Index: BOL/script_install/install_lmdz.sh =================================================================== --- BOL/script_install/install_lmdz.sh (revision 4223) +++ BOL/script_install/install_lmdz.sh (revision 4235) @@ -19,6 +19,6 @@ # # The sources of the models can be found in the "modeles" directory. -# In the present case, LMDZ, ORCHIDEE, and IOIPSL or XIOS (handling of input-outputs -# using the NetCDF library). +# In the present case, LMDZ, ORCHIDEE, and IOIPSL or XIOS (handling of +# input-outputs using the NetCDF library). # # The script downloads various source files (including a version of NetCDF) @@ -47,16 +47,17 @@ ################################################################ 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 --no-check-certificate -nv http://lmdz.lmd.jussieu.fr/pub/$1 - save_pub_locally=0 - if [ $save_pub_locally = 1 ] ; then # saving wget files on ~/LMDZ/pub - dir=~/LMDZ/pub/`dirname $1` ; mkdir -p $dir ; cp -r `basename $1` $dir - fi - fi + # 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 --no-check-certificate -nv http://lmdz.lmd.jussieu.fr/pub/$1 + save_pub_locally=0 + if [ $save_pub_locally = 1 ] ; then # saving wget files on ~/LMDZ/pub + dir=~/LMDZ/pub/`dirname $1` ; mkdir -p $dir + cp -r `basename $1` $dir + fi + fi } @@ -74,8 +75,7 @@ getlmdzor=1 -netcdf=1 # 1 for automatic installation - # 0 for no installation - # /.../../netcdf-4.0.1 if wanting to link with an already - # compiled netcdf library (implies to check option compatibility) +netcdf=0 # 1: for automatic installation; +# or 0: do not install NetCDF and look for it in standard locations; +# or absolute path: look for NetCDF there check_linux=1 ioipsl=1 @@ -138,7 +138,7 @@ ######################################################################### while (($# > 0)) - do - case $1 in - "-h") cat <<........fin +do + case $1 in + "-h") cat <<........fin $0 [ -v version ] [ -r svn_release ] [ -parallel PARA ] [ -d GRID_RESOLUTION ] [ -bench 0/1 ] @@ -163,6 +163,8 @@ -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) + -netcdf 0, 1 or PATH + 0: do not download NetCDF, look for it in standard locations + 1: download and compile NetCDF + PATH: full path to an existing installed NetCDF library -xios also download and compile the XIOS library @@ -191,46 +193,60 @@ ........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=$2 - case $cosp in - "none"|"v1"|"v2") cosp=$2 ; shift ; shift ;; - *) echo Only none v1 v2 for cosp option ; exit - esac ;; - "-nofcm") compile_with_fcm=0 ; shift ;; - "-SCM") SCM=1 ; shift ;; - "-opt_makelmdz") OPT_MAKELMDZ="$2" ; shift ; shift ;; - "-rrtm") rrtm="$2" ; if [ "$2" = "false" ] ; then rad="oldrad" ; else rad="rrtm" ; fi ; shift ; shift ;; - "-rad") rad=$2 - case $rad in - "oldrad"|"rrtm"|"ecrad") rad=$2 ; shift ; shift ;; - *) echo Only oldrad rrtm ecrad for rad option ; exit - esac ;; - "-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 ;; - "-veget") veget=$2 ; shift ; shift ;; - *) ./install_lmdz.sh -h ; exit - esac + 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=$2 + case $cosp in + "none"|"v1"|"v2") cosp=$2 ; shift ; shift ;; + *) echo Only none v1 v2 for cosp option ; exit + esac ;; + "-nofcm") compile_with_fcm=0 ; shift ;; + "-SCM") SCM=1 ; shift ;; + "-opt_makelmdz") OPT_MAKELMDZ="$2" ; shift ; shift ;; + "-rrtm") rrtm="$2" + if [ "$2" = "false" ] ; then + rad="oldrad" + else + rad="rrtm" + fi + shift ; shift ;; + "-rad") rad=$2 + case $rad in + "oldrad"|"rrtm"|"ecrad") rad=$2 ; shift ; shift ;; + *) echo Only oldrad rrtm ecrad for rad option ; exit + esac ;; + "-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 ;; + "-veget") veget=$2 ; shift ; shift ;; + *) ./install_lmdz.sh -h ; exit + esac done -# Option de compilation du rayonnement : depend de $mysvn ><= r4185, sera donc definie plus bas +# Option de compilation du rayonnement : depend de $mysvn ><= r4185, +# sera donc definie plus bas + #opt_rad="" #case $rad in @@ -243,6 +259,6 @@ opt_cosp="" case cosp in - v1) opt_cosp="-cosp true" ;; - v2) opt_cosp="-cospv2 true" ;; + v1) opt_cosp="-cosp true" ;; + v2) opt_cosp="-cospv2 true" ;; esac @@ -260,5 +276,6 @@ if [ "$veget" = 'NONE' ] ; then suff_orc='' - #For use with tutorial, orchidee_rev is also defined (will be written in surface_env at the end of the script) + #For use with tutorial, orchidee_rev is also defined (will be + #written in surface_env at the end of the script) orchidee_rev='' else @@ -267,5 +284,9 @@ -if [ $parallel = none ] ; then sequential=1; suff_exe='_seq' ; else sequential=0; suff_exe='_para_mem' ; fi +if [ $parallel = none ] ; then + sequential=1; suff_exe='_seq' +else + sequential=0; suff_exe='_para_mem' +fi #Chemin pour placer le modele @@ -287,76 +308,84 @@ 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 - else - echo "Cannot find mpif90" ; - if [ $parallel = none ] ; then exit ; fi ; - fi ; - if [ $parallel != none ] ; then - root_mpi=$(which mpif90 | sed -e s:/bin/mpif90::) - path_mpi=$(which mpif90 | sed -e s:/mpif90::) - export LD_LIBRARY_PATH=${root_mpi}/lib:$LD_LIBRARY_PATH - fi - par_comp=${path_mpi}/mpif90 ; - mpirun=${path_mpi}/mpirun ; - arch=local ; - make=make ; - o_ins_make="-t g95" + 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" ; + module purge + module load gnu/10.2.0 + module load openmpi/4.0.5 + module load hdf5/1.10.7-mpi + module load netcdf-c/4.7.4-mpi + module load netcdf-fortran/4.5.3-mpi + netcdf=/net/nfs/tools/PrgEnv/linux-scientific6-x86_64/gcc-10.2.0/netcdf-fortran-4.5.3-k3drgfqok3lip62hnm3tsyof4cjen5sk + module load svn/1.14.0 + + if [ $parallel != none ] ; then + root_mpi=/net/nfs/tools/meso-sl6/openmpi/4.0.5-gcc-10.2.0 + path_mpi=$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 + else + echo "Cannot find mpif90" ; + if [ $parallel = none ] ; then exit ; fi ; + fi ; + if [ $parallel != none ] ; then + root_mpi=$(which mpif90 | sed -e s:/bin/mpif90::) + path_mpi=$(which mpif90 | sed -e s:/mpif90::) + export LD_LIBRARY_PATH=${root_mpi}/lib:$LD_LIBRARY_PATH + fi + par_comp=${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 + # 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 [ "$compiler" = "ifort" ] ; then + MPI_FLAGS="" + OMP_FLAGS="-openmp" + OMP_LD="-openmp" + else # pgf90 + MPI_FLAGS="" + OMP_FLAGS="-mp" + OMP_LD="-mp" + fi fi @@ -370,19 +399,19 @@ if [ "$compiler" = "gfortran" ] ; then - gfortran=gfortran - gfortranv=`gfortran --version | \ + gfortran=gfortran + gfortranv=`gfortran --version | \ head -1 | awk ' { print $NF } ' | awk -F. ' { print $1 * 10 + $2 } '` - if [ $gfortranv -le 43 ] ; then - echo ERROR : Your gfortran compiler is too old - echo 'Please choose a new one (ifort) and change the line' - echo compiler=xxx - echo in the install_lmdz.sh script and rerun it - if [ `which gfortran44 | wc -w` -ne 0 ] ; then - gfortran=gfortran44 - else - echo gfotran trop vieux ; exit - fi - fi - compiler=$gfortran + if [ $gfortranv -le 43 ] ; then + echo ERROR : Your gfortran compiler is too old + echo 'Please choose a new one (ifort) and change the line' + echo compiler=xxx + echo in the install_lmdz.sh script and rerun it + if [ `which gfortran44 | wc -w` -ne 0 ] ; then + gfortran=gfortran44 + else + echo gfotran trop vieux ; exit + fi + fi + compiler=$gfortran fi ##################################################################### @@ -390,15 +419,15 @@ ## 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 + echo "Error, you must set -parallel mpi_omp if you want XIOS" + exit fi if [ "$with_xios" = "y" ] ; then - opt_makelmdz_xios="-io xios" + opt_makelmdz_xios="-io xios" fi if [ "$cosp" = "v2" -a "$with_xios" = "n" ] ; then - echo "Error, Cospv2 cannot run without Xios" - exit + echo "Error, Cospv2 cannot run without Xios" + exit fi @@ -414,72 +443,78 @@ BASE_LD="$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 +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" = "$gfortran" ] ; then - OPTIM='-O3' - OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all -fbacktrace -finit-real=snan" - OPTDEV="-Wall -fbounds-check" - fmod='I ' - OPTPREC="$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=" $OPTIMNC" - export CC=gcc - export CXX=g++ - export fpp_flags="-P -C -traditional -ffreestanding" + OPTIM='-O3' + OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all -fbacktrace -finit-real=snan" + OPTDEV="-Wall -fbounds-check" + fmod='I ' + OPTPREC="$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=" $OPTIMNC" - export CC=gcc - export CXX=g++ + OPTIM='-O3' + OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all" + OPTDEV="-Wall -fbounds-check" + BASE_LD="$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 - + 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 || $compiler = mpiifort ]] ; 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 else - echo unexpected compiler $compiler ; exit + echo unexpected compiler $compiler ; exit fi @@ -492,14 +527,14 @@ # 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" + 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 $OPTPREC" fi ########################################################################## @@ -513,108 +548,117 @@ echo '################################################################' if [ "$check_linux" = 1 ] ; then -echo Check if required software is available -echo '################################################################' - -#### Ehouarn: test if the required shell is available -#### Maj FH-LF-AS 2021-04 : default=bash ; if bash missing, use ksh -use_shell="bash" # default -if [ "`which bash`" = "" ] ; then - echo "no bash ; we will use ksh" - use_shell="ksh" - if [ "`which ksh`" = "" ] ; then - echo "bash (or ksh) needed!! Install it!" - exit - 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 + echo Check if required software is available + echo '################################################################' + + #### Ehouarn: test if the required shell is available + #### Maj FH-LF-AS 2021-04 : default=bash ; if bash missing, use ksh + use_shell="bash" # default + if [ "`which bash`" = "" ] ; then + echo "no bash ; we will use ksh" + use_shell="ksh" + if [ "`which ksh`" = "" ] ; then + echo "bash (or ksh) needed!! Install it!" + exit + fi + fi + + for logiciel in wget tar gzip make $compiler gcc cmake ; 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 + $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 -a ! -d $MODEL/modipsl ] ; then + ########################################################################### + echo '##########################################################' + echo Download a slightly modified version of LMDZ + echo '##########################################################' + cd $MODEL + myget src/modipsl.$version.tar.gz + echo install_lmdz.sh wget_OK `date` + gunzip modipsl.$version.tar.gz + tar xf modipsl.$version.tar + \rm modipsl.$version.tar +fi + ########################################################################### - echo '##########################################################' - echo Download a slightly modified version of LMDZ - echo '##########################################################' - cd $MODEL - myget src/modipsl.$version.tar.gz - echo install_lmdz.sh wget_OK `date` - gunzip modipsl.$version.tar.gz - tar xf modipsl.$version.tar - \rm modipsl.$version.tar -fi - -########################################################################### -if [ $netcdf = 1 -a ! -d $MODEL/netcdf ] ; 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 - - 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 >> $netcdflog 2>&1 - #LF rajout d'une verrue, pour une raison non encore expliquee, la librairie est parfois rangée dans lib64 - # et non dans lib par certains compilateurs - if [ ! -e lib -a -d lib64 ] ; then ln -s lib64 lib; fi - else - # download and compile hdf5 and netcdf, etc. using the install_netcdf4_hdf5.bash script - #wget http://www.lmd.jussieu.fr/~lmdz/Distrib/install_netcdf4_hdf5.bash - myget import/install_netcdf4_hdf5.bash - chmod u=rwx install_netcdf4_hdf5.bash - if [ "$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_lmdz.sh netcdf_OK `date` +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" && ! -d $MODEL/netcdf4_hdf5_seq ]] ; then + myget import/install_netcdf4_hdf5_seq.bash + chmod +x install_netcdf4_hdf5_seq.bash + + if [ "$compiler" = "gfortran" ] + then + ./install_netcdf4_hdf5_seq.bash -prefix $MODEL/netcdf4_hdf5_seq \ + -compiler gnu > $netcdflog 2>&1 + elif [ "$compiler" = "ifort" ] + then + ./install_netcdf4_hdf5_seq.bash -prefix $MODEL/netcdf4_hdf5_seq \ + -compiler intel > $netcdflog 2>&1 + else + echo "unexpected compiler $compiler" ; exit + fi + + # LF rajout d'une verrue, pour une raison non encore expliquee, + # la librairie est parfois rangée dans lib64 et non dans lib + # par certains compilateurs + if [ ! -e lib -a -d lib64 ] ; then ln -s lib64 lib; fi + elif [[ "$with_xios" = "y" && ! -d $MODEL/netcdf4_hdf5 ]] + then + # download and compile hdf5 and netcdf, etc. using the + # install_netcdf4_hdf5.bash script + myget import/install_netcdf4_hdf5.bash + chmod u=rwx install_netcdf4_hdf5.bash + if [ "$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_lmdz.sh netcdf_OK `date` fi # of if [ $netcdf = 1 ] # ncdfdir contains the directory where netcdf is installed -if [ $netcdf = 0 -o $netcdf = 1 ] ; then - if [ "$with_xios" = "y" ] ; then - ncdfdir=$MODEL/netcdf4_hdf5 - else - ncdfdir=$MODEL/netcdf-4.0.1 - fi +if [ $netcdf = 1 ] ; then + if [ "$with_xios" = "y" ] ; then + ncdfdir=$MODEL/netcdf4_hdf5 + else + ncdfdir=$MODEL/netcdf4_hdf5_seq + fi +elif [ $netcdf = 0 ] +then + ncdfdir=/usr else - ncdfdir=$netcdf + ncdfdir=$netcdf fi @@ -622,140 +666,149 @@ if [[ ! -f $MODEL/modipsl/lib/libioipsl.a ]] then -if [ $ioipsl = 1 ] ; then -#========================================================================= - echo OK ioipsl=$ioipsl - echo '##########################################################' - echo 'Installing MODIPSL, the installation package manager for the ' - echo 'IPSL models and tools' - echo '##########################################################' - echo `date` - - 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 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" ] - - echo install_lmdz.sh MODIPSL_OK `date` - - cd $MODEL/modipsl/modeles/IOIPSL/src - ioipsllog=`pwd`/ioipsl.log - echo '##########################################################' - echo 'Compiling IOIPSL, the interface library with Netcdf' - echo '##########################################################' - echo `date` - 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_lmdz.sh ioipsl_OK `date` -fi # of if [ $ioipsl = 1 ] + if [ $ioipsl = 1 ] ; then + #===================================================================== + echo OK ioipsl=$ioipsl + echo '##########################################################' + echo 'Installing MODIPSL, the installation package manager for the ' + echo 'IPSL models and tools' + echo '##########################################################' + echo `date` + + 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 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" ] + + echo install_lmdz.sh MODIPSL_OK `date` + + cd $MODEL/modipsl/modeles/IOIPSL/src + ioipsllog=`pwd`/ioipsl.log + echo '##########################################################' + echo 'Compiling IOIPSL, the interface library with Netcdf' + echo '##########################################################' + echo `date` + 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_lmdz.sh ioipsl_OK `date` + fi # of if [ $ioipsl = 1 ] fi # Saving ioipsl lib for possible parallel compile - cd $MODEL/modipsl - tar cf ioipsl.tar lib/ bin/ +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 - #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 - svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5 XIOS - 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 + 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 import/install_xios.bash + chmod u=rwx install_xios.bash + if [ ${hostname:0:5} = jean- ] ; then + svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5 \ + XIOS + 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 $arch > xios.log 2>&1 + fi # of case Jean-Zay + if [ -f XIOS/lib/libxios.a ] ; then + echo "XIOS library successfully generated" + echo install_lmdz.sh XIOS_OK `date` + fi fi @@ -763,92 +816,112 @@ veget_version=false if [ "$veget" != 'NONE' ] ; then - cd $MODEL/modipsl/modeles/ORCHIDEE - set +e ; svn upgrade ; set -e - if [ "$veget" = "CMIP6" ] ; then - veget_version=orchidee2.0 - orchidee_rev=6592 - else # specific orchidee revision newer than CMIP6, on 2_1 or 2_2 branches - veget_version=orchidee2.1 - orchidee_rev=$veget - if [ $veget -lt 4465 ] ; then - echo 'Stopping, ORCHIDEE version too old, script needs work on the CPP flags to pass to makelmdz' - exit 1 - fi - set +e - # which branch is my version on? - orcbranch=`svn log -v -q svn://forge.ipsl.jussieu.fr/orchidee/ -r $veget |grep ORCHIDEE |head -1| sed -e 's:ORCHIDEE/.