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source: BOL/script_install/install_lmdz.sh @ 3063

Last change on this file since 3063 was 3063, checked in by fhourdin, 7 years ago
Add an "-Wl,-rpath=" to the netcdf library for the "flio_rbld" program used by the "rebuild" script. EM
File size: 33.1 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	LMDZ_HOME="/u/lmdz/WWW/Distrib"
46	if [ -f $LMDZ_HOME/$1 ] ; then
47	\cp -f -p $LMDZ_HOME/$1 .
48	else
49	wget http://www.lmd.jussieu.fr/~lmdz/Distrib/$1
50	fi
51	}
52
53
54	#real=r4
55	real=r8
56
57	# WARNING !!!! For versions before october 2009, use
58	# install.v2.sh instead of install.sh
59
60	#########################################################################
61	# Valeur par défaut des parametres
62	#########################################################################
63	svn=""
64	version=testing
65	getlmdzor=1
66	netcdf=1 # 1 for automatic installation
67	# 0 for no installation
68	# /.../../netcdf-4.0.1 if wanting to link with an already
69	# compiled netcdf library (implies to check option compatibility)
70	check_linux=1
71	ioipsl=1
72	veget=1
73	bench=1
74	pclinux=1
75	SCM=0
76	# use the old orchidee interface without the calculation of z0h
77	no_z0h_orc=1
78	# choose the resolution for the bench runs
79	# grid_resolution= 32x24x11 or 48x36x19 for tests (test without ORCHIDEE)
80	# 96x71x19 standard configuration
81	grid_resolution=144x142x79
82	grid_resolution=48x36x19
83
84	## parallel can take the values none/mpi/omp/mpi_omp
85	parallel=mpi_omp
86	parallel=none
87	OPT_GPROF=""
88	OPT_MAKELMDZ=""
89	MODEL=""
90
91	## also compile XIOS? (and more recent NetCDF/HDF5 libraries) Default=no
92	with_xios="n"
93	opt_makelmdz_xios=""
94
95	#########################################################################
96	# Options interactives
97	#########################################################################
98	while (($# > 0))
99	do
100	case $1 in
101	"-h") cat <<........fin
102	$0 [ -v version ] [ -r svn_release ]
103	[ -parallel PARA ] [ -d GRID_RESOLUTION ] [ -bench 0/1 ]
104	[-name LOCAL_MODEL_NAME] [-gprof] [-opt_makelmdz]
105
106	-v "version" like 20150828.trunk
107	see http://www.lmd.jussieu.fr/~lmdz/Distrib/LISMOI.trunk
108
109	-r "svn_release" : either the svn release number or "last"
110
111	-parallel PARA : can be mpi_omp (mpi with openMP) or none (for sequential)
112
113	-d GRID_RESOLUTION should be among the available benchs if -bench 1
114	among which : 48x36x19, 48x36x39
115	if wanting to run a bench simulation in addition to compilation
116	default : 48x36x19
117
118	-bench activating the bench or not (0/1). Default 1
119
120	-name LOCAL_MODEL_NAME : default = LMDZversion.release
121
122	-netcdf PATH : full path to an existing installed NetCDF library
123	(without -netcdf: also download and install the NetCDF library)
124
125	-xios also download and compile the XIOS library
126	(requires the NetCDF4-HDF5 library, also installed by default)
127	(requires to also have -parallel mpi_omp)
128
129	-gprof to compile with -pg to enable profiling with gprof
130
131	-SCM install 1D version automatically
132
133	-opt_makelmdz to call makelmdz or makelmdz_fcm with additional options
134	........fin
135	exit ;;
136	"-v") version=$2 ; shift ; shift ;;
137	"-r") svn=$2 ; shift ; shift ;;
138	"-d") grid_resolution=$2 ; shift ; shift ;;
139	"-gprof") OPT_GPROF="-pg" ; shift ;;
140	"-SCM") SCM=1 ; shift ;;
141	"-opt_makelmdz") OPT_MAKELMDZ="$2" ; shift ; shift ;;
142	"-parallel") parallel=$2
143	case $parallel in
144	"mpi"\|"omp"\|"mpi_omp") parallel=$2 ; shift ; shift ;;
145	*) echo Only mpi omp mpi_omp for the parallel option ; exit
146	esac ;;
147	"-bench") bench=$2 ; shift ; shift ;;
148	"-name") MODEL=$2 ; shift ; shift ;;
149	"-netcdf") netcdf=$2 ; shift ; shift ;;
150	"-xios") with_xios="y" ; shift ;;
151	*) ./install_lmdz.sh -h ; exit
152	esac
153	done
154
155	if [ $parallel = none ] ; then sequential=1 ; else sequential=0 ; fi
156
157
