Index: BOL/script_install_amaury/install_lmdz.sh =================================================================== --- BOL/script_install_amaury/install_lmdz.sh (revision 4862) +++ BOL/script_install_amaury/install_lmdz.sh (revision 4871) @@ -38,16 +38,12 @@ ### Functions -function myget { - # A function to fetch files either locally or on the internet - - local file_name=$1 - # Path on local computer where to look for the datafile - if [[ -f "/u/lmdz/WWW/LMDZ/pub/$file_name" ]]; then - \cp -f -p "/u/lmdz/WWW/LMDZ/pub/$file_name" . - elif [[ -f ~"/LMDZ/pub/$file_name" ]]; then - \cp -f -p ~"/LMDZ/pub/$file_name" . - else - wget --no-check-certificate -nv "http://lmdz.lmd.jussieu.fr/pub/$file_name" - fi +function myget { # Get a file from LMDZ repository + local url=$1 + + local filename + filename=$(basename "$url") + + wget --no-check-certificate -nv "http://lmdz.lmd.jussieu.fr/pub/$url" + if [[ $filename =~ .*\.(ba)?sh ]]; then chmod +x "$filename"; fi } @@ -323,4 +319,29 @@ \rm "modipsl.$version.tar" fi + + if [[ $svn != "" ]]; then + mysvn=$svn + else + mysvn="$(grep 'Revision: [0-9]' "$MODEL"/Read*.md | awk ' { print $2 } ' 2>/dev/null)" + fi + echo "SVN revision used: $mysvn" +} + +function setup_local_arch { + # Setup local arch, and correspondance between arch names accross different programs + + case $arch in + local) + arch_ioipsl="gfortran" + arch_xios="local" + + cat <"$MODEL/modipsl/modeles/IOIPSL/arch/arch-${arch_ioipsl}.path" # fix bad IOIPSL arch files... +NETCDF_INCDIR="\$(nf-config --fflags)" +NETCDF_LIBDIR="\$(nf-config --flibs)" +EOF + ;; + *) arch_ioipsl=$arch + arch_xios=$arch + esac } @@ -405,5 +426,5 @@ echo "Compiling IOIPSL, the interface library with Netcdf $(date) (log: $ioipsllog)" - if ! ./makeioipsl_fcm -job 8 > "$ioipsllog" 2>&1; then + if ! ./makeioipsl_fcm -arch "$arch_ioipsl" -job 8 > "$ioipsllog" 2>&1; then echo "IOIPSL compile failed, exiting"; exit 1 fi @@ -413,4 +434,21 @@ } +function install_XIOS { + if [[ $with_xios = "y" && ! -f "$MODEL/modipsl/modeles/XIOS/lib/libxios.a" ]]; then + cd "$MODEL/modipsl/modeles" + xioslog="$(pwd)/xios.log" + echo "##########################################################" + echo "Compiling XIOS (log $xioslog) $(date)" + echo "##########################################################" + myget script_install/install_xios.bash + + if ! ./install_xios.bash -prefix "$MODEL/modipsl/modeles" -arch "$arch_xios" > "$xioslog" 2>&1; then + echo "XIOS compilation failed, exiting"; exit 1 + fi + + echo "Compiled XIOS $(date)" + fi +} + echo "install_lmdz.sh DEBUT $(date)" @@ -419,6 +457,10 @@ check_available_software download_model +setup_local_arch install_netcdf install_IOIPSL +install_XIOS + +exit 0 @@ -562,48 +604,10 @@ -if [[ "$with_xios" = "y" ]]; then - echo '##########################################################' - echo 'Compiling XIOS' - echo '##########################################################' - cd "$MODEL/modipsl/modeles" - xioslog="$(pwd)/xios.log" - #wget http://www.lmd.jussieu.fr/~lmdz/Distrib/install_xios.bash - myget script_install/install_xios.bash - chmod u=rwx install_xios.bash -# following will be recalculated later on once LMDZ is updated -# mysvn=`svnversion LMDZ | egrep || "[0-9]+" 2>/dev/null` - mysvn=$(grep 'Revision: [0-9]' "$MODEL"/Read*.md | awk ' { print $2 } ' 2>/dev/null) - if [[ $svn != "" ]]; then mysvn=$svn; fi - echo "mysvn $mysvn" - - if [[ ${hostname:0:5} = jean- ]]; then - if [[ $mysvn -ge 4619 ]]; then - svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS2/branches/xios-2.6 XIOS - else - svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS2/branches/xios-2.5 XIOS - fi - cd XIOS/arch - svn update - cd .. - echo "Compiling XIOS, start $(date) (it takes about 20 min on Jean-Zay)" - echo "log file: $xioslog" - ./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 $arch > xios.log 2>&1 - fi # of case Jean-Zay - if [[ -f XIOS/lib/libxios.a ]]; then - echo "XIOS library successfully generated" - echo install_lmdz.sh XIOS_OK "$(date)" - fi -fi - #============================================================================ veget_version=false -if [[ "$veget" != 'NONE' ]]; then +if [[ $veget != 'NONE' ]]; then cd "$MODEL/modipsl/modeles/ORCHIDEE" set +e; svn upgrade; set -e - if [[ "$veget" = "CMIP6" ]]; then + if [[ $veget = "CMIP6" ]]; then veget_version=orchidee2.0 orchidee_rev=6592 @@ -652,9 +656,4 @@ # Pour les experts qui voudraient changer de version d'orchidee. # Attention : necessite d'avoir le password pour orchidee - - # Correctif suite debug Jean-Zay - if [[ -f src_global/time.f90 ]]; then - sed -i -e 's/CALL tlen2itau/\!CALL tlen2itau/' src_global/time.f90 - fi ################################################################### if [[ "$veget_version" == "false" ]]; then Index: BOL/script_install_amaury/install_xios.bash =================================================================== --- BOL/script_install_amaury/install_xios.bash (revision 4862) +++ BOL/script_install_amaury/install_xios.bash (revision 4871) @@ -1,129 +1,115 @@ -#!/bin/bash -######################################################################### -# Defaults -######################################################################### -hostname=`hostname` -install_dir=$(pwd) -netcdf_home="/usr/local/netcdf" -hdf5_home="/usr/local/hdf5" -if [ -d /usr/lib64/openmpi ] ; then - mpi_home="/usr/lib64/openmpi" -else - mpi_home="/usr" -fi -arch="local" -#xios_branch="trunk" -xios_branch="2.6" -#xios_rev="HEAD" -xios_rev="2568" +#!/bin/bash +set -e -u # exit on most (not all!) error codes, and error on unset variables -######################################################################### -# Options -######################################################################### -while (($# > 0)) - do - case $1 in - "-h") cat <<........fin - $0 [ -prefix path ] where (path) to install - (default: $install_dir) - [ -netcdf path ] top directory of the netcdf library - (default: $netcdf_home) - [ -hdf5 path ] top directory of the hdf5 library - (default: $hdf5_home) - [ -MPI path ] top directory