*$:ORCHIDEE:' | awk '{print $2}'` - # switch to that branch - echo IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at orchidee-help@listes.ipsl.fr - svn switch -r $veget --accept theirs-full svn://forge.ipsl.jussieu.fr/orchidee/$orcbranch - svn log -r $veget | grep $veget - 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 $veget ; set -e - fi - # Correctif suite debug Jean-Zay - sed -i -e 's/9010 FORMAT(A52,F17.14)/9010 FORMAT(A52,F20.14)/' src_stomate/stomate.f90 - opt_orc="-prod" ; if [ "$optim" = "-debug" ] ; then opt_orc="-debug" ; fi - - orchideelog=`pwd`/orchidee.log - echo '########################################################' - echo 'Compiling ORCHIDEE, the continental surface model ' - echo '########################################################' - echo Start of the first compilation of orchidee, in sequential mode: `date` - echo log file : $orchideelog - - export ORCHPATH=`pwd` - xios_orchid="-noxios" - if [ "$with_xios" = "y" ] ; then - xios_orchid="-xios" - fi - if [ -d tools ] ; then -################################################################### -# 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 [ "$veget_version" == "false" ] ; then veget_version=orchidee2.0 ; fi - cd arch - sed -e s:"%COMPILER .*.$":"%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 ../ - - echo ./makeorchidee_fcm -j $xios_orchid $opt_orc -parallel none -arch $arch - ./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel none -arch $arch > $orchideelog 2>&1 - pwd - else # of "if [ -d tools ]" - if [ -d src_parallel ] ; then - liste_src="parallel parameters global stomate sechiba driver" - if [ "$veget_version" == "false" ] ; then veget_version=orchidee2.0 ; 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 # of "if [ -d tools ]" - echo install_lmdz.sh orchidee_compil_seq_OK `date` + cd $MODEL/modipsl/modeles/ORCHIDEE + set +e ; svn upgrade ; set -e + if [ "$veget" = "CMIP6" ] ; then + veget_version=orchidee2.0 + orchidee_rev=6592 + else # specific orchidee revision newer than CMIP6, on 2_1 or 2_2 branches + veget_version=orchidee2.1 + orchidee_rev=$veget + if [ $veget -lt 4465 ] ; then + echo 'Stopping, ORCHIDEE version too old, script needs work on ' \ + 'the CPP flags to pass to makelmdz' + exit 1 + fi + set +e + # which branch is my version on? + orcbranch=`svn log -v -q svn://forge.ipsl.jussieu.fr/orchidee/ -r $veget |grep ORCHIDEE |head -1| sed -e 's:ORCHIDEE/.*$:ORCHIDEE:' | awk '{print $2}'` + # switch to that branch + echo IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at \ + orchidee-help@listes.ipsl.fr + svn switch -r $veget --accept theirs-full \ + svn://forge.ipsl.jussieu.fr/orchidee/$orcbranch + svn log -r $veget | grep $veget + 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 $veget ; set -e + fi + # Correctif suite debug Jean-Zay + sed -i -e 's/9010 FORMAT(A52,F17.14)/9010 FORMAT(A52,F20.14)/' \ + src_stomate/stomate.f90 + opt_orc="-prod" ; if [ "$optim" = "-debug" ] ; then opt_orc="-debug" ; fi + + orchideelog=`pwd`/orchidee.log + echo '########################################################' + echo 'Compiling ORCHIDEE, the continental surface model ' + echo '########################################################' + echo Start of the first compilation of orchidee, in sequential mode: `date` + echo log file : $orchideelog + + export ORCHPATH=`pwd` + xios_orchid="-noxios" + if [ "$with_xios" = "y" ] ; then + xios_orchid="-xios" + fi + if [ -d tools ] ; then + ################################################################### + # 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 [ "$veget_version" == "false" ] ; then + veget_version=orchidee2.0 + fi + cd arch + sed -e s:"%COMPILER .*.$":"%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 ../ + + echo ./makeorchidee_fcm -j $xios_orchid $opt_orc -parallel none \ + -arch $arch + ./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel none \ + -arch $arch > $orchideelog 2>&1 + pwd + else # of "if [ -d tools ]" + if [ -d src_parallel ] ; then + liste_src="parallel parameters global stomate sechiba driver" + if [ "$veget_version" == "false" ] ; then + veget_version=orchidee2.0 + 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 # of "if [ -d tools ]" + echo install_lmdz.sh orchidee_compil_seq_OK `date` fi # of if [ "$veget" != 'NONE' ] @@ -857,12 +930,12 @@ # Ehouarn: the directory name LMDZ* depends on version/tar file... if [ -d $MODEL/modipsl/modeles/LMD* ] ; then - echo '###############################################################' - echo 'Preparing LMDZ compilation : arch file, svn switch if needed...' - echo '###############################################################' - cd $MODEL/modipsl/modeles/LMD* - LMDZPATH=`pwd` + echo '###############################################################' + echo 'Preparing LMDZ compilation : arch file, svn switch if needed...' + echo '###############################################################' + cd $MODEL/modipsl/modeles/LMD* + LMDZPATH=`pwd` else - echo "ERROR: No LMD* directory !!!" - exit + echo "ERROR: No LMD* directory !!!" + exit fi @@ -872,41 +945,44 @@ ############################################################ -if [ "$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 $whereisthatshell" >> bld.cfg +if [[ "$pclinux" = "1" && ! -f arch/arch-local.path ]] ; 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 'NETCDF95_INCDIR=$LMDGCM/../../include' >> arch-local.path + echo 'NETCDF95_LIBDIR=$LMDGCM/../../lib' >> 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 ] @@ -926,5 +1002,6 @@ set +e ; svn info | grep -q 'http:' if [ $? = 0 ] ; then - svn switch --relocate http://svn.lmd.jussieu.fr/LMDZ https://svn.lmd.jussieu.fr/LMDZ + svn switch --relocate http://svn.lmd.jussieu.fr/LMDZ \ + https://svn.lmd.jussieu.fr/LMDZ fi svn update $svnopt @@ -933,5 +1010,6 @@ ################################################################## -# Retrieve the final svn release number, and adjust compilation options accordingly +# Retrieve the final svn release number, and adjust compilation +# options accordingly mysvn=`svnversion . | egrep -o "[0-9]+"` @@ -941,12 +1019,35 @@ case $rad in oldrad) iflag_rrtm=0 ; NSW=2 ; opt_rad="" ;; - rrtm) iflag_rrtm=1 ; NSW=6 ; if [ $mysvn -le 4185 ] ; then opt_rad="-rrtm true" ; else opt_rad="-rad rrtm" ; fi ;; + rrtm) iflag_rrtm=1 ; NSW=6 + if [ $mysvn -le 4185 ] ; then + opt_rad="-rrtm true" + else + opt_rad="-rad rrtm" + fi ;; ecrad) iflag_rrtm=2 ; NSW=6 ; opt_rad="-rad ecrad" ;; *) echo Only oldrad rrtm ecrad for rad option ; exit esac -if [ $mysvn -le 4185 -a $rad = "ecrad" ] ; then echo "ecrad only available for LMDZ rev starting with 4186 " ; exit ; fi +if [ $mysvn -le 4185 -a $rad = "ecrad" ] ; then + echo "ecrad only available for LMDZ rev starting with 4186 " ; exit +fi ################################################################## + + +if [[ ! -f libf/misc/netcdf95.F90 && ! -d $MODEL/NetCDF95-0.2 ]] +then + cd $MODEL + myget import/NetCDF95-0.2.tar.gz + tar -xf NetCDF95-0.2.tar.gz + rm NetCDF95-0.2.tar.gz + cd NetCDF95-0.2 + mkdir build + cd build + cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=$ncdfdir \ + -DCMAKE_INSTALL_PREFIX=$MODEL/modipsl + make install + cd $MODEL/modipsl/modeles/LMDZ* +fi echo '##################################################################' @@ -956,101 +1057,128 @@ echo '##################################################################' -if [ "$env_file" != "" ] ; then mv arch/arch-${arch}.env arch/arch-${arch}.orig ; \cp -f $env_file arch/arch-${arch}.env ; fi - -if [ $compile_with_fcm = 1 ] ; then makelmdz="makelmdz_fcm $optim -arch $arch -j 8 " ; else makelmdz="makelmdz $optim -arch $arch" ; fi +if [ "$env_file" != "" ] ; then + mv arch/arch-${arch}.env arch/arch-${arch}.orig + \cp -f $env_file arch/arch-${arch}.env +fi + +if [ $compile_with_fcm = 1 ] ; then + makelmdz="makelmdz_fcm $optim -arch $arch -j 8 " +else + makelmdz="makelmdz $optim -arch $arch" +fi # sequential compilation if [ "$sequential" = 1 ] ; then - echo Sequential compilation command, saved in compile.sh: - echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp -d ${grid_resolution} -v $veget_version gcm " - echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp -d ${grid_resolution} -v $veget_version gcm " > compile.sh - chmod +x ./compile.sh - if [ $bench = 1 ] ; then - echo install_lmdz.sh start_lmdz_seq_compilation `date` - echo log file: $lmdzlog - ./compile.sh > $lmdzlog 2>&1 - echo install_lmdz.sh end_lmdz_seq_compilation `date` - fi + echo Sequential compilation command, saved in compile.sh: + echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp " \ + "-d ${grid_resolution} -v $veget_version gcm " + echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp " \ + "-d ${grid_resolution} -v $veget_version gcm " > compile.sh + chmod +x ./compile.sh + if [ $bench = 1 ] ; then + echo install_lmdz.sh start_lmdz_seq_compilation `date` + echo log file: $lmdzlog + ./compile.sh > $lmdzlog 2>&1 + echo install_lmdz.sh end_lmdz_seq_compilation `date` + fi fi # fin sequential # compiling in parallel mode if [ $parallel != "none" ] ; then - echo '##########################################################' - echo ' Parallel compile ' - echo '##########################################################' - echo "(after 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 $veget != 'NONE' ] ; then - cd arch - sed \ - -e s:"%COMPILER.