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compile_ipslcm7.sh

Last change on this file was 6886, checked in by cetlod, 4 days ago
Being able to compile NEMO in debug mode without changing arch file
Property svn:executable set to ``*
File size: 31.8 KB

Rev	Line
[5479]	1	#!/bin/bash
	2	# Default options
	3	#
	4	#
	5	#
	6	date
	7	#### 1 Set up the compiling options
	8	#### Define some directories
	9	submitdir=$( pwd )
	10	modipsl=$submitdir/../..
	11	arch_path=$submitdir/ARCH
	12	mysrc_path=$submitdir/SOURCES
[6722]	13	export ROOT=$modipsl/modeles/IOIPSL
[6641]	14	#### Set default options
	15	# Activate compilation of LMDZ for regular latlon grid without DYNAMICO
[6856]	16	regular_latlon=n
[6677]	17	# Atmospheric resolution for regular grid for LMDZ/ORCHIDEE, if regular_latlon=y
[5479]	18	resol_atm=144x142x79
	19	# Coupled with ocean biogeochemistry (y/n)
[6346]	20	nemotop=y
[5479]	21	# Optimization mode
	22	# optmode=prod/dev/debug
	23	optmode=prod
	24	# fcm_arch
	25	fcm_arch=default
	26	# Default values to be overritten
	27	parallel=mpi_omp
	28	export fcm_arch parallel xios
	29	full_flag=""
	30	full_nemo=n
	31	full_inca=""
	32	full_xios=""
	33	full_lmdz=""
	34	full_orch=""
	35	full_dyna=""
[6648]	36	full_oasis=n
[6296]	37	# choose radiative code compilation option
	38	rad=rrtm
	39	opt_rad=""
[6544]	40	#choose chemistry inca configuration
	41	optchimie=GES
[6462]	42
[6638]	43	# subconfig : which sub-configuration to compile. By default, the full extracted configuration is compiled.
	44	subconfig=default
	45
[6707]	46	# orchversion tells if ORCHIDEE_2_2 or ORCHIDEE_4 is compiled. This is used as argument and also in the suffix of the executables.
[6462]	47	orchversion=orch22
[6691]	48	# orchdriver : Permet to compile the ORCHIDEE offline drivers. This option is activated by setting -orchdriver as argument.
[6705]	49	# Drivers are now compiled by default
	50	orchdriver="-driver"
[6462]	51
[5479]	52	# Default netcdf_lib is used for XIOS but can be change by argument
	53	netcdf_lib=""
	54
[6827]	55	## Arguments in order to compress temporary files after compilation
	56	tar=no
	57	comp_tar=yes
	58
[5479]	59	# Output text file for compilation of each component
	60	datestr=`LC_ALL=C date +"%Y%m%dT%H%M"`
	61	outfile=$submitdir/out_compile_ipslcm7.$datestr
	62	echo > $outfile
	63	echo; echo "Text output from compilation will be stored in file out_compile_ipslcm7.$datestr"; echo
	64
[6538]	65
	66	rm -f out_compile_ipslcm7
	67	ln -s ${outfile} out_compile_ipslcm7
	68
	69
[5479]	70	#### Read arguments
	71	# Loop over all arguments to modify default set up
	72	while (($# > 0)) ; do
	73	case $1 in
[6677]	74	"-h"\|"-help") cat <<end_help
[5479]	75	########################################################################
	76	# Usage of the script compile_ipslcm7.sh
	77	#
	78	########################################################################
	79
	80	./compile_ipslcm7.sh [Options]
	81
[6677]	82	Description of all options:
[5479]	83
[6677]	84	[-full] Full recompilation of all components. This option can be added to all other options.
	85	[-cleannemo] Full recompilation of NEMO component only.
[6856]	86	[-regular_latlon yes/y/no/n] Activate or deactivate compilation of LMDZ dynamics for regular latlon grid.
	87	Default resol_atm size is used. This option is set in addition to the compilation of the icosahedric grid.
[6677]	88	[-resol_atm XXXxYYYxZZ] Define which regular grid to compile. A default grid is set if this option is not used.
	89	[-debug / -dev / -prod] Level of optimization. One of these can be added to all other compile options. Default: -prod.
	90	[-subconfig X] Set this option if you want to compile a sub-configuration. X can be one of following sub-configurations :
	91	ICOLMDZORINCA, ICOLMDZOR, LMDZORINCA, LMDZOR, IPSLCM-reg or IPSLCM
	92	By default, all available components are compiled.
[6707]	93	[-orch4 / -orch22] Choice of ORCHIDEE version. The source code are found in modeles/ORCHIDEE_4 or modeles/ORCHIDEE_2_2
[6677]	94	and a link will be set to the choosen model version. Default version is currently ORCHIDEE_2_2 (-orch22).
[6691]	95	[-orchdriver] Activate compilation of orchidee offline drivers
[6827]	96	[-tar]: option to compress XIOS repository that takes many inodes without compilation
	97	[-comp_tar]: option to compile and compress XIOS repository if compilation succed
	98	[-notar]: do not compress XIOS repository
[5479]	99
[6827]	100
[6677]	101	Example 1: Default compilation of IPSLCM7
[5479]	102	./compile_ipslcm7.sh
	103
[6677]	104	Example 2: Default compilation in debug mode
[5479]	105	./compile_ipslcm7.sh -debug
	106
	107	Example 3: Default compilation with full recompilation of all components. No clean is needed.
	108	./compile_ipslcm7.sh -full
	109
[6677]	110	Example 4: Compilation in addition of LMDZ in regular lat-lon for a specific resolution :
[6641]	111	./compile_ipslcm7.sh -resol_atm 144x142x95
[5479]	112
[6856]	113	Example 4b: Add compilation of LMDZ in regular grid with default resolution.
