Bugfixes and hard coded path removal

Hard coded path are removed
env.sh added to hep update environment variables (in particular PATH)
Update the separator used to build pack directori names

INSTALL_pack

@@ -5,16 +5,16 @@ This document describes how to build reference packs on sxphynh and belenos.
 The following instructions focuse on the 'phyex' pack in which the physics
 have been put in a new gmkpack project, named phyex.
 
-An other pack ('main') have been produced as a super-reference without code
-move. Only a recompilation have been done.
+Another pack ('main') have been produced as a super-reference without code
+move. Only a recompilation has been done.
 
 This document ends with instruction on how to use these packs. This step
 is now automatically performed with the prep_code.sh script.
 
-On belenos, it is not possible to use the wget used on sxphynh. The file
-must be put on a reachable place. On sxphynh:
-cd /cnrm/phynh/data1/riette/DATA/202005_externalisation_physique/pack/
-wget http://anonymous:mto@webdav.cnrm.meteo.fr/public/algo/khatib/src/48t1_main.01.tgz
+In these instructions, the git package have been installed in:
+sxphynh:/cnrm/phynh/data1/riette/DATA/202005_externalisation_physique
+belenos:/scratch/work/riette/202005_externalisation_physique
+Pathes must be adapted.
 
 #######################################################################
 Creation on sxphynh, to be done only once and to be shared among users:
@@ -65,7 +65,7 @@ gmkpack -a -r 48t1 -b phyex -n $version -l MIMPIIFC1805 -o 2y -p masterodb -h /s
 
 #populate main pack with source code
 cd /scratch/work/riette/202005_externalisation_physique/pack/48t1_phyex.${version}.MIMPIIFC1805.2y/src/local/
-scp sxphynh.cnrm.meteo.fr:/cnrm/phynh/data1/riette/DATA/202005_externalisation_physique/pack/48t1_main.01.tgz .
+ssh sxphynh.cnrm.meteo.fr "wget http://anonymous:mto@webdav.cnrm.meteo.fr/public/algo/khatib/src/48t1_main.01.tgz -O -" > 48t1_main.01.tg
 tar xf 48t1_main.01.tgz
 rm -f 48t1_main.01.tgz
 for rep in turb micro conv; do

check_commit.sh

@@ -17,19 +17,21 @@ set -e
 specialPack="ori split recompil"
 availTests="small_3D,small_3D_np2,small_3D_alt1,small_3D_alt2,small_3D_alt3,small_3D_alt4,small_3D_alt5"
 defaultTest="small_3D"
+separator='_' #- be carrefull, gmkpack (at least on belenos) has multiple allergies (':', '.', '@')
+              #- seprator must be in sync with prep_code.sh separator
 
-if [ $(hostname | cut -c 1-7) == 'belenos' ]; then
+PHYEXTOOLSDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+
+dirpack=$PHYEXTOOLSDIR/pack
+dirconf=$PHYEXTOOLSDIR/conf_tests
+if [ $(hostname | cut -c 1-7) == 'belenos' -o $(hostname | cut -c 1-7) == 'taranis' ]; then
   HPC=1
-  dirpack=/scratch/work/riette/202005_externalisation_physique/pack
-  dirconf=/scratch/work/riette/202005_externalisation_physique/conf_tests
   gmkpack_l=MIMPIIFC1805
   gmkpack_o=2y
   defaultMainPackVersion=01
   defaultRef=split
 else
   HPC=0
-  dirpack=/cnrm/phynh/data1/riette/DATA/202005_externalisation_physique/pack
-  dirconf=/cnrm/phynh/data1/riette/DATA/202005_externalisation_physique/conf_tests
   gmkpack_l=MPIGFORTRAN920DBL
   gmkpack_o=xfftw
   defaultMainPackVersion=01
@@ -99,6 +101,7 @@ while [ -n "$1" ]; do
 done
 
