#!/bin/bash ########################################################################### # Author : Laurent Fairhead et Frédéric Hourdin # Usage : install_lmdz.sh -help # # bash installation script of the LMDZ model on a Linux PC. # the model is downloaded in the following direcory tree # $MODEL/modipsl/modeles/... # using the "modipsl" infrastructure created by the "IPSL" # for coupled (atmosphere/ocean/vegetation/chemistry) climate modeling # activities. # Here we only download atmospheric (LMDZ) and vegetation (ORCHIDEE) # components. # # The sources of the models can be found in the "modeles" directory. # In the present case, LMDZ5, ORCHIDEE and IOIPSL (handling of input-outputs # using the NetCDF library. # # The script downloads various source files (including a version of NetCDF) # and utilities, compiles the model, and runs a test simulation in a # munimal configuration. # # Prerequisites : pgf90/gfortran, ksh, wget , gunzip, tar, ... # # Modif 18/11/2011 # changes for option real 8. # We comopile with -r8 (or equivalent) and -DNC_DOUBLE for the GCM # but with -r4 for netcdf. Variable real must be set to # r4 or r8 at the beginning of the script below. # ########################################################################### echo install.sh DEBUT `date` set -e ################################################################ # Choice of installation options ################################################################ # A function to fetch files either locally or on the internet function myget { #1st and only argument should be file name # Path on local computer where to look for the datafile if [ -f /u/lmdz/WWW/LMDZ/pub/$1 ] ; then \cp -f -p /u/lmdz/WWW/LMDZ/pub/$1 . elif [ -f ~/LMDZ/pub/$1 ] ; then \cp -f -p ~/LMDZ/pub/$1 . else wget -nv http://www.lmd.jussieu.fr/~lmdz/pub/$1 #dir=~/LMDZ/pub/`dirname $1` ; mkdir -p $dir ; cp -r `basename $1` $dir fi } #real=r4 real=r8 # WARNING !!!! For versions before october 2009, use # install.v2.sh instead of install.sh ######################################################################### # Valeur par défaut des parametres ######################################################################### svn="" version=trunk getlmdzor=1 netcdf=1 # 1 for automatic installation # 0 for no installation # /.../../netcdf-4.0.1 if wanting to link with an already # compiled netcdf library (implies to check option compatibility) check_linux=1 ioipsl=1 veget=0 orchidee_rev="" # default revision of ORCHIDEE bench=1 pclinux=1 pcmac=0 # default: not on a Mac compiler=gfortran SCM=0 # use the old orchidee interface without the calculation of z0h no_z0h_orc=1 # orchidee_version: defined to use the CMIP6 version of ORCHIDEE # (and eventually anyother) # values=CMIP6 orchidee_version="" # choose the resolution for the bench runs # grid_resolution= 32x24x11 or 48x36x19 for tests (test without ORCHIDEE) # 96x71x19 standard configuration grid_resolution=144x142x79 grid_resolution=96x95x39 grid_resolution=48x36x19 grid_resolution=32x32x39 # choose the physiq version you want to test #physiq=NPv6.0.14splith physiq= ## parallel can take the values none/mpi/omp/mpi_omp parallel=mpi_omp idris_acct=lmd parallel=none OPT_GPROF="" OPT_MAKELMDZ="" MODEL="" ## also compile XIOS? (and more recent NetCDF/HDF5 libraries) Default=no with_xios="n" opt_makelmdz_xios="" ## compile_with_fcm=1 : use makelmdz_fcm (1) or makelmdz (0) compile_with_fcm=1 cosp=0 ; opt_cosp1="" cosp=0 ; opt_cosp2="" cosp=0 ; opt_cospv2="" opt_cosp="" # Check if on a Mac if [ `uname` = "Darwin" ] then pcmac=1 export MAKE=make fi #echo "pcmac="$pcmac env_file="" ######################################################################### # Options interactives ######################################################################### while (($# > 0)) do case $1 in "-h") cat <<........fin $0 [ -v version ] [ -r svn_release ] [ -parallel PARA ] [ -d GRID_RESOLUTION ] [ -bench 0/1 ] [-name LOCAL_MODEL_NAME] [-gprof] [-opt_makelmdz] -v "version" like 20150828.trunk see http://www.lmd.jussieu.fr/~lmdz/Distrib/LISMOI.trunk -r "svn_release" : either the svn release number or "last" -compiler gfortran|ifort|pgf90 (default: gfortran) -parallel PARA : can be mpi_omp (mpi with openMP) or none (for sequential) -d GRID_RESOLUTION should be among the available benchs if -bench 1 among which : 48x36x19, 48x36x39 if wanting to run a bench simulation in addition to compilation default : 48x36x19 -bench activating the bench or not (0/1). Default 1 -name LOCAL_MODEL_NAME : default = LMDZversion.release -netcdf PATH : full path to an existing installed NetCDF library (without -netcdf: also download and install the NetCDF library) -xios also download and compile the XIOS library (requires the NetCDF4-HDF5 library, also installed by default) (requires to also have -parallel mpi_omp) -gprof to compile with -pg to enable profiling with gprof -orchidee_rev "svn_release" : upgrade included