diff --git a/README.md b/README.md
index 3a92475719248be492eeb91b9e75c63380b71148..b9629700f0270caa806041b07fdc19a0a5345cb1 100644
--- a/README.md
+++ b/README.md
@@ -16,4 +16,7 @@ Instructions can be found in INSTALL file.
Help on check_commit_ial.sh, check_commit_mesonh.sh and prep_code.sh can be printed with the '-h' option.
-For check_commit_mesonh.sh, it is mandatory to source the env.sh file
+For check_commit_mesonh.sh the following environment variables can be set:
+* MNHPACK: directory in which MNH pack will be created (default is $HOME/MesoNH/PHYEX)
+* REFDIR: directory in which reference pack can be found (default is the pack directory near the check_commit_mesonh.sh file)
+* TARGZDIR: directory in which the tar.gz file can be found (default is the pack directory near the check_commit_mesonh.sh file)
diff --git a/check_commit_ial.sh b/check_commit_ial.sh
index 6a44641839699f4b8f5f6bfd342b302f70061c52..24f841a2e5f9aca9495da86064a786b56f3ed9c5 100755
--- a/check_commit_ial.sh
+++ b/check_commit_ial.sh
@@ -218,11 +218,11 @@ if [ $compilation -eq 1 ]; then
reftree='local'
subs="" #There is nothing to exclude from compilation because (normally) only needed files are copied into the pack
fi
+ cd $HOMEPACK/$name/src/local/phyex
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
if [ $useexpand == 1 ]; then
expand_options="-D MNH_EXPAND -D MNH_EXPAND_LOOP"
else
diff --git a/check_commit_mesonh.sh b/check_commit_mesonh.sh
index 167a45769a6125c07b4eee3456e7c02a9553747d..e3ae44e6e2d728b995088edcb54eca4307e673c4 100755
--- a/check_commit_mesonh.sh
+++ b/check_commit_mesonh.sh
@@ -8,19 +8,27 @@ set -e
# Repertoire où MNH-V5-5-0_PHYEX.tar.gz modifie pour accueillir PHYEX se trouve
#TARGZDIR=$HOME
-MNHPACK=${MNHPACK:=$HOME/MesoNH/PHYEX}
-PHYEXTOOLSDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+availTests="007_16janvier/008_run2"
+defaultTest="007_16janvier/008_run2"
+separator='_' #- be carrefull, gmkpack (at least on belenos) has multiple allergies (':', '.', '@')
+ #- seprator must be in sync with prep_code.sh separator
+PHYEXTOOLSDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
function usage {
- echo "Usage: $0 [-h] [-c] [-r] [-C] commit reference"
- echo "commit commit hash"
- echo "reference commit hash or nothing for ref"
+ echo "Usage: $0 [-h] [-c] [-r] [-C] [-s] [--expand] commit reference"
+ echo "commit commit hash (or a directory)"
+ echo "reference commit hash or a directory or nothing for ref"
echo "-s suppress compilation pack"
echo "-c performs compilation"
- echo "-r runs the tests, if option appears twice, run is also executed on only 2 procs (instead of 4 procs)"
+ echo "-r runs the tests"
echo "-C checks the result against the reference"
+ echo "--expand use mnh_expand (code will use do loops)"
echo ""
echo "If nothing is asked (compilation, running, check) everything is done"
+ echo
+ echo "The directory (for commit only, not ref) can take the form server:directory"
+ echo
+ echo "If using a directory (for commit or reference) it must contain at least one '/'"
}
compilation=0
@@ -28,7 +36,9 @@ run=0
check=0
commit=""
reference=""
+tests=""
suppress=0
+useexpand=0
while [ -n "$1" ]; do
