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source: BOL/script_install/install_lmdz.sh @ 3774

Last change on this file since 3774 was 3736, checked in by idelkadi, 5 years ago
Updating install_lmdz.sh script in order to run simulations with Cosp(v2) simulator. Note that for the update for Jean-Zay, svn is used to download XIOS and that the model is compiled in dev mode with Cospv2
File size: 42.9 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` $dir
52	fi
53	}
54
55
56	#real=r4
57	real=r8
58
59	# WARNING !!!! For versions before october 2009, use
60	# install.v2.sh instead of install.sh
61
62	#########################################################################
63	# Valeur par défaut des parametres
64	#########################################################################
65	svn=""
66	version=trunk
67	getlmdzor=1
68	netcdf=1 # 1 for automatic installation
69	# 0 for no installation
70	# /.../../netcdf-4.0.1 if wanting to link with an already
71	# compiled netcdf library (implies to check option compatibility)
72	check_linux=1
73	ioipsl=1
74	veget=0
75	orchidee_rev="" # default revision of ORCHIDEE
76	bench=1
77	pclinux=1
78	pcmac=0 # default: not on a Mac
79	compiler=gfortran
80	SCM=0
81	# use the old orchidee interface without the calculation of z0h
82	no_z0h_orc=1
83	# orchidee_version: defined to use the CMIP6 version of ORCHIDEE
84	# (and eventually anyother)
85	# values=CMIP6
86	orchidee_version=""
87	# choose the resolution for the bench runs
88	# grid_resolution= 32x24x11 or 48x36x19 for tests (test without ORCHIDEE)
89	# 96x71x19 standard configuration
90	grid_resolution=144x142x79
91	grid_resolution=96x95x39
92	grid_resolution=48x36x19
93	grid_resolution=32x32x39
94	# choose the physiq version you want to test
95	#physiq=NPv6.0.14splith
96	physiq=
97
98	## parallel can take the values none/mpi/omp/mpi_omp
99	parallel=mpi_omp
100	idris_acct=lmd
101	parallel=none
102	OPT_GPROF=""
103	OPT_MAKELMDZ=""
104	MODEL=""
105
106	## also compile XIOS? (and more recent NetCDF/HDF5 libraries) Default=no
107	with_xios="n"
108	opt_makelmdz_xios=""
109
110	## compile_with_fcm=1 : use makelmdz_fcm (1) or makelmdz (0)
111	compile_with_fcm=1
112	cosp=0 ; opt_cosp1=""
113	cosp=0 ; opt_cosp2=""
114	cosp=0 ; opt_cospv2=""
115	opt_cosp=""
116
117	# Check if on a Mac
118	if [ `uname` = "Darwin" ]
119	then
120	pcmac=1
121	export MAKE=make
122	fi
123	#echo "pcmac="$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 [ $netcdf = 1 ]
602
603
604	#=======================================================================================
605	echo OK2 ioipsl=$ioipsl
606	echo '##########################################################'
607	echo 'Installing MODIPSL, the installation package manager for the '
608	echo 'IPSL models and tools'
609	echo '##########################################################'
610
611	if [ $netcdf = 0 -o $netcdf = 1 ] ; then
612	if [ "$with_xios" = "y" ] ; then
613	ncdfdir=$MODEL/netcdf4_hdf5
614	else
615	ncdfdir=$MODEL/netcdf-4.0.1
616	fi
617	else
618	ncdfdir=$netcdf
619	fi
620
621	if [ $ioipsl = 1 ] ; then
622	cd $MODEL/modipsl
623	\rm -rf lib/*
624
625	cd util
626
627	cp AA_make.gdef AA_make.orig
628	F_C="$compiler -c " ; if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then F_C="$compiler -c -cpp " ; fi
629	if [ "$compiler" = "pgf90" ] ; then F_C="$compiler -c -Mpreprocess" ; fi
630	sed -e 's/^\#..g95..\#.*.$/\#/' AA_make.gdef > tmp
631	sed -e "s:F_L = g95:F_L = $compiler:" -e "s:F_C = g95 -c -cpp:F_C = $F_C": \
632	-e 's/g95..w_w..(F_D)/g95 w_w = '"$OPTIMGCM"'/' \
633	-e 's:g95..NCDF_INC..$:g95 NCDF_INC= '"$ncdfdir"'/include:' \
634	-e 's:g95..NCDF_LIB..$:g95 NCDF_LIB= -L'"$ncdfdir"'/lib -lnetcdff -lnetcdf:' \