	114	./compile_ipslcm7.sh -regular_latlon yes
[6677]	115
[6707]	116	Example 5: Compilation of ORCHIDEE_4 version
[6462]	117	./compile_ipslcm7.sh -orch4
	118
[6544]	119	Example 6: compilation of a specific chemistry for INCA (default is GES)
	120	./compile_ipslcm7.sh -chimie NMHC_AER_S
	121
[6677]	122	Example 7: Compilation of sub-configuration LMDZOR :
	123	./compile_ipslcm7.sh -subconfig LMDZOR
	124
[6827]	125	Example 5: Compile without compressing XIOS and LMDZ/libo in tar files
	126	./compile_ipslcm7.sh -notar
	127
[5479]	128	end_help
	129	exit;;
	130
	131	"-parallel") parallel=$2 ; shift ; shift ;;
	132	"-arch") fcm_arch="$2" ; shift ; shift ;;
	133	"-debug") optmode=debug ; shift ;;
	134	"-dev") optmode=dev ; shift ;;
	135	"-prod") optmode=prod ; shift ;;
[6677]	136	"-regular_latlon") regular_latlon=$2 ; shift ; shift ;;
	137	"-resol_atm") regular_latlon=y ; resol_atm=$2 ; shift ; shift ;;
[6638]	138	"-subconfig") subconfig=$2 ; shift ; shift ;;
[6649]	139	"-full") full_flag="-full"; full_nemo=y ; full_xios="--full" ; full_lmdz="-full" ; full_orch="-full" ; full_oasis=y ; full_inca="-clean" ; full_dyna="-full" ; shift ;;
[5479]	140	"-full_xios") full_xios="--full" ; shift ;; # Note only full_xios is using double dash: --full
	141	"-full_lmdz") full_lmdz="-full" ; shift ;;
	142	"-full_orch") full_orch="-full" ; shift ;;
	143	"-full_nemo") full_nemo=y ; shift ;;
	144	"-full_inca") full_inca="-clean"; shift ;;
[6648]	145	"-full_dyna") full_dyna="-full" ; shift ;;
	146	"-full_oasis") full_oasis=y ; shift ;;
[5479]	147	"-cleannemo") full_nemo=y ; shift ;;
[6296]	148	"-rad") rad=$2; shift ; shift ;;
[6640]	149	"-orch22") orchversion="orch22"; shift ;;
	150	"-orch4") orchversion="orch4"; shift ;;
[6691]	151	"-orchdriver") orchdriver="-driver"; shift ;;
[6544]	152	"-chimie") optchimie=$2; shift ; shift;;
[6827]	153	"-tar") tar=yes ; shift ;;
	154	"-comp_tar") comp_tar=yes ; shift ;;
	155	"-notar") comp_tar=no ; shift ;;
[5479]	156	*) echo "unknown option "$1" , exiting..." ; exit
	157	esac
	158	done
	159
[6638]	160
	161	# Define which sub-configuration to compile. By default all extracted source components are compiled.
	162	source define_config.sh
	163
[5479]	164	echo "Following options are set in current compiling:" >> $outfile
	165	echo " regular_latlon=$regular_latlon (if yes, then resol_atm=${resol_atm})" >> $outfile
[6641]	166	echo " resol_atm=${resol_atm}, nemotop=${nemotop}" >> $outfile
[5479]	167	echo " optmode = $optmode, parallel = $parallel, fcm_arch = $fcm_arch " >> $outfile
[6648]	168	echo " full_flag=$full_flag, full_xios=$full_xios, full_lmdz=$full_lmdz, full_orch=$full_orch, full_nemo=$full_nemo, full_dyna=$full_dyna, full_oasis=$full_oasis" >> $outfile
[6827]	169	echo " tar=$tar, comp_tar=$comp_tar" >> $outfile
[6638]	170	echo " compinca=$compinca compnemo=$compnemo compoasis=$compoasis compdyna=$compdyna complmdz=y comporch=y compxios=y" >> $outfile
[5479]	171	echo >> $outfile
[6640]	172	### Verification of argument
	173	# Set argorch depeinding on the version of ORCHIDEE. This is argument needed for the compilation of LMDZ to consider coherent interface.
	174	if [ $orchversion == orch22 ] ; then
	175	argorch=orchidee2.1
	176	elif [ $orchversion == orch4 ] ; then
	177	argorch=orchideetrunk
	178	else
	179	echo "ERROR in version of ORCHIDEE. It is only possible to have orch22 or orch4 for now"
	180	fi
[6638]	181
[6827]	182	# Compress XIOS and LMDZ/libo without compiling if tar=yes
	183	if [ $tar == yes ] ; then
	184	echo "Option tar activated to compress XIOS and LMDZ/libo. No compilation will be done."
	185	echo >> $outfile
	186	echo "Option tar activated to compress XIOS and LMDZ/libo. No compilation will be done." >> $outfile
	187	if [[ -d $modipsl/modeles/XIOS ]] ; then
	188	echo " Now tar XIOS repository"
	189	echo " Now tar XIOS repository" >> $outfile
[6840]	190	cd $modipsl/modeles
	191	tar -cf XIOS.tar XIOS
	192	rm -rf XIOS
[6827]	193	else
	194	echo " No XIOS repository to compress"
	195	echo " No XIOS repository to compress" >> $outfile
	196	fi
	197
	198	if [[ -d $modipsl/modeles/LMDZ/libo ]] ; then
	199	echo "Now tar LMDZ/libo repository"
	200	echo "Now tar LMDZ/libo repository" >> $outfile
[6840]	201	cd $modipsl/modeles/LMDZ
	202	tar -cf libo.tar libo
	203	rm -rf libo
[6827]	204	else
	205	echo " No LMDZ/libo repository to compress"
	206	echo " No LMDZ/libo repository to compress" >> $outfile
	207	fi
	208
	209	echo "END OF SCRIPT"
	210	echo "END OF SCRIPT" >> $outfile
	211	exit
	212	fi
	213
[5479]	214	### Read host dependent default values
	215	### These variables will not be changed if they were set as argument
	216	###./host.sh $host
	217	# Later : Following lines should be set in host.sh file
	218	# begin host.sh
	219	if [ $fcm_arch == default ] ; then
	220	# Find out current host and source specific paths and commands for the host
	221	case $( hostname -s ) in
	222	jean-zay*)
[6629]	223	if [[ $( hostname -s ) != "pp" ]] ; then
	224	echo "Warning! You MUST compile on jean-zay-pp."
