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source: BOL/script_install/install_lmdz.sh @ 3783

Last change on this file since 3783 was 3783, checked in by Laurent Fairhead, 4 years ago
Back to sequential version by default Switch/relocate LMDZ depository to https://.... Added some exe name (needs work #116)
File size: 43.0 KB

Line
1	#!/bin/bash
2
3	###########################################################################
4	# Author : Laurent Fairhead et Frédéric Hourdin
5	# Usage : install_lmdz.sh -help
6	#
7	# bash installation script of the LMDZ model on a Linux PC.
8	# the model is downloaded in the following direcory tree
9	# $MODEL/modipsl/modeles/...
10	# using the "modipsl" infrastructure created by the "IPSL"
11	# for coupled (atmosphere/ocean/vegetation/chemistry) climate modeling
12	# activities.
13	# Here we only download atmospheric (LMDZ) and vegetation (ORCHIDEE)
14	# components.
15	#
16	# The sources of the models can be found in the "modeles" directory.
17	# In the present case, LMDZ5, ORCHIDEE and IOIPSL (handling of input-outputs
18	# using the NetCDF library.
19	#
20	# The script downloads various source files (including a version of NetCDF)
21	# and utilities, compiles the model, and runs a test simulation in a
22	# munimal configuration.
23	#
24	# Prerequisites : pgf90/gfortran, ksh, wget , gunzip, tar, ...
25	#
26	# Modif 18/11/2011
27	# changes for option real 8.
28	# We comopile with -r8 (or equivalent) and -DNC_DOUBLE for the GCM
29	# but with -r4 for netcdf. Variable real must be set to
30	# r4 or r8 at the beginning of the script below.
31	#
32	###########################################################################
33
34	echo install.sh DEBUT `date`
35
36	set -e
37
38	################################################################
39	# Choice of installation options
40	################################################################
41
42	# A function to fetch files either locally or on the internet
43	function myget { #1st and only argument should be file name
44	# Path on local computer where to look for the datafile
45	if [ -f /u/lmdz/WWW/LMDZ/pub/$1 ] ; then
46	\cp -f -p /u/lmdz/WWW/LMDZ/pub/$1 .
47	elif [ -f ~/LMDZ/pub/$1 ] ; then
48	\cp -f -p ~/LMDZ/pub/$1 .
49	else
50	wget -nv http://www.lmd.jussieu.fr/~lmdz/pub/$1
51	#dir=~/LMDZ/pub/`dirname $1` ; mkdir -p $dir ; cp -r `basename $1` $dir
52	fi
53	}
54
55
56	#real=r4
57	real=r8
58
59	# WARNING !!!! For versions before october 2009, use
60	# install.v2.sh instead of install.sh
61
62	#########################################################################
63	# Valeur par défaut des parametres
64	#########################################################################
65	svn=""
66	version=trunk
67	getlmdzor=1
68	netcdf=1 # 1 for automatic installation
69	# 0 for no installation
70	# /.../../netcdf-4.0.1 if wanting to link with an already
71	# compiled netcdf library (implies to check option compatibility)
72	check_linux=1
73	ioipsl=1
74	veget=0
75	orchidee_rev="" # default revision of ORCHIDEE
76	bench=1
77	pclinux=1
78	pcmac=0 # default: not on a Mac
79	compiler=gfortran
80	SCM=0
81	# use the old orchidee interface without the calculation of z0h
82	no_z0h_orc=1
83	# orchidee_version: defined to use the CMIP6 version of ORCHIDEE
84	# (and eventually anyother)
85	# values=CMIP6
86	orchidee_version=""
87	# choose the resolution for the bench runs
88	# grid_resolution= 32x24x11 or 48x36x19 for tests (test without ORCHIDEE)
89	# 96x71x19 standard configuration
90	grid_resolution=144x142x79
91	grid_resolution=96x95x39
92	grid_resolution=48x36x19
93	grid_resolution=32x32x39
94	# choose the physiq version you want to test
95	#physiq=NPv6.0.14splith
96	physiq=
97
98	## parallel can take the values none/mpi/omp/mpi_omp
99	parallel=mpi_omp
100	parallel=none
101	idris_acct=lmd
102	OPT_GPROF=""
103	OPT_MAKELMDZ=""
104	MODEL=""
105
106	## also compile XIOS? (and more recent NetCDF/HDF5 libraries) Default=no
107	with_xios="n"
108	opt_makelmdz_xios=""
109
110	## compile_with_fcm=1 : use makelmdz_fcm (1) or makelmdz (0)
111	compile_with_fcm=1
112	cosp=0 ; opt_cosp1=""
113	cosp=0 ; opt_cosp2=""
114	cosp=0 ; opt_cospv2=""
115	opt_cosp=""
116
117	# Check if on a Mac
118	if [ `uname` = "Darwin" ]
119	then
120	pcmac=1
121	export MAKE=make
122	fi
123	#echo "pcmac="$pcmac
124
125	env_file=""
126
127	#########################################################################
128	# Options interactives
129	#########################################################################
130	while (($# > 0))
131	do
132	case $1 in
133	"-h") cat <<........fin
134	$0 [ -v version ] [ -r svn_release ]
135	[ -parallel PARA ] [ -d GRID_RESOLUTION ] [ -bench 0/1 ]
136	[-name LOCAL_MODEL_NAME] [-gprof] [-opt_makelmdz]
137
138	-v "version" like 20150828.trunk
139	see http://www.lmd.jussieu.fr/~lmdz/Distrib/LISMOI.trunk
140
141	-r "svn_release" : either the svn release number or "last"
142
143	-compiler gfortran\|ifort\|pgf90 (default: gfortran)
144
145	-parallel PARA : can be mpi_omp (mpi with openMP) or none (for sequential)
146
147	-d GRID_RESOLUTION should be among the available benchs if -bench 1
148	among which : 48x36x19, 48x36x39
149	if wanting to run a bench simulation in addition to compilation
150	default : 48x36x19
151
152	-bench activating the bench or not (0/1). Default 1
153
154	-name LOCAL_MODEL_NAME : default = LMDZversion.release
155
156	-netcdf PATH : full path to an existing installed NetCDF library
157	(without -netcdf: also download and install the NetCDF library)
158
159	-xios also download and compile the XIOS library
160	(requires the NetCDF4-HDF5 library, also installed by default)
161	(requires to also have -parallel mpi_omp)
162
163	-gprof to compile with -pg to enable profiling with gprof
164
165	-orchidee_rev "svn_release" : upgrade included ORCHIDEE model to