635	-e 's:g95 L_O =:g95 L_O = -Wl,-rpath='"$ncdfdir"'/lib:' \
636	-e "s:-fmod=:-$fmod:" -e 's/-fno-second-underscore//' \
637	-e 's:#-Q- g95 M_K = gmake:#-Q- g95 M_K = make:' \
638	tmp >\| AA_make.gdef
639
640	if [ $pcmac == 1 ]
641	then
642	cp AA_make.gdef tmp
643	sed -e 's/rpath=/rpath,/g' tmp > AA_make.gdef
644	fi
645
646
647	# We use lines for g95 even for the other compilers to run ins_make
648	if [ "$use_shell" = "ksh" ] ; then
649	./ins_make $o_ins_make
650	else # bash
651	sed -e s:/bin/ksh:/bin/bash:g ins_make > ins_make.bash
652	#if [ "`grep ada AA_make.gdef`" = "" ] ; then # Bidouille pour compiler sur ada des vieux modipsl.tar
653	# \cp -f ~rdzt401/bin/AA_make.gdef .
654	#fi
655	if [ "`grep jeanzay AA_make.gdef`" = "" ] ; then # Bidouille pour compiler sur ada des vieux modipsl.tar
656	echo 'Warning jean-zay not in AA_make.gdef'
657	echo 'Think about updating'
658	exit 1
659	fi
660
661	chmod u=rwx ins_make.bash
662	./ins_make.bash $o_ins_make
663	fi # of if [ "$use_shell" = "ksh" ]
664
665	#=======================================================================================
666	cd $MODEL/modipsl/modeles/IOIPSL/src
667	ioipsllog=`pwd`/ioipsl.log
668	echo '##########################################################'
669	echo 'Compiling IOIPSL, the interface library with Netcdf'
670	echo '##########################################################'
671	echo log file : $ioipsllog
672
673	if [ "$use_shell" = "bash" ] ; then
674	cp Makefile Makefile.ksh
675	sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile
676	fi
677	# if [ "$pclinux" = 1 ] ; then
678	# Build IOIPSL modules and library
679	$make clean
680	$make > $ioipsllog 2>&1
681	if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then # copy module files to lib
682	cp -f *.mod ../../../lib
683	fi
684	# Build IOIPSL tools (ie: "rebuild", if present)
685	if [ -f $MODEL/modipsl/modeles/IOIPSL/tools/rebuild ] ; then
686	cd $MODEL/modipsl/modeles/IOIPSL/tools
687	# adapt Makefile & rebuild script if in bash
688	if [ "$use_shell" = "bash" ] ; then
689	cp Makefile Makefile.ksh
690	sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile
691	cp rebuild rebuild.ksh
692	sed -e 's:/bin/ksh:/bin/bash:g' \
693	-e 's:print -u2:echo:g' \
694	-e 's:print:echo:g' rebuild.ksh > rebuild
695	fi
696	$make clean
697	$make > $ioipsllog 2>&1
698	fi
699	# fi # of if [ "$pclinux" = 1 ]
700
701	else # of if [ $ioipsl = 1 ]
702	if [ ${hostname:0:5} = jean- ] ; then
703	cd $MODEL/modipsl
704	cd util
705	if [ "`grep jeanzay AA_make.gdef`" = "" ] ; then
706	echo 'Warning jean-zay not in AA_make.gdef'
707	echo 'Think about updating'
708	exit 1
709	fi
710	./ins_make $o_ins_make
711	# Compile IOIPSL on jean-zay
712	cd $MODEL/modipsl/modeles/IOIPSL/src
713	gmake > ioipsl.log
714	cd $MODEL/modipsl/modeles/IOIPSL/tools
715	gmake > ioipsl.log
716
717	fi
718	echo install.sh ioipsl_OK `date`
719	fi # of if [ $ioipsl = 1 ]
720	# Saving ioipsl lib for possible parallel compile
721	cd $MODEL/modipsl
722	tar cf ioipsl.tar lib/ bin/
723
724	#===========================================================================
725	if [ "$with_xios" = "y" ] ; then
726	echo '##########################################################'
727	echo 'Compiling XIOS'
728	echo '##########################################################'
729	cd $MODEL/modipsl/modeles
730	xioslog=`pwd`/xios.log
731	echo "log file: $xioslog"
732	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/install_xios.bash
733	myget import/install_xios.bash
734	chmod u=rwx install_xios.bash
735	if [ ${hostname:0:5} = jean- ] ; then
736	# echo 'Need to work on install_xios implementation for jean-zay'
737	# exit
738	svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5 XIOS
739	cd XIOS/arch
740	svn update
741	cd ..
