Merge branch 'main' into 100-revise-bdy-structure-of-top-boundary-conditions

.gitignore

@@ -4,12 +4,16 @@ cfgs/work_cfgs.txt
 cfgs/*/BLD
 cfgs/*/EXP00
 cfgs/*/WORK
+cfgs/*/NEMOFILES
+cfgs/*/AGRIFLIB
 cfgs/*_ST
 
 tests/work_cfgs.txt
 tests/*/BLD
 tests/*/EXP00
 tests/*/WORK
+tests/*/NEMOFILES
+tests/*/AGRIFLIB
 tests/*_ST
 
 tools/*/BLD

.gitlab-ci-cnrs.yml

+# HPC & configs lists to be tested with SETTE
+.parallel_HPC_CFG:
+  parallel:
+    matrix:
+      - HPC: [irene,jean-zay]
+        CONFIG: [ORCA2_ICE_PISCES,ORCA2_OFF_PISCES,AMM12,AGRIF,WED025,GYRE_PISCES,SAS,ORCA2_ICE_OBS]
+
+# HPC & testcases lists to be tested with SETTE
+.parallel_HPC_TST:
+  parallel:
+    matrix:
+      - HPC: [irene,jean-zay]
+        CONFIG: [SWG,ICE_AGRIF,OVERFLOW,LOCK_EXCHANGE,VORTEX,ISOMIP+]
+
+
+# variables declared hereafter will be avaible in all jobs
+# these 2 variables are needed for each HPC to be tested:
+# - SETTE_CFG: SETTE param.cfg file path
+# - SETTE_MOD: SETTE modules list
+
+variables:
+  # JEAN-ZAY
+  JZ_SETTE_CFG: "/linkhome/rech/genloc01/reee217/nemo_CI/param.cfg"
+  JZ_SETTE_MOD: "intel-compilers/19.1.3 intel-mpi/2019.9 hdf5/1.12.0-mpi netcdf-c/4.7.4-mpi netcdf-fortran/4.5.3-mpi git/2.25.0"
+  # IRENE
+  IR_SETTE_CFG: "/ccc/cont005/dsku/leger/home/user/locean/massons/nemo_CI/param.cfg"
+  IR_SETTE_MOD: "intel/19.0.5.281 mpi/openmpi/4.0.2 flavor/hdf5/parallel flavor/buildmpi/openmpi/4.0 netcdf-c/4.6.0 netcdf-fortran/4.4.4 hdf5/1.8.20 boost/1.69.0 blitz/0.10 c++/gnu/7.3.0 c/gnu/7.3.0"

.gitlab-ci-default.yml

+# default (but willingly wrong) values
+
+# HPC & configs lists to be tested with SETTE
+.parallel_HPC_CFG:
+  parallel:
+    matrix:
+      - HPC: [default]
+        CONFIG: [default]
+
+# HPC & testcases lists to be tested with SETTE
+.parallel_HPC_TST:
+  parallel:
+    matrix:
+      - HPC: [default]
+        CONFIG: [default]