166	given svn release number (default: $orchidee_rev)
167	(only valid for orchidee2.0 and later)
168
169	-cosp to compile with cosp(v1)
170
171	-cosp2 to compile with cosp(1v2)
172
173	-cospv2 to compile with cosp(v2)
174
175	-nofcm to compile without fcm
176
177	-SCM install 1D version automatically
178
179	-debug compile everything in debug mode
180
181	-opt_makelmdz to call makelmdz or makelmdz_fcm with additional options
182
183	-physiq to choose which physics package to use
184
185	-env_file specify an arch.env file to overwrite the existing one
186
187	-orc_version to chose some tagged ORCHIDEE version (CMIP6 only for the present)
188
189	........fin
190	exit ;;
191	"-v") version=$2 ; shift ; shift ;;
192	"-r") svn=$2 ; shift ; shift ;;
193	"-compiler") compiler=$2
194	case $compiler in
195	"gfortran"\|"ifort"\|"pgf90") compiler=$2 ; shift ; shift ;;
196	*) echo "Only gfortran , ifort or pgf90 for the compiler option" ; exit
197	esac ;;
198	"-d") grid_resolution=$2 ; shift ; shift ;;
199	"-gprof") OPT_GPROF="-pg" ; shift ;;
200	"-cosp") cosp=1 ; opt_cosp1="-cosp true" ; shift ;;
201	"-cosp2") cosp2=1 ; opt_cosp2="-cosp2 true" ; shift ;;
202	"-cospv2") cospv2=1 ; opt_cospv2="-cospv2 true" ; shift ;;
203	"-orchidee_rev") orchidee_rev=$2 ; shift ; shift ;;
204	"-nofcm") compile_with_fcm=0 ; shift ;;
205	"-SCM") SCM=1 ; shift ;;
206	"-opt_makelmdz") OPT_MAKELMDZ="$2" ; shift ; shift ;;
207	"-parallel") parallel=$2
208	case $parallel in
209	"none"\|"mpi"\|"omp"\|"mpi_omp") parallel=$2 ; shift ; shift ;;
210	*) echo Only none mpi omp mpi_omp for the parallel option ; exit
211	esac ;;
212	"-bench") bench=$2 ; shift ; shift ;;
213	"-debug") optim=-debug ; shift ;;
214	"-name") MODEL=$2 ; shift ; shift ;;
215	"-netcdf") netcdf=$2 ; shift ; shift ;;
216	"-physiq") physiq=$2 ; shift ; shift ;;
217	"-xios") with_xios="y" ; shift ;;
218	"-env_file") env_file=$2 ; shift ; shift ;;
219	"-orc_version") orchidee_version=$2 ; shift ; shift ;;
220	*) ./install_lmdz.sh -h ; exit
221	esac
222	done
223
224	if [ $parallel = none ] ; then sequential=1 ; else sequential=0 ; fi
225
226	#Chemin pour placer le modele
227	if [ "$MODEL" = "" ] ; then MODEL=./LMDZ$version$svn$optim ; fi
228
229
230	arch=local
231
232
233	if [ $compiler = g95 ] ; then echo g95 is not supported anymore ; exit ; fi
234
235	################################################################
236	# Specificite des machines
237	################################################################
238
239	hostname=`hostname`
240	if [ "$pclinux" = 1 ] ; then o_ins_make="-t g95" ; else o_ins_make="" ; fi
241
242	case ${hostname:0:5} in
243
244	jean-) compiler="mpiifort" ;
245	par_comp="mpiifort" ;
246	o_ins_make="-t jeanzay" ;
247	make=gmake ;
248	module purge
249	module load intel-compilers/19.0.4 ;
250	#module load intel-mpi/19.0.4 ;
251	#module load intel-mkl/19.0.4 ;
252	module load hdf5/1.10.5-mpi ;
253	module load netcdf/4.7.2-mpi ;
254	module load netcdf-fortran/4.5.2-mpi ;
255	module load subversion/1.9.7 ;
256	export NETCDF_LIBDIR=./
257	export NETCDFFORTRAN_INCDIR=./
258	export NETCDFFORTRAN_LIBDIR=./
259	arch=X64_JEANZAY ;;
260
261	cicla\|camel) compiler="gfortran" ;
262	if [ $parallel != none ] ; then
263	module load openmpi/1.6.5-gfortran ;
264	root_mpi=$MPI_HOME ;
265	path_mpi=$root_mpi/bin ;
266	par_comp=${path_mpi}/mpif90 ;
267	mpirun=${path_mpi}/mpirun ;
268	fi ;
269	arch=local ;
270	make=make ;
271	o_ins_make="-t g95" ;;
272
273	*) if [ $parallel = none -o -f /usr/bin/mpif90 ] ; then
274	path_mpi=`which mpif90 \| sed -e s:/mpif90::` ;
275	if [ -d /usr/lib64/openmpi ] ; then
276	root_mpi="/usr/lib64/openmpi"
277	else
278	root_mpi="/usr"
279	fi
280	# For Scientifique Linux with gfortran at LMD :
281	elif [ -f /usr/lib64/openmpi/1.4.5-gfortran/bin/mpif90 -a $compiler = "gfortran" ] ; then
282	path_mpi=/usr/lib64/openmpi/1.4.5-gfortran/bin ;
283	root_mpi=/usr/lib64/openmpi/1.4.5-gfortran ;
284	export LD_LIBRARY_PATH=${root_mpi}/lib:$LD_LIBRARY_PATH
285	# For Scientifique Linux with ifort at LMD :
286	elif [ -f /usr/lib64/openmpi/1.4.5-ifort/bin/mpif90 -a $compiler = "ifort" ] ; then
287	path_mpi=/usr/lib64/openmpi/1.4.5-ifort/bin ;
288	root_mpi=/usr/lib64/openmpi/1.4.5-ifort ;
289	export LD_LIBRARY_PATH=${root_mpi}/lib:$LD_LIBRARY_PATH
290	# For Scientifique Linux with pgf90 at LMD :
291	elif [ -f /usr/lib64/openmpi/1.4.5-ifort/bin/mpif90 -a $compiler = "pgf90" ] ; then
292	path_mpi=/usr/lib64/openmpi/1.4.5-pgf/bin ;
293	root_mpi=/usr/lib64/openmpi/1.4.5-pgf ;
294	export LD_LIBRARY_PATH=${root_mpi}/lib:$LD_LIBRARY_PATH
295	else
296	echo "Cannot find mpif90" ;
297	if [ $parallel = none ] ; then exit ; fi ;
298	fi ;
299	par_comp=${path_mpi}/mpif90 ;
300	mpirun=${path_mpi}/mpirun ;
301	arch=local ;
302	make=make ;
303	o_ins_make="-t g95"
304	esac
305
306	# Flags for parallelism:
307	if [ $parallel != none ] ; then
308	# MPI_LD are the flags needed for linking with MPI
309	MPI_LD="-L${root_mpi}/lib -lmpi"
310	if [ "$compiler" = "gfortran" ] ; then
311	# MPI_FLAGS are the flags needed for compilation with MPI
312	MPI_FLAGS="-fcray-pointer"
313	# OMP_FLAGS are the flags needed for compilation with OpenMP
314	OMP_FLAGS="-fopenmp -fcray-pointer"
315	# OMP_LD are the flags needed for linking with OpenMP
316	OMP_LD="-fopenmp"
317	elif [ "$compiler" = "ifort" ] ; then
318	MPI_FLAGS=""
319	OMP_FLAGS="-openmp"
320	OMP_LD="-openmp"
321	else # pgf90
322	MPI_FLAGS=""
323	OMP_FLAGS="-mp"
324	OMP_LD="-mp"
325	fi
326	fi
327
328	#####################################################################
329	# Test for old gfortran compilers
330	# If the compiler is too old (older than 4.3.x) we test if the
331	# temporary gfortran44 patch is available on the computer in which
332	# case the compiler is changed from gfortran to gfortran44
333	# Must be aware than parallelism can not be activated in this case