ORCHIDEE model to given svn release number (default: $orchidee_rev) (only valid for orchidee2.0 and later) -cosp to compile with cosp(v1) -cosp2 to compile with cosp(1v2) -cospv2 to compile with cosp(v2) -nofcm to compile without fcm -SCM install 1D version automatically -debug compile everything in debug mode -opt_makelmdz to call makelmdz or makelmdz_fcm with additional options -physiq to choose which physics package to use -env_file specify an arch.env file to overwrite the existing one -orc_version to chose some tagged ORCHIDEE version (CMIP6 only for the present) ........fin exit ;; "-v") version=$2 ; shift ; shift ;; "-r") svn=$2 ; shift ; shift ;; "-compiler") compiler=$2 case $compiler in "gfortran"|"ifort"|"pgf90") compiler=$2 ; shift ; shift ;; *) echo "Only gfortran , ifort or pgf90 for the compiler option" ; exit esac ;; "-d") grid_resolution=$2 ; shift ; shift ;; "-gprof") OPT_GPROF="-pg" ; shift ;; "-cosp") cosp=1 ; opt_cosp1="-cosp true" ; shift ;; "-cosp2") cosp2=1 ; opt_cosp2="-cosp2 true" ; shift ;; "-cospv2") cospv2=1 ; opt_cospv2="-cospv2 true" ; shift ;; "-orchidee_rev") orchidee_rev=$2 ; shift ; shift ;; "-nofcm") compile_with_fcm=0 ; shift ;; "-SCM") SCM=1 ; shift ;; "-opt_makelmdz") OPT_MAKELMDZ="$2" ; shift ; shift ;; "-parallel") parallel=$2 case $parallel in "none"|"mpi"|"omp"|"mpi_omp") parallel=$2 ; shift ; shift ;; *) echo Only none mpi omp mpi_omp for the parallel option ; exit esac ;; "-bench") bench=$2 ; shift ; shift ;; "-debug") optim=-debug ; shift ;; "-name") MODEL=$2 ; shift ; shift ;; "-netcdf") netcdf=$2 ; shift ; shift ;; "-physiq") physiq=$2 ; shift ; shift ;; "-xios") with_xios="y" ; shift ;; "-env_file") env_file=$2 ; shift ; shift ;; "-orc_version") orchidee_version=$2 ; shift ; shift ;; *) ./install_lmdz.sh -h ; exit esac done if [ $parallel = none ] ; then sequential=1 ; else sequential=0 ; fi #Chemin pour placer le modele if [ "$MODEL" = "" ] ; then MODEL=./LMDZ$version$svn$optim ; fi arch=local if [ $compiler = g95 ] ; then echo g95 is not supported anymore ; exit ; fi ################################################################ # Specificite des machines ################################################################ hostname=`hostname` if [ "$pclinux" = 1 ] ; then o_ins_make="-t g95" ; else o_ins_make="" ; fi case ${hostname:0:5} in jean-) compiler="mpiifort" ; par_comp="mpiifort" ; o_ins_make="-t jeanzay" ; make=gmake ; module purge module load intel-compilers/19.0.4 ; #module load intel-mpi/19.0.4 ; #module load intel-mkl/19.0.4 ; module load hdf5/1.10.5-mpi ; module load netcdf/4.7.2-mpi ; module load netcdf-fortran/4.5.2-mpi ; module load subversion/1.9.7 ; export NETCDF_LIBDIR=./ export NETCDFFORTRAN_INCDIR=./ export NETCDFFORTRAN_LIBDIR=./ arch=X64_JEANZAY ;; cicla|camel) compiler="gfortran" ; if [ $parallel != none ] ; then module load openmpi/1.6.5-gfortran ; root_mpi=$MPI_HOME ; path_mpi=$root_mpi/bin ; par_comp=${path_mpi}/mpif90 ; mpirun=${path_mpi}/mpirun ; fi ; arch=local ; make=make ; o_ins_make="-t g95" ;; *) if [ $parallel = none -o -f /usr/bin/mpif90 ] ; then path_mpi=`which mpif90 | sed -e s:/mpif90::` ; if [ -d /usr/lib64/openmpi ] ; then root_mpi="/usr/lib64/openmpi" else root_mpi="/usr" fi # For Scientifique Linux with gfortran at LMD : elif [ -f /usr/lib64/openmpi/1.4.5-gfortran/bin/mpif90 -a $compiler = "gfortran" ] ; then path_mpi=/usr/lib64/openmpi/1.4.5-gfortran/bin ; root_mpi=/usr/lib64/openmpi/1.4.5-gfortran ; export LD_LIBRARY_PATH=${root_mpi}/lib:$LD_LIBRARY_PATH # For Scientifique Linux with ifort at LMD : elif [ -f /usr/lib64/openmpi/1.4.5-ifort/bin/mpif90 -a $compiler = "ifort" ] ; then path_mpi=/usr/lib64/openmpi/1.4.5-ifort/bin ; root_mpi=/usr/lib64/openmpi/1.4.5-ifort ; export LD_LIBRARY_PATH=${root_mpi}/lib:$LD_LIBRARY_PATH # For Scientifique Linux with pgf90 at LMD : elif [ -f /usr/lib64/openmpi/1.4.5-ifort/bin/mpif90 -a $compiler = "pgf90" ] ; then path_mpi=/usr/lib64/openmpi/1.4.5-pgf/bin ; root_mpi=/usr/lib64/openmpi/1.4.5-pgf ; export LD_LIBRARY_PATH=${root_mpi}/lib:$LD_LIBRARY_PATH else echo "Cannot find mpif90" ; if [ $parallel = none ] ; then exit ; fi ; fi ; par_comp=${path_mpi}/mpif90 ; mpirun=${path_mpi}/mpirun ; arch=local ; make=make ; o_ins_make="-t g95" esac # Flags for parallelism: if [ $parallel != none ] ; then # MPI_LD are the flags needed for linking with MPI MPI_LD="-L${root_mpi}/lib -lmpi" if [ "$compiler" = "gfortran" ] ; then # MPI_FLAGS are the flags needed for compilation with MPI MPI_FLAGS="-fcray-pointer" # OMP_FLAGS are the flags needed for compilation with OpenMP OMP_FLAGS="-fopenmp -fcray-pointer" # OMP_LD are the flags needed for linking with OpenMP OMP_LD="-fopenmp" elif [ "$compiler" = "ifort" ] ; then MPI_FLAGS="" OMP_FLAGS="-openmp" OMP_LD="-openmp" else # pgf90 MPI_FLAGS="" OMP_FLAGS="-mp" OMP_LD="-mp" fi fi ##################################################################### # Test for old gfortran compilers # If the compiler is too old (older than 4.3.x) we test if the # temporary gfortran44 patch is available on the computer in which # case the compiler is changed from gfortran to gfortran44 # Must be aware than parallelism can not be activated in this case ##################################################################### if [ "$compiler" = "gfortran" ] ; then gfortran=gfortran gfortranv=`gfortran --version | \ head -1 | awk ' { print $NF } ' | awk -F. ' { print $1 * 10 + $2 } '` if [ $gfortranv -le 43 ] ; then echo ERROR : Your gfortran compiler is too old echo 'Please choose a new one (ifort) and change the line' echo compiler=xxx echo in the install.sh script and rerun it if [ `which gfortran44 | wc -w` -ne 0 ] ; then gfortran=gfortran44 else echo gfotran trop vieux ; exit fi fi compiler=$gfortran fi ##################################################################### ## if also compiling XIOS, parallel must be mpi_omp if [ "$with_xios" = "y" -a "$parallel" != "mpi_omp" ] ; then echo "Error, you must set -parallel mpi_omp if you want XIOS" exit fi ## We can't compile with -cosp and -cosp2 if [ "$cosp" = 1 -a "$cosp2" = 1 ] ; then echo "Error, you can't run with cosp1 and cosp2" exit fi if [ "$cosp" = 1 ] ; then opt_cosp="$opt_cosp1" fi if [ "$cosp2" = 1 ] ; then opt_cosp="$opt_cosp2" fi if [ "$cospv2" = 1 ] ; then opt_cosp="$opt_cospv2" fi ## if also compiling XIOS, cosp must be activate to define axis in *.xml if [ "$with_xios" = "y" ] ; then if [ "$cosp" = 0 -a "$cosp2" = 0 -a "$cospv2" = 0 ] ; then echo "Error, you must use -cosp option when compiling with -xios" echo "You need to call Cosp in physical first step to define axis variables" exit fi opt_makelmdz_xios="-io xios" fi if [ "$cospv2" = 1 -a "$with_xios" = "n" ] ; then echo "Error, Cospv2 cannot run without Xios" exit fi echo '################################################################' echo Choix des options de compilation echo '################################################################' export FC=$compiler export F90=$compiler export F77=$compiler export CPPFLAGS= OPTIMNC=$OPTIM BASE_LD="$OPT_GPROF" OPTPREC="$OPT_GPROF" ARFLAGS="rs" ; if [ -f /etc/issue ] ; then if [ "`grep -i ubuntu /etc/issue`" != "" ] ; then if [ "`grep -i ubuntu /etc/issue | awk ' { print $2 } ' | cut -d. -f1`" -ge 16 ] ; then ARFLAGS="rU" ; fi ; fi ; fi if [ "$compiler" = "$gfortran" ] ; then OPTIM='-O3' OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all -fbacktrace -finit-real=nan" OPTDEV="-Wall -fbounds-check" fmod='I ' OPTPREC="$OPTPREC -cpp -ffree-line-length-0" if [ $real = r8 ] ; then OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE" ; fi export F90FLAGS=" -ffree-form $OPTIMNC" export FFLAGS=" $OPTIMNC" export CC=gcc export CXX=g++ export fpp_flags="-P -C -traditional -ffreestanding" elif [ $compiler = mpif90 ] ; then OPTIM='-O3' OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all" OPTDEV="-Wall -fbounds-check" BASE_LD="$BASE_LD -lblas" fmod='I ' if [ $real = r8 ] ; then OPTPREC="$OPTPREC -fdefault-real-8 -DNC_DOUBLE -fcray-pointer" ; fi export F90FLAGS=" -ffree-form $OPTIMNC" export FFLAGS=" $OPTIMNC" export CC=gcc export CXX=g++ elif [ $compiler = pgf90 ] ; then OPTIM='-O2 -Mipa -Munroll -Mnoframe -Mautoinline -Mcache_align' OPTDEB='-g -Mdclchk -Mbounds -Mchkfpstk -Mchkptr -Minform=inform -Mstandard -Ktrap=fp -traceback' OPTDEV='-g -Mbounds -Ktrap=fp -traceback' fmod='module ' if [ $real = r8 ] ; then OPTPREC="$OPTPREC -r8 -DNC_DOUBLE" ; fi export CPPFLAGS="-DpgiFortran" export CC=pgcc export CFLAGS="-O2 -Msignextend" export CXX=pgCC export CXXFLAGS="-O2 -Msignextend" export FFLAGS="-O2 $OPTIMNC" export F90FLAGS="-O2 $OPTIMNC" compile_with_fcm=1 elif [ $compiler = ifort ] ; then OPTIM="-O2 -fp-model strict -ip -align all " OPTDEV="-p -g -O2 -traceback -fp-stack-check -ftrapuv -check" OPTDEB="-g -no-ftz -traceback -ftrapuv -fp-stack-check -check" fmod='module ' if [ $real = r8 ] ; then OPTPREC="$OPTPREC -real-size 64 -DNC_DOUBLE" ; fi export CPP="icc -E" export FFLAGS="-O2 -ip -fpic -mcmodel=large" export FCFLAGS="-O2 -ip -fpic -mcmodel=large" export CC=icc export CFLAGS="-O2 -ip -fpic -mcmodel=large" export CXX=icpc export CXXFLAGS="-O2 -ip -fpic -mcmodel=large" export fpp_flags="-P -traditional" # Pourquoi forcer la compilation fcm. Marche mieux sans #compile_with_fcm=1 elif [ $compiler = mpiifort ] ; then echo on ne fait rien la # Pourquoi forcer la compilation fcm. Marche mieux sans #compile_with_fcm=1 else echo unexpected compiler $compiler ; exit fi OPTIMGCM="$OPTIM $OPTPREC" hostname=`hostname` ########################################################################## # If installing on know machines such as IBM x3750 (Ada) # at IDRIS, don't check for available software and don"t install netcdf if [ ${hostname:0:5} = jean- ] ; then netcdf=0 # no need to recompile netcdf, alreday available check_linux=0 pclinux=0 ioipsl=0 # no need to recompile ioipsl, already