.gitlab-ci-mercator.yml

+# HPC & configs lists to be tested with SETTE
+.parallel_HPC_CFG:
+  parallel:
+    matrix:
+      - HPC: [aa,belenos]
+        #CONFIG: [ORCA2_ICE_PISCES,ORCA2_OFF_PISCES,AMM12,AGRIF_DEMO,WED025,GYRE_PISCES,ORCA2_SAS_ICE,ORCA2_ICE_OBS]
+        CONFIG: [ORCA2_ICE_PISCES,ORCA2_OFF_PISCES,AMM12,WED025,GYRE_PISCES,ORCA2_SAS_ICE,ORCA2_ICE_OBS]
+
+# HPC & testcases lists to be tested with SETTE
+.parallel_HPC_TST:
+  parallel:
+    matrix:
+      - HPC: [aa,belenos]
+        #CONFIG: [SWG,ICE_AGRIF,OVERFLOW,LOCK_EXCHANGE,VORTEX,ISOMIP+]
+        CONFIG: [SWG,OVERFLOW,LOCK_EXCHANGE,VORTEX,ISOMIP+]
+
+
+# variables declared hereafter will be avaible in all jobs
+# these 2 variables are needed for each HPC to be tested:
+# - SETTE_CFG: SETTE param.cfg file path
+# - SETTE_MOD: SETTE modules list
+
+variables:
+  # METEO-FRANCE BELENOS (INTEL_2018+INTEL-MPI)
+  BL_SETTE_CFG: "/home/ext/mr/smer/samsong/SRC/NEMO/main/sette/param.ci"
+  BL_SETTE_MOD: "gcc/9.2.0 intel/2018.5.274 intelmpi/2018.5.274 phdf5/1.8.18 netcdf_par/4.7.1_V2 xios/trunk/r2320_intel-impi git/2.27.0"
+  # ECMWF AA (INTEL_2021+OPEN-MPI)
+  AA_SETTE_CFG: "/home/ar0s/SRC/NEMO/main/sette/param.ci"
+  AA_SETTE_MOD: "prgenv/intel intel/2021.4.0 openmpi/4.1.1.1 hdf5-parallel/1.10.6 netcdf4-parallel/4.7.4 xios/trunk/r2320_intel-ompi"
+  # MERCATOR KARA (TODO)
+  #KR_SETTE_CFG: "/kara/data1/gsamson/SRC/NEMO/nemo/sette/param.ci"
+  #KR_SETTE_MOD: "gcc/9.3.0 openmpi/4.0.5_gcc9.3.0 hdf5/1.8.18_gcc9.3.0 netcdf/4.7.1_gcc9.3.0 xios/trunk_rev2136_gcc9.3.0 git/2.34.1"