334	#####################################################################
335
336	if [ "$compiler" = "gfortran" ] ; then
337	gfortran=gfortran
338	gfortranv=`gfortran --version \| \
339	head -1 \| awk ' { print $NF } ' \| awk -F. ' { print $1 * 10 + $2 } '`
340	if [ $gfortranv -le 43 ] ; then
341	echo ERROR : Your gfortran compiler is too old
342	echo 'Please choose a new one (ifort) and change the line'
343	echo compiler=xxx
344	echo in the install.sh script and rerun it
345	if [ `which gfortran44 \| wc -w` -ne 0 ] ; then
346	gfortran=gfortran44
347	else
348	echo gfotran trop vieux ; exit
349	fi
350	fi
351	compiler=$gfortran
352	fi
353	#####################################################################
354
355	## if also compiling XIOS, parallel must be mpi_omp
356	if [ "$with_xios" = "y" -a "$parallel" != "mpi_omp" ] ; then
357	echo "Error, you must set -parallel mpi_omp if you want XIOS"
358	exit
359	fi
360
361	## We can't compile with -cosp and -cosp2
362	if [ "$cosp" = 1 -a "$cosp2" = 1 ] ; then
363	echo "Error, you can't run with cosp1 and cosp2"
364	exit
365	fi
366	if [ "$cosp" = 1 ] ; then
367	opt_cosp="$opt_cosp1"
368	fi
369	if [ "$cosp2" = 1 ] ; then
370	opt_cosp="$opt_cosp2"
371	fi
372	if [ "$cospv2" = 1 ] ; then
373	opt_cosp="$opt_cospv2"
374	fi
375
376	## if also compiling XIOS, cosp must be activate to define axis in *.xml
377	if [ "$with_xios" = "y" ] ; then
378	if [ "$cosp" = 0 -a "$cosp2" = 0 -a "$cospv2" = 0 ] ; then
379	echo "Error, you must use -cosp option when compiling with -xios"
380	echo "You need to call Cosp in physical first step to define axis variables"
381	exit
382	fi
383	opt_makelmdz_xios="-io xios"
384	fi
385
386	if [ "$cospv2" = 1 -a "$with_xios" = "n" ] ; then
387	echo "Error, Cospv2 cannot run without Xios"
388	exit
389	fi
390
391	echo '################################################################'
392	echo Choix des options de compilation
393	echo '################################################################'
394
395	export FC=$compiler
396	export F90=$compiler
397	export F77=$compiler
398	export CPPFLAGS=
399	OPTIMNC=$OPTIM
400	BASE_LD="$OPT_GPROF"
401	OPTPREC="$OPT_GPROF"
402	ARFLAGS="rs" ; if [ -f /etc/issue ] ; then if [ "`grep -i ubuntu /etc/issue`" != "" ] ; then if [ "`grep -i ubuntu /etc/issue \| awk ' { print $2 } ' \| cut -d. -f1`" -ge 16 ] ; then ARFLAGS="rU" ; fi ; fi ; fi
403
404
405
406	if [ "$compiler" = "$gfortran" ] ; then
407	OPTIM='-O3'
408	OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all -fbacktrace -finit-real=nan"
409	OPTDEV="-Wall -fbounds-check"
410	fmod='I '
411	OPTPREC="$OPTPREC -cpp -ffree-line-length-0"
412	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE" ; fi
413	export F90FLAGS=" -ffree-form $OPTIMNC"
414	export FFLAGS=" $OPTIMNC"
415	export CC=gcc
416	export CXX=g++
417	export fpp_flags="-P -C -traditional -ffreestanding"
418
419	elif [ $compiler = mpif90 ] ; then
420	OPTIM='-O3'
421	OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all"
422	OPTDEV="-Wall -fbounds-check"
423	BASE_LD="$BASE_LD -lblas"
424	fmod='I '
425	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE -fcray-pointer" ; fi
426	export F90FLAGS=" -ffree-form $OPTIMNC"
427	export FFLAGS=" $OPTIMNC"
428	export CC=gcc
429	export CXX=g++
430
431	elif [ $compiler = pgf90 ] ; then
432	OPTIM='-O2 -Mipa -Munroll -Mnoframe -Mautoinline -Mcache_align'
433	OPTDEB='-g -Mdclchk -Mbounds -Mchkfpstk -Mchkptr -Minform=inform -Mstandard -Ktrap=fp -traceback'
434	OPTDEV='-g -Mbounds -Ktrap=fp -traceback'
435	fmod='module '
436	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -r8 -DNC_DOUBLE" ; fi
437	export CPPFLAGS="-DpgiFortran"
438	export CC=pgcc
439	export CFLAGS="-O2 -Msignextend"
440	export CXX=pgCC
441	export CXXFLAGS="-O2 -Msignextend"
442	export FFLAGS="-O2 $OPTIMNC"
443	export F90FLAGS="-O2 $OPTIMNC"
444	compile_with_fcm=1
445
446	elif [ $compiler = ifort ] ; then
447	OPTIM="-O2 -fp-model strict -ip -align all "
448	OPTDEV="-p -g -O2 -traceback -fp-stack-check -ftrapuv -check"
449	OPTDEB="-g -no-ftz -traceback -ftrapuv -fp-stack-check -check"
450	fmod='module '
451	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -real-size 64 -DNC_DOUBLE" ; fi
452	export CPP="icc -E"
453	export FFLAGS="-O2 -ip -fpic -mcmodel=large"
454	export FCFLAGS="-O2 -ip -fpic -mcmodel=large"
455	export CC=icc
456	export CFLAGS="-O2 -ip -fpic -mcmodel=large"
457	export CXX=icpc
458	export CXXFLAGS="-O2 -ip -fpic -mcmodel=large"
459	export fpp_flags="-P -traditional"
460	# Pourquoi forcer la compilation fcm. Marche mieux sans
461	#compile_with_fcm=1
462
463	elif [ $compiler = mpiifort ] ; then
464	echo on ne fait rien la
465	# Pourquoi forcer la compilation fcm. Marche mieux sans
466	#compile_with_fcm=1
467
468	else
469	echo unexpected compiler $compiler ; exit
470	fi
471
472	OPTIMGCM="$OPTIM $OPTPREC"
473
474	hostname=`hostname`
475
476	##########################################################################
477	# If installing on know machines such as IBM x3750 (Ada)
478	# at IDRIS, don't check for available software and don"t install netcdf
479	if [ ${hostname:0:5} = jean- ] ; then
480	netcdf=0 # no need to recompile netcdf, alreday available
481	check_linux=0
482	pclinux=0
483	ioipsl=0 # no need to recompile ioipsl, already available
484	#netcdf="/smplocal/pub/NetCDF/4.1.3"
485	compiler="mpiifort"
486	fmod='module '
487	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -i4 -r8 -DNC_DOUBLE" ; fi
488	OPTIM="-auto -align all -O2 -fp-model strict -xHost "
489	OPTIMGCM="$OPTIM $OPTPREC"
490	fi
491	##########################################################################
492
493
494
495	mkdir -p $MODEL
496	echo $MODEL
497	MODEL=`( cd $MODEL ; pwd )` # to get absolute path, if necessary
498
499
500
501	# Option -fendian=big is only to be used with ARPEGE1D.