case "$1" in
@@ -37,6 +47,7 @@ while [ -n "$1" ]; do
'-c') compilation=1;;
'-r') run=$(($run+1));;
'-C') check=1;;
+ '--expand') useexpand=1;;
#-b) param="$2"; shift ;;
#--) shift; break ;;
*) if [ -z "${commit-}" ]; then
@@ -53,6 +64,17 @@ while [ -n "$1" ]; do
shift
done
+[ "$reference" == 'REF' ] && reference="" #Compatibility with check_commit_arome.sh
+
+MNHPACK=${MNHPACK:=$HOME/MesoNH/PHYEX}
+REFDIR=${REFDIR:=$PHYEXTOOLSDIR/pack/}
+TARGZDIR=${TARGZDIR:=$PHYEXTOOLSDIR/pack/}
+if [ -z "${tests-}" ]; then
+ tests=$defaultTest
+elif [ $tests == 'ALL' ]; then
+ tests=$availTests
+fi
+
if [ $compilation -eq 0 -a \
$run -eq 0 -a \
$check -eq 0 ]; then
@@ -66,42 +88,53 @@ if [ -z "${commit-}" ]; then
exit 2
fi
-#if [ $check -eq 1 -a -z "${reference-}" ]; then
-# echo "To perform a comparison two commit hashes are mandatory on the command line"
-# exit 3
-#fi
-
-if echo $commit | grep '/' > /dev/null; then
- name=MNH-V5-5-0-$(echo $commit | sed 's/\//_/g')
- [ $suppress -eq 1 -a -d $MNHPACK/$name ] && rm -rf $MNHPACK/$name
-else
- name=MNH-V5-5-0-$commit
- [ $suppress -eq 1 -a -d $MNHPACK/$name ] && rm -rf $MNHPACK/$name
-fi
-
#Two possibilities are supported for the simulations
# - they can be done in the the pack we are currently checking
# - they can be done in the reference pack
#They are done in the current pack except if the reference pack
#already contains a tested simulation
-run_in_ref=$(ls -d $REFDIR/MNH-V5-5-0/MY_RUN/KTEST/007_16janvier/008_run2_* | tail -1 |wc -l)
+run_in_ref=$(ls -d $REFDIR/MNH-V5-5-0/MY_RUN/KTEST/007_16janvier/008_run2_* 2> /dev/null | tail -1 |wc -l)
+
+#Name and directory for compiling and executing user pack
+fromdir=''
+if echo $commit | grep '/' > /dev/null; then
+ fromdir=$commit
+ tag=$(echo $commit | sed 's/\//'${separator}'/g' | sed 's/:/'${separator}'/g' | sed 's/\./'${separator}'/g')
+else
+ tag=$commit
+fi
+name=MNH-V5-5-0-$tag
+[ $suppress -eq 1 -a -d $MNHPACK/$name ] && rm -rf $MNHPACK/$name
+if [ $run_in_ref -eq 1 ]; then
+ path_user_beg=$REFDIR/MNH-V5-5-0 #pack directory containing the simulation
+ path_user_end=_$tag #to be appended to the 'run' simulation directory
+else
+ path_user_beg=$MNHPACK/$name #pack directory containing the simulation
+ path_user_end= #to be appended to the 'run' simulation directory
+fi
+
+#Name and directory for the reference
+reffromdir=''
+if echo $reference | grep '/' > /dev/null; then
+ reffromdir=$reference
+ reftag=$(echo $reference | sed 's/\//'${separator}'/g' | sed 's/:/'${separator}'/g' | sed 's/\./'${separator}'/g')
+else
+ reftag=$reference
+fi
+refname=MNH-V5-5-0-$reftag
if [ $run_in_ref -eq 1 ]; then
- path_user_beg=$REFDIR/MNH-V5-5-0
- path_user_end=_$commit
path_ref_beg=$REFDIR/MNH-V5-5-0
if [ "$reference" == "" ]; then
path_ref_end=
else
- path_ref_end=_$reference
+ path_ref_end=_$reftag
fi
else
- path_user_beg=$MNHPACK/$name
- path_user_end=
path_ref_end=
if [ "$reference" == "" ]; then
path_ref_beg=$REFDIR/MNH-V5-5-0
else
- path_ref_beg=$MNHPACK/MNH-V5-5-0-$reference
+ path_ref_beg=$MNHPACK/MNH-V5-5-0-$reftag
fi
fi
@@ -116,48 +149,42 @@ if [ $compilation -eq 1 ]; then
# Prepare the pack
cd $MNHPACK
cp $TARGZDIR/MNH-V5-5-0_PHYEX.tar.gz .