742	./make_xios --prod --arch $arch --job 4 > xios.log 2>&1
743	else
744	./install_xios.bash -prefix $MODEL/modipsl/modeles \
745	-netcdf ${ncdfdir} -hdf5 ${ncdfdir} \
746	-MPI $root_mpi -arch $arch > xios.log 2>&1
747	fi
748	if [ -f XIOS/lib/libxios.a ] ; then
749	echo "OK, XIOS library successfully generated"
750	fi
751	fi
752
753	#============================================================================
754	veget_version=false
755	if [ "$veget" = 1 ] ; then
756	cd $MODEL/modipsl/modeles/ORCHIDEE
757	if [ "$orchidee_version" = "CMIP6" ] ; then
758	set +e
759	svn upgrade
760	svn switch -r 5661 --accept theirs-full svn://forge.ipsl.jussieu.fr/orchidee/tags/ORCHIDEE_2_0/ORCHIDEE
761	orchidee_rev=5661
762	veget_version=orchidee2.0
763	no_z0h_orc=0
764	set -e
765	fi
766	# Correctif suite debug Jean-Zay
767	sed -i -e 's/9010 FORMAT(A52,F17.14)/9010 FORMAT(A52,F20.14)/' src_stomate/stomate.f90
768	opt_orc="-prod" ; if [ "$optim" = "-debug" ] ; then opt_orc="-debug" ; fi
769
770	orchideelog=`pwd`/orchidee.log
771	echo '########################################################'
772	echo 'Compiling ORCHIDEE, the continental surfaces model '
773	echo '########################################################'
774	echo log file : $orchideelog
775	export ORCHPATH=`pwd`
776	if [ -d tools ] ; then
777	###################################################################
778	# Pour les experts qui voudraient changer de version d'orchidee.
779	# Attention : necessite d'avoir le password pour orchidee
780	set +e ; svn upgrade ; set -e
781	if [ "$orchidee_rev" != "" ] ; then
782	# test qu'on est sur la bonne branche pour faire le update
783	set +e
784	svn log -r $orchidee_rev \| grep $orchidee_rev
785	if [ $? -gt 0 ] ; then
786	echo 'Cannot update ORCHIDEE as not on the right branch for ORCHIDEE'
787	exit
788	fi
789	set -e
790	set +e ; svn update -r $orchidee_rev ; set -e
791	fi
792	# Correctif suite debug Jean-Zay
793	if [ -f src_global/time.f90 ] ; then sed -i -e 's/CALL tlen2itau/\!CALL tlen2itau/' src_global/time.f90 ; fi
794	###################################################################
795	if [ "$veget_version" == "false" ] ; then veget_version=orchidee2.0 ; fi
796	cd arch
797	sed -e s:"%COMPILER .*.$":"%COMPILER $compiler":1 \
798	-e s:"%LINK .*.$":"%LINK $compiler":1 \
799	-e s:"%FPP_FLAGS .*.$":"%FPP_FLAGS $fpp_flags":1 \
800	-e s:"%PROD_FFLAGS .*.$":"%PROD_FFLAGS $OPTIM":1 \
801	-e s:"%DEV_FFLAGS .*.$":"%DEV_FFLAGS $OPTDEV":1 \
802	-e s:"%DEBUG_FFLAGS .*.$":"%DEBUG_FFLAGS $OPTDEB":1 \
803	-e s:"%BASE_FFLAGS .*.$":"%BASE_FFLAGS $OPTPREC":1 \
804	-e s:"%BASE_LD .*.$":"%BASE_LD $BASE_LD":1 \
805	-e s:"%ARFLAGS .*.$":"%ARFLAGS $ARFLAGS":1 \
806	arch-gfortran.fcm > arch-local.fcm
807	echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib -lnetcdff -lnetcdf\"" > arch-local.path
808	echo "NETCDF_INCDIR=${ncdfdir}/include" >> arch-local.path
809	echo "IOIPSL_INCDIR=$ORCHPATH/../../lib" >> arch-local.path
810	echo "IOIPSL_LIBDIR=$ORCHPATH/../../lib" >> arch-local.path
811	echo 'XIOS_INCDIR=${ORCHDIR}/../XIOS/inc' >> arch-local.path
812	echo 'XIOS_LIBDIR="${ORCHDIR}/../XIOS/lib -lxios"' >> arch-local.path
813	cd ../
814	# compiling ORCHIDEE sequential mode
815	./makeorchidee_fcm -j 8 -noxios $opt_orc -parallel none -arch $arch > $orchideelog 2>&1