	225	echo "EXIT"
	226	exit
	227	else
	228	fcm_arch=X64_JEANZAY
	229	fi ;;
[5479]	230	irene170\|irene171\|irene190\|irene191\|irene192\|irene193)
	231	fcm_arch=X64_IRENE;;
	232	irene172\|irene173\|irene194\|irene195)
	233	fcm_arch=X64_IRENE-AMD;;
	234	asterix\|obelix)
	235	fcm_arch=ifort_LSCE
	236	if [ "${parallel}" == "mpi_omp" ] ; then
	237	echo "Warning!! Currently at Obelix hybrid mode is not possible."
	238	echo " Option -parallel mpi_omp is now changed to -parallel mpi"
	239	echo ""
	240	parallel=mpi
	241	else
	242	echo "You used -parallel" $parallel
	243	fi ;;
[6296]	244	spirit*)
	245	fcm_arch=ifort_MESOIPSL;;
[5479]	246	ciclad\|climserv\|loholt\|camelot)
	247	fcm_arch=ifort_CICLAD;;
	248	*)
	249	echo Current host is not known. You must use option -arch to specify which architecuture files to use.
	250	echo Exit now.
	251	exit
	252	esac
	253	fi
	254
	255	# Set a link to arch.env if arch-${fcm_arch}.env file exist for current fcm_arch.
	256	# The link arch.env is also set in config.card and will be used by libIGCM to ensure the same running environnement.
	257	if [ -f ARCH/arch-${fcm_arch}.env ] ; then
	258	echo >> $outfile
	259	echo "The file ARCH/arch-${fcm_arch}.env will now be sourced with modules needed for compilation for all components."
[6296]	260	echo "Note that this new environement might be kept after compilation."
	261	echo "If this is the case, source again your personal environment after compilation."
	262	echo " Personal module list before sourcing of ARCH/arch.env file:" >> $outfile
	263	module list >> $outfile 2>&1
[6808]	264	svn_version=$(module -t list \| grep subversion)
[6296]	265
[5479]	266	# Make a link to this file, to be used also in config.card
	267	rm -f ARCH/arch.env
	268	ln -s arch-${fcm_arch}.env ARCH/arch.env
	269
	270	# Source the file
[6296]	271	source ARCH/arch.env >> $outfile 2>&1
	272	if [ X$svn_version != X ] ; then
	273	module load ${svn_version}
	274	fi
	275	echo >> $outfile
	276	echo " New module list after sourcing of ARCH/arch.env file:" >> $outfile
	277	module list >> $outfile 2>&1
[5479]	278	fi
	279
[6462]	280
	281	#### Clean if full_orch
	282	# If full recompilation of ORCHIDEE then first clean modipsl/lib folder
	283	if [ X${full_orch} == X"-full" ] ; then
	284	rm -f $modipsl/lib/*
	285	fi
	286
[5479]	287	#### 2 Do the compilation
	288	## 2.1 Compile ioipsl
	289	cd $modipsl/modeles/IOIPSL
	290	echo; echo "NOW COMPILE IOIPSL"
	291	echo >> $outfile ; echo " NOW COMPILE IOIPSL" >> $outfile
	292
	293	echo ./makeioipsl_fcm -$optmode -parallel -arch ${fcm_arch} -arch_path $arch_path -j 8 $full_flag >> $outfile
	294	./makeioipsl_fcm -$optmode -parallel -arch ${fcm_arch} -arch_path $arch_path -j 8 $full_flag >> $outfile 2>&1
	295	# Test if compiling succeded
	296	if [[ $? != 0 ]] ; then
	297	echo "THERE IS A PROBLEM IN IOIPSL COMPILATION - STOP"
	298	exit
	299	fi
	300
[6638]	301	if [ $compoasis == y ] ; then
[5479]	302	## 2.2 Compile oasis3-mct
[6648]	303	if [ $full_oasis == y ] ; then
	304	rm -rf $modipsl/oasis3-mct/BLD
	305	fi
[5479]	306	cd $modipsl/oasis3-mct/util/make_dir
	307	echo; echo "NOW COMPILE OASIS3-MCT"
	308	echo >> $outfile ; echo " NOW COMPILE OASIS3-MCT" >> $outfile
	309	cp $mysrc_path/OASIS3-MCT/make_${fcm_arch} make.inc
	310
	311	echo make -f TopMakefileOasis3 >> $outfile
	312	make -f TopMakefileOasis3 >> $outfile 2>&1
[6686]	313	if [[ $? != 0 ]] ; then
	314	echo "THERE IS A PROBLEM IN OASIS COMPILATION - STOP"
	315	exit
	316	fi
	317
[5479]	318
[6638]	319	else
	320	echo ; echo No compilation of OASIS
	321	fi
[5479]	322
	323	## 2.3 Compile xios
[6840]	324	cd $modipsl/modeles
[6827]	325	echo; echo "NOW DECOMPRESS XIOS IF NEEDED"
	326	# First check if XIOS needs to be decompressed
	327	# In priority search for modeles/XIOS_${optmode}.tar but if it doesn't exist take
	328	# the first which is found.
