From e3a0ad20dc001b44e4ae003732c6f3353ae28311 Mon Sep 17 00:00:00 2001
From: Guillaume S <gsamson@mercator-ocean.fr>
Date: Wed, 9 Nov 2022 12:29:23 +0100
Subject: [PATCH 01/31] fix tests dir

---
 sette/sette_test-cases.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sette/sette_test-cases.sh b/sette/sette_test-cases.sh
index db9c81dc..ba507fe9 100755
--- a/sette/sette_test-cases.sh
+++ b/sette/sette_test-cases.sh
@@ -108,7 +108,7 @@ if [ ${USING_MPMD} == "no" ]
 fi
 #
 # Directory to run the tests
-CONFIG_DIR0=${MAIN_DIR}/cfgs
+CONFIG_DIR0=${MAIN_DIR}/tests
 TOOLS_DIR=${MAIN_DIR}/tools
 
 if [ -n "${CUSTOM_DIR}" ]; then
-- 
GitLab


From 0e03932e20a609087443afb634ce1506b9a61af1 Mon Sep 17 00:00:00 2001
From: Guillaume S <gsamson@mercator-ocean.fr>
Date: Wed, 9 Nov 2022 19:04:57 +0100
Subject: [PATCH 02/31] change makenemo arguments to avoid using "-t" option
 when not needed

---
 sette/sette_reference-configurations.sh | 18 +++++++++---------
 sette/sette_test-cases.sh               | 12 ++++++------
 2 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/sette/sette_reference-configurations.sh b/sette/sette_reference-configurations.sh
index 4d22ddff..90678bfd 100755
--- a/sette/sette_reference-configurations.sh
+++ b/sette/sette_reference-configurations.sh
@@ -157,7 +157,7 @@ if [ ${config} == "GYRE_PISCES" ] ;  then
     clean_config GYRE_PISCES ${SETTE_CONFIG} 'cfgs'
     #
     # GYRE uses linssh so remove key_qco if added by default
-    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r GYRE_PISCES -t ${CMP_DIR:-${CONFIG_DIR0}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS/key_qco/}" del_key "${DEL_KEYS}"
+    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r GYRE_PISCES ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS/key_qco/}" del_key "${DEL_KEYS}"
 fi
 if [ ${config} == "GYRE_PISCES" ] && [ ${DO_RESTART} == "1" ] ;  then
 ## Restartability tests for GYRE_PISCES
@@ -303,7 +303,7 @@ if [ ${config} == "ORCA2_ICE_PISCES" ] ;  then
     sync_config  ORCA2_ICE_PISCES ${SETTE_CONFIG} 'cfgs'
     clean_config ORCA2_ICE_PISCES ${SETTE_CONFIG} 'cfgs'
     #
-    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r ORCA2_ICE_PISCES -t ${CMP_DIR:-${CONFIG_DIR0}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS}" del_key "${DEL_KEYS}"
+    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r ORCA2_ICE_PISCES ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS}" del_key "${DEL_KEYS}"
 fi
 if [ ${config} == "ORCA2_ICE_PISCES" ] && [ ${DO_RESTART} == "1" ] ;  then
 ## Restartability tests for ORCA2_ICE_PISCES
@@ -591,7 +591,7 @@ if [ ${config} == "ORCA2_OFF_PISCES" ] ;  then
     clean_config ${SETTE_CONFIG} ORCA2_OFF_PISCES_ST 'cfgs'
     #
     # ORCA2_OFF_PISCES uses linssh so remove key_qco if added by default
-    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r ORCA2_OFF_PISCES -t ${CMP_DIR:-${CONFIG_DIR0}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS/key_qco/}" del_key "${DEL_KEYS}"
+    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r ORCA2_OFF_PISCES ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS/key_qco/}" del_key "${DEL_KEYS}"
 fi
 if [ ${config} == "ORCA2_OFF_PISCES" ] && [ ${DO_RESTART} == "1" ] ;  then
 ## Restartability tests for ORCA2_OFF_PISCES
@@ -767,7 +767,7 @@ if [ ${config} == "AMM12" ] ;  then
     sync_config  AMM12 ${SETTE_CONFIG} 'cfgs'
     clean_config AMM12 ${SETTE_CONFIG} 'cfgs'
     #
-    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r AMM12 -t ${CMP_DIR:-${CONFIG_DIR0}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS}" del_key "${DEL_KEYS}"
+    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r AMM12 ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS}" del_key "${DEL_KEYS}"
 fi
 if [ ${config} == "AMM12" ] && [ ${DO_RESTART} == "1" ] ;  then
     ## Restartability tests for AMM12
@@ -902,7 +902,7 @@ if [ ${config} == "SAS" ] ;  then
     clean_config ORCA2_SAS_ICE ${SETTE_CONFIG} 'cfgs'
     #
     # ORCA2_SAS_ICE uses linssh so remove key_qco if added by default
-    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r ORCA2_SAS_ICE -t ${CMP_DIR:-${CONFIG_DIR0}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS/key_qco/}" del_key "${DEL_KEYS}"
+    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r ORCA2_SAS_ICE ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS/key_qco/}" del_key "${DEL_KEYS}"
 fi
 if [ ${config} == "SAS" ] && [ ${DO_RESTART} == "1" ] ;  then
 ## Restartability tests
@@ -1049,7 +1049,7 @@ if [ ${config} == "ORCA2_ICE_OBS" ] ;  then
     sync_config  ORCA2_ICE_PISCES ${SETTE_CONFIG} 'cfgs'
     clean_config ORCA2_ICE_PISCES ${SETTE_CONFIG} 'cfgs'
     #
-    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r ORCA2_ICE_PISCES -d "OCE ICE" -t ${CMP_DIR:-${CONFIG_DIR0}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "key_asminc ${ADD_KEYS}" del_key "key_top ${DEL_KEYS}"
+    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r ORCA2_ICE_PISCES -d "OCE ICE" ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "key_asminc ${ADD_KEYS}" del_key "key_top ${DEL_KEYS}"
 fi
 if [ ${config} == "ORCA2_ICE_OBS" ] && [ ${DO_RESTART} == "1" ] ;  then
 ## Reproducibility tests
@@ -1175,7 +1175,7 @@ if [ ${config} == "AGRIF" ] ;  then
     #
     # AGRIF_DEMO does not yet support nn_hls=2 => key_loop_fusion can not be used
 #    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r AGRIF_DEMO -j ${CMPL_CORES} add_key "${ADD_KEYS/key_loop_fusion}" del_key "${DEL_KEYS}"
-    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r AGRIF_DEMO -t ${CMP_DIR:-${CONFIG_DIR0}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS}" del_key "${DEL_KEYS}"
+    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r AGRIF_DEMO ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS}" del_key "${DEL_KEYS}"
 fi
 if [ ${config} == "AGRIF" ] && [ ${DO_RESTART} == "1" ] ;  then
 ## Restartability tests
@@ -1491,7 +1491,7 @@ if [ ${config} == "AGRIF" ] && [ ${DO_CORRUPT} == "1" ] ;  then
     clean_config AGRIF_DEMO ${SETTE_CONFIG} 'cfgs'
     #
     # AGRIF_DEMO does not yet support nn_hls=2 => key_loop_fusion can not be used
-    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r AGRIF_DEMO -t ${CMP_DIR:-${CONFIG_DIR0}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS/key_loop_fusion}" del_key "key_agrif ${DEL_KEYS}"
+    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r AGRIF_DEMO ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS/key_loop_fusion}" del_key "key_agrif ${DEL_KEYS}"
     cd ${SETTE_DIR}
     . ./prepare_exe_dir.sh
     set_valid_dir
@@ -1539,7 +1539,7 @@ if [ ${config} == "WED025" ] ;  then
     clean_config WED025 ${SETTE_CONFIG} 'cfgs'
     #
     # WED025 uses ln_hpg_isf so remove key_qco if added by default
-    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r WED025 -t ${CMP_DIR:-${CONFIG_DIR0}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS/key_qco/}" del_key "${DEL_KEYS}"
+    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r WED025 ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS/key_qco/}" del_key "${DEL_KEYS}"
 fi
 if [ ${config} == "WED025" ] && [ ${DO_RESTART} == "1" ] ;  then
 ## Restartability tests
diff --git a/sette/sette_test-cases.sh b/sette/sette_test-cases.sh
index ba507fe9..34e1bf7f 100755
--- a/sette/sette_test-cases.sh
+++ b/sette/sette_test-cases.sh
@@ -157,7 +157,7 @@ if [ ${config} == "OVERFLOW" ] ;  then
     #
     sync_config  OVERFLOW ${SETTE_CONFIG} 'tests'
     #
-    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -a OVERFLOW -t ${CMP_DIR:-${CONFIG_DIR0}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS}" del_key "${DEL_KEYS}"
+    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -a OVERFLOW ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS}" del_key "${DEL_KEYS}"
 fi
 if [ ${config} == "OVERFLOW" ] && [ ${DO_RESTART} == "1" ] ;  then
     ## Restartability tests for OVERFLOW
@@ -274,7 +274,7 @@ if [ ${config} == "LOCK_EXCHANGE" ] ;  then
     #
     sync_config  LOCK_EXCHANGE ${SETTE_CONFIG} 'tests'
     #
-    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -a LOCK_EXCHANGE -t ${CMP_DIR:-${CONFIG_DIR0}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS}" del_key "${DEL_KEYS}"
+    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -a LOCK_EXCHANGE ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS}" del_key "${DEL_KEYS}"
 fi
 if [ ${config} == "LOCK_EXCHANGE" ] && [ ${DO_RESTART} == "1" ] ;  then
     ## Restartability tests for LOCK_EXCHANGE
@@ -393,7 +393,7 @@ if [ ${config} == "VORTEX" ] ;  then
     #
     sync_config  VORTEX ${SETTE_CONFIG} 'tests'
     #
-    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -a VORTEX -t ${CMP_DIR:-${CONFIG_DIR0}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES}  add_key "${ADD_KEYS}" del_key "${DEL_KEYS}"
+    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -a VORTEX ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES}  add_key "${ADD_KEYS}" del_key "${DEL_KEYS}"
 fi
 if [ ${config} == "VORTEX" ] && [ ${DO_RESTART} == "1" ] ;  then
 ## Restartability tests for VORTEX
@@ -588,7 +588,7 @@ if [ ${config} == "ICE_AGRIF" ] ;  then
     sync_config  ICE_AGRIF ${SETTE_CONFIG} 'tests'
     #
     # ICE_AGRIF uses linssh so remove key_qco if added by default
-    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -a ICE_AGRIF -t ${CMP_DIR:-${CONFIG_DIR0}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES}  add_key "${ADD_KEYS/key_qco/}" del_key "${DEL_KEYS}"
+    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -a ICE_AGRIF ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES}  add_key "${ADD_KEYS/key_qco/}" del_key "${DEL_KEYS}"
 fi
 if [ ${config} == "ICE_AGRIF" ] && [ ${DO_RESTART} == "1" ] ;  then
 ## Restartability tests for ICE_AGRIF
@@ -786,7 +786,7 @@ if [ ${config} == "ISOMIP+" ] ;  then
     sync_config  ISOMIP+ ${SETTE_CONFIG} 'tests'
     #
     # ISOMIP+ uses ln_hpg_isf so remove key_qco if added by default
-    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -a ISOMIP+ -t ${CMP_DIR:-${CONFIG_DIR0}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS/key_qco/}" del_key "${DEL_KEYS}"
+    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -a ISOMIP+ ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS/key_qco/}" del_key "${DEL_KEYS}"
 fi
 if [ ${config} == "ISOMIP+" ] && [ ${DO_RESTART} == "1" ] ;  then
 ## Restartability tests
@@ -930,7 +930,7 @@ if [ ${config} == "SWG" ] && [ ${USING_QCO} == "yes" ] ;  then
     #
     sync_config  SWG ${SETTE_CONFIG} 'tests'
     #
-    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -a SWG -t ${CMP_DIR:-${CONFIG_DIR0}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES}  add_key "${ADD_KEYS}" del_key "${DEL_KEYS}"
+    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -a SWG ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES}  add_key "${ADD_KEYS}" del_key "${DEL_KEYS}"
 fi
 if [ ${config} == "SWG" ] && [ ${DO_RESTART} == "1" ] && [ ${USING_QCO} == "yes" ] ;  then
 ## Restartability tests for SWG
-- 
GitLab


From 2619bda189491bc520f9697b4d567d5364ca374d Mon Sep 17 00:00:00 2001
From: Guillaume S <gsamson@mercator-ocean.fr>
Date: Thu, 10 Nov 2022 08:24:06 +0100
Subject: [PATCH 03/31] add same change to makenemo in clean_config function

---
 sette/all_functions.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/sette/all_functions.sh b/sette/all_functions.sh
index 4be4be5a..6c07afd2 100755
--- a/sette/all_functions.sh
+++ b/sette/all_functions.sh
@@ -153,12 +153,12 @@ clean_config() {
       echo '-------------------------------------------------------------------------------'
       echo '                         CLEANING CONFIGURATION                                '
       echo ''
-      echo "./makenemo -n $lCFG -a/-r $lREF -t ${CMP_DIR:-${CONFIG_DIR0}} clean"
+      echo "./makenemo -n $lCFG -a/-r $lREF ${CUSTOM_DIR:+-t ${CMP_DIR}} clean"
       echo ''
       if [ ${lTYP} == 'tests' ]; then
-         ./makenemo -n $lCFG -t ${CMP_DIR:-${CONFIG_DIR0}} -a $lREF clean
+         ./makenemo -n $lCFG ${CUSTOM_DIR:+-t ${CMP_DIR}} -a $lREF clean
       elif [ ${lTYP} == 'cfgs' ]; then
-         ./makenemo -n $lCFG -t ${CMP_DIR:-${CONFIG_DIR0}} -r $lREF clean
+         ./makenemo -n $lCFG ${CUSTOM_DIR:+-t ${CMP_DIR}} -r $lREF clean
       else
          echo 'ERROR in the cleaning process'; exit 42
       fi
-- 
GitLab


From b9eb7b48c9e965a99ba31c0a69d7e70a6fb3aff2 Mon Sep 17 00:00:00 2001
From: Guillaume S <gsamson@mercator-ocean.fr>
Date: Thu, 10 Nov 2022 18:32:50 +0100
Subject: [PATCH 04/31] add the possibility to install a new configuration
 anywhere using "-t" makenemo option (continuation of #84)

---
 makenemo                 | 53 +++++++++++++++++++++-------------------
 mk/Fadd_keys.sh          |  6 ++---
 mk/Fdef_keys.sh          |  2 +-
 mk/Fdel_keys.sh          | 14 +++++------
 mk/Fmake_WORK.sh         |  8 +++---
 mk/Fmake_bld.sh          | 10 ++++----
 mk/Fmake_config.sh       | 11 +++++----
 mk/bldxag.cfg            |  2 +-
 sette/prepare_exe_dir.sh | 16 ++++++------
 9 files changed, 64 insertions(+), 58 deletions(-)

diff --git a/makenemo b/makenemo
index 8de8150e..d1a48ca3 100755
--- a/makenemo
+++ b/makenemo
@@ -88,18 +88,12 @@ x_u=''; x_a=''; x_m=''; x_t=''; x_b='';
 x_j='1'; x_e='none'; x_s='src'; x_v='1'
 x_c_cfg=0
 x_nocdf=0
-x_name=''
+#x_name=''
 
 ##- Local variables ---
 b_n=$(basename ${0})
 OPTIND='1'
 MAIN_DIR=$(cd $(dirname "$0"); pwd)
-MAIN_DIR=${MAIN_DIR%/sette*}
-MAIN_DIR=${MAIN_DIR%/tools*}
-MAIN_DIR=${MAIN_DIR%/cfgs*}
-MAIN_DIR=${MAIN_DIR%/tests*}
-MAIN_DIR=${MAIN_DIR%/ext*}
-MAIN_DIR=${MAIN_DIR%/arch*}
 export MAIN_DIR
 #
 export CFGS_DIR=${MAIN_DIR}/cfgs
@@ -195,7 +189,8 @@ EOF
 	-d|--dirs|--comp)
 	    x_d=${2} ; shift ;;
 	-n|--name)
-	    x_name=${2} ; shift ;;
+	    #x_name=${2} ; shift ;;
+	    x_n=${2} ; shift ;;
 	-r|--ref)
 	    x_r=${2} ; shift ;;
 	-a|--academic|--test)
@@ -229,31 +224,38 @@ EOF
     shift
 done
 
-if [ -n "$x_name" ]   # is the configuration existing in cfgs or tests? or is it a new conf?
+#if [ -n "$x_name" ]   # is the configuration existing in cfgs or tests? or is it a new conf?
+if [ -n "$x_n" ]   # is the configuration existing in cfgs or tests? or is it a new conf?
 then
-    incfg=$( find $CFGS_DIR   -type d -name $x_name | wc -l )   # this configuration exists in CFGS_DIR
-    intst=$( find $TESTS_DIR  -type d -name $x_name | wc -l )   # this configuration exists in TESTS_DIR
+    #incfg=$( find $CFGS_DIR   -type d -name $x_name | wc -l )   # this configuration exists in CFGS_DIR
+    #intst=$( find $TESTS_DIR  -type d -name $x_name | wc -l )   # this configuration exists in TESTS_DIR
+    incfg=$( find $CFGS_DIR   -type d -name $x_n | wc -l )   # this configuration exists in CFGS_DIR
+    intst=$( find $TESTS_DIR  -type d -name $x_n | wc -l )   # this configuration exists in TESTS_DIR
     if [ $(( $incfg + $intst )) -eq 2 ] ; then
-	echo -e "\033[0;31m\nERROR: the $x_name directory is found twice: in $CFGS_DIR and in $TESTS_DIR\033[0m\n"
+	#echo -e "\033[0;31m\nERROR: the $x_name directory is found twice: in $CFGS_DIR and in $TESTS_DIR\033[0m\n"
+	echo -e "\033[0;31m\nERROR: the $x_n directory is found twice: in $CFGS_DIR and in $TESTS_DIR\033[0m\n"
 	exit 4
     fi
     if [ $(( $incfg + $intst )) -gt 0 ] ; then
 	if [ $x_c_cfg -eq 1 ] ; then   # if we just want to clean the config (do it here as it must exist)
-	    x_n=$x_name                # must define x_n as it is used in Fclean_config.sh
+	    #x_n=$x_name                # must define x_n as it is used in Fclean_config.sh
 	    . ${COMPIL_DIR}/Fclean_config.sh
 	    exit 0
 	fi
-	[ -n "$x_r" ] && echo -e "\nWARNING: $x_name configuration is already existing, we ignore \"-r $x_r\"\n"
-	[ -n "$x_a" ] && echo -e "\nWARNING: $x_name configuration is already existing, we ignore \"-a $x_a\"\n"
+	#[ -n "$x_r" ] && echo -e "\nWARNING: $x_name configuration is already existing, we ignore \"-r $x_r\"\n"
+	#[ -n "$x_a" ] && echo -e "\nWARNING: $x_name configuration is already existing, we ignore \"-a $x_a\"\n"
+	[ -n "$x_r" ] && echo -e "\nWARNING: $x_n configuration is already existing, we ignore \"-r $x_r\"\n"
+	[ -n "$x_a" ] && echo -e "\nWARNING: $x_n configuration is already existing, we ignore \"-a $x_a\"\n"
     fi
-    if   [ $incfg -eq 1 ] ; then
-	x_r=$x_name ; x_a=''  # reference configuration existing -> define/overwrite x_r
-    elif [ $intst -eq 1 ] ; then
-	x_a=$x_name ; x_r=''   # test      configuration existing -> define/overwrite x_a
-    else
+    #if   [ $incfg -eq 1 ] ; then
+	#x_r=$x_name ; x_a=''  # reference configuration existing -> define/overwrite x_r
+    #elif [ $intst -eq 1 ] ; then
+	#x_a=$x_name ; x_r=''   # test      configuration existing -> define/overwrite x_a
+    #else
+    if [[ $incfg -eq 0 && $intst -eq 0 ]]; then
 	[  ${#x_c} -ne 0 ] && echo -e "\nWARNING: Compilation cleaning of a non-existing configuration, we ignore\n" && exit 0
 	[ $x_c_cfg -eq 1 ] && echo -e "\nWARNING: Configuration cleaning of a non-existing configuration, we ignore\n" && exit 0
-	x_n=$x_name            # this is a new configuration      -> define
+	#x_n=$x_name            # this is a new configuration      -> define
     fi
 fi
 
@@ -270,7 +272,7 @@ NEMO_DBG=${x_b}
 
 
 ## No ref. cfg or demo selected
-if [[ -z "${REF_CONF}" && -z "${DEMO_CONF}" ]]; then
+if [[ -z "${REF_CONF}" && -z "${DEMO_CONF}" && $(( $incfg + $intst )) -eq 0 ]]; then
     echo -e "\033[0;31m\nAt least a reference configuration ('-r'), a test case ('-a'), "
     echo -e "a remote configuration ('-u') has to be choosen to build a new configuration!!!\033[0m"
     ${COMPIL_DIR}/Flist_cfgs.sh
@@ -332,10 +334,11 @@ echo ${NEW_CONF} "${NEM_SUBDIR}" >> ${CONFIG_DIR}/work_cfgs.txt
 cd ${CONFIG_DIR}
 
 ## Create new config even in existing one (mkdir with -p option, cp with -n)
-${COMPIL_DIR}/Fmake_config.sh ${NEW_CONF} ${TML_CONF}
+${COMPIL_DIR}/Fmake_config.sh ${NEMO_TDIR}/${NEW_CONF} ${TML_CONF}
 
 ## create EXP00 if needed
-[ ! -d ${CONFIG_DIR}/${NEW_CONF}/EXP00 ] && \cp -R -n ${CONFIG_DIR}/${NEW_CONF}/EXPREF ${CONFIG_DIR}/${NEW_CONF}/EXP00
+[[ ! -d ${NEMO_TDIR}/${NEW_CONF}/EXP00 && -n "${REF_CONF}" ]] && \cp -R -n ${CONFIG_DIR}/${REF_CONF}/EXPREF ${NEMO_TDIR}/${NEW_CONF}/EXP00
+[[ ! -d ${NEMO_TDIR}/${NEW_CONF}/EXP00 && -n "${DEMO_CONF}" ]] && \cp -R -n ${CONFIG_DIR}/${DEMO_CONF}/EXPREF ${NEMO_TDIR}/${NEW_CONF}/EXP00
 
 #- Create the WORK ---
 #- Clean links and librairies ---
@@ -410,7 +413,7 @@ if [ "${NBR_PRC}" -gt 0 ]; then
     fcm build ${x_c} --ignore-lock -v ${x_v} -j ${NBR_PRC} ${COMPIL_DIR}/$USEBLD ||{ cd - ; exit 1 ;}
 
     if [ -f ${NEMO_TDIR}/${NEW_CONF}/BLD/bin/nemo.exe ]; then
-	ln -sf ${NEMO_TDIR}/${NEW_CONF}/BLD/bin/nemo.exe  ${CONFIG_DIR}/${NEW_CONF}/EXP00/nemo
+	ln -sf ${NEMO_TDIR}/${NEW_CONF}/BLD/bin/nemo.exe  ${NEMO_TDIR}/${NEW_CONF}/EXP00/nemo
     fi
 
     ## add remove for clean option
diff --git a/mk/Fadd_keys.sh b/mk/Fadd_keys.sh
index 0aa554c1..e4fc8c78 100755
--- a/mk/Fadd_keys.sh
+++ b/mk/Fadd_keys.sh
@@ -64,11 +64,11 @@ set -o posix
 #-
  echo "Adding keys in : ${NEW_CONF}" 
  for i in ${list_add_key} ; do
-	if [ "$(cat ${CONFIG_DIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm | grep -c "\<$i\>" )" -ne 0 ] ; then
+	if [ "$(cat ${NEMO_TDIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm | grep -c "\<$i\>" )" -ne 0 ] ; then
  	   echo "key $i already present in cpp_${NEW_CONF}.fcm" 
 	else
-	   sed -e "s/$/ ${i}/"  ${CONFIG_DIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm >  ${CONFIG_DIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm.tmp
- 	   mv ${CONFIG_DIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm.tmp   ${CONFIG_DIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm
+	   sed -e "s/$/ ${i}/"  ${NEMO_TDIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm >  ${NEMO_TDIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm.tmp
+ 	   mv ${NEMO_TDIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm.tmp   ${NEMO_TDIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm
  	   echo "added key $i in ${NEW_CONF}" 
 	fi
  done
diff --git a/mk/Fdef_keys.sh b/mk/Fdef_keys.sh
index f0edd7d8..bf94a481 100755
--- a/mk/Fdef_keys.sh
+++ b/mk/Fdef_keys.sh
@@ -58,6 +58,6 @@ set -o posix
 
 echo "Defining keys in : ${NEW_CONF}"
 
-echo " bld::tool::fppkeys ${list_def_key}" > ${CONFIG_DIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm
+echo " bld::tool::fppkeys ${list_def_key}" > ${NEMO_TDIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm
 
 unset -v list_def_key
diff --git a/mk/Fdel_keys.sh b/mk/Fdel_keys.sh
index 88aafc23..ff95aa2b 100755
--- a/mk/Fdel_keys.sh
+++ b/mk/Fdel_keys.sh
@@ -65,14 +65,14 @@ echo "Removing keys in : ${NEW_CONF}"
 for i in ${list_del_key} ; do
 
      if [ "$(echo ${i} | grep -c key_nproc )" -ne 0                                      ]; then
-        sed -e "s/key_nproc[ij]=.* //" ${CONFIG_DIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm \
-	    >  ${CONFIG_DIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm.tmp
-        mv ${CONFIG_DIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm.tmp ${CONFIG_DIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm
+        sed -e "s/key_nproc[ij]=.* //" ${NEMO_TDIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm \
+	    >  ${NEMO_TDIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm.tmp
+        mv ${NEMO_TDIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm.tmp ${NEMO_TDIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm
         echo " "
-     elif [ "$(cat ${CONFIG_DIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm | grep -c "$i" )" -ne 0 ]; then
-         sed -e "s/\b${i}\b//" ${CONFIG_DIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm \
-	     >  ${CONFIG_DIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm.tmp
-         mv ${CONFIG_DIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm.tmp ${CONFIG_DIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm
+     elif [ "$(cat ${NEMO_TDIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm | grep -c "$i" )" -ne 0 ]; then
+         sed -e "s/\b${i}\b//" ${NEMO_TDIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm \
+	     >  ${NEMO_TDIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm.tmp
+         mv ${NEMO_TDIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm.tmp ${NEMO_TDIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm
          echo "deleted key $i in ${NEW_CONF}"
      fi
 
diff --git a/mk/Fmake_WORK.sh b/mk/Fmake_WORK.sh
index 372bca57..780fb996 100755
--- a/mk/Fmake_WORK.sh
+++ b/mk/Fmake_WORK.sh
@@ -64,14 +64,14 @@ set -o posix
 #
 #-
 declare ZSRC=${@}
-ZCONF=${NEW_CONF}
+ZCONF=${NEMO_TDIR}/${NEW_CONF}
 ZTAB=${NEM_SUBDIR[@]}
 declare NDIR=${#ZTAB[@]}
 
-echo 'Creating '${ZCONF}'/WORK = '${ZTAB[*]}' for '${ZCONF}
+echo 'Creating '${ZCONF}'/WORK = '${ZTAB[*]}' for '${ZCONF##*/}
 