available #netcdf="/smplocal/pub/NetCDF/4.1.3" compiler="mpiifort" fmod='module ' if [ $real = r8 ] ; then OPTPREC="$OPTPREC -i4 -r8 -DNC_DOUBLE" ; fi OPTIM="-auto -align all -O2 -fp-model strict -xHost " OPTIMGCM="$OPTIM $OPTPREC" fi ########################################################################## mkdir -p $MODEL echo $MODEL MODEL=`( cd $MODEL ; pwd )` # to get absolute path, if necessary # Option -fendian=big is only to be used with ARPEGE1D. # The -r8 should probably be avoided if running on 32 bit machines # Option r8 is not mandatory and generates larger executables. # It is however mandatory if using ARPEGE1D # Better optimization options might be a better choice (e.g. -O3) echo '################################################################' if [ "$check_linux" = 1 ] ; then echo Check if required software is available echo '################################################################' #### Ehouarn: test if ksh and/or bash are available use_shell="ksh" # default: use ksh if [ "`which ksh`" = "" ] ; then echo "no ksh ... we will use bash" use_shell="bash" if [ "`which bash`" = "" ] ; then echo "ksh (or bash) needed!! Install it!" fi fi for logiciel in wget tar gzip make $compiler gcc ; do if [ "`which $logiciel`" = "" ] ; then echo You must first install $logiciel on your system exit fi done if [ $pclinux = 1 ] ; then cd $MODEL cat < tt.f90 print*,'coucou' end eod $compiler tt.f90 -o a.out ./a.out >| tt if [ "`cat tt | sed -e 's/ //g' `" != "coucou" ] ; then echo problem installing with compiler $compiler ; exit ; fi \rm tt a.out tt.f90 fi fi ########################################################################### if [ $getlmdzor = 1 ] ; then echo '##########################################################' echo Download a slightly modified version of LMDZ echo '##########################################################' cd $MODEL myget src/modipsl.$version.tar.gz echo install.sh wget_OK `date` gunzip modipsl.$version.tar.gz tar xvf modipsl.$version.tar \rm modipsl.$version.tar fi echo OK1 if [ $netcdf = 1 ] ; then cd $MODEL netcdflog=`pwd`/netcdf.log echo '##########################################################' echo Compiling the Netcdf library echo '##########################################################' echo log file : $netcdflog if [ "$with_xios" = "n" ] ; then # keep it simple #wget http://www.lmd.jussieu.fr/~lmdz/Distrib/netcdf-4.0.1.tar.gz myget import/netcdf-4.0.1.tar.gz gunzip netcdf-4.0.1.tar.gz tar xvf netcdf-4.0.1.tar \rm -f netcdf-4.0.1.tar cd netcdf-4.0.1 # seds to possibly use gfortran44 obsolete nowdays (Ehouarn: 10/2017) #sed -e 's/gfortran/'$gfortran'/g' configure >| tmp ; mv -f tmp configure ; chmod +x configure localdir=`pwd -P` ./configure --prefix=$localdir --enable-shared --disable-cxx #sed -e 's/gfortran/'$gfortran'/g' Makefile >| tmp ; mv -f tmp Makefile $make check > $netcdflog 2>&1 $make install >> $netcdflog 2>&1 else # download and compile hdf5 and netcdf, etc. using the install_netcdf4_hdf5.bash script #wget http://www.lmd.jussieu.fr/~lmdz/Distrib/install_netcdf4_hdf5.bash myget import/install_netcdf4_hdf5.bash chmod u=rwx install_netcdf4_hdf5.bash if [ "$compiler" = "gfortran" ] ; then ./install_netcdf4_hdf5.bash -prefix $MODEL/netcdf4_hdf5 -CC gcc -FC gfortran -CXX g++ -MPI $root_mpi > $netcdflog 2>&1 elif [ "$compiler" = "ifort" ] ; then ./install_netcdf4_hdf5.bash -prefix $MODEL/netcdf4_hdf5 -CC icc -FC ifort -CXX icpc -MPI $root_mpi > $netcdflog 2>&1 elif [ "$compiler" = "pgf90" ] ; then ./install_netcdf4_hdf5.bash -prefix $MODEL/netcdf4_hdf5 -CC pgcc -FC pgf90 -CXX pgCC -MPI $root_mpi > $netcdflog 2>&1 else echo "unexpected compiler $compiler" ; exit fi fi # of if [ "$with_xios" = "n" ] echo install.sh netcdf_OK `date` fi # of if [ $netcdf = 1 ] #======================================================================================= echo OK2 ioipsl=$ioipsl echo '##########################################################' echo 'Installing MODIPSL, the installation package manager for the ' echo 'IPSL models and tools' echo '##########################################################' if [ $netcdf = 0 -o $netcdf = 1 ] ; then if [ "$with_xios" = "y" ] ; then ncdfdir=$MODEL/netcdf4_hdf5 else ncdfdir=$MODEL/netcdf-4.0.1 fi else ncdfdir=$netcdf fi if [ $ioipsl = 1 ] ; then cd $MODEL/modipsl \rm -rf lib/* cd util cp AA_make.gdef AA_make.orig F_C="$compiler -c " ; if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then F_C="$compiler -c -cpp " ; fi if [ "$compiler" = "pgf90" ] ; then F_C="$compiler -c -Mpreprocess" ; fi sed -e 's/^\#.*.g95.*.\#.*.$/\#/' AA_make.gdef > tmp sed -e "s:F_L = g95:F_L = $compiler:" -e "s:F_C = g95 -c -cpp:F_C = $F_C": \ -e 's/g95.*.w_w.*.(F_D)/g95 w_w = '"$OPTIMGCM"'/' \ -e 's:g95.*.NCDF_INC.*.$:g95 NCDF_INC= '"$ncdfdir"'/include:' \ -e 's:g95.*.NCDF_LIB.*.