816	echo ./makeorchidee_fcm -j 8 -noxios $opt_orc -parallel none -arch $arch
817	echo End of the first compilation of orchidee ; pwd
818	else
819	if [ -d src_parallel ] ; then
820	liste_src="parallel parameters global stomate sechiba driver"
821	if [ "$veget_version" == "false" ] ; then veget_version=orchidee2.0 ; fi
822	else
823	# Obsolete, for ORCHIDEE_beton only
824	liste_src="parameters stomate sechiba "
825	# A trick to compile ORCHIDEE depending on if we are using real4 or real8
826	cd src_parameters ; \cp reqdprec.$real reqdprec.f90 ; cd ..
827	if [ "$veget_version" == "false" ] ; then veget_version=orchidee1.9 ; fi
828	fi
829	for d in $liste_src ; do src_d=src_$d
830	echo src_d $src_d
831	echo ls ; ls
832	if [ ! -d $src_d ] ; then echo Problem orchidee : no $src_d ; exit ; fi
833	cd $src_d ; \rm -f *.mod make ; $make clean
834	$make > $orchideelog 2>&1 ; if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then cp -f *.mod ../../../lib ; fi
835	cd ..
836	done
837	fi
838	echo install.sh orchidee_OK `date`
839	fi # of if [ "$veget" = 1 ]
840
841
842	#============================================================================
843	# Ehouarn: it may be directory LMDZ4 or LMDZ5 depending on tar file...
844	if [ -d $MODEL/modipsl/modeles/LMD* ] ; then
845	echo '##########################################################'
846	echo 'Compiling LMDZ'
847	echo '##########################################################'
848	cd $MODEL/modipsl/modeles/LMD*
849	LMDZPATH=`pwd`
850	else
851	echo "ERROR: No LMD* directory !!!"
852	exit
853	fi
854
855	###########################################################
856	# For those who want to use fcm to compile via :
857	# makelmdz_fcm -arch local .....
858	############################################################
859
860	if [ "$pclinux" = "1" ] ; then
861
862	# create local 'arch' files (if on Linux PC):
863	cd arch
864	# arch-local.path file
865	echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib -lnetcdff -lnetcdf\"" > arch-local.path
866	echo "NETCDF_INCDIR=-I${ncdfdir}/include" >> arch-local.path
867	echo 'IOIPSL_INCDIR=$LMDGCM/../../lib' >> arch-local.path
868	echo 'IOIPSL_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
869	echo 'XIOS_INCDIR=$LMDGCM/../XIOS/inc' >> arch-local.path
870	echo 'XIOS_LIBDIR=$LMDGCM/../XIOS/lib' >> arch-local.path
871	echo 'ORCH_INCDIR=$LMDGCM/../../lib' >> arch-local.path
872	echo 'ORCH_LIBDIR=$LMDGCM/../../lib' >> arch-local.path
873
874	if [ $pcmac == 1 ] ; then
875	BASE_LD="$BASE_LD -Wl,-rpath,${ncdfdir}/lib"
876	else
877	BASE_LD="$BASE_LD -Wl,-rpath=${ncdfdir}/lib"
878	fi
879	# Arch-local.fcm file (adapted from arch-linux-32bit.fcm)
880
881	if [ $real = r8 ] ; then FPP_DEF=NC_DOUBLE ; else FPP_DEF="" ; fi
882	sed -e s:"%COMPILER .*.$":"%COMPILER $compiler":1 \
883	-e s:"%LINK .*.$":"%LINK $compiler":1 \
884	-e s:"%PROD_FFLAGS .*.$":"%PROD_FFLAGS $OPTIM":1 \
885	-e s:"%DEV_FFLAGS .*.$":"%DEV_FFLAGS $OPTDEV":1 \
886	-e s:"%DEBUG_FFLAGS .*.$":"%DEBUG_FFLAGS $OPTDEB":1 \
887	-e s:"%BASE_FFLAGS .*.$":"%BASE_FFLAGS $OPTPREC":1 \
888	-e s:"%FPP_DEF .*.$":"%FPP_DEF $FPP_DEF":1 \
889	-e s:"%BASE_LD .*.$":"%BASE_LD $BASE_LD":1 \
890	-e s:"%ARFLAGS .*.$":"%ARFLAGS $ARFLAGS":1 \
891	arch-linux-32bit.fcm > arch-local.fcm
892
893	cd ..
