# Pour les experts qui voudraient changer de version d'orchidee.
863	# Attention : necessite d'avoir le password pour orchidee
864
865	# Correctif suite debug Jean-Zay
866	if [ -f src_global/time.f90 ] ; then
867	sed -i -e 's/CALL tlen2itau/\!CALL tlen2itau/' src_global/time.f90
868	fi
869	###################################################################
870	if [ "$veget_version" == "false" ] ; then
871	veget_version=orchidee2.0
872	fi
873	cd arch
874	sed -e s:"%COMPILER .*.$":"%COMPILER $compiler":1 \
875	-e s:"%LINK .*.$":"%LINK $compiler":1 \
876	-e s:"%FPP_FLAGS .*.$":"%FPP_FLAGS $fpp_flags":1 \
877	-e s:"%PROD_FFLAGS .*.$":"%PROD_FFLAGS $OPTIM":1 \
878	-e s:"%DEV_FFLAGS .*.$":"%DEV_FFLAGS $OPTDEV":1 \
879	-e s:"%DEBUG_FFLAGS .*.$":"%DEBUG_FFLAGS $OPTDEB":1 \
880	-e s:"%BASE_FFLAGS .*.$":"%BASE_FFLAGS $OPTPREC":1 \
881	-e s:"%BASE_LD .*.$":"%BASE_LD $BASE_LD":1 \
882	-e s:"%ARFLAGS .*.$":"%ARFLAGS $ARFLAGS":1 \
883	arch-gfortran.fcm > arch-local.fcm
884	echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib -lnetcdff -lnetcdf\"" \
885	> arch-local.path
886	echo "NETCDF_INCDIR=${ncdfdir}/include" >> arch-local.path
887	echo "IOIPSL_INCDIR=$ORCHPATH/../../lib" >> arch-local.path
888	echo "IOIPSL_LIBDIR=$ORCHPATH/../../lib" >> arch-local.path
889	echo 'XIOS_INCDIR=${ORCHDIR}/../XIOS/inc' >> arch-local.path
890	echo 'XIOS_LIBDIR="${ORCHDIR}/../XIOS/lib -lxios"' >> arch-local.path
891	cd ../
892
893	echo ./makeorchidee_fcm -j $xios_orchid $opt_orc -parallel none \
894	-arch $arch
895	./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel none \
896	-arch $arch > $orchideelog 2>&1
897	pwd
898	else # of "if [ -d tools ]"
899	if [ -d src_parallel ] ; then
900	liste_src="parallel parameters global stomate sechiba driver"
901	if [ "$veget_version" == "false" ] ; then
902	veget_version=orchidee2.0
903	fi
904	fi
905	for d in $liste_src ; do
906	src_d=src_$d
907	echo src_d $src_d
908	echo ls ; ls
909	if [ ! -d $src_d ] ; then
910	echo Problem orchidee : no $src_d ; exit
911	fi
912	cd $src_d ; \rm -f *.mod make ; $make clean
913	$make > $orchideelog 2>&1
914	if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then
915	cp -f *.mod ../../../lib
916	fi
917	cd ..
918	done
919	fi # of "if [ -d tools ]"
920	echo install_lmdz.sh orchidee_compil_seq_OK `date`
921	fi # of if [ "$veget" != 'NONE' ]
922
923
924	#============================================================================
925	# Ehouarn: the directory name LMDZ* depends on version/tar file...
926	if [ -d $MODEL/modipsl/modeles/LMD* ] ; then
927	echo '###############################################################'
928	echo 'Preparing LMDZ compilation : arch file, svn switch if needed...'
929	echo '###############################################################'
930	cd $MODEL/modipsl/modeles/LMD*
931	LMDZPATH=`pwd`
932	else
933	echo "ERROR: No LMD* directory !!!"
934	exit
935	fi
936
937	###########################################################
938	# For those who want to use fcm to compile via :
939	# makelmdz_fcm -arch local .....