-[ ! -d ${ZCONF}/MY_SRC ] && \mkdir ${ZCONF}/MY_SRC
-[   -d ${ZCONF}/WORK   ] || \mkdir ${ZCONF}/WORK
+[ ! -d ${ZCONF}/MY_SRC ] && \mkdir -p ${ZCONF}/MY_SRC
+[   -d ${ZCONF}/WORK   ] || \mkdir -p ${ZCONF}/WORK
 
 for comp in ${ZTAB[*]}; do
 	find ${NEMO_DIR}/$comp -name *.[Ffh]90 -exec ln -sf {} ${ZCONF}/WORK \;
diff --git a/mk/Fmake_bld.sh b/mk/Fmake_bld.sh
index 53d9f7e3..9973af3f 100755
--- a/mk/Fmake_bld.sh
+++ b/mk/Fmake_bld.sh
@@ -57,8 +57,8 @@ set -o posix
 #   * creation
 #
 #-
-[ ! -d ${3}/${2}     ] && \mkdir ${3}/${2}
-[ ! -d ${3}/${2}/BLD ] && \mkdir ${3}/${2}/BLD
-[ ! -d ${1}/${2}/BLD ] && ln -sf ${3}/${2}/BLD ${1}/${2}/BLD
-[ -f ${1}/${NEW_CONF}/cpp_${NEW_CONF}.fcm ] && ln -sf ${1}/${NEW_CONF}/cpp_${NEW_CONF}.fcm ${COMPIL_DIR}/cpp.fcm
-rm -f  ${1}/${NEW_CONF}/BLD/fcm.bld.lock
+[ ! -d ${3}/${2}     ] && \mkdir -p ${3}/${2}
+[ ! -d ${3}/${2}/BLD ] && \mkdir -p ${3}/${2}/BLD
+#[ ! -d ${1}/${2}/BLD ] && ln -sf ${3}/${2}/BLD ${1}/${2}/BLD
+[ -f ${3}/${2}/cpp_${2}.fcm ] && ln -sf ${3}/${2}/cpp_${2}.fcm ${COMPIL_DIR}/cpp.fcm
+rm -f  ${1}/${2}/BLD/fcm.bld.lock
diff --git a/mk/Fmake_config.sh b/mk/Fmake_config.sh
index 12babc42..3ad6bb65 100755
--- a/mk/Fmake_config.sh
+++ b/mk/Fmake_config.sh
@@ -59,8 +59,9 @@ set -o posix
 \mkdir -p ${1}
 \mkdir -p ${1}/EXP00
 \mkdir -p ${1}/MY_SRC
-\cp -R -n ${2}/cpp_${2}.fcm ${1}/cpp_${1}.fcm
-\cp -R -n ${2}/EXPREF/*namelist* ${1}/EXP00/.
-\cp -R -n ${2}/EXPREF/*.xml ${1}/EXP00/.
-[ -f ${2}/EXPREF/AGRIF_FixedGrids.in ] &&  \cp -R -n ${2}/EXPREF/AGRIF_FixedGrids.in ${1}/EXP00/.
-[ -d    ${2}/MY_SRC ] && \cp -n ${2}/MY_SRC/* ${1}/MY_SRC/. 2> /dev/null
+\cp -R -n ${2}/cpp_${2}.fcm ${1}/cpp_${1##*/}.fcm
+for f in ${2}/EXPREF/*.xml ${2}/EXPREF/*namelist*; do
+  if [ -L ${f} ]; then ln -sf $(readlink -f ${f}) ${1}/EXP00/$(basename ${f}); else cp -R -n ${f} ${1}/EXP00/.; fi
+done
+[ -f ${2}/EXPREF/AGRIF_FixedGrids.in ] &&  \cp -a -n ${2}/EXPREF/AGRIF_FixedGrids.in ${1}/EXP00/.
+[ -d    ${2}/MY_SRC ] && \cp -an ${2}/MY_SRC/* ${1}/MY_SRC/. 2> /dev/null
diff --git a/mk/bldxag.cfg b/mk/bldxag.cfg
index 19ea8475..5b4db893 100644
--- a/mk/bldxag.cfg
+++ b/mk/bldxag.cfg
@@ -13,7 +13,7 @@ inc $COMPIL_DIR/cpp.fcm
 search_src           1
 
 src::ioipsl               $MAIN_DIR/ext/IOIPSL/src
-src::nemo                 $CONFIG_DIR/$NEW_CONF/WORK
+src::nemo                 $NEMO_TDIR/$NEW_CONF/WORK
 src::ppr_1d               $MAIN_DIR/ext/PPR/src
 
 bld::target nemo.exe
diff --git a/sette/prepare_exe_dir.sh b/sette/prepare_exe_dir.sh
index 47d5207f..33ede807 100755
--- a/sette/prepare_exe_dir.sh
+++ b/sette/prepare_exe_dir.sh
@@ -67,22 +67,24 @@ set -o posix
 # PREPARE EXEC_DIR
 #==================
 if [ -z "${CUSTOM_DIR}" ]; then
-  export EXE_DIR=${CONFIG_DIR}/${NEW_CONF}/${TEST_NAME}
+  EXE_DIR=${CONFIG_DIR}/${NEW_CONF}
 else
   if [[ -n "${NEMO_DEBUG}" || ${CMP_NAM,,} =~ ("debug"|"dbg") ]]; then
-    export EXE_DIR=${CUSTOM_DIR}/${SETTE_SUB_VAL}_${NEMO_REV}_DEBUG/${NEW_CONF}/${TEST_NAME}
+    EXE_DIR=${CUSTOM_DIR}/${SETTE_SUB_VAL}_${NEMO_REV}_DEBUG/${NEW_CONF}
   else
-    export EXE_DIR=${CUSTOM_DIR}/${SETTE_SUB_VAL}_${NEMO_REV}/${NEW_CONF}/${TEST_NAME}
+    EXE_DIR=${CUSTOM_DIR}/${SETTE_SUB_VAL}_${NEMO_REV}/${NEW_CONF}
   fi
 fi
-mkdir -p ${EXE_DIR}
+mkdir -p ${EXE_DIR}/${TEST_NAME}
 
-cp -RL ${CONFIG_DIR}/${NEW_CONF}/EXP00/* ${EXE_DIR}/.
-#cat ${SETTE_DIR}/iodef_sette.xml | sed -e"s;DEF_SHARED;${CONFIG_DIR0}/SHARED;" > ${EXE_DIR}/iodef.xml
+#cp -RL ${EXE_DIR:-${CONFIG_DIR}/${NEW_CONF}}/EXP00/* ${EXE_DIR}/${TEST_NAME}/.
+cp -an ${EXE_DIR:-${CONFIG_DIR}/${NEW_CONF}}/EXP00/* ${EXE_DIR}/${TEST_NAME}/.
+COMP_KEYS="`cat ${EXE_DIR}/cpp_${NEW_CONF}.fcm | sed -e 's/.*fppkeys *//'`"
+
+export EXE_DIR=${EXE_DIR}/${TEST_NAME}
 cd ${EXE_DIR}
 #
 # Add summary of the sette.sh set-up used and the current list of keys added or deleted
-COMP_KEYS="`cat ${CONFIG_DIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm | sed -e 's/.*fppkeys *//'`"
 echo "Summary of sette environment"                                > ./sette_config
 echo "----------------------------"                               >> ./sette_config
 echo "requested by the command          : "$cmd $cmdargs          >> ./sette_config
-- 
GitLab


From f1b38a32715ddeabdba1f0fcecd1493bf91d809d Mon Sep 17 00:00:00 2001
From: Guillaume S <gsamson@mercator-ocean.fr>
Date: Sun, 13 Nov 2022 19:56:06 +0100
Subject: [PATCH 05/31] adapt sette to work with any path (custom or not)

---
 sette/all_functions.sh                  | 20 +++++---------
 sette/prepare_job.sh                    |  4 +--
 sette/sette_reference-configurations.sh | 36 ++++++++++++-------------
 sette/sette_test-cases.sh               | 30 +++++++++------------
 4 files changed, 38 insertions(+), 52 deletions(-)

diff --git a/sette/all_functions.sh b/sette/all_functions.sh
index 6c07afd2..6eee8ebb 100755
--- a/sette/all_functions.sh
+++ b/sette/all_functions.sh
@@ -94,8 +94,8 @@ usage=" if value is a string ths is neede syntax : ./set_namelist namelist_name
 sync_config() {
    if [ ${SYNC_CONFIGS} == "yes" ]; then
 
-      lREF=$3/$1    # reference 
-      lCFG=$3/$2    # target
+      lREF=$1    # reference
+      lCFG=$2    # target
 
       echo '-------------------------------------------------------------------------------'
       echo '                    SOURCE AND CONFIG FILES SYNCHRONISATION                    '
@@ -146,24 +146,16 @@ sync_config() {
 # clean _STg config (input CFG CFG_STg TYPE (test or ref))
 clean_config() {
    if [ ${CLEAN_CONFIGS} == "yes" ]; then
-      lREF=$1
-      lCFG=$2
-      lTYP=$3
+      lCFG=$1
       echo ''
       echo '-------------------------------------------------------------------------------'
       echo '                         CLEANING CONFIGURATION                                '
       echo ''
-      echo "./makenemo -n $lCFG -a/-r $lREF ${CUSTOM_DIR:+-t ${CMP_DIR}} clean"
+      echo "./makenemo -n $(basename $lCFG) ${CUSTOM_DIR:+-t ${CMP_DIR}} clean"
       echo ''
-      if [ ${lTYP} == 'tests' ]; then
-         ./makenemo -n $lCFG ${CUSTOM_DIR:+-t ${CMP_DIR}} -a $lREF clean
-      elif [ ${lTYP} == 'cfgs' ]; then
-         ./makenemo -n $lCFG ${CUSTOM_DIR:+-t ${CMP_DIR}} -r $lREF clean
-      else
-         echo 'ERROR in the cleaning process'; exit 42
-      fi
+      ./makenemo -n $(basename $lCFG) ${CUSTOM_DIR:+-t ${CMP_DIR}} clean
       echo ''
-      echo "$lCFG configuration has been cleaned"
+      echo "$(basename $lCFG) configuration has been cleaned"
       echo ''
       echo '-------------------------------------------------------------------------------'
    fi
diff --git a/sette/prepare_job.sh b/sette/prepare_job.sh
index 335daedb..80d3fa1e 100755
--- a/sette/prepare_job.sh
+++ b/sette/prepare_job.sh
@@ -104,7 +104,7 @@ echo "" >> ${SETTE_DIR}/output.sette
 echo "running config: ${NEW_CONF}" >> ${SETTE_DIR}/output.sette
 echo "" >> ${SETTE_DIR}/output.sette
 echo "list of cpp_keys: " >> ${SETTE_DIR}/output.sette
-echo "`more ${CONFIG_DIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm`" >> ${SETTE_DIR}/output.sette 
+echo "`more ${NEMO_TDIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm`" >> ${SETTE_DIR}/output.sette
 echo "" >> ${SETTE_DIR}/output.sette
 echo "compiling with: ${CMP_NAM}" >> ${SETTE_DIR}/output.sette
 echo "" >> ${SETTE_DIR}/output.sette
@@ -269,7 +269,7 @@ fi
              -e"s/NXIOPROCS/${NXIO_PROC}/" \
              -e"s:DEF_SETTE_DIR:${SETTE_DIR}:" -e"s:DEF_INPUT_DIR:${INPUT_DIR}:" \
              -e"s:DEF_EXE_DIR:${EXE_DIR}:" \
-             -e"s:DEF_CONFIG_DIR:${CONFIG_DIR}:" \
+             -e"s:DEF_CONFIG_DIR:${NEMO_TDIR}:" \
              -e"s:DEF_TOOLS_DIR:${TOOLS_DIR}:" \
              -e"s:MPI_FLAG:${MPI_FLAG}:" \
              -e"s:DEF_NEMO_VALIDATION:${NEMO_VALID}:" -e"s:DEF_NEW_CONF:${NEW_CONF}:" \
diff --git a/sette/sette_reference-configurations.sh b/sette/sette_reference-configurations.sh
index 90678bfd..cb0b80d4 100755
--- a/sette/sette_reference-configurations.sh
+++ b/sette/sette_reference-configurations.sh
@@ -153,8 +153,8 @@ if [ ${config} == "GYRE_PISCES" ] ;  then
     cd ${MAIN_DIR}
     #
     # syncronisation if target directory/file exist (not done by makenemo)
-    sync_config  GYRE_PISCES ${SETTE_CONFIG} 'cfgs'
-    clean_config GYRE_PISCES ${SETTE_CONFIG} 'cfgs'
+    clean_config ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
+    sync_config  ${CONFIG_DIR0}/${config} ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
     #
     # GYRE uses linssh so remove key_qco if added by default
     . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r GYRE_PISCES ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS/key_qco/}" del_key "${DEL_KEYS}"
@@ -300,8 +300,8 @@ if [ ${config} == "ORCA2_ICE_PISCES" ] ;  then
     cd ${MAIN_DIR}
     #
     # syncronisation if target directory/file exist (not done by makenemo)
-    sync_config  ORCA2_ICE_PISCES ${SETTE_CONFIG} 'cfgs'
-    clean_config ORCA2_ICE_PISCES ${SETTE_CONFIG} 'cfgs'
+    clean_config ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
+    sync_config  ${CONFIG_DIR0}/${config} ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
     #
     . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r ORCA2_ICE_PISCES ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS}" del_key "${DEL_KEYS}"
 fi
@@ -587,8 +587,8 @@ if [ ${config} == "ORCA2_OFF_PISCES" ] ;  then
     cd ${MAIN_DIR}
     #
     # syncronisation if target directory/file exist (not done by makenemo)
-    sync_config  ${SETTE_CONFIG} ORCA2_OFF_PISCES_ST 'cfgs'
-    clean_config ${SETTE_CONFIG} ORCA2_OFF_PISCES_ST 'cfgs'
+    clean_config ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
+    sync_config  ${CONFIG_DIR0}/${config} ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
     #
     # ORCA2_OFF_PISCES uses linssh so remove key_qco if added by default
     . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r ORCA2_OFF_PISCES ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS/key_qco/}" del_key "${DEL_KEYS}"
@@ -764,8 +764,8 @@ if [ ${config} == "AMM12" ] ;  then
     cd ${MAIN_DIR}
     #
     # syncronisation if target directory/file exist (not done by makenemo)
-    sync_config  AMM12 ${SETTE_CONFIG} 'cfgs'
-    clean_config AMM12 ${SETTE_CONFIG} 'cfgs'
+    clean_config ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
+    sync_config  ${CONFIG_DIR0}/${config} ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
     #
     . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r AMM12 ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS}" del_key "${DEL_KEYS}"
 fi
@@ -898,8 +898,8 @@ if [ ${config} == "SAS" ] ;  then
     cd ${MAIN_DIR}
     #
     # syncronisation if target directory/file exist (not done by makenemo)
-    sync_config  ORCA2_SAS_ICE ${SETTE_CONFIG} 'cfgs'
-    clean_config ORCA2_SAS_ICE ${SETTE_CONFIG} 'cfgs'
+    clean_config ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
+    sync_config  ${CONFIG_DIR0}/${config} ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
     #
     # ORCA2_SAS_ICE uses linssh so remove key_qco if added by default
     . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r ORCA2_SAS_ICE ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS/key_qco/}" del_key "${DEL_KEYS}"
@@ -1046,8 +1046,8 @@ if [ ${config} == "ORCA2_ICE_OBS" ] ;  then
     cd ${MAIN_DIR}
     #
     # syncronisation if target directory/file exist (not done by makenemo)
-    sync_config  ORCA2_ICE_PISCES ${SETTE_CONFIG} 'cfgs'
-    clean_config ORCA2_ICE_PISCES ${SETTE_CONFIG} 'cfgs'
+    clean_config ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
+    sync_config  ${CONFIG_DIR0}/${config} ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
     #
     . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r ORCA2_ICE_PISCES -d "OCE ICE" ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "key_asminc ${ADD_KEYS}" del_key "key_top ${DEL_KEYS}"
 fi
@@ -1170,8 +1170,8 @@ if [ ${config} == "AGRIF" ] ;  then
     cd ${MAIN_DIR}
     #
     # syncronisation if target directory/file exist (not done by makenemo)
-    sync_config  AGRIF_DEMO ${SETTE_CONFIG} 'cfgs'
-    clean_config AGRIF_DEMO ${SETTE_CONFIG} 'cfgs'
+    clean_config ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
+    sync_config  ${CONFIG_DIR0}/${config} ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
     #
     # AGRIF_DEMO does not yet support nn_hls=2 => key_loop_fusion can not be used
 #    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r AGRIF_DEMO -j ${CMPL_CORES} add_key "${ADD_KEYS/key_loop_fusion}" del_key "${DEL_KEYS}"
@@ -1487,8 +1487,8 @@ if [ ${config} == "AGRIF" ] && [ ${DO_CORRUPT} == "1" ] ;  then
     cd ${MAIN_DIR}
     #
     # syncronisation if target directory/file exist (not done by makenemo)
-    sync_config  AGRIF_DEMO ${SETTE_CONFIG} 'cfgs'
-    clean_config AGRIF_DEMO ${SETTE_CONFIG} 'cfgs'
+    clean_config ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
+    sync_config  ${CONFIG_DIR0}/${config} ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
     #
     # AGRIF_DEMO does not yet support nn_hls=2 => key_loop_fusion can not be used
     . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r AGRIF_DEMO ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS/key_loop_fusion}" del_key "key_agrif ${DEL_KEYS}"
@@ -1535,8 +1535,8 @@ if [ ${config} == "WED025" ] ;  then
     cd ${MAIN_DIR}
     #
     # syncronisation if target directory/file exist (not done by makenemo)
-    sync_config  WED025 ${SETTE_CONFIG} 'cfgs'
-    clean_config WED025 ${SETTE_CONFIG} 'cfgs'
+    clean_config ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
+    sync_config  ${CONFIG_DIR0}/${config} ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
     #
     # WED025 uses ln_hpg_isf so remove key_qco if added by default
     . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r WED025 ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS/key_qco/}" del_key "${DEL_KEYS}"
diff --git a/sette/sette_test-cases.sh b/sette/sette_test-cases.sh
index 34e1bf7f..aec16728 100755
--- a/sette/sette_test-cases.sh
+++ b/sette/sette_test-cases.sh
@@ -153,9 +153,8 @@ if [ ${config} == "OVERFLOW" ] ;  then
     cd ${MAIN_DIR}
     #
     #
-    clean_config OVERFLOW ${SETTE_CONFIG} 'tests'
-    #
-    sync_config  OVERFLOW ${SETTE_CONFIG} 'tests'
+    clean_config ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
+    sync_config  ${CONFIG_DIR0}/${config} ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
     #
     . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -a OVERFLOW ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS}" del_key "${DEL_KEYS}"
 fi
@@ -270,9 +269,8 @@ if [ ${config} == "LOCK_EXCHANGE" ] ;  then
     #
     # syncronisation if target directory/file exist (not done by makenemo)
     #
-    clean_config LOCK_EXCHANGE ${SETTE_CONFIG} 'tests'
-    #
-    sync_config  LOCK_EXCHANGE ${SETTE_CONFIG} 'tests'
+    clean_config ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
+    sync_config  ${CONFIG_DIR0}/${config} ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
     #
     . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -a LOCK_EXCHANGE ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS}" del_key "${DEL_KEYS}"
 fi
@@ -389,9 +387,8 @@ if [ ${config} == "VORTEX" ] ;  then
     #
     # syncronisation if target directory/file exist (not done by makenemo)
     #
-    clean_config VORTEX ${SETTE_CONFIG} 'tests'
-    #
-    sync_config  VORTEX ${SETTE_CONFIG} 'tests'
+    clean_config ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
+    sync_config  ${CONFIG_DIR0}/${config} ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
     #
     . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -a VORTEX ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES}  add_key "${ADD_KEYS}" del_key "${DEL_KEYS}"
 fi
@@ -583,9 +580,8 @@ if [ ${config} == "ICE_AGRIF" ] ;  then
     #
     # syncronisation if target directory/file exist (not done by makenemo)
     #
-    clean_config ICE_AGRIF ${SETTE_CONFIG} 'tests'
-    #
-    sync_config  ICE_AGRIF ${SETTE_CONFIG} 'tests'
+    clean_config ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
+    sync_config  ${CONFIG_DIR0}/${config} ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
     #
     # ICE_AGRIF uses linssh so remove key_qco if added by default
     . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -a ICE_AGRIF ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES}  add_key "${ADD_KEYS/key_qco/}" del_key "${DEL_KEYS}"
@@ -781,9 +777,8 @@ if [ ${config} == "ISOMIP+" ] ;  then
     #
     # syncronisation if target directory/file exist (not done by makenemo)
     #
-    clean_config ISOMIP+ ${SETTE_CONFIG} 'tests'
-    #
-    sync_config  ISOMIP+ ${SETTE_CONFIG} 'tests'
+    clean_config ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
+    sync_config  ${CONFIG_DIR0}/${config} ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
     #
     # ISOMIP+ uses ln_hpg_isf so remove key_qco if added by default
     . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -a ISOMIP+ ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS/key_qco/}" del_key "${DEL_KEYS}"
@@ -926,9 +921,8 @@ if [ ${config} == "SWG" ] && [ ${USING_QCO} == "yes" ] ;  then
     #
     # syncronisation if target directory/file exist (not done by makenemo)
     #
-    clean_config SWG ${SETTE_CONFIG} 'tests'
-    #
-    sync_config  SWG ${SETTE_CONFIG} 'tests'
+    clean_config ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
+    sync_config  ${CONFIG_DIR0}/${config} ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
     #
     . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -a SWG ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES}  add_key "${ADD_KEYS}" del_key "${DEL_KEYS}"
 fi
-- 
GitLab


From e8d1a34e06d7a5f483191d3433905528ea820955 Mon Sep 17 00:00:00 2001
From: Guillaume S <gsamson@mercator-ocean.fr>
Date: Sun, 13 Nov 2022 19:57:44 +0100
Subject: [PATCH 06/31] adapt mk scripts and fcm cfg files to compile nemo
 completely outside nemo directory

---
 mk/Fcheck_archfile.sh | 99 ++++++++++++++++++++++---------------------
 mk/Fmake_bld.sh       |  2 +-
 mk/Fmake_config.sh    |  2 +-
 mk/bldxag.cfg         |  4 +-
 mk/bldxagxcdf.cfg     |  4 +-
 mk/bldxcdf.cfg        |  4 +-
 mk/conv.cfg           |  2 +-
 7 files changed, 59 insertions(+), 58 deletions(-)

diff --git a/mk/Fcheck_archfile.sh b/mk/Fcheck_archfile.sh
index b6145132..f7aad910 100755
--- a/mk/Fcheck_archfile.sh
+++ b/mk/Fcheck_archfile.sh
@@ -73,19 +73,20 @@ EOF
 	eval "echo \"$line\" >> $2"
     done < $1
 }
+
 # cleaning related to the old version
-rm -f $( find ${COMPIL_DIR} -type f -name $1 -print )
+rm -f $( find $(dirname $1) -type f -name $(basename $1) -print )
 
 #
 if [ ${#3} -eq 0 ]; then # arch not specified
-    if [ ! -f ${COMPIL_DIR}/arch.history ]; then
+    if [ ! -f $(dirname $1)/arch.history ]; then
 	echo "Warning !!!"
 	echo "NO compiler chosen"
 	echo "Try makenemo -h for help"
 	echo "EXITING..."
 	exit 1 
     else # use the arch file defined in arch.history
-	myarch=$( cat ${COMPIL_DIR}/arch.history )	
+	myarch=$( cat $(dirname $1)/arch.history )
 	if [ ! -f $myarch ]; then
 	    echo "Warning !!!"
 	    echo "previously used arch file no more found:"
@@ -93,26 +94,26 @@ if [ ${#3} -eq 0 ]; then # arch not specified
 	    echo "EXITING..."
 	    exit 1 
 	else
-	    if [ -f ${COMPIL_DIR}/$1 ]; then
-		if [ "$2" != "nocpp" ] 
+	    if [ -f $1 ]; then
+		if [[ ! "$2" =~ "nocpp" ]]
 		then
 		    # has the cpp keys file been changed since we copied the arch file in ${COMPIL_DIR}?
-		    mycpp=$( ls -l ${COMPIL_DIR}/$2 | sed -e "s/.* -> //" )
-		    if [ "$mycpp" != "$( cat ${COMPIL_DIR}/cpp.history )" ]; then
-			echo $mycpp > ${COMPIL_DIR}/cpp.history
-			cpeval ${myarch} ${COMPIL_DIR}/$1
+		    mycpp=$( ls -l $2 | sed -e "s/.* -> //" )
+		    if [ "$mycpp" != "$( cat $(dirname $2)/cpp.history )" ]; then
+			echo $mycpp > $(dirname $2)/cpp.history
+			cpeval ${myarch} $1
 		    fi
 		    # has the cpp keys file been updated since we copied the arch file in ${COMPIL_DIR}?
-		    mycpp=$( find -L ${COMPIL_DIR} -cnewer ${COMPIL_DIR}/$1 -name $2 -print )
-		    [ ${#mycpp} -ne 0 ] && cpeval ${myarch} ${COMPIL_DIR}/$1
+		    mycpp=$( find -L $(dirname $2) -cnewer $(basename $1) -name $(basename $2) -print )
+		    [ ${#mycpp} -ne 0 ] && cpeval ${myarch} $1
 		fi
 		# has myarch file been updated since we copied it in ${COMPIL_DIR}?
 		myarchdir=$( dirname ${myarch} )
 		myarchname=$( basename ${myarch} )
-		myarch=$( find -L $myarchdir -cnewer ${COMPIL_DIR}/$1 -name $myarchname -print )
-		[ ${#myarch} -ne 0 ] && cpeval ${myarch} ${COMPIL_DIR}/$1
+		myarch=$( find -L $myarchdir -cnewer $(basename $1) -name $myarchname -print )
+		[ ${#myarch} -ne 0 ] && cpeval ${myarch} $1
 	    else
-		cpeval ${myarch} ${COMPIL_DIR}/$1
+		cpeval ${myarch} $1
 	    fi
 	fi
     fi
@@ -135,68 +136,68 @@ else
     fi
     myarch=$( find ${MAIN_DIR}/arch -name arch-${3}.fcm -print )
     # we were already using this arch file ?
-    if [ "$myarch" == "$( cat ${COMPIL_DIR}/arch.history )" ]; then 
-	if [ -f ${COMPIL_DIR}/$1 ]; then
-	    if [ "$2" != "nocpp" ] 
+    if [ "$myarch" == "$( cat $(dirname $1)/arch.history 2>/dev/null)" ]; then 
+	if [ -f $1 ]; then
+	    if [[ ! "$2" =~ "nocpp" ]]
 	    then
 		# has the cpp keys file been changed since we copied the arch file in ${COMPIL_DIR}?
-		mycpp=$( ls -l ${COMPIL_DIR}/$2 | sed -e "s/.* -> //" )
-		if [ "$mycpp" != "$( cat ${COMPIL_DIR}/cpp.history )" ]; then
-		    echo $mycpp > ${COMPIL_DIR}/cpp.history
-		    cpeval ${myarch} ${COMPIL_DIR}/$1
+		mycpp=$( ls -l $2 | sed -e "s/.* -> //" )
+		if [ "$mycpp" != "$( cat $(dirname $2)/cpp.history )" ]; then
+		    echo $mycpp > $(dirname $2)/cpp.history
+		    cpeval ${myarch} $1
 		fi
 		# has the cpp keys file been updated since we copied the arch file in ${COMPIL_DIR}?
-		mycpp=$( find -L ${COMPIL_DIR} -cnewer ${COMPIL_DIR}/$1 -name $2 -print )
-		[ ${#mycpp} -ne 0 ] && cpeval ${myarch} ${COMPIL_DIR}/$1
+		mycpp=$( find -L $(dirname $2) -cnewer $(basename $1) -name $(basename $2) -print )
+		[ ${#mycpp} -ne 0 ] && cpeval ${myarch} $1
 	    fi
 	    # has myarch file been updated since we copied it in ${COMPIL_DIR}?
-	    myarch=$( find -L ${MAIN_DIR}/arch -cnewer ${COMPIL_DIR}/$1 -name arch-${3}.fcm -print )
-	    [ ${#myarch} -ne 0 ] && cpeval ${myarch} ${COMPIL_DIR}/$1
+	    myarch=$( find -L ${MAIN_DIR}/arch -cnewer $(basename $1) -name arch-${3}.fcm -print )
+	    [ ${#myarch} -ne 0 ] && cpeval ${myarch} $1
 	else
-	    cpeval ${myarch} ${COMPIL_DIR}/$1
+	    cpeval ${myarch} $1
 	fi
     else
-	if [ "$2" != "nocpp" ] 
+	if [[ ! "$2" =~ "nocpp" ]]
 	then
-	    ls -l ${COMPIL_DIR}/$2 | sed -e "s/.* -> //" > ${COMPIL_DIR}/cpp.history
+	    ls -l $2 | sed -e "s/.* -> //" > $(dirname $2)/cpp.history
 	fi
-	echo ${myarch} > ${COMPIL_DIR}/arch.history
-	cpeval ${myarch} ${COMPIL_DIR}/$1
+	echo ${myarch} > $(dirname $1)/arch.history
+	cpeval ${myarch} $1
     fi
 fi
 