894	### Adapt "bld.cfg" (add the shell):
895	whereisthatshell=$(which ${use_shell})
896	echo "bld::tool::SHELL $whereisthatshell" >> bld.cfg
897
898	fi # of if [ "$pclinux" = 1 ]
899
900
901	cd $MODEL/modipsl/modeles/LMDZ*
902	lmdzlog=`pwd`/lmdz.log
903
904	##################################################################
905	# Possibly update LMDZ if a specific svn release is requested
906	##################################################################
907
908	set +e ; svn upgrade ; set -e
909	if [ "$svn" = "last" ] ; then svnopt="" ; else svnopt="-r $svn" ; fi
910	if [ "$svn" != "" ] ; then svn update $svnopt ; fi
911
912	echo '##################################################################'
913	echo Compile LMDZ
914	echo '##################################################################'
915	echo log file : $lmdzlog
916
917	if [ "$env_file" != "" ] ; then mv arch/arch-${arch}.env arch/arch-${arch}.orig ; \cp -f $env_file arch/arch-${arch}.env ; fi
918
919	echo install.sh avant_compilation `date`
920	if [ $compile_with_fcm = 1 ] ; then makelmdz="makelmdz_fcm $optim -arch $arch -j 8 " ; else makelmdz="makelmdz $optim -arch $arch" ; fi
921
922	# use the orchidee interface that has no z0h
923	if [ "$no_z0h_orc" = 1 ] ; then
924	veget_version="$veget_version -cpp ORCHIDEE_NOZ0H"
925	fi
926
927	# sequential compilation and bench
928	if [ "$sequential" = 1 ] ; then
929	echo "./$makelmdz $optim $OPT_MAKELMDZ $optim -rrtm true $opt_cosp -d ${grid_resolution} -v $veget_version gcm " >> compile.sh
930	chmod +x ./compile.sh
931	if [ $bench != 0 ] ; then ./compile.sh > $lmdzlog 2>&1 ; fi
932	echo install.sh apres_compilation `date`
933
934
935	fi # fin sequential
936
937
938
939	# compiling in parallel mode
940	if [ $parallel != "none" ] ; then
941	echo '##########################################################'
942	echo ' Parallel compile '
943	echo '##########################################################'
944	# saving the sequential libs and binaries
945	cd $MODEL/modipsl
946	tar cf sequential.tar bin/ lib/
947	\rm -rf bin/ lib/
948	tar xf ioipsl.tar
949	#
950	# Orchidee
951	#
952	cd $ORCHPATH
953	if [ -d src_parallel -a $veget = 1 ] ; then
954	cd arch
955	sed \
956	-e s:"%COMPILER.*.$":"%COMPILER $par_comp":1 \
957	-e s:"%LINK.*.$":"%LINK $par_comp":1 \
958	-e s:"%MPI_FFLAG.*.$":"%MPI_FFLAGS $MPI_FLAGS":1 \
959	-e s:"%OMP_FFLAG.*.$":"%OMP_FFLAGS $OMP_FLAGS":1 \
960	-e s:"%MPI_LD.*.$":"%MPI_LD $MPI_LD":1 \
961	-e s:"%OMP_LD.*.$":"%OMP_LD $OMP_LD":1 \
962	arch-local.fcm > tmp.fcm
963
964	mv tmp.fcm arch-local.fcm
965	cd ../
966	echo compiling ORCHIDEE parallel mode
967	echo logfile $orchideelog
968	./makeorchidee_fcm -j 8 -clean -noxios $opt_orc -parallel $parallel -arch $arch > $orchideelog 2>&1