	329	if [[ -d $modipsl/modeles/XIOS ]] ; then
	330	echo "Found XIOS -> no decompress needs to be do"; >> $outfile
	331	elif [[ -f $modipsl/modeles/XIOS_${optmode}.tar ]]; then
	332	echo >> $outfile
	333	echo "Found XIOS_${optmode}.tar -> decompress repository" >> $outfile
[6840]	334	tar -xf XIOS_${optmode}.tar >> $outfile 2>&1
[6827]	335	elif [[ -f $modipsl/modeles/XIOS_prod.tar ]]; then
	336	echo >> $outfile
	337	echo "Found XIOS_prod.tar -> decompress repository" >> $outfile
[6840]	338	tar -xf $modipsl/modeles/XIOS_prod.tar >> $outfile 2>&1
[6827]	339	elif [[ -f $modipsl/modeles/XIOS_debug.tar ]]; then
	340	echo >> $outfile
	341	echo "Found XIOS_debug.tar -> decompress repository" >> $outfile
[6840]	342	tar -xf $modipsl/modeles/XIOS_debug.tar >> $outfile 2>&1
[6827]	343	elif [[ -f $modipsl/modeles/XIOS_dev.tar ]]; then
	344	echo >> $outfile
	345	echo "Found XIOS_dev.tar -> decompress repository" >> $outfile
[6840]	346	tar -xf $modipsl/modeles/XIOS_dev.tar >> $outfile 2>&1
[6827]	347	elif [[ -f $modipsl/modeles/XIOS.tar ]]; then
	348	echo >> $outfile
	349	echo "Found XIOS.tar -> decompress repository" >> $outfile
[6840]	350	tar -xf $modipsl/modeles/XIOS.tar >> $outfile 2>&1
[6827]	351	else
	352	echo "XIOS source code was not found. Exit"
	353	echo "XIOS source code was not found. Exit" >> $outfile
	354	exit
	355	fi
	356
[5479]	357	cd $modipsl/modeles/XIOS
	358	echo; echo "NOW COMPILE XIOS"
	359	echo >> $outfile ; echo " NOW COMPILE XIOS" >> $outfile
[6638]	360	if [ $compoasis == y ] ; then
	361	argoasis="--use_oasis oasis3_mct "
	362	else
	363	argoasis=" "
	364	fi
	365	echo ./make_xios $argoasis --$optmode --arch $fcm_arch --arch_path $arch_path ${netcdf_lib} --job 4 $full_xios >> $outfile
	366	./make_xios $argoasis --$optmode --arch $fcm_arch --arch_path $arch_path ${netcdf_lib} --job 4 $full_xios >> $outfile 2>&1
[5479]	367	# Test if compiling succeded
	368	if [[ $? != 0 ]] ; then
	369	echo "THERE IS A PROBLEM IN XIOS COMPILATION - STOP"
	370	exit
	371	fi
	372	# Move executables to modipsl/bin
	373	if [ -f $modipsl/modeles/XIOS/bin/xios_server.exe ] ; then
	374	mv $modipsl/modeles/XIOS/bin/xios_server.exe $modipsl/bin/xios_server_${optmode}.exe
	375	else
	376	echo "THERE IS A PROBLEM IN XIOS COMPILATION EXECUTABLE MISSING - STOP"
	377	exit
	378	fi
	379
	380
[6462]	381	## 2.4 Compile ORCHIDEE
	382	# Choose ORCHIDEE version to compile and create a link to generic folder name ORCHIDEE.
	383	# This link is needed for the compilation of ICOSA_LMDZ for it to find the orchidee librarie.
	384	cd $modipsl/modeles
	385	rm -f ORCHIDEE
	386	if [ $orchversion == orch22 ] ; then
	387	ln -s ORCHIDEE_2_2 ORCHIDEE
	388	cd $modipsl/modeles/ORCHIDEE_2_2
	389	echo; echo "NOW COMPILE ORCHIDEE_2_2"
	390	echo >> $outfile ; echo " NOW COMPILE ORCHIDEE_2_2" >> $outfile
	391	else
[6707]	392	ln -s ORCHIDEE_4 ORCHIDEE
	393	cd $modipsl/modeles/ORCHIDEE_4
	394	echo; echo "NOW COMPILE ORCHIDEE_4 (trunk)"
	395	echo >> $outfile ; echo " NOW COMPILE ORCHIDEE_4 (trunk)" >> $outfile
[6462]	396	fi
[5479]	397
	398	# Check if the compilation of ORCHIDEE was previsouly interupted prematured.
	399	# In that case, the files fcm.bld.lock exist. If the file exist, it is here removed to avoid makeorchidee_fcm
	400	# to ask question and wait for interactivly answer from the user.
	401	if [ -f build/fcm.bld.lock ] ; then
	402	echo >> $outfile
	403	echo " WARNING!! The file ORCHIDEE/build/fcm.bld.lock exist. " >> $outfile
	404	echo " This means that the compilation is either currently on going in another terminal was previous interupted before the end." >> $outfile
	405	echo " The file will now be removed. " >> $outfile
	406	echo >> $outfile
	407	rm -f build/fcm.bld.lock
	408	fi
	409
[6725]	410	if [ $compoasis == y ] ; then
	411	# For this case, XIOS library needs to be linked with OASIS library
	412	argoasis="-linkwithoasis"
	413	else
	414	argoasis=""
	415	fi
	416
	417	echo ./makeorchidee_fcm -j 8 -xios -parallel $parallel -$optmode -arch ${fcm_arch} -arch_path $arch_path ${argoasis} $full_orch $orchdriver >> $outfile
	418	./makeorchidee_fcm -j 8 -xios -parallel $parallel -$optmode -arch ${fcm_arch} -arch_path $arch_path ${argoasis} $full_orch $orchdriver >> $outfile 2>&1
[5479]	419	# Test if compiling finished
	420	if [[ $? != 0 ]] ; then
	421	echo "THERE IS A PROBLEM IN ORCHIDEE COMPILATION - STOP"
	422	exit
	423	fi
	424
[6462]	425	# Rename exetubles for ORCHIDEE offline driver with suffix version
	426	cd $modipsl/bin
[6705]	427	if [ -f orchideedriver ] ; then
	428	mv orchideedriver orchideedriver.${orchversion}_$optmode
	429	ln -sf orchideedriver.${orchversion}_$optmode orchideedriver_$optmode
	430	fi
	431	if [ -f orchidee_ol ] ; then
	432	mv orchidee_ol orchidee_ol.${orchversion}_$optmode
	433	ln -sf orchidee_ol.${orchversion}_$optmode orchidee_ol_$optmode
	434	fi
[5479]	435
[6639]	436	## 2.5 Compile NEMO
[6638]	437	if [ $compnemo == y ] ; then
[6639]	438	nemo_root=$modipsl/modeles/NEMO
	439	cfg_ref=ORCA2_ICE_PISCES
	440	cfg_wrk=ORCA_ICE_TRC
	441	addkeys="key_oasis3 key_top key_si3 key_isf"
	442	delkeys=""
	443
	444	if [ ${nemotop} == n ] ; then
	445	cfg_wrk=ORCA_ICE
	446	delkeys="key_top"
	447	fi
	448
	449	if [ ${nemotop} == n ] ; then
	450	echo; echo "NOW COMPILE NEMO with ice model SI3 without passive tracer model TOP"
	451	echo >> $outfile ; echo " NOW COMPILE NEMO with ice model SI3 without passive tracer model TOP" >> $outfile
	452	else
	453	echo; echo "NOW COMPILE NEMO with ice model SI3 and passive tracer model TOP"
	454	echo >> $outfile ; echo " NOW COMPILE NEMO with ice model SI3 and passive tracer model TOP" >> $outfile
	455	fi
[6886]	456
	457	# Compilation management
	458	# Nemo debug ?