- tar xvfz MNH-V5-5-0_PHYEX.tar.gz
+ tar xfz MNH-V5-5-0_PHYEX.tar.gz
rm MNH-V5-5-0_PHYEX.tar.gz
mv MNH-V5-5-0 $name
cd $name/src
+ rm -rf PHYEX
- cd $MNHPACK
- echo "Clone repository, and checkout commit $commit"
- git clone https://github.com/QuentinRodier/PHYEX.git
- cd PHYEX
- git checkout $commit
-
- cd src/common/turb
- # Rename all *.F90 to *.f90
- for rep in turb micro aux; do
- cd ../$rep
- for f in *.F90; do
- mv -- "$f" "${f%.F90}.f90"
- done
- done
- cd ../../../
+ MNH_EXPAND_DIR=$PHYEXTOOLSDIR/mnh_expand
+ export PATH=$MNH_EXPAND_DIR/filepp:$MNH_EXPAND_DIR/MNH_Expand_Array:$PATH
- for rep in turb micro conv ext aux; do
- [ ! -d ../$rep ] && mkdir ../$rep
- [ -d src/common/$rep ] && mv -f src/common/$rep/* ../$rep/
- [ -d src/mesonh/$rep ] && mv -f src/mesonh/$rep/* ../$rep/
- touch ../$rep/*
- done
- cd ..
- # Move PHYEX files inside MNH/src/PHYEX
- for rep in turb micro conv aux; do
- mv $rep/* $name/src/PHYEX/$rep/.
- rmdir $rep
- done
+ if [ $useexpand == 1 ]; then
+ expand_options="-D MNH_EXPAND -D MNH_EXPAND_LOOP"
+ else
+ expand_options=""
+ fi
+ subs="-s turb -s micro -s aux -s ext -s conv"
+ prep_code=$PHYEXTOOLSDIR/prep_code.sh
+ if [ "$fromdir" == '' ]; then
+ echo "Clone repository, and checkout commit $commit (using prep_code.sh)"
+ if [[ $commit == mesonh${separator}* ]]; then
+ $prep_code --renameFf -c $commit PHYEX #This commit is ready for inclusion
+ else
+ $prep_code --renameFf -c $commit $expand_options $subs -m mesonh PHYEX
+ fi
+ else
+ echo "Copy $fromdir"
+ scp -q -r $fromdir PHYEX
+ $prep_code --renameFf $expand_options $subs -m mesonh PHYEX
+ fi
+ rm -rf PHYEX/.git
+ find PHYEX -type f -exec touch {} \; #to be sure a recompilation occurs
# Move manually ext/ files in src/MNH
- mv -f ext/* $name/src/MNH/.
-
- # Clean folder
- rmdir ext
- rm -Rf PHYEX
+ mv -f PHYEX/ext/* MNH/
+ rmdir PHYEX/ext
- cd $name/src/PHYEX/turb
+ cd $MNHPACK/$name/src/PHYEX/turb
# Delete files of MNH-V5-5-0/src/MNH and MNH/src/LIB/SURCOUCHE/src with same name
for rep in turb micro conv aux ; do
cd ../$rep
@@ -185,76 +212,87 @@ if [ $compilation -eq 1 ]; then
#Configure and compilation
./configure
set +e #file ends with a test that can return false
- . ../conf/profile_mesonh-LXgfortran-R8I4-MNH-V5-5-0-MPIAUTO-DEBUG
+ . ../conf/profile_mesonh-*
set -e
- make -j 8
- make installmaster
+ make -j 8 | tee ../Output_compilation
+ make installmaster | tee -a ../Output_compilation
fi
if [ $run -ge 1 ]; then
echo "### Running of commit $commit"
- echo $commit
+
if [ ! -f $MNHPACK/$name/exe/MESONH* ]; then
echo "Pack does not exist ($MNHPACK/$name) or compilation has failed, please check"
exit 6
fi
- if [ $run_in_ref -eq 1 ]; then
- cd $REFDIR/MNH-V5-5-0/MY_RUN/KTEST/007_16janvier/
- [ ! -d 008_run2_$commit ] && cp -R 008_run2 008_run2_$commit
- cd $REFDIR/MNH-V5-5-0/MY_RUN/KTEST/007_16janvier/008_run2_$commit
- else
- cd $MNHPACK/$name/MY_RUN/KTEST/007_16janvier/
- for rep in ???_*; do
- if [ $rep != 008_run2 ]; then
- rm -rf $rep
- ln -s $REFDIR/MNH-V5-5-0/MY_RUN/KTEST/007_16janvier/$rep .