158	compilo=gfortran # compilo=pgf90 or gfortran or ifort sur PC linux
159	#Chemin pour placer le modele
160	if [ "$MODEL" = "" ] ; then MODEL=./LMDZ$version$svn ; fi
161
162
163	## compile_with_fcm=1 : use makelmdz_fcm (1) or makelmdz (0)
164	compile_with_fcm=1
165	arch=local
166
167
168	if [ $compilo = g95 ] ; then echo g95 is not supported anymore ; exit ; fi
169
170	################################################################
171	# Specificite des machines
172	################################################################
173
174	hostname=`hostname`
175	if [ "$pclinux" = 1 ] ; then o_ins_make="-t g95" ; else o_ins_make="" ; fi
176
177	case ${hostname:0:5} in
178
179	ada33) compilo="ifort" ;
180	par_comp="ifort" ;
181	o_ins_make="-t ada" ;
182	make=gmake ;
183	# module load intel/2013.0 ;
184	arch=X64_ADA ;;
185
186	cicla) compilo="gfortran" ;
187	if [ $parallel != none ] ; then
188	module load openmpi/1.4.5-gfortran ;
189	root_mpi=$MPI_HOME ;
190	path_mpi=$root_mpi/bin ;
191	par_comp=${path_mpi}/mpif90 ;
192	mpirun=${path_mpi}/mpirun ;
193	fi ;
194	arch=local ;
195	make=make ;
196	o_ins_make="-t g95" ;;
197
198	*) compilo="gfortran" ;
199	if [ $parallel = none -o -f /usr/bin/mpif90 ] ; then
200	path_mpi=`which mpif90 \| sed -e 's:/mpif90::'` ;
201	if [ -d /usr/lib64/openmpi ] ; then
202	root_mpi="/usr/lib64/openmpi"
203	else
204	root_mpi="/usr"
205	fi
206	# For Scientifique Linux at LMD :
207	elif [ -f /usr/lib64/openmpi/1.4.5-gfortran/bin/mpif90 ] ; then
208	path_mpi=/usr/lib64/openmpi/1.4.5-gfortran/bin ;
209	root_mpi=/usr/lib64/openmpi/1.4.5-gfortran ;
210	export LD_LIBRARY_PATH=${root_mpi}/lib:$LD_LIBRARY_PATH
211	else
212	echo "Cannot find mpif90" ;
213	exit ;
214	fi ;
215	par_comp=${path_mpi}/mpif90 ;
216	mpirun=${path_mpi}/mpirun ;
217	arch=local ;
218	make=make ;
219	o_ins_make="-t g95"
220	esac
221
222
223	# MPI_FLAGS are the flags needed for compilation with MPI
224	#MPI_FLAGS="-I/usr/include/openmpi-x86_64 -fcray-pointer"
225	MPI_FLAGS="-fcray-pointer"
226	# MPI_LD are the flags needed for linking with MPI
227	MPI_LD="-L/usr/lib64/openmpi/lib -lmpi"
228	# OMP_FLAGS are the flags needed for compilation with OpenMP
229	OMP_FLAGS="-fopenmp -fcray-pointer"
230	# OMP_LD are the flags needed for linking with OpenMP
231	#OMP_LD="-fopenmp -L/usr/lib64 -lnuma"
232	OMP_LD="-fopenmp"
233
234
235	#####################################################################
236	# Test for old gfortran compilers
237	# If the compiler is too old (older than 4.3.x) we test if the
238	# temporary gfortran44 patch is available on the computer in which
239	# case the compiler is changed from gfortran to gfortran44
240	# Must be aware than parallelism can not be activated in this case
241	#####################################################################
242
243	if [ "$compilo" = "gfortran" ] ; then
244	gfortran=gfortran
245	gfortranv=`gfortran --version \| \
246	head -1 \| awk ' { print $NF } ' \| awk -F. ' { print $1 * 10 + $2 } '`
247	if [ $gfortranv -le 43 ] ; then
248	echo ERROR : Your gfortran compiler is too old
249	echo 'Please choose a new one (ifort) and change the line'
250	echo compilo=xxx
251	echo in the install.sh script and rerun it
252	if [ `which gfortran44 \| wc -w` -ne 0 ] ; then
253	gfortran=gfortran44
254	else
255	echo gfotran trop vieux ; exit
256	fi
257	fi
258	compilo=$gfortran
259	fi
260	#####################################################################
261
262	## if also compiling XIOS, parallel must be mpi_omp
263	if [ "$with_xios" = "y" -a "$parallel" != "mpi_omp" ] ; then
264	echo "Error, you must set -parallel mpi_omp if you want XIOS"
265	exit
266	fi
267	if [ "$with_xios" = "y" ] ; then
268	opt_makelmdz_xios="-io xios"
269	fi
270
271	echo '################################################################'
272	echo Choix des options de compilation
273	echo '################################################################'
274
275	export FC=$compilo
276	export F90=$compilo
277	export F77=$compilo
278	export CPPFLAGS=