940	############################################################
941
942	if [[ "$pclinux" = "1" && ! -f arch/arch-local.path ]] ; then
943
944	# create local 'arch' files (if on Linux PC):
945	cd arch
946	# arch-local.path file
947	echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib -lnetcdff -lnetcdf\"" \
948	> arch-local.path
949	echo "NETCDF_INCDIR=-I${ncdfdir}/include" >> arch-local.path
950	echo 'NETCDF95_INCDIR=$LMDGCM/../../include' >> arch-local.path
951	echo 'NETCDF95_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
952	echo 'IOIPSL_INCDIR=$LMDGCM/../../lib' >> arch-local.path
953	echo 'IOIPSL_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
954	echo 'XIOS_INCDIR=$LMDGCM/../XIOS/inc' >> arch-local.path
955	echo 'XIOS_LIBDIR=$LMDGCM/../XIOS/lib' >> arch-local.path
956	echo 'ORCH_INCDIR=$LMDGCM/../../lib' >> arch-local.path
957	echo 'ORCH_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
958
959	if [ $pcmac == 1 ] ; then
960	BASE_LD="$BASE_LD -Wl,-rpath,${ncdfdir}/lib"
961	else
962	BASE_LD="$BASE_LD -Wl,-rpath=${ncdfdir}/lib"
963	fi
964	# Arch-local.fcm file (adapted from arch-linux-32bit.fcm)
965
966	if [ $real = r8 ] ; then FPP_DEF=NC_DOUBLE ; else FPP_DEF="" ; fi
967	sed -e s:"%COMPILER .*.$":"%COMPILER $compiler":1 \
968	-e s:"%LINK .*.$":"%LINK $compiler":1 \
969	-e s:"%PROD_FFLAGS .*.$":"%PROD_FFLAGS $OPTIM":1 \
970	-e s:"%DEV_FFLAGS .*.$":"%DEV_FFLAGS $OPTDEV":1 \
971	-e s:"%DEBUG_FFLAGS .*.$":"%DEBUG_FFLAGS $OPTDEB":1 \
972	-e s:"%BASE_FFLAGS .*.$":"%BASE_FFLAGS $OPTPREC":1 \
973	-e s:"%FPP_DEF .*.$":"%FPP_DEF $FPP_DEF":1 \
974	-e s:"%BASE_LD .*.$":"%BASE_LD $BASE_LD":1 \
975	-e s:"%ARFLAGS .*.$":"%ARFLAGS $ARFLAGS":1 \
976	arch-linux-32bit.fcm > arch-local.fcm
977
978	cd ..
979	### Adapt "bld.cfg" (add the shell):
980	#whereisthatshell=$(which ${use_shell})
981	#echo "bld::tool::SHELL $whereisthatshell" >> bld.cfg
982
983	fi # of if [ "$pclinux" = 1 ]
984
985
986	cd $MODEL/modipsl/modeles/LMDZ*
987	lmdzlog=`pwd`/lmdz.log
988
989	##################################################################
990	# Possibly update LMDZ if a specific svn release is requested
991	##################################################################
992
993	set +e ; svn upgrade ; set -e
994
995	if [ "$svn" = "last" ] ; then svnopt="" ; else svnopt="-r $svn" ; fi
996	if [ "$svn" != "" ] ; then
997	set +e ; svn info \| grep -q 'http:'
998	if [ $? = 0 ] ; then
999	svn switch --relocate http://svn.lmd.jussieu.fr/LMDZ \
1000	https://svn.lmd.jussieu.fr/LMDZ
1001	fi
1002	svn update $svnopt
1003	fi
1004	set -e
1005
1006	##################################################################
1007	# Retrieve the final svn release number, and adjust compilation
1008	# options accordingly
1009	mysvn=`svnversion . \| egrep -o "[0-9]+"`
1010
1011	# Option de compilation du rayonnement : depend de $mysvn ><= r4185
1012	opt_rad=""
1013
1014	case $rad in
1015	oldrad) iflag_rrtm=0 ; NSW=2 ; opt_rad="" ;;
1016	rrtm) iflag_rrtm=1 ; NSW=6
1017	if [ $mysvn -le 4185 ] ; then
1018	opt_rad="-rrtm true"
1019	else
1020	opt_rad="-rad rrtm"
1021	fi ;;
1022	ecrad) iflag_rrtm=2 ; NSW=6 ; opt_rad="-rad ecrad" ;;
1023	*) echo Only oldrad rrtm ecrad for rad option ; exit
1024	esac
1025
1026	if [ $mysvn -le 4185 -a $rad = "ecrad" ] ; then
1027	echo "ecrad only available for LMDZ rev starting with 4186 " ; exit
1028	fi
1029
1030	##################################################################
1031
1032
1033	if [[ ! -f libf/misc/netcdf95.F90 && ! -d $MODEL/NetCDF95-0.2 ]]
1034	then
1035	cd $MODEL
1036	myget import/NetCDF95-0.2.tar.gz
1037	tar -xf NetCDF95-0.2.tar.gz
1038	rm NetCDF95-0.2.tar.gz
1039	cd NetCDF95-0.2
1040	mkdir build
1041	cd build
1042	cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=$ncdfdir \
