Index: BOL/script_install/install_lmdz.sh
===================================================================
--- BOL/script_install/install_lmdz.sh	(revision 3983)
+++ BOL/script_install/install_lmdz.sh	(revision 4018)
@@ -34,5 +34,5 @@
 ###########################################################################
 
-echo install.sh DEBUT `date`
+echo install_lmdz.sh DEBUT `date`
 
 set -e
@@ -81,5 +81,5 @@
 # - NONE: bucket scheme (default)
 # - CMIP6: orchidee version used in CMIP exercise, rev 5661
-# - number: orchidee version number (not yet implemented)
+# - number: orchidee version number
 veget=NONE
 # choose the resolution for the bench runs
@@ -380,5 +380,5 @@
        echo 'Please choose a new one (ifort) and change the line'
        echo compiler=xxx
-       echo in the install.sh script and rerun it
+       echo in the install_lmdz.sh script and rerun it
        if [ `which gfortran44 | wc -w` -ne 0 ] ; then
           gfortran=gfortran44
@@ -559,11 +559,9 @@
 cd $MODEL
 myget src/modipsl_orc_cmip6.$version.tar.gz
-echo install.sh wget_OK `date`
+echo install_lmdz.sh wget_OK `date`
 gunzip modipsl_orc_cmip6.$version.tar.gz
 tar xvf modipsl_orc_cmip6.$version.tar
 \rm modipsl_orc_cmip6.$version.tar
 fi
-
-echo OK1
 
 if [ $netcdf = 1 ] ; then
@@ -607,13 +605,14 @@
   fi
 fi  # of if [ "$with_xios" = "n" ]
-echo install.sh netcdf_OK `date`
+echo install_lmdz.sh netcdf_OK `date`
 fi # of if [ $netcdf = 1 ]
 
 #======================================================================================
-echo OK2 ioipsl=$ioipsl
+echo OK ioipsl=$ioipsl
 echo '##########################################################'
 echo 'Installing MODIPSL, the installation package manager for the '
 echo 'IPSL models and tools'
 echo '##########################################################'
+echo `date`
 
 if [ $netcdf = 0 -o $netcdf = 1 ] ; then
@@ -671,4 +670,5 @@
   fi # of if [ "$use_shell" = "ksh" ]
 
+echo install_lmdz.sh MODIPSL_OK `date`
 #=======================================================================================
   cd $MODEL/modipsl/modeles/IOIPSL/src
@@ -677,4 +677,5 @@
   echo 'Compiling IOIPSL, the interface library with Netcdf'
   echo '##########################################################'
+  echo `date`
   echo log file : $ioipsllog
 
@@ -724,5 +725,5 @@
    
   fi
-  echo install.sh ioipsl_OK `date`
+  echo install_lmdz.sh ioipsl_OK `date`
 fi # of if [ $ioipsl = 1 ]
 # Saving ioipsl lib for possible parallel compile
@@ -737,24 +738,24 @@
   cd $MODEL/modipsl/modeles
   xioslog=`pwd`/xios.log
-  echo "log file: $xioslog"
   #wget http://www.lmd.jussieu.fr/~lmdz/Distrib/install_xios.bash
   myget import/install_xios.bash
   chmod u=rwx install_xios.bash
-   if [ ${hostname:0:5} = jean- ] ; then
-#    echo 'Need to work on install_xios implementation for jean-zay'
-#    exit
-   svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5 XIOS
-   cd XIOS/arch
-   svn update
-   cd ..
-   ./make_xios --prod --arch $arch --job 4 > xios.log 2>&1
-   else
+  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
-   if [ -f XIOS/lib/libxios.a ] ; then
-     echo "OK, XIOS library successfully generated"
-   fi
+  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
 
@@ -778,4 +779,5 @@
      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
@@ -793,7 +795,9 @@
   orchideelog=`pwd`/orchidee.log
   echo '########################################################'
-  echo 'Compiling ORCHIDEE, the continental surfaces model '
+  echo 'Compiling ORCHIDEE, the continental surface model '
   echo '########################################################'
+  echo Start of the first compilation of orchidee, in sequential mode: `date`
   echo log file : $orchideelog
+
   export ORCHPATH=`pwd`
   xios_orchid="-noxios"
@@ -828,10 +832,9 @@
      echo 'XIOS_LIBDIR="${ORCHDIR}/../XIOS/lib -lxios"' >> arch-local.path
      cd ../ 
-# compiling ORCHIDEE sequential mode
-	     
+
+     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
-     echo ./makeorchidee_fcm -j $xios_orchid $opt_orc -parallel none -arch $arch
-     echo End of the first compilation of orchidee ; pwd
-  else
+     pwd
+  else # of "if [ -d tools ]"
      if [ -d src_parallel ] ; then
        liste_src="parallel parameters global stomate sechiba driver"
@@ -846,7 +849,7 @@
         cd ..
      done
-  fi
-  echo install.sh orchidee_OK `date`
-fi # of if [ "$veget" = 1 ]
+  fi # of "if [ -d tools ]" 
+  echo install_lmdz.sh orchidee_compil_seq_OK `date`
+fi # of if [ "$veget" != 'NONE' ] 
 
