Changeset 3922

Timestamp:

Jun 1, 2021, 6:25:58 PM (3 years ago)

Author:

Laurent Fairhead

Message:

New install with updated CMIP6 vegetation by default
LF/AS

File:

• BOL/script_install/install_lmdz.sh (modified) (31 diffs)

BOL/script_install/install_lmdz.sh

@@ -5 +5 @@
 # Usage  : install_lmdz.sh -help
 #
-# bash installation script of the LMDZ model on a Linux PC.
-# the model is downloaded in the following direcory tree
+# 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"
@@ -15 +17 @@
 #
 # The sources of the models can be found in the "modeles" directory.
-# In the present case, LMDZ5, ORCHIDEE and IOIPSL (handling of input-outputs
-# using the NetCDF library.
+# 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
-# munimal configuration.
+# minimal configuration.
 #
-# Prerequisites : pgf90/gfortran, wget , gunzip, tar, ... 
+# Prerequisites : pgf90/gfortran, bash or ksh, wget , gunzip, tar, ... 
 #
 # Modif 18/11/2011
 #    changes for option real 8.
-#      We comopile with -r8 (or equivalent) and -DNC_DOUBLE for the GCM
+#      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.
@@ -53 +55 @@
 }
 
-
+# 04_2021 : tester si r4 marche encore !
 #real=r4
 real=r8
-
-# WARNING !!!! For versions before october 2009, use
-# install.v2.sh instead of install.sh
 
 #########################################################################
@@ -64 +63 @@
 #########################################################################
 svn=""
-version=trunk
+#version=trunk
+version=20210320.trunk
 getlmdzor=1
 netcdf=1   #  1 for automatic installation
@@ -72 +72 @@
 check_linux=1
 ioipsl=1
-veget=1
-orchidee_rev=""  # default revision of ORCHIDEE
 bench=1
 pclinux=1
@@ -79 +77 @@
 compiler=gfortran
 SCM=0
-# use the old orchidee interface without the calculation of z0h
-no_z0h_orc=1
-# orchidee_version: defined to use the CMIP6 version of ORCHIDEE 
-#                   (and eventually anyother)
-#                   values=CMIP6
-orchidee_version=""
+# 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 (not yet implemented)
+veget=NONE
 # choose the resolution for the bench runs
 # grid_resolution= 32x24x11 or 48x36x19 for tests (test without ORCHIDEE)
@@ -163 +161 @@
     -gprof     to compile with -pg to enable profiling with gprof
 
-    -orchidee_rev "svn_release" : upgrade included ORCHIDEE model to
-               given svn release number (default: $orchidee_rev)
-               (only valid for orchidee2.0 and later)
-
     -cosp      to compile with cosp(v1)
  
@@ -185 +179 @@
     -env_file  specify an arch.env file to overwrite the existing one
 
-    -orc_version      to chose some tagged ORCHIDEE version (CMIP6 only for the present)
+    -veget surface model to run [NONE/CMIP6/xxxx]
 
 ........fin
@@ -201 +195 @@
      "-cosp2") cosp2=1 ; opt_cosp2="-cosp2 true" ; shift ;;
      "-cospv2") cospv2=1 ; opt_cospv2="-cospv2 true" ; shift ;;
-     "-orchidee_rev") orchidee_rev=$2 ; shift ; shift ;;
      "-nofcm") compile_with_fcm=0 ; shift ;;
      "-SCM") SCM=1 ; shift ;;
@@ -217 +210 @@
      "-xios") with_xios="y" ; shift ;;
      "-env_file") env_file=$2 ; shift ; shift ;;
-     "-orc_version") orchidee_version=$2 ; shift ; shift ;;
+     "-veget") veget=$2 ; shift ; shift ;;
      *) ./install_lmdz.sh -h ; exit
    esac
 done
 
-if [ $parallel = none ] ; then sequential=1 ; else sequential=0 ; fi 
+# Check on veget version
+#if [ "$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
@@ -271 +284 @@
             o_ins_make="-t g95" ;;
             