 #- do we need xios library?
 #- 2 cases: 
 #- in CONFIG directory looking for key_xios or key_iomput
-if [ "$1" == "arch_nemo.fcm" ]
+if [ "$(basename $1)" == "arch_nemo.fcm" ]
 then
-    if [ "$2" != "nocpp" ] 
+    if [[ ! "$2" =~ "nocpp" ]]
     then
-        use_iom=$( sed -e "s/#.*$//" ${COMPIL_DIR}/$2 | grep -c "key_xios\|key_iomput" )
+        use_iom=$( sed -e "s/#.*$//" $2 | grep -c "key_xios\|key_iomput" )
     else
         use_iom=0
     fi
-    have_lxios=$( sed -e "s/#.*$//" ${COMPIL_DIR}/$1 | grep -c "\-lxios" )
+    have_lxios=$( sed -e "s/#.*$//" $1 | grep -c "\-lxios" )
     if [[ ( $use_iom -eq 0 ) && ( $have_lxios -ge 1 ) ]]
     then 
-        sed -e "s/-lxios//g" ${COMPIL_DIR}/$1 > ${COMPIL_DIR}/tmp$$
-        mv -f ${COMPIL_DIR}/tmp$$ ${COMPIL_DIR}/$1
+        sed -e "s/-lxios//g" $1 > $(dirname $1)/tmp$$
+        mv -f $(dirname $1)/tmp$$ $1
     fi
 #- in TOOLS directory looking for USE xios
 else
-    use_iom=$( egrep --exclude-dir=.svn -r USE ${NEW_CONF}/src/* | grep -c xios )
-    have_lxios=$( sed -e "s/#.*$//" ${COMPIL_DIR}/$1 | grep -c "\-lxios" )
+    use_iom=$( egrep --exclude-dir=.svn -r USE ${MAIN_DIR}/src/* | grep -c xios )
+    have_lxios=$( sed -e "s/#.*$//" $1 | grep -c "\-lxios" )
     if [[ ( $use_iom -eq 0 ) || ( $have_lxios != 1 ) ]]
     then 
-        sed -e "s/-lxios//g" ${COMPIL_DIR}/$1 > ${COMPIL_DIR}/tmp$$
-        mv -f ${COMPIL_DIR}/tmp$$ ${COMPIL_DIR}/$1
+        sed -e "s/-lxios//g" $1 > $(dirname $1)/tmp$$
+        mv -f $(dirname $1)/tmp$$ $1
     fi
 fi
 
 #- do we need oasis libraries?
-if [ "$2" != "nocpp" ] 
+if [[ ! "$2" =~ "nocpp" ]]
 then
-    use_oasis=$( sed -e "s/#.*$//" ${COMPIL_DIR}/$2 | grep -c key_oasis3 )
+    use_oasis=$( sed -e "s/#.*$//" $2 | grep -c key_oasis3 )
 else
     use_oasis=0
 fi
@@ -206,26 +207,26 @@ if [[ ! -z "$XIOS_OASIS" ]]; then
 fi 
 for liboa in psmile.MPI1 mct mpeu scrip mpp_io
 do
-    have_liboa=$( sed -e "s/#.*$//" ${COMPIL_DIR}/$1 | grep -c "\-l${liboa}" )
+    have_liboa=$( sed -e "s/#.*$//" $1 | grep -c "\-l${liboa}" )
     if [[ ( $use_oasis -eq 0 ) && ( $have_liboa -ge 1 ) ]]
     then 
-	sed -e "s/-l${liboa}//g" ${COMPIL_DIR}/$1 > ${COMPIL_DIR}/tmp$$
-	mv -f ${COMPIL_DIR}/tmp$$ ${COMPIL_DIR}/$1
+	sed -e "s/-l${liboa}//g" $1 > $(dirname $1)/tmp$$
+	mv -f $(dirname $1)/tmp$$ $1
     fi
 done
 
 # Nemo debug ?
 if [ -n "${NEMO_DBG}" ]; then
-    if (! grep -q "^%DEBUG_FCFLAGS" ${COMPIL_DIR}/$1 ); then
+    if (! grep -q "^%DEBUG_FCFLAGS" $1 ); then
        echo "ERROR: You must defined '%DEBUG_FCFLAGS' in your arch file if you want to compile Nemo in debug mode using '-d' option"
        exit 1
     fi
     # duplicate the lines starting with %DEBUG_XXX and replace, in the duplicated line, %DEBUG_XXX by %XXX
-    sed -i "/^%DEBUG_/{p;s/^%DEBUG_\([^ ]*\)/%\1/;}" ${COMPIL_DIR}/$1
+    sed -i "/^%DEBUG_/{p;s/^%DEBUG_\([^ ]*\)/%\1/;}" $1
 else
-    if (! grep -q "^%PROD_FCFLAGS" ${COMPIL_DIR}/$1 ); then
+    if (! grep -q "^%PROD_FCFLAGS" $1 ); then
         echo "WARNING: '%PROD_FCFLAGS' not defined in your arch file, makenemo will use '%FCFLAGS' instead"
     fi
     # duplicate the lines starting with %PROD_XXX and replace, in the duplicated line, %PROD_XXX by %XXX
-    sed -i "/^%PROD_/{p;s/^%PROD_\([^ ]*\)/%\1/;}" ${COMPIL_DIR}/$1
+    sed -i "/^%PROD_/{p;s/^%PROD_\([^ ]*\)/%\1/;}" $1
 fi
diff --git a/mk/Fmake_bld.sh b/mk/Fmake_bld.sh
index 9973af3f..ebb2e48c 100755
--- a/mk/Fmake_bld.sh
+++ b/mk/Fmake_bld.sh
@@ -60,5 +60,5 @@ set -o posix
 [ ! -d ${3}/${2}     ] && \mkdir -p ${3}/${2}
 [ ! -d ${3}/${2}/BLD ] && \mkdir -p ${3}/${2}/BLD
 #[ ! -d ${1}/${2}/BLD ] && ln -sf ${3}/${2}/BLD ${1}/${2}/BLD
-[ -f ${3}/${2}/cpp_${2}.fcm ] && ln -sf ${3}/${2}/cpp_${2}.fcm ${COMPIL_DIR}/cpp.fcm
+[ -f ${3}/${2}/cpp_${2}.fcm ] && ln -sf ${3}/${2}/cpp_${2}.fcm ${3}/${2}/BLD/cpp.fcm
 rm -f  ${1}/${2}/BLD/fcm.bld.lock
diff --git a/mk/Fmake_config.sh b/mk/Fmake_config.sh
index 3ad6bb65..79673f0e 100755
--- a/mk/Fmake_config.sh
+++ b/mk/Fmake_config.sh
@@ -59,7 +59,7 @@ set -o posix
 \mkdir -p ${1}
 \mkdir -p ${1}/EXP00
 \mkdir -p ${1}/MY_SRC
-\cp -R -n ${2}/cpp_${2}.fcm ${1}/cpp_${1##*/}.fcm
+\cp -R -n ${2}/cpp_${2##*/}.fcm ${1}/cpp_${1##*/}.fcm
 for f in ${2}/EXPREF/*.xml ${2}/EXPREF/*namelist*; do
   if [ -L ${f} ]; then ln -sf $(readlink -f ${f}) ${1}/EXP00/$(basename ${f}); else cp -R -n ${f} ${1}/EXP00/.; fi
 done
diff --git a/mk/bldxag.cfg b/mk/bldxag.cfg
index 5b4db893..78a775d5 100644
--- a/mk/bldxag.cfg
+++ b/mk/bldxag.cfg
@@ -7,8 +7,8 @@ cfg::version                        1.0
 # Build information
 # ------------------------------------------------------------------------------
 
-inc $COMPIL_DIR/arch_nemo.fcm
-inc $COMPIL_DIR/cpp.fcm
+inc $NEMO_TDIR/$NEW_CONF/BLD/arch_nemo.fcm
+inc $NEMO_TDIR/$NEW_CONF/BLD/cpp.fcm
 
 search_src           1
 
diff --git a/mk/bldxagxcdf.cfg b/mk/bldxagxcdf.cfg
index d562b61b..28361348 100644
--- a/mk/bldxagxcdf.cfg
+++ b/mk/bldxagxcdf.cfg
@@ -7,8 +7,8 @@ cfg::version                        1.0
 # Build information
 # ------------------------------------------------------------------------------
 
-inc $COMPIL_DIR/arch_nemo.fcm
-inc $COMPIL_DIR/cpp.fcm
+inc $NEMO_TDIR/$NEW_CONF/BLD/arch_nemo.fcm
+inc $NEMO_TDIR/$NEW_CONF/BLD/cpp.fcm
 
 search_src           1
 
diff --git a/mk/bldxcdf.cfg b/mk/bldxcdf.cfg
index 0d752da9..5a175b45 100644
--- a/mk/bldxcdf.cfg
+++ b/mk/bldxcdf.cfg
@@ -7,8 +7,8 @@ cfg::version                        1.0
 # Build information
 # ------------------------------------------------------------------------------
 
-inc $COMPIL_DIR/arch_nemo.fcm
-inc $COMPIL_DIR/cpp.fcm
+inc $NEMO_TDIR/$NEW_CONF/BLD/arch_nemo.fcm
+inc $NEMO_TDIR/$NEW_CONF/BLD/cpp.fcm
 
 search_src           1
 
diff --git a/mk/conv.cfg b/mk/conv.cfg
index 759e5f26..f8757962 100644
--- a/mk/conv.cfg
+++ b/mk/conv.cfg
@@ -7,7 +7,7 @@ cfg::version                        1.0
 # ------------------------------------------------------------------------------
 # Build information
 # ------------------------------------------------------------------------------
-inc $COMPIL_DIR/$MYARCH
+inc $NEMO_TDIR/$NEW_CONF/BLD/$MYARCH
 
 bld::tool::cc        %CC
 bld::tool::cflags    %CFLAGS
-- 
GitLab


From cce977dcd4413ba1a5d0dad67b58166243551205 Mon Sep 17 00:00:00 2001
From: Guillaume S <gsamson@mercator-ocean.fr>
Date: Sun, 13 Nov 2022 20:36:43 +0100
Subject: [PATCH 07/31] adapt makenemo to compile nemo in any directory +
 improve "clean" option

---
 makenemo | 169 ++++++++++++++++++++++++-------------------------------
 1 file changed, 72 insertions(+), 97 deletions(-)

diff --git a/makenemo b/makenemo
index d1a48ca3..dd884a5b 100755
--- a/makenemo
+++ b/makenemo
@@ -88,7 +88,6 @@ x_u=''; x_a=''; x_m=''; x_t=''; x_b='';
 x_j='1'; x_e='none'; x_s='src'; x_v='1'
 x_c_cfg=0
 x_nocdf=0
-#x_name=''
 
 ##- Local variables ---
 b_n=$(basename ${0})
@@ -189,7 +188,6 @@ EOF
 	-d|--dirs|--comp)
 	    x_d=${2} ; shift ;;
 	-n|--name)
-	    #x_name=${2} ; shift ;;
 	    x_n=${2} ; shift ;;
 	-r|--ref)
 	    x_r=${2} ; shift ;;
@@ -224,41 +222,6 @@ EOF
     shift
 done
 
-#if [ -n "$x_name" ]   # is the configuration existing in cfgs or tests? or is it a new conf?
-if [ -n "$x_n" ]   # is the configuration existing in cfgs or tests? or is it a new conf?
-then
-    #incfg=$( find $CFGS_DIR   -type d -name $x_name | wc -l )   # this configuration exists in CFGS_DIR
-    #intst=$( find $TESTS_DIR  -type d -name $x_name | wc -l )   # this configuration exists in TESTS_DIR
-    incfg=$( find $CFGS_DIR   -type d -name $x_n | wc -l )   # this configuration exists in CFGS_DIR
-    intst=$( find $TESTS_DIR  -type d -name $x_n | wc -l )   # this configuration exists in TESTS_DIR
-    if [ $(( $incfg + $intst )) -eq 2 ] ; then
-	#echo -e "\033[0;31m\nERROR: the $x_name directory is found twice: in $CFGS_DIR and in $TESTS_DIR\033[0m\n"
-	echo -e "\033[0;31m\nERROR: the $x_n directory is found twice: in $CFGS_DIR and in $TESTS_DIR\033[0m\n"
-	exit 4
-    fi
-    if [ $(( $incfg + $intst )) -gt 0 ] ; then
-	if [ $x_c_cfg -eq 1 ] ; then   # if we just want to clean the config (do it here as it must exist)
-	    #x_n=$x_name                # must define x_n as it is used in Fclean_config.sh
-	    . ${COMPIL_DIR}/Fclean_config.sh
-	    exit 0
-	fi
-	#[ -n "$x_r" ] && echo -e "\nWARNING: $x_name configuration is already existing, we ignore \"-r $x_r\"\n"
-	#[ -n "$x_a" ] && echo -e "\nWARNING: $x_name configuration is already existing, we ignore \"-a $x_a\"\n"
-	[ -n "$x_r" ] && echo -e "\nWARNING: $x_n configuration is already existing, we ignore \"-r $x_r\"\n"
-	[ -n "$x_a" ] && echo -e "\nWARNING: $x_n configuration is already existing, we ignore \"-a $x_a\"\n"
-    fi
-    #if   [ $incfg -eq 1 ] ; then
-	#x_r=$x_name ; x_a=''  # reference configuration existing -> define/overwrite x_r
-    #elif [ $intst -eq 1 ] ; then
-	#x_a=$x_name ; x_r=''   # test      configuration existing -> define/overwrite x_a
-    #else
-    if [[ $incfg -eq 0 && $intst -eq 0 ]]; then
-	[  ${#x_c} -ne 0 ] && echo -e "\nWARNING: Compilation cleaning of a non-existing configuration, we ignore\n" && exit 0
-	[ $x_c_cfg -eq 1 ] && echo -e "\nWARNING: Configuration cleaning of a non-existing configuration, we ignore\n" && exit 0
-	#x_n=$x_name            # this is a new configuration      -> define
-    fi
-fi
-
 export NEW_CONF=${x_n}
 NBR_PRC=${x_j}
 CMP_NAM=${x_m}
@@ -270,21 +233,10 @@ NEMO_DBG=${x_b}
 
 [ "${CMP_NAM}" == 'all' ] && . ${COMPIL_DIR}/Flist_archfile.sh all && exit
 
-
-## No ref. cfg or demo selected
-if [[ -z "${REF_CONF}" && -z "${DEMO_CONF}" && $(( $incfg + $intst )) -eq 0 ]]; then
-    echo -e "\033[0;31m\nAt least a reference configuration ('-r'), a test case ('-a'), "
-    echo -e "a remote configuration ('-u') has to be choosen to build a new configuration!!!\033[0m"
-    ${COMPIL_DIR}/Flist_cfgs.sh
-    exit 2
-fi
-## At least one config has been requested
-
 ## 'all' arg: list all available configurations
 if [[ "${REF_CONF}" == 'all' || "${DEMO_CONF}" == 'all' ]]; then
     ${COMPIL_DIR}/Flist_cfgs.sh
     exit 2
-    ## Probably useless but who knows?
 elif [[ -n "${REF_CONF}" && -n "${DEMO_CONF}" ]]; then
     echo -e "\033[0;31m\nYou have to choose whether you work with:"
     echo -e "  - LTS configurations in ./cfgs  ('-r') or"
@@ -294,29 +246,62 @@ elif [ -n "${REF_CONF}" ]; then
     conf_file=ref_cfgs.txt ; export CONFIG_DIR=${CFGS_DIR} ; TML_CONF=${REF_CONF}
 elif [ -n "${DEMO_CONF}" ]; then
     conf_file=demo_cfgs.txt; export CONFIG_DIR=${TESTS_DIR}; TML_CONF=${DEMO_CONF}
-fi
- 
-## Reuse a working cfg
-grep -q "${TML_CONF} " ${CONFIG_DIR}/work_cfgs.txt 2>/dev/null && conf_file=work_cfgs.txt
-
-## Test if ref. cfg or demo case does exist
-if (! grep -q "${TML_CONF} " ${CONFIG_DIR}/$conf_file ); then
+elif grep -q "${NEW_CONF} " ${CFGS_DIR}/work_cfgs.txt ${TESTS_DIR}/work_cfgs.txt; then
+    conf_file=$( grep -l "${NEW_CONF} " ${CFGS_DIR}/work_cfgs.txt ${TESTS_DIR}/work_cfgs.txt )
+    export CONFIG_DIR=$( dirname $conf_file ); conf_file=$( basename $conf_file )
+    TML_CONF=${NEW_CONF}
+elif ! grep -q "${NEW_CONF} " ${CFGS_DIR}/work_cfgs.txt ${TESTS_DIR}/work_cfgs.txt; then
     echo -e "\033[0;31m\nThe reference configuration ('-r') or "
     echo -e "demonstration case ('-a') selected is not available!!!"
     echo -e "Check the option used and the available items in .txt files\033[0m"
     ${COMPIL_DIR}/Flist_cfgs.sh
     exit 2
 fi
+if [ -z "${NEW_CONF}" ]; then NEW_CONF=$TML_CONF; fi
+export NEMO_TDIR=${x_t:-$CONFIG_DIR}
 
-## If new cfg exists, work in it
-if [ -n "${NEW_CONF}" ]
-then
-    echo
-    printf "\nYou are installing a new configuration %s from %s " ${NEW_CONF} ${TML_CONF}
-    printf  "with sub-components: %s\n"  "${NEM_SUBDIR}"
-    echo
-else
-    NEW_CONF=${TML_CONF}
+
+# check configuration existence & clean it if asked
+if [ -n "$x_n" ]; then
+    incfg=$( find $NEMO_TDIR -type d -name $x_n | wc -l )   # this configuration exists in CFGS_DIR
+    if [ $incfg -eq 1 ] ; then
+        # CLEANING
+	if [ $x_c_cfg -eq 1 ] ; then
+	    . ${COMPIL_DIR}/Fclean_config.sh
+	    exit 0
+        elif [ ${#x_c} -ne 0 ]; then
+            # We coose the default light file
+            [ $x_nocdf -eq 1 ] && export USEBLD=bldxagxcdf.cfg || export USEBLD=bldxag.cfg
+            # We look after agrif
+            grep key_agrif ${NEMO_TDIR}/BLD/cpp.fcm 2>/dev/null && export AGRIFUSE=1 && export USEBLD=${USEBLD/xag/}
+            # fcm clean
+            fcm build ${x_c} --ignore-lock -v ${x_v} -j ${NBR_PRC} ${COMPIL_DIR}/$USEBLD || exit 1
+            # add remove for clean option
+    	    echo -e '\nCleaning '${NEW_CONF}' building directories and variables\n'
+    	    for dir in AGRIFLIB BLD LONG NEMOFILES REPRO_* SHORT WORK; do
+    	        rm -rf ${NEMO_TDIR}/${NEW_CONF}/$dir
+    	    done
+    	    for file in cpp.history cpp.fcm full_key_list.txt; do
+    	        rm -f ${NEMO_TDIR}/${NEW_CONF}/BLD/$file
+    	    done
+            exit 0
+	fi
+	if [ -n "$REF_CONF"  ]; then echo -e "\nWARNING: $x_n configuration is already existing, we ignore \"-r $REF_CONF\"\n"; REF_CONF=""; fi
+	if [ -n "$DEMO_CONF" ]; then echo -e "\nWARNING: $x_n configuration is already existing, we ignore \"-a $DEMO_CONF\"\n"; DEMO_CONF=""; fi
+    fi
+    if [ $incfg -eq 0 ]; then
+	[ $x_c_cfg -eq 1 ] && echo -e "\nWARNING: Configuration cleaning of a non-existing configuration, we ignore\n" && exit 0
+	[  ${#x_c} -ne 0 ] && echo -e "\nWARNING: Compilation cleaning of a non-existing configuration, we ignore\n" && exit 0
+    fi
+fi
+
+
+## No ref. cfg or demo selected
+if [[ -z "${REF_CONF}" && -z "${DEMO_CONF}" && $incfg -eq 0 ]]; then
+    echo -e "\033[0;31m\nAt least a reference configuration ('-r'), a test case ('-a'), "
+    echo -e "a remote configuration ('-u') has to be choosen to build a new configuration!!!\033[0m"
+    ${COMPIL_DIR}/Flist_cfgs.sh
+    exit 2
 fi
 
 ## Update sub-comps if needed
@@ -324,17 +309,22 @@ if [ -z "${NEM_SUBDIR}" ]; then
     NEM_SUBDIR=$( grep "${TML_CONF} " ${CONFIG_DIR}/${conf_file}  | awk '{$1 = ""; print $0}' )
 fi
 
-export NEMO_TDIR=${x_t:-$CONFIG_DIR}
 export NEM_SUBDIR="${NEM_SUBDIR}" NEW_CONF="${NEW_CONF}"
 
+## If new cfg exists, work in it
+if [ ${TML_CONF} != ${NEW_CONF} ]; then
+    echo
+    printf "\nYou are installing a new configuration %s from %s " ${NEW_CONF} ${TML_CONF}
+    if [ -n "${NEM_SUBDIR}" ]; then printf  "with sub-components: %s\n"  "${NEM_SUBDIR}"; fi
+    echo
+fi
+
 ## Save new configuration with sub-components set in work_cfgs.txt
 [ -f ${CONFIG_DIR}/work_cfgs.txt ] && sed -i "/${NEW_CONF} /d" ${CONFIG_DIR}/work_cfgs.txt
 echo ${NEW_CONF} "${NEM_SUBDIR}" >> ${CONFIG_DIR}/work_cfgs.txt
 
-cd ${CONFIG_DIR}
-
 ## Create new config even in existing one (mkdir with -p option, cp with -n)
-${COMPIL_DIR}/Fmake_config.sh ${NEMO_TDIR}/${NEW_CONF} ${TML_CONF}
+${COMPIL_DIR}/Fmake_config.sh ${NEMO_TDIR}/${NEW_CONF} ${CONFIG_DIR}/${TML_CONF}
 
 ## create EXP00 if needed
 [[ ! -d ${NEMO_TDIR}/${NEW_CONF}/EXP00 && -n "${REF_CONF}" ]] && \cp -R -n ${CONFIG_DIR}/${REF_CONF}/EXPREF ${NEMO_TDIR}/${NEW_CONF}/EXP00
@@ -349,12 +339,12 @@ ${COMPIL_DIR}/Fmake_config.sh ${NEMO_TDIR}/${NEW_CONF} ${TML_CONF}
 
 # build the complete list of the cpp keys of this configuration
 if [[ ${chk_key} -eq 1 || ${list_key} -eq 1 ]] ; then
-    for i in $( grep "^ *#.* key_" ${NEW_CONF}/WORK/* ); do
+    for i in $( grep "^ *#.* key_" ${NEMO_TDIR}/${NEW_CONF}/WORK/* ); do
 	echo $i | grep key_ | sed -e "s/=.*//"
     done \
-	| sort -d | uniq > ${COMPIL_DIR}/full_key_list.txt
+	| sort -d | uniq > ${NEMO_TDIR}/${NEW_CONF}/BLD/full_key_list.txt
     
-    [ ${list_key} -eq 1 ] && echo && cat ${COMPIL_DIR}/full_key_list.txt && exit 0
+    [ ${list_key} -eq 1 ] && echo && cat ${NEMO_TDIR}/${NEW_CONF}/BLD/full_key_list.txt && exit 0
 fi
 
 #- At this stage new configuration has been added, we add or remove keys
@@ -364,12 +354,12 @@ fi
 
 #- check that all keys are really existing...
 if [ $chk_key -eq 1 ] ; then
-    for kk in $( cat ${NEW_CONF}/cpp_${NEW_CONF}.fcm ); do
+    for kk in $( cat ${NEMO_TDIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm ); do
 	if [ "$( echo $kk | cut -c 1-4 )" == "key_" ]; then
 	    kk=${kk/=*/}
-	    if [ ! $( grep -w $kk ${COMPIL_DIR}/full_key_list.txt ) ]; then
+	    if [ ! $( grep -w $kk ${NEMO_TDIR}/${NEW_CONF}/BLD/full_key_list.txt ) ]; then
 		echo
-		echo "E R R O R : key "$kk" is not found in ${NEW_CONF}/WORK routines..."
+		echo "E R R O R : key "$kk" is not found in ${NEMO_TDIR}/${NEW_CONF}/WORK routines..."
 		echo "we stop..."
 		echo
 		exit 1
@@ -380,14 +370,9 @@ fi
 
 #- At this stage cpp keys have been updated. we can check the arch file
 #- When used for the first time, choose a compiler ---
-. ${COMPIL_DIR}/Fcheck_archfile.sh arch_nemo.fcm cpp.fcm ${CMP_NAM} || exit 3
-
-#- At this stage the configuration has beeen chosen
-#- We coose the default light file
-[ $x_nocdf -eq 1 ] && export USEBLD=bldxagxcdf.cfg || export USEBLD=bldxag.cfg
+. ${COMPIL_DIR}/Fcheck_archfile.sh ${NEMO_TDIR}/${NEW_CONF}/BLD/arch_nemo.fcm ${NEMO_TDIR}/${NEW_CONF}/BLD/cpp.fcm ${CMP_NAM} || exit 3
 
 #- We look after agrif
-grep key_agrif ${COMPIL_DIR}/cpp.fcm && export AGRIFUSE=1 && export USEBLD=${USEBLD/xag/}
 . ${COMPIL_DIR}/Fprep_agrif.sh ${NEW_CONF} ${NEMO_TDIR} arch_nemo.fcm || exit 3
 
 #-
@@ -398,40 +383,30 @@ grep key_agrif ${COMPIL_DIR}/cpp.fcm && export AGRIFUSE=1 && export USEBLD=${USE
 #- Compile ---
 
 if [ "${NBR_PRC}" -gt 0 ]; then
-    cd ${NEMO_TDIR}/${NEW_CONF} || cd -
 
     ## if AGRIF we do a first preprocessing
     if [[ ${#x_c} -eq 0 && "$AGRIFUSE" -eq 1 ]]; then
-	fcm build --ignore-lock -j 1 ${COMPIL_DIR}/bld_preproagr.cfg ||{ cd - ; exit 1 ;}
+	fcm build --ignore-lock -j 1 ${COMPIL_DIR}/bld_preproagr.cfg || exit 1
 	echo ''
 	echo "---------------------------------"
 	echo "CONV preprocessing successfull !!"
 	echo "---------------------------------"
 	echo ''
     fi
+
+    # We coose the default light file
+    [ $x_nocdf -eq 1 ] && export USEBLD=bldxagxcdf.cfg || export USEBLD=bldxag.cfg
+    # We look after agrif
+    grep key_agrif ${NEMO_TDIR}/BLD/cpp.fcm 2>/dev/null && export AGRIFUSE=1 && export USEBLD=${USEBLD/xag/}
     
-    fcm build ${x_c} --ignore-lock -v ${x_v} -j ${NBR_PRC} ${COMPIL_DIR}/$USEBLD ||{ cd - ; exit 1 ;}
+    fcm build ${x_c} --ignore-lock -v ${x_v} -j ${NBR_PRC} ${COMPIL_DIR}/$USEBLD || exit 1
 
     if [ -f ${NEMO_TDIR}/${NEW_CONF}/BLD/bin/nemo.exe ]; then
 	ln -sf ${NEMO_TDIR}/${NEW_CONF}/BLD/bin/nemo.exe  ${NEMO_TDIR}/${NEW_CONF}/EXP00/nemo
     fi
 
-    ## add remove for clean option
-    if [ ${#x_c} -ne 0 ]; then
-	echo -e '\nCleaning '${NEW_CONF}' building directories and variables\n'
-	for dir in AGRIFLIB BLD LONG NEMOFILES REPRO_* SHORT WORK; do
-	    rm -rf ${NEMO_TDIR}/${NEW_CONF}/$dir
-	done
-	for file in cpp.history cpp.fcm full_key_list.txt; do
-	    rm -f ${COMPIL_DIR}/$file
-	done
-    fi
     
 fi
 
-#- Come back to original directory ---
-cd -
-
-#-
 #- Unset variables
 ${COMPIL_DIR}/Fclean_var.sh
-- 
GitLab