 
@@ -854,7 +857,7 @@
 # Ehouarn: the directory name LMDZ* depends on version/tar file...
 if [ -d $MODEL/modipsl/modeles/LMD* ] ; then
-  echo '##########################################################'
-  echo 'Compiling LMDZ'
-  echo '##########################################################'
+  echo '###############################################################'
+  echo 'Preparing LMDZ compilation : arch file, svn switch if needed...'
+  echo '###############################################################'
   cd $MODEL/modipsl/modeles/LMD*
   LMDZPATH=`pwd`
@@ -930,24 +933,26 @@
 
 echo '##################################################################'
-echo Compile LMDZ
+echo "Preparing script compile.sh for LMDZ compilation" 
+echo "It will only be run automatically if bench=1" 
+echo Here bench=$bench
 echo '##################################################################'
-echo log file : $lmdzlog
 
 if [ "$env_file" != "" ] ; then mv arch/arch-${arch}.env arch/arch-${arch}.orig ; \cp -f $env_file arch/arch-${arch}.env ; fi
 
-echo install.sh avant_compilation `date`
 if [ $compile_with_fcm = 1 ] ; then makelmdz="makelmdz_fcm $optim -arch $arch -j 8 " ; else makelmdz="makelmdz $optim -arch $arch" ; fi
 
-# sequential compilation and bench
+# sequential compilation 
 if [ "$sequential" = 1 ] ; then
-echo "./$makelmdz $optim $OPT_MAKELMDZ $optim $opt_rad $opt_cosp -d ${grid_resolution} -v $veget_version gcm " >> compile.sh
-chmod +x ./compile.sh
-if [ $bench != 0 ] ; then ./compile.sh > $lmdzlog 2>&1 ; fi
-echo install.sh apres_compilation `date`
-
-
+  echo Sequential compilation command, saved in compile.sh:
+  echo "./$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 != 0 ] ; 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
@@ -956,5 +961,5 @@
   echo ' Parallel compile '
   echo '##########################################################'
-  # saving the sequential libs and binaries
+  echo "(after saving the sequential libs and binaries)"
   cd $MODEL/modipsl
   tar cf sequential.tar bin/ lib/
@@ -978,10 +983,14 @@
      mv tmp.fcm arch-local.fcm
      cd ../
-     echo compiling ORCHIDEE parallel mode
+     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 ./makeorchidee_fcm -j 8 -clean $xios_orchid $opt_orc -parallel $parallel -arch $arch
-     echo ./makeorchidee_fcm -j 8 $xios_orchid $opt_orc -parallel $parallel -arch $arch
+     echo End of ORCHIDEE compilation in parallel mode `date`
   elif [ $veget != 'NONE' ] ; then
     echo '##########################################################'
@@ -990,5 +999,6 @@
     echo '##########################################################'
     exit
-  fi # of if [ -d src_parallel ]
+  fi # of [ -d src_parallel -a $veget != 'NONE' ]
+
   # LMDZ
   cd $LMDZPATH
@@ -1010,5 +1020,7 @@
   echo resol=${grid_resolution} >> compile.sh
   if [ ${hostname:0:5} = jean- -a "$cosp" = "v2" ] ; then
-  echo ATTENTION le probleme de cospv2 sur jean-zay en mode prod n est pas corrige
+ 
+  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
@@ -1019,7 +1031,10 @@
   fi 
   chmod +x ./compile.sh
-  if [ $bench != 0 ] ; then ./compile.sh > $lmdzlog 2>&1 ; fi
-
-  echo "Compilation finished"
+
+  if [ $bench != 0 ] ; then 
+    echo Compiling LMDZ in parallel mode `date`
+    echo LMDZ log file: $lmdzlog
+    ./compile.sh > $lmdzlog 2>&1
+  fi
   
 fi # of if [ $parallel != "none" ]
@@ -1045,5 +1060,5 @@
 else
    echo '##########################################################'
-   echo 'Compilation successfull !! '
+   echo 'Compilation successfull !! ' `date`
    echo '##########################################################'
    echo The executable is $gcm
@@ -1062,8 +1077,8 @@
 \rm -rf BENCH${grid_resolution}
 bench=bench_lmdz_${grid_resolution}
-echo install.sh before bench download  `date`
+echo install_lmdz.sh before bench download  `date`
 #wget http://www.lmd.jussieu.fr/~lmdz/Distrib/$bench.tar.gz
 myget 3DBenchs/$bench.tar.gz
-echo install.sh after bench download  `date`
+echo install_lmdz.sh after bench download  `date`
 tar xvf $bench.tar.gz