502	# The -r8 should probably be avoided if running on 32 bit machines
503	# Option r8 is not mandatory and generates larger executables.
504	# It is however mandatory if using ARPEGE1D
505	# Better optimization options might be a better choice (e.g. -O3)
506
507
508	echo '################################################################'
509	if [ "$check_linux" = 1 ] ; then
510	echo Check if required software is available
511	echo '################################################################'
512
513	#### Ehouarn: test if ksh and/or bash are available
514	use_shell="ksh" # default: use ksh
515	if [ "`which ksh`" = "" ] ; then
516	echo "no ksh ... we will use bash"
517	use_shell="bash"
518	if [ "`which bash`" = "" ] ; then
519	echo "ksh (or bash) needed!! Install it!"
520	fi
521	fi
522
523
524	for logiciel in wget tar gzip make $compiler gcc ; do
525	if [ "`which $logiciel`" = "" ] ; then
526	echo You must first install $logiciel on your system
527	exit
528	fi
529	done
530
531	if [ $pclinux = 1 ] ; then
532	cd $MODEL
533	cat <<eod > tt.f90
534	print*,'coucou'
535	end
536	eod
537	$compiler tt.f90 -o a.out
538	./a.out >\| tt
539	if [ "`cat tt \| sed -e 's/ //g' `" != "coucou" ] ; then
540	echo problem installing with compiler $compiler ; exit ; fi
541	\rm tt a.out tt.f90
542	fi
543	fi
544
545	###########################################################################
546	if [ $getlmdzor = 1 ] ; then
547	echo '##########################################################'
548	echo Download a slightly modified version of LMDZ
549	echo '##########################################################'
550	cd $MODEL
551	myget src/modipsl.$version.tar.gz
552	echo install.sh wget_OK `date`
553	gunzip modipsl.$version.tar.gz
554	tar xvf modipsl.$version.tar
555	\rm modipsl.$version.tar
556
557	fi
558
559	echo OK1
560
561	if [ $netcdf = 1 ] ; then
562	cd $MODEL
563	netcdflog=`pwd`/netcdf.log
564	echo '##########################################################'
565	echo Compiling the Netcdf library
566	echo '##########################################################'
567	echo log file : $netcdflog
568	if [ "$with_xios" = "n" ] ; then
569	# keep it simple
570	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/netcdf-4.0.1.tar.gz
571	myget import/netcdf-4.0.1.tar.gz
572	gunzip netcdf-4.0.1.tar.gz
573	tar xvf netcdf-4.0.1.tar
574	\rm -f netcdf-4.0.1.tar
575
576	cd netcdf-4.0.1
577
578	# seds to possibly use gfortran44 obsolete nowdays (Ehouarn: 10/2017)
579	#sed -e 's/gfortran/'$gfortran'/g' configure >\| tmp ; mv -f tmp configure ; chmod +x configure
580	localdir=`pwd -P`
581	./configure --prefix=$localdir --enable-shared --disable-cxx
582	#sed -e 's/gfortran/'$gfortran'/g' Makefile >\| tmp ; mv -f tmp Makefile
583	$make check > $netcdflog 2>&1
584	$make install >> $netcdflog 2>&1
585	else
586	# download and compile hdf5 and netcdf, etc. using the install_netcdf4_hdf5.bash script
587	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/install_netcdf4_hdf5.bash
588	myget import/install_netcdf4_hdf5.bash
589	chmod u=rwx install_netcdf4_hdf5.bash
590	if [ "$compiler" = "gfortran" ] ; then
591	./install_netcdf4_hdf5.bash -prefix $MODEL/netcdf4_hdf5 -CC gcc -FC gfortran -CXX g++ -MPI $root_mpi > $netcdflog 2>&1
592	elif [ "$compiler" = "ifort" ] ; then
593	./install_netcdf4_hdf5.bash -prefix $MODEL/netcdf4_hdf5 -CC icc -FC ifort -CXX icpc -MPI $root_mpi > $netcdflog 2>&1
594	elif [ "$compiler" = "pgf90" ] ; then
595	./install_netcdf4_hdf5.bash -prefix $MODEL/netcdf4_hdf5 -CC pgcc -FC pgf90 -CXX pgCC -MPI $root_mpi > $netcdflog 2>&1
596	else
597	echo "unexpected compiler $compiler" ; exit
598	fi
599	fi # of if [ "$with_xios" = "n" ]
600	echo install.sh netcdf_OK `date`
601	fi # of if [ $netcdf = 1 ]
602
603	#======================================================================================
604	echo OK2 ioipsl=$ioipsl
605	echo '##########################################################'
606	echo 'Installing MODIPSL, the installation package manager for the '
607	echo 'IPSL models and tools'
608	echo '##########################################################'
609
610	if [ $netcdf = 0 -o $netcdf = 1 ] ; then
611	if [ "$with_xios" = "y" ] ; then
612	ncdfdir=$MODEL/netcdf4_hdf5
613	else
614	ncdfdir=$MODEL/netcdf-4.0.1
615	fi
616	else
617	ncdfdir=$netcdf
618	fi
619
620	if [ $ioipsl = 1 ] ; then
621	cd $MODEL/modipsl
622	\rm -rf lib/*
623
624	cd util
625
626	cp AA_make.gdef AA_make.orig
627	F_C="$compiler -c " ; if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then F_C="$compiler -c -cpp " ; fi
628	if [ "$compiler" = "pgf90" ] ; then F_C="$compiler -c -Mpreprocess" ; fi
629	sed -e 's/^\#..g95..\#.*.$/\#/' AA_make.gdef > tmp
630	sed -e "s:F_L = g95:F_L = $compiler:" -e "s:F_C = g95 -c -cpp:F_C = $F_C": \
631	-e 's/g95..w_w..(F_D)/g95 w_w = '"$OPTIMGCM"'/' \
632	-e 's:g95..NCDF_INC..$:g95 NCDF_INC= '"$ncdfdir"'/include:' \
633	-e 's:g95..NCDF_LIB..$:g95 NCDF_LIB= -L'"$ncdfdir"'/lib -lnetcdff -lnetcdf:' \
634	-e 's:g95 L_O =:g95 L_O = -Wl,-rpath='"$ncdfdir"'/lib:' \
635	-e "s:-fmod=:-$fmod:" -e 's/-fno-second-underscore//' \
636	-e 's:#-Q- g95 M_K = gmake:#-Q- g95 M_K = make:' \
637	tmp >\| AA_make.gdef
638
639	if [ $pcmac == 1 ]
640	then
641	cp AA_make.gdef tmp
642	sed -e 's/rpath=/rpath,/g' tmp > AA_make.gdef
643	fi
644
645
646	# We use lines for g95 even for the other compilers to run ins_make
647	if [ "$use_shell" = "ksh" ] ; then
648	./ins_make $o_ins_make
649	else # bash
650	sed -e s:/bin/ksh:/bin/bash:g ins_make > ins_make.bash
651	#if [ "`grep ada AA_make.gdef`" = "" ] ; then # Bidouille pour compiler sur ada des vieux modipsl.tar
652	# \cp -f ~rdzt401/bin/AA_make.gdef .