*.$":"%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 in parallel mode `date` - echo logfile $orchideelog - echo "NOTE : to recompile it when necessary, use ./compile_orc.sh in modipsl/modeles/ORCHIDEE" - echo ./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc -parallel $parallel -arch $arch > compile_orc.sh - echo ./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel $parallel -arch $arch >> compile_orc.sh - echo echo Now you must also recompile LMDZ, by running ./compile.sh in modeles/LMDZ >> compile_orc.sh - chmod u+x compile_orc.sh - ./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc -parallel $parallel -arch $arch > $orchideelog 2>&1 - ./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel $parallel -arch $arch >> $orchideelog 2>&1 - echo End of ORCHIDEE compilation in parallel mode `date` - elif [ $veget != 'NONE' ] ; then echo '##########################################################' - echo ' Orchidee version too old ' - echo ' Please update to new version ' + echo ' Parallel compile ' echo '##########################################################' - exit - fi # of [ -d src_parallel -a $veget != 'NONE' ] - - # 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 [ ${hostname:0:5} = jean- -a "$cosp" = "v2" ] ; then - - echo LMDZ compilation command in parallel mode, saved in compile.sh, is : - echo "(ATTENTION le probleme de cospv2 sur jean-zay en mode prod n est pas corrige ! )" -# ATTENTION le probleme de cospv2 sur jean-zay en mode prod n est pas corrige - echo ./$makelmdz -dev $optim $OPT_MAKELMDZ $opt_rad $opt_cosp $opt_makelmdz_xios -d \$resol -v $veget_version -mem -parallel $parallel gcm >> compile.sh - echo ./$makelmdz -dev $optim $OPT_MAKELMDZ $opt_rad $opt_cosp $opt_makelmdz_xios -d \$resol -v $veget_version -mem -parallel $parallel gcm - else - echo ./$makelmdz $optim $OPT_MAKELMDZ $opt_rad $opt_cosp $opt_makelmdz_xios -d \$resol -v $veget_version -mem -parallel $parallel gcm >> compile.sh - echo ./$makelmdz $optim $OPT_MAKELMDZ $opt_rad $opt_cosp $opt_makelmdz_xios -d \$resol -v $veget_version -mem -parallel $parallel gcm - fi - chmod +x ./compile.sh - - if [ $bench = 1 ] ; then - echo Compiling LMDZ in parallel mode `date`, LMDZ log file: $lmdzlog ; ./compile.sh > $lmdzlog 2>&1 - fi + echo "(after 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 $veget != 'NONE' ] ; then + cd arch + sed \ + -e s:"%COMPILER.*.$":"%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 in parallel mode `date` + echo logfile $orchideelog + echo "NOTE : to recompile it when necessary, use ./compile_orc.sh " \ + "in modipsl/modeles/ORCHIDEE" + echo ./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc \ + -parallel $parallel -arch $arch > compile_orc.sh + echo ./makeorchidee_fcm -j 8 $xios_orchid $opt_orc \ + -parallel $parallel -arch $arch >> compile_orc.sh + echo echo Now you must also recompile LMDZ, by running ./compile.sh \ + in modeles/LMDZ >> compile_orc.sh + chmod u+x compile_orc.sh + ./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc \ + -parallel $parallel -arch $arch > $orchideelog 2>&1 + ./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel $parallel \ + -arch $arch >> $orchideelog 2>&1 + echo End of ORCHIDEE compilation in parallel mode `date` + elif [ $veget != 'NONE' ] ; then + echo '##########################################################' + echo ' Orchidee version too old ' + echo ' Please update to new version ' + echo '##########################################################' + exit + fi # of [ -d src_parallel -a $veget != 'NONE' ] + + # 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 [ ${hostname:0:5} = jean- -a "$cosp" = "v2" ] ; then + + echo LMDZ compilation command in parallel mode, saved in compile.sh, \ + is : + echo "(ATTENTION le probleme de cospv2 sur jean-zay en mode prod " \ + "n est pas corrige ! )" + # ATTENTION le probleme de cospv2 sur jean-zay en mode prod n + # est pas corrige + echo ./$makelmdz -dev $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \ + $opt_makelmdz_xios -d \$resol -v $veget_version -mem \ + -parallel $parallel gcm >> compile.sh + echo ./$makelmdz -dev $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \ + $opt_makelmdz_xios -d \$resol -v $veget_version -mem \ + -parallel $parallel gcm + else + echo ./$makelmdz $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \ + $opt_makelmdz_xios -d \$resol -v $veget_version -mem \ + -parallel $parallel gcm >> compile.sh + echo ./$makelmdz $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \ + $opt_makelmdz_xios -d \$resol -v $veget_version -mem \ + -parallel $parallel gcm + fi + chmod +x ./compile.sh + + if [ $bench = 1 ] ; then + echo Compiling LMDZ in parallel mode `date`, LMDZ log file: $lmdzlog + ./compile.sh > $lmdzlog 2>&1 + fi fi # of if [ $parallel != "none" ] @@ -1065,20 +1193,22 @@ if [ $mysvn -ge 4186 ] ; then suff_exe=_${rad}${suff_exe} ; fi gcm="" -#for exe in gcm.e bin/gcm_${grid_resolution}_phylmd_seq_orch.e bin/gcm_${grid_resolution}_phylmd_seq.e bin/gcm_${grid_resolution}_phylmd_para_mem_orch.e bin/gcm_${grid_resolution}_phylmd_para_mem.e ; do -for exe in gcm.e bin/gcm_${grid_resolution}_phylmd${suff_exe}${suff_orc}.e ; do if [ -f $exe ] ; then gcm=$exe ; fi + +for exe in gcm.e bin/gcm_${grid_resolution}_phylmd${suff_exe}${suff_orc}.e +do + if [ -f $exe ] ; then gcm=$exe ; fi done if [ "$gcm" = "" ] ; then - if [ $bench = 1 ] ; then - echo 'Compilation failed !! Cannot run the benchmark;' - exit - else - echo 'Compilation not done (only done when bench=1)' - fi + if [ $bench = 1 ] ; 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 !! ' `date` - echo '##########################################################' - echo The executable is $gcm + echo '##########################################################' + echo 'Compilation successfull !! ' `date` + echo '##########################################################' + echo The executable is $gcm fi @@ -1088,205 +1218,253 @@ if [ $bench = tuto ] ; then - myget Training/tutorial.tar ; tar xvf tutorial.tar ; cd TUTORIAL ; ./init.sh + myget Training/tutorial.tar ; tar xvf tutorial.tar ; cd TUTORIAL + ./init.sh elif [[ $bench = 1 && ! -d BENCH${grid_resolution} ]] ; then - # TOUTE CETTE SECTION DEVRAIT DISPARAITRE POUR UNE COMMANDE - # OU DES BENCHS PAR MOTS CLES COMME tuto - - echo '##########################################################' - echo ' Running a test run ' - echo '##########################################################' - - \rm -rf BENCH${grid_resolution} - bench=bench_lmdz_${grid_resolution} - echo install_lmdz.sh before bench download `date` - #wget http://www.lmd.jussieu.fr/~lmdz/Distrib/$bench.tar.gz - myget 3DBenchs/$bench.tar.gz - echo install_lmdz.sh after bench download `date` - tar xvf $bench.tar.gz - - if [ "$cosp" = "v1" -o "$cosp" = "v2" ] ; then - cd BENCH${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${grid_resolution} - cp ../DefLists/iodef.xml . - cp ../DefLists/context_lmdz.xml . - cp ../DefLists/field_def_lmdz.xml . - # A raffiner par la suite - echo A FAIRE : Copier les *xml en fonction de l option cosp - cp ../DefLists/field_def_cosp*.xml . - cp ../DefLists/file_def_hist*xml . - # adapt iodef.xml to use attached mode - sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' iodef.xml > tmp - \mv -f tmp iodef.xml - - # and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE. - # except for histday - for histfile in file_def_hist*xml - do - if [ "$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" = "v1" ] ; 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 $histfile - fi - if [ "$cosp" = "v2" ] ; 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 - sed -e 's@src="./file_def_histmthCOSP_lmdz.xml"@src="./file_def_histmthCOSPv2_lmdz.xml"@' $contextfile > tmp ; \mv -f tmp $contextfile - sed -e 's@src="./file_def_histhfCOSP_lmdz.xml"@src="./file_def_histhfCOSPv2_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 $fieldfile - fi - - cd .. - fi - - # Cas Bensh avec ecrad - if [ "$rad" = "ecrad" ] ; then - cd BENCH${grid_resolution} - cp ../DefLists/namelist_ecrad . - cp -r ../libf/phylmd/ecrad/data . - cd .. - fi - - # Adjusting bench physiq.def to radiative code chosen - cd BENCH${grid_resolution} - sed -e 's/iflag_rrtm=.