$:g95 NCDF_LIB= -L'"$ncdfdir"'/lib -lnetcdff -lnetcdf:' \ -e 's:g95 L_O =:g95 L_O = -Wl,-rpath='"$ncdfdir"'/lib:' \ -e "s:-fmod=:-$fmod:" -e 's/-fno-second-underscore//' \ -e 's:#-Q- g95 M_K = gmake:#-Q- g95 M_K = make:' \ tmp >| AA_make.gdef if [ $pcmac == 1 ] then cp AA_make.gdef tmp sed -e 's/rpath=/rpath,/g' tmp > AA_make.gdef fi # We use lines for g95 even for the other compilers to run ins_make if [ "$use_shell" = "ksh" ] ; then ./ins_make $o_ins_make else # bash sed -e s:/bin/ksh:/bin/bash:g ins_make > ins_make.bash #if [ "`grep ada AA_make.gdef`" = "" ] ; then # Bidouille pour compiler sur ada des vieux modipsl.tar # \cp -f ~rdzt401/bin/AA_make.gdef . #fi if [ "`grep jeanzay AA_make.gdef`" = "" ] ; then # Bidouille pour compiler sur ada des vieux modipsl.tar echo 'Warning jean-zay not in AA_make.gdef' echo 'Think about updating' exit 1 fi chmod u=rwx ins_make.bash ./ins_make.bash $o_ins_make fi # of if [ "$use_shell" = "ksh" ] #======================================================================================= cd $MODEL/modipsl/modeles/IOIPSL/src ioipsllog=`pwd`/ioipsl.log echo '##########################################################' echo 'Compiling IOIPSL, the interface library with Netcdf' echo '##########################################################' echo log file : $ioipsllog if [ "$use_shell" = "bash" ] ; then cp Makefile Makefile.ksh sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile fi # if [ "$pclinux" = 1 ] ; then # Build IOIPSL modules and library $make clean $make > $ioipsllog 2>&1 if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then # copy module files to lib cp -f *.mod ../../../lib fi # Build IOIPSL tools (ie: "rebuild", if present) if [ -f $MODEL/modipsl/modeles/IOIPSL/tools/rebuild ] ; then cd $MODEL/modipsl/modeles/IOIPSL/tools # adapt Makefile & rebuild script if in bash if [ "$use_shell" = "bash" ] ; then cp Makefile Makefile.ksh sed -e s:/bin/ksh:/bin/bash:g Makefile.ksh > Makefile cp rebuild rebuild.ksh sed -e 's:/bin/ksh:/bin/bash:g' \ -e 's:print -u2:echo:g' \ -e 's:print:echo:g' rebuild.ksh > rebuild fi $make clean $make > $ioipsllog 2>&1 fi # fi # of if [ "$pclinux" = 1 ] else # of if [ $ioipsl = 1 ] if [ ${hostname:0:5} = jean- ] ; then cd $MODEL/modipsl cd util if [ "`grep jeanzay AA_make.gdef`" = "" ] ; then echo 'Warning jean-zay not in AA_make.gdef' echo 'Think about updating' exit 1 fi ./ins_make $o_ins_make # Compile IOIPSL on jean-zay cd $MODEL/modipsl/modeles/IOIPSL/src gmake > ioipsl.log cd $MODEL/modipsl/modeles/IOIPSL/tools gmake > ioipsl.log fi echo install.sh ioipsl_OK `date` fi # of if [ $ioipsl = 1 ] # Saving ioipsl lib for possible parallel compile cd $MODEL/modipsl tar cf ioipsl.tar lib/ bin/ #=========================================================================== if [ "$with_xios" = "y" ] ; then echo '##########################################################' echo 'Compiling XIOS' echo '##########################################################' cd $MODEL/modipsl/modeles xioslog=`pwd`/xios.log echo "log file: $xioslog" #wget http://www.lmd.jussieu.fr/~lmdz/Distrib/install_xios.bash myget import/install_xios.bash chmod u=rwx install_xios.bash if [ ${hostname:0:5} = jean- ] ; then # echo 'Need to work on install_xios implementation for jean-zay' # exit svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5 XIOS cd XIOS/arch svn update cd .. ./make_xios --prod --arch $arch --job 4 > xios.log 2>&1 else ./install_xios.bash -prefix $MODEL/modipsl/modeles \ -netcdf ${ncdfdir} -hdf5 ${ncdfdir} \ -MPI $root_mpi -arch $arch > xios.log 2>&1 fi if [ -f XIOS/lib/libxios.a ] ; then echo "OK, XIOS library successfully generated" fi fi #============================================================================ veget_version=false if [ "$veget" = 1 ] ; then cd $MODEL/modipsl/modeles/ORCHIDEE if [ "$orchidee_version" = "CMIP6" ] ; then set +e svn upgrade svn switch -r 5661 --accept theirs-full svn://forge.ipsl.jussieu.fr/orchidee/tags/ORCHIDEE_2_0/ORCHIDEE orchidee_rev=5661 veget_version=orchidee2.0 no_z0h_orc=0 set -e fi # Correctif suite debug Jean-Zay sed -i -e 's/9010 FORMAT(A52,F17.14)/9010 FORMAT(A52,F20.14)/' src_stomate/stomate.f90 opt_orc="-prod" ; if [ "$optim" = "-debug" ] ; then opt_orc="-debug" ; fi orchideelog=`pwd`/orchidee.log echo '########################################################' echo 'Compiling ORCHIDEE, the continental surfaces model ' echo '########################################################' echo log file : $orchideelog export ORCHPATH=`pwd` if [ -d tools ] ; then ################################################################### # Pour les experts qui voudraient changer de version d'orchidee. # Attention : necessite d'avoir le password pour orchidee set +e ; svn upgrade ; set -e if [ "$orchidee_rev" != "" ] ; then # test qu'on est sur la bonne branche pour faire le update set +e svn log -r $orchidee_rev | grep $orchidee_rev if [ $? -gt 0 ] ; then echo 'Cannot update ORCHIDEE as not on the right branch for ORCHIDEE' exit fi set -e set +e ; svn update -r $orchidee_rev ; set -e fi # Correctif suite debug Jean-Zay if [ -f src_global/time.f90 ] ; then sed -i -e 's/CALL tlen2itau/\!CALL tlen2itau/' src_global/time.f90 ; fi ################################################################### if [ "$veget_version" == "false" ] ; then veget_version=orchidee2.0 ; fi cd arch sed -e s:"%COMPILER .