.gitlab-ci.yml

+#----------#
+# SETTE CI #
+#----------#
+
+
+include:
+  # default values will be overwritten depending on commit author
+  - local: '.gitlab-ci-default.yml'
+  - local: '.gitlab-ci-cnrs.yml'
+    rules:
+    - if: '$CI_COMMIT_AUTHOR =~ /.*masson.*/'
+  - local: '.gitlab-ci-mercator.yml'
+    rules:
+    - if: $CI_PIPELINE_SOURCE == "schedule"
+    #- if: '$CI_COMMIT_AUTHOR =~ /.*samson.*/ || $CI_COMMIT_AUTHOR =~ /.*chanut.*/'
+
+
+.cache: &cache_CFG
+  key: ${CONFIG}_${CI_COMMIT_SHORT_SHA}_${CI_PIPELINE_ID}
+  paths:
+    - cfgs/${CONFIG}_ST/EXP*
+    - cfgs/${CONFIG}_ST/BLD/bin
+    - cfgs/${CONFIG}_ST/cpp_${CONFIG}_ST.fcm
+
+.cache: &cache_TST
+  key: ${CONFIG}_${CI_COMMIT_SHORT_SHA}_${CI_PIPELINE_ID}
+  paths:
+    - tests/${CONFIG}_ST/EXP*
+    - tests/${CONFIG}_ST/BLD/bin
+    - tests/${CONFIG}_ST/cpp_${CONFIG}_ST.fcm
+
+
+stages:
+  - compile
+  - run
+  - check
+
+
+before_script:
+# the following commands will be executed at the beginning of each job
+# they are needed to copy param.cfg to SETTE directory and to load the modules
+  - declare -A HOST_NAME=( ["kara"]="KR" ["aa"]="AA" ["belenoslogin"]="BL" ["irene"]="IR" ["jean-zay"]="JZ" )
+  - SETTE_MOD=${HOST_NAME[${HOSTNAME//[0-9,-,.]*}]}_SETTE_MOD
+  - if [ -d ${HOME}/modules ]; then module use ${HOME}/modules; fi
+  - module purge || true   # force to always have 0 as error code (needed for irene)
+  - module load ${!SETTE_MOD}
+  - set -x   # debug prints
+  - SETTE_CFG=${HOST_NAME[${HOSTNAME//[0-9,-,.]*}]}_SETTE_CFG
+  - cp -av ${!SETTE_CFG} sette/param.cfg
+  - git config core.filemode false   # ignore git(lab) symlinks permissions changes when pushing then pulling cache ("old mode 100755 -> new mode 100644")
+  - SETTE_OPT="-b -u -w"
+
+
+# JOBS
+# sette_cmp_cfgs : compile reference configurations
+# sette_cmp_tsts : compile test cases
+# sette_run_cfgs : run reference configurations
+# sette_run_tsts : run test cases
+# sette_rpt_cfgs : check reference configurations results
+# sette_rpt_tsts : check test cases results
+
+sette_cmp_cfgs:
+  stage: compile
+  rules:
+    - if: $CI_PIPELINE_SOURCE == "schedule"
+  extends: .parallel_HPC_CFG   # HPC + configs loop 
+  cache:
+    <<: *cache_CFG
+    policy: push
+  tags:
+    - $HPC
+  script:
+    - cd sette
+    - ./sette.sh ${SETTE_OPT} -n ${CONFIG} -x "COMPILE" | tee -a sette_cmp_${CONFIG}_${CI_COMMIT_SHORT_SHA}_${HPC}.log
+    - cd -
+  artifacts:
+    paths:
+      - sette/sette_cmp_${CONFIG}_${CI_COMMIT_SHORT_SHA}_${HPC}.log
+    when: always
+
+sette_cmp_tsts:
+  stage: compile
+  rules:
+    - if: $CI_PIPELINE_SOURCE == "schedule"
+  extends: .parallel_HPC_TST   # HPC + tests loop
+  cache:
+    <<: *cache_TST
+    policy: push
+  tags:
+    - $HPC
+  script:
+    - cd sette
+    - ./sette.sh ${SETTE_OPT} -n ${CONFIG} -x "COMPILE" | tee -a sette_cmp_${CONFIG}_${CI_COMMIT_SHORT_SHA}_${HPC}.log
+    - cd -
+  artifacts:
+    paths:
+      - sette/sette_cmp_${CONFIG}_${CI_COMMIT_SHORT_SHA}_${HPC}.log
+    when: always
+
+sette_run_cfgs:
+  stage: run
+  rules:
+    - if: $CI_PIPELINE_SOURCE == "schedule"
+  needs: [sette_cmp_cfgs]   # limited to 50 jobs
+  dependencies: []   # do not retrieve previous artifacts
+  extends: .parallel_HPC_CFG   # HPC + configs loop
+  cache:
+    <<: *cache_CFG
+    policy: pull
+  tags:
+    - $HPC
+  script:
+    - cd sette
+    - ./sette.sh ${SETTE_OPT} -n ${CONFIG} -x "RESTART REPRO PHYOPTS CORRUPT" | tee -a sette_run_${CONFIG}_${CI_COMMIT_SHORT_SHA}_${HPC}.log
+    - cd -
+  artifacts:
+    paths:
+      - sette/sette_run_${CONFIG}_${CI_COMMIT_SHORT_SHA}_${HPC}.log
+      - cfgs/${CONFIG}_ST/*/sette.*.out
+      - cfgs/${CONFIG}_ST/*/sette.*.err
+      - cfgs/${CONFIG}_ST/*/ocean.output*
+    when: always
+
+sette_run_tsts:
+  stage: run
+  rules:
+    - if: $CI_PIPELINE_SOURCE == "schedule"
+  needs: [sette_cmp_tsts]   # limited to 50 jobs
+  dependencies: []   # do not retrieve previous artifacts
+  extends: .parallel_HPC_TST   # HPC + tests loop
+  cache:
+    <<: *cache_TST
+    policy: pull
+  tags:
+    - $HPC
+  script:
+    - cd sette
+    - ./sette.sh ${SETTE_OPT} -n ${CONFIG} -x "RESTART REPRO PHYOPTS CORRUPT" | tee -a sette_run_${CONFIG}_${CI_COMMIT_SHORT_SHA}_${HPC}.log
+    - cd -
+  artifacts:
+    paths:
+      - sette/sette_run_${CONFIG}_${CI_COMMIT_SHORT_SHA}_${HPC}.log
+      - tests/${CONFIG}_ST/*/sette.*.out
+      - tests/${CONFIG}_ST/*/sette.*.err
+      - tests/${CONFIG}_ST/*/ocean.output*
+    when: always
+
+sette_rpt_cfgs:
+  stage: check
+  rules:
+    - if: $CI_PIPELINE_SOURCE == "schedule"
+  needs: [sette_run_cfgs]   # limited to 50 jobs
+  dependencies: []   # do not retrieve previous artifacts
+  extends: .parallel_HPC_CFG   # HPC + configs loop
+  tags:
+    - $HPC
+  script:
+    - cd sette
+    - ./sette_rpt.sh -b -u -n "${CONFIG}" | tee -a sette_rpt_${CONFIG}_${CI_COMMIT_SHORT_SHA}_${HPC}.log
+  artifacts:
+    paths:
+      - sette/sette_rpt_${CONFIG}_${CI_COMMIT_SHORT_SHA}_${HPC}.log
+    when: always
+
+sette_rpt_tsts:
+  stage: check
+  rules:
+    - if: $CI_PIPELINE_SOURCE == "schedule"
+  needs: [sette_run_tsts]   # limited to 50 jobs
+  dependencies: []   # do not retrieve previous artifacts
+  extends: .parallel_HPC_TST   # HPC + tests loop
+  tags:
+    - $HPC
+  script:
+    - cd sette
+    - ./sette_rpt.sh -b -u -n "${CONFIG}" | tee -a sette_rpt_${CONFIG}_${CI_COMMIT_SHORT_SHA}_${HPC}.log
+  artifacts:
+    paths:
+      - sette/sette_rpt_${CONFIG}_${CI_COMMIT_SHORT_SHA}_${HPC}.log
+    when: always
\ No newline at end of file