1043	-DCMAKE_INSTALL_PREFIX=$MODEL/modipsl
1044	make install
1045	cd $MODEL/modipsl/modeles/LMDZ*
1046	fi
1047
1048	echo '##################################################################'
1049	echo "Preparing script compile.sh for LMDZ compilation"
1050	echo "It will only be run automatically if bench=1/tuto"
1051	echo Here bench=$bench
1052	echo '##################################################################'
1053
1054	if [ "$env_file" != "" ] ; then
1055	mv arch/arch-${arch}.env arch/arch-${arch}.orig
1056	\cp -f $env_file arch/arch-${arch}.env
1057	fi
1058
1059	if [ $compile_with_fcm = 1 ] ; then
1060	makelmdz="makelmdz_fcm $optim -arch $arch -j 8 "
1061	else
1062	makelmdz="makelmdz $optim -arch $arch"
1063	fi
1064
1065	# sequential compilation
1066	if [ "$sequential" = 1 ] ; then
1067	echo Sequential compilation command, saved in compile.sh:
1068	echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp " \
1069	"-d ${grid_resolution} -v $veget_version gcm "
1070	echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp " \
1071	"-d ${grid_resolution} -v $veget_version gcm " > compile.sh
1072	chmod +x ./compile.sh
1073	if [ $bench = 1 ] ; then
1074	echo install_lmdz.sh start_lmdz_seq_compilation `date`
1075	echo log file: $lmdzlog
1076	./compile.sh > $lmdzlog 2>&1
1077	echo install_lmdz.sh end_lmdz_seq_compilation `date`
1078	fi
1079	fi # fin sequential
1080
1081	# compiling in parallel mode
1082	if [ $parallel != "none" ] ; then
1083	echo '##########################################################'
1084	echo ' Parallel compile '
1085	echo '##########################################################'
1086	echo "(after saving the sequential libs and binaries)"
1087	cd $MODEL/modipsl
1088	tar cf sequential.tar bin/ lib/
1089	\rm -rf bin/ lib/
1090	tar xf ioipsl.tar
1091	#
1092	# Orchidee
1093	#
1094	cd $ORCHPATH
1095	if [ -d src_parallel -a $veget != 'NONE' ] ; then
1096	cd arch
1097	sed \
1098	-e s:"%COMPILER.*.$":"%COMPILER $par_comp":1 \
1099	-e s:"%LINK.*.$":"%LINK $par_comp":1 \
1100	-e s:"%MPI_FFLAG.*.$":"%MPI_FFLAGS $MPI_FLAGS":1 \
1101	-e s:"%OMP_FFLAG.*.$":"%OMP_FFLAGS $OMP_FLAGS":1 \
1102	-e s:"%MPI_LD.*.$":"%MPI_LD $MPI_LD":1 \
1103	-e s:"%OMP_LD.*.$":"%OMP_LD $OMP_LD":1 \
1104	arch-local.fcm > tmp.fcm
1105
1106	mv tmp.fcm arch-local.fcm
1107	cd ../
1108	echo Compiling ORCHIDEE in parallel mode `date`
1109	echo logfile $orchideelog
1110	echo "NOTE : to recompile it when necessary, use ./compile_orc.sh " \
1111	"in modipsl/modeles/ORCHIDEE"
1112	echo ./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc \
1113	-parallel $parallel -arch $arch > compile_orc.sh
1114	echo ./makeorchidee_fcm -j 8 $xios_orchid $opt_orc \
1115	-parallel $parallel -arch $arch >> compile_orc.sh
1116	echo echo Now you must also recompile LMDZ, by running ./compile.sh \
1117	in modeles/LMDZ >> compile_orc.sh
1118	chmod u+x compile_orc.sh
1119	./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc \
1120	-parallel $parallel -arch $arch > $orchideelog 2>&1
1121	./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel $parallel \
1122	-arch $arch >> $orchideelog 2>&1
1123	echo End of ORCHIDEE compilation in parallel mode `date`
1124	elif [ $veget != 'NONE' ] ; then
1125	echo '##########################################################'
1126	echo ' Orchidee version too old '
1127	echo ' Please update to new version '
1128	echo '##########################################################'
1129	exit
1130	fi # of [ -d src_parallel -a $veget != 'NONE' ]
1131
1132	# LMDZ
1133	cd $LMDZPATH
1134	if [ $arch = local ] ; then
1135	cd arch
1136	sed -e s:"%COMPILER.*.$":"%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 $OMP_FLAGS":1 \
1140	-e s:"%ARFLAGS.*.$":"%ARFLAGS $ARFLAGS":1 \
1141	-e s@"%BASE_LD.*.$"@"%BASE_LD -Wl,-rpath=${root_mpi}/lib:${ncdfdir}/lib"@1 \