From 865b28981487c07b05bb952f64eaa0e05ba0eca0 Mon Sep 17 00:00:00 2001
From: Guillaume S <gsamson@mercator-ocean.fr>
Date: Mon, 14 Nov 2022 12:20:08 +0100
Subject: [PATCH 08/31] agrif compilation bugfix

---
 makenemo             | 18 ++++++++----------
 mk/bld.cfg           |  4 ++--
 mk/bld_preproagr.cfg |  6 +++---
 3 files changed, 13 insertions(+), 15 deletions(-)

diff --git a/makenemo b/makenemo
index dd884a5b..cdddf458 100755
--- a/makenemo
+++ b/makenemo
@@ -263,7 +263,7 @@ export NEMO_TDIR=${x_t:-$CONFIG_DIR}
 
 # check configuration existence & clean it if asked
 if [ -n "$x_n" ]; then
-    incfg=$( find $NEMO_TDIR -type d -name $x_n | wc -l )   # this configuration exists in CFGS_DIR
+    incfg=$( find $NEMO_TDIR -type d -name $x_n 2>/dev/null | wc -l )   # this configuration exists in CFGS_DIR
     if [ $incfg -eq 1 ] ; then
         # CLEANING
 	if [ $x_c_cfg -eq 1 ] ; then
@@ -371,10 +371,6 @@ fi
 #- At this stage cpp keys have been updated. we can check the arch file
 #- When used for the first time, choose a compiler ---
 . ${COMPIL_DIR}/Fcheck_archfile.sh ${NEMO_TDIR}/${NEW_CONF}/BLD/arch_nemo.fcm ${NEMO_TDIR}/${NEW_CONF}/BLD/cpp.fcm ${CMP_NAM} || exit 3
-
-#- We look after agrif
-. ${COMPIL_DIR}/Fprep_agrif.sh ${NEW_CONF} ${NEMO_TDIR} arch_nemo.fcm || exit 3
-
 #-
 #_ END OF CONFIGURATION PHASE
 #_
@@ -384,6 +380,13 @@ fi
 
 if [ "${NBR_PRC}" -gt 0 ]; then
 
+    # We coose the default light file
+    [ $x_nocdf -eq 1 ] && export USEBLD=bldxagxcdf.cfg || export USEBLD=bldxag.cfg
+
+    # We look after agrif
+    grep key_agrif ${NEMO_TDIR}/${NEW_CONF}/BLD/cpp.fcm 2>/dev/null && export AGRIFUSE=1 && export USEBLD=${USEBLD/xag/}
+    . ${COMPIL_DIR}/Fprep_agrif.sh ${NEW_CONF} ${NEMO_TDIR} arch_nemo.fcm || exit 3
+    
     ## if AGRIF we do a first preprocessing
     if [[ ${#x_c} -eq 0 && "$AGRIFUSE" -eq 1 ]]; then
 	fcm build --ignore-lock -j 1 ${COMPIL_DIR}/bld_preproagr.cfg || exit 1
@@ -394,11 +397,6 @@ if [ "${NBR_PRC}" -gt 0 ]; then
 	echo ''
     fi
 
-    # We coose the default light file
-    [ $x_nocdf -eq 1 ] && export USEBLD=bldxagxcdf.cfg || export USEBLD=bldxag.cfg
-    # We look after agrif
-    grep key_agrif ${NEMO_TDIR}/BLD/cpp.fcm 2>/dev/null && export AGRIFUSE=1 && export USEBLD=${USEBLD/xag/}
-    
     fcm build ${x_c} --ignore-lock -v ${x_v} -j ${NBR_PRC} ${COMPIL_DIR}/$USEBLD || exit 1
 
     if [ -f ${NEMO_TDIR}/${NEW_CONF}/BLD/bin/nemo.exe ]; then
diff --git a/mk/bld.cfg b/mk/bld.cfg
index 67352be6..ebc688aa 100644
--- a/mk/bld.cfg
+++ b/mk/bld.cfg
@@ -7,8 +7,8 @@ cfg::version                        1.0
 # Build information
 # ------------------------------------------------------------------------------
 
-inc $COMPIL_DIR/arch_nemo.fcm
-inc $COMPIL_DIR/cpp.fcm
+inc $NEMO_TDIR/$NEW_CONF/BLD/arch_nemo.fcm
+inc $NEMO_TDIR/$NEW_CONF/BLD/cpp.fcm
 
 search_src           1
 
diff --git a/mk/bld_preproagr.cfg b/mk/bld_preproagr.cfg
index e901d829..3f015aa1 100644
--- a/mk/bld_preproagr.cfg
+++ b/mk/bld_preproagr.cfg
@@ -7,11 +7,11 @@ cfg::version                        1.0
 # Build information
 # ------------------------------------------------------------------------------
 
-inc $COMPIL_DIR/arch_nemo.fcm
-inc $COMPIL_DIR/cpp.fcm
+inc $NEMO_TDIR/$NEW_CONF/BLD/arch_nemo.fcm
+inc $NEMO_TDIR/$NEW_CONF/BLD/cpp.fcm
 search_src           1
 
-src::nemo                 $CONFIG_DIR/$NEW_CONF/WORK
+src::nemo                 $NEMO_TDIR/$NEW_CONF/WORK
 
 bld::target  lib_cray.f90 nemo.f90 agrif_user.f90 agrif2model.f90 
 
-- 
GitLab


From 2836ff662d697ff02b36ad0b9b03521fa9c0de4a Mon Sep 17 00:00:00 2001
From: Guillaume S <gsamson@mercator-ocean.fr>
Date: Mon, 14 Nov 2022 12:53:44 +0100
Subject: [PATCH 09/31] fix physics tests for LOCK_EXCHANGE & OVERFLOW

---
 sette/sette_test-cases.sh | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/sette/sette_test-cases.sh b/sette/sette_test-cases.sh
index aec16728..b55dd0c5 100755
--- a/sette/sette_test-cases.sh
+++ b/sette/sette_test-cases.sh
@@ -220,12 +220,12 @@ if [ ${config} == "OVERFLOW" ] && [ ${DO_PHYOPTS} == "1" ] ;  then
     else
 	ITEND=6120
     fi
-    cd ${CONFIG_DIR}/${NEW_CONF}/EXP00
+    cd ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}/EXP00
 
     for file in $(echo `ls namelist_*_cfg `) ; do
         TEST_NAME=`echo $file | sed -e "s/namelist_//" | sed -e "s/_cfg//"`
         TEST_NAME="EXP-${TEST_NAME}"
-        if [ ! -d ${CONFIG_DIR}/${NEW_CONF}/${TEST_NAME} ] ; then mkdir ${CONFIG_DIR}/${NEW_CONF}/${TEST_NAME} ; fi
+        if [ ! -d ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}/${TEST_NAME} ] ; then mkdir -p ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}/${TEST_NAME} ; fi
         export TEST_NAME="${TEST_NAME}"
          ##
         cd ${SETTE_DIR}
@@ -237,7 +237,7 @@ if [ ${config} == "OVERFLOW" ] && [ ${DO_PHYOPTS} == "1" ] ;  then
         if [ -f ${JOB_FILE} ] ; then \rm ${JOB_FILE} ; fi
         cd ${EXE_DIR}
         rm namelist_*_*_*_*
-        cp -pL ${CONFIG_DIR}/${NEW_CONF}/EXP00/$file namelist_cfg
+        cp -pL ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}/EXP00/$file namelist_cfg
 	set_namelist namelist_cfg nn_it000 1
 	set_namelist namelist_cfg nn_itend ${ITEND}
         set_namelist_opt namelist_cfg ln_timing ${USING_TIMING} .true. .false.
@@ -335,13 +335,14 @@ if [ ${config} == "LOCK_EXCHANGE" ] && [ ${DO_PHYOPTS} == "1" ] ;  then
     else
 	ITEND=61200
     fi
-    cd ${CONFIG_DIR}/${NEW_CONF}/EXP00
+    cd ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}/EXP00
+
 
     for file in $(echo `ls namelist_*_cfg `) ; do
         echo ''
         TEST_NAME=`echo $file | sed -e "s/namelist_//" | sed -e "s/_cfg//"`
         TEST_NAME="EXP-${TEST_NAME}"
-        `mkdir ${CONFIG_DIR}/${NEW_CONF}/${TEST_NAME}`
+        mkdir -p ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}/${TEST_NAME}
         export TEST_NAME="${TEST_NAME}"
         ##  
         cd ${SETTE_DIR}
@@ -353,7 +354,7 @@ if [ ${config} == "LOCK_EXCHANGE" ] && [ ${DO_PHYOPTS} == "1" ] ;  then
         if [ -f ${JOB_FILE} ] ; then \rm ${JOB_FILE} ; fi
         cd ${EXE_DIR}
         rm namelist_*_*_*_*
-        cp -pL ${CONFIG_DIR}/${NEW_CONF}/EXP00/$file namelist_cfg
+        cp -pL ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}/EXP00/$file namelist_cfg
 	set_namelist namelist_cfg nn_it000 1
         set_namelist namelist_cfg nn_itend ${ITEND}
         set_namelist_opt namelist_cfg ln_timing ${USING_TIMING} .true. .false.
-- 
GitLab


From f462b1fa8e240d89daa2ad38c48c1cc8a39c29f5 Mon Sep 17 00:00:00 2001
From: Guillaume S <gsamson@mercator-ocean.fr>
Date: Tue, 29 Nov 2022 09:19:08 +0100
Subject: [PATCH 10/31] apply Simon suggestions from !178

---
 makenemo | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/makenemo b/makenemo
index cdddf458..96464483 100755
--- a/makenemo
+++ b/makenemo
@@ -246,10 +246,15 @@ elif [ -n "${REF_CONF}" ]; then
     conf_file=ref_cfgs.txt ; export CONFIG_DIR=${CFGS_DIR} ; TML_CONF=${REF_CONF}
 elif [ -n "${DEMO_CONF}" ]; then
     conf_file=demo_cfgs.txt; export CONFIG_DIR=${TESTS_DIR}; TML_CONF=${DEMO_CONF}
-elif grep -q "${NEW_CONF} " ${CFGS_DIR}/work_cfgs.txt ${TESTS_DIR}/work_cfgs.txt; then
-    conf_file=$( grep -l "${NEW_CONF} " ${CFGS_DIR}/work_cfgs.txt ${TESTS_DIR}/work_cfgs.txt )
+elif [ $( grep -l "^${NEW_CONF} " */work_cfgs.txt | wc -l ) -eq 1 ]; then
+    conf_file=$( grep -l "^${NEW_CONF} " ${CFGS_DIR}/work_cfgs.txt ${TESTS_DIR}/work_cfgs.txt )
     export CONFIG_DIR=$( dirname $conf_file ); conf_file=$( basename $conf_file )
     TML_CONF=${NEW_CONF}
+elif [ $( grep -l "^${NEW_CONF} " */work_cfgs.txt | wc -l ) -eq 2 ]; then
+    echo -e "\033[0;31m\nUser configuration is present in both"
+    echo -e "cfgs/work_cfgs.txt and tests/work_cfgs.txt files"
+    echo -e "Please choose only one \033[0m"
+    exit 2
 elif ! grep -q "${NEW_CONF} " ${CFGS_DIR}/work_cfgs.txt ${TESTS_DIR}/work_cfgs.txt; then
     echo -e "\033[0;31m\nThe reference configuration ('-r') or "
     echo -e "demonstration case ('-a') selected is not available!!!"
-- 
GitLab


From fa8fd0c00e689da08aba9921ee6b6f1971411329 Mon Sep 17 00:00:00 2001
From: Guillaume S <gsamson@mercator-ocean.fr>
Date: Wed, 14 Dec 2022 17:01:15 +0100
Subject: [PATCH 11/31] apply Simon review

---
 makenemo           | 62 ++++++++++++++++++++++++----------------------
 mk/Fmake_config.sh |  4 +--
 2 files changed, 34 insertions(+), 32 deletions(-)

diff --git a/makenemo b/makenemo
index 96464483..668eed08 100755
--- a/makenemo
+++ b/makenemo
@@ -246,35 +246,39 @@ elif [ -n "${REF_CONF}" ]; then
     conf_file=ref_cfgs.txt ; export CONFIG_DIR=${CFGS_DIR} ; TML_CONF=${REF_CONF}
 elif [ -n "${DEMO_CONF}" ]; then
     conf_file=demo_cfgs.txt; export CONFIG_DIR=${TESTS_DIR}; TML_CONF=${DEMO_CONF}
-elif [ $( grep -l "^${NEW_CONF} " */work_cfgs.txt | wc -l ) -eq 1 ]; then
+elif [ $( grep -l "^${NEW_CONF} " */work_cfgs.txt 2> /dev/null | wc -l ) -eq 1 ]; then
     conf_file=$( grep -l "^${NEW_CONF} " ${CFGS_DIR}/work_cfgs.txt ${TESTS_DIR}/work_cfgs.txt )
     export CONFIG_DIR=$( dirname $conf_file ); conf_file=$( basename $conf_file )
     TML_CONF=${NEW_CONF}
-elif [ $( grep -l "^${NEW_CONF} " */work_cfgs.txt | wc -l ) -eq 2 ]; then
+elif [ $( grep -l "^${NEW_CONF} " */work_cfgs.txt 2> /dev/null | wc -l ) -eq 2 ]; then
     echo -e "\033[0;31m\nUser configuration is present in both"
     echo -e "cfgs/work_cfgs.txt and tests/work_cfgs.txt files"
     echo -e "Please choose only one \033[0m"
     exit 2
-elif ! grep -q "${NEW_CONF} " ${CFGS_DIR}/work_cfgs.txt ${TESTS_DIR}/work_cfgs.txt; then
+elif ! grep -q "^${NEW_CONF} " ${CFGS_DIR}/work_cfgs.txt ${TESTS_DIR}/work_cfgs.txt 2> /dev/null; then
     echo -e "\033[0;31m\nThe reference configuration ('-r') or "
     echo -e "demonstration case ('-a') selected is not available!!!"
     echo -e "Check the option used and the available items in .txt files\033[0m"
     ${COMPIL_DIR}/Flist_cfgs.sh
     exit 2
+else
+    exit 2
 fi
+
 if [ -z "${NEW_CONF}" ]; then NEW_CONF=$TML_CONF; fi
 export NEMO_TDIR=${x_t:-$CONFIG_DIR}
 
 
 # check configuration existence & clean it if asked
-if [ -n "$x_n" ]; then
-    incfg=$( find $NEMO_TDIR -type d -name $x_n 2>/dev/null | wc -l )   # this configuration exists in CFGS_DIR
-    if [ $incfg -eq 1 ] ; then
-        # CLEANING
-	if [ $x_c_cfg -eq 1 ] ; then
-	    . ${COMPIL_DIR}/Fclean_config.sh
-	    exit 0
-        elif [ ${#x_c} -ne 0 ]; then
+incfg=$( find $NEMO_TDIR -type d -maxdepth 1 -name ${TML_CONF} 2>/dev/null | wc -l )   # this configuration exists in CFGS_DIR
+if [ $incfg -eq 1 ] ; then
+    # CLEANING
+    if [ $x_c_cfg -eq 1 ] ; then
+        . ${COMPIL_DIR}/Fclean_config.sh
+        exit 0
+    elif [ ${#x_c} -ne 0 ]; then
+        read -p "Are you sure that you want to clean $TML_CONF configuration ? " -n 1 -r; echo
+        if [[ $REPLY =~ ^[Yy]$ ]]; then
             # We coose the default light file
             [ $x_nocdf -eq 1 ] && export USEBLD=bldxagxcdf.cfg || export USEBLD=bldxag.cfg
             # We look after agrif
@@ -282,22 +286,24 @@ if [ -n "$x_n" ]; then
             # fcm clean
             fcm build ${x_c} --ignore-lock -v ${x_v} -j ${NBR_PRC} ${COMPIL_DIR}/$USEBLD || exit 1
             # add remove for clean option
-    	    echo -e '\nCleaning '${NEW_CONF}' building directories and variables\n'
-    	    for dir in AGRIFLIB BLD LONG NEMOFILES REPRO_* SHORT WORK; do
-    	        rm -rf ${NEMO_TDIR}/${NEW_CONF}/$dir
-    	    done
-    	    for file in cpp.history cpp.fcm full_key_list.txt; do
-    	        rm -f ${NEMO_TDIR}/${NEW_CONF}/BLD/$file
-    	    done
+            echo -e '\nCleaning '${NEW_CONF}' building directories and variables\n'
+            for dir in AGRIFLIB BLD LONG NEMOFILES REPRO_* SHORT WORK; do
+               rm -rf ${NEMO_TDIR}/${NEW_CONF}/$dir
+            done
+            for file in cpp.history cpp.fcm full_key_list.txt; do
+               rm -f ${NEMO_TDIR}/${NEW_CONF}/BLD/$file
+            done
             exit 0
-	fi
-	if [ -n "$REF_CONF"  ]; then echo -e "\nWARNING: $x_n configuration is already existing, we ignore \"-r $REF_CONF\"\n"; REF_CONF=""; fi
-	if [ -n "$DEMO_CONF" ]; then echo -e "\nWARNING: $x_n configuration is already existing, we ignore \"-a $DEMO_CONF\"\n"; DEMO_CONF=""; fi
-    fi
-    if [ $incfg -eq 0 ]; then
-	[ $x_c_cfg -eq 1 ] && echo -e "\nWARNING: Configuration cleaning of a non-existing configuration, we ignore\n" && exit 0
-	[  ${#x_c} -ne 0 ] && echo -e "\nWARNING: Compilation cleaning of a non-existing configuration, we ignore\n" && exit 0
+        else
+            echo "cleaning cancelled"
+            exit 2
+        fi
     fi
+    if [[ -n "$x_n" && -n "$REF_CONF"  ]]; then echo -e "\nWARNING: $x_n configuration is already existing, we ignore \"-r $REF_CONF\"\n"; REF_CONF=""; fi
+    if [[ -n "$x_n" && -n "$DEMO_CONF" ]]; then echo -e "\nWARNING: $x_n configuration is already existing, we ignore \"-a $DEMO_CONF\"\n"; DEMO_CONF=""; fi
+elif [ $incfg -eq 0 ]; then
+    [ $x_c_cfg -eq 1 ] && echo -e "\nWARNING: Configuration cleaning of a non-existing configuration, we ignore\n" && exit 0
+    [  ${#x_c} -ne 0 ] && echo -e "\nWARNING: Compilation cleaning of a non-existing configuration, we ignore\n" && exit 0
 fi
 
 
@@ -325,16 +331,12 @@ if [ ${TML_CONF} != ${NEW_CONF} ]; then
 fi
 
 ## Save new configuration with sub-components set in work_cfgs.txt
-[ -f ${CONFIG_DIR}/work_cfgs.txt ] && sed -i "/${NEW_CONF} /d" ${CONFIG_DIR}/work_cfgs.txt
+[ -f ${CONFIG_DIR}/work_cfgs.txt ] && sed -i "/^${NEW_CONF} /d" ${CONFIG_DIR}/work_cfgs.txt
 echo ${NEW_CONF} "${NEM_SUBDIR}" >> ${CONFIG_DIR}/work_cfgs.txt
 
 ## Create new config even in existing one (mkdir with -p option, cp with -n)
 ${COMPIL_DIR}/Fmake_config.sh ${NEMO_TDIR}/${NEW_CONF} ${CONFIG_DIR}/${TML_CONF}
 
-## create EXP00 if needed
-[[ ! -d ${NEMO_TDIR}/${NEW_CONF}/EXP00 && -n "${REF_CONF}" ]] && \cp -R -n ${CONFIG_DIR}/${REF_CONF}/EXPREF ${NEMO_TDIR}/${NEW_CONF}/EXP00
-[[ ! -d ${NEMO_TDIR}/${NEW_CONF}/EXP00 && -n "${DEMO_CONF}" ]] && \cp -R -n ${CONFIG_DIR}/${DEMO_CONF}/EXPREF ${NEMO_TDIR}/${NEW_CONF}/EXP00
-
 #- Create the WORK ---
 #- Clean links and librairies ---
 #- Creating the good links, at first on OCE ---
diff --git a/mk/Fmake_config.sh b/mk/Fmake_config.sh
index 79673f0e..6a3e942b 100755
--- a/mk/Fmake_config.sh
+++ b/mk/Fmake_config.sh
@@ -59,9 +59,9 @@ set -o posix
 \mkdir -p ${1}
 \mkdir -p ${1}/EXP00
 \mkdir -p ${1}/MY_SRC
-\cp -R -n ${2}/cpp_${2##*/}.fcm ${1}/cpp_${1##*/}.fcm
+[ "${2}/cpp_${2##*/}.fcm" != "${1}/cpp_${1##*/}.fcm" ] && \cp -R -n ${2}/cpp_${2##*/}.fcm ${1}/cpp_${1##*/}.fcm
 for f in ${2}/EXPREF/*.xml ${2}/EXPREF/*namelist*; do
   if [ -L ${f} ]; then ln -sf $(readlink -f ${f}) ${1}/EXP00/$(basename ${f}); else cp -R -n ${f} ${1}/EXP00/.; fi
 done
-[ -f ${2}/EXPREF/AGRIF_FixedGrids.in ] &&  \cp -a -n ${2}/EXPREF/AGRIF_FixedGrids.in ${1}/EXP00/.
+[ -f ${2}/EXPREF/AGRIF_FixedGrids.in ] && \cp -a -n ${2}/EXPREF/AGRIF_FixedGrids.in ${1}/EXP00/.
 [ -d    ${2}/MY_SRC ] && \cp -an ${2}/MY_SRC/* ${1}/MY_SRC/. 2> /dev/null
-- 
GitLab


From 3477947b7f764545095e7bdcc1b01a5353397e77 Mon Sep 17 00:00:00 2001
From: Guillaume S <gsamson@mercator-ocean.fr>
Date: Wed, 9 Nov 2022 12:29:23 +0100
Subject: [PATCH 12/31] fix tests dir

---
 sette/sette_test-cases.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sette/sette_test-cases.sh b/sette/sette_test-cases.sh
index 1d879f30..ee12e28f 100755
--- a/sette/sette_test-cases.sh
+++ b/sette/sette_test-cases.sh
@@ -108,7 +108,7 @@ if [ ${USING_MPMD} == "no" ]
 fi
 #
 # Directory to run the tests
-CONFIG_DIR0=${MAIN_DIR}/cfgs
+CONFIG_DIR0=${MAIN_DIR}/tests
 TOOLS_DIR=${MAIN_DIR}/tools
 
 if [ -n "${CUSTOM_DIR}" ]; then
-- 
GitLab


From d46abc33964ab0b15b80b64bb98c6d7fefe5c75b Mon Sep 17 00:00:00 2001
From: Guillaume S <gsamson@mercator-ocean.fr>
Date: Wed, 9 Nov 2022 19:04:57 +0100
Subject: [PATCH 13/31] change makenemo arguments to avoid using "-t" option
 when not needed