*.$/iflag_rrtm='$iflag_rrtm'/' -e 's/NSW=.*.$/NSW='$NSW'/' physiq.def > tmpdef - \mv tmpdef physiq.def - cd .. - - 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 [ "$cosp" = "v1" -o "$cosp" = "v2" ] ; 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 [ ${hostname:0:5} = jean- ] ; then - . ../arch/arch-${arch}.env - 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 - # Add rebuild, using reb.sh if it is there - echo 'if [ -f reb.sh ] ; then' >> bench.sh - echo ' ./reb.sh histday ; ./reb.sh histmth ; ./reb.sh histhf ; ./reb.sh histins ; ./reb.sh stomate_history ; ./reb.sh sechiba_history ; ./reb.sh sechiba_out_2 ' >> bench.sh - echo 'fi' >> bench.sh - else - echo "./gcm.e > listing 2>&1" > bench.sh - fi - # Getting orchidee stuff - if [ $veget == 'CMIP6' ] ; then - #echo 'myget 3DBenchs/BENCHorch11.tar.gz' - #myget 3DBenchs/BENCHorch11.tar.gz - #tar xvzf BENCHorch11.tar.gz - echo 'myget 3DBenchs/BENCHCMIP6.tar.gz' - myget 3DBenchs/BENCHCMIP6.tar.gz - tar xvzf BENCHCMIP6.tar.gz - sed -e "s:VEGET=n:VEGET=y:" config.def > tmp - mv -f tmp config.def - if [ "$with_xios" = "y" ] ; then - cp ../../ORCHIDEE/src_xml/context_orchidee.xml . - echo '' > add.tmp - cp ../../ORCHIDEE/src_xml/field_def_orchidee.xml . - cp ../../ORCHIDEE/src_xml/file_def_orchidee.xml . - cp ../../ORCHIDEE/src_xml/file_def_input_orchidee.xml . - if [ -f ../../ORCHIDEE/src_xml/context_input_orchidee.xml ] ; then - cp ../../ORCHIDEE/src_xml/context_input_orchidee.xml . - echo '' >> add.tmp - fi - sed -e '/id="LMDZ"/r add.tmp' iodef.xml > tmp - mv tmp iodef.xml - sed -e'{/sechiba1/ s/enabled="_AUTO_"/type="one_file" enabled=".TRUE."/}' file_def_orchidee.xml > tmp ; \mv -f tmp file_def_orchidee.xml - sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' file_def_orchidee.xml > tmp ; \mv -f tmp file_def_orchidee.xml - sed -e 's@output_level="_AUTO_"@output_level="1"@' file_def_orchidee.xml > tmp ; \mv -f tmp file_def_orchidee.xml - sed -e 's@output_freq="_AUTO_"@output_freq="1d"@' file_def_orchidee.xml > tmp ; \mv -f tmp file_def_orchidee.xml - sed -e 's@compression_level="4"@compression_level="0"@' file_def_orchidee.xml > tmp ; \mv -f tmp file_def_orchidee.xml - sed -e 's@XIOS_ORCHIDEE_OK = n@XIOS_ORCHIDEE_OK = y@' orchidee.def > tmp ; \mv -f tmp orchidee.def - fi - 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 '##########################################################' + # TOUTE CETTE SECTION DEVRAIT DISPARAITRE POUR UNE COMMANDE + # OU DES BENCHS PAR MOTS CLES COMME tuto + + echo '##########################################################' + echo ' Running a test run ' + echo '##########################################################' + + \rm -rf BENCH${grid_resolution} + bench=bench_lmdz_${grid_resolution} + echo install_lmdz.sh before bench download `date` + #wget http://www.lmd.jussieu.fr/~lmdz/Distrib/$bench.tar.gz + myget 3DBenchs/$bench.tar.gz + echo install_lmdz.sh after bench download `date` + tar xvf $bench.tar.gz + + if [ "$cosp" = "v1" -o "$cosp" = "v2" ] ; then + cd BENCH${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${grid_resolution} + cp ../DefLists/iodef.xml . + cp ../DefLists/context_lmdz.xml . + cp ../DefLists/field_def_lmdz.xml . + # A raffiner par la suite + echo A FAIRE : Copier les *xml en fonction de l option cosp + cp ../DefLists/field_def_cosp*.xml . + cp ../DefLists/file_def_hist*xml . + # adapt iodef.xml to use attached mode + sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' \ + iodef.xml > tmp + \mv -f tmp iodef.xml + + # and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE. + # except for histday + for histfile in file_def_hist*xml + do + if [ "$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" = "v1" ] ; 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 $histfile + fi + if [ "$cosp" = "v2" ] ; 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 + sed -e 's@src="./file_def_histmthCOSP_lmdz.xml"@src="./file_def_histmthCOSPv2_lmdz.xml"@' \ + $contextfile > tmp + \mv -f tmp $contextfile + sed -e 's@src="./file_def_histhfCOSP_lmdz.xml"@src="./file_def_histhfCOSPv2_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 $fieldfile + fi + + cd .. + fi + + # Cas Bensh avec ecrad + if [ "$rad" = "ecrad" ] ; then + cd BENCH${grid_resolution} + cp ../DefLists/namelist_ecrad . + cp -r ../libf/phylmd/ecrad/data . + cd .. + fi + + # Adjusting bench physiq.def to radiative code chosen + cd BENCH${grid_resolution} + sed -e 's/iflag_rrtm=.*.$/iflag_rrtm='$iflag_rrtm'/' \ + -e 's/NSW=.*.$/NSW='$NSW'/' physiq.def > tmpdef + \mv tmpdef physiq.def + cd .. + + 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 [ "$cosp" = "v1" -o "$cosp" = "v2" ] ; 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 [ ${hostname:0:5} = jean- ] ; then + . ../arch/arch-${arch}.env + 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 + # Add rebuild, using reb.sh if it is there + echo 'if [ -f reb.sh ] ; then' >> bench.sh + echo ' ./reb.sh histday ; ./reb.sh histmth ; ./reb.sh histhf ; ' \ + './reb.sh histins ; ./reb.sh stomate_history ; ' \ + './reb.sh sechiba_history ; ./reb.sh sechiba_out_2 ' >> bench.sh + echo 'fi' >> bench.sh + else + echo "./gcm.e > listing 2>&1" > bench.sh + fi + # Getting orchidee stuff + if [ $veget == 'CMIP6' ] ; then + #echo 'myget 3DBenchs/BENCHorch11.tar.gz' + #myget 3DBenchs/BENCHorch11.tar.gz + #tar xvzf BENCHorch11.tar.gz + echo 'myget 3DBenchs/BENCHCMIP6.tar.gz' + myget 3DBenchs/BENCHCMIP6.tar.gz + tar xvzf BENCHCMIP6.tar.gz + sed -e "s:VEGET=n:VEGET=y:" config.def > tmp + mv -f tmp config.def + if [ "$with_xios" = "y" ] ; then + cp ../../ORCHIDEE/src_xml/context_orchidee.xml . + echo '' \ + > add.tmp + cp ../../ORCHIDEE/src_xml/field_def_orchidee.xml . + cp ../../ORCHIDEE/src_xml/file_def_orchidee.xml . + cp ../../ORCHIDEE/src_xml/file_def_input_orchidee.xml . + if [ -f ../../ORCHIDEE/src_xml/context_input_orchidee.xml ] ; then + cp ../../ORCHIDEE/src_xml/context_input_orchidee.xml . + echo '' >> add.tmp + fi + sed -e '/id="LMDZ"/r add.tmp' iodef.xml > tmp + mv tmp iodef.xml + sed -e'{/sechiba1/ s/enabled="_AUTO_"/type="one_file" enabled=".TRUE."/}' \ + file_def_orchidee.xml > tmp + \mv -f tmp file_def_orchidee.xml + sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \ + file_def_orchidee.xml > tmp + \mv -f tmp file_def_orchidee.xml + sed -e 's@output_level="_AUTO_"@output_level="1"@' \ + file_def_orchidee.xml > tmp + \mv -f tmp file_def_orchidee.xml + sed -e 's@output_freq="_AUTO_"@output_freq="1d"@' \ + file_def_orchidee.xml > tmp + \mv -f tmp file_def_orchidee.xml + sed -e 's@compression_level="4"@compression_level="0"@' \ + file_def_orchidee.xml > tmp + \mv -f tmp file_def_orchidee.xml + sed -e 's@XIOS_ORCHIDEE_OK = n@XIOS_ORCHIDEE_OK = y@' \ + orchidee.def > tmp + \mv -f tmp orchidee.def + fi + fi + + if [[ -f ../arch.env ]] + then + source ../arch.env + 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 # bench @@ -1298,10 +1476,10 @@ 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 -rad $rad + 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 -rad $rad fi #set -vx @@ -1318,6 +1496,2 @@ echo 'orchidee_rev='$orchidee_rev >> surface_env echo 'suforch='$suff_orc >> surface_env - - - - Index: BOL/script_install/install_lmdz_new.sh =================================================================== --- BOL/script_install/install_lmdz_new.sh (revision 4223) +++ (revision ) @@ -1,1497 +1,0 @@ -#!/bin/bash - -#set -vx - -########################################################################### -# Author : Laurent Fairhead et Frédéric Hourdin -# Usage : install_lmdz.sh -help -# -# bash installation script of the LMDZ model on different computer types : -# Linux PC, "mesocentre" (IPSL-UPMC, IPSL-X), super-computer (IDRIS) -# -# The model is downloaded in the following directory 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, LMDZ, ORCHIDEE, and IOIPSL or XIOS (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 -# minimal configuration. -# -# Prerequisites : pgf90/gfortran, bash or ksh, wget , gunzip, tar, ... -# -# Modif 18/11/2011 -# changes for option real 8. -# We compile 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_lmdz.