653	#fi
654	if [ "`grep jeanzay AA_make.gdef`" = "" ] ; then # Bidouille pour compiler sur ada des vieux modipsl.tar
655	echo 'Warning jean-zay not in AA_make.gdef'
656	echo 'Think about updating'
657	exit 1
658	fi
659
660	chmod u=rwx ins_make.bash
661	./ins_make.bash $o_ins_make
662	fi # of if [ "$use_shell" = "ksh" ]
663
664	#=======================================================================================
665	cd $MODEL/modipsl/modeles/IOIPSL/src
666	ioipsllog=`pwd`/ioipsl.log
667	echo '##########################################################'
668	echo 'Compiling IOIPSL, the interface library with Netcdf'
669	echo '##########################################################'
670	echo log file : $ioipsllog
671
672	if [ "$use_shell" = "bash" ] ; then
673	cp Makefile Makefile.ksh
674	sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile
675	fi
676	# if [ "$pclinux" = 1 ] ; then
677	# Build IOIPSL modules and library
678	$make clean
679	$make > $ioipsllog 2>&1
680	if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then # copy module files to lib
681	cp -f *.mod ../../../lib
682	fi
683	# Build IOIPSL tools (ie: "rebuild", if present)
684	if [ -f $MODEL/modipsl/modeles/IOIPSL/tools/rebuild ] ; then
685	cd $MODEL/modipsl/modeles/IOIPSL/tools
686	# adapt Makefile & rebuild script if in bash
687	if [ "$use_shell" = "bash" ] ; then
688	cp Makefile Makefile.ksh
689	sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile
690	cp rebuild rebuild.ksh
691	sed -e 's:/bin/ksh:/bin/bash:g' \
692	-e 's:print -u2:echo:g' \
693	-e 's:print:echo:g' rebuild.ksh > rebuild
694	fi
695	$make clean
696	$make > $ioipsllog 2>&1
697	fi
698	# fi # of if [ "$pclinux" = 1 ]
699
700	else # of if [ $ioipsl = 1 ]
701	if [ ${hostname:0:5} = jean- ] ; then
702	cd $MODEL/modipsl
703	cd util
704	if [ "`grep jeanzay AA_make.gdef`" = "" ] ; then
705	echo 'Warning jean-zay not in AA_make.gdef'
706	echo 'Think about updating'
707	exit 1
708	fi
709	./ins_make $o_ins_make
710	# Compile IOIPSL on jean-zay
711	cd $MODEL/modipsl/modeles/IOIPSL/src
712	gmake > ioipsl.log
713	cd $MODEL/modipsl/modeles/IOIPSL/tools
714	gmake > ioipsl.log
715
716	fi
717	echo install.sh ioipsl_OK `date`
718	fi # of if [ $ioipsl = 1 ]
719	# Saving ioipsl lib for possible parallel compile
720	cd $MODEL/modipsl
721	tar cf ioipsl.tar lib/ bin/
722
723	#===========================================================================
724	if [ "$with_xios" = "y" ] ; then
725	echo '##########################################################'
726	echo 'Compiling XIOS'
727	echo '##########################################################'
728	cd $MODEL/modipsl/modeles
729	xioslog=`pwd`/xios.log
730	echo "log file: $xioslog"
731	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/install_xios.bash
732	myget import/install_xios.bash
733	chmod u=rwx install_xios.bash
734	if [ ${hostname:0:5} = jean- ] ; then
735	# echo 'Need to work on install_xios implementation for jean-zay'
736	# exit
737	svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5 XIOS
738	cd XIOS/arch
739	svn update
740	cd ..
741	./make_xios --prod --arch $arch --job 4 > xios.log 2>&1
742	else
743	./install_xios.bash -prefix $MODEL/modipsl/modeles \
744	-netcdf ${ncdfdir} -hdf5 ${ncdfdir} \
745	-MPI $root_mpi -arch $arch > xios.log 2>&1
746	fi
747	if [ -f XIOS/lib/libxios.a ] ; then
748	echo "OK, XIOS library successfully generated"
749	fi
750	fi
751
752	#============================================================================
753	veget_version=false
754	if [ "$veget" = 1 ] ; then
755	cd $MODEL/modipsl/modeles/ORCHIDEE
756	if [ "$orchidee_version" = "CMIP6" ] ; then
757	set +e
758	svn upgrade
759	svn switch -r 5661 --accept theirs-full svn://forge.ipsl.jussieu.fr/orchidee/tags/ORCHIDEE_2_0/ORCHIDEE
760	orchidee_rev=5661
761	veget_version=orchidee2.0
762	no_z0h_orc=0
763	set -e
764	fi
765	# Correctif suite debug Jean-Zay
766	sed -i -e 's/9010 FORMAT(A52,F17.14)/9010 FORMAT(A52,F20.14)/' src_stomate/stomate.f90
767	opt_orc="-prod" ; if [ "$optim" = "-debug" ] ; then opt_orc="-debug" ; fi
768
769	orchideelog=`pwd`/orchidee.log
770	echo '########################################################'
771	echo 'Compiling ORCHIDEE, the continental surfaces model '
772	echo '########################################################'
773	echo log file : $orchideelog
774	export ORCHPATH=`pwd`
775	if [ -d tools ] ; then
776	###################################################################
777	# Pour les experts qui voudraient changer de version d'orchidee.