1142	-e s:"%MPI_LD.*.$":"%MPI_LD $MPI_LD":1 \
1143	-e s:"%OMP_LD.*.$":"%OMP_LD $OMP_LD":1 \
1144	arch-local.fcm > tmp.fcm
1145	mv tmp.fcm arch-local.fcm
1146	cd ../
1147	fi
1148	rm -f compile.sh
1149	echo resol=${grid_resolution} >> compile.sh
1150	if [ ${hostname:0:5} = jean- -a "$cosp" = "v2" ] ; then
1151
1152	echo LMDZ compilation command in parallel mode, saved in compile.sh, \
1153	is :
1154	echo "(ATTENTION le probleme de cospv2 sur jean-zay en mode prod " \
1155	"n est pas corrige ! )"
1156	# ATTENTION le probleme de cospv2 sur jean-zay en mode prod n
1157	# est pas corrige
1158	echo ./$makelmdz -dev $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
1159	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
1160	-parallel $parallel gcm >> compile.sh
1161	echo ./$makelmdz -dev $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
1162	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
1163	-parallel $parallel gcm
1164	else
1165	echo ./$makelmdz $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
1166	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
1167	-parallel $parallel gcm >> compile.sh
1168	echo ./$makelmdz $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \
1169	$opt_makelmdz_xios -d \$resol -v $veget_version -mem \
1170	-parallel $parallel gcm
1171	fi
1172	chmod +x ./compile.sh
1173
1174	if [ $bench = 1 ] ; then
1175	echo Compiling LMDZ in parallel mode `date`, LMDZ log file: $lmdzlog
1176	./compile.sh > $lmdzlog 2>&1
1177	fi
1178
1179	fi # of if [ $parallel != "none" ]
1180
1181
1182	##################################################################
1183	# Verification du succes de la compilation
1184	##################################################################
1185
1186	# Recherche de l'executable dont le nom a change au fil du temps ...
1187	# suffix contains radiative option starting with revision 4186
1188	if [ $mysvn -ge 4186 ] ; then suff_exe=_${rad}${suff_exe} ; fi
1189	gcm=""
1190
1191	for exe in gcm.e bin/gcm_${grid_resolution}_phylmd${suff_exe}${suff_orc}.e
1192	do
1193	if [ -f $exe ] ; then gcm=$exe ; fi
1194	done
1195
1196	if [ "$gcm" = "" ] ; then
1197	if [ $bench = 1 ] ; then
1198	echo 'Compilation failed !! Cannot run the benchmark;'
1199	exit
1200	else
1201	echo 'Compilation not done (only done when bench=1)'
1202	fi
1203	else
1204	echo '##########################################################'
1205	echo 'Compilation successfull !! ' `date`
1206	echo '##########################################################'
1207	echo The executable is $gcm
1208	fi
1209
1210	##################################################################
1211	# Below, we run a benchmark if bench=1 or tuto
1212	##################################################################
1213
1214	if [ $bench = tuto ] ; then
1215	myget Training/tutorial.tar ; tar xvf tutorial.tar ; cd TUTORIAL
1216	./init.sh
1217
1218	elif [[ $bench = 1 && ! -d BENCH${grid_resolution} ]] ; then
1219	# TOUTE CETTE SECTION DEVRAIT DISPARAITRE POUR UNE COMMANDE
1220	# OU DES BENCHS PAR MOTS CLES COMME tuto
1221
1222	echo '##########################################################'
1223	echo ' Running a test run '
1224	echo '##########################################################'
1225
1226	\rm -rf BENCH${grid_resolution}
1227	bench=bench_lmdz_${grid_resolution}
1228	echo install_lmdz.sh before bench download `date`
1229	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/$bench.tar.gz
1230	myget 3DBenchs/$bench.tar.gz
1231	echo install_lmdz.sh after bench download `date`
1232	tar xvf $bench.tar.gz
1233
1234	if [ "$cosp" = "v1" -o "$cosp" = "v2" ] ; then
1235	cd BENCH${grid_resolution}
1236	# copier les fichiers namelist input et output our COSP
1237	cp ../DefLists/cosp*_input_nl.txt .