969	./makeorchidee_fcm -j 8 -noxios $opt_orc -parallel $parallel -arch $arch >> $orchideelog 2>&1
970	echo ./makeorchidee_fcm -j 8 -clean -noxios $opt_orc -parallel $parallel -arch $arch
971	echo ./makeorchidee_fcm -j 8 -noxios $opt_orc -parallel $parallel -arch $arch
972	elif [ $veget = 1 ] ; then
973	echo '##########################################################'
974	echo ' Orchidee version too old '
975	echo ' Please update to new version '
976	echo '##########################################################'
977	exit
978	fi # of if [ -d src_parallel ]
979	# LMDZ
980	cd $LMDZPATH
981	if [ $arch = local ] ; then
982	cd arch
983	sed -e s:"%COMPILER.*.$":"%COMPILER $par_comp":1 \
984	-e s:"%LINK.*.$":"%LINK $par_comp":1 \
985	-e s:"%MPI_FFLAG.*.$":"%MPI_FFLAGS $MPI_FLAGS":1 \
986	-e s:"%OMP_FFLAG.*.$":"%OMP_FFLAGS $OMP_FLAGS":1 \
987	-e s:"%ARFLAGS.*.$":"%ARFLAGS $ARFLAGS":1 \
988	-e s@"%BASE_LD.*.$"@"%BASE_LD -Wl,-rpath=${root_mpi}/lib:${ncdfdir}/lib"@1 \
989	-e s:"%MPI_LD.*.$":"%MPI_LD $MPI_LD":1 \
990	-e s:"%OMP_LD.*.$":"%OMP_LD $OMP_LD":1 \
991	arch-local.fcm > tmp.fcm
992	mv tmp.fcm arch-local.fcm
993	cd ../
994	fi
995	rm -f compile.sh
996	echo resol=${grid_resolution} >> compile.sh
997	if [ ${hostname:0:5} = jean- -a "$cospv2" = 1 ] ; then
998	echo ./$makelmdz -dev $optim $OPT_MAKELMDZ -rrtm true $opt_cosp $opt_makelmdz_xios -d \$resol -v $veget_version -mem -parallel $parallel gcm >> compile.sh
999	echo ./$makelmdz -dev $optim $OPT_MAKELMDZ -rrtm true $opt_cosp $opt_makelmdz_xios -d \$resol -v $veget_version -mem -parallel $parallel gcm
1000	else
1001	echo ./$makelmdz $optim $OPT_MAKELMDZ -rrtm true $opt_cosp $opt_makelmdz_xios -d \$resol -v $veget_version -mem -parallel $parallel gcm >> compile.sh
1002	echo ./$makelmdz $optim $OPT_MAKELMDZ -rrtm true $opt_cosp $opt_makelmdz_xios -d \$resol -v $veget_version -mem -parallel $parallel gcm
1003	fi
1004	chmod +x ./compile.sh
1005	if [ $bench != 0 ] ; then ./compile.sh > $lmdzlog 2>&1 ; fi
1006
1007	echo "Compilation finished"
1008
1009	fi # of if [ $parallel != "none" ]
1010
1011	#echo LLLLLLLLLLLLLLLLLLLLLLLLLLL
1012	if [ "$gfortran" = "gfortran44" ] ; then
1013	echo Your gfortran compiler was too old so that the model was automatically
1014	echo compiled with gfortran44 instead. It can not be used in parallel mode.
1015	echo You can change the compiler at the begining of the install.sh
1016	echo script and reinstall.
1017	fi
1018
1019	##################################################################
1020	# Verification du succes de la compilation
1021	##################################################################
1022
1023	# Recherche de l'executable dont le nom a change au fil du temps ...