---
 sette/sette_reference-configurations.sh | 18 +++++++++---------
 sette/sette_test-cases.sh               | 12 ++++++------
 2 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/sette/sette_reference-configurations.sh b/sette/sette_reference-configurations.sh
index 379ee02a..49bcbaca 100755
--- a/sette/sette_reference-configurations.sh
+++ b/sette/sette_reference-configurations.sh
@@ -159,7 +159,7 @@ if [ ${config} == "GYRE_PISCES" ] ;  then
     clean_config GYRE_PISCES ${SETTE_CONFIG} 'cfgs'
     #
     # GYRE uses linssh so remove key_qco if added by default
-    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r GYRE_PISCES -t ${CMP_DIR:-${CONFIG_DIR0}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS/key_qco/}" del_key "${DEL_KEYS}"
+    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r GYRE_PISCES ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS/key_qco/}" del_key "${DEL_KEYS}"
 fi
 if [ ${config} == "GYRE_PISCES" ] && [ ${DO_RESTART} == "1" ] ;  then
 ## Restartability tests for GYRE_PISCES
@@ -305,7 +305,7 @@ if [ ${config} == "ORCA2_ICE_PISCES" ] ;  then
     sync_config  ORCA2_ICE_PISCES ${SETTE_CONFIG} 'cfgs'
     clean_config ORCA2_ICE_PISCES ${SETTE_CONFIG} 'cfgs'
     #
-    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r ORCA2_ICE_PISCES -t ${CMP_DIR:-${CONFIG_DIR0}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS}" del_key "${DEL_KEYS}"
+    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r ORCA2_ICE_PISCES ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS}" del_key "${DEL_KEYS}"
 fi
 if [ ${config} == "ORCA2_ICE_PISCES" ] && [ ${DO_RESTART} == "1" ] ;  then
 ## Restartability tests for ORCA2_ICE_PISCES
@@ -593,7 +593,7 @@ if [ ${config} == "ORCA2_OFF_PISCES" ] ;  then
     clean_config ${SETTE_CONFIG} ORCA2_OFF_PISCES_ST 'cfgs'
     #
     # ORCA2_OFF_PISCES uses linssh so remove key_qco if added by default
-    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r ORCA2_OFF_PISCES -t ${CMP_DIR:-${CONFIG_DIR0}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS/key_qco/}" del_key "${DEL_KEYS}"
+    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r ORCA2_OFF_PISCES ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS/key_qco/}" del_key "${DEL_KEYS}"
 fi
 if [ ${config} == "ORCA2_OFF_PISCES" ] && [ ${DO_RESTART} == "1" ] ;  then
 ## Restartability tests for ORCA2_OFF_PISCES
@@ -769,7 +769,7 @@ if [ ${config} == "AMM12" ] ;  then
     sync_config  AMM12 ${SETTE_CONFIG} 'cfgs'
     clean_config AMM12 ${SETTE_CONFIG} 'cfgs'
     #
-    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r AMM12 -t ${CMP_DIR:-${CONFIG_DIR0}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS}" del_key "${DEL_KEYS}"
+    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r AMM12 ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS}" del_key "${DEL_KEYS}"
 fi
 if [ ${config} == "AMM12" ] && [ ${DO_RESTART} == "1" ] ;  then
     ## Restartability tests for AMM12
@@ -904,7 +904,7 @@ if [ ${config} == "SAS" ] ;  then
     clean_config ORCA2_SAS_ICE ${SETTE_CONFIG} 'cfgs'
     #
     # ORCA2_SAS_ICE uses linssh so remove key_qco if added by default
-    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r ORCA2_SAS_ICE -t ${CMP_DIR:-${CONFIG_DIR0}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS/key_qco/}" del_key "${DEL_KEYS}"
+    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r ORCA2_SAS_ICE ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS/key_qco/}" del_key "${DEL_KEYS}"
 fi
 if [ ${config} == "SAS" ] && [ ${DO_RESTART} == "1" ] ;  then
 ## Restartability tests
@@ -1051,7 +1051,7 @@ if [ ${config} == "ORCA2_ICE_OBS" ] ;  then
     sync_config  ORCA2_ICE_PISCES ${SETTE_CONFIG} 'cfgs'
     clean_config ORCA2_ICE_PISCES ${SETTE_CONFIG} 'cfgs'
     #
-    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r ORCA2_ICE_PISCES -d "OCE ICE" -t ${CMP_DIR:-${CONFIG_DIR0}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "key_asminc ${ADD_KEYS}" del_key "key_top ${DEL_KEYS}"
+    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r ORCA2_ICE_PISCES -d "OCE ICE" ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "key_asminc ${ADD_KEYS}" del_key "key_top ${DEL_KEYS}"
 fi
 if [ ${config} == "ORCA2_ICE_OBS" ] && [ ${DO_RESTART} == "1" ] ;  then
 ## Reproducibility tests
@@ -1177,7 +1177,7 @@ if [ ${config} == "AGRIF" ] ;  then
     #
     # AGRIF_DEMO does not yet support nn_hls=2 => key_loop_fusion can not be used
 #    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r AGRIF_DEMO -j ${CMPL_CORES} add_key "${ADD_KEYS/key_loop_fusion}" del_key "${DEL_KEYS}"
-    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r AGRIF_DEMO -t ${CMP_DIR:-${CONFIG_DIR0}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS}" del_key "${DEL_KEYS}"
+    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r AGRIF_DEMO ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS}" del_key "${DEL_KEYS}"
 fi
 if [ ${config} == "AGRIF" ] && [ ${DO_RESTART} == "1" ] ;  then
 ## Restartability tests
@@ -1493,7 +1493,7 @@ if [ ${config} == "AGRIF" ] && [ ${DO_CORRUPT} == "1" ] ;  then
     clean_config AGRIF_DEMO ${SETTE_CONFIG} 'cfgs'
     #
     # AGRIF_DEMO does not yet support nn_hls=2 => key_loop_fusion can not be used
-    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r AGRIF_DEMO -t ${CMP_DIR:-${CONFIG_DIR0}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS/key_loop_fusion}" del_key "key_agrif ${DEL_KEYS}"
+    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r AGRIF_DEMO ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS/key_loop_fusion}" del_key "key_agrif ${DEL_KEYS}"
     cd ${SETTE_DIR}
     . ./prepare_exe_dir.sh
     set_valid_dir
@@ -1541,7 +1541,7 @@ if [ ${config} == "WED025" ] ;  then
     clean_config WED025 ${SETTE_CONFIG} 'cfgs'
     #
     # WED025 uses ln_hpg_isf so remove key_qco if added by default
-    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r WED025 -t ${CMP_DIR:-${CONFIG_DIR0}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS/key_qco/}" del_key "${DEL_KEYS}"
+    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r WED025 ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS/key_qco/}" del_key "${DEL_KEYS}"
 fi
 if [ ${config} == "WED025" ] && [ ${DO_RESTART} == "1" ] ;  then
 ## Restartability tests
diff --git a/sette/sette_test-cases.sh b/sette/sette_test-cases.sh
index ee12e28f..3a77b2e6 100755
--- a/sette/sette_test-cases.sh
+++ b/sette/sette_test-cases.sh
@@ -159,7 +159,7 @@ if [ ${config} == "OVERFLOW" ] ;  then
     #
     sync_config  OVERFLOW ${SETTE_CONFIG} 'tests'
     #
-    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -a OVERFLOW -t ${CMP_DIR:-${CONFIG_DIR0}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS}" del_key "${DEL_KEYS}"
+    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -a OVERFLOW ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS}" del_key "${DEL_KEYS}"
 fi
 if [ ${config} == "OVERFLOW" ] && [ ${DO_RESTART} == "1" ] ;  then
     ## Restartability tests for OVERFLOW
@@ -276,7 +276,7 @@ if [ ${config} == "LOCK_EXCHANGE" ] ;  then
     #
     sync_config  LOCK_EXCHANGE ${SETTE_CONFIG} 'tests'
     #
-    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -a LOCK_EXCHANGE -t ${CMP_DIR:-${CONFIG_DIR0}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS}" del_key "${DEL_KEYS}"
+    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -a LOCK_EXCHANGE ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS}" del_key "${DEL_KEYS}"
 fi
 if [ ${config} == "LOCK_EXCHANGE" ] && [ ${DO_RESTART} == "1" ] ;  then
     ## Restartability tests for LOCK_EXCHANGE
@@ -395,7 +395,7 @@ if [ ${config} == "VORTEX" ] ;  then
     #
     sync_config  VORTEX ${SETTE_CONFIG} 'tests'
     #
-    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -a VORTEX -t ${CMP_DIR:-${CONFIG_DIR0}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES}  add_key "${ADD_KEYS}" del_key "${DEL_KEYS}"
+    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -a VORTEX ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES}  add_key "${ADD_KEYS}" del_key "${DEL_KEYS}"
 fi
 if [ ${config} == "VORTEX" ] && [ ${DO_RESTART} == "1" ] ;  then
 ## Restartability tests for VORTEX
@@ -590,7 +590,7 @@ if [ ${config} == "ICE_AGRIF" ] ;  then
     sync_config  ICE_AGRIF ${SETTE_CONFIG} 'tests'
     #
     # ICE_AGRIF uses linssh so remove key_qco if added by default
-    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -a ICE_AGRIF -t ${CMP_DIR:-${CONFIG_DIR0}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES}  add_key "${ADD_KEYS/key_qco/}" del_key "${DEL_KEYS}"
+    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -a ICE_AGRIF ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES}  add_key "${ADD_KEYS/key_qco/}" del_key "${DEL_KEYS}"
 fi
 if [ ${config} == "ICE_AGRIF" ] && [ ${DO_RESTART} == "1" ] ;  then
 ## Restartability tests for ICE_AGRIF
@@ -788,7 +788,7 @@ if [ ${config} == "ISOMIP+" ] ;  then
     sync_config  ISOMIP+ ${SETTE_CONFIG} 'tests'
     #
     # ISOMIP+ uses ln_hpg_isf so remove key_qco if added by default
-    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -a ISOMIP+ -t ${CMP_DIR:-${CONFIG_DIR0}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS/key_qco/}" del_key "${DEL_KEYS}"
+    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -a ISOMIP+ ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS/key_qco/}" del_key "${DEL_KEYS}"
 fi
 if [ ${config} == "ISOMIP+" ] && [ ${DO_RESTART} == "1" ] ;  then
 ## Restartability tests
@@ -932,7 +932,7 @@ if [ ${config} == "SWG" ] && [ ${USING_QCO} == "yes" ] ;  then
     #
     sync_config  SWG ${SETTE_CONFIG} 'tests'
     #
-    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -a SWG -t ${CMP_DIR:-${CONFIG_DIR0}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES}  add_key "${ADD_KEYS}" del_key "${DEL_KEYS}"
+    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -a SWG ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES}  add_key "${ADD_KEYS}" del_key "${DEL_KEYS}"
 fi
 if [ ${config} == "SWG" ] && [ ${DO_RESTART} == "1" ] && [ ${USING_QCO} == "yes" ] ;  then
 ## Restartability tests for SWG
-- 
GitLab


From afbdad111883e98348e3396a6b6a8c3c73009cc7 Mon Sep 17 00:00:00 2001
From: Guillaume S <gsamson@mercator-ocean.fr>
Date: Thu, 10 Nov 2022 08:24:06 +0100
Subject: [PATCH 14/31] add same change to makenemo in clean_config function

---
 sette/all_functions.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/sette/all_functions.sh b/sette/all_functions.sh
index f75cfe3d..6c99ef46 100755
--- a/sette/all_functions.sh
+++ b/sette/all_functions.sh
@@ -153,12 +153,12 @@ clean_config() {
       echo '-------------------------------------------------------------------------------'
       echo '                         CLEANING CONFIGURATION                                '
       echo ''
-      echo "./makenemo -n $lCFG -a/-r $lREF -t ${CMP_DIR:-${CONFIG_DIR0}} clean"
+      echo "./makenemo -n $lCFG -a/-r $lREF ${CUSTOM_DIR:+-t ${CMP_DIR}} clean"
       echo ''
       if [ ${lTYP} == 'tests' ]; then
-         ./makenemo -n $lCFG -t ${CMP_DIR:-${CONFIG_DIR0}} -a $lREF clean
+         ./makenemo -n $lCFG ${CUSTOM_DIR:+-t ${CMP_DIR}} -a $lREF clean
       elif [ ${lTYP} == 'cfgs' ]; then
-         ./makenemo -n $lCFG -t ${CMP_DIR:-${CONFIG_DIR0}} -r $lREF clean
+         ./makenemo -n $lCFG ${CUSTOM_DIR:+-t ${CMP_DIR}} -r $lREF clean
       else
          echo 'ERROR in the cleaning process'; exit 42
       fi
-- 
GitLab


From a64f52e54cacc9bf371b102fba9c030cca6e4020 Mon Sep 17 00:00:00 2001
From: Guillaume S <gsamson@mercator-ocean.fr>
Date: Thu, 10 Nov 2022 18:32:50 +0100
Subject: [PATCH 15/31] add the possibility to install a new configuration
 anywhere using "-t" makenemo option (continuation of #84)

---
 makenemo                 | 53 +++++++++++++++++++++-------------------
 mk/Fadd_keys.sh          |  6 ++---
 mk/Fdef_keys.sh          |  2 +-
 mk/Fdel_keys.sh          | 14 +++++------
 mk/Fmake_WORK.sh         |  8 +++---
 mk/Fmake_bld.sh          | 10 ++++----
 mk/Fmake_config.sh       | 11 +++++----
 mk/bldxag.cfg            |  2 +-
 sette/prepare_exe_dir.sh | 14 ++++++-----
 9 files changed, 63 insertions(+), 57 deletions(-)

diff --git a/makenemo b/makenemo
index 8de8150e..d1a48ca3 100755
--- a/makenemo
+++ b/makenemo
@@ -88,18 +88,12 @@ x_u=''; x_a=''; x_m=''; x_t=''; x_b='';
 x_j='1'; x_e='none'; x_s='src'; x_v='1'
 x_c_cfg=0
 x_nocdf=0
-x_name=''
+#x_name=''
 
 ##- Local variables ---
 b_n=$(basename ${0})
 OPTIND='1'
 MAIN_DIR=$(cd $(dirname "$0"); pwd)
-MAIN_DIR=${MAIN_DIR%/sette*}
-MAIN_DIR=${MAIN_DIR%/tools*}
-MAIN_DIR=${MAIN_DIR%/cfgs*}
-MAIN_DIR=${MAIN_DIR%/tests*}
-MAIN_DIR=${MAIN_DIR%/ext*}
-MAIN_DIR=${MAIN_DIR%/arch*}
 export MAIN_DIR
 #
 export CFGS_DIR=${MAIN_DIR}/cfgs
@@ -195,7 +189,8 @@ EOF
 	-d|--dirs|--comp)
 	    x_d=${2} ; shift ;;
 	-n|--name)
-	    x_name=${2} ; shift ;;
+	    #x_name=${2} ; shift ;;
+	    x_n=${2} ; shift ;;
 	-r|--ref)
 	    x_r=${2} ; shift ;;
 	-a|--academic|--test)
@@ -229,31 +224,38 @@ EOF
     shift
 done
 
-if [ -n "$x_name" ]   # is the configuration existing in cfgs or tests? or is it a new conf?
+#if [ -n "$x_name" ]   # is the configuration existing in cfgs or tests? or is it a new conf?
+if [ -n "$x_n" ]   # is the configuration existing in cfgs or tests? or is it a new conf?
 then
-    incfg=$( find $CFGS_DIR   -type d -name $x_name | wc -l )   # this configuration exists in CFGS_DIR
-    intst=$( find $TESTS_DIR  -type d -name $x_name | wc -l )   # this configuration exists in TESTS_DIR
+    #incfg=$( find $CFGS_DIR   -type d -name $x_name | wc -l )   # this configuration exists in CFGS_DIR
+    #intst=$( find $TESTS_DIR  -type d -name $x_name | wc -l )   # this configuration exists in TESTS_DIR
+    incfg=$( find $CFGS_DIR   -type d -name $x_n | wc -l )   # this configuration exists in CFGS_DIR
+    intst=$( find $TESTS_DIR  -type d -name $x_n | wc -l )   # this configuration exists in TESTS_DIR
     if [ $(( $incfg + $intst )) -eq 2 ] ; then
-	echo -e "\033[0;31m\nERROR: the $x_name directory is found twice: in $CFGS_DIR and in $TESTS_DIR\033[0m\n"
+	#echo -e "\033[0;31m\nERROR: the $x_name directory is found twice: in $CFGS_DIR and in $TESTS_DIR\033[0m\n"
+	echo -e "\033[0;31m\nERROR: the $x_n directory is found twice: in $CFGS_DIR and in $TESTS_DIR\033[0m\n"
 	exit 4
     fi
     if [ $(( $incfg + $intst )) -gt 0 ] ; then
 	if [ $x_c_cfg -eq 1 ] ; then   # if we just want to clean the config (do it here as it must exist)
-	    x_n=$x_name                # must define x_n as it is used in Fclean_config.sh
+	    #x_n=$x_name                # must define x_n as it is used in Fclean_config.sh
 	    . ${COMPIL_DIR}/Fclean_config.sh
 	    exit 0
 	fi
-	[ -n "$x_r" ] && echo -e "\nWARNING: $x_name configuration is already existing, we ignore \"-r $x_r\"\n"
-	[ -n "$x_a" ] && echo -e "\nWARNING: $x_name configuration is already existing, we ignore \"-a $x_a\"\n"
+	#[ -n "$x_r" ] && echo -e "\nWARNING: $x_name configuration is already existing, we ignore \"-r $x_r\"\n"
+	#[ -n "$x_a" ] && echo -e "\nWARNING: $x_name configuration is already existing, we ignore \"-a $x_a\"\n"
+	[ -n "$x_r" ] && echo -e "\nWARNING: $x_n configuration is already existing, we ignore \"-r $x_r\"\n"
+	[ -n "$x_a" ] && echo -e "\nWARNING: $x_n configuration is already existing, we ignore \"-a $x_a\"\n"
     fi
-    if   [ $incfg -eq 1 ] ; then
-	x_r=$x_name ; x_a=''  # reference configuration existing -> define/overwrite x_r
-    elif [ $intst -eq 1 ] ; then
-	x_a=$x_name ; x_r=''   # test      configuration existing -> define/overwrite x_a
-    else
+    #if   [ $incfg -eq 1 ] ; then
+	#x_r=$x_name ; x_a=''  # reference configuration existing -> define/overwrite x_r
+    #elif [ $intst -eq 1 ] ; then
+	#x_a=$x_name ; x_r=''   # test      configuration existing -> define/overwrite x_a
+    #else
+    if [[ $incfg -eq 0 && $intst -eq 0 ]]; then
 	[  ${#x_c} -ne 0 ] && echo -e "\nWARNING: Compilation cleaning of a non-existing configuration, we ignore\n" && exit 0
 	[ $x_c_cfg -eq 1 ] && echo -e "\nWARNING: Configuration cleaning of a non-existing configuration, we ignore\n" && exit 0
-	x_n=$x_name            # this is a new configuration      -> define
+	#x_n=$x_name            # this is a new configuration      -> define
     fi
 fi
 
@@ -270,7 +272,7 @@ NEMO_DBG=${x_b}
 
 
 ## No ref. cfg or demo selected
-if [[ -z "${REF_CONF}" && -z "${DEMO_CONF}" ]]; then
+if [[ -z "${REF_CONF}" && -z "${DEMO_CONF}" && $(( $incfg + $intst )) -eq 0 ]]; then
     echo -e "\033[0;31m\nAt least a reference configuration ('-r'), a test case ('-a'), "
     echo -e "a remote configuration ('-u') has to be choosen to build a new configuration!!!\033[0m"
     ${COMPIL_DIR}/Flist_cfgs.sh
@@ -332,10 +334,11 @@ echo ${NEW_CONF} "${NEM_SUBDIR}" >> ${CONFIG_DIR}/work_cfgs.txt
 cd ${CONFIG_DIR}
 
 ## Create new config even in existing one (mkdir with -p option, cp with -n)
-${COMPIL_DIR}/Fmake_config.sh ${NEW_CONF} ${TML_CONF}
+${COMPIL_DIR}/Fmake_config.sh ${NEMO_TDIR}/${NEW_CONF} ${TML_CONF}
 
 ## create EXP00 if needed
-[ ! -d ${CONFIG_DIR}/${NEW_CONF}/EXP00 ] && \cp -R -n ${CONFIG_DIR}/${NEW_CONF}/EXPREF ${CONFIG_DIR}/${NEW_CONF}/EXP00
+[[ ! -d ${NEMO_TDIR}/${NEW_CONF}/EXP00 && -n "${REF_CONF}" ]] && \cp -R -n ${CONFIG_DIR}/${REF_CONF}/EXPREF ${NEMO_TDIR}/${NEW_CONF}/EXP00
+[[ ! -d ${NEMO_TDIR}/${NEW_CONF}/EXP00 && -n "${DEMO_CONF}" ]] && \cp -R -n ${CONFIG_DIR}/${DEMO_CONF}/EXPREF ${NEMO_TDIR}/${NEW_CONF}/EXP00
 
 #- Create the WORK ---
 #- Clean links and librairies ---
@@ -410,7 +413,7 @@ if [ "${NBR_PRC}" -gt 0 ]; then
     fcm build ${x_c} --ignore-lock -v ${x_v} -j ${NBR_PRC} ${COMPIL_DIR}/$USEBLD ||{ cd - ; exit 1 ;}
 
     if [ -f ${NEMO_TDIR}/${NEW_CONF}/BLD/bin/nemo.exe ]; then
-	ln -sf ${NEMO_TDIR}/${NEW_CONF}/BLD/bin/nemo.exe  ${CONFIG_DIR}/${NEW_CONF}/EXP00/nemo
+	ln -sf ${NEMO_TDIR}/${NEW_CONF}/BLD/bin/nemo.exe  ${NEMO_TDIR}/${NEW_CONF}/EXP00/nemo
     fi
 
     ## add remove for clean option
diff --git a/mk/Fadd_keys.sh b/mk/Fadd_keys.sh
index 0aa554c1..e4fc8c78 100755
--- a/mk/Fadd_keys.sh
+++ b/mk/Fadd_keys.sh
@@ -64,11 +64,11 @@ set -o posix
 #-
  echo "Adding keys in : ${NEW_CONF}" 
  for i in ${list_add_key} ; do
-	if [ "$(cat ${CONFIG_DIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm | grep -c "\<$i\>" )" -ne 0 ] ; then
+	if [ "$(cat ${NEMO_TDIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm | grep -c "\<$i\>" )" -ne 0 ] ; then
  	   echo "key $i already present in cpp_${NEW_CONF}.fcm" 
 	else
-	   sed -e "s/$/ ${i}/"  ${CONFIG_DIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm >  ${CONFIG_DIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm.tmp
- 	   mv ${CONFIG_DIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm.tmp   ${CONFIG_DIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm
+	   sed -e "s/$/ ${i}/"  ${NEMO_TDIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm >  ${NEMO_TDIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm.tmp
+ 	   mv ${NEMO_TDIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm.tmp   ${NEMO_TDIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm
  	   echo "added key $i in ${NEW_CONF}" 
 	fi
  done
diff --git a/mk/Fdef_keys.sh b/mk/Fdef_keys.sh
index f0edd7d8..bf94a481 100755
--- a/mk/Fdef_keys.sh
+++ b/mk/Fdef_keys.sh
@@ -58,6 +58,6 @@ set -o posix
 
 echo "Defining keys in : ${NEW_CONF}"
 
-echo " bld::tool::fppkeys ${list_def_key}" > ${CONFIG_DIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm
+echo " bld::tool::fppkeys ${list_def_key}" > ${NEMO_TDIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm
 
 unset -v list_def_key
diff --git a/mk/Fdel_keys.sh b/mk/Fdel_keys.sh
index 88aafc23..ff95aa2b 100755
--- a/mk/Fdel_keys.sh
+++ b/mk/Fdel_keys.sh
@@ -65,14 +65,14 @@ echo "Removing keys in : ${NEW_CONF}"
 for i in ${list_del_key} ; do
 
      if [ "$(echo ${i} | grep -c key_nproc )" -ne 0                                      ]; then
-        sed -e "s/key_nproc[ij]=.* //" ${CONFIG_DIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm \
-	    >  ${CONFIG_DIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm.tmp
-        mv ${CONFIG_DIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm.tmp ${CONFIG_DIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm
+        sed -e "s/key_nproc[ij]=.* //" ${NEMO_TDIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm \
+	    >  ${NEMO_TDIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm.tmp
+        mv ${NEMO_TDIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm.tmp ${NEMO_TDIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm
         echo " "
-     elif [ "$(cat ${CONFIG_DIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm | grep -c "$i" )" -ne 0 ]; then
-         sed -e "s/\b${i}\b//" ${CONFIG_DIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm \
-	     >  ${CONFIG_DIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm.tmp
-         mv ${CONFIG_DIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm.tmp ${CONFIG_DIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm
+     elif [ "$(cat ${NEMO_TDIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm | grep -c "$i" )" -ne 0 ]; then
+         sed -e "s/\b${i}\b//" ${NEMO_TDIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm \
+	     >  ${NEMO_TDIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm.tmp
+         mv ${NEMO_TDIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm.tmp ${NEMO_TDIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm
          echo "deleted key $i in ${NEW_CONF}"
      fi
 
diff --git a/mk/Fmake_WORK.sh b/mk/Fmake_WORK.sh
index 372bca57..780fb996 100755
--- a/mk/Fmake_WORK.sh
+++ b/mk/Fmake_WORK.sh
@@ -64,14 +64,14 @@ set -o posix
 #
 #-
 declare ZSRC=${@}
-ZCONF=${NEW_CONF}
+ZCONF=${NEMO_TDIR}/${NEW_CONF}
 ZTAB=${NEM_SUBDIR[@]}
 declare NDIR=${#ZTAB[@]}
 
-echo 'Creating '${ZCONF}'/WORK = '${ZTAB[*]}' for '${ZCONF}
+echo 'Creating '${ZCONF}'/WORK = '${ZTAB[*]}' for '${ZCONF##*/}
 
-[ ! -d ${ZCONF}/MY_SRC ] && \mkdir ${ZCONF}/MY_SRC
-[   -d ${ZCONF}/WORK   ] || \mkdir ${ZCONF}/WORK
+[ ! -d ${ZCONF}/MY_SRC ] && \mkdir -p ${ZCONF}/MY_SRC
+[   -d ${ZCONF}/WORK   ] || \mkdir -p ${ZCONF}/WORK
 
 for comp in ${ZTAB[*]}; do
 	find ${NEMO_DIR}/$comp -name *.[Ffh]90 -exec ln -sf {} ${ZCONF}/WORK \;
diff --git a/mk/Fmake_bld.sh b/mk/Fmake_bld.sh
index 53d9f7e3..9973af3f 100755
--- a/mk/Fmake_bld.sh
+++ b/mk/Fmake_bld.sh
@@ -57,8 +57,8 @@ set -o posix
 #   * creation
 #
 #-
-[ ! -d ${3}/${2}     ] && \mkdir ${3}/${2}
-[ ! -d ${3}/${2}/BLD ] && \mkdir ${3}/${2}/BLD
-[ ! -d ${1}/${2}/BLD ] && ln -sf ${3}/${2}/BLD ${1}/${2}/BLD
-[ -f ${1}/${NEW_CONF}/cpp_${NEW_CONF}.fcm ] && ln -sf ${1}/${NEW_CONF}/cpp_${NEW_CONF}.fcm ${COMPIL_DIR}/cpp.fcm
-rm -f  ${1}/${NEW_CONF}/BLD/fcm.bld.lock
+[ ! -d ${3}/${2}     ] && \mkdir -p ${3}/${2}
+[ ! -d ${3}/${2}/BLD ] && \mkdir -p ${3}/${2}/BLD
+#[ ! -d ${1}/${2}/BLD ] && ln -sf ${3}/${2}/BLD ${1}/${2}/BLD
+[ -f ${3}/${2}/cpp_${2}.fcm ] && ln -sf ${3}/${2}/cpp_${2}.fcm ${COMPIL_DIR}/cpp.fcm
+rm -f  ${1}/${2}/BLD/fcm.bld.lock
diff --git a/mk/Fmake_config.sh b/mk/Fmake_config.sh
index 12babc42..3ad6bb65 100755
--- a/mk/Fmake_config.sh
+++ b/mk/Fmake_config.sh
@@ -59,8 +59,9 @@ set -o posix
 \mkdir -p ${1}
 \mkdir -p ${1}/EXP00
 \mkdir -p ${1}/MY_SRC
-\cp -R -n ${2}/cpp_${2}.fcm ${1}/cpp_${1}.fcm
-\cp -R -n ${2}/EXPREF/*namelist* ${1}/EXP00/.
-\cp -R -n ${2}/EXPREF/*.xml ${1}/EXP00/.
-[ -f ${2}/EXPREF/AGRIF_FixedGrids.in ] &&  \cp -R -n ${2}/EXPREF/AGRIF_FixedGrids.in ${1}/EXP00/.
-[ -d    ${2}/MY_SRC ] && \cp -n ${2}/MY_SRC/* ${1}/MY_SRC/. 2> /dev/null
+\cp -R -n ${2}/cpp_${2}.fcm ${1}/cpp_${1##*/}.fcm
+for f in ${2}/EXPREF/*.xml ${2}/EXPREF/*namelist*; do
+  if [ -L ${f} ]; then ln -sf $(readlink -f ${f}) ${1}/EXP00/$(basename ${f}); else cp -R -n ${f} ${1}/EXP00/.; fi
+done
+[ -f ${2}/EXPREF/AGRIF_FixedGrids.in ] &&  \cp -a -n ${2}/EXPREF/AGRIF_FixedGrids.in ${1}/EXP00/.
+[ -d    ${2}/MY_SRC ] && \cp -an ${2}/MY_SRC/* ${1}/MY_SRC/. 2> /dev/null
diff --git a/mk/bldxag.cfg b/mk/bldxag.cfg
index 19ea8475..5b4db893 100644
--- a/mk/bldxag.cfg
+++ b/mk/bldxag.cfg
@@ -13,7 +13,7 @@ inc $COMPIL_DIR/cpp.fcm
 search_src           1
 
 src::ioipsl               $MAIN_DIR/ext/IOIPSL/src
-src::nemo                 $CONFIG_DIR/$NEW_CONF/WORK
+src::nemo                 $NEMO_TDIR/$NEW_CONF/WORK
 src::ppr_1d               $MAIN_DIR/ext/PPR/src
 
 bld::target nemo.exe
diff --git a/sette/prepare_exe_dir.sh b/sette/prepare_exe_dir.sh
index b446a7e3..d43feec5 100755
--- a/sette/prepare_exe_dir.sh
+++ b/sette/prepare_exe_dir.sh
@@ -67,23 +67,25 @@ set -o posix
 # PREPARE EXEC_DIR
 #==================
 if [ -z "${CUSTOM_DIR}" ]; then
-  export EXE_DIR=${CONFIG_DIR}/${NEW_CONF}/${TEST_NAME}
+  EXE_DIR=${CONFIG_DIR}/${NEW_CONF}
 else
   CMP_NAM_L=$(echo ${CMP_NAM} | tr '[:upper:]' '[:lower:]')
   if [[ -n "${NEMO_DEBUG}" || ${CMP_NAM_L} =~ ("debug"|"dbg") ]]; then
     export EXE_DIR=${CUSTOM_DIR}/${SETTE_SUB_VAL}_${NEMO_REV}_DEBUG/${NEW_CONF}/${TEST_NAME}
   else
-    export EXE_DIR=${CUSTOM_DIR}/${SETTE_SUB_VAL}_${NEMO_REV}/${NEW_CONF}/${TEST_NAME}
+    EXE_DIR=${CUSTOM_DIR}/${SETTE_SUB_VAL}_${NEMO_REV}/${NEW_CONF}
   fi
 fi
-mkdir -p ${EXE_DIR}
+mkdir -p ${EXE_DIR}/${TEST_NAME}
 
-cp -RL ${CONFIG_DIR}/${NEW_CONF}/EXP00/* ${EXE_DIR}/.
-#cat ${SETTE_DIR}/iodef_sette.xml | sed -e"s;DEF_SHARED;${CONFIG_DIR0}/SHARED;" > ${EXE_DIR}/iodef.xml
+#cp -RL ${EXE_DIR:-${CONFIG_DIR}/${NEW_CONF}}/EXP00/* ${EXE_DIR}/${TEST_NAME}/.
+cp -an ${EXE_DIR:-${CONFIG_DIR}/${NEW_CONF}}/EXP00/* ${EXE_DIR}/${TEST_NAME}/.
+COMP_KEYS="`cat ${EXE_DIR}/cpp_${NEW_CONF}.fcm | sed -e 's/.*fppkeys *//'`"
+
+export EXE_DIR=${EXE_DIR}/${TEST_NAME}
 cd ${EXE_DIR}
 #
 # Add summary of the sette.sh set-up used and the current list of keys added or deleted
-COMP_KEYS="`cat ${CONFIG_DIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm | sed -e 's/.*fppkeys *//'`"
 echo "Summary of sette environment"                                > ./sette_config
 echo "----------------------------"                               >> ./sette_config
 echo "requested by the command          : "$cmd $cmdargs          >> ./sette_config
-- 
GitLab