	459	cp $mysrc_path/NEMO/arch-${fcm_arch}.fcm $mysrc_path/NEMO/arch-nemo.fcm
	460	if [ $optmode == debug ] ; then
	461	if (! grep -q "^%DEBUG_FCFLAGS" $mysrc_path/NEMO/arch-nemo.fcm); then
	462	echo "ERROR: You must defined '%DEBUG_FCFLAGS' in your arch file if you want to compile Nemo in debug mode using '-d' option"
	463	exit 1
	464	fi
	465	# duplicate the lines starting with %DEBUG_XXX and replace, in the duplicated line, %DEBUG_XXX by %XXX
	466	sed -i'' -e "/^%DEBUG_/{p;s/^%DEBUG_$[^ ]*$/%\1/;}" $mysrc_path/NEMO/arch-nemo.fcm
	467	else
	468	if (! grep -q "^%PROD_FCFLAGS" $mysrc_path/NEMO/arch-nemo.fcm ); then
	469	echo "WARNING: '%PROD_FCFLAGS' not defined in your arch file, makenemo will use '%FCFLAGS' instead"
	470	fi
	471	# duplicate the lines starting with %PROD_XXX and replace, in the duplicated line, %PROD_XXX by %XXX
	472	sed -i'' -e "/^%PROD_/{p;s/^%PROD_$[^ ]*$/%\1/;}" $mysrc_path/NEMO/arch-nemo.fcm
	473	fi
	474
[6639]	475	echo >> $outfile ; echo cd $nemo_root >> $outfile
[6886]	476	echo >> $outfile ; echo cp $mysrc_path/NEMO/arch-nemo.fcm arch/CNRS/arch-${fcm_arch}.fcm >> $outfile
[6639]	477	echo >> $outfile
[6886]	478
	479	cd $nemo_root ; mv $mysrc_path/NEMO/arch-nemo.fcm arch/CNRS/arch-${fcm_arch}.fcm
	480
[6639]	481	# creation of config
	482	echo >> $outfile ; echo cd $nemo_root >> $outfile
	483	echo ./makenemo -m ${fcm_arch} -n $cfg_wrk -r $cfg_ref -j0 add_key "$addkeys" del_key "$delkeys" >> $outfile
	484	echo >> $outfile
	485	cd $nemo_root
	486	./makenemo -m ${fcm_arch} -n $cfg_wrk -r $cfg_ref -j0 add_key "$addkeys" del_key "$delkeys" >> $outfile 2>&1
	487
	488
	489	# Copy of specfic source files
	490	echo >> $outfile ; echo cp $mysrc_path/NEMO/.90 $nemo_root/cfgs/$cfg_wrk/MY_SRC/. >> $outfile
	491	echo >> $outfile
	492	cp $mysrc_path/NEMO/.90 $nemo_root/cfgs/$cfg_wrk/MY_SRC/.
	493
	494
	495	if [ $full_nemo == y ] ; then
	496	# To make a full compilation, first make a clean to remove all files produced during previous compilation
	497	echo ./makenemo -m ${fcm_arch} -n $cfg_wrk -r $cfg_ref clean >> $outfile
	498	echo >> $outfile
	499	./makenemo -m ${fcm_arch} -n $cfg_wrk -r $cfg_ref clean >> $outfile 2>&1
	500	fi
	501	echo ./makenemo -m ${fcm_arch} -n $cfg_wrk -r $cfg_ref -j8 >> $outfile
	502	echo >> $outfile
	503	./makenemo -m ${fcm_arch} -n $cfg_wrk -r $cfg_ref -j8 >> $outfile 2>&1
	504
	505	echo >> $outfile
	506	echo "Move nemo executable to modipsl/bin" >> $outfile
	507	echo ls -lrt $nemo_root/cfgs/$cfg_wrk/BLD/bin >> $outfile
	508	ls -lrt $nemo_root/cfgs/$cfg_wrk/BLD/bin >> $outfile
	509	echo >> $outfile
	510
	511	if [ -f $nemo_root/cfgs/$cfg_wrk/BLD/bin/nemo.exe ] ; then
	512	mv $nemo_root/cfgs/$cfg_wrk/BLD/bin/nemo.exe $modipsl/bin/opa_${optmode}.exe
	513	else
	514	echo "ERROR nemo.exe executable does not exist."