279	OPTIMNC=$OPTIM
280	BASE_LD="$OPT_GPROF"
281	OPTPREC="$OPT_GPROF"
282
283	if [ "$compilo" = "$gfortran" ] ; then
284	OPTIM='-O3'
285	OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all -fbacktrace -finit-real=nan"
286	OPTDEV="-Wall -fbounds-check"
287	fmod='I '
288	OPTPREC="$OPTPREC -cpp -ffree-line-length-0"
289	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE" ; fi
290	export F90FLAGS=" -ffree-form $OPTIMNC"
291	export FFLAGS=" $OPTIMNC"
292	export CC=gcc
293	export CXX=g++
294	export fpp_flags="-P -C -traditional -ffreestanding"
295
296	elif [ $compilo = mpif90 ] ; then
297	OPTIM='-O3'
298	OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all"
299	OPTDEV="-Wall -fbounds-check"
300	BASE_LD="$BASE_LD -lblas"
301	fmod='I '
302	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE -fcray-pointer" ; fi
303	export F90FLAGS=" -ffree-form $OPTIMNC"
304	export FFLAGS=" $OPTIMNC"
305	export CC=gcc
306	export CXX=g++
307
308	elif [ $compilo = pgf90 ] ; then
309	OPTIM='-O2 -Mipa -Munroll -Mnoframe -Mautoinline -Mcache_align'
310	OPTDEB='-g -Mdclchk -Mbounds -Mchkfpstk -Mchkptr -Minform=inform -Mstandard -Ktrap=fp -traceback'
311	OPTDEV='-g -Mbounds -Ktrap=fp -traceback'
312	fmod='module '
313	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -r8 -DNC_DOUBLE" ; fi
314	export CPPFLAGS="-DpgiFortran"
315	export CC=pgcc
316	export CFLAGS="-O2 -Msignextend"
317	export CXX=pgCC
318	export CXXFLAGS="-O2 -Msignextend"
319	export FFLAGS="-O2 $OPTIMNC"
320	export F90FLAGS="-O2 $OPTIMNC"
321	compile_with_fcm=1
322
323	elif [ $compilo = ifort ] ; then
324	OPTIM="-O2 -fp-model strict -ip -align all "
325	OPTDEV="-p -g -O2 -traceback -fp-stack-check -ftrapuv -check"
326	OPTDEB="-g -no-ftz -traceback -ftrapuv -fp-stack-check -check"
327	fmod='module '
328	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -real-size 64 -DNC_DOUBLE" ; fi
329	export CPP="icc -E"
330	export FFLAGS="-O2 -ip -fpic -mcmodel=large"
331	export FCFLAGS="-O2 -ip -fpic -mcmodel=large"
332	export CC=icc
333	export CFLAGS="-O2 -ip -fpic -mcmodel=large"
334	export CXX=icpc
335	export CXXFLAGS="-O2 -ip -fpic -mcmodel=large"
336	compile_with_fcm=1
337
338	else
339	echo unexpected compiler $compilo ; exit
340	fi
341
342	OPTIMGCM="$OPTIM $OPTPREC"
343
344	hostname=`hostname`
345
346	##########################################################################
347	# If installing on know machines such as IBM x3750 (Ada)
348	# at IDRIS, don't check for available software and don"t install netcdf
349	if [ ${hostname:0:5} = ada33 ] ; then
350	netcdf=0 # no need to recompile netcdf, alreday available
351	check_linux=0
352	pclinux=0
353	ioipsl=1 # no need to recompile ioipsl, already available
354	#netcdf="/smplocal/pub/NetCDF/4.1.3"
355	compilo="ifort"
356	fmod='module '
357	if [ $real = r8 ] ; then OPTPREC="$OPTPREC -real-size 64 -DNC_DOUBLE" ; fi
358	OPTIM="-O2 -fp-model strict -ip -axAVX,SSE4.2 -align all "
359	OPTIMGCM="$OPTIM $OPTPREC"
360	fi
361	##########################################################################
362
363
364
365	mkdir -p $MODEL
366	echo $MODEL
367	MODEL=`( cd $MODEL ; pwd )` # to get absolute path, if necessary
368
369
370
371	# Option -fendian=big is only to be used with ARPEGE1D.
372	# The -r8 should probably be avoided if running on 32 bit machines
373	# Option r8 is not mandatory and generates larger executables.
374	# It is however mandatory if using ARPEGE1D
375	# Better optimization options might be a better choice (e.g. -O3)
376
377
378	echo '################################################################'
379	if [ "$check_linux" = 1 ] ; then
380	echo Check if required software is available
381	echo '################################################################'
382
383	#### Ehouarn: test if ksh and/or bash are available
384	use_shell="ksh" # default: use ksh
385	if [ "`which ksh`" = "" ] ; then
386	echo "no ksh ... we will use bash"
387	use_shell="bash"
388	if [ "`which bash`" = "" ] ; then
389	echo "ksh (or bash) needed!! Install it!"