- fi
- done
- [ -d 008_run2 ] && rm -rf 008_run2
- cp -R $REFDIR/MNH-V5-5-0/MY_RUN/KTEST/007_16janvier/008_run2 .
- cd 008_run2
- fi
-
- set +e #file ends with a test that can return false
- [ $compilation -eq 0 ] && . $MNHPACK/$name/conf/profile_mesonh-LXgfortran-R8I4-MNH-V5-5-0-MPIAUTO-DEBUG
- set -e
- ./clean_mesonh_xyz
- ./run_mesonh_xyz
-fi
+ for t in $(echo $tests | sed 's/,/ /g'); do
+ case=$(echo $t | cut -d / -f 1)
+ exedir=$(echo $t | cut -d / -f 2)
+ if [ $run_in_ref -eq 1 ]; then
+ cd $REFDIR/MNH-V5-5-0/MY_RUN/KTEST/$case/
+ [ ! -d ${exedir}_$commit ] && cp -R ${exedir} ${exedir}_$commit
+ cd $REFDIR/MNH-V5-5-0/MY_RUN/KTEST/$case/${exedir}_$commit
+ else
+ cd $MNHPACK/$name/MY_RUN/KTEST/$case/
+ for rep in ???_*; do
+ if [ $rep != ${exedir} ]; then
+ rm -rf $rep
+ ln -s $REFDIR/MNH-V5-5-0/MY_RUN/KTEST/$case/$rep .
+ fi
+ done
+ [ -d ${exedir} ] && rm -rf ${exedir}
+ cp -R $REFDIR/MNH-V5-5-0/MY_RUN/KTEST/$case/${exedir} .
+ cd ${exedir}
+ fi
+ set +e #file ends with a test that can return false
+ [ $compilation -eq 0 ] && . $MNHPACK/$name/conf/profile_mesonh-*
+ set -e
+ ./clean_mesonh_xyz
+ ./run_mesonh_xyz | tee Output_run
+ done
+fi
+
if [ $check -eq 1 ]; then
- allt=0
echo "### Check commit $commit against commit $reference"
- path_user=$path_user_beg/MY_RUN/KTEST/007_16janvier/008_run2$path_user_end
- path_ref=$path_ref_beg/MY_RUN/KTEST/007_16janvier/008_run2$path_ref_end
- if [ ! -d $path_user ]; then
- echo "$path_user is missing, please run the simulation"
- exit 7
- fi
- if [ ! -d $path_ref ]; then
- echo "$path_ref is missing, please run the reference simulation"
- exit 8
- fi
+ allt=0
+ for t in $(echo $tests | sed 's/,/ /g'); do
+ case=$(echo $t | cut -d / -f 1)
+ exedir=$(echo $t | cut -d / -f 2)
- echo "Compare with python..."
- # Compare variable of both Synchronous and Diachronic files with printing difference
- set +e
- $PHYEXTOOLSDIR/compare.py $path_user $path_ref
- t=$?