	515	echo "THERE IS A PROBLEM IN NEMO COMPILATION - STOP"
	516	exit
	517	fi
	518
[5479]	519	else
[6639]	520	echo ; echo No compilation of NEMO
[5479]	521	fi
[6346]	522
[6639]	523	##2.6 Compile INCA
[6638]	524	if [ $compinca == y ] ; then
[6544]	525	cd $modipsl/modeles/INCA
[6639]	526
[6544]	527	echo; echo "NOW COMPILE INCA ${optchimie}"
[6588]	528	echo >> $outfile ; echo " NOW COMPILE INCA ${optchimie}" >> $outfile
	529
[6649]	530	echo ./makeinca_fcm -chimie ${optchimie} -$optmode -xios -parallel mpi_omp -j 8 -arch ${fcm_arch} -arch_path $arch_path $full_inca >> $outfile
	531	./makeinca_fcm -chimie ${optchimie} -$optmode -xios -parallel mpi_omp -j 8 -arch ${fcm_arch} -arch_path $arch_path $full_inca >> $outfile 2>&1
[6639]	532
[6544]	533	# Test if compiling finished
	534	if [[ $? != 0 ]] ; then
	535	echo "THERE IS A PROBLEM IN INCA COMPILATION - STOP"
	536	echo "ALL INFORMATION IN FILE $outfile"
	537	exit
	538	fi
[6639]	539
[6544]	540	echo "Move inca.dat modipsl/bin"
	541	if [[ -f $modipsl/modeles/INCA/SIMULATIONS/${optchimie}/inca.dat ]] ; then
	542	mv $modipsl/modeles/INCA/SIMULATIONS/${optchimie}/inca.dat $modipsl/bin/inca_${optchimie}.dat ;
	543	else
	544	echo "THERE IS A PROBLEM IN INCA COMPILATION - STOP"
	545	echo "ALL INFORMATION IN FILE $outfile"
	546	exit
	547	fi
[6639]	548
[6544]	549	echo "Move tracer.def to modipsl/bin"
	550	if [[ -f $modipsl/modeles/INCA/tracer.def ]] ; then
	551	mv $modipsl/modeles/INCA/tracer.def $modipsl/bin/tracer_${optchimie}.def ;
	552	fi
[6639]	553
[6638]	554	else
[6639]	555	echo ; echo No compilation of INCA
[6638]	556	fi
[6544]	557
	558	## 2.7 Compile LMDZ
[6703]	559
[6827]	560	# First check if LMDZ/libo exist or if it could be decompressed
	561	# If neither LMDZ/libo or LMDZ/libo_${optmode}.tar exists, nothing is done. It'll be created
	562	# during the compilation.
	563	echo; echo "NOW DECOMPRESS LMDZ/libo IF NEEDED"
	564	if [[ -d $modipsl/modeles/LMDZ/libo ]] ; then
	565	echo "Found LMDZ/libo -> no decompress needs to be done"; >> $outfile
	566	elif [[ -f $modipsl/modeles/LMDZ/libo_${optmode}.tar ]]; then
	567	echo "Found LMDZ/libo_${optmode}.tar -> decompress repository"; >> $outfile
	568	echo >> $outfile
[6840]	569	cd $modipsl/modeles/LMDZ
	570	tar -xf libo_${optmode}.tar >> $outfile 2>&1
[6827]	571	fi
	572
	573
[5479]	574	# Compile LMDZ as library to couple to DYNAMICO
[6639]	575	if [ $compdyna == y ] ; then
	576	echo; echo "NOW COMPILE LMDZ FOR COUPLING TO DYNAMICO"
	577	echo >> $outfile ; echo " NOW COMPILE LMDZ FOR COUPLING TO DYNAMICO" >> $outfile
[6840]	578	cd $modipsl/modeles/LMDZ
[6639]	579
	580	# Check if the compilation of LMDZ was previsouly interupted prematured.
	581	# In that case, the files dimension.h and .lock exist. If the files exist, they are here removed to avoid makelmdz_fcm
	582	# to ask question and wait for interactivly answer from the user.
	583	if [ -f libf/grid/dimensions.h ] \|\| [ -f .lock ] ; then
	584	echo >> $outfile
	585	echo " WARNING!! The file LMDZ/libf/grid/dimension.h and/or the LMDZ/.lock exist. " >> $outfile
	586	echo " This means that the compilation is either currently on going in another terminal was previous interupted before the end." >> $outfile
	587	echo " The files dimension.h and .lock will now be removed. " >> $outfile
	588	echo >> $outfile
	589	rm -f libf/grid/dimensions.h
	590	rm -f .lock
	591	fi
	592
	593	# Need to define the proper option for radiative code compilation. By default, we use rrtm
	594	case $rad in
	595	oldrad) opt_rad="" ;;
[6692]	596	rrtm) opt_rad="-rad rrtm" ;;
[6639]	597	ecrad) opt_rad="-rad ecrad" ;;
	598	*) echo Only oldrad rrtm ecrad for rad option ; exit
	599	esac
	600
	601
	602	if [ $compinca == y ] ; then
	603	arginca="-chimie INCA "
	604	else
	605	arginca=" "
	606	fi
	607
	608	if [ $compoasis == y ] ; then
	609	argoasis="-c OMCT "
	610	else
	611	argoasis=" "
	612	fi
[6640]	613
	614	echo ./makelmdz_fcm -p lmd $argoasis $opt_rad -$optmode -mem -parallel $parallel -libphy -v $argorch $arginca -io xios -arch $fcm_arch -arch_path $arch_path -j 8 $full_lmdz >> $outfile
	615	./makelmdz_fcm -p lmd $argoasis $opt_rad -$optmode -mem -parallel $parallel -libphy -v $argorch $arginca -io xios -arch $fcm_arch -arch_path $arch_path -j 8 $full_lmdz >> $outfile 2>&1
[6639]	616
	617
	618	# Test if compiling finished
	619	if [[ $? != 0 ]] ; then
	620	echo "THERE IS A PROBLEM IN LMDZ PHYSICS COMPILATION - STOP"
	621	exit
	622	fi
[5479]	623	fi
	624
	625
[6544]	626	## 2.8 Compile DYNAMICO
[6639]	627	if [ $compdyna == y ] ; then
	628	cd $modipsl/modeles/DYNAMICO
	629	echo; echo "NOW COMPILE DYNAMICO "
	630	echo >> $outfile ; echo " NOW COMPILE DYNAMICO" >> $outfile
	631
	632	if [ $compoasis == y ] ; then
	633	argoasis="-with_oasis "
	634	else
	635	argoasis=" "
	636	fi
	637	if [ $compinca == y ] ; then
	638	arginca="-with_inca "
	639	else
	640	arginca=" "
	641	fi
	642
	643
[6789]	644	echo ./make_icosa -$optmode -parallel $parallel -external_ioipsl $argoasis -with_xios -arch $fcm_arch -arch_path $arch_path -job 8 $full_dyna >> $outfile
	645	./make_icosa -$optmode -parallel $parallel -external_ioipsl $argoasis -with_xios -arch $fcm_arch -arch_path $arch_path -job 8 $full_dyna >> $outfile 2>&1
[6639]	646	# Test if compiling finished
	647	if [[ $? != 0 ]] ; then