*.$":"%COMPILER $compiler":1 \ -e s:"%LINK .*.$":"%LINK $compiler":1 \ -e s:"%FPP_FLAGS .*.$":"%FPP_FLAGS $fpp_flags":1 \ -e s:"%PROD_FFLAGS .*.$":"%PROD_FFLAGS $OPTIM":1 \ -e s:"%DEV_FFLAGS .*.$":"%DEV_FFLAGS $OPTDEV":1 \ -e s:"%DEBUG_FFLAGS .*.$":"%DEBUG_FFLAGS $OPTDEB":1 \ -e s:"%BASE_FFLAGS .*.$":"%BASE_FFLAGS $OPTPREC":1 \ -e s:"%BASE_LD .*.$":"%BASE_LD $BASE_LD":1 \ -e s:"%ARFLAGS .*.$":"%ARFLAGS $ARFLAGS":1 \ arch-gfortran.fcm > arch-local.fcm echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib -lnetcdff -lnetcdf\"" > arch-local.path echo "NETCDF_INCDIR=${ncdfdir}/include" >> arch-local.path echo "IOIPSL_INCDIR=$ORCHPATH/../../lib" >> arch-local.path echo "IOIPSL_LIBDIR=$ORCHPATH/../../lib" >> arch-local.path echo 'XIOS_INCDIR=${ORCHDIR}/../XIOS/inc' >> arch-local.path echo 'XIOS_LIBDIR="${ORCHDIR}/../XIOS/lib -lxios"' >> arch-local.path cd ../ # compiling ORCHIDEE sequential mode ./makeorchidee_fcm -j 8 -noxios $opt_orc -parallel none -arch $arch > $orchideelog 2>&1 echo ./makeorchidee_fcm -j 8 -noxios $opt_orc -parallel none -arch $arch echo End of the first compilation of orchidee ; pwd else if [ -d src_parallel ] ; then liste_src="parallel parameters global stomate sechiba driver" if [ "$veget_version" == "false" ] ; then veget_version=orchidee2.0 ; fi else # Obsolete, for ORCHIDEE_beton only liste_src="parameters stomate sechiba " # A trick to compile ORCHIDEE depending on if we are using real*4 or real*8 cd src_parameters ; \cp reqdprec.$real reqdprec.f90 ; cd .. if [ "$veget_version" == "false" ] ; then veget_version=orchidee1.9 ; fi fi for d in $liste_src ; do src_d=src_$d echo src_d $src_d echo ls ; ls if [ ! -d $src_d ] ; then echo Problem orchidee : no $src_d ; exit ; fi cd $src_d ; \rm -f *.mod make ; $make clean $make > $orchideelog 2>&1 ; if [ "$compiler" = "$gfortran" -o "$compiler" = "mpif90" ] ; then cp -f *.mod ../../../lib ; fi cd .. done fi echo install.sh orchidee_OK `date` fi # of if [ "$veget" = 1 ] #============================================================================ # Ehouarn: it may be directory LMDZ4 or LMDZ5 depending on tar file... if [ -d $MODEL/modipsl/modeles/LMD* ] ; then echo '##########################################################' echo 'Compiling LMDZ' echo '##########################################################' cd $MODEL/modipsl/modeles/LMD* LMDZPATH=`pwd` else echo "ERROR: No LMD* directory !!!" exit fi ########################################################### # For those who want to use fcm to compile via : # makelmdz_fcm -arch local ..... ############################################################ if [ "$pclinux" = "1" ] ; then # create local 'arch' files (if on Linux PC): cd arch # arch-local.path file echo "NETCDF_LIBDIR=\"-L${ncdfdir}/lib -lnetcdff -lnetcdf\"" > arch-local.path echo "NETCDF_INCDIR=-I${ncdfdir}/include" >> arch-local.path echo 'IOIPSL_INCDIR=$LMDGCM/../../lib' >> arch-local.path echo 'IOIPSL_LIBDIR=$LMDGCM/../../lib' >> arch-local.path echo 'XIOS_INCDIR=$LMDGCM/../XIOS/inc' >> arch-local.path echo 'XIOS_LIBDIR=$LMDGCM/../XIOS/lib' >> arch-local.path echo 'ORCH_INCDIR=$LMDGCM/../../lib' >> arch-local.path echo 'ORCH_LIBDIR=$LMDGCM/../../lib' >> arch-local.path if [ $pcmac == 1 ] ; then BASE_LD="$BASE_LD -Wl,-rpath,${ncdfdir}/lib" else BASE_LD="$BASE_LD -Wl,-rpath=${ncdfdir}/lib" fi # Arch-local.fcm file (adapted from arch-linux-32bit.fcm) if [ $real = r8 ] ; then FPP_DEF=NC_DOUBLE ; else FPP_DEF="" ; fi sed -e s:"%COMPILER .*.$":"%COMPILER $compiler":1 \ -e s:"%LINK .*.$":"%LINK $compiler":1 \ -e s:"%PROD_FFLAGS .*.$":"%PROD_FFLAGS $OPTIM":1 \ -e s:"%DEV_FFLAGS .*.$":"%DEV_FFLAGS $OPTDEV":1 \ -e s:"%DEBUG_FFLAGS .*.$":"%DEBUG_FFLAGS $OPTDEB":1 \ -e s:"%BASE_FFLAGS .*.$":"%BASE_FFLAGS $OPTPREC":1 \ -e s:"%FPP_DEF .*.$":"%FPP_DEF $FPP_DEF":1 \ -e s:"%BASE_LD .*.$":"%BASE_LD $BASE_LD":1 \ -e s:"%ARFLAGS .*.