1238	cp ../DefLists/cosp*_output_nl.txt .
1239	# Activer la cles ok_cosp pour tourner avec COSP
1240	sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp
1241	\mv -f tmp config.def
1242	cd ..
1243	fi
1244
1245	if [ -n "$physiq" ]; then
1246	cd BENCH${grid_resolution}
1247	if [ -f physiq.def_${physiq} ]; then
1248	cp physiq.def_${physiq} physiq.def
1249	echo using physiq.def_${physiq}
1250	else
1251	echo using standard physiq.def
1252	fi
1253	cd ..
1254	else
1255	echo using standard physiq.def
1256	fi
1257
1258	if [ "$with_xios" = "y" ] ; then
1259	cd BENCH${grid_resolution}
1260	cp ../DefLists/iodef.xml .
1261	cp ../DefLists/context_lmdz.xml .
1262	cp ../DefLists/field_def_lmdz.xml .
1263	# A raffiner par la suite
1264	echo A FAIRE : Copier les *xml en fonction de l option cosp
1265	cp ../DefLists/field_def_cosp*.xml .
1266	cp ../DefLists/file_def_hist*xml .
1267	# adapt iodef.xml to use attached mode
1268	sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' \
1269	iodef.xml > tmp
1270	\mv -f tmp iodef.xml
1271
1272	# and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
1273	# except for histday
1274	for histfile in file_def_hist*xml
1275	do
1276	if [ "$histfile" = "file_def_histday_lmdz.xml" ] ; then
1277	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' \
1278	$histfile > tmp
1279	\mv -f tmp $histfile
1280	sed -e 's@output_level="_AUTO_"@output_level="5"@' $histfile \
1281	> tmp
1282	\mv -f tmp $histfile
1283	sed -e 's@compression_level="2"@compression_level="0"@' \
1284	$histfile > tmp
1285	\mv -f tmp $histfile
1286	else
1287	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
1288	$histfile > tmp
1289	\mv -f tmp $histfile
1290	fi
1291	done
1292	# and add option "ok_all_xml=y" in config.def
1293	echo "### XIOS outputs" >> config.def
1294	echo 'ok_all_xml=.true.' >> config.def
1295
1296	#activer les sorties pour Cosp
1297	if [ "$cosp" = "v1" ] ; then
1298	histfile=file_def_histdayCOSP_lmdz.xml
1299	sed -e 's@enabled=".FALSE."@enabled=".TRUE."@' $histfile > tmp
1300	\mv -f tmp $histfile
1301	sed -e 's@output_level="_AUTO_"@output_level="5"@' $histfile > tmp
1302	\mv -f tmp $histfile
1303	sed -e 's@compression_level="2"@compression_level="0"@' \
1304	$histfile > tmp
1305	\mv -f tmp $histfile
1306	fi
1307	if [ "$cosp" = "v2" ] ; then
1308	histfile=file_def_histdayCOSPv2_lmdz.xml
1309	sed -e 's@compression_level="2"@compression_level="0"@' \
1310	$histfile > tmp
1311	\mv -f tmp $histfile
1312	contextfile=context_lmdz.xml
1313	sed -e 's@src="./file_def_histdayCOSP_lmdz.xml"@src="./file_def_histdayCOSPv2_lmdz.xml"@' \
1314	$contextfile > tmp
1315	\mv -f tmp $contextfile
1316	sed -e 's@src="./file_def_histmthCOSP_lmdz.xml"@src="./file_def_histmthCOSPv2_lmdz.xml"@' \
1317	$contextfile > tmp
1318	\mv -f tmp $contextfile
1319	sed -e 's@src="./file_def_histhfCOSP_lmdz.xml"@src="./file_def_histhfCOSPv2_lmdz.xml"@' \
1320	$contextfile > tmp
1321	\mv -f tmp $contextfile
1322	fieldfile=field_def_lmdz.xml
1323	sed -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' $fieldfile \
1324	> tmp
1325	\mv -f tmp $fieldfile
1326	fi
1327
1328	cd ..