	648	echo "THERE IS A PROBLEM IN DYNAMICO COMPILATION - STOP"
	649	exit
	650	fi
[6638]	651	fi
[6639]	652
[6544]	653	## 2.9 Compile interface ICOSA_LMDZ
[6642]	654	if [ $compdyna == y ] ; then
[6639]	655	cd $modipsl/modeles/ICOSA_LMDZ
	656	echo; echo "NOW COMPILE ICOSA_LMDZ "
	657	echo >> $outfile ; echo " NOW COMPILE ICOSA_LMDZ" >> $outfile
	658
	659	echo ./make_icosa_lmdz -nodeps -p lmd -$optmode -parallel $parallel $argoasis -with_orchidee $arginca -arch ${fcm_arch} -arch_path ${arch_path} -job 8 $full_dyna >> $outfile
	660	./make_icosa_lmdz -nodeps -p lmd -$optmode -parallel $parallel $argoasis -with_orchidee $arginca -arch ${fcm_arch} -arch_path ${arch_path} -job 8 $full_dyna >> $outfile 2>&1
	661	# Test if compiling finished
	662	if [[ $? != 0 ]] ; then
	663	echo "THERE IS A PROBLEM IN ICOSA_LMDZ COMPILATION - STOP"
	664	exit
	665	fi
	666	# Move executables to modipsl/bin
	667	if [ -f $modipsl/modeles/ICOSA_LMDZ/bin/icosa_lmdz.exe ] ; then
	668	if [ $compinca == y ] ; then
	669	mv $modipsl/modeles/ICOSA_LMDZ/bin/icosa_lmdz.exe $modipsl/bin/icosa_lmdz_${orchversion}_${optmode}_${optchimie}.exe
	670	# Create link to be use by IPSLCM and LMDZOR without any change in the executable name
	671	cd $modipsl/bin
	672	rm -f icosa_lmdz_${orchversion}_${optmode}.exe
	673	ln -s icosa_lmdz_${orchversion}_${optmode}_${optchimie}.exe icosa_lmdz_${orchversion}_${optmode}.exe
	674	else
	675	mv $modipsl/modeles/ICOSA_LMDZ/bin/icosa_lmdz.exe $modipsl/bin/icosa_lmdz_${orchversion}_${optmode}.exe
	676	fi
[6638]	677	else
[6639]	678	echo "THERE IS A PROBLEM IN ICOSA_LMDZ COMPILATION EXECUTABLE MISSING - STOP"
	679	exit
[6638]	680	fi
[5479]	681	fi
	682
	683
[6544]	684	## 2.10 Compile LMDZ for regular latlon configuration
[6727]	685	if [ $regular_latlon = y ] && [ $complmdz = y ] ; then
[5479]	686
	687	cd $modipsl/modeles/LMDZ
[6840]	688
[5479]	689	# Compile LMDZ regular lat-lon exectuable
	690	echo; echo "NOW COMPILE LMDZ REGULAR LAT-LON MODE. Resolution = ${resol_atm}"
	691	echo >> $outfile ; echo " NOW COMPILE LMDZ REGULAR LAT-LON MODE. Resolution = ${resol_atm}" >> $outfile
	692	# Check if the compilation of LMDZ was previsouly interupted prematured.
	693	# In that case, the files dimension.h and .lock exist. If the files exist, they are here removed to avoid makelmdz_fcm
	694	# to ask question and wait for interactivly answer from the user.
	695	if [ -f libf/grid/dimensions.h ] \|\| [ -f .lock ] ; then
	696	echo >> $outfile
	697	echo " WARNING!! The file LMDZ/libf/grid/dimension.h and/or the LMDZ/.lock exist. " >> $outfile
	698	echo " This means that the compilation is either currently on going in another terminal was previous interupted before the end." >> $outfile
	699	echo " The files dimension.h and .lock will now be removed. " >> $outfile
	700	echo >> $outfile
	701	rm -f libf/grid/dimensions.h
	702	rm -f .lock
	703	fi
[6638]	704
[6692]	705	# Need to define the proper option for radiative code compilation. By default, we use rrtm
	706	case $rad in
	707	oldrad) opt_rad="" ;;
	708	rrtm) opt_rad="-rad rrtm" ;;
	709	ecrad) opt_rad="-rad ecrad" ;;
	710	*) echo Only oldrad rrtm ecrad for rad option ; exit
	711	esac
	712
[6638]	713	if [ $compinca == y ] ; then
	714	arginca="-chimie INCA"
	715	else
	716	arginca=""
	717	fi
	718
	719	if [ $compoasis == y ] ; then
	720	argoasis="-c OMCT"
	721	else
	722	argoasis=""
	723	fi
[6640]	724	echo ./makelmdz_fcm -d ${resol_atm} $argoasis -p lmd $opt_rad -$optmode -mem -parallel $parallel $arginca -io xios -v $argorch -arch $fcm_arch -arch_path $arch_path -j 8 $full_lmdz gcm >> $outfile
	725	./makelmdz_fcm -d ${resol_atm} $argoasis -p lmd $opt_rad -$optmode -mem -parallel $parallel $arginca -io xios -v $argorch -arch $fcm_arch -arch_path $arch_path -j 8 $full_lmdz gcm >> $outfile 2>&1
[5479]	726	# Test if compiling finished
	727	if [[ $? != 0 ]] ; then
	728	echo "THERE IS A PROBLEM IN LMDZ REGULAR LATLON COMPILATION - STOP"
	729	exit
	730	fi
	731
[6457]	732	# Find executable suffix
	733	suffix=_${resol_atm}_phylmd
[6692]	734	suffix=${suffix}_${rad}
[6457]	735	if [ $parallel == seq ] \|\| [ $parallel == none ] ; then
[6544]	736	suffix=${suffix}_seq_orch_inca.e
[6457]	737	else
[6638]	738	if [ $compoasis == y ] ; then
	739	suffix=${suffix}_para_mem_orch_couple
	740	else
	741	suffix=${suffix}_para_mem_orch
	742	fi
	743	if [ $compinca == y ] ; then
	744	suffix=${suffix}_inca.e
	745	else
	746	suffix=${suffix}.e
	747	fi
[6457]	748	fi
	749	echo gcm suffix = $suffix
	750
[6462]	751	# Move executables to modipsl/bin folder
[6457]	752	echo "Move gcm.e executable to modipsl/bin"
	753	if [ -f $modipsl/modeles/LMDZ/bin/gcm${suffix} ] ; then
[6638]	754	if [ $compinca == y ] ; then
	755	mv $modipsl/modeles/LMDZ/bin/gcm${suffix} $modipsl/bin/gcm_${resol_atm}_${orchversion}_${optmode}_${optchimie}.e
	756	# Create link to be use by IPSLCM and LMDZOR without any change in the executable name
	757	cd $modipsl/bin
	758	rm -f gcm_${resol_atm}_${orchversion}_${optmode}.e
	759	ln -s gcm_${resol_atm}_${orchversion}_${optmode}_${optchimie}.e gcm_${resol_atm}_${orchversion}_${optmode}.e
	760	else
	761	mv $modipsl/modeles/LMDZ/bin/gcm${suffix} $modipsl/bin/gcm_${resol_atm}_${orchversion}_${optmode}.e
	762	fi
[6457]	763	else
	764	echo "ERROR gcm${suffix} executable does not exist."