390	fi
391	fi
392
393
394	for logiciel in csh wget tar gzip make $compilo gcc ; do
395	if [ "`which $logiciel`" = "" ] ; then
396	echo You must first install $logiciel on your system
397	exit
398	fi
399	done
400
401	if [ $pclinux = 1 ] ; then
402	cd $MODEL
403	cat <<eod > tt.f90
404	print*,'coucou'
405	end
406	eod
407	$compilo tt.f90 -o a.out
408	./a.out >\| tt
409	if [ "`cat tt \| sed -e 's/ //g' `" != "coucou" ] ; then
410	echo problem installing with compiler $compilo ; exit ; fi
411	\rm tt a.out tt.f90
412	fi
413	fi
414
415	###########################################################################
416	if [ $getlmdzor = 1 ] ; then
417	echo '##########################################################'
418	echo Download a slightly modified version of LMDZ
419	echo '##########################################################'
420	cd $MODEL
421	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/modipsl.$version.tar.gz
422	myget modipsl.$version.tar.gz
423	echo install.sh wget_OK `date`
424	gunzip modipsl.$version.tar.gz
425	tar xvf modipsl.$version.tar
426	\rm modipsl.$version.tar
427
428	fi
429
430	echo OK1
431
432	if [ $netcdf = 1 ] ; then
433	echo '##########################################################'
434	echo Compiling the Netcdf library
435	echo '##########################################################'
436	cd $MODEL
437	if [ "$with_xios" = "n" ] ; then
438	# keep it simple
439	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/netcdf-4.0.1.tar.gz
440	myget netcdf-4.0.1.tar.gz
441	gunzip netcdf-4.0.1.tar.gz
442	tar xvf netcdf-4.0.1.tar
443	\rm -f netcdf-4.0.1.tar
444
445	cd netcdf-4.0.1
446
447	# seds to possibly use gfortran44 obsolete nowdays (Ehouarn: 10/2017)
448	#sed -e 's/gfortran/'$gfortran'/g' configure >\| tmp ; mv -f tmp configure ; chmod +x configure
449	localdir=`pwd -P`
450	./configure --prefix=$localdir --enable-shared --disable-cxx
451	#sed -e 's/gfortran/'$gfortran'/g' Makefile >\| tmp ; mv -f tmp Makefile
452	$make check
453	$make install
454	else
455	# download and compile hdf5 and netcdf, etc. using the install_netcdf4_hdf5.bash script
456	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/install_netcdf4_hdf5.bash
457	myget install_netcdf4_hdf5.bash
458	chmod u=rwx install_netcdf4_hdf5.bash
459	if [ "$compilo" = "gfortran" ] ; then
460	./install_netcdf4_hdf5.bash -prefix $MODEL/netcdf4_hdf5 -CC gcc -FC gfortran -CXX g++ -MPI $root_mpi
461	elif [ "$compilo" = "ifort" ] ; then
462	./install_netcdf4_hdf5.bash -prefix $MODEL/netcdf4_hdf5 -CC icc -FC ifort -CXX icpc -MPI $root_mpi
463	elif [ "$compilo" = "pgf90" ] ; then
464	./install_netcdf4_hdf5.bash -prefix $MODEL/netcdf4_hdf5 -CC pgcc -FC pgf90 -CXX pgCC -MPI $root_mpi
465	else
466	echo "unexpected compiler $compilo" ; exit
467	fi
468	fi # of if [ "$with_xios" = "n" ]
469	echo install.sh netcdf_OK `date`
470	fi # of if [ $netcdf = 1 ]
471
472
473	#=======================================================================================
474	echo OK2 ioipsl=$ioipsl
475	echo '##########################################################'
476	echo 'Installing MODIPSL, the installation package manager for the '
477	echo 'IPSL models and tools'
478	echo '##########################################################'
479
480	if [ $netcdf = 0 -o $netcdf = 1 ] ; then
481	if [ "$with_xios" = "y" ] ; then
482	ncdfdir=$MODEL/netcdf4_hdf5
483	else
484	ncdfdir=$MODEL/netcdf-4.0.1
485	fi
486	else
487	ncdfdir=$netcdf
488	fi
489
490	if [ $ioipsl = 1 ] ; then
491	cd $MODEL/modipsl
492	\rm -rf lib/*
493
494	cd util
495
496	cp AA_make.gdef AA_make.orig
497	F_C="$compilo -c " ; if [ "$compilo" = "$gfortran" -o "$compilo" = "mpif90" ] ; then F_C="$compilo -c -cpp " ; fi
498	if [ "$compilo" = "pgf90" ] ; then F_C="$compilo -c -Mpreprocess" ; fi
499	sed -e 's/^\#..g95..\#.*.$/\#/' AA_make.gdef > tmp
500	sed -e "s:F_L = g95:F_L = $compilo:" -e "s:F_C = g95 -c -cpp:F_C = $F_C": \
501	-e 's/g95..w_w..(F_D)/g95 w_w = '"$OPTIMGCM"'/' \
502	-e 's:g95..NCDF_INC..$:g95 NCDF_INC= '"$ncdfdir"'/include:' \
503	-e 's:g95..NCDF_LIB..$:g95 NCDF_LIB= -L'"$ncdfdir"'/lib -lnetcdff -lnetcdf:' \
504	-e 's:g95 L_O =:g95 L_O = -Wl,-rpath='"$ncdfdir"'/lib:' \
505	-e "s:-fmod=:-$fmod:" -e 's/-fno-second-underscore//' \
506	-e 's:#-Q- g95 M_K = gmake:#-Q- g95 M_K = make:' \
507	tmp >\| AA_make.gdef
508
509
510	# We use lines for g95 even for the other compilers to run ins_make
511	if [ "$use_shell" = "ksh" ] ; then
512	./ins_make $o_ins_make
513	else # bash
514	sed -e s:/bin/ksh:/bin/bash:g ins_make > ins_make.bash
515	if [ "`grep ada AA_make.gdef`" = "" ] ; then # Bidouille pour compiler sur ada des vieux modipsl.tar
516	\cp -f ~rdzt401/bin/AA_make.gdef .