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 --no-check-certificate -nv http://lmdz.lmd.jussieu.fr/pub/$1 - save_pub_locally=0 - if [ $save_pub_locally = 1 ] ; then # saving wget files on ~/LMDZ/pub - dir=~/LMDZ/pub/`dirname $1` ; mkdir -p $dir - cp -r `basename $1` $dir - fi - fi -} - -# 04_2021 : tester si r4 marche encore ! -#real=r4 -real=r8 - - -######################################################################### -# Valeur par défaut des parametres -######################################################################### -svn="" -#version=trunk -version=20220131.trunk - -getlmdzor=1 -netcdf=0 # 1: for automatic installation; -# or 0: do not install NetCDF and look for it in standard locations; -# or absolute path: look for NetCDF there -check_linux=1 -ioipsl=1 -bench=1 -pclinux=1 -pcmac=0 # default: not on a Mac -compiler=gfortran -SCM=0 -# surface/vegetation scheme treatment -# controlled by the single variable veget which can have the following values -# - NONE: bucket scheme (default) -# - CMIP6: orchidee version used in CMIP exercise, rev 5661 -# - number: orchidee version number -veget=NONE -# choose the resolution for the bench runs -# grid_resolution= 32x24x11 or 48x36x19 for tests (test without ORCHIDEE) -# 96x71x19 standard configuration -grid_resolution=144x142x79 -grid_resolution=96x95x39 -grid_resolution=48x36x19 -grid_resolution=32x32x39 -# choose the physiq version you want to test -#physiq=NPv6.0.14splith -physiq= - -## parallel can take the values none/mpi/omp/mpi_omp -parallel=mpi_omp -parallel=none -idris_acct=lmd -OPT_GPROF="" -OPT_MAKELMDZ="" -MODEL="" - -## also compile XIOS? (and more recent NetCDF/HDF5 libraries) Default=no -with_xios="n" -opt_makelmdz_xios="" - -## compile with oldrad/rrtm/ecrad radiatif code (Default=rrtm) -rad=rrtm - -## compile_with_fcm=1 : use makelmdz_fcm (1) or makelmdz (0) -compile_with_fcm=1 - -#Compilation with Cosp (cosp=NONE/v1/v2 ; default=NONE) -cosp=NONE -opt_cosp="" - -# Check if on a Mac -if [ `uname` = "Darwin" ] -then - pcmac=1 - export MAKE=make -fi -#echo "pcmac="$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] [-rad RADIATIF] - - -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 0, 1 or PATH - 0: do not download NetCDF, look for it in standard locations - 1: download and compile NetCDF - PATH: full path to an existing installed 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 - - -cosp to run without our with cospv1 or cospv2 [none/v1/v2] - - -rad RADIATIF can be oldrad, rrtm or ecrad radiatif code - - -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 - - -veget surface model to run [NONE/CMIP6/xxxx] - -........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=$2 - case $cosp in - "none"|"v1"|"v2") cosp=$2 ; shift ; shift ;; - *) echo Only none v1 v2 for cosp option ; exit - esac ;; - "-nofcm") compile_with_fcm=0 ; shift ;; - "-SCM") SCM=1 ; shift ;; - "-opt_makelmdz") OPT_MAKELMDZ="$2" ; shift ; shift ;; - "-rrtm") rrtm="$2" - if [ "$2" = "false" ] ; then - rad="oldrad" - else - rad="rrtm" - fi - shift ; shift ;; - "-rad") rad=$2 - case $rad in - "oldrad"|"rrtm"|"ecrad") rad=$2 ; shift ; shift ;; - *) echo Only oldrad rrtm ecrad for rad option ; exit - esac ;; - "-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 ;; - "-veget") veget=$2 ; shift ; shift ;; - *) ./install_lmdz.sh -h ; exit - esac -done - -# Option de compilation du rayonnement : depend de $mysvn ><= r4185, -# sera donc definie plus bas - -#opt_rad="" -#case $rad in -# rrtm) opt_rad="-rad rrtm" ;; -# ecrad) opt_rad="-rad ecrad" ;; -#esac - - -# Option de compilation pour Cosp -opt_cosp="" -case cosp in - v1) opt_cosp="-cosp true" ;; - v2) opt_cosp="-cospv2 true" ;; -esac - -# Check on veget version -#if [ "$veget" != 'NONE' -a "$veget" != "CMIP6" -a "$veget" != +([0-9]) ] ; then -if [ $veget != 'NONE' -a $veget != "CMIP6" ] ; then - re='^[0-9]+$' - if ! [[ $veget =~ $re ]] ; then - echo 'Valeur de l option veget non valable' - exit - fi -fi - -#Define veget-related suffix for gcm name -if [ "$veget" = 'NONE' ] ; then - suff_orc='' - #For use with tutorial, orchidee_rev is also defined (will be - #written in surface_env at the end of the script) - orchidee_rev='' -else - suff_orc='_orch' -fi - - -if [ $parallel = none ] ; then - sequential=1; suff_exe='_seq' -else - sequential=0; suff_exe='_para_mem' -fi - -#Chemin pour placer le modele -if [ "$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" ; - module purge - module load gnu/10.2.0 - module load openmpi/4.0.5 - module load hdf5/1.10.7-mpi - module load netcdf-c/4.7.4-mpi - module load netcdf-fortran/4.5.3-mpi - netcdf=/net/nfs/tools/PrgEnv/linux-scientific6-x86_64/gcc-10.2.0/netcdf-fortran-4.5.3-k3drgfqok3lip62hnm3tsyof4cjen5sk - module load svn/1.14.0 - - if [ $parallel != none ] ; then - root_mpi=/net/nfs/tools/meso-sl6/openmpi/4.0.5-gcc-10.2.0 - path_mpi=$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 - else - echo "Cannot find mpif90" ; - if [ $parallel = none ] ; then exit ; fi ; - fi ; - if [ $parallel != none ] ; then - root_mpi=$(which mpif90 | sed -e s:/bin/mpif90::) - path_mpi=$(which mpif90 | sed -e s:/mpif90::) - export LD_LIBRARY_PATH=${root_mpi}/lib:$LD_LIBRARY_PATH - fi - par_comp=${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 [ $gfortranv -le 43 ] ; then - echo ERROR : Your gfortran compiler is too old - echo 'Please choose a new one (ifort) and change the line' - echo compiler=xxx - echo in the install_lmdz.sh script and rerun it - if [ `which gfortran44 | wc -w` -ne 0 ] ; then - gfortran=gfortran44 - else - echo gfotran trop vieux ; exit - fi - fi - compiler=$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 - -if [ "$with_xios" = "y" ] ; then - opt_makelmdz_xios="-io xios" -fi - -if [ "$cosp" = "v2" -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" = "$gfortran" ] ; then - OPTIM='-O3' - OPTDEB="-g3 -Wall -fbounds-check -ffpe-trap=invalid,zero,overflow -O0 -fstack-protector-all -fbacktrace -finit-real=snan" - OPTDEV="-Wall -fbounds-check" - fmod='I ' - OPTPREC="$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 || $compiler = mpiifort ]] ; 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 -else - echo unexpected compiler $compiler ; exit -fi - -OPTIMGCM="$OPTIM $OPTPREC" - -hostname=`hostname` - -########################################################################## -# If installing on known machines such as Jean-Zay 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 $MODEL ; pwd )` # to get absolute path, if necessary - - -echo '################################################################' -if [ "$check_linux" = 1 ] ; then - echo Check if required software is available - echo '################################################################' - - #### Ehouarn: test if the required shell is available - #### Maj FH-LF-AS 2021-04 : default=bash ; if bash missing, use ksh - use_shell="bash" # default - if [ "`which bash`" = "" ] ; then - echo "no bash ; we will use ksh" - use_shell="ksh" - if [ "`which ksh`" = "" ] ; then - echo "bash (or ksh) needed!! Install it!" - exit - fi - fi - - for logiciel in wget tar gzip make $compiler gcc cmake ; 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 -a ! -d $MODEL/modipsl ] ; then - ########################################################################### - echo '##########################################################' - echo Download a slightly modified version of LMDZ - echo '##########################################################' - cd $MODEL - myget src/modipsl.$version.tar.gz - echo install_lmdz.sh wget_OK `date` - gunzip modipsl.$version.tar.gz - tar xf modipsl.$version.tar - \rm modipsl.