778	# Attention : necessite d'avoir le password pour orchidee
779	set +e ; svn upgrade ; set -e
780	if [ "$orchidee_rev" != "" ] ; then
781	# test qu'on est sur la bonne branche pour faire le update
782	set +e
783	svn log -r $orchidee_rev \| grep $orchidee_rev
784	if [ $? -gt 0 ] ; then
785	echo 'Cannot update ORCHIDEE as not on the right branch for ORCHIDEE'
786	exit
787	fi
788	set -e
789	set +e ; svn update -r $orchidee_rev ; set -e
790	fi
791	# Correctif suite debug Jean-Zay
792	if [ -f src_global/time.f90 ] ; then sed -i -e 's/CALL tlen2itau/\!CALL tlen2itau/' src_global/time.f90 ; fi
793	###################################################################
794	if [ "$veget_version" == "false" ] ; then veget_version=orchidee2.0 ; fi
795	cd arch
796	sed -e s:"%COMPILER .*.$":"%COMPILER $compiler":1 \
797	-e s:"%LINK .*.$":"%LINK $compiler":1 \
798	-e s:"%FPP_FLAGS .*.$":"%FPP_FLAGS $fpp_flags":1 \
799	-e s:"%PROD_FFLAGS .*.$":"%PROD_FFLAGS $OPTIM":1 \
800	-e s:"%DEV_FFLAGS .*.$":"%DEV_FFLAGS $OPTDEV":1 \
801	-e s:"%DEBUG_FFLAGS .*.$":"%DEBUG_FFLAGS $OPTDEB":1 \
802	-e s:"%BASE_FFLAGS .*.$":"%BASE_FFLAGS $OPTPREC":1 \
803	-e s:"%BASE_LD .*.$":"%BASE_LD $BASE_LD":1 \
804	-e s:"%ARFLAGS .*.$":"%ARFLAGS $ARFLAGS":1 \
805	arch-gfortran.fcm > arch-local.fcm
806	echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib -lnetcdff -lnetcdf\"" > arch-local.path
807	echo "NETCDF_INCDIR=${ncdfdir}/include" >> arch-local.path
808	echo "IOIPSL_INCDIR=$ORCHPATH/../../lib" >> arch-local.path
809	echo "IOIPSL_LIBDIR=$ORCHPATH/../../lib" >> arch-local.path
810	echo 'XIOS_INCDIR=${ORCHDIR}/../XIOS/inc' >> arch-local.path
811	echo 'XIOS_LIBDIR="${ORCHDIR}/../XIOS/lib -lxios"' >> arch-local.path
812	cd ../
813	# compiling ORCHIDEE sequential mode
814	./makeorchidee_fcm -j 8 -noxios $opt_orc -parallel none -arch $arch > $orchideelog 2>&1
815	echo ./makeorchidee_fcm -j 8 -noxios $opt_orc -parallel none -arch $arch
816	echo End of the first compilation of orchidee ; pwd
817	else
818	if [ -d src_parallel ] ; then
819	liste_src="parallel parameters global stomate sechiba driver"
820	if [ "$veget_version" == "false" ] ; then veget_version=orchidee2.0 ; fi
821	else
822	# Obsolete, for ORCHIDEE_beton only
823	liste_src="parameters stomate sechiba "
824	# A trick to compile ORCHIDEE depending on if we are using real4 or real8
825	cd src_parameters ; \cp reqdprec.$real reqdprec.f90 ; cd ..
826	if [ "$veget_version" == "false" ] ; then veget_version=orchidee1.9 ; fi
827	fi
828	for d in $liste_src ; do src_d=src_$d
829	echo src_d $src_d
830	echo ls ; ls
831	if [ ! -d $src_d ] ; then echo Problem orchidee : no $src_d ; exit ; fi
832	cd $src_d ; \rm -f *.mod make ; $make clean
833	$make > $orchideelog 2>&1 ; if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then cp -f *.mod ../../../lib ; fi
834	cd ..
835	done
836	fi
837	echo install.sh orchidee_OK `date`
838	fi # of if [ "$veget" = 1 ]
839
840
841	#============================================================================
842	# Ehouarn: it may be directory LMDZ4 or LMDZ5 depending on tar file...
843	if [ -d $MODEL/modipsl/modeles/LMD* ] ; then
844	echo '##########################################################'
845	echo 'Compiling LMDZ'
846	echo '##########################################################'
847	cd $MODEL/modipsl/modeles/LMD*
848	LMDZPATH=`pwd`
849	else
850	echo "ERROR: No LMD* directory !!!"
851	exit
852	fi
853
854	###########################################################
855	# For those who want to use fcm to compile via :
856	# makelmdz_fcm -arch local .....
857	############################################################
858
859	if [ "$pclinux" = "1" ] ; then
860
861	# create local 'arch' files (if on Linux PC):
862	cd arch
863	# arch-local.path file
864	echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib -lnetcdff -lnetcdf\"" > arch-local.path
865	echo "NETCDF_INCDIR=-I${ncdfdir}/include" >> arch-local.path
866	echo 'IOIPSL_INCDIR=$LMDGCM/../../lib' >> arch-local.path
867	echo 'IOIPSL_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
868	echo 'XIOS_INCDIR=$LMDGCM/../XIOS/inc' >> arch-local.path
869	echo 'XIOS_LIBDIR=$LMDGCM/../XIOS/lib' >> arch-local.path
870	echo 'ORCH_INCDIR=$LMDGCM/../../lib' >> arch-local.path
871	echo 'ORCH_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
872
873	if [ $pcmac == 1 ] ; then
874	BASE_LD="$BASE_LD -Wl,-rpath,${ncdfdir}/lib"
875	else
876	BASE_LD="$BASE_LD -Wl,-rpath=${ncdfdir}/lib"
877	fi
878	# Arch-local.fcm file (adapted from arch-linux-32bit.fcm)
879
880	if [ $real = r8 ] ; then FPP_DEF=NC_DOUBLE ; else FPP_DEF="" ; fi
881	sed -e s:"%COMPILER .*.$":"%COMPILER $compiler":1 \
882	-e s:"%LINK .*.$":"%LINK $compiler":1 \
883	-e s:"%PROD_FFLAGS .*.$":"%PROD_FFLAGS $OPTIM":1 \
884	-e s:"%DEV_FFLAGS .*.$":"%DEV_FFLAGS $OPTDEV":1 \
885	-e s:"%DEBUG_FFLAGS .*.$":"%DEBUG_FFLAGS $OPTDEB":1 \
886	-e s:"%BASE_FFLAGS .*.$":"%BASE_FFLAGS $OPTPREC":1 \
887	-e s:"%FPP_DEF .*.$":"%FPP_DEF $FPP_DEF":1 \
888	-e s:"%BASE_LD .*.$":"%BASE_LD $BASE_LD":1 \
889	-e s:"%ARFLAGS .*.$":"%ARFLAGS $ARFLAGS":1 \
890	arch-linux-32bit.fcm > arch-local.fcm
891
892	cd ..