- set -e
- allt=$(($allt+$t))
-
- #Check bit-repro before date of creation of Synchronous file from ncdump of all values (pb with direct .nc file checks)
- file1=$path_user/16JAN.1.12B18.001.nc
- file2=$path_ref/16JAN.1.12B18.001.nc
- echo "Compare with ncdump..."
- set +e
- diff <(ncdump $file1 | head -c 62889) <(ncdump $file2 | head -c 62889)
- t=$?
- set -e
- allt=$(($allt+$t))
+ path_user=$path_user_beg/MY_RUN/KTEST/007_16janvier/008_run2$path_user_end
+ path_ref=$path_ref_beg/MY_RUN/KTEST/007_16janvier/008_run2$path_ref_end
+ if [ ! -d $path_user ]; then
+ echo "$path_user is missing, please run the simulation"
+ exit 7
+ fi
+ if [ ! -d $path_ref ]; then
+ echo "$path_ref is missing, please run the reference simulation"
+ exit 8
+ fi
+
+ if [ $case == 007_16janvier ]; then
+ echo "Compare with python..."
+ # Compare variable of both Synchronous and Diachronic files with printing difference
+ set +e
+ $PHYEXTOOLSDIR/compare.py $path_user $path_ref
+ t=$?
+ set -e
+ allt=$(($allt+$t))
+
+ #Check bit-repro before date of creation of Synchronous file from ncdump of all values (pb with direct .nc file checks)
+ file1=$path_user/16JAN.1.12B18.001.nc
+ file2=$path_ref/16JAN.1.12B18.001.nc
+ echo "Compare with ncdump..."
+ set +e
+ diff <(ncdump $file1 | head -c 62889) <(ncdump $file2 | head -c 62889)
+ t=$?
+ set -e
+ allt=$(($allt+$t))
+ fi
+ done
if [ $allt -eq 0 ]; then
status="OK"
diff --git a/env.sh b/env.sh
index 1d52bba34111dccc931031f646444107c74c9a4d..1bec04b6d4f2486ecf5c15117ceca0a3aa584607 100644
--- a/env.sh
+++ b/env.sh
@@ -2,6 +2,3 @@ DIR="$( 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:$PATH
-
-export REFDIR=$DIR/pack/
-export TARGZDIR=$DIR/pack/
diff --git a/prep_code.sh b/prep_code.sh
index 3c3cb1ba01268b020457d34d2f893dd921f06367..8b894913ad8e39f0dc069d0297ad969424295a0b 100755
--- a/prep_code.sh
+++ b/prep_code.sh
@@ -111,6 +111,14 @@ else
from='git'
fi
+###### RENAME .F90 into .f90
+if [ $renameFf -eq 1 ]; then
+ find . -type f -name \*.F90 -print0 | \
+ while IFS= read -r -d '' file; do
+ mv -- "$file" "${file%.F90}.f90"
+ done
+fi
+
###### MERGE
if [ -n "${model-}" ]; then
if [ ! -d src/$model ]; then
@@ -129,8 +137,8 @@ if [ -n "${model-}" ]; then
for sub in $subs; do
[ $verbose -gt 1 ] && echo "Merging $sub directory/file"
if [ -e $sub ]; then
- echo "$sub must not exist in the repository, this is a limitation of the script"
- exit 7
+ echo "$sub must not exist in the repository root, this is a limitation of the script"
+ exit 7
fi
[ -e src/common/$sub ] && mv src/common/$sub .
[ -e src/$model/$sub ] && cp -rlf src/$model/$sub . && rm -rf src/$model/$sub
@@ -179,14 +187,6 @@ if [ -n "${mnh_expand_options-}" ]; then
done
fi
-###### RENAME .F90 into .f90
-if [ $renameFf -eq 1 ]; then
- find . -type f -name \*.F90 -print0 | \
- while IFS= read -r -d '' file; do
- mv -- "$file" "${file%.F90}.f90"
- done
-fi
-
###### PUSH
if [ -n "${branch-}" ]; then
[ $verbose -gt 0 ] && echo "commit and push"