From 297615941d68cd9c643cd8142b6169b469c9dad2 Mon Sep 17 00:00:00 2001
From: Guillaume S <gsamson@mercator-ocean.fr>
Date: Sun, 13 Nov 2022 19:56:06 +0100
Subject: [PATCH 16/31] adapt sette to work with any path (custom or not)

---
 sette/all_functions.sh                  | 20 +++++---------
 sette/prepare_job.sh                    |  4 +--
 sette/sette_reference-configurations.sh | 36 ++++++++++++-------------
 sette/sette_test-cases.sh               | 30 +++++++++------------
 4 files changed, 38 insertions(+), 52 deletions(-)

diff --git a/sette/all_functions.sh b/sette/all_functions.sh
index 6c99ef46..f5befee2 100755
--- a/sette/all_functions.sh
+++ b/sette/all_functions.sh
@@ -94,8 +94,8 @@ usage=" if value is a string ths is neede syntax : ./set_namelist namelist_name
 sync_config() {
    if [ ${SYNC_CONFIGS} == "yes" ]; then
 
-      lREF=$3/$1    # reference 
-      lCFG=$3/$2    # target
+      lREF=$1    # reference
+      lCFG=$2    # target
 
       echo '-------------------------------------------------------------------------------'
       echo '                    SOURCE AND CONFIG FILES SYNCHRONISATION                    '
@@ -146,24 +146,16 @@ sync_config() {
 # clean _STg config (input CFG CFG_STg TYPE (test or ref))
 clean_config() {
    if [ ${CLEAN_CONFIGS} == "yes" ]; then
-      lREF=$1
-      lCFG=$2
-      lTYP=$3
+      lCFG=$1
       echo ''
       echo '-------------------------------------------------------------------------------'
       echo '                         CLEANING CONFIGURATION                                '
       echo ''
-      echo "./makenemo -n $lCFG -a/-r $lREF ${CUSTOM_DIR:+-t ${CMP_DIR}} clean"
+      echo "./makenemo -n $(basename $lCFG) ${CUSTOM_DIR:+-t ${CMP_DIR}} clean"
       echo ''
-      if [ ${lTYP} == 'tests' ]; then
-         ./makenemo -n $lCFG ${CUSTOM_DIR:+-t ${CMP_DIR}} -a $lREF clean
-      elif [ ${lTYP} == 'cfgs' ]; then
-         ./makenemo -n $lCFG ${CUSTOM_DIR:+-t ${CMP_DIR}} -r $lREF clean
-      else
-         echo 'ERROR in the cleaning process'; exit 42
-      fi
+      ./makenemo -n $(basename $lCFG) ${CUSTOM_DIR:+-t ${CMP_DIR}} clean
       echo ''
-      echo "$lCFG configuration has been cleaned"
+      echo "$(basename $lCFG) configuration has been cleaned"
       echo ''
       echo '-------------------------------------------------------------------------------'
    fi
diff --git a/sette/prepare_job.sh b/sette/prepare_job.sh
index 335daedb..80d3fa1e 100755
--- a/sette/prepare_job.sh
+++ b/sette/prepare_job.sh
@@ -104,7 +104,7 @@ echo "" >> ${SETTE_DIR}/output.sette
 echo "running config: ${NEW_CONF}" >> ${SETTE_DIR}/output.sette
 echo "" >> ${SETTE_DIR}/output.sette
 echo "list of cpp_keys: " >> ${SETTE_DIR}/output.sette
-echo "`more ${CONFIG_DIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm`" >> ${SETTE_DIR}/output.sette 
+echo "`more ${NEMO_TDIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm`" >> ${SETTE_DIR}/output.sette
 echo "" >> ${SETTE_DIR}/output.sette
 echo "compiling with: ${CMP_NAM}" >> ${SETTE_DIR}/output.sette
 echo "" >> ${SETTE_DIR}/output.sette
@@ -269,7 +269,7 @@ fi
              -e"s/NXIOPROCS/${NXIO_PROC}/" \
              -e"s:DEF_SETTE_DIR:${SETTE_DIR}:" -e"s:DEF_INPUT_DIR:${INPUT_DIR}:" \
              -e"s:DEF_EXE_DIR:${EXE_DIR}:" \
-             -e"s:DEF_CONFIG_DIR:${CONFIG_DIR}:" \
+             -e"s:DEF_CONFIG_DIR:${NEMO_TDIR}:" \
              -e"s:DEF_TOOLS_DIR:${TOOLS_DIR}:" \
              -e"s:MPI_FLAG:${MPI_FLAG}:" \
              -e"s:DEF_NEMO_VALIDATION:${NEMO_VALID}:" -e"s:DEF_NEW_CONF:${NEW_CONF}:" \
diff --git a/sette/sette_reference-configurations.sh b/sette/sette_reference-configurations.sh
index 49bcbaca..6fdae259 100755
--- a/sette/sette_reference-configurations.sh
+++ b/sette/sette_reference-configurations.sh
@@ -155,8 +155,8 @@ if [ ${config} == "GYRE_PISCES" ] ;  then
     cd ${MAIN_DIR}
     #
     # syncronisation if target directory/file exist (not done by makenemo)
-    sync_config  GYRE_PISCES ${SETTE_CONFIG} 'cfgs'
-    clean_config GYRE_PISCES ${SETTE_CONFIG} 'cfgs'
+    clean_config ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
+    sync_config  ${CONFIG_DIR0}/${config} ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
     #
     # GYRE uses linssh so remove key_qco if added by default
     . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r GYRE_PISCES ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS/key_qco/}" del_key "${DEL_KEYS}"
@@ -302,8 +302,8 @@ if [ ${config} == "ORCA2_ICE_PISCES" ] ;  then
     cd ${MAIN_DIR}
     #
     # syncronisation if target directory/file exist (not done by makenemo)
-    sync_config  ORCA2_ICE_PISCES ${SETTE_CONFIG} 'cfgs'
-    clean_config ORCA2_ICE_PISCES ${SETTE_CONFIG} 'cfgs'
+    clean_config ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
+    sync_config  ${CONFIG_DIR0}/${config} ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
     #
     . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r ORCA2_ICE_PISCES ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS}" del_key "${DEL_KEYS}"
 fi
@@ -589,8 +589,8 @@ if [ ${config} == "ORCA2_OFF_PISCES" ] ;  then
     cd ${MAIN_DIR}
     #
     # syncronisation if target directory/file exist (not done by makenemo)
-    sync_config  ${SETTE_CONFIG} ORCA2_OFF_PISCES_ST 'cfgs'
-    clean_config ${SETTE_CONFIG} ORCA2_OFF_PISCES_ST 'cfgs'
+    clean_config ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
+    sync_config  ${CONFIG_DIR0}/${config} ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
     #
     # ORCA2_OFF_PISCES uses linssh so remove key_qco if added by default
     . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r ORCA2_OFF_PISCES ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS/key_qco/}" del_key "${DEL_KEYS}"
@@ -766,8 +766,8 @@ if [ ${config} == "AMM12" ] ;  then
     cd ${MAIN_DIR}
     #
     # syncronisation if target directory/file exist (not done by makenemo)
-    sync_config  AMM12 ${SETTE_CONFIG} 'cfgs'
-    clean_config AMM12 ${SETTE_CONFIG} 'cfgs'
+    clean_config ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
+    sync_config  ${CONFIG_DIR0}/${config} ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
     #
     . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r AMM12 ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS}" del_key "${DEL_KEYS}"
 fi
@@ -900,8 +900,8 @@ if [ ${config} == "SAS" ] ;  then
     cd ${MAIN_DIR}
     #
     # syncronisation if target directory/file exist (not done by makenemo)
-    sync_config  ORCA2_SAS_ICE ${SETTE_CONFIG} 'cfgs'
-    clean_config ORCA2_SAS_ICE ${SETTE_CONFIG} 'cfgs'
+    clean_config ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
+    sync_config  ${CONFIG_DIR0}/${config} ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
     #
     # ORCA2_SAS_ICE uses linssh so remove key_qco if added by default
     . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r ORCA2_SAS_ICE ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS/key_qco/}" del_key "${DEL_KEYS}"
@@ -1048,8 +1048,8 @@ if [ ${config} == "ORCA2_ICE_OBS" ] ;  then
     cd ${MAIN_DIR}
     #
     # syncronisation if target directory/file exist (not done by makenemo)
-    sync_config  ORCA2_ICE_PISCES ${SETTE_CONFIG} 'cfgs'
-    clean_config ORCA2_ICE_PISCES ${SETTE_CONFIG} 'cfgs'
+    clean_config ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
+    sync_config  ${CONFIG_DIR0}/${config} ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
     #
     . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r ORCA2_ICE_PISCES -d "OCE ICE" ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "key_asminc ${ADD_KEYS}" del_key "key_top ${DEL_KEYS}"
 fi
@@ -1172,8 +1172,8 @@ if [ ${config} == "AGRIF" ] ;  then
     cd ${MAIN_DIR}
     #
     # syncronisation if target directory/file exist (not done by makenemo)
-    sync_config  AGRIF_DEMO ${SETTE_CONFIG} 'cfgs'
-    clean_config AGRIF_DEMO ${SETTE_CONFIG} 'cfgs'
+    clean_config ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
+    sync_config  ${CONFIG_DIR0}/${config} ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
     #
     # AGRIF_DEMO does not yet support nn_hls=2 => key_loop_fusion can not be used
 #    . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r AGRIF_DEMO -j ${CMPL_CORES} add_key "${ADD_KEYS/key_loop_fusion}" del_key "${DEL_KEYS}"
@@ -1489,8 +1489,8 @@ if [ ${config} == "AGRIF" ] && [ ${DO_CORRUPT} == "1" ] ;  then
     cd ${MAIN_DIR}
     #
     # syncronisation if target directory/file exist (not done by makenemo)
-    sync_config  AGRIF_DEMO ${SETTE_CONFIG} 'cfgs'
-    clean_config AGRIF_DEMO ${SETTE_CONFIG} 'cfgs'
+    clean_config ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
+    sync_config  ${CONFIG_DIR0}/${config} ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
     #
     # AGRIF_DEMO does not yet support nn_hls=2 => key_loop_fusion can not be used
     . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r AGRIF_DEMO ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS/key_loop_fusion}" del_key "key_agrif ${DEL_KEYS}"
@@ -1537,8 +1537,8 @@ if [ ${config} == "WED025" ] ;  then
     cd ${MAIN_DIR}
     #
     # syncronisation if target directory/file exist (not done by makenemo)
-    sync_config  WED025 ${SETTE_CONFIG} 'cfgs'
-    clean_config WED025 ${SETTE_CONFIG} 'cfgs'
+    clean_config ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
+    sync_config  ${CONFIG_DIR0}/${config} ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
     #
     # WED025 uses ln_hpg_isf so remove key_qco if added by default
     . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -r WED025 ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS/key_qco/}" del_key "${DEL_KEYS}"
diff --git a/sette/sette_test-cases.sh b/sette/sette_test-cases.sh
index 3a77b2e6..eb7b5d44 100755
--- a/sette/sette_test-cases.sh
+++ b/sette/sette_test-cases.sh
@@ -155,9 +155,8 @@ if [ ${config} == "OVERFLOW" ] ;  then
     cd ${MAIN_DIR}
     #
     #
-    clean_config OVERFLOW ${SETTE_CONFIG} 'tests'
-    #
-    sync_config  OVERFLOW ${SETTE_CONFIG} 'tests'
+    clean_config ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
+    sync_config  ${CONFIG_DIR0}/${config} ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
     #
     . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -a OVERFLOW ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS}" del_key "${DEL_KEYS}"
 fi
@@ -272,9 +271,8 @@ if [ ${config} == "LOCK_EXCHANGE" ] ;  then
     #
     # syncronisation if target directory/file exist (not done by makenemo)
     #
-    clean_config LOCK_EXCHANGE ${SETTE_CONFIG} 'tests'
-    #
-    sync_config  LOCK_EXCHANGE ${SETTE_CONFIG} 'tests'
+    clean_config ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
+    sync_config  ${CONFIG_DIR0}/${config} ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
     #
     . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -a LOCK_EXCHANGE ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS}" del_key "${DEL_KEYS}"
 fi
@@ -391,9 +389,8 @@ if [ ${config} == "VORTEX" ] ;  then
     #
     # syncronisation if target directory/file exist (not done by makenemo)
     #
-    clean_config VORTEX ${SETTE_CONFIG} 'tests'
-    #
-    sync_config  VORTEX ${SETTE_CONFIG} 'tests'
+    clean_config ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
+    sync_config  ${CONFIG_DIR0}/${config} ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
     #
     . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -a VORTEX ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES}  add_key "${ADD_KEYS}" del_key "${DEL_KEYS}"
 fi
@@ -585,9 +582,8 @@ if [ ${config} == "ICE_AGRIF" ] ;  then
     #
     # syncronisation if target directory/file exist (not done by makenemo)
     #
-    clean_config ICE_AGRIF ${SETTE_CONFIG} 'tests'
-    #
-    sync_config  ICE_AGRIF ${SETTE_CONFIG} 'tests'
+    clean_config ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
+    sync_config  ${CONFIG_DIR0}/${config} ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
     #
     # ICE_AGRIF uses linssh so remove key_qco if added by default
     . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -a ICE_AGRIF ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES}  add_key "${ADD_KEYS/key_qco/}" del_key "${DEL_KEYS}"
@@ -783,9 +779,8 @@ if [ ${config} == "ISOMIP+" ] ;  then
     #
     # syncronisation if target directory/file exist (not done by makenemo)
     #
-    clean_config ISOMIP+ ${SETTE_CONFIG} 'tests'
-    #
-    sync_config  ISOMIP+ ${SETTE_CONFIG} 'tests'
+    clean_config ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
+    sync_config  ${CONFIG_DIR0}/${config} ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
     #
     # ISOMIP+ uses ln_hpg_isf so remove key_qco if added by default
     . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -a ISOMIP+ ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES} add_key "${ADD_KEYS/key_qco/}" del_key "${DEL_KEYS}"
@@ -928,9 +923,8 @@ if [ ${config} == "SWG" ] && [ ${USING_QCO} == "yes" ] ;  then
     #
     # syncronisation if target directory/file exist (not done by makenemo)
     #
-    clean_config SWG ${SETTE_CONFIG} 'tests'
-    #
-    sync_config  SWG ${SETTE_CONFIG} 'tests'
+    clean_config ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
+    sync_config  ${CONFIG_DIR0}/${config} ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}
     #
     . ./makenemo -m ${CMP_NAM} -n ${SETTE_CONFIG} -a SWG ${CUSTOM_DIR:+-t ${CMP_DIR}} -k 0 ${NEMO_DEBUG} -j ${CMPL_CORES}  add_key "${ADD_KEYS}" del_key "${DEL_KEYS}"
 fi
-- 
GitLab


From 9572960ff30122734b748b18bbc9c4edfef9e52e Mon Sep 17 00:00:00 2001
From: Guillaume S <gsamson@mercator-ocean.fr>
Date: Sun, 13 Nov 2022 19:57:44 +0100
Subject: [PATCH 17/31] adapt mk scripts and fcm cfg files to compile nemo
 completely outside nemo directory

---
 mk/Fcheck_archfile.sh | 99 ++++++++++++++++++++++---------------------
 mk/Fmake_bld.sh       |  2 +-
 mk/Fmake_config.sh    |  2 +-
 mk/bldxag.cfg         |  4 +-
 mk/bldxagxcdf.cfg     |  4 +-
 mk/bldxcdf.cfg        |  4 +-
 mk/conv.cfg           |  2 +-
 7 files changed, 59 insertions(+), 58 deletions(-)

diff --git a/mk/Fcheck_archfile.sh b/mk/Fcheck_archfile.sh
index b6145132..f7aad910 100755
--- a/mk/Fcheck_archfile.sh
+++ b/mk/Fcheck_archfile.sh
@@ -73,19 +73,20 @@ EOF
 	eval "echo \"$line\" >> $2"
     done < $1
 }
+
 # cleaning related to the old version
-rm -f $( find ${COMPIL_DIR} -type f -name $1 -print )
+rm -f $( find $(dirname $1) -type f -name $(basename $1) -print )
 
 #
 if [ ${#3} -eq 0 ]; then # arch not specified
-    if [ ! -f ${COMPIL_DIR}/arch.history ]; then
+    if [ ! -f $(dirname $1)/arch.history ]; then
 	echo "Warning !!!"
 	echo "NO compiler chosen"
 	echo "Try makenemo -h for help"
 	echo "EXITING..."
 	exit 1 
     else # use the arch file defined in arch.history
-	myarch=$( cat ${COMPIL_DIR}/arch.history )	
+	myarch=$( cat $(dirname $1)/arch.history )
 	if [ ! -f $myarch ]; then
 	    echo "Warning !!!"
 	    echo "previously used arch file no more found:"
@@ -93,26 +94,26 @@ if [ ${#3} -eq 0 ]; then # arch not specified
 	    echo "EXITING..."
 	    exit 1 
 	else
-	    if [ -f ${COMPIL_DIR}/$1 ]; then
-		if [ "$2" != "nocpp" ] 
+	    if [ -f $1 ]; then
+		if [[ ! "$2" =~ "nocpp" ]]
 		then
 		    # has the cpp keys file been changed since we copied the arch file in ${COMPIL_DIR}?
-		    mycpp=$( ls -l ${COMPIL_DIR}/$2 | sed -e "s/.* -> //" )
-		    if [ "$mycpp" != "$( cat ${COMPIL_DIR}/cpp.history )" ]; then
-			echo $mycpp > ${COMPIL_DIR}/cpp.history
-			cpeval ${myarch} ${COMPIL_DIR}/$1
+		    mycpp=$( ls -l $2 | sed -e "s/.* -> //" )
+		    if [ "$mycpp" != "$( cat $(dirname $2)/cpp.history )" ]; then
+			echo $mycpp > $(dirname $2)/cpp.history
+			cpeval ${myarch} $1
 		    fi
 		    # has the cpp keys file been updated since we copied the arch file in ${COMPIL_DIR}?
-		    mycpp=$( find -L ${COMPIL_DIR} -cnewer ${COMPIL_DIR}/$1 -name $2 -print )
-		    [ ${#mycpp} -ne 0 ] && cpeval ${myarch} ${COMPIL_DIR}/$1
+		    mycpp=$( find -L $(dirname $2) -cnewer $(basename $1) -name $(basename $2) -print )
+		    [ ${#mycpp} -ne 0 ] && cpeval ${myarch} $1
 		fi
 		# has myarch file been updated since we copied it in ${COMPIL_DIR}?
 		myarchdir=$( dirname ${myarch} )
 		myarchname=$( basename ${myarch} )
-		myarch=$( find -L $myarchdir -cnewer ${COMPIL_DIR}/$1 -name $myarchname -print )
-		[ ${#myarch} -ne 0 ] && cpeval ${myarch} ${COMPIL_DIR}/$1
+		myarch=$( find -L $myarchdir -cnewer $(basename $1) -name $myarchname -print )
+		[ ${#myarch} -ne 0 ] && cpeval ${myarch} $1
 	    else
-		cpeval ${myarch} ${COMPIL_DIR}/$1
+		cpeval ${myarch} $1
 	    fi
 	fi
     fi
@@ -135,68 +136,68 @@ else
     fi
     myarch=$( find ${MAIN_DIR}/arch -name arch-${3}.fcm -print )
     # we were already using this arch file ?
-    if [ "$myarch" == "$( cat ${COMPIL_DIR}/arch.history )" ]; then 
-	if [ -f ${COMPIL_DIR}/$1 ]; then
-	    if [ "$2" != "nocpp" ] 
+    if [ "$myarch" == "$( cat $(dirname $1)/arch.history 2>/dev/null)" ]; then 
+	if [ -f $1 ]; then
+	    if [[ ! "$2" =~ "nocpp" ]]
 	    then
 		# has the cpp keys file been changed since we copied the arch file in ${COMPIL_DIR}?
-		mycpp=$( ls -l ${COMPIL_DIR}/$2 | sed -e "s/.* -> //" )
-		if [ "$mycpp" != "$( cat ${COMPIL_DIR}/cpp.history )" ]; then
-		    echo $mycpp > ${COMPIL_DIR}/cpp.history
-		    cpeval ${myarch} ${COMPIL_DIR}/$1
+		mycpp=$( ls -l $2 | sed -e "s/.* -> //" )
+		if [ "$mycpp" != "$( cat $(dirname $2)/cpp.history )" ]; then
+		    echo $mycpp > $(dirname $2)/cpp.history
+		    cpeval ${myarch} $1
 		fi
 		# has the cpp keys file been updated since we copied the arch file in ${COMPIL_DIR}?
-		mycpp=$( find -L ${COMPIL_DIR} -cnewer ${COMPIL_DIR}/$1 -name $2 -print )
-		[ ${#mycpp} -ne 0 ] && cpeval ${myarch} ${COMPIL_DIR}/$1
+		mycpp=$( find -L $(dirname $2) -cnewer $(basename $1) -name $(basename $2) -print )
+		[ ${#mycpp} -ne 0 ] && cpeval ${myarch} $1
 	    fi
 	    # has myarch file been updated since we copied it in ${COMPIL_DIR}?
-	    myarch=$( find -L ${MAIN_DIR}/arch -cnewer ${COMPIL_DIR}/$1 -name arch-${3}.fcm -print )
-	    [ ${#myarch} -ne 0 ] && cpeval ${myarch} ${COMPIL_DIR}/$1
+	    myarch=$( find -L ${MAIN_DIR}/arch -cnewer $(basename $1) -name arch-${3}.fcm -print )
+	    [ ${#myarch} -ne 0 ] && cpeval ${myarch} $1
 	else
-	    cpeval ${myarch} ${COMPIL_DIR}/$1
+	    cpeval ${myarch} $1
 	fi
     else
-	if [ "$2" != "nocpp" ] 
+	if [[ ! "$2" =~ "nocpp" ]]
 	then
-	    ls -l ${COMPIL_DIR}/$2 | sed -e "s/.* -> //" > ${COMPIL_DIR}/cpp.history
+	    ls -l $2 | sed -e "s/.* -> //" > $(dirname $2)/cpp.history
 	fi
-	echo ${myarch} > ${COMPIL_DIR}/arch.history
-	cpeval ${myarch} ${COMPIL_DIR}/$1
+	echo ${myarch} > $(dirname $1)/arch.history
+	cpeval ${myarch} $1
     fi
 fi
 
 #- do we need xios library?
 #- 2 cases: 
 #- in CONFIG directory looking for key_xios or key_iomput
-if [ "$1" == "arch_nemo.fcm" ]
+if [ "$(basename $1)" == "arch_nemo.fcm" ]
 then
-    if [ "$2" != "nocpp" ] 
+    if [[ ! "$2" =~ "nocpp" ]]
     then
-        use_iom=$( sed -e "s/#.*$//" ${COMPIL_DIR}/$2 | grep -c "key_xios\|key_iomput" )
+        use_iom=$( sed -e "s/#.*$//" $2 | grep -c "key_xios\|key_iomput" )
     else
         use_iom=0
     fi
-    have_lxios=$( sed -e "s/#.*$//" ${COMPIL_DIR}/$1 | grep -c "\-lxios" )
+    have_lxios=$( sed -e "s/#.*$//" $1 | grep -c "\-lxios" )
     if [[ ( $use_iom -eq 0 ) && ( $have_lxios -ge 1 ) ]]
     then 
-        sed -e "s/-lxios//g" ${COMPIL_DIR}/$1 > ${COMPIL_DIR}/tmp$$
-        mv -f ${COMPIL_DIR}/tmp$$ ${COMPIL_DIR}/$1
+        sed -e "s/-lxios//g" $1 > $(dirname $1)/tmp$$
+        mv -f $(dirname $1)/tmp$$ $1
     fi
 #- in TOOLS directory looking for USE xios
 else
-    use_iom=$( egrep --exclude-dir=.svn -r USE ${NEW_CONF}/src/* | grep -c xios )
-    have_lxios=$( sed -e "s/#.*$//" ${COMPIL_DIR}/$1 | grep -c "\-lxios" )
+    use_iom=$( egrep --exclude-dir=.svn -r USE ${MAIN_DIR}/src/* | grep -c xios )
+    have_lxios=$( sed -e "s/#.*$//" $1 | grep -c "\-lxios" )
     if [[ ( $use_iom -eq 0 ) || ( $have_lxios != 1 ) ]]
     then 
-        sed -e "s/-lxios//g" ${COMPIL_DIR}/$1 > ${COMPIL_DIR}/tmp$$
-        mv -f ${COMPIL_DIR}/tmp$$ ${COMPIL_DIR}/$1
+        sed -e "s/-lxios//g" $1 > $(dirname $1)/tmp$$
+        mv -f $(dirname $1)/tmp$$ $1
     fi
 fi
 
 #- do we need oasis libraries?
-if [ "$2" != "nocpp" ] 
+if [[ ! "$2" =~ "nocpp" ]]
 then
-    use_oasis=$( sed -e "s/#.*$//" ${COMPIL_DIR}/$2 | grep -c key_oasis3 )
+    use_oasis=$( sed -e "s/#.*$//" $2 | grep -c key_oasis3 )
 else
     use_oasis=0
 fi
@@ -206,26 +207,26 @@ if [[ ! -z "$XIOS_OASIS" ]]; then
 fi 
 for liboa in psmile.MPI1 mct mpeu scrip mpp_io
 do
-    have_liboa=$( sed -e "s/#.*$//" ${COMPIL_DIR}/$1 | grep -c "\-l${liboa}" )
+    have_liboa=$( sed -e "s/#.*$//" $1 | grep -c "\-l${liboa}" )
     if [[ ( $use_oasis -eq 0 ) && ( $have_liboa -ge 1 ) ]]
     then 
-	sed -e "s/-l${liboa}//g" ${COMPIL_DIR}/$1 > ${COMPIL_DIR}/tmp$$
-	mv -f ${COMPIL_DIR}/tmp$$ ${COMPIL_DIR}/$1
+	sed -e "s/-l${liboa}//g" $1 > $(dirname $1)/tmp$$
+	mv -f $(dirname $1)/tmp$$ $1
     fi
 done
 
 # Nemo debug ?
 if [ -n "${NEMO_DBG}" ]; then
-    if (! grep -q "^%DEBUG_FCFLAGS" ${COMPIL_DIR}/$1 ); then
+    if (! grep -q "^%DEBUG_FCFLAGS" $1 ); then
        echo "ERROR: You must defined '%DEBUG_FCFLAGS' in your arch file if you want to compile Nemo in debug mode using '-d' option"
        exit 1
     fi
     # duplicate the lines starting with %DEBUG_XXX and replace, in the duplicated line, %DEBUG_XXX by %XXX
-    sed -i "/^%DEBUG_/{p;s/^%DEBUG_\([^ ]*\)/%\1/;}" ${COMPIL_DIR}/$1
+    sed -i "/^%DEBUG_/{p;s/^%DEBUG_\([^ ]*\)/%\1/;}" $1
 else
-    if (! grep -q "^%PROD_FCFLAGS" ${COMPIL_DIR}/$1 ); then
+    if (! grep -q "^%PROD_FCFLAGS" $1 ); then
         echo "WARNING: '%PROD_FCFLAGS' not defined in your arch file, makenemo will use '%FCFLAGS' instead"
     fi
     # duplicate the lines starting with %PROD_XXX and replace, in the duplicated line, %PROD_XXX by %XXX
-    sed -i "/^%PROD_/{p;s/^%PROD_\([^ ]*\)/%\1/;}" ${COMPIL_DIR}/$1
+    sed -i "/^%PROD_/{p;s/^%PROD_\([^ ]*\)/%\1/;}" $1
 fi
diff --git a/mk/Fmake_bld.sh b/mk/Fmake_bld.sh
index 9973af3f..ebb2e48c 100755
--- a/mk/Fmake_bld.sh
+++ b/mk/Fmake_bld.sh
@@ -60,5 +60,5 @@ set -o posix
 [ ! -d ${3}/${2}     ] && \mkdir -p ${3}/${2}
 [ ! -d ${3}/${2}/BLD ] && \mkdir -p ${3}/${2}/BLD
 #[ ! -d ${1}/${2}/BLD ] && ln -sf ${3}/${2}/BLD ${1}/${2}/BLD
-[ -f ${3}/${2}/cpp_${2}.fcm ] && ln -sf ${3}/${2}/cpp_${2}.fcm ${COMPIL_DIR}/cpp.fcm
+[ -f ${3}/${2}/cpp_${2}.fcm ] && ln -sf ${3}/${2}/cpp_${2}.fcm ${3}/${2}/BLD/cpp.fcm
 rm -f  ${1}/${2}/BLD/fcm.bld.lock
diff --git a/mk/Fmake_config.sh b/mk/Fmake_config.sh
index 3ad6bb65..79673f0e 100755
--- a/mk/Fmake_config.sh
+++ b/mk/Fmake_config.sh
@@ -59,7 +59,7 @@ set -o posix
 \mkdir -p ${1}
 \mkdir -p ${1}/EXP00
 \mkdir -p ${1}/MY_SRC
-\cp -R -n ${2}/cpp_${2}.fcm ${1}/cpp_${1##*/}.fcm
+\cp -R -n ${2}/cpp_${2##*/}.fcm ${1}/cpp_${1##*/}.fcm
 for f in ${2}/EXPREF/*.xml ${2}/EXPREF/*namelist*; do
   if [ -L ${f} ]; then ln -sf $(readlink -f ${f}) ${1}/EXP00/$(basename ${f}); else cp -R -n ${f} ${1}/EXP00/.; fi
 done
diff --git a/mk/bldxag.cfg b/mk/bldxag.cfg
index 5b4db893..78a775d5 100644
--- a/mk/bldxag.cfg
+++ b/mk/bldxag.cfg
@@ -7,8 +7,8 @@ cfg::version                        1.0
 # Build information
 # ------------------------------------------------------------------------------
 