893	### Adapt "bld.cfg" (add the shell):
894	whereisthatshell=$(which ${use_shell})
895	echo "bld::tool::SHELL $whereisthatshell" >> bld.cfg
896
897	fi # of if [ "$pclinux" = 1 ]
898
899
900	cd $MODEL/modipsl/modeles/LMDZ*
901	lmdzlog=`pwd`/lmdz.log
902
903	##################################################################
904	# Possibly update LMDZ if a specific svn release is requested
905	##################################################################
906
907	set +e ; svn upgrade
908	if [ "$svn" = "last" ] ; then svnopt="" ; else svnopt="-r $svn" ; fi
909	if [ "$svn" != "" ] ; then
910	svn info \| grep -q 'http:'
911	if [ $? = 0 ] ; then
912	svn switch --relocate http://svn.lmd.jussieu.fr/LMDZ https://svn.lmd.jussieu.fr/LMDZ
913	fi
914	svn update $svnopt
915	fi
916	set -e
917
918	echo '##################################################################'
919	echo Compile LMDZ
920	echo '##################################################################'
921	echo log file : $lmdzlog
922
923	if [ "$env_file" != "" ] ; then mv arch/arch-${arch}.env arch/arch-${arch}.orig ; \cp -f $env_file arch/arch-${arch}.env ; fi
924
925	echo install.sh avant_compilation `date`
926	if [ $compile_with_fcm = 1 ] ; then makelmdz="makelmdz_fcm $optim -arch $arch -j 8 " ; else makelmdz="makelmdz $optim -arch $arch" ; fi
927
928	# use the orchidee interface that has no z0h
929	if [ "$no_z0h_orc" = 1 ] ; then
930	veget_version="$veget_version -cpp ORCHIDEE_NOZ0H"
931	fi
932
933	# sequential compilation and bench
934	if [ "$sequential" = 1 ] ; then
935	echo "./$makelmdz $optim $OPT_MAKELMDZ $optim -rrtm true $opt_cosp -d ${grid_resolution} -v $veget_version gcm " >> compile.sh
936	chmod +x ./compile.sh
937	if [ $bench != 0 ] ; then ./compile.sh > $lmdzlog 2>&1 ; fi
938	echo install.sh apres_compilation `date`
939
940
941	fi # fin sequential
942
943
944
945	# compiling in parallel mode
946	if [ $parallel != "none" ] ; then
947	echo '##########################################################'
948	echo ' Parallel compile '
949	echo '##########################################################'
950	# saving the sequential libs and binaries
951	cd $MODEL/modipsl
952	tar cf sequential.tar bin/ lib/
953	\rm -rf bin/ lib/
954	tar xf ioipsl.tar
955	#
956	# Orchidee
957	#
958	cd $ORCHPATH
959	if [ -d src_parallel -a $veget = 1 ] ; then
960	cd arch
961	sed \
962	-e s:"%COMPILER.*.$":"%COMPILER $par_comp":1 \
963	-e s:"%LINK.*.$":"%LINK $par_comp":1 \
964	-e s:"%MPI_FFLAG.*.$":"%MPI_FFLAGS $MPI_FLAGS":1 \
965	-e s:"%OMP_FFLAG.*.$":"%OMP_FFLAGS $OMP_FLAGS":1 \
966	-e s:"%MPI_LD.*.$":"%MPI_LD $MPI_LD":1 \
967	-e s:"%OMP_LD.*.$":"%OMP_LD $OMP_LD":1 \
968	arch-local.fcm > tmp.fcm
969
970	mv tmp.fcm arch-local.fcm
971	cd ../
972	echo compiling ORCHIDEE parallel mode
973	echo logfile $orchideelog
974	./makeorchidee_fcm -j 8 -clean -noxios $opt_orc -parallel $parallel -arch $arch > $orchideelog 2>&1
975	./makeorchidee_fcm -j 8 -noxios $opt_orc -parallel $parallel -arch $arch >> $orchideelog 2>&1
976	echo ./makeorchidee_fcm -j 8 -clean -noxios $opt_orc -parallel $parallel -arch $arch
977	echo ./makeorchidee_fcm -j 8 -noxios $opt_orc -parallel $parallel -arch $arch
978	elif [ $veget = 1 ] ; then
979	echo '##########################################################'
980	echo ' Orchidee version too old '
981	echo ' Please update to new version '
982	echo '##########################################################'
983	exit
984	fi # of if [ -d src_parallel ]
985	# LMDZ
986	cd $LMDZPATH
987	if [ $arch = local ] ; then
988	cd arch
989	sed -e s:"%COMPILER.*.$":"%COMPILER $par_comp":1 \
990	-e s:"%LINK.*.$":"%LINK $par_comp":1 \
991	-e s:"%MPI_FFLAG.*.$":"%MPI_FFLAGS $MPI_FLAGS":1 \
992	-e s:"%OMP_FFLAG.*.$":"%OMP_FFLAGS $OMP_FLAGS":1 \
993	-e s:"%ARFLAGS.*.$":"%ARFLAGS $ARFLAGS":1 \
994	-e s@"%BASE_LD.*.$"@"%BASE_LD -Wl,-rpath=${root_mpi}/lib:${ncdfdir}/lib"@1 \
995	-e s:"%MPI_LD.*.$":"%MPI_LD $MPI_LD":1 \
996	-e s:"%OMP_LD.*.$":"%OMP_LD $OMP_LD":1 \
997	arch-local.fcm > tmp.fcm
998	mv tmp.fcm arch-local.fcm
999	cd ../
1000	fi
1001	rm -f compile.sh
1002	echo resol=${grid_resolution} >> compile.sh
1003	if [ ${hostname:0:5} = jean- -a "$cospv2" = 1 ] ; then
1004	echo ./$makelmdz -dev $optim $OPT_MAKELMDZ -rrtm true $opt_cosp $opt_makelmdz_xios -d \$resol -v $veget_version -mem -parallel $parallel gcm >> compile.sh
1005	echo ./$makelmdz -dev $optim $OPT_MAKELMDZ -rrtm true $opt_cosp $opt_makelmdz_xios -d \$resol -v $veget_version -mem -parallel $parallel gcm
1006	else
1007	echo ./$makelmdz $optim $OPT_MAKELMDZ -rrtm true $opt_cosp $opt_makelmdz_xios -d \$resol -v $veget_version -mem -parallel $parallel gcm >> compile.sh
1008	echo ./$makelmdz $optim $OPT_MAKELMDZ -rrtm true $opt_cosp $opt_makelmdz_xios -d \$resol -v $veget_version -mem -parallel $parallel gcm
1009	fi
1010	chmod +x ./compile.sh
1011	if [ $bench != 0 ] ; then ./compile.sh > $lmdzlog 2>&1 ; fi
1012
1013	echo "Compilation finished"
1014
1015	fi # of if [ $parallel != "none" ]
1016
1017	#echo LLLLLLLLLLLLLLLLLLLLLLLLLLL
1018	if [ "$gfortran" = "gfortran44" ] ; then
1019	echo Your gfortran compiler was too old so that the model was automatically
1020	echo compiled with gfortran44 instead. It can not be used in parallel mode.
1021	echo You can change the compiler at the begining of the install.sh
1022	echo script and reinstall.
1023	fi
1024
1025	##################################################################
1026	# Verification du succes de la compilation
1027	##################################################################
1028
1029	# Recherche de l'executable dont le nom a change au fil du temps ...
1030	gcm=""
1031	for exe in gcm.e bin/gcm_${grid_resolution}_phylmd_seq_orch.e bin/gcm_${grid_resolution}_phylmd_seq.e bin/gcm_${grid_resolution}_phylmd_para_mem_orch.e bin/gcm_${grid_resolution}_phylmd_para_mem.e ; do
1032	if [ -f $exe ] ; then gcm=$exe ; fi
1033	done
1034
1035	if [ "$gcm" = "" ] ; then
1036	if [ $bench != 0 ] ; then
1037	echo 'Compilation failed !! Cannot run the benchmark;'
1038	exit
1039	else
1040	echo 'Compilation not done (only done when bench=1)'
1041	fi
1042	else
1043	echo '##########################################################'
1044	echo 'Compilation successfull !! '
1045	echo '##########################################################'
1046	echo The executable is $gcm
1047	fi
1048
1049	##################################################################
1050	# Below, we run a benchmark test (if bench=0)
1051	##################################################################
1052
1053	if [ $bench != 0 ] ; then
1054
1055	echo '##########################################################'
1056	echo ' Running a test run '
1057	echo '##########################################################'
1058
1059	\rm -rf BENCH${grid_resolution}
1060	bench=bench_lmdz_${grid_resolution}
1061	echo install.sh before bench download `date`
1062	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/$bench.tar.gz
1063	myget 3DBenchs/$bench.tar.gz
1064	echo install.sh after bench download `date`
1065	tar xvf $bench.tar.gz
1066
1067	if [ "$cosp" = 1 -o "$cosp2" = 1 -o "$cospv2" = 1 ] ; then
1068	cd BENCH${grid_resolution}
1069	# copier les fichiers namelist input et output our COSP
1070	cp ../DefLists/cosp*_input_nl.txt .