of the MPI library - (default: $mpi_home) - [ -branch branch] XIOS branch trunk|2.5|2.6 - (default: $xios_branch) - [ -rev number ] XIOS revision - (default: $xios_rev) - [ -arch ARCH ] Use ARCH file (provided by XIOS) - (default: make/use a local arch file) -........fin - exit ;; - "-prefix") install_dir=$2 ; shift ; shift ;; - "-netcdf") netcdf_home=$2 ; shift ; shift ;; - "-hdf5" ) hdf5_home=$2 ; shift ; shift ;; - "-MPI") mpi_home=$2 ; shift ; shift ;; - "-branch") xios_branch=$2 ; shift ; shift ;; - "-rev") xios_rev=$2 ; shift ; shift ;; - "-arch") arch=$2 ; shift ; shift ;; - *) echo "Error, bad argument $1" ; $0 -h ; exit - esac -done +# Installs xios +# Rewritten 02/2024 A. Barral -# Install directory (get full path) -mkdir -p $install_dir -install_dir=$(cd $install_dir ; pwd -P ) +function read_args { + ## Defaults + install_dir=$(pwd) -# Download XIOS -case $xios_branch in - "trunk") - xios_http="http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/trunk" ;; - "2.5") - xios_http="http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5" ;; - "2.6") - xios_http="http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS2/branches/xios-2.6" ;; -*) -echo "Error, bad argument for -branch ! Did not expect $xios_branch" ; exit ;; -esac + xios_branch="2.6" + xios_rev="2568" + arch="local" + make_j="8" + # Not inputs + hdf5_home=$(dirname "$(dirname "$(readlink -f "$(which h5pcc)")")") + mpi_home=$(dirname "$(dirname "$(readlink -f "$(which mpif90)")")") -cd $install_dir -svn co --revision $xios_rev $xios_http XIOS + while (($# > 0)); do + case $1 in + "-h") cat < arch-local.env -echo '' >> arch-local.env -echo 'export NETCDFC='${netcdf_home} >> arch-local.env -echo 'export NETCDFC_LIB=$NETCDFC/lib' >> arch-local.env -echo 'export NETCDFC_INC=$NETCDFC/include' >> arch-local.env -echo '' >> arch-local.env -echo 'export NETCDFF='${netcdf_home} >> arch-local.env -echo 'export NETCDFF_LIB=$NETCDFF/lib' >> arch-local.env -echo 'export NETCDFF_INC=$NETCDFF/include' >> arch-local.env -echo '' >> arch-local.env -echo 'export NETCDFCXX='${netcdf_home} >> arch-local.env -echo 'export NETCDFCXX_LIB=$NETCDFCXX/lib' >> arch-local.env -echo 'export NETCDFCXX_INC=$NETCDFCXX/include' >> arch-local.env +function download_xios { + # Install directory (get full path) + mkdir -p "$install_dir" + install_dir=$(cd "$install_dir" || exit 1; pwd -P) -# arch-local.fcm -echo '%CCOMPILER '${mpi_home}'/bin/mpicc' > arch-local.fcm -echo '%FCOMPILER '${mpi_home}'/bin/mpif90' >> arch-local.fcm -echo '%LINKER '${mpi_home}'/bin/mpif90' >> arch-local.fcm -echo '' >> arch-local.fcm -if [ ${hostname:0:5} = cicla ] ; then -echo '%BASE_CFLAGS -w -ansi' >> arch-local.fcm -else -echo '%BASE_CFLAGS -w -std=c++11 -D__XIOS_EXCEPTION' >> arch-local.fcm -fi -echo '%PROD_CFLAGS -O3 -D BOOST_DISABLE_ASSERTS' >> arch-local.fcm -echo '%DEV_CFLAGS -g -O2' >> arch-local.fcm -echo '%DEBUG_CFLAGS -g -DBZ_DEBUG' >> arch-local.fcm -echo '' >> arch-local.fcm -echo '%BASE_FFLAGS -D__NONE__ -ffree-line-length-none' >> arch-local.fcm -echo '%PROD_FFLAGS -O3' >> arch-local.fcm -echo '%DEV_FFLAGS -g -O2' >> arch-local.fcm -echo '%DEBUG_FFLAGS -g' >> arch-local.fcm -echo '' >> arch-local.fcm -echo '%BASE_INC -D__NONE__' >> arch-local.fcm -echo '%BASE_LD -lstdc++ -Wl,-rpath='${mpi_home}'/lib' >> arch-local.fcm -echo '' >> arch-local.fcm -echo '%CPP '${mpi_home}'/bin/mpicc -EP' >> arch-local.fcm -echo '%FPP cpp -P' >> arch-local.fcm -echo '%MAKE make' >> arch-local.fcm + local xios_http + case $xios_branch in + "trunk") xios_http="http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/trunk";; + "2.5") xios_http="http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5";; + "2.6") xios_http="http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS2/branches/xios-2.6";; + *) echo "Error, bad argument for -branch ! Did not expect $xios_branch"; exit 1;; + esac -# arch-local.path -echo 'NETCDF_INCDIR="-I${NETCDFC_INC} -I${NETCDFF_INC} -I${NETCDFCXX_INC} "' > arch-local.path -echo 'NETCDF_LIBDIR="-L${NETCDFC_LIB} -L${NETCDFF_LIB} -L${NETCDFCXX_LIB} "' >> arch-local.path -echo 'NETCDF_LIB="-lnetcdf -lnetcdff -lnetcdf_c++4"' >> arch-local.path -echo 'HDF5_INCDIR="-I'${hdf5_home}'/include"' >> arch-local.path -echo 'HDF5_LIBDIR="-L'${hdf5_home}'/lib"' >> arch-local.path -echo 'HDF5_LIB="-lhdf5_hl -lhdf5 -lhdf5 -lz -lcurl"' >> arch-local.path -fi + cd "$install_dir" || exit 1 + svn co --revision "$xios_rev" "$xios_http" XIOS +} -# make XIOS -cd $install_dir/XIOS -./make_xios --arch $arch --job 8 2>&1 | tee make_xios.out +function create_local_arch { + cd "$install_dir/XIOS/arch" || exit 1 + cat < arch-local.env +export MPI_LIB="-L${mpi_home}/lib -lmpi" + +export NETCDFC_INC="\$(nc-config --includedir)" +export NETCDFC_LIB="\$(nc-config --libdir)" + +export NETCDFF_INC="\$(nf-config --includedir)" +export NETCDFF_LIB="\$(nf-config --prefix)/lib" + +export NETCDFCXX_INC="\$(ncxx4-config --includedir)" +export NETCDFCXX_LIB="\$(ncxx4-config --libdir)" +eof + + cat < arch-local.fcm +%CCOMPILER "$(which mpicc)" +%FCOMPILER "$(which mpif90)" +%LINKER "$(which mpif90)" + +%BASE_CFLAGS -w -std=c++11 -D__XIOS_EXCEPTION +%PROD_CFLAGS -O3 -D BOOST_DISABLE_ASSERTS +%DEV_CFLAGS -g -O2 +%DEBUG_CFLAGS -g -DBZ_DEBUG + +%BASE_FFLAGS -D__NONE__ -ffree-line-length-none +%PROD_FFLAGS -O3 +%DEV_FFLAGS -g -O2 +%DEBUG_FFLAGS -g + +%BASE_INC -D__NONE__ +%BASE_LD -lstdc++ -Wl,-rpath=${mpi_home}/lib + +%CPP $(which mpicc) -EP +%FPP cpp -P +%MAKE make +eof + cat < arch-local.path +NETCDF_INCDIR="-I\${NETCDFC_INC} -I\${NETCDFF_INC} -I\${NETCDFCXX_INC}" +NETCDF_LIBDIR="-L\${NETCDFC_LIB} -L\${NETCDFF_LIB} -L\${NETCDFCXX_LIB}" +NETCDF_LIB="-lnetcdf -lnetcdff -lnetcdf_c++4" + +HDF5_INCDIR="-I${hdf5_home}/include" +HDF5_LIBDIR="-L${hdf5_home}/lib" +HDF5_LIB="-lhdf5_hl -lhdf5 -lz -lcurl" +eof +} + +function make_xios { + cd "$install_dir/XIOS" + echo "Compiling xios, see $(pwd)/make_xios.out" + ./make_xios --arch "$arch" --job "$make_j" >make_xios.out 2>&1 +} + +read_args "$@" +download_xios +if [[ $arch = "local" ]]; then create_local_arch; fi +make_xios +