1024	gcm=""
1025	for exe in gcm.e bin/gcm_${grid_resolution}_phylmd_seq_orch.e bin/gcm_${grid_resolution}_phylmd_seq.e bin/gcm_${grid_resolution}_phylmd_para_mem.e bin/gcm_${grid_resolution}_phylmd_para_mem_orch.e ; do
1026	if [ -f $exe ] ; then gcm=$exe ; fi
1027	done
1028
1029	if [ "$gcm" = "" ] ; then
1030	if [ $bench != 0 ] ; then
1031	echo 'Compilation failed !! Cannot run the benchmark;'
1032	exit
1033	else
1034	echo 'Compilation not done (only done when bench=1)'
1035	fi
1036	else
1037	echo '##########################################################'
1038	echo 'Compilation successfull !! '
1039	echo '##########################################################'
1040	echo The executable is $gcm
1041	fi
1042
1043	##################################################################
1044	# Below, we run a benchmark test (if bench=0)
1045	##################################################################
1046
1047	if [ $bench != 0 ] ; then
1048
1049	echo '##########################################################'
1050	echo ' Running a test run '
1051	echo '##########################################################'
1052
1053	\rm -rf BENCH${grid_resolution}
1054	bench=bench_lmdz_${grid_resolution}
1055	echo install.sh before bench download `date`
1056	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/$bench.tar.gz
1057	myget 3DBenchs/$bench.tar.gz
1058	echo install.sh after bench download `date`
1059	tar xvf $bench.tar.gz
1060
1061	if [ "$cosp" = 1 -o "$cosp2" = 1 -o "$cospv2" = 1 ] ; then
1062	cd BENCH${grid_resolution}
1063	# copier les fichiers namelist input et output our COSP
1064	cp ../DefLists/cosp*_input_nl.txt .
1065	cp ../DefLists/cosp*_output_nl.txt .
1066	# Activer la cles ok_cosp pour tourner avec COSP
1067	sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp
1068	\mv -f tmp config.def
1069	cd ..
1070	fi
1071
1072	if [ -n "$physiq" ]; then
1073	cd BENCH${grid_resolution}
1074	if [ -f physiq.def_${physiq} ]; then
1075	cp physiq.def_${physiq} physiq.def
1076	echo using physiq.def_${physiq}
1077	else
1078	echo using standard physiq.def
1079	fi
1080	cd ..
1081	else
1082	echo using standard physiq.def
1083	fi
1084
1085	if [ "$with_xios" = "y" ] ; then
1086	cd BENCH${grid_resolution}
1087	cp ../DefLists/iodef.xml .
1088	cp ../DefLists/context_lmdz.xml .
1089	cp ../DefLists/field_def_lmdz.xml .
1090	cp ../DefLists/field_def_cosp*.xml .
1091	cp ../DefLists/file_def_hist*xml .
1092	# adapt iodef.xml to use attached mode
1093	sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' iodef.xml > tmp
1094	\mv -f tmp iodef.xml
1095
1096	# and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE.
1097	# except for histday
1098	for histfile in file_def_hist*xml
1099	do
1100	if [ "$histfile" = "file_def_histday_lmdz.xml" ] ; then
1101	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' $histfile > tmp ; \mv -f tmp $histfile
1102	sed -e 's@output_level="_AUTO_"@output_level="5"@' $histfile > tmp ; \mv -f tmp $histfile
1103	sed -e 's@compression_level="2"@compression_level="0"@' $histfile > tmp ; \mv -f tmp $histfile
1104	else
1105	sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' $histfile > tmp ; \mv -f tmp $histfile
1106	fi
1107	done
1108	# and add option "ok_all_xml=y" in config.def
1109	echo "### XIOS outputs" >> config.def
1110	echo 'ok_all_xml=.true.' >> config.def
1111
1112	#activer les sorties pour Cosp
1113	if [ "$cosp" = 1 -o "$cosp2" = 1 ] ; then
1114	histfile=file_def_histdayCOSP_lmdz.xml
1115	sed -e 's@enabled=".FALSE."@enabled=".TRUE."@' $histfile > tmp ; \mv -f tmp $histfile
1116	sed -e 's@output_level="_AUTO_"@output_level="5"@' $histfile > tmp ; \mv -f tmp $histfile
1117	sed -e 's@compression_level="2"@compression_level="0"@' $histfile > tmp ; \mv -f tmp $histfile
1118	fi
1119	if [ "$cospv2" = 1 ] ; then
1120	histfile=file_def_histdayCOSPv2_lmdz.xml
1121	sed -e 's@compression_level="2"@compression_level="0"@' $histfile > tmp ; \mv -f tmp $histfile
1122	contextfile=context_lmdz.xml
1123	sed -e 's@src="./file_def_histdayCOSP_lmdz.xml"@src="./file_def_histdayCOSPv2_lmdz.xml"@' $contextfile > tmp ; \mv -f tmp $contextfile
1124	fieldfile=field_def_lmdz.xml
1125	sed -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' $fieldfile > tmp ; \mv -f tmp $fieldfile
1126	fi
1127
1128	cd ..