1071	cp ../DefLists/cosp*_output_nl.txt .
1072	# Activer la cles ok_cosp pour tourner avec COSP
1073	sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp
1074	\mv -f tmp config.def
1075	cd ..
1076	fi
1077
1078	if [ -n "$physiq" ]; then
1079	cd BENCH${grid_resolution}
1080	if [ -f physiq.def_${physiq} ]; then
1081	cp physiq.def_${physiq} physiq.def
1082	echo using physiq.def_${physiq}
1083	else
1084	echo using standard physiq.def
1085	fi
1086	cd ..
1087	else
1088	echo using standard physiq.def
1089	fi
1090
1091	if [ "$with_xios" = "y" ] ; then
1092	cd BENCH${grid_resolution}
1093	cp ../DefLists/iodef.xml .
1094	cp ../DefLists/context_lmdz.xml .
1095	cp ../DefLists/field_def_lmdz.xml .
1096	cp ../DefLists/field_def_cosp*.xml .
1097	cp ../DefLists/file_def_hist*xml .
1098	# adapt iodef.xml to use attached mode
1099	sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' iodef.xml > tmp
1100	\mv -f tmp iodef.xml
1101
1102	# and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
1103	# except for histday
1104	for histfile in file_def_hist*xml
1105	do
1106	if [ "$histfile" = "file_def_histday_lmdz.xml" ] ; then
1107	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' $histfile > tmp ; \mv -f tmp $histfile
1108	sed -e 's@output_level="_AUTO_"@output_level="5"@' $histfile > tmp ; \mv -f tmp $histfile
1109	sed -e 's@compression_level="2"@compression_level="0"@' $histfile > tmp ; \mv -f tmp $histfile
1110	else
1111	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' $histfile > tmp ; \mv -f tmp $histfile
1112	fi
1113	done
1114	# and add option "ok_all_xml=y" in config.def
1115	echo "### XIOS outputs" >> config.def
1116	echo 'ok_all_xml=.true.' >> config.def
1117
1118	#activer les sorties pour Cosp
1119	if [ "$cosp" = 1 -o "$cosp2" = 1 ] ; then
1120	histfile=file_def_histdayCOSP_lmdz.xml
1121	sed -e 's@enabled=".FALSE."@enabled=".TRUE."@' $histfile > tmp ; \mv -f tmp $histfile
1122	sed -e 's@output_level="_AUTO_"@output_level="5"@' $histfile > tmp ; \mv -f tmp $histfile
1123	sed -e 's@compression_level="2"@compression_level="0"@' $histfile > tmp ; \mv -f tmp $histfile
1124	fi
1125	if [ "$cospv2" = 1 ] ; then
1126	histfile=file_def_histdayCOSPv2_lmdz.xml
1127	sed -e 's@compression_level="2"@compression_level="0"@' $histfile > tmp ; \mv -f tmp $histfile
1128	contextfile=context_lmdz.xml
1129	sed -e 's@src="./file_def_histdayCOSP_lmdz.xml"@src="./file_def_histdayCOSPv2_lmdz.xml"@' $contextfile > tmp ; \mv -f tmp $contextfile
1130	fieldfile=field_def_lmdz.xml
1131	sed -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' $fieldfile > tmp ; \mv -f tmp $fieldfile
1132	fi
1133
1134	cd ..
1135	fi
1136
1137	cp $gcm BENCH${grid_resolution}/gcm.e
1138
1139	cd BENCH${grid_resolution}
1140	# On cree le fichier bench.sh au besoin
1141	# Dans le cas 48x36x39 le bench.sh existe deja en parallele
1142
1143	if [ "$grid_resolution" = "48x36x39" ] ; then
1144	echo On ne touche pas au bench.sh
1145	# But we have to adapt "run_local.sh" for $mpirun
1146	sed -e "s@mpirun@$mpirun@g" run_local.sh > tmp
1147	mv -f tmp run_local.sh
1148	chmod u=rwx run_local.sh
1149	elif [ "${parallel:0:3}" = "mpi" ] ; then
1150	# Lancement avec deux procs mpi et 2 openMP
1151	echo "export OMP_STACKSIZE=800M" > bench.sh
1152	if [ "${parallel:4:3}" = "omp" ] ; then
1153	echo "export OMP_NUM_THREADS=2" >> bench.sh
1154	fi
1155	if [ "$cospv2" = 1 -o "$cosp" = 1 -o "$cosp2" = 1 ] ; then
1156	if [ ${hostname:0:5} = jean- ] ; then
1157	chmod +x ../arch.env
1158	../arch.env
1159	echo "ulimit -s 2000000" >> bench.sh
1160	else
1161	echo "ulimit -s 200000" >> bench.sh
1162	fi
1163	else
1164	echo "ulimit -s unlimited" >> bench.sh
1165	fi
1166	if [ ${hostname:0:5} = jean- ] ; then
1167	echo "srun -n 2 -A $idris_acct@cpu gcm.e > listing 2>&1" >> bench.sh
1168	else
1169	echo "$mpirun -np 2 gcm.e > listing 2>&1" >> bench.sh
1170	fi
1171	else
1172	echo "./gcm.e > listing 2>&1" > bench.sh
1173	fi
1174	echo EXECUTION DU BENCH
1175	set +e
1176	date ; ./bench.sh > out.bench 2>&1 ; date
1177	set -e
1178	tail listing
1179
1180
1181	echo '##########################################################'
1182	echo 'Simulation finished in' `pwd`
1183	echo 'You have compiled with:'
1184	cat ../compile.sh
1185	if [ $parallel = "none" ] ; then
1186	echo 'You may re-run it with : cd ' `pwd` ' ; gcm.e'
1187	echo 'or ./bench.sh'
1188	else
1189	echo 'You may re-run it with : '
1190	echo 'cd ' `pwd` '; ./bench.sh'
1191	# echo 'ulimit -s unlimited'
1192	# echo 'export OMP_NUM_THREADS=2'
1193	# echo 'export OMP_STACKSIZE=800M'
1194	# echo "$mpirun -np 2 gcm.e "
1195	fi
1196	echo '##########################################################'
1197
1198	fi
1199
1200
1201	#################################################################
1202	# Installation eventuelle du 1D
1203	#################################################################
1204
1205	if [ $SCM = 1 ] ; then
1206	cd $MODEL
1207	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/1D.tar.gz
1208	myget 1D/1D.tar.gz
1209	tar xvf 1D.tar.gz
1210	cd 1D
1211	./run.sh
1212	fi

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