	765	echo "THERE IS A PROBLEM IN LMDZ REGULAR LATLON COMPILATION - STOP"
	766	exit
[6462]	767	fi
	768
[6588]	769	# Find executable suffix
	770	suffix=_${resol_atm}_phylmd
[6692]	771	suffix=${suffix}_${rad}
[6588]	772	if [ $parallel == seq ] \|\| [ $parallel == none ] ; then
	773	suffix=${suffix}_seq_orch.e
	774	else
[6638]	775	if [ $compoasis == y ] ; then
	776	suffix=${suffix}_para_mem_orch_couple.e
	777	else
	778	suffix=${suffix}_para_mem_orch.e
	779	fi
[6588]	780	fi
	781	echo ce0l suffix = $suffix
[6638]	782
[5479]	783	# Compile ce0l initialization program for LMDZ regular lat-lon exectuable
[6544]	784	cd $modipsl/modeles/LMDZ
[5479]	785	echo; echo "NOW COMPILE CE0L OF LMDZ. Resolution = ${resol_atm}"
	786	echo >> $outfile ; echo " NOW COMPILE CE0L OF LMDZ. Resolution = ${resol_atm}" >> $outfile
	787
[6640]	788	echo ./makelmdz_fcm -d ${resol_atm} $argoasis -p lmd -rrtm true -$optmode -mem -parallel $parallel -io xios -v $argorch -arch $fcm_arch -arch_path $arch_path -j 8 $full_lmdz ce0l >> $outfile
	789	./makelmdz_fcm -d ${resol_atm} $argoasis -p lmd -rrtm true -$optmode -mem -parallel $parallel -io xios -v $argorch -arch $fcm_arch -arch_path $arch_path -j 8 $full_lmdz ce0l >> $outfile 2>&1
[5479]	790	# Test if compiling finished
	791	if [[ $? != 0 ]] ; then
	792	echo "THERE IS A PROBLEM IN CE0L (LMDZ) REGULAR LATLON COMPILATION - STOP"
	793	exit
	794	fi
[6462]	795
	796
[6457]	797	# Move executable ce0l to modipsl/bin folder
	798	echo "Move ce0l executable to modipsl/bin"
[5479]	799	if [ -f $modipsl/modeles/LMDZ/bin/ce0l${suffix} ] ; then
	800	mv $modipsl/modeles/LMDZ/bin/ce0l${suffix} $modipsl/bin/ce0l_${resol_atm}_${optmode}.e
	801	else
	802	echo "ERROR ce0l${suffix} executable does not exist."
	803	echo "THERE IS A PROBLEM IN LMDZ REGULAR LATLON COMPILATION - STOP"
	804	exit
	805	fi
	806	fi
	807
[6827]	808	# Compress XIOS and LMDZ/libo
	809	if [ $comp_tar == yes ] && [ -d $modipsl/modeles/XIOS ] ; then
[6828]	810	echo "Option comp_tar activated, now compress XIOS"
	811	echo "Option comp_tar activated, now compress XIOS" >> $outfile
[6840]	812	cd $modipsl/modeles
	813	tar -cf XIOS_${optmode}.tar XIOS
	814	rm -rf XIOS
[6828]	815	fi
[6840]	816
[6828]	817	if [ $comp_tar == yes ] && [ -d $modipsl/modeles/LMDZ/libo ] ; then
	818	echo "Option comp_tar activated, now compress LMDZ/libo"
	819	echo "Option comp_tar activated, now compress LMDZ/libo" >> $outfile
[6840]	820	cd $modipsl/modeles/LMDZ
	821	tar -cf libo_${optmode}.tar libo
	822	rm -rf libo
[6827]	823	fi
[6840]	824
[5479]	825	echo >>$outfile ; echo "ALL COMPILING FINISHED" >> $outfile
	826	echo ls -lrt modipsl/bin >> $outfile
	827	ls -lrt $modipsl/bin >> $outfile
	828
	829	echo; echo "ALL COMPILING FINISHED" ; echo
	830	echo "Executables are found in modipsl/bin"
	831	echo "Check that executable names correspond with the name set in config.card before launching the job"
	832	echo ls -lrt modipsl/bin
	833	ls -lrt $modipsl/bin
	834
	835	date
	836
	837	exit
	838
	839

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source: CONFIG/UNIFORM/v7/IPSLCM7/compile_ipslcm7.sh

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