517	fi
518	chmod u=rwx ins_make.bash
519	./ins_make.bash $o_ins_make
520	fi # of if [ "$use_shell" = "ksh" ]
521
522	#=======================================================================================
523	echo '##########################################################'
524	echo 'Compiling IOIPSL, the interface library with Netcdf'
525	echo '##########################################################'
526
527	cd $MODEL/modipsl/modeles/IOIPSL/src
528	if [ "$use_shell" = "bash" ] ; then
529	cp Makefile Makefile.ksh
530	sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile
531	fi
532	# if [ "$pclinux" = 1 ] ; then
533	# Build IOIPSL modules and library
534	echo EOEOFOOEOOOOOOOOOOOOOOOOOOOOOOOOOOOO
535	$make clean
536	$make
537	if [ "$compilo" = "$gfortran" -o "$compilo" = "mpif90" ] ; then # copy module files to lib
538	cp -f *.mod ../../../lib
539	fi
540	# Build IOIPSL tools (ie: "rebuild", if present)
541	if [ -f $MODEL/modipsl/modeles/IOIPSL/tools/rebuild ] ; then
542	cd $MODEL/modipsl/modeles/IOIPSL/tools
543	# adapt Makefile & rebuild script if in bash
544	if [ "$use_shell" = "bash" ] ; then
545	cp Makefile Makefile.ksh
546	sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile
547	cp rebuild rebuild.ksh
548	sed -e 's:/bin/ksh:/bin/bash:g' \
549	-e 's:print -u2:echo:g' \
550	-e 's:print:echo:g' rebuild.ksh > rebuild
551	fi
552	$make clean
553	$make
554	fi
555	# fi # of if [ "$pclinux" = 1 ]
556
557	else # of if [ $ioipsl = 1 ]
558	if [ ${hostname:0:5} = ada33 ] ; then
559	cd $MODEL/modipsl
560	cd util
561
562	cp AA_make.gdef AA_make.orig
563	sed -e 's/^\#..g95..\#.*.$/\#/' AA_make.gdef > tmp
564	sed -e "s:F_L = g95:F_L = $compilo:" -e "s:F_C = g95 -c:F_C = $compilo -c": \
565	-e 's/g95..w_w..(F_D)/g95 w_w = '"$OPTIMGCM"'/' \
566	-e 's:g95..NCDF_INC..$:g95 NCDF_INC= -I/smplocal/pub/HDF5/1.8.9/seq/include -I/smplocal/pub/NetCDF/4.1.3/include:' \
567	-e 's:g95..NCDF_LIB..$:g95 NCDF_LIB= -L/smplocal/pub/NetCDF/4.1.3/lib -lnetcdff -lnetcdf:' \
568	-e "s:-fmod=:-$fmod:" -e 's/-fno-second-underscore//' \
569	-e 's:#-Q- g95 M_K = gmake:#-Q- g95 M_K = make:' \
570	tmp >\| AA_make.gdef
571
572	./ins_make $o_ins_make # We use lines for g95 even for the other compilers
573
574	# on Ada, IOIPSL is already installed in ~rpsl035/IOIPSL_PLUS
575	# so link it to current settings
576	cd $MODEL/modipsl/modeles/
577	\rm -r -f IOIPSL
578	ln -s ~rpsl035/IOIPSL_PLUS IOIPSL
579	cd ..
580	ln -s ~rpsl035/IOIPSL_PLUS/modipsl_Tagv2_2_3/bin/* bin/
581	ln -s ~rpsl035/IOIPSL_PLUS/modipsl_Tagv2_2_3/lib/* lib/
582
583	fi # of if [ ${hostname:0:5} = ada33 ]
584	echo install.sh ioipsl_OK `date`
585	fi # of if [ $ioipsl = 1 ]
586	# Saving ioipsl lib for possible parallel compile
587	cd $MODEL/modipsl
588	tar cf ioipsl.tar lib/ bin/
589
590	#===========================================================================
591	if [ "$with_xios" = "y" ] ; then
592	echo '##########################################################'
593	echo 'Compiling XIOS'
594	echo '##########################################################'
595	cd $MODEL/modipsl/modeles
596	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/install_xios.bash
597	myget install_xios.bash
598	chmod u=rwx install_xios.bash
599	./install_xios.bash -prefix $MODEL/modipsl/modeles \
600	-netcdf ${ncdfdir} -hdf5 ${ncdfdir} \
601	-MPI $root_mpi -arch $arch
602	fi
603
604	#============================================================================
605	veget_version=false
606	if [ "$veget" = 1 ] ; then
607	echo '########################################################'
608	echo 'Compiling ORCHIDEE, the continental surfaces model '
609	echo '########################################################'
610	cd $MODEL/modipsl/modeles/ORCHIDEE
611	export ORCHPATH=`pwd`
612	if [ -d tools ] ; then
613	orchidee_rev=2247
614	veget_version=orchidee2.0
615	cd arch