-#   *)       if [ $parallel = none -o ] ; then
-   *)       if [ $parallel = none ] ; then
+   *)       if [ $parallel = none -o -f /usr/bin/mpif90 ] ; then
                 path_mpi=`which mpif90 | sed -e s:/mpif90::` ;
                 if [ -d /usr/lib64/openmpi ] ; then
@@ -279 +291 @@
                   root_mpi="/usr"
                 fi
-                # Ehouarn: but why do we need path_mpi and root_mpi 
-                # if not in parallel ?
+            # For Scientifique Linux with gfortran at LMD :
+            elif [ -f /usr/lib64/openmpi/1.4.5-gfortran/bin/mpif90 -a $compiler = "gfortran" ] ; then
+                path_mpi=/usr/lib64/openmpi/1.4.5-gfortran/bin ;
+                root_mpi=/usr/lib64/openmpi/1.4.5-gfortran ;
+                export LD_LIBRARY_PATH=${root_mpi}/lib:$LD_LIBRARY_PATH
+            # For Scientifique Linux with ifort at LMD :
+            elif [ -f /usr/lib64/openmpi/1.4.5-ifort/bin/mpif90 -a $compiler = "ifort" ] ; then
+                path_mpi=/usr/lib64/openmpi/1.4.5-ifort/bin ;
+                root_mpi=/usr/lib64/openmpi/1.4.5-ifort ;
+                export LD_LIBRARY_PATH=${root_mpi}/lib:$LD_LIBRARY_PATH
+            # For Scientifique Linux with pgf90 at LMD :
+            elif [ -f /usr/lib64/openmpi/1.4.5-ifort/bin/mpif90 -a $compiler = "pgf90" ] ; then
+                path_mpi=/usr/lib64/openmpi/1.4.5-pgf/bin ;
+                root_mpi=/usr/lib64/openmpi/1.4.5-pgf ;
+                export LD_LIBRARY_PATH=${root_mpi}/lib:$LD_LIBRARY_PATH
             else
-               path_mpi=`which mpif90 | sed -e s:/mpif90::` ;
-               root_mpi=`which mpif90 | sed -e s:/bin/mpif90::` ;
-               if [ ! -x ${path_mpi}/mpif90 ] ; then 
-                 echo "Error: cannot find mpif90" ;
-                 exit ;
-               fi ;
-               export LD_LIBRARY_PATH=${root_mpi}/lib:$LD_LIBRARY_PATH
+               echo "Cannot find mpif90" ;
+               if [ $parallel = none ] ; then exit ; fi ;
             fi ;
             par_comp=${path_mpi}/mpif90 ;
@@ -468 +488 @@
 
 ##########################################################################
-# If installing on know machines such as IBM x3750 (Ada)
-# at IDRIS, don't check for available software and don"t install netcdf
+# 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
@@ -485 +505 @@
 
 
-
 mkdir -p $MODEL
 echo $MODEL
 MODEL=`( cd $MODEL ; pwd )` # to get absolute path, if necessary
-
-
-
-# Option -fendian=big is only to be used with ARPEGE1D.
-# The -r8 should probably be avoided if running on 32 bit machines
-# Option r8 is not mandatory and generates larger executables.
-# It is however mandatory if using ARPEGE1D
-# Better optimization options might be a better choice (e.g. -O3)
 
 
@@ -504 +515 @@
 echo '################################################################'
 
-#### Ehouarn: test if ksh and/or bash are available
-#use_shell="ksh" # default: use ksh
-#if [ "`which ksh`" = "" ] ; then
-#  echo "no ksh ... we will use bash"
-  use_shell="bash"
-  if [ "`which bash`" = "" ] ; then
-    echo "bash needed!! Install it!"
-  fi
-#fi
-
+#### 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
@@ -542 +554 @@
 echo '##########################################################'
 cd $MODEL
-myget src/modipsl.$version.tar.gz
+myget src/modipsl_orc_cmip6.$version.tar.gz
 echo install.sh wget_OK `date`
-gunzip modipsl.$version.tar.gz
-tar xvf modipsl.$version.tar
-\rm modipsl.$version.tar
-
+gunzip modipsl_orc_cmip6.$version.tar.gz
+tar xvf modipsl_orc_cmip6.$version.tar
+\rm modipsl_orc_cmip6.$version.tar
 fi
 