-inc $COMPIL_DIR/arch_nemo.fcm
-inc $COMPIL_DIR/cpp.fcm
+inc $NEMO_TDIR/$NEW_CONF/BLD/arch_nemo.fcm
+inc $NEMO_TDIR/$NEW_CONF/BLD/cpp.fcm
 
 search_src           1
 
diff --git a/mk/bldxagxcdf.cfg b/mk/bldxagxcdf.cfg
index d562b61b..28361348 100644
--- a/mk/bldxagxcdf.cfg
+++ b/mk/bldxagxcdf.cfg
@@ -7,8 +7,8 @@ cfg::version                        1.0
 # Build information
 # ------------------------------------------------------------------------------
 
-inc $COMPIL_DIR/arch_nemo.fcm
-inc $COMPIL_DIR/cpp.fcm
+inc $NEMO_TDIR/$NEW_CONF/BLD/arch_nemo.fcm
+inc $NEMO_TDIR/$NEW_CONF/BLD/cpp.fcm
 
 search_src           1
 
diff --git a/mk/bldxcdf.cfg b/mk/bldxcdf.cfg
index 0d752da9..5a175b45 100644
--- a/mk/bldxcdf.cfg
+++ b/mk/bldxcdf.cfg
@@ -7,8 +7,8 @@ cfg::version                        1.0
 # Build information
 # ------------------------------------------------------------------------------
 
-inc $COMPIL_DIR/arch_nemo.fcm
-inc $COMPIL_DIR/cpp.fcm
+inc $NEMO_TDIR/$NEW_CONF/BLD/arch_nemo.fcm
+inc $NEMO_TDIR/$NEW_CONF/BLD/cpp.fcm
 
 search_src           1
 
diff --git a/mk/conv.cfg b/mk/conv.cfg
index 759e5f26..f8757962 100644
--- a/mk/conv.cfg
+++ b/mk/conv.cfg
@@ -7,7 +7,7 @@ cfg::version                        1.0
 # ------------------------------------------------------------------------------
 # Build information
 # ------------------------------------------------------------------------------
-inc $COMPIL_DIR/$MYARCH
+inc $NEMO_TDIR/$NEW_CONF/BLD/$MYARCH
 
 bld::tool::cc        %CC
 bld::tool::cflags    %CFLAGS
-- 
GitLab


From 5f40b08016c3b01a0b3bd31bad1eba7e5854d807 Mon Sep 17 00:00:00 2001
From: Guillaume S <gsamson@mercator-ocean.fr>
Date: Sun, 13 Nov 2022 20:36:43 +0100
Subject: [PATCH 18/31] adapt makenemo to compile nemo in any directory +
 improve "clean" option

---
 makenemo | 169 ++++++++++++++++++++++++-------------------------------
 1 file changed, 72 insertions(+), 97 deletions(-)

diff --git a/makenemo b/makenemo
index d1a48ca3..dd884a5b 100755
--- a/makenemo
+++ b/makenemo
@@ -88,7 +88,6 @@ x_u=''; x_a=''; x_m=''; x_t=''; x_b='';
 x_j='1'; x_e='none'; x_s='src'; x_v='1'
 x_c_cfg=0
 x_nocdf=0
-#x_name=''
 
 ##- Local variables ---
 b_n=$(basename ${0})
@@ -189,7 +188,6 @@ EOF
 	-d|--dirs|--comp)
 	    x_d=${2} ; shift ;;
 	-n|--name)
-	    #x_name=${2} ; shift ;;
 	    x_n=${2} ; shift ;;
 	-r|--ref)
 	    x_r=${2} ; shift ;;
@@ -224,41 +222,6 @@ EOF
     shift
 done
 
-#if [ -n "$x_name" ]   # is the configuration existing in cfgs or tests? or is it a new conf?
-if [ -n "$x_n" ]   # is the configuration existing in cfgs or tests? or is it a new conf?
-then
-    #incfg=$( find $CFGS_DIR   -type d -name $x_name | wc -l )   # this configuration exists in CFGS_DIR
-    #intst=$( find $TESTS_DIR  -type d -name $x_name | wc -l )   # this configuration exists in TESTS_DIR
-    incfg=$( find $CFGS_DIR   -type d -name $x_n | wc -l )   # this configuration exists in CFGS_DIR
-    intst=$( find $TESTS_DIR  -type d -name $x_n | wc -l )   # this configuration exists in TESTS_DIR
-    if [ $(( $incfg + $intst )) -eq 2 ] ; then
-	#echo -e "\033[0;31m\nERROR: the $x_name directory is found twice: in $CFGS_DIR and in $TESTS_DIR\033[0m\n"
-	echo -e "\033[0;31m\nERROR: the $x_n directory is found twice: in $CFGS_DIR and in $TESTS_DIR\033[0m\n"
-	exit 4
-    fi
-    if [ $(( $incfg + $intst )) -gt 0 ] ; then
-	if [ $x_c_cfg -eq 1 ] ; then   # if we just want to clean the config (do it here as it must exist)
-	    #x_n=$x_name                # must define x_n as it is used in Fclean_config.sh
-	    . ${COMPIL_DIR}/Fclean_config.sh
-	    exit 0
-	fi
-	#[ -n "$x_r" ] && echo -e "\nWARNING: $x_name configuration is already existing, we ignore \"-r $x_r\"\n"
-	#[ -n "$x_a" ] && echo -e "\nWARNING: $x_name configuration is already existing, we ignore \"-a $x_a\"\n"
-	[ -n "$x_r" ] && echo -e "\nWARNING: $x_n configuration is already existing, we ignore \"-r $x_r\"\n"
-	[ -n "$x_a" ] && echo -e "\nWARNING: $x_n configuration is already existing, we ignore \"-a $x_a\"\n"
-    fi
-    #if   [ $incfg -eq 1 ] ; then
-	#x_r=$x_name ; x_a=''  # reference configuration existing -> define/overwrite x_r
-    #elif [ $intst -eq 1 ] ; then
-	#x_a=$x_name ; x_r=''   # test      configuration existing -> define/overwrite x_a
-    #else
-    if [[ $incfg -eq 0 && $intst -eq 0 ]]; then
-	[  ${#x_c} -ne 0 ] && echo -e "\nWARNING: Compilation cleaning of a non-existing configuration, we ignore\n" && exit 0
-	[ $x_c_cfg -eq 1 ] && echo -e "\nWARNING: Configuration cleaning of a non-existing configuration, we ignore\n" && exit 0
-	#x_n=$x_name            # this is a new configuration      -> define
-    fi
-fi
-
 export NEW_CONF=${x_n}
 NBR_PRC=${x_j}
 CMP_NAM=${x_m}
@@ -270,21 +233,10 @@ NEMO_DBG=${x_b}
 
 [ "${CMP_NAM}" == 'all' ] && . ${COMPIL_DIR}/Flist_archfile.sh all && exit
 
-
-## No ref. cfg or demo selected
-if [[ -z "${REF_CONF}" && -z "${DEMO_CONF}" && $(( $incfg + $intst )) -eq 0 ]]; then
-    echo -e "\033[0;31m\nAt least a reference configuration ('-r'), a test case ('-a'), "
-    echo -e "a remote configuration ('-u') has to be choosen to build a new configuration!!!\033[0m"
-    ${COMPIL_DIR}/Flist_cfgs.sh
-    exit 2
-fi
-## At least one config has been requested
-
 ## 'all' arg: list all available configurations
 if [[ "${REF_CONF}" == 'all' || "${DEMO_CONF}" == 'all' ]]; then
     ${COMPIL_DIR}/Flist_cfgs.sh
     exit 2
-    ## Probably useless but who knows?
 elif [[ -n "${REF_CONF}" && -n "${DEMO_CONF}" ]]; then
     echo -e "\033[0;31m\nYou have to choose whether you work with:"
     echo -e "  - LTS configurations in ./cfgs  ('-r') or"
@@ -294,29 +246,62 @@ elif [ -n "${REF_CONF}" ]; then
     conf_file=ref_cfgs.txt ; export CONFIG_DIR=${CFGS_DIR} ; TML_CONF=${REF_CONF}
 elif [ -n "${DEMO_CONF}" ]; then
     conf_file=demo_cfgs.txt; export CONFIG_DIR=${TESTS_DIR}; TML_CONF=${DEMO_CONF}
-fi
- 
-## Reuse a working cfg
-grep -q "${TML_CONF} " ${CONFIG_DIR}/work_cfgs.txt 2>/dev/null && conf_file=work_cfgs.txt
-
-## Test if ref. cfg or demo case does exist
-if (! grep -q "${TML_CONF} " ${CONFIG_DIR}/$conf_file ); then
+elif grep -q "${NEW_CONF} " ${CFGS_DIR}/work_cfgs.txt ${TESTS_DIR}/work_cfgs.txt; then
+    conf_file=$( grep -l "${NEW_CONF} " ${CFGS_DIR}/work_cfgs.txt ${TESTS_DIR}/work_cfgs.txt )
+    export CONFIG_DIR=$( dirname $conf_file ); conf_file=$( basename $conf_file )
+    TML_CONF=${NEW_CONF}
+elif ! grep -q "${NEW_CONF} " ${CFGS_DIR}/work_cfgs.txt ${TESTS_DIR}/work_cfgs.txt; then
     echo -e "\033[0;31m\nThe reference configuration ('-r') or "
     echo -e "demonstration case ('-a') selected is not available!!!"
     echo -e "Check the option used and the available items in .txt files\033[0m"
     ${COMPIL_DIR}/Flist_cfgs.sh
     exit 2
 fi
+if [ -z "${NEW_CONF}" ]; then NEW_CONF=$TML_CONF; fi
+export NEMO_TDIR=${x_t:-$CONFIG_DIR}
 
-## If new cfg exists, work in it
-if [ -n "${NEW_CONF}" ]
-then
-    echo
-    printf "\nYou are installing a new configuration %s from %s " ${NEW_CONF} ${TML_CONF}
-    printf  "with sub-components: %s\n"  "${NEM_SUBDIR}"
-    echo
-else
-    NEW_CONF=${TML_CONF}
+
+# check configuration existence & clean it if asked
+if [ -n "$x_n" ]; then
+    incfg=$( find $NEMO_TDIR -type d -name $x_n | wc -l )   # this configuration exists in CFGS_DIR
+    if [ $incfg -eq 1 ] ; then
+        # CLEANING
+	if [ $x_c_cfg -eq 1 ] ; then
+	    . ${COMPIL_DIR}/Fclean_config.sh
+	    exit 0
+        elif [ ${#x_c} -ne 0 ]; then
+            # We coose the default light file
+            [ $x_nocdf -eq 1 ] && export USEBLD=bldxagxcdf.cfg || export USEBLD=bldxag.cfg
+            # We look after agrif
+            grep key_agrif ${NEMO_TDIR}/BLD/cpp.fcm 2>/dev/null && export AGRIFUSE=1 && export USEBLD=${USEBLD/xag/}
+            # fcm clean
+            fcm build ${x_c} --ignore-lock -v ${x_v} -j ${NBR_PRC} ${COMPIL_DIR}/$USEBLD || exit 1
+            # add remove for clean option
+    	    echo -e '\nCleaning '${NEW_CONF}' building directories and variables\n'
+    	    for dir in AGRIFLIB BLD LONG NEMOFILES REPRO_* SHORT WORK; do
+    	        rm -rf ${NEMO_TDIR}/${NEW_CONF}/$dir
+    	    done
+    	    for file in cpp.history cpp.fcm full_key_list.txt; do
+    	        rm -f ${NEMO_TDIR}/${NEW_CONF}/BLD/$file
+    	    done
+            exit 0
+	fi
+	if [ -n "$REF_CONF"  ]; then echo -e "\nWARNING: $x_n configuration is already existing, we ignore \"-r $REF_CONF\"\n"; REF_CONF=""; fi
+	if [ -n "$DEMO_CONF" ]; then echo -e "\nWARNING: $x_n configuration is already existing, we ignore \"-a $DEMO_CONF\"\n"; DEMO_CONF=""; fi
+    fi
+    if [ $incfg -eq 0 ]; then
+	[ $x_c_cfg -eq 1 ] && echo -e "\nWARNING: Configuration cleaning of a non-existing configuration, we ignore\n" && exit 0
+	[  ${#x_c} -ne 0 ] && echo -e "\nWARNING: Compilation cleaning of a non-existing configuration, we ignore\n" && exit 0
+    fi
+fi
+
+
+## No ref. cfg or demo selected
+if [[ -z "${REF_CONF}" && -z "${DEMO_CONF}" && $incfg -eq 0 ]]; then
+    echo -e "\033[0;31m\nAt least a reference configuration ('-r'), a test case ('-a'), "
+    echo -e "a remote configuration ('-u') has to be choosen to build a new configuration!!!\033[0m"
+    ${COMPIL_DIR}/Flist_cfgs.sh
+    exit 2
 fi
 
 ## Update sub-comps if needed
@@ -324,17 +309,22 @@ if [ -z "${NEM_SUBDIR}" ]; then
     NEM_SUBDIR=$( grep "${TML_CONF} " ${CONFIG_DIR}/${conf_file}  | awk '{$1 = ""; print $0}' )
 fi
 
-export NEMO_TDIR=${x_t:-$CONFIG_DIR}
 export NEM_SUBDIR="${NEM_SUBDIR}" NEW_CONF="${NEW_CONF}"
 
+## If new cfg exists, work in it
+if [ ${TML_CONF} != ${NEW_CONF} ]; then
+    echo
+    printf "\nYou are installing a new configuration %s from %s " ${NEW_CONF} ${TML_CONF}
+    if [ -n "${NEM_SUBDIR}" ]; then printf  "with sub-components: %s\n"  "${NEM_SUBDIR}"; fi
+    echo
+fi
+
 ## Save new configuration with sub-components set in work_cfgs.txt
 [ -f ${CONFIG_DIR}/work_cfgs.txt ] && sed -i "/${NEW_CONF} /d" ${CONFIG_DIR}/work_cfgs.txt
 echo ${NEW_CONF} "${NEM_SUBDIR}" >> ${CONFIG_DIR}/work_cfgs.txt
 
-cd ${CONFIG_DIR}
-
 ## Create new config even in existing one (mkdir with -p option, cp with -n)
-${COMPIL_DIR}/Fmake_config.sh ${NEMO_TDIR}/${NEW_CONF} ${TML_CONF}
+${COMPIL_DIR}/Fmake_config.sh ${NEMO_TDIR}/${NEW_CONF} ${CONFIG_DIR}/${TML_CONF}
 
 ## create EXP00 if needed
 [[ ! -d ${NEMO_TDIR}/${NEW_CONF}/EXP00 && -n "${REF_CONF}" ]] && \cp -R -n ${CONFIG_DIR}/${REF_CONF}/EXPREF ${NEMO_TDIR}/${NEW_CONF}/EXP00
@@ -349,12 +339,12 @@ ${COMPIL_DIR}/Fmake_config.sh ${NEMO_TDIR}/${NEW_CONF} ${TML_CONF}
 
 # build the complete list of the cpp keys of this configuration
 if [[ ${chk_key} -eq 1 || ${list_key} -eq 1 ]] ; then
-    for i in $( grep "^ *#.* key_" ${NEW_CONF}/WORK/* ); do
+    for i in $( grep "^ *#.* key_" ${NEMO_TDIR}/${NEW_CONF}/WORK/* ); do
 	echo $i | grep key_ | sed -e "s/=.*//"
     done \
-	| sort -d | uniq > ${COMPIL_DIR}/full_key_list.txt
+	| sort -d | uniq > ${NEMO_TDIR}/${NEW_CONF}/BLD/full_key_list.txt
     
-    [ ${list_key} -eq 1 ] && echo && cat ${COMPIL_DIR}/full_key_list.txt && exit 0
+    [ ${list_key} -eq 1 ] && echo && cat ${NEMO_TDIR}/${NEW_CONF}/BLD/full_key_list.txt && exit 0
 fi
 
 #- At this stage new configuration has been added, we add or remove keys
@@ -364,12 +354,12 @@ fi
 
 #- check that all keys are really existing...
 if [ $chk_key -eq 1 ] ; then
-    for kk in $( cat ${NEW_CONF}/cpp_${NEW_CONF}.fcm ); do
+    for kk in $( cat ${NEMO_TDIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm ); do
 	if [ "$( echo $kk | cut -c 1-4 )" == "key_" ]; then
 	    kk=${kk/=*/}
-	    if [ ! $( grep -w $kk ${COMPIL_DIR}/full_key_list.txt ) ]; then
+	    if [ ! $( grep -w $kk ${NEMO_TDIR}/${NEW_CONF}/BLD/full_key_list.txt ) ]; then
 		echo
-		echo "E R R O R : key "$kk" is not found in ${NEW_CONF}/WORK routines..."
+		echo "E R R O R : key "$kk" is not found in ${NEMO_TDIR}/${NEW_CONF}/WORK routines..."
 		echo "we stop..."
 		echo
 		exit 1
@@ -380,14 +370,9 @@ fi
 
 #- At this stage cpp keys have been updated. we can check the arch file
 #- When used for the first time, choose a compiler ---
-. ${COMPIL_DIR}/Fcheck_archfile.sh arch_nemo.fcm cpp.fcm ${CMP_NAM} || exit 3
-
-#- At this stage the configuration has beeen chosen
-#- We coose the default light file
-[ $x_nocdf -eq 1 ] && export USEBLD=bldxagxcdf.cfg || export USEBLD=bldxag.cfg
+. ${COMPIL_DIR}/Fcheck_archfile.sh ${NEMO_TDIR}/${NEW_CONF}/BLD/arch_nemo.fcm ${NEMO_TDIR}/${NEW_CONF}/BLD/cpp.fcm ${CMP_NAM} || exit 3
 
 #- We look after agrif
-grep key_agrif ${COMPIL_DIR}/cpp.fcm && export AGRIFUSE=1 && export USEBLD=${USEBLD/xag/}
 . ${COMPIL_DIR}/Fprep_agrif.sh ${NEW_CONF} ${NEMO_TDIR} arch_nemo.fcm || exit 3
 
 #-
@@ -398,40 +383,30 @@ grep key_agrif ${COMPIL_DIR}/cpp.fcm && export AGRIFUSE=1 && export USEBLD=${USE
 #- Compile ---
 
 if [ "${NBR_PRC}" -gt 0 ]; then
-    cd ${NEMO_TDIR}/${NEW_CONF} || cd -
 
     ## if AGRIF we do a first preprocessing
     if [[ ${#x_c} -eq 0 && "$AGRIFUSE" -eq 1 ]]; then
-	fcm build --ignore-lock -j 1 ${COMPIL_DIR}/bld_preproagr.cfg ||{ cd - ; exit 1 ;}
+	fcm build --ignore-lock -j 1 ${COMPIL_DIR}/bld_preproagr.cfg || exit 1
 	echo ''
 	echo "---------------------------------"
 	echo "CONV preprocessing successfull !!"
 	echo "---------------------------------"
 	echo ''
     fi
+
+    # We coose the default light file
+    [ $x_nocdf -eq 1 ] && export USEBLD=bldxagxcdf.cfg || export USEBLD=bldxag.cfg
+    # We look after agrif
+    grep key_agrif ${NEMO_TDIR}/BLD/cpp.fcm 2>/dev/null && export AGRIFUSE=1 && export USEBLD=${USEBLD/xag/}
     
-    fcm build ${x_c} --ignore-lock -v ${x_v} -j ${NBR_PRC} ${COMPIL_DIR}/$USEBLD ||{ cd - ; exit 1 ;}
+    fcm build ${x_c} --ignore-lock -v ${x_v} -j ${NBR_PRC} ${COMPIL_DIR}/$USEBLD || exit 1
 
     if [ -f ${NEMO_TDIR}/${NEW_CONF}/BLD/bin/nemo.exe ]; then
 	ln -sf ${NEMO_TDIR}/${NEW_CONF}/BLD/bin/nemo.exe  ${NEMO_TDIR}/${NEW_CONF}/EXP00/nemo
     fi
 
-    ## add remove for clean option
-    if [ ${#x_c} -ne 0 ]; then
-	echo -e '\nCleaning '${NEW_CONF}' building directories and variables\n'
-	for dir in AGRIFLIB BLD LONG NEMOFILES REPRO_* SHORT WORK; do
-	    rm -rf ${NEMO_TDIR}/${NEW_CONF}/$dir
-	done
-	for file in cpp.history cpp.fcm full_key_list.txt; do
-	    rm -f ${COMPIL_DIR}/$file
-	done
-    fi
     
 fi
 
-#- Come back to original directory ---
-cd -
-
-#-
 #- Unset variables
 ${COMPIL_DIR}/Fclean_var.sh
-- 
GitLab


From dca802ef6fe72cb5cff99e8bb87394cbabca5152 Mon Sep 17 00:00:00 2001
From: Guillaume S <gsamson@mercator-ocean.fr>
Date: Mon, 14 Nov 2022 12:20:08 +0100
Subject: [PATCH 19/31] agrif compilation bugfix

---
 makenemo             | 18 ++++++++----------
 mk/bld.cfg           |  4 ++--
 mk/bld_preproagr.cfg |  6 +++---
 3 files changed, 13 insertions(+), 15 deletions(-)

diff --git a/makenemo b/makenemo
index dd884a5b..cdddf458 100755
--- a/makenemo
+++ b/makenemo
@@ -263,7 +263,7 @@ export NEMO_TDIR=${x_t:-$CONFIG_DIR}
 
 # check configuration existence & clean it if asked
 if [ -n "$x_n" ]; then
-    incfg=$( find $NEMO_TDIR -type d -name $x_n | wc -l )   # this configuration exists in CFGS_DIR
+    incfg=$( find $NEMO_TDIR -type d -name $x_n 2>/dev/null | wc -l )   # this configuration exists in CFGS_DIR
     if [ $incfg -eq 1 ] ; then
         # CLEANING
 	if [ $x_c_cfg -eq 1 ] ; then
@@ -371,10 +371,6 @@ fi
 #- At this stage cpp keys have been updated. we can check the arch file
 #- When used for the first time, choose a compiler ---
 . ${COMPIL_DIR}/Fcheck_archfile.sh ${NEMO_TDIR}/${NEW_CONF}/BLD/arch_nemo.fcm ${NEMO_TDIR}/${NEW_CONF}/BLD/cpp.fcm ${CMP_NAM} || exit 3
-
-#- We look after agrif
-. ${COMPIL_DIR}/Fprep_agrif.sh ${NEW_CONF} ${NEMO_TDIR} arch_nemo.fcm || exit 3
-
 #-
 #_ END OF CONFIGURATION PHASE
 #_
@@ -384,6 +380,13 @@ fi
 
 if [ "${NBR_PRC}" -gt 0 ]; then
 
+    # We coose the default light file
+    [ $x_nocdf -eq 1 ] && export USEBLD=bldxagxcdf.cfg || export USEBLD=bldxag.cfg
+
+    # We look after agrif
+    grep key_agrif ${NEMO_TDIR}/${NEW_CONF}/BLD/cpp.fcm 2>/dev/null && export AGRIFUSE=1 && export USEBLD=${USEBLD/xag/}
+    . ${COMPIL_DIR}/Fprep_agrif.sh ${NEW_CONF} ${NEMO_TDIR} arch_nemo.fcm || exit 3
+    
     ## if AGRIF we do a first preprocessing
     if [[ ${#x_c} -eq 0 && "$AGRIFUSE" -eq 1 ]]; then
 	fcm build --ignore-lock -j 1 ${COMPIL_DIR}/bld_preproagr.cfg || exit 1
@@ -394,11 +397,6 @@ if [ "${NBR_PRC}" -gt 0 ]; then
 	echo ''
     fi
 
-    # We coose the default light file
-    [ $x_nocdf -eq 1 ] && export USEBLD=bldxagxcdf.cfg || export USEBLD=bldxag.cfg
-    # We look after agrif
-    grep key_agrif ${NEMO_TDIR}/BLD/cpp.fcm 2>/dev/null && export AGRIFUSE=1 && export USEBLD=${USEBLD/xag/}
-    
     fcm build ${x_c} --ignore-lock -v ${x_v} -j ${NBR_PRC} ${COMPIL_DIR}/$USEBLD || exit 1
 
     if [ -f ${NEMO_TDIR}/${NEW_CONF}/BLD/bin/nemo.exe ]; then
diff --git a/mk/bld.cfg b/mk/bld.cfg
index 67352be6..ebc688aa 100644
--- a/mk/bld.cfg
+++ b/mk/bld.cfg
@@ -7,8 +7,8 @@ cfg::version                        1.0
 # Build information
 # ------------------------------------------------------------------------------
 
-inc $COMPIL_DIR/arch_nemo.fcm
-inc $COMPIL_DIR/cpp.fcm
+inc $NEMO_TDIR/$NEW_CONF/BLD/arch_nemo.fcm
+inc $NEMO_TDIR/$NEW_CONF/BLD/cpp.fcm
 
 search_src           1
 
diff --git a/mk/bld_preproagr.cfg b/mk/bld_preproagr.cfg
index e901d829..3f015aa1 100644
--- a/mk/bld_preproagr.cfg
+++ b/mk/bld_preproagr.cfg
@@ -7,11 +7,11 @@ cfg::version                        1.0
 # Build information
 # ------------------------------------------------------------------------------
 
-inc $COMPIL_DIR/arch_nemo.fcm
-inc $COMPIL_DIR/cpp.fcm
+inc $NEMO_TDIR/$NEW_CONF/BLD/arch_nemo.fcm
+inc $NEMO_TDIR/$NEW_CONF/BLD/cpp.fcm
 search_src           1
 
-src::nemo                 $CONFIG_DIR/$NEW_CONF/WORK
+src::nemo                 $NEMO_TDIR/$NEW_CONF/WORK
 
 bld::target  lib_cray.f90 nemo.f90 agrif_user.f90 agrif2model.f90 
 
-- 
GitLab


From aa6450b8aacfd8ca0fe3343d2f2ae5a2a8971156 Mon Sep 17 00:00:00 2001
From: Guillaume S <gsamson@mercator-ocean.fr>
Date: Mon, 14 Nov 2022 12:53:44 +0100
Subject: [PATCH 20/31] fix physics tests for LOCK_EXCHANGE & OVERFLOW