616	sed -e s:"%COMPILER .*.$":"%COMPILER $compilo":1 \
617	-e s:"%LINK .*.$":"%LINK $compilo":1 \
618	-e s:"%FPP_FLAGS .*.$":"%FPP_FLAGS $fpp_flags":1 \
619	-e s:"%PROD_FFLAGS .*.$":"%PROD_FFLAGS $OPTIM":1 \
620	-e s:"%DEV_FFLAGS .*.$":"%DEV_FFLAGS $OPTDEV":1 \
621	-e s:"%DEBUG_FFLAGS .*.$":"%DEBUG_FFLAGS $OPTDEB":1 \
622	-e s:"%BASE_FFLAGS .*.$":"%BASE_FFLAGS $OPTPREC":1 \
623	-e s:"%BASE_LD .*.$":"%BASE_LD $BASE_LD":1 \
624	arch-gfortran.fcm > arch-local.fcm
625	echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib -lnetcdff -lnetcdf\"" > arch-local.path
626	echo "NETCDF_INCDIR=${ncdfdir}/include" >> arch-local.path
627	echo "IOIPSL_INCDIR=$ORCHPATH/../../lib" >> arch-local.path
628	echo "IOIPSL_LIBDIR=$ORCHPATH/../../lib" >> arch-local.path
629	cd ../
630	# compiling ORCHIDEE sequential mode
631	./makeorchidee_fcm -j 8 -noxios -prod -parallel none -arch $arch
632	echo ./makeorchidee_fcm -j 8 -noxios -prod -parallel none -arch $arch
633	echo Fin de la premiere compilation orchidee ; pwd
634	else
635	if [ -d src_parallel ] ; then
636	liste_src="parallel parameters global stomate sechiba driver"
637	veget_version=orchidee2.0
638	else
639	# Obsolete, for ORCHIDEE_beton only
640	liste_src="parameters stomate sechiba "
641	# A trick to compile ORCHIDEE depending on if we are using real4 or real8
642	cd src_parameters ; \cp reqdprec.$real reqdprec.f90 ; cd ..
643	veget_version=orchidee1.9
644	fi
645	for d in $liste_src ; do src_d=src_$d
646	echo src_d $src_d
647	echo ls ; ls
648	if [ ! -d $src_d ] ; then echo Problem orchidee : no $src_d ; exit ; fi
649	cd $src_d ; \rm -f *.mod make ; $make clean
650	$make ; if [ "$compilo" = "$gfortran" -o "$compilo" = "mpif90" ] ; then cp -f *.mod ../../../lib ; fi
651	cd ..
652	done
653	fi
654	echo install.sh orchidee_OK `date`
655	fi # of if [ "$veget" = 1 ]
656
657
658	#============================================================================
659	# Ehouarn: it may be directory LMDZ4 or LMDZ5 depending on tar file...
660	if [ -d $MODEL/modipsl/modeles/LMD* ] ; then
661	echo '##########################################################'
662	echo 'Compiling LMDZ'
663	echo '##########################################################'
664	cd $MODEL/modipsl/modeles/LMD*
665	LMDZPATH=`pwd`
666	else
667	echo "ERROR: No LMD* directory !!!"
668	exit
669	fi
670
671	###########################################################
672	# For those who want to use fcm to compile via :
673	# makelmdz_fcm -arch local .....
674	############################################################
675
676	if [ "$pclinux" = "1" ] ; then
677
678	# create local 'arch' files (if on Linux PC):
679	cd arch
680	# arch-local.path file
681	echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib -lnetcdff -lnetcdf\"" > arch-local.path
682	echo "NETCDF_INCDIR=-I${ncdfdir}/include" >> arch-local.path
683	echo 'IOIPSL_INCDIR=$LMDGCM/../../lib' >> arch-local.path
684	echo 'IOIPSL_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
685	echo 'XIOS_INCDIR=$LMDGCM/../XIOS/inc' >> arch-local.path
686	echo 'XIOS_LIBDIR=$LMDGCM/../XIOS/lib' >> arch-local.path
687	echo 'ORCH_INCDIR=$LMDGCM/../../lib' >> arch-local.path
688	echo 'ORCH_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
689
690	BASE_LD="$BASE_LD -Wl,-rpath=${ncdfdir}/lib"
691	# arch-local.fcm file (adapted from arch-linux-32bit.fcm)
692
693	if [ $real = r8 ] ; then FPP_DEF=NC_DOUBLE ; else FPP_DEF="" ; fi
694	sed -e s:"%COMPILER .*.$":"%COMPILER $compilo":1 \
695	-e s:"%LINK .*.$":"%LINK $compilo":1 \
696	-e s:"%PROD_FFLAGS .*.$":"%PROD_FFLAGS $OPTIM":1 \
697	-e s:"%DEV_FFLAGS .*.$":"%DEV_FFLAGS $OPTDEV":1 \
698	-e s:"%DEBUG_FFLAGS .*.$":"%DEBUG_FFLAGS $OPTDEB":1 \
699	-e s:"%BASE_FFLAGS .*.$":"%BASE_FFLAGS $OPTPREC":1 \
700	-e s:"%FPP_DEF .*.$":"%FPP_DEF $FPP_DEF":1 \
701	-e s:"%BASE_LD .*.$":"%BASE_LD $BASE_LD":1 \
702	arch-linux-32bit.fcm > arch-local.fcm
703
704	cd ..