1329	fi
1330
1331	# Cas Bensh avec ecrad
1332	if [ "$rad" = "ecrad" ] ; then
1333	cd BENCH${grid_resolution}
1334	cp ../DefLists/namelist_ecrad .
1335	cp -r ../libf/phylmd/ecrad/data .
1336	cd ..
1337	fi
1338
1339	# Adjusting bench physiq.def to radiative code chosen
1340	cd BENCH${grid_resolution}
1341	sed -e 's/iflag_rrtm=.*.$/iflag_rrtm='$iflag_rrtm'/' \
1342	-e 's/NSW=.*.$/NSW='$NSW'/' physiq.def > tmpdef
1343	\mv tmpdef physiq.def
1344	cd ..
1345
1346	cp $gcm BENCH${grid_resolution}/gcm.e
1347
1348	cd BENCH${grid_resolution}
1349	# On cree le fichier bench.sh au besoin
1350	# Dans le cas 48x36x39 le bench.sh existe deja en parallele
1351
1352	if [ "$grid_resolution" = "48x36x39" ] ; then
1353	echo On ne touche pas au bench.sh
1354	# But we have to adapt "run_local.sh" for $mpirun
1355	sed -e "s@mpirun@$mpirun@g" run_local.sh > tmp
1356	mv -f tmp run_local.sh
1357	chmod u=rwx run_local.sh
1358	elif [ "${parallel:0:3}" = "mpi" ] ; then
1359	# Lancement avec deux procs mpi et 2 openMP
1360	echo "export OMP_STACKSIZE=800M" > bench.sh
1361	if [ "${parallel:4:3}" = "omp" ] ; then
1362	echo "export OMP_NUM_THREADS=2" >> bench.sh
1363	fi
1364	if [ "$cosp" = "v1" -o "$cosp" = "v2" ] ; then
1365	if [ ${hostname:0:5} = jean- ] ; then
1366	chmod +x ../arch.env
1367	../arch.env
1368	echo "ulimit -s 2000000" >> bench.sh
1369	else
1370	echo "ulimit -s 200000" >> bench.sh
1371	fi
1372	else
1373	echo "ulimit -s unlimited" >> bench.sh
1374	fi
1375	if [ ${hostname:0:5} = jean- ] ; then
1376	. ../arch/arch-${arch}.env
1377	echo "srun -n 2 -A $idris_acct@cpu gcm.e > listing 2>&1" \
1378	>> bench.sh
1379	else
1380	echo "$mpirun -np 2 gcm.e > listing 2>&1" >> bench.sh
1381	fi
1382	# Add rebuild, using reb.sh if it is there
1383	echo 'if [ -f reb.sh ] ; then' >> bench.sh
1384	echo ' ./reb.sh histday ; ./reb.sh histmth ; ./reb.sh histhf ; ' \
1385	'./reb.sh histins ; ./reb.sh stomate_history ; ' \
1386	'./reb.sh sechiba_history ; ./reb.sh sechiba_out_2 ' >> bench.sh
1387	echo 'fi' >> bench.sh
1388	else
1389	echo "./gcm.e > listing 2>&1" > bench.sh
1390	fi
1391	# Getting orchidee stuff
1392	if [ $veget == 'CMIP6' ] ; then
1393	#echo 'myget 3DBenchs/BENCHorch11.tar.gz'
1394	#myget 3DBenchs/BENCHorch11.tar.gz
1395	#tar xvzf BENCHorch11.tar.gz
1396	echo 'myget 3DBenchs/BENCHCMIP6.tar.gz'
1397	myget 3DBenchs/BENCHCMIP6.tar.gz
1398	tar xvzf BENCHCMIP6.tar.gz
1399	sed -e "s:VEGET=n:VEGET=y:" config.def > tmp
1400	mv -f tmp config.def
1401	if [ "$with_xios" = "y" ] ; then
1402	cp ../../ORCHIDEE/src_xml/context_orchidee.xml .