 HOMEPACK=${HOMEPACK:=$HOME/pack}
+
 function exescript () {
   #usage: exescript <output file> <script> [arg [arg ...]]
   output=$1
@@ -139,7 +142,7 @@ fi
 fromdir=''
 if echo $commit | grep '/' > /dev/null; then
   fromdir=$commit
-  packBranch=$(echo $commit | sed 's/\//@/g' | sed 's/:/@/g')
+  packBranch=$(echo $commit | sed 's/\//'${separator}'/g' | sed 's/:/'${separator}'/g' | sed 's/\./'${separator}'/g')
   name="PHYEX/48t1_${packBranch}.01.${gmkpack_l}.${gmkpack_o}"
   [ $suppress -eq 1 -a -d $HOMEPACK/$name ] && rm -rf $HOMEPACK/$name
 elif echo $specialPack | grep -w $commit > /dev/null; then
@@ -154,7 +157,7 @@ if [ ! -z "${reference-}" ]; then
   reffromdir=''
   if echo $reference | grep '/' > /dev/null; then
     reffromdir=$reference
-    name="PHYEX/48t1_$(echo $reference | sed 's/\//@/g' | sed 's/:/@/g').01.${gmkpack_l}.${gmkpack_o}"
+    name="PHYEX/48t1_$(echo $reference | sed 's/\//'${separator}'/g' | sed 's/:/'${separator}'/g' | sed 's/\./'${separator}'/g').01.${gmkpack_l}.${gmkpack_o}"
   elif echo $specialPack | grep -w $reference > /dev/null; then
     refname="PHYEX/$reference"
   else
@@ -190,7 +193,11 @@ if [ $compilation -eq 1 ]; then
     gmkpack -a -r 48t1 -b ${packBranch} -n 01 -l ${gmkpack_l} -o ${gmkpack_o} -p masterodb -h $HOMEPACK/PHYEX
     #Populate (we keep everything from the official source code except internals and module subdirectories of mpa)
     cd $HOMEPACK/$name/src/local/
-    scp sxphynh.cnrm.meteo.fr:/cnrm/phynh/data1/riette/DATA/202005_externalisation_physique/pack/48t1_main.01.tgz .
+    if [ $HPC -eq 1 ]; then
+      ssh sxphynh.cnrm.meteo.fr "wget http://anonymous:mto@webdav.cnrm.meteo.fr/public/algo/khatib/src/48t1_main.01.tgz -O -" > 48t1_main.01.tgz
+    else
+      wget http://anonymous:mto@webdav.cnrm.meteo.fr/public/algo/khatib/src/48t1_main.01.tgz
+    fi
     tar xf 48t1_main.01.tgz
     rm -f 48t1_main.01.tgz
     for rep in turb micro conv; do
@@ -211,7 +218,7 @@ if [ $compilation -eq 1 ]; then
     subs="" #There is nothing to exclude from compilation because (normally) only needed files are copied into the pack
   fi
 
-  MNH_EXPAND_DIR=$(dirname "${BASH_SOURCE[0]}")/mnh_expand
+  MNH_EXPAND_DIR=$PHYEXTOOLSDIR/mnh_expand
   export PATH=$MNH_EXPAND_DIR/filepp:$MNH_EXPAND_DIR/MNH_Expand_Array:$PATH
 
   cd $HOMEPACK/$name/src/local/phyex
@@ -221,10 +228,10 @@ if [ $compilation -eq 1 ]; then
     expand_options=""
   fi
   subs="$subs -s turb -s micro -s aux -s ext -s conv -s externals" #externals is the old name for aux/ext
-  prep_code=$(dirname "${BASH_SOURCE[0]}")/prep_code.sh
+  prep_code=$PHYEXTOOLSDIR/prep_code.sh
   if [ "$fromdir" == '' ]; then
     echo "Clone repository, and checkout commit $commit (using prep_code.sh)"
-    if [[ $commit == arome@* ]]; then
+    if [[ $commit == arome${separator}* ]]; then
       $prep_code -c $commit PHYEX #This commit is ready for inclusion
     else
       $prep_code -c $commit $expand_options $subs -m arome PHYEX
@@ -366,7 +373,7 @@ if [ $check -eq 1 ]; then
             [ ! -d /d0/images/$USER ] && mkdir /d0/images/$USER
             ddh_images="$ddh_images /d0/images/$USER/ddh_diff_${tag}.png"
           fi
-          cmd="$(dirname "${BASH_SOURCE[0]}")/comp_DDH.py"
+          cmd="$PHYEXTOOLSDIR/comp_DDH.py"
           if [ ! -x $cmd ]; then
             echo "Command not found: \"$cmd\""
             exit 10
@@ -375,7 +382,7 @@ if [ $check -eq 1 ]; then
           output='stdout'
         elif [ $(basename $file) == NODE.001_01 ]; then
           #Output listing
-          cmd="$(dirname "${BASH_SOURCE[0]}")/diffNODE.001_01"
+          cmd="$PHYEXTOOLSDIR/diffNODE.001_01"
           if [ ! -x $cmd ]; then
             echo "Command not found: \"$cmd\""
             exit 11

env.sh

+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+
+MNH_EXPAND_DIR=$DIR/mnh_expand
+export PATH=$DIR:$MNH_EXPAND_DIR/filepp:$MNH_EXPAND_DIR/MNH_Expand_Array:$PATH

prep_code.sh

@@ -39,7 +39,9 @@ function usage {
   echo "To use mnh_expand... it must be installed (alongside the filepp tool)"
 }
 
-full_command="${BASH_SOURCE[0]} $@"
+full_command="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd ) $@"
+separator='_' #- be carrefull, gmkpack (at least on belenos) has multiple allergies (':', '.', '@')
+              #- seprator must be in sync with prep_code.sh separator
 
 directory=""
 checkout_point=""
@@ -73,7 +75,7 @@ fi
 
 ###### BRANCH OR NOT BRANCH
 if [ -n "${checkout_point-}" -a -n "${model-}" -a $push == 1 ]; then
-  branch=${model}@${checkout_point}
+  branch=${model}${separator}${checkout_point}
 fi
 
 ###### WORKING DIRECTORY