$version.tar -fi - -########################################################################### -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" && ! -d $MODEL/netcdf4_hdf5_seq ]] ; then - myget import/install_netcdf4_hdf5_seq.bash - chmod +x install_netcdf4_hdf5_seq.bash - - if [ "$compiler" = "gfortran" ] - then - ./install_netcdf4_hdf5_seq.bash -prefix $MODEL/netcdf4_hdf5_seq \ - -compiler gnu > $netcdflog 2>&1 - elif [ "$compiler" = "ifort" ] - then - ./install_netcdf4_hdf5_seq.bash -prefix $MODEL/netcdf4_hdf5_seq \ - -compiler intel > $netcdflog 2>&1 - else - echo "unexpected compiler $compiler" ; exit - fi - - # LF rajout d'une verrue, pour une raison non encore expliquee, - # la librairie est parfois rangée dans lib64 et non dans lib - # par certains compilateurs - if [ ! -e lib -a -d lib64 ] ; then ln -s lib64 lib; fi - elif [[ "$with_xios" = "y" && ! -d $MODEL/netcdf4_hdf5 ]] - then - # download and compile hdf5 and netcdf, etc. using the - # install_netcdf4_hdf5.bash script - myget import/install_netcdf4_hdf5.bash - chmod u=rwx install_netcdf4_hdf5.bash - if [ "$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_lmdz.sh netcdf_OK `date` -fi # of if [ $netcdf = 1 ] - -# ncdfdir contains the directory where netcdf is installed -if [ $netcdf = 1 ] ; then - if [ "$with_xios" = "y" ] ; then - ncdfdir=$MODEL/netcdf4_hdf5 - else - ncdfdir=$MODEL/netcdf4_hdf5_seq - fi -elif [ $netcdf = 0 ] -then - ncdfdir=/usr -else - ncdfdir=$netcdf -fi - -#========================================================================= -if [[ ! -f $MODEL/modipsl/lib/libioipsl.a ]] -then - if [ $ioipsl = 1 ] ; then - #===================================================================== - echo OK ioipsl=$ioipsl - echo '##########################################################' - echo 'Installing MODIPSL, the installation package manager for the ' - echo 'IPSL models and tools' - echo '##########################################################' - echo `date` - - 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 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" ] - - echo install_lmdz.sh MODIPSL_OK `date` - - cd $MODEL/modipsl/modeles/IOIPSL/src - ioipsllog=`pwd`/ioipsl.log - echo '##########################################################' - echo 'Compiling IOIPSL, the interface library with Netcdf' - echo '##########################################################' - echo `date` - 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_lmdz.sh ioipsl_OK `date` - fi # of if [ $ioipsl = 1 ] -fi -# 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 - #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 - svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5 \ - XIOS - 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 - cd $MODEL/modipsl/modeles/ORCHIDEE - set +e ; svn upgrade ; set -e - if [ "$veget" = "CMIP6" ] ; then - veget_version=orchidee2.0 - orchidee_rev=6592 - else # specific orchidee revision newer than CMIP6, on 2_1 or 2_2 branches - veget_version=orchidee2.1 - orchidee_rev=$veget - if [ $veget -lt 4465 ] ; then - echo 'Stopping, ORCHIDEE version too old, script needs work on ' \ - 'the CPP flags to pass to makelmdz' - exit 1 - fi - set +e - # which branch is my version on? - orcbranch=`svn log -v -q svn://forge.ipsl.jussieu.fr/orchidee/ -r $veget |grep ORCHIDEE |head -1| sed -e 's:ORCHIDEE/.*$:ORCHIDEE:' | awk '{print $2}'` - # switch to that branch - echo IF YOU INSTALL ORCHIDEE THE VERY FIRST TIME, ASK for PASSWORD at \ - orchidee-help@listes.ipsl.fr - svn switch -r $veget --accept theirs-full \ - svn://forge.ipsl.jussieu.fr/orchidee/$orcbranch - svn log -r $veget | grep $veget - 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 $veget ; set -e - fi - # Correctif suite debug Jean-Zay - sed -i -e 's/9010 FORMAT(A52,F17.14)/9010 FORMAT(A52,F20.14)/' \ - src_stomate/stomate.f90 - opt_orc="-prod" ; if [ "$optim" = "-debug" ] ; then opt_orc="-debug" ; fi - - orchideelog=`pwd`/orchidee.log - echo '########################################################' - echo 'Compiling ORCHIDEE, the continental surface model ' - echo '########################################################' - echo Start of the first compilation of orchidee, in sequential mode: `date` - echo log file : $orchideelog - - export ORCHPATH=`pwd` - xios_orchid="-noxios" - if [ "$with_xios" = "y" ] ; then - xios_orchid="-xios" - fi - if [ -d tools ] ; then - ################################################################### - # 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 [ "$veget_version" == "false" ] ; then - veget_version=orchidee2.0 - fi - cd arch - sed -e s:"%COMPILER .*.$":"%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 ../ - - echo ./makeorchidee_fcm -j $xios_orchid $opt_orc -parallel none \ - -arch $arch - ./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel none \ - -arch $arch > $orchideelog 2>&1 - pwd - else # of "if [ -d tools ]" - if [ -d src_parallel ] ; then - liste_src="parallel parameters global stomate sechiba driver" - if [ "$veget_version" == "false" ] ; then - veget_version=orchidee2.0 - 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 # of "if [ -d tools ]" - echo install_lmdz.sh orchidee_compil_seq_OK `date` -fi # of if [ "$veget" != 'NONE' ] - - -#============================================================================ -# Ehouarn: the directory name LMDZ* depends on version/tar file... -if [ -d $MODEL/modipsl/modeles/LMD* ] ; then - echo '###############################################################' - echo 'Preparing LMDZ compilation : arch file, svn switch if needed...' - 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" && ! -f arch/arch-local.path ]] ; 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 'NETCDF95_INCDIR=$LMDGCM/../../include' >> arch-local.path - echo 'NETCDF95_LIBDIR=$LMDGCM/../../lib' >> 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 - set +e ; svn info | grep -q 'http:' - if [ $? = 0 ] ; then - svn switch --relocate http://svn.lmd.jussieu.fr/LMDZ \ - https://svn.lmd.jussieu.fr/LMDZ - fi - svn update $svnopt -fi -set -e - -################################################################## -# Retrieve the final svn release number, and adjust compilation -# options accordingly -mysvn=`svnversion . | egrep -o "[0-9]+"` - -# Option de compilation du rayonnement : depend de $mysvn ><= r4185 -opt_rad="" - -case $rad in - oldrad) iflag_rrtm=0 ; NSW=2 ; opt_rad="" ;; - rrtm) iflag_rrtm=1 ; NSW=6 - if [ $mysvn -le 4185 ] ; then - opt_rad="-rrtm true" - else - opt_rad="-rad rrtm" - fi ;; - ecrad) iflag_rrtm=2 ; NSW=6 ; opt_rad="-rad ecrad" ;; - *) echo Only oldrad rrtm ecrad for rad option ; exit -esac - -if [ $mysvn -le 4185 -a $rad = "ecrad" ] ; then - echo "ecrad only available for LMDZ rev starting with 4186 " ; exit -fi - -################################################################## - - -if [[ ! -f libf/misc/netcdf95.F90 && ! -d $MODEL/NetCDF95-0.2 ]] -then - cd $MODEL - myget import/NetCDF95-0.2.tar.gz - tar -xf NetCDF95-0.2.tar.gz - rm NetCDF95-0.2.tar.gz - cd NetCDF95-0.2 - mkdir build - cd build - cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=$ncdfdir \ - -DCMAKE_INSTALL_PREFIX=$MODEL/modipsl - make install - cd $MODEL/modipsl/modeles/LMDZ* -fi - -echo '##################################################################' -echo "Preparing script compile.sh for LMDZ compilation" -echo "It will only be run automatically if bench=1/tuto" -echo Here bench=$bench -echo '##################################################################' - -if [ "$env_file" != "" ] ; then - mv arch/arch-${arch}.env arch/arch-${arch}.orig - \cp -f $env_file arch/arch-${arch}.env -fi - -if [ $compile_with_fcm = 1 ] ; then - makelmdz="makelmdz_fcm $optim -arch $arch -j 8 " -else - makelmdz="makelmdz $optim -arch $arch" -fi - -# sequential compilation -if [ "$sequential" = 1 ] ; then - echo Sequential compilation command, saved in compile.sh: - echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp " \ - "-d ${grid_resolution} -v $veget_version gcm " - echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp " \ - "-d ${grid_resolution} -v $veget_version gcm " > compile.sh - chmod +x ./compile.sh - if [ $bench = 1 ] ; then - echo install_lmdz.sh start_lmdz_seq_compilation `date` - echo log file: $lmdzlog - ./compile.sh > $lmdzlog 2>&1 - echo install_lmdz.sh end_lmdz_seq_compilation `date` - fi -fi # fin sequential - -# compiling in parallel mode -if [ $parallel != "none" ] ; then - echo '##########################################################' - echo ' Parallel compile ' - echo '##########################################################' - echo "(after 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 $veget != 'NONE' ] ; then - cd arch - sed \ - -e s:"%COMPILER.*.