1129	fi
1130
1131	cp $gcm BENCH${grid_resolution}/gcm.e
1132
1133	cd BENCH${grid_resolution}
1134	# On cree le fichier bench.sh au besoin
1135	# Dans le cas 48x36x39 le bench.sh existe deja en parallele
1136
1137	if [ "$grid_resolution" = "48x36x39" ] ; then
1138	echo On ne touche pas au bench.sh
1139	# But we have to adapt "run_local.sh" for $mpirun
1140	sed -e "s@mpirun@$mpirun@g" run_local.sh > tmp
1141	mv -f tmp run_local.sh
1142	chmod u=rwx run_local.sh
1143	elif [ "${parallel:0:3}" = "mpi" ] ; then
1144	# Lancement avec deux procs mpi et 2 openMP
1145	echo "export OMP_STACKSIZE=800M" > bench.sh
1146	if [ "${parallel:4:3}" = "omp" ] ; then
1147	echo "export OMP_NUM_THREADS=2" >> bench.sh
1148	fi
1149	if [ "$cospv2" = 1 -o "$cosp" = 1 -o "$cosp2" = 1 ] ; then
1150	if [ ${hostname:0:5} = jean- ] ; then
1151	chmod +x ../arch.env
1152	../arch.env
1153	echo "ulimit -s 2000000" >> bench.sh
1154	else
1155	echo "ulimit -s 200000" >> bench.sh
1156	fi
1157	else
1158	echo "ulimit -s unlimited" >> bench.sh
1159	fi
1160	if [ ${hostname:0:5} = jean- ] ; then
1161	echo "srun -n 2 -A $idris_acct@cpu gcm.e > listing 2>&1" >> bench.sh
1162	else
1163	echo "$mpirun -np 2 gcm.e > listing 2>&1" >> bench.sh
1164	fi
1165	else
1166	echo "./gcm.e > listing 2>&1" > bench.sh
1167	fi
1168	echo EXECUTION DU BENCH
1169	set +e
1170	date ; ./bench.sh > out.bench 2>&1 ; date
1171	set -e
1172	tail listing
1173
1174
1175	echo '##########################################################'
1176	echo 'Simulation finished in' `pwd`
1177	echo 'You have compiled with:'
1178	cat ../compile.sh
1179	if [ $parallel = "none" ] ; then
1180	echo 'You may re-run it with : cd ' `pwd` ' ; gcm.e'
1181	echo 'or ./bench.sh'
1182	else
1183	echo 'You may re-run it with : '
1184	echo 'cd ' `pwd` '; ./bench.sh'
1185	# echo 'ulimit -s unlimited'
1186	# echo 'export OMP_NUM_THREADS=2'
1187	# echo 'export OMP_STACKSIZE=800M'
1188	# echo "$mpirun -np 2 gcm.e "
1189	fi
1190	echo '##########################################################'
1191
1192	fi
1193
1194
1195	#################################################################
1196	# Installation eventuelle du 1D
1197	#################################################################
1198
1199	if [ $SCM = 1 ] ; then
1200	cd $MODEL
1201	#wget http://www.lmd.jussieu.fr/~lmdz/Distrib/1D.tar.gz
1202	myget 1D/1D.tar.gz
1203	tar xvf 1D.tar.gz
1204	cd 1D
1205	./run.sh
1206	fi

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