@@ -569 +580 @@
   cd netcdf-4.0.1
 
-  # seds to possibly use gfortran44 obsolete nowdays (Ehouarn: 10/2017)
-  #sed -e 's/gfortran/'$gfortran'/g' configure >| tmp ; mv -f tmp configure ; chmod +x configure
   localdir=`pwd -P`
   ./configure --prefix=$localdir --enable-shared --disable-cxx
@@ -748 +757 @@
 #============================================================================
 veget_version=false
-if [ "$veget" = 1 ] ; then
+if [ "$veget" != 'NONE' ] ; then
   cd $MODEL/modipsl/modeles/ORCHIDEE
-  if [ "$orchidee_version" = "CMIP6" ] ; then
-    set +e
-    svn upgrade
-    svn switch -r 5661 --accept theirs-full svn://forge.ipsl.jussieu.fr/orchidee/tags/ORCHIDEE_2_0/ORCHIDEE
-    orchidee_rev=5661
-    veget_version=orchidee2.0
-    no_z0h_orc=0
-    set -e
+  set +e ; svn upgrade ; set -e
+  if [ "$veget" = "CMIP6" ] ; then
+    veget_version=orchidee2.0  
+    orchidee_rev=6592
+  else # specific orchidee revision
+     set +e
+     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 $veget ; set -e  
   fi
   # Correctif suite debug Jean-Zay
@@ -773 +787 @@
 # Pour les experts qui voudraient changer de version d'orchidee.
 # Attention : necessite d'avoir le password pour orchidee
-      set +e ; svn upgrade ; set -e
-      if [ "$orchidee_rev" != "" ] ; then
-          # test qu'on est sur la bonne branche pour faire le update
-          set +e
-          svn log -r $orchidee_rev | grep  $orchidee_rev
-          if [  $? -gt 0 ] ; then
-              echo 'Cannot update ORCHIDEE as not on the right branch for ORCHIDEE'
-              exit
-          fi
-          set -e
-          set +e ; svn update -r $orchidee_rev ; set -e 
-      fi
+
       # Correctif suite debug Jean-Zay
       if [ -f src_global/time.f90 ] ; then sed -i -e 's/CALL tlen2itau/\!CALL tlen2itau/' src_global/time.f90 ; fi
@@ -815 +818 @@
        liste_src="parallel parameters global stomate sechiba driver"
        if [ "$veget_version" == "false" ] ; then veget_version=orchidee2.0 ; fi
-     else
-       # Obsolete, for ORCHIDEE_beton only
-       liste_src="parameters stomate sechiba "
-       # A trick to compile ORCHIDEE depending on if we are using real*4 or real*8
-       cd src_parameters ; \cp reqdprec.$real reqdprec.f90 ; cd ..
-       if [ "$veget_version" == "false" ] ; then veget_version=orchidee1.9 ; fi
      fi
      for d in $liste_src ; do src_d=src_$d
@@ -836 +833 @@
 
 #============================================================================
-# Ehouarn: it may be directory LMDZ4 or LMDZ5 depending on tar file...
+# Ehouarn: the directory name LMDZ* depends on version/tar file...
 if [ -d $MODEL/modipsl/modeles/LMD* ] ; then
   echo '##########################################################'
@@ -901 +898 @@
 ##################################################################
 
-set +e ; svn upgrade
+
+set +e ; svn upgrade ; set -e
 if [ "$svn" = "last" ] ; then svnopt="" ; else svnopt="-r $svn" ; fi
 if [ "$svn" != "" ] ; then
@@ -921 +919 @@
 echo install.sh avant_compilation `date`
 if [ $compile_with_fcm = 1 ] ; then makelmdz="makelmdz_fcm $optim -arch $arch -j 8 " ; else makelmdz="makelmdz $optim -arch $arch" ; fi
-
-# use the orchidee interface that has no z0h
-if [ "$no_z0h_orc" = 1 ] ; then
-veget_version="$veget_version -cpp ORCHIDEE_NOZ0H"
-fi
 
 # sequential compilation and bench
@@ -953 +946 @@
   #
   cd $ORCHPATH
-  if [ -d src_parallel -a $veget = 1 ] ; then
+  if [ -d src_parallel -a $veget != 'NONE' ] ; then
      cd arch
      sed  \
@@ -972 +965 @@
      echo ./makeorchidee_fcm -j 8 -clean -noxios $opt_orc -parallel $parallel -arch $arch
      echo ./makeorchidee_fcm -j 8 -noxios $opt_orc -parallel $parallel -arch $arch
-  elif [ $veget = 1 ] ; then
+  elif [ $veget != 'NONE' ] ; then
     echo '##########################################################'
     echo ' Orchidee version too old                                 '
@@ -1011 +1004 @@
 fi # of if [ $parallel != "none" ]
 
-#echo LLLLLLLLLLLLLLLLLLLLLLLLLLL
-if [ "$gfortran" = "gfortran44" ] ; then
-    echo Your gfortran compiler was too old so that the model was automatically
-    echo compiled with gfortran44 instead. It can not be used in parallel mode.
-    echo You can change the compiler at the begining of the install.sh
-    echo script and reinstall.
-fi
 
 ##################################################################
@@ -1025 +1011 @@
 # Recherche de l'executable dont le nom a change au fil du temps ...
 gcm=""
-for exe in gcm.e bin/gcm_${grid_resolution}_phylmd_seq_orch.e bin/gcm_${grid_resolution}_phylmd_seq.e bin/gcm_${grid_resolution}_phylmd_para_mem_orch.e bin/gcm_${grid_resolution}_phylmd_para_mem.e  ; do
-   if [ -f $exe ] ; then gcm=$exe ; fi
+#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
 done
 
@@ -1161 +1147 @@
    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
@@ -1167 +1154 @@
    # 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 ; ./reh.sh histins' >> 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
 fi
 echo EXECUTION DU BENCH
@@ -1196 +1194 @@
 echo '##########################################################'
 
-fi
+fi # bench
 
 
@@ -1211 +1209 @@
 ./run.sh
 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
+   
+
+
+