$":"%ARFLAGS $ARFLAGS":1 \ arch-linux-32bit.fcm > arch-local.fcm cd .. ### Adapt "bld.cfg" (add the shell): whereisthatshell=$(which ${use_shell}) echo "bld::tool::SHELL $whereisthatshell" >> bld.cfg fi # of if [ "$pclinux" = 1 ] cd $MODEL/modipsl/modeles/LMDZ* lmdzlog=`pwd`/lmdz.log ################################################################## # Possibly update LMDZ if a specific svn release is requested ################################################################## set +e ; svn upgrade ; set -e if [ "$svn" = "last" ] ; then svnopt="" ; else svnopt="-r $svn" ; fi if [ "$svn" != "" ] ; then svn update $svnopt ; fi echo '##################################################################' echo Compile LMDZ echo '##################################################################' echo log file : $lmdzlog if [ "$env_file" != "" ] ; then mv arch/arch-${arch}.env arch/arch-${arch}.orig ; \cp -f $env_file arch/arch-${arch}.env ; fi echo install.sh avant_compilation `date` if [ $compile_with_fcm = 1 ] ; then makelmdz="makelmdz_fcm $optim -arch $arch -j 8 " ; else makelmdz="makelmdz $optim -arch $arch" ; fi # use the orchidee interface that has no z0h if [ "$no_z0h_orc" = 1 ] ; then veget_version="$veget_version -cpp ORCHIDEE_NOZ0H" fi # sequential compilation and bench if [ "$sequential" = 1 ] ; then echo "./$makelmdz $optim $OPT_MAKELMDZ $optim -rrtm true $opt_cosp -d ${grid_resolution} -v $veget_version gcm " >> compile.sh chmod +x ./compile.sh if [ $bench != 0 ] ; then ./compile.sh > $lmdzlog 2>&1 ; fi echo install.sh apres_compilation `date` fi # fin sequential # compiling in parallel mode if [ $parallel != "none" ] ; then echo '##########################################################' echo ' Parallel compile ' echo '##########################################################' # saving the sequential libs and binaries cd $MODEL/modipsl tar cf sequential.tar bin/ lib/ \rm -rf bin/ lib/ tar xf ioipsl.tar # # Orchidee # cd $ORCHPATH if [ -d src_parallel -a $veget = 1 ] ; then cd arch sed \ -e s:"%COMPILER.*.$":"%COMPILER $par_comp":1 \ -e s:"%LINK.*.$":"%LINK $par_comp":1 \ -e s:"%MPI_FFLAG.*.$":"%MPI_FFLAGS $MPI_FLAGS":1 \ -e s:"%OMP_FFLAG.*.$":"%OMP_FFLAGS $OMP_FLAGS":1 \ -e s:"%MPI_LD.*.$":"%MPI_LD $MPI_LD":1 \ -e s:"%OMP_LD.*.$":"%OMP_LD $OMP_LD":1 \ arch-local.fcm > tmp.fcm mv tmp.fcm arch-local.fcm cd ../ echo compiling ORCHIDEE parallel mode echo logfile $orchideelog ./makeorchidee_fcm -j 8 -clean -noxios $opt_orc -parallel $parallel -arch $arch > $orchideelog 2>&1 ./makeorchidee_fcm -j 8 -noxios $opt_orc -parallel $parallel -arch $arch >> $orchideelog 2>&1 echo ./makeorchidee_fcm -j 8 -clean -noxios $opt_orc -parallel $parallel -arch $arch echo ./makeorchidee_fcm -j 8 -noxios $opt_orc -parallel $parallel -arch $arch elif [ $veget = 1 ] ; then echo '##########################################################' echo ' Orchidee version too old ' echo ' Please update to new version ' echo '##########################################################' exit fi # of if [ -d src_parallel ] # LMDZ cd $LMDZPATH if [ $arch = local ] ; then cd arch sed -e s:"%COMPILER.*.$":"%COMPILER $par_comp":1 \ -e s:"%LINK.*.$":"%LINK $par_comp":1 \ -e s:"%MPI_FFLAG.*.$":"%MPI_FFLAGS $MPI_FLAGS":1 \ -e s:"%OMP_FFLAG.*.$":"%OMP_FFLAGS $OMP_FLAGS":1 \ -e s:"%ARFLAGS.*.$":"%ARFLAGS $ARFLAGS":1 \ -e s@"%BASE_LD.*.$"@"%BASE_LD -Wl,-rpath=${root_mpi}/lib:${ncdfdir}/lib"@1 \ -e s:"%MPI_LD.*.$":"%MPI_LD $MPI_LD":1 \ -e s:"%OMP_LD.*.$":"%OMP_LD $OMP_LD":1 \ arch-local.fcm > tmp.fcm mv tmp.fcm arch-local.fcm cd ../ fi rm -f compile.sh echo resol=${grid_resolution} >> compile.sh if [ ${hostname:0:5} = jean- -a "$cospv2" = 1 ] ; then echo ./$makelmdz -dev $optim $OPT_MAKELMDZ -rrtm true $opt_cosp $opt_makelmdz_xios -d \$resol -v $veget_version -mem -parallel $parallel gcm >> compile.sh echo ./$makelmdz -dev $optim $OPT_MAKELMDZ -rrtm true $opt_cosp $opt_makelmdz_xios -d \$resol -v $veget_version -mem -parallel $parallel gcm else echo ./$makelmdz $optim $OPT_MAKELMDZ -rrtm true $opt_cosp $opt_makelmdz_xios -d \$resol -v $veget_version -mem -parallel $parallel gcm >> compile.sh echo ./$makelmdz $optim $OPT_MAKELMDZ -rrtm true $opt_cosp $opt_makelmdz_xios -d \$resol -v $veget_version -mem -parallel $parallel gcm fi chmod +x ./compile.sh if [ $bench != 0 ] ; then ./compile.sh > $lmdzlog 2>&1 ; fi echo "Compilation finished" fi # of if [ $parallel != "none" ] #echo LLLLLLLLLLLLLLLLLLLLLLLLLLL if [ "$gfortran" = "gfortran44" ] ; then echo Your gfortran compiler was too old so that the model was automatically echo compiled with gfortran44 instead. It can not be used in parallel mode. echo You can change the compiler at the begining of the install.sh echo script and reinstall. fi ################################################################## # Verification du succes de la compilation ################################################################## # Recherche de l'executable dont le nom a change au fil du temps ... gcm="" 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 if [ -f $exe ] ; then gcm=$exe ; fi done if [ "$gcm" = "" ] ; then if [ $bench != 0 ] ; then echo 'Compilation failed !! Cannot run the benchmark;' exit else echo 'Compilation not done (only done when bench=1)' fi else echo '##########################################################' echo 'Compilation successfull !! ' echo '##########################################################' echo The executable is $gcm fi ################################################################## # Below, we run a benchmark test (if bench=0) ################################################################## if [ $bench != 0 ] ; then echo '##########################################################' echo ' Running a test run ' echo '##########################################################' \rm -rf BENCH${grid_resolution} bench=bench_lmdz_${grid_resolution} echo install.sh before bench download `date` #wget http://www.lmd.jussieu.fr/~lmdz/Distrib/$bench.tar.gz myget 3DBenchs/$bench.tar.gz echo install.sh after bench download `date` tar xvf $bench.tar.gz if [ "$cosp" = 1 -o "$cosp2" = 1 -o "$cospv2" = 1 ] ; then cd BENCH${grid_resolution} # copier les fichiers namelist input et output our COSP cp ../DefLists/cosp*_input_nl.txt . cp ../DefLists/cosp*_output_nl.txt . # Activer la cles ok_cosp pour tourner avec COSP sed -e 's@ok_cosp=n@ok_cosp=y@' config.def > tmp \mv -f tmp config.def cd .. fi if [ -n "$physiq" ]; then cd BENCH${grid_resolution} if [ -f physiq.def_${physiq} ]; then cp physiq.def_${physiq} physiq.def echo using physiq.def_${physiq} else echo using standard physiq.def fi cd .. else echo using standard physiq.def fi if [ "$with_xios" = "y" ] ; then cd BENCH${grid_resolution} cp ../DefLists/iodef.xml . cp ../DefLists/context_lmdz.xml . cp ../DefLists/field_def_lmdz.xml . cp ../DefLists/field_def_cosp*.xml . cp ../DefLists/file_def_hist*xml . # adapt iodef.xml to use attached mode sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' iodef.xml > tmp \mv -f tmp iodef.xml # and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE. # except for histday for histfile in file_def_hist*xml do if [ "$histfile" = "file_def_histday_lmdz.xml" ] ; then sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".TRUE."@' $histfile > tmp ; \mv -f tmp $histfile sed -e 's@output_level="_AUTO_"@output_level="5"@' $histfile > tmp ; \mv -f tmp $histfile sed -e 's@compression_level="2"@compression_level="0"@' $histfile > tmp ; \mv -f tmp $histfile else sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' $histfile > tmp ; \mv -f tmp $histfile fi done # and add option "ok_all_xml=y" in config.def echo "### XIOS outputs" >> config.def echo 'ok_all_xml=.true.' >> config.def #activer les sorties pour Cosp if [ "$cosp" = 1 -o "$cosp2" = 1 ] ; then histfile=file_def_histdayCOSP_lmdz.xml sed -e 's@enabled=".FALSE."@enabled=".TRUE."@' $histfile > tmp ; \mv -f tmp $histfile sed -e 's@output_level="_AUTO_"@output_level="5"@' $histfile > tmp ; \mv -f tmp $histfile sed -e 's@compression_level="2"@compression_level="0"@' $histfile > tmp ; \mv -f tmp $histfile fi if [ "$cospv2" = 1 ] ; then histfile=file_def_histdayCOSPv2_lmdz.xml sed -e 's@compression_level="2"@compression_level="0"@' $histfile > tmp ; \mv -f tmp $histfile contextfile=context_lmdz.xml sed -e 's@src="./file_def_histdayCOSP_lmdz.xml"@src="./file_def_histdayCOSPv2_lmdz.xml"@' $contextfile > tmp ; \mv -f tmp $contextfile fieldfile=field_def_lmdz.xml sed -e 's@field_def_cosp1.xml@field_def_cospv2.xml@' $fieldfile > tmp ; \mv -f tmp $fieldfile fi cd .. fi cp $gcm BENCH${grid_resolution}/gcm.e cd BENCH${grid_resolution} # On cree le fichier bench.sh au besoin # Dans le cas 48x36x39 le bench.sh existe deja en parallele if [ "$grid_resolution" = "48x36x39" ] ; then echo On ne touche pas au bench.sh # But we have to adapt "run_local.sh" for $mpirun sed -e "s@mpirun@$mpirun@g" run_local.sh > tmp mv -f tmp run_local.sh chmod u=rwx run_local.sh elif [ "${parallel:0:3}" = "mpi" ] ; then # Lancement avec deux procs mpi et 2 openMP echo "export OMP_STACKSIZE=800M" > bench.sh if [ "${parallel:4:3}" = "omp" ] ; then echo "export OMP_NUM_THREADS=2" >> bench.sh fi if [ "$cospv2" = 1 -o "$cosp" = 1 -o "$cosp2" = 1 ] ; then if [ ${hostname:0:5} = jean- ] ; then chmod +x ../arch.env ../arch.env echo "ulimit -s 2000000" >> bench.sh else echo "ulimit -s 200000" >> bench.sh fi else echo "ulimit -s unlimited" >> bench.sh fi if [ ${hostname:0:5} = jean- ] ; then echo "srun -n 2 -A $idris_acct@cpu gcm.e > listing 2>&1" >> bench.sh else echo "$mpirun -np 2 gcm.e > listing 2>&1" >> bench.sh fi else echo "./gcm.e > listing 2>&1" > bench.sh fi echo EXECUTION DU BENCH set +e date ; ./bench.sh > out.bench 2>&1 ; date set -e tail listing echo '##########################################################' echo 'Simulation finished in' `pwd` echo 'You have compiled with:' cat ../compile.sh if [ $parallel = "none" ] ; then echo 'You may re-run it with : cd ' `pwd` ' ; gcm.e' echo 'or ./bench.sh' else echo 'You may re-run it with : ' echo 'cd ' `pwd` '; ./bench.sh' # echo 'ulimit -s unlimited' # echo 'export OMP_NUM_THREADS=2' # echo 'export OMP_STACKSIZE=800M' # echo "$mpirun -np 2 gcm.e " fi echo '##########################################################' fi ################################################################# # Installation eventuelle du 1D ################################################################# if [ $SCM = 1 ] ; then cd $MODEL #wget http://www.lmd.jussieu.fr/~lmdz/Distrib/1D.tar.gz myget 1D/1D.tar.gz tar xvf 1D.tar.gz cd 1D ./run.sh fi