705	### Adapt "bld.cfg" (add the shell):
706	whereisthatshell=$(which ${use_shell})
707	echo "bld::tool::SHELL $whereisthatshell" >> bld.cfg
708
709	fi # of if [ "$pclinux" = 1 ]
710
711
712	cd $MODEL/modipsl/modeles/LMDZ*
713
714	##################################################################
715	# Possibly update LMDZ if a specific svn release is requested
716	##################################################################
717
718	if [ "$svn" = "last" ] ; then svnopt="" ; else svnopt="-r $svn" ; fi
719	if [ "$svn" != "" ] ; then set +e ; svn upgrade ; set -e ; svn update $svnopt ; fi
720
721	##################################################################
722	# Compile LMDZ
723	##################################################################
724
725	echo install.sh avant_compilation `date`
726	if [ $compile_with_fcm = 1 ] ; then makelmdz="makelmdz_fcm -arch $arch -j 8" ; else makelmdz="makelmdz -arch $arch" ; fi
727
728	# use the orchidee interface that has no z0h
729	if [ "$no_z0h_orc" = 1 ] ; then
730	veget_version="$veget_version -cpp ORCHIDEE_NOZ0H"
731	fi
732
733	# sequential compilation and bench
734	if [ "$sequential" = 1 ] ; then
735	echo "./$makelmdz $OPT_MAKELMDZ -rrtm true -d ${grid_resolution} -v $veget_version gcm" >> compile.sh
736	chmod +x ./compile.sh ; ./compile.sh
737	echo install.sh apres_compilation `date`
738
739
740	fi # fin sequential
741
742
743
744	# compiling in parallel mode
745	if [ $parallel != "none" ] ; then
746	echo '##########################################################'
747	echo ' Parallel compile '
748	echo '##########################################################'
749	# saving the sequential libs and binaries
750	cd $MODEL/modipsl
751	tar cf sequential.tar bin/ lib/
752	\rm -rf bin/ lib/
753	tar xf ioipsl.tar
754	#
755	# Orchidee
756	#
757	cd $ORCHPATH
758	if [ -d src_parallel ] ; then
759	cd arch
760	sed \
761	-e s:"%COMPILER.*.$":"%COMPILER $par_comp":1 \
762	-e s:"%LINK.*.$":"%LINK $par_comp":1 \
763	-e s:"%MPI_FFLAG.*.$":"%MPI_FFLAGS $MPI_FLAGS":1 \
764	-e s:"%OMP_FFLAG.*.$":"%OMP_FFLAGS $OMP_FLAGS":1 \
765	-e s:"%MPI_LD.*.$":"%MPI_LD $MPI_LD":1 \
766	-e s:"%OMP_LD.*.$":"%OMP_LD $OMP_LD":1 \
767	arch-local.fcm > tmp.fcm
768
769	mv tmp.fcm arch-local.fcm
770	cd ../
771	# compiling ORCHIDEE parallel mode
772	./makeorchidee_fcm -j 8 -clean -noxios -prod -parallel $parallel -arch $arch
773	./makeorchidee_fcm -j 8 -noxios -prod -parallel $parallel -arch $arch
774	echo ./makeorchidee_fcm -j 8 -clean -noxios -prod -parallel $parallel -arch $arch
775	echo ./makeorchidee_fcm -j 8 -noxios -prod -parallel $parallel -arch $arch
776	echo deuxieme compilation orchidee ; pwd
777	else
778	echo '##########################################################'
779	echo ' Orchidee version too old '
780	echo ' Please update to new version '
781	echo '##########################################################'
782	exit
783	fi # of if [ -d src_parallel ]
784	# LMDZ
785	cd $LMDZPATH
786	if [ $arch = local ] ; then
787	cd arch
788	sed -e s:"%COMPILER.*.$":"%COMPILER $par_comp":1 \
789	-e s:"%LINK.*.$":"%LINK $par_comp":1 \
790	-e s:"%MPI_FFLAG.*.$":"%MPI_FFLAGS $MPI_FLAGS":1 \
791	-e s:"%OMP_FFLAG.*.$":"%OMP_FFLAGS $OMP_FLAGS":1 \
792	-e s@"%BASE_LD.*.$"@"%BASE_LD -Wl,-rpath=${root_mpi}/lib:${ncdfdir}/lib"@1 \
793	-e s:"%MPI_LD.*.$":"%MPI_LD $MPI_LD":1 \
794	-e s:"%OMP_LD.*.$":"%OMP_LD $OMP_LD":1 \
795	arch-local.fcm > tmp.fcm
796	mv tmp.fcm arch-local.fcm
797	cd ../
798	fi
799	rm -f compile.sh
800	if [ ${hostname:0:5} = ada33 ] ; then echo "module load intel/2013.0" > compile.sh ; fi
801	echo resol=${grid_resolution} >> compile.sh
802	echo ./$makelmdz $OPT_MAKELMDZ -rrtm true $opt_makelmdz_xios -d \$resol -v $veget_version -mem -parallel $parallel gcm >> compile.sh
803	chmod +x ./compile.sh ; ./compile.sh
804
805	echo "Compilation finished"
806
807	fi # of if [ $parallel != "none" ]
808
809	echo LLLLLLLLLLLLLLLLLLLLLLLLLLL
810	if [ "$gfortran" = "gfortran44" ] ; then
811	echo Your gfortran compiler was too old so that the model was automatically
812	echo compiled with gfortran44 instead. It can not be used in parallel mode.