$":"%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 in parallel mode `date` - echo logfile $orchideelog - echo "NOTE : to recompile it when necessary, use ./compile_orc.sh " \ - "in modipsl/modeles/ORCHIDEE" - echo ./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc \ - -parallel $parallel -arch $arch > compile_orc.sh - echo ./makeorchidee_fcm -j 8 $xios_orchid $opt_orc \ - -parallel $parallel -arch $arch >> compile_orc.sh - echo echo Now you must also recompile LMDZ, by running ./compile.sh \ - in modeles/LMDZ >> compile_orc.sh - chmod u+x compile_orc.sh - ./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc \ - -parallel $parallel -arch $arch > $orchideelog 2>&1 - ./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel $parallel \ - -arch $arch >> $orchideelog 2>&1 - echo End of ORCHIDEE compilation in parallel mode `date` - elif [ $veget != 'NONE' ] ; then - echo '##########################################################' - echo ' Orchidee version too old ' - echo ' Please update to new version ' - echo '##########################################################' - exit - fi # of [ -d src_parallel -a $veget != 'NONE' ] - - # 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 [ ${hostname:0:5} = jean- -a "$cosp" = "v2" ] ; then - - echo LMDZ compilation command in parallel mode, saved in compile.sh, \ - is : - echo "(ATTENTION le probleme de cospv2 sur jean-zay en mode prod " \ - "n est pas corrige ! )" - # ATTENTION le probleme de cospv2 sur jean-zay en mode prod n - # est pas corrige - echo ./$makelmdz -dev $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \ - $opt_makelmdz_xios -d \$resol -v $veget_version -mem \ - -parallel $parallel gcm >> compile.sh - echo ./$makelmdz -dev $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \ - $opt_makelmdz_xios -d \$resol -v $veget_version -mem \ - -parallel $parallel gcm - else - echo ./$makelmdz $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \ - $opt_makelmdz_xios -d \$resol -v $veget_version -mem \ - -parallel $parallel gcm >> compile.sh - echo ./$makelmdz $optim $OPT_MAKELMDZ $opt_rad $opt_cosp \ - $opt_makelmdz_xios -d \$resol -v $veget_version -mem \ - -parallel $parallel gcm - fi - chmod +x ./compile.sh - - if [ $bench = 1 ] ; then - echo Compiling LMDZ in parallel mode `date`, LMDZ log file: $lmdzlog - ./compile.sh > $lmdzlog 2>&1 - fi - -fi # of if [ $parallel != "none" ] - - -################################################################## -# Verification du succes de la compilation -################################################################## - -# Recherche de l'executable dont le nom a change au fil du temps ... -# suffix contains radiative option starting with revision 4186 -if [ $mysvn -ge 4186 ] ; then suff_exe=_${rad}${suff_exe} ; fi -gcm="" - -for exe in gcm.e bin/gcm_${grid_resolution}_phylmd${suff_exe}${suff_orc}.e -do - if [ -f $exe ] ; then gcm=$exe ; fi -done - -if [ "$gcm" = "" ] ; then - if [ $bench = 1 ] ; 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 !! ' `date` - echo '##########################################################' - echo The executable is $gcm -fi - -################################################################## -# Below, we run a benchmark if bench=1 or tuto -################################################################## - -if [ $bench = tuto ] ; then - myget Training/tutorial.tar ; tar xvf tutorial.tar ; cd TUTORIAL - ./init.sh - -elif [[ $bench = 1 && ! -d BENCH${grid_resolution} ]] ; then - # TOUTE CETTE SECTION DEVRAIT DISPARAITRE POUR UNE COMMANDE - # OU DES BENCHS PAR MOTS CLES COMME tuto - - echo '##########################################################' - echo ' Running a test run ' - echo '##########################################################' - - \rm -rf BENCH${grid_resolution} - bench=bench_lmdz_${grid_resolution} - echo install_lmdz.sh before bench download `date` - #wget http://www.lmd.jussieu.fr/~lmdz/Distrib/$bench.tar.gz - myget 3DBenchs/$bench.tar.gz - echo install_lmdz.sh after bench download `date` - tar xvf $bench.tar.gz - - if [ "$cosp" = "v1" -o "$cosp" = "v2" ] ; then - cd BENCH${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${grid_resolution} - cp ../DefLists/iodef.xml . - cp ../DefLists/context_lmdz.xml . - cp ../DefLists/field_def_lmdz.xml . - # A raffiner par la suite - echo A FAIRE : Copier les *xml en fonction de l option cosp - cp ../DefLists/field_def_cosp*.xml . - cp ../DefLists/file_def_hist*xml . - # adapt iodef.xml to use attached mode - sed -e 's@"using_server" type="bool">true@"using_server" type="bool">false@' \ - iodef.xml > tmp - \mv -f tmp iodef.xml - - # and convert all the enabled="_AUTO_" (for libIGCM) to enabled=.FALSE. - # except for histday - for histfile in file_def_hist*xml - do - if [ "$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" = "v1" ] ; 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 $histfile - fi - if [ "$cosp" = "v2" ] ; 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 - sed -e 's@src="./file_def_histmthCOSP_lmdz.xml"@src="./file_def_histmthCOSPv2_lmdz.xml"@' \ - $contextfile > tmp - \mv -f tmp $contextfile - sed -e 's@src="./file_def_histhfCOSP_lmdz.xml"@src="./file_def_histhfCOSPv2_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 $fieldfile - fi - - cd .. - fi - - # Cas Bensh avec ecrad - if [ "$rad" = "ecrad" ] ; then - cd BENCH${grid_resolution} - cp ../DefLists/namelist_ecrad . - cp -r ../libf/phylmd/ecrad/data . - cd .. - fi - - # Adjusting bench physiq.def to radiative code chosen - cd BENCH${grid_resolution} - sed -e 's/iflag_rrtm=.*.$/iflag_rrtm='$iflag_rrtm'/' \ - -e 's/NSW=.*.$/NSW='$NSW'/' physiq.def > tmpdef - \mv tmpdef physiq.def - cd .. - - 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 [ "$cosp" = "v1" -o "$cosp" = "v2" ] ; 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 [ ${hostname:0:5} = jean- ] ; then - . ../arch/arch-${arch}.env - 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 - # Add rebuild, using reb.sh if it is there - echo 'if [ -f reb.sh ] ; then' >> bench.sh - echo ' ./reb.sh histday ; ./reb.sh histmth ; ./reb.sh histhf ; ' \ - './reb.sh histins ; ./reb.sh stomate_history ; ' \ - './reb.sh sechiba_history ; ./reb.sh sechiba_out_2 ' >> bench.sh - echo 'fi' >> bench.sh - else - echo "./gcm.e > listing 2>&1" > bench.sh - fi - # Getting orchidee stuff - if [ $veget == 'CMIP6' ] ; then - #echo 'myget 3DBenchs/BENCHorch11.tar.gz' - #myget 3DBenchs/BENCHorch11.tar.gz - #tar xvzf BENCHorch11.tar.gz - echo 'myget 3DBenchs/BENCHCMIP6.tar.gz' - myget 3DBenchs/BENCHCMIP6.tar.gz - tar xvzf BENCHCMIP6.tar.gz - sed -e "s:VEGET=n:VEGET=y:" config.def > tmp - mv -f tmp config.def - if [ "$with_xios" = "y" ] ; then - cp ../../ORCHIDEE/src_xml/context_orchidee.xml . - echo '' \ - > add.tmp - cp ../../ORCHIDEE/src_xml/field_def_orchidee.xml . - cp ../../ORCHIDEE/src_xml/file_def_orchidee.xml . - cp ../../ORCHIDEE/src_xml/file_def_input_orchidee.xml . - if [ -f ../../ORCHIDEE/src_xml/context_input_orchidee.xml ] ; then - cp ../../ORCHIDEE/src_xml/context_input_orchidee.xml . - echo '' >> add.tmp - fi - sed -e '/id="LMDZ"/r add.tmp' iodef.xml > tmp - mv tmp iodef.xml - sed -e'{/sechiba1/ s/enabled="_AUTO_"/type="one_file" enabled=".TRUE."/}' \ - file_def_orchidee.xml > tmp - \mv -f tmp file_def_orchidee.xml - sed -e 's@enabled="_AUTO_"@type="one_file" enabled=".FALSE."@' \ - file_def_orchidee.xml > tmp - \mv -f tmp file_def_orchidee.xml - sed -e 's@output_level="_AUTO_"@output_level="1"@' \ - file_def_orchidee.xml > tmp - \mv -f tmp file_def_orchidee.xml - sed -e 's@output_freq="_AUTO_"@output_freq="1d"@' \ - file_def_orchidee.xml > tmp - \mv -f tmp file_def_orchidee.xml - sed -e 's@compression_level="4"@compression_level="0"@' \ - file_def_orchidee.xml > tmp - \mv -f tmp file_def_orchidee.xml - sed -e 's@XIOS_ORCHIDEE_OK = n@XIOS_ORCHIDEE_OK = y@' \ - orchidee.def > tmp - \mv -f tmp orchidee.def - fi - fi - - if [[ -f ../arch.env ]] - then - source ../arch.env - 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 # bench - - -################################################################# -# 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 -rad $rad -fi -#set -vx - -################################################################# -# sauvegarde des options veget pour utilisation eventuelle tutorial_prod -################################################################# -cd $MODEL/modipsl/modeles -#echo surface_env file created in $MODEL -echo 'veget='$veget > surface_env -#opt_veget="-v $veget_version" -#echo 'opt_veget="'$opt_veget\" >> surface_env -echo 'opt_veget="'-v $veget_version\" >> surface_env -echo 'orchidee_rev='$orchidee_rev >> surface_env -echo 'suforch='$suff_orc >> surface_env