README.rst

+.. image:: https://forge.nemo-ocean.eu/nemo/nemo/badges/main/pipeline.svg
+           :target: https://forge.nemo-ocean.eu/nemo/nemo/-/commits/main
+
 **Contents**
 
 .. contents::

arch/MERCATOR/arch-X64_BELENOS_INTEL_OMPI.fcm

@@ -55,7 +55,8 @@
 
 %CPP                 cpp
 %FC                  mpifort -c -cpp
-%FCFLAGS             -march=core-avx2 -i4 -r8 -O3 -fp-model strict -fno-alias -align array64byte
+%PROD_FCFLAGS        -march=core-avx2 -i4 -r8 -O3 -fp-model strict -fno-alias -align array64byte
+%DEBUG_FCFLAGS       -march=core-avx2 -i4 -r8 -g -O0 -debug all -traceback -fp-model strict -ftrapuv -check all,noarg_temp_created -fpe-all0 -ftz -init=arrays,snan,huge
 %FFLAGS              %FCFLAGS
 %LD                  mpifort
 %LDFLAGS             

cfgs/ORCA2_ICE_PISCES/EXPREF/namelist_top_cfg

@@ -114,7 +114,7 @@
    sn_trcsbc(14) = 'dust.orca.new'   ,       -1          , 'dustfer'     ,  .true.      , .true. , 'yearly'  , ''       , ''    , ''
    sn_trcsbc(23) = 'ndeposition.orca',      -12          , 'ndep'        ,  .false.     , .true. , 'yearly'  , ''       , ''    , ''
    rn_trsfac(5)  = 3.774194e-02     !  (  1E-3 / 31. * 117 )
-   rn_trsfac(7)  = 9.572954e-03     !  ( 8.8   / 28.1 )
+   rn_trsfac(7)  = 9.572954e-03     !  (  0.269 / 28.1 )
    rn_trsfac(14) = 6.2667860e-04    !  (  0.035 / 55.85 )
    rn_trsfac(23) = 5.2232143e-01    !  ( From kgN m-2 s-1 to molC l-1 ====> zfact = 7.3125/14 )
    rn_sbc_time   = 1.               !  Time scaling factor for SBC and CBC data (seconds in a day)