1403	echo '<context id="orchidee" src="./context_orchidee.xml"/>' \
1404	> add.tmp
1405	cp ../../ORCHIDEE/src_xml/field_def_orchidee.xml .
1406	cp ../../ORCHIDEE/src_xml/file_def_orchidee.xml .
1407	cp ../../ORCHIDEE/src_xml/file_def_input_orchidee.xml .
1408	if [ -f ../../ORCHIDEE/src_xml/context_input_orchidee.xml ] ; then
1409	cp ../../ORCHIDEE/src_xml/context_input_orchidee.xml .
1410	echo '<context id="orchidee" ' \
1411	'src="./context_input_orchidee.xml"/>' >> add.tmp
1412	fi
1413	sed -e '/id="LMDZ"/r add.tmp' iodef.xml > tmp
1414	mv tmp iodef.xml
1415	sed -e'{/sechiba1/ s/enabled="_AUTO_"/type="one_file" enabled=".TRUE."/}' \
1416	file_def_orchidee.xml > tmp
1417	\mv -f tmp file_def_orchidee.xml
1418	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \
1419	file_def_orchidee.xml > tmp
1420	\mv -f tmp file_def_orchidee.xml
1421	sed -e 's@output_level="_AUTO_"@output_level="1"@' \
1422	file_def_orchidee.xml > tmp
1423	\mv -f tmp file_def_orchidee.xml
1424	sed -e 's@output_freq="_AUTO_"@output_freq="1d"@' \
1425	file_def_orchidee.xml > tmp
1426	\mv -f tmp file_def_orchidee.xml
1427	sed -e 's@compression_level="4"@compression_level="0"@' \
1428	file_def_orchidee.xml > tmp
1429	\mv -f tmp file_def_orchidee.xml
1430	sed -e 's@XIOS_ORCHIDEE_OK = n@XIOS_ORCHIDEE_OK = y@' \
1431	orchidee.def > tmp
1432	\mv -f tmp orchidee.def
1433	fi
1434	fi
1435
1436	if [[ -f ../arch.env ]]
1437	then
1438	source ../arch.env
1439	fi
1440
1441	echo EXECUTION DU BENCH
1442	set +e
1443	date ; ./bench.sh > out.bench 2>&1 ; date
1444	set -e
1445	tail listing
1446
1447
1448	echo '##########################################################'
1449	echo 'Simulation finished in' `pwd`
1450	echo 'You have compiled with:'
1451	cat ../compile.sh
1452	if [ $parallel = "none" ] ; then
1453	echo 'You may re-run it with : cd ' `pwd` ' ; gcm.e'
1454	echo 'or ./bench.sh'
1455	else
1456	echo 'You may re-run it with : '
1457	echo 'cd ' `pwd` '; ./bench.sh'
1458	# echo 'ulimit -s unlimited'
1459	# echo 'export OMP_NUM_THREADS=2'
1460	# echo 'export OMP_STACKSIZE=800M'
1461	# echo "$mpirun -np 2 gcm.e "
1462	fi
1463	echo '##########################################################'
1464
1465	fi # bench
1466
1467
1468	#################################################################
1469	# Installation eventuelle du 1D
1470	#################################################################
1471
1472	if [ $SCM = 1 ] ; then
1473	cd $MODEL
1474	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/1D.tar.gz
1475	myget 1D/1D.tar.gz
1476	tar xvf 1D.tar.gz
1477	cd 1D
1478	./run.sh -rad $rad
1479	fi
1480	#set -vx
1481
1482	#################################################################
1483	# sauvegarde des options veget pour utilisation eventuelle tutorial_prod
1484	#################################################################
1485	cd $MODEL/modipsl/modeles
1486	#echo surface_env file created in $MODEL
1487	echo 'veget='$veget > surface_env
1488	#opt_veget="-v $veget_version"
1489	#echo 'opt_veget="'$opt_veget\" >> surface_env
1490	echo 'opt_veget="'-v $veget_version\" >> surface_env
1491	echo 'orchidee_rev='$orchidee_rev >> surface_env
1492	echo 'suforch='$suff_orc >> surface_env

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