---
 sette/sette_test-cases.sh | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/sette/sette_test-cases.sh b/sette/sette_test-cases.sh
index eb7b5d44..e76ae95b 100755
--- a/sette/sette_test-cases.sh
+++ b/sette/sette_test-cases.sh
@@ -222,12 +222,12 @@ if [ ${config} == "OVERFLOW" ] && [ ${DO_PHYOPTS} == "1" ] ;  then
     else
 	ITEND=6120
     fi
-    cd ${CONFIG_DIR}/${NEW_CONF}/EXP00
+    cd ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}/EXP00
 
     for file in $(echo `ls namelist_*_cfg `) ; do
         TEST_NAME=`echo $file | sed -e "s/namelist_//" | sed -e "s/_cfg//"`
         TEST_NAME="EXP-${TEST_NAME}"
-        if [ ! -d ${CONFIG_DIR}/${NEW_CONF}/${TEST_NAME} ] ; then mkdir ${CONFIG_DIR}/${NEW_CONF}/${TEST_NAME} ; fi
+        if [ ! -d ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}/${TEST_NAME} ] ; then mkdir -p ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}/${TEST_NAME} ; fi
         export TEST_NAME="${TEST_NAME}"
          ##
         cd ${SETTE_DIR}
@@ -239,7 +239,7 @@ if [ ${config} == "OVERFLOW" ] && [ ${DO_PHYOPTS} == "1" ] ;  then
         if [ -f ${JOB_FILE} ] ; then \rm ${JOB_FILE} ; fi
         cd ${EXE_DIR}
         rm namelist_*_*_*_*
-        cp -pL ${CONFIG_DIR}/${NEW_CONF}/EXP00/$file namelist_cfg
+        cp -pL ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}/EXP00/$file namelist_cfg
 	set_namelist namelist_cfg nn_it000 1
 	set_namelist namelist_cfg nn_itend ${ITEND}
         set_namelist_opt namelist_cfg ln_timing ${USING_TIMING} .true. .false.
@@ -337,13 +337,14 @@ if [ ${config} == "LOCK_EXCHANGE" ] && [ ${DO_PHYOPTS} == "1" ] ;  then
     else
 	ITEND=61200
     fi
-    cd ${CONFIG_DIR}/${NEW_CONF}/EXP00
+    cd ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}/EXP00
+
 
     for file in $(echo `ls namelist_*_cfg `) ; do
         echo ''
         TEST_NAME=`echo $file | sed -e "s/namelist_//" | sed -e "s/_cfg//"`
         TEST_NAME="EXP-${TEST_NAME}"
-        `mkdir ${CONFIG_DIR}/${NEW_CONF}/${TEST_NAME}`
+        mkdir -p ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}/${TEST_NAME}
         export TEST_NAME="${TEST_NAME}"
         ##  
         cd ${SETTE_DIR}
@@ -355,7 +356,7 @@ if [ ${config} == "LOCK_EXCHANGE" ] && [ ${DO_PHYOPTS} == "1" ] ;  then
         if [ -f ${JOB_FILE} ] ; then \rm ${JOB_FILE} ; fi
         cd ${EXE_DIR}
         rm namelist_*_*_*_*
-        cp -pL ${CONFIG_DIR}/${NEW_CONF}/EXP00/$file namelist_cfg
+        cp -pL ${CMP_DIR:-${CONFIG_DIR0}}/${SETTE_CONFIG}/EXP00/$file namelist_cfg
 	set_namelist namelist_cfg nn_it000 1
         set_namelist namelist_cfg nn_itend ${ITEND}
         set_namelist_opt namelist_cfg ln_timing ${USING_TIMING} .true. .false.
-- 
GitLab


From 9dff9e49c2f3da196e74f605fe7452bc374e8f90 Mon Sep 17 00:00:00 2001
From: Guillaume S <gsamson@mercator-ocean.fr>
Date: Tue, 29 Nov 2022 09:19:08 +0100
Subject: [PATCH 21/31] apply Simon suggestions from !178

---
 makenemo | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/makenemo b/makenemo
index cdddf458..96464483 100755
--- a/makenemo
+++ b/makenemo
@@ -246,10 +246,15 @@ elif [ -n "${REF_CONF}" ]; then
     conf_file=ref_cfgs.txt ; export CONFIG_DIR=${CFGS_DIR} ; TML_CONF=${REF_CONF}
 elif [ -n "${DEMO_CONF}" ]; then
     conf_file=demo_cfgs.txt; export CONFIG_DIR=${TESTS_DIR}; TML_CONF=${DEMO_CONF}
-elif grep -q "${NEW_CONF} " ${CFGS_DIR}/work_cfgs.txt ${TESTS_DIR}/work_cfgs.txt; then
-    conf_file=$( grep -l "${NEW_CONF} " ${CFGS_DIR}/work_cfgs.txt ${TESTS_DIR}/work_cfgs.txt )
+elif [ $( grep -l "^${NEW_CONF} " */work_cfgs.txt | wc -l ) -eq 1 ]; then
+    conf_file=$( grep -l "^${NEW_CONF} " ${CFGS_DIR}/work_cfgs.txt ${TESTS_DIR}/work_cfgs.txt )
     export CONFIG_DIR=$( dirname $conf_file ); conf_file=$( basename $conf_file )
     TML_CONF=${NEW_CONF}
+elif [ $( grep -l "^${NEW_CONF} " */work_cfgs.txt | wc -l ) -eq 2 ]; then
+    echo -e "\033[0;31m\nUser configuration is present in both"
+    echo -e "cfgs/work_cfgs.txt and tests/work_cfgs.txt files"
+    echo -e "Please choose only one \033[0m"
+    exit 2
 elif ! grep -q "${NEW_CONF} " ${CFGS_DIR}/work_cfgs.txt ${TESTS_DIR}/work_cfgs.txt; then
     echo -e "\033[0;31m\nThe reference configuration ('-r') or "
     echo -e "demonstration case ('-a') selected is not available!!!"
-- 
GitLab


From fae8dc5c6113599fa0e12c2bcf8ea6811eb49b58 Mon Sep 17 00:00:00 2001
From: Guillaume S <gsamson@mercator-ocean.fr>
Date: Wed, 14 Dec 2022 17:01:15 +0100
Subject: [PATCH 22/31] apply Simon review

---
 makenemo           | 62 ++++++++++++++++++++++++----------------------
 mk/Fmake_config.sh |  4 +--
 2 files changed, 34 insertions(+), 32 deletions(-)

diff --git a/makenemo b/makenemo
index 96464483..668eed08 100755
--- a/makenemo
+++ b/makenemo
@@ -246,35 +246,39 @@ elif [ -n "${REF_CONF}" ]; then
     conf_file=ref_cfgs.txt ; export CONFIG_DIR=${CFGS_DIR} ; TML_CONF=${REF_CONF}
 elif [ -n "${DEMO_CONF}" ]; then
     conf_file=demo_cfgs.txt; export CONFIG_DIR=${TESTS_DIR}; TML_CONF=${DEMO_CONF}
-elif [ $( grep -l "^${NEW_CONF} " */work_cfgs.txt | wc -l ) -eq 1 ]; then
+elif [ $( grep -l "^${NEW_CONF} " */work_cfgs.txt 2> /dev/null | wc -l ) -eq 1 ]; then
     conf_file=$( grep -l "^${NEW_CONF} " ${CFGS_DIR}/work_cfgs.txt ${TESTS_DIR}/work_cfgs.txt )
     export CONFIG_DIR=$( dirname $conf_file ); conf_file=$( basename $conf_file )
     TML_CONF=${NEW_CONF}
-elif [ $( grep -l "^${NEW_CONF} " */work_cfgs.txt | wc -l ) -eq 2 ]; then
+elif [ $( grep -l "^${NEW_CONF} " */work_cfgs.txt 2> /dev/null | wc -l ) -eq 2 ]; then
     echo -e "\033[0;31m\nUser configuration is present in both"
     echo -e "cfgs/work_cfgs.txt and tests/work_cfgs.txt files"
     echo -e "Please choose only one \033[0m"
     exit 2
-elif ! grep -q "${NEW_CONF} " ${CFGS_DIR}/work_cfgs.txt ${TESTS_DIR}/work_cfgs.txt; then
+elif ! grep -q "^${NEW_CONF} " ${CFGS_DIR}/work_cfgs.txt ${TESTS_DIR}/work_cfgs.txt 2> /dev/null; then
     echo -e "\033[0;31m\nThe reference configuration ('-r') or "
     echo -e "demonstration case ('-a') selected is not available!!!"
     echo -e "Check the option used and the available items in .txt files\033[0m"
     ${COMPIL_DIR}/Flist_cfgs.sh
     exit 2
+else
+    exit 2
 fi
+
 if [ -z "${NEW_CONF}" ]; then NEW_CONF=$TML_CONF; fi
 export NEMO_TDIR=${x_t:-$CONFIG_DIR}
 
 
 # check configuration existence & clean it if asked
-if [ -n "$x_n" ]; then
-    incfg=$( find $NEMO_TDIR -type d -name $x_n 2>/dev/null | wc -l )   # this configuration exists in CFGS_DIR
-    if [ $incfg -eq 1 ] ; then
-        # CLEANING
-	if [ $x_c_cfg -eq 1 ] ; then
-	    . ${COMPIL_DIR}/Fclean_config.sh
-	    exit 0
-        elif [ ${#x_c} -ne 0 ]; then
+incfg=$( find $NEMO_TDIR -type d -maxdepth 1 -name ${TML_CONF} 2>/dev/null | wc -l )   # this configuration exists in CFGS_DIR
+if [ $incfg -eq 1 ] ; then
+    # CLEANING
+    if [ $x_c_cfg -eq 1 ] ; then
+        . ${COMPIL_DIR}/Fclean_config.sh
+        exit 0
+    elif [ ${#x_c} -ne 0 ]; then
+        read -p "Are you sure that you want to clean $TML_CONF configuration ? " -n 1 -r; echo
+        if [[ $REPLY =~ ^[Yy]$ ]]; then
             # We coose the default light file
             [ $x_nocdf -eq 1 ] && export USEBLD=bldxagxcdf.cfg || export USEBLD=bldxag.cfg
             # We look after agrif
@@ -282,22 +286,24 @@ if [ -n "$x_n" ]; then
             # fcm clean
             fcm build ${x_c} --ignore-lock -v ${x_v} -j ${NBR_PRC} ${COMPIL_DIR}/$USEBLD || exit 1
             # add remove for clean option
-    	    echo -e '\nCleaning '${NEW_CONF}' building directories and variables\n'
-    	    for dir in AGRIFLIB BLD LONG NEMOFILES REPRO_* SHORT WORK; do
-    	        rm -rf ${NEMO_TDIR}/${NEW_CONF}/$dir
-    	    done
-    	    for file in cpp.history cpp.fcm full_key_list.txt; do
-    	        rm -f ${NEMO_TDIR}/${NEW_CONF}/BLD/$file
-    	    done
+            echo -e '\nCleaning '${NEW_CONF}' building directories and variables\n'
+            for dir in AGRIFLIB BLD LONG NEMOFILES REPRO_* SHORT WORK; do
+               rm -rf ${NEMO_TDIR}/${NEW_CONF}/$dir
+            done
+            for file in cpp.history cpp.fcm full_key_list.txt; do
+               rm -f ${NEMO_TDIR}/${NEW_CONF}/BLD/$file
+            done
             exit 0
-	fi
-	if [ -n "$REF_CONF"  ]; then echo -e "\nWARNING: $x_n configuration is already existing, we ignore \"-r $REF_CONF\"\n"; REF_CONF=""; fi
-	if [ -n "$DEMO_CONF" ]; then echo -e "\nWARNING: $x_n configuration is already existing, we ignore \"-a $DEMO_CONF\"\n"; DEMO_CONF=""; fi
-    fi
-    if [ $incfg -eq 0 ]; then
-	[ $x_c_cfg -eq 1 ] && echo -e "\nWARNING: Configuration cleaning of a non-existing configuration, we ignore\n" && exit 0
-	[  ${#x_c} -ne 0 ] && echo -e "\nWARNING: Compilation cleaning of a non-existing configuration, we ignore\n" && exit 0
+        else
+            echo "cleaning cancelled"
+            exit 2
+        fi
     fi
+    if [[ -n "$x_n" && -n "$REF_CONF"  ]]; then echo -e "\nWARNING: $x_n configuration is already existing, we ignore \"-r $REF_CONF\"\n"; REF_CONF=""; fi
+    if [[ -n "$x_n" && -n "$DEMO_CONF" ]]; then echo -e "\nWARNING: $x_n configuration is already existing, we ignore \"-a $DEMO_CONF\"\n"; DEMO_CONF=""; fi
+elif [ $incfg -eq 0 ]; then
+    [ $x_c_cfg -eq 1 ] && echo -e "\nWARNING: Configuration cleaning of a non-existing configuration, we ignore\n" && exit 0
+    [  ${#x_c} -ne 0 ] && echo -e "\nWARNING: Compilation cleaning of a non-existing configuration, we ignore\n" && exit 0
 fi
 
 
@@ -325,16 +331,12 @@ if [ ${TML_CONF} != ${NEW_CONF} ]; then
 fi
 
 ## Save new configuration with sub-components set in work_cfgs.txt
-[ -f ${CONFIG_DIR}/work_cfgs.txt ] && sed -i "/${NEW_CONF} /d" ${CONFIG_DIR}/work_cfgs.txt
+[ -f ${CONFIG_DIR}/work_cfgs.txt ] && sed -i "/^${NEW_CONF} /d" ${CONFIG_DIR}/work_cfgs.txt
 echo ${NEW_CONF} "${NEM_SUBDIR}" >> ${CONFIG_DIR}/work_cfgs.txt
 
 ## Create new config even in existing one (mkdir with -p option, cp with -n)
 ${COMPIL_DIR}/Fmake_config.sh ${NEMO_TDIR}/${NEW_CONF} ${CONFIG_DIR}/${TML_CONF}
 
-## create EXP00 if needed
-[[ ! -d ${NEMO_TDIR}/${NEW_CONF}/EXP00 && -n "${REF_CONF}" ]] && \cp -R -n ${CONFIG_DIR}/${REF_CONF}/EXPREF ${NEMO_TDIR}/${NEW_CONF}/EXP00
-[[ ! -d ${NEMO_TDIR}/${NEW_CONF}/EXP00 && -n "${DEMO_CONF}" ]] && \cp -R -n ${CONFIG_DIR}/${DEMO_CONF}/EXPREF ${NEMO_TDIR}/${NEW_CONF}/EXP00
-
 #- Create the WORK ---
 #- Clean links and librairies ---
 #- Creating the good links, at first on OCE ---
diff --git a/mk/Fmake_config.sh b/mk/Fmake_config.sh
index 79673f0e..6a3e942b 100755
--- a/mk/Fmake_config.sh
+++ b/mk/Fmake_config.sh
@@ -59,9 +59,9 @@ set -o posix
 \mkdir -p ${1}
 \mkdir -p ${1}/EXP00
 \mkdir -p ${1}/MY_SRC
-\cp -R -n ${2}/cpp_${2##*/}.fcm ${1}/cpp_${1##*/}.fcm
+[ "${2}/cpp_${2##*/}.fcm" != "${1}/cpp_${1##*/}.fcm" ] && \cp -R -n ${2}/cpp_${2##*/}.fcm ${1}/cpp_${1##*/}.fcm
 for f in ${2}/EXPREF/*.xml ${2}/EXPREF/*namelist*; do
   if [ -L ${f} ]; then ln -sf $(readlink -f ${f}) ${1}/EXP00/$(basename ${f}); else cp -R -n ${f} ${1}/EXP00/.; fi
 done
-[ -f ${2}/EXPREF/AGRIF_FixedGrids.in ] &&  \cp -a -n ${2}/EXPREF/AGRIF_FixedGrids.in ${1}/EXP00/.
+[ -f ${2}/EXPREF/AGRIF_FixedGrids.in ] && \cp -a -n ${2}/EXPREF/AGRIF_FixedGrids.in ${1}/EXP00/.
 [ -d    ${2}/MY_SRC ] && \cp -an ${2}/MY_SRC/* ${1}/MY_SRC/. 2> /dev/null
-- 
GitLab


From 2e0edf9379a22d15e3caca16c145ede426ac5097 Mon Sep 17 00:00:00 2001
From: Guillaume S <gsamson@mercator-ocean.fr>
Date: Fri, 16 Dec 2022 19:16:33 +0100
Subject: [PATCH 23/31] adapt maketools to Fcheck_archfile.sh modifications

---
 tools/maketools | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/maketools b/tools/maketools
index 99aab337..857f9643 100755
--- a/tools/maketools
+++ b/tools/maketools
@@ -156,7 +156,7 @@ echo "${NEW_CONF} "  > ${COMPIL_DIR}/tools.txt
 
 #- At this stage cpp keys have been updated. we can check the arch file
 #- When used for the first time, choose a compiler ---
-. ${COMPIL_DIR}/Fcheck_archfile.sh arch_tools.fcm cpp_tools.fcm ${CMP_NAM} || exit
+. ${COMPIL_DIR}/Fcheck_archfile.sh ${COMPIL_DIR}/arch_tools.fcm ${COMPIL_DIR}/cpp_tools.fcm ${CMP_NAM} || exit
 
 #- At this stage the configuration has beeen chosen
 #- We coose the default light file
-- 
GitLab


From 244b4deaacf45331af8fab2acbe6caadf26fd2ab Mon Sep 17 00:00:00 2001
From: Guillaume S <gsamson@mercator-ocean.fr>
Date: Mon, 19 Dec 2022 10:57:07 +0100
Subject: [PATCH 24/31] move tools.txt (generated bu maketools) to tools
 directory to avoid any modification of mk directory

---
 mk/tools.txt | 1 -
 1 file changed, 1 deletion(-)
 delete mode 100644 mk/tools.txt

diff --git a/mk/tools.txt b/mk/tools.txt
deleted file mode 100644
index a6cb4ae5..00000000
--- a/mk/tools.txt
+++ /dev/null
@@ -1 +0,0 @@
-DOMAINcfg 
-- 
GitLab


From 0333f7b332234201545b57ce931b55c3433c1781 Mon Sep 17 00:00:00 2001
From: Guillaume S <gsamson@mercator-ocean.fr>
Date: Mon, 19 Dec 2022 10:58:05 +0100
Subject: [PATCH 25/31] cleaning

---
 mk/Fmake_bld.sh | 1 -
 1 file changed, 1 deletion(-)

diff --git a/mk/Fmake_bld.sh b/mk/Fmake_bld.sh
index ebb2e48c..bd4b331c 100755
--- a/mk/Fmake_bld.sh
+++ b/mk/Fmake_bld.sh
@@ -59,6 +59,5 @@ set -o posix
 #-
 [ ! -d ${3}/${2}     ] && \mkdir -p ${3}/${2}
 [ ! -d ${3}/${2}/BLD ] && \mkdir -p ${3}/${2}/BLD
-#[ ! -d ${1}/${2}/BLD ] && ln -sf ${3}/${2}/BLD ${1}/${2}/BLD
 [ -f ${3}/${2}/cpp_${2}.fcm ] && ln -sf ${3}/${2}/cpp_${2}.fcm ${3}/${2}/BLD/cpp.fcm
 rm -f  ${1}/${2}/BLD/fcm.bld.lock
-- 
GitLab


From 7f835414a047af7c3114587528ad190b40f6d3c1 Mon Sep 17 00:00:00 2001
From: Guillaume S <gsamson@mercator-ocean.fr>
Date: Mon, 19 Dec 2022 10:58:36 +0100
Subject: [PATCH 26/31] harmonize Fmake_tools_bld.sh script with Fmake_bld.sh
 version

---
 mk/Fmake_tools_bld.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mk/Fmake_tools_bld.sh b/mk/Fmake_tools_bld.sh
index b5e67c8c..3a9a5041 100755
--- a/mk/Fmake_tools_bld.sh
+++ b/mk/Fmake_tools_bld.sh
@@ -62,5 +62,5 @@ set -o posix
 [ ! -d ${1}/${2}/BLD ] && ln -sf ${3}/${2}/BLD ${1}/${2}/BLD
 # enforce presence of cpp_tools.fcm (write a blank one if not present in the tools directory)
 # cp instead of ln to avoid overwiting previous tool cpp_XXX.fcm file when compiling a file without cpp_YYY.fcm file.
-[ -f ${1}/${NEW_CONF}/cpp_${NEW_CONF}.fcm ] && cp -f ${1}/${NEW_CONF}/cpp_${NEW_CONF}.fcm ${COMPIL_DIR}/cpp_tools.fcm || echo 'bld::tool::fppkeys ' > ${COMPIL_DIR}/cpp_tools.fcm
+[ -f ${3}/${2}/cpp_${2}.fcm ] && ln -sf -f ${3}/${2}/cpp_${2}.fcm ${3}/${2}/BLD/cpp_tools.fcm || echo 'bld::tool::fppkeys ' > ${3}/${2}/BLD/cpp_tools.fcm
 rm -f  ${1}/${NEW_CONF}/BLD/fcm.bld.lock
-- 
GitLab


From a445fe6cb2a162cf556d760bf4391afead135d22 Mon Sep 17 00:00:00 2001
From: Guillaume S <gsamson@mercator-ocean.fr>
Date: Mon, 19 Dec 2022 10:59:14 +0100
Subject: [PATCH 27/31] change cpp & arch files path from mk directory to BLD
 tools directory (as for makenemo)

---
 mk/bldxag_tools.cfg | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/mk/bldxag_tools.cfg b/mk/bldxag_tools.cfg
index 45282637..7f54517b 100644
--- a/mk/bldxag_tools.cfg
+++ b/mk/bldxag_tools.cfg
@@ -7,8 +7,8 @@ cfg::version                        1.0
 # Build information
 # ------------------------------------------------------------------------------
 
-inc $COMPIL_DIR/arch_tools.fcm
-inc $COMPIL_DIR/cpp_tools.fcm
+inc $TOOLS_DIR/$NEW_CONF/BLD/arch_tools.fcm
+inc $TOOLS_DIR/$NEW_CONF/BLD/cpp_tools.fcm
 
 search_src           1
 
-- 
GitLab


From 01ae4c2b51ccaca88c5660e8f46526217c5b86ca Mon Sep 17 00:00:00 2001
From: Guillaume S <gsamson@mercator-ocean.fr>
Date: Mon, 19 Dec 2022 11:00:27 +0100
Subject: [PATCH 28/31] adjust maketools for new cpp, arch & tools.txt paths

---
 tools/maketools | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tools/maketools b/tools/maketools
index 857f9643..cc420971 100755
--- a/tools/maketools
+++ b/tools/maketools
@@ -146,24 +146,24 @@ export NEMO_TDIR=${NEMO_TDIR:-$TOOLS_DIR}
 
 #- Choose a default tool if needed ---
 #- REBUILD or last one used ---
-. ${COMPIL_DIR}/Fcheck_config.sh tools.txt ${NEW_CONF} || exit
+. ${COMPIL_DIR}/Fcheck_config.sh ${TOOLS_DIR}/tools.txt ${NEW_CONF} || exit
 
 #- Save new configuration ---
-echo "${NEW_CONF} "  > ${COMPIL_DIR}/tools.txt
+echo "${NEW_CONF} "  > ${TOOLS_DIR}/tools.txt
 
 #- Make the building directory
 . ${COMPIL_DIR}/Fmake_tools_bld.sh ${TOOLS_DIR} ${NEW_CONF} ${NEMO_TDIR} || exit
 
 #- At this stage cpp keys have been updated. we can check the arch file
 #- When used for the first time, choose a compiler ---
-. ${COMPIL_DIR}/Fcheck_archfile.sh ${COMPIL_DIR}/arch_tools.fcm ${COMPIL_DIR}/cpp_tools.fcm ${CMP_NAM} || exit
+. ${COMPIL_DIR}/Fcheck_archfile.sh ${TOOLS_DIR}/${NEW_CONF}/BLD/arch_tools.fcm ${TOOLS_DIR}/${NEW_CONF}/BLD/cpp_tools.fcm ${CMP_NAM} || exit
 
 #- At this stage the configuration has beeen chosen
 #- We coose the default light file
 export USEBLD=bldxag_tools.cfg
 
 #- We look after agrif
-grep key_agrif ${COMPIL_DIR}/cpp_tools.fcm && export AGRIFUSE=1 && export USEBLD=${USEBLD/xag/}
+grep key_agrif ${TOOLS_DIR}/${NEW_CONF}/BLD/cpp_tools.fcm && export AGRIFUSE=1 && export USEBLD=${USEBLD/xag/}
 
 
 . ${COMPIL_DIR}/Fprep_agrif.sh ${NEW_CONF} ${TOOLS_DIR} arch_tools.fcm|| exit 3
-- 
GitLab


From 0f0a295b4e9455fd45d963c55797b932903b2e01 Mon Sep 17 00:00:00 2001
From: Guillaume S <gsamson@mercator-ocean.fr>
Date: Mon, 19 Dec 2022 11:05:57 +0100
Subject: [PATCH 29/31] adat gitignore to mk changes

---
 .gitignore | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/.gitignore b/.gitignore
index 403ab425..ab4a609c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,16 +1,20 @@
-# configurations & testcases
+# configurations, testcases & tools
 
-*/work_cfgs.txt
+cfgs/work_cfgs.txt
 cfgs/*/BLD
 cfgs/*/EXP00
 cfgs/*/WORK
 cfgs/*_ST
+
+tests/work_cfgs.txt
 tests/*/BLD
 tests/*/EXP00
 tests/*/WORK
 tests/*_ST
 
+tools/*/BLD
+tools/*/*.exe
+tools/tools.txt
+
 # mk
-mk/arch*
-mk/cpp.*
 mk/full_key_list.txt
-- 
GitLab


From 8dbe59be944888c67e0ad8e903c60177387ab6cc Mon Sep 17 00:00:00 2001
From: Guillaume S <gsamson@mercator-ocean.fr>
Date: Mon, 19 Dec 2022 11:24:01 +0100
Subject: [PATCH 30/31] finishing applying Simon review

---
 makenemo | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/makenemo b/makenemo
index 668eed08..a774d878 100755
--- a/makenemo
+++ b/makenemo
@@ -270,14 +270,14 @@ export NEMO_TDIR=${x_t:-$CONFIG_DIR}
 
 
 # check configuration existence & clean it if asked
-incfg=$( find $NEMO_TDIR -type d -maxdepth 1 -name ${TML_CONF} 2>/dev/null | wc -l )   # this configuration exists in CFGS_DIR
+incfg=$( find $NEMO_TDIR -type d -maxdepth 1 -name ${NEW_CONF} 2>/dev/null | wc -l )   # this configuration exists in CFGS_DIR
 if [ $incfg -eq 1 ] ; then
     # CLEANING
     if [ $x_c_cfg -eq 1 ] ; then
         . ${COMPIL_DIR}/Fclean_config.sh
         exit 0
     elif [ ${#x_c} -ne 0 ]; then
-        read -p "Are you sure that you want to clean $TML_CONF configuration ? " -n 1 -r; echo
+        read -p "Are you sure that you want to clean $NEW_CONF configuration ? " -n 1 -r; echo
         if [[ $REPLY =~ ^[Yy]$ ]]; then
             # We coose the default light file
             [ $x_nocdf -eq 1 ] && export USEBLD=bldxagxcdf.cfg || export USEBLD=bldxag.cfg
-- 
GitLab


From 7add42f97130db23ffa26553ccc4c41b2b39875c Mon Sep 17 00:00:00 2001
From: Guillaume S <gsamson@mercator-ocean.fr>
Date: Mon, 19 Dec 2022 11:31:17 +0100
Subject: [PATCH 31/31] put back MAIN_DIR path modification (in case of needed
 by someone)

---
 makenemo | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/makenemo b/makenemo
index a774d878..0d648679 100755
--- a/makenemo
+++ b/makenemo
@@ -93,6 +93,12 @@ x_nocdf=0
 b_n=$(basename ${0})
 OPTIND='1'
 MAIN_DIR=$(cd $(dirname "$0"); pwd)
+MAIN_DIR=${MAIN_DIR%/sette}
+MAIN_DIR=${MAIN_DIR%/tools}
+MAIN_DIR=${MAIN_DIR%/cfgs}
+MAIN_DIR=${MAIN_DIR%/tests}
+MAIN_DIR=${MAIN_DIR%/ext}
+MAIN_DIR=${MAIN_DIR%/arch}
 export MAIN_DIR
 #
 export CFGS_DIR=${MAIN_DIR}/cfgs
-- 
GitLab