813	echo You can change the compiler at the begining of the install.sh
814	echo script and reinstall.
815	fi
816
817	##################################################################
818	# Verification du succes de la compilation
819	##################################################################
820
821	# Recherche de l'executable dont le nom a change au fil du temps ...
822	gcm=""
823	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 ; do
824	if [ -f $exe ] ; then gcm=$exe ; fi
825	done
826
827	if [ "$gcm" = "" ] ; then
828	echo 'Compilation failed !!'
829	# Ehouarn : temporary, do not exit and let job finish (to set up bench case)
830	#exit
831	set +e
832	else
833	echo '##########################################################'
834	echo 'Compilation successfull !! '
835	echo '##########################################################'
836	echo The executable is $gcm
837	fi
838
839	##################################################################
840	# Below, we run a benchmark test (if bench=0)
841	##################################################################
842
843	if [ $bench != 0 ] ; then
844
845	echo '##########################################################'
846	echo ' Running a test run '
847	echo '##########################################################'
848
849	\rm -rf BENCH${grid_resolution}
850	bench=bench_lmdz_${grid_resolution}
851	echo install.sh avant_chargement_bench `date`
852	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/$bench.tar.gz
853	myget $bench.tar.gz
854	echo install.sh after bench download `date`
855	tar xvf $bench.tar.gz
856
857	if [ "$with_xios" = "y" ] ; then
858	cd BENCH${grid_resolution}
859	cp ../DefLists/iodef.xml .
860	cp ../DefLists/context_lmdz.xml .
861	cp ../DefLists/field_def_lmdz.xml .
862	cp ../DefLists/file_def_hist*xml .
863	# adapt iodef.xml to use attached mode
864	sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' iodef.xml > tmp
865	\mv -f tmp iodef.xml
866	# and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
867	# except for histday
868	for histfile in file_def_hist*xml
869	do
870	if [ "$histfile" = "file_def_histday_lmdz.xml" ] ; then
871	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' $histfile > tmp ; \mv -f tmp $histfile
872	else
873	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' $histfile > tmp ; \mv -f tmp $histfile
874	fi
875	done
876	# and add option "ok_all_xml=y" in config.def
877	echo "### XIOS outputs" >> config.def
878	echo 'ok_all_xml=.true.' >> config.def
879	cd ..
880	fi
881
882	cp $gcm BENCH${grid_resolution}/gcm.e
883
884	cd BENCH${grid_resolution}
885	# On cree le fichier bench.sh au besoin
886	# Dans le cas 48x36x39 le bench.sh existe deja en parallele
887
888	if [ "$grid_resolution" = "48x36x39" ] ; then
889	echo On ne touche pas au bench.sh
890	# But we have to adapt "run_local.sh" for $mpirun
891	sed -e "s@mpirun@$mpirun@g" run_local.sh > tmp
892	mv -f tmp run_local.sh
893	chmod u=rwx run_local.sh
894	elif [ "${parallel:0:3}" = "mpi" ] ; then
895	# Lancement avec deux procs mpi et 2 openMP
896	echo "export OMP_STACKSIZE=800M" > bench.sh
897	if [ "${parallel:4:3}" = "omp" ] ; then
898	echo "export OMP_NUM_THREADS=2" >> bench.sh
899	fi
900	echo "ulimit -s unlimited" >> bench.sh
901	echo "$mpirun -np 2 gcm.e > listing 2>&1" >> bench.sh
902	else
903	echo "./gcm.e > listing 2>&1" > bench.sh
904	fi
905	echo EXECUTION DU BENCH
906	date ; ./bench.sh > out.bench 2>&1 ; date
907	tail listing
908
909
910	echo '##########################################################'
911	echo 'Simulation finished in' `pwd`
912	echo 'You have compiled with:'
913	cat ../compile.sh
914	if [ $parallel = "none" ] ; then
915	echo 'You may re-run it with : cd ' `pwd` ' ; gcm.e'
916	echo 'or ./bench.sh'
917	else
918	echo 'You may re-run it with : '
919	echo 'cd ' `pwd` '; ./bench.sh'
920	echo 'ulimit -s unlimited'
921	echo 'export OMP_NUM_THREADS=2'
922	echo 'export OMP_STACKSIZE=800M'
923	echo "$mpirun -np 2 gcm.e "
924	fi
925	echo '##########################################################'
926
927	fi
928
929
930	#################################################################
931	# Installation eventuelle du 1D
932	#################################################################
933
934	if [ $SCM = 1 ] ; then
935	cd $MODEL
936	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/1D.tar.gz
937	myget 1D.tar.gz
938	tar xvf 1D.tar.gz
939	cd 1D
940	./run.sh
941	fi

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