cfgs/ORCA2_OFF_PISCES/EXPREF/namelist_top_cfg

@@ -114,7 +114,7 @@
    sn_trcsbc(14) = 'dust.orca.new'   ,       -1          , 'dustfer'     ,  .true.      , .true. , 'yearly'  , ''       , ''    , ''
    sn_trcsbc(23) = 'ndeposition.orca',      -12          , 'ndep'        ,  .false.     , .true. , 'yearly'  , ''       , ''    , ''
    rn_trsfac(5)  = 3.774194e-02     !  (  1E-3 / 31. * 117 )
-   rn_trsfac(7)  = 9.572954e-03     !  ( 8.8   / 28.1 )
+   rn_trsfac(7)  = 9.572954e-03     !  (  0.269 / 28.1 )
    rn_trsfac(14) = 6.2667860e-04    !  (  0.035 / 55.85 )
    rn_trsfac(23) = 5.2232143e-01    !  ( From kgN m-2 s-1 to molC l-1 ====> zfact = 7.3125/14 )
    rn_sbc_time   = 1.               !  Time scaling factor for SBC and CBC data (seconds in a day)

ext/FCM/bin/fcm_internal

@@ -9,6 +9,7 @@ use strict;
 use warnings;
 
 use Fcm::Timer qw{timestamp_command};
+use File::Spec;
 
 # Function declarations
 sub catfile;

makenemo

 #!/bin/bash
-#set -x
 set -o posix
+#set -x
 #set -u
 #set -e
-#+
 #
 # ===============
 # makenemo
@@ -16,15 +15,12 @@ set -o posix
 # SYNOPSIS
 # ========
 #
-# ::
-#
 #  $ makenemo
 #
 #
 # DESCRIPTION
 # ===========
 #
-#
 # This script aims :
 #
 # - to choose MYCONFIG
@@ -44,11 +40,8 @@ set -o posix
 #
 #  Locally defined :
 #
-# - TAB         : NEMO subdirectory used (read)
 # - MAIN_DIR    : self explaining
 # - CONFIG_DIR  :   "    "    "
-# - MODELES_DIR :   "    "    "
-# - TOOLS_DIR   :   "    "    "
 # - NEMO_DIR    :   "    "    "
 # - REMOTE_CTL  : URL link to a remote resource list for an external configuration
 #                 which is not part of the reference suite
@@ -59,62 +52,26 @@ set -o posix
 # EXAMPLES
 # ========
 #
-# ::
-#
-#  $ ./makenemo -m ifort_osx - j3 -n ORCA2_SI3_PISCES
-#
-#
-# TODO
-# ====
-#
-# option debug
-#
-#
-# EVOLUTIONS
-# ==========
-#
-# $Id: makenemo 15186 2021-08-12 16:39:09Z gsamson $
-#
-#
-#
-#   * creation
-#
-#-
+#  $ ./makenemo -m ifort_osx -j 3 -r ORCA2_ICE_PISCES -n MY_ORCA2
 
-#-
-##- Initialization of the options ---
+
+# Initialization of the options
 x_d=''; x_h=''; x_n=''; x_r=''; x_c='';
 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
-
-##- 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
-export TESTS_DIR=${MAIN_DIR}/tests
-export TOOLS_DIR=${MAIN_DIR}/tools
-export COMPIL_DIR=${MAIN_DIR}/mk
-export NEMO_DIR=${MAIN_DIR}/${x_s}
-export AGRIFUSE='10'
+x_j='1'; x_e=''; x_s='src'; x_v='1'
 list_key='0'; chk_key='1'
 list_add_key=''; list_def_key=''; list_del_key=''
-#-
-#- FCM and functions location ---
-export PATH=${MAIN_DIR}/ext/FCM/bin:$PATH
+x_c_cfg=0; x_nocdf=0
+
+
+# Local variables
+MAIN_DIR=$(cd $(dirname "$0"); pwd)
+MAIN_DIR=${MAIN_DIR%/+(sette|tools|cfgs|tests|ext|arch)}
+COMPIL_DIR=${MAIN_DIR}/mk
+PATH=${MAIN_DIR}/ext/FCM/bin:$PATH
 
-#-
-#- Choice of the options ---
+
+# Choice of the options
 while [ ${#1} -gt 0 ]; do
     
     case "$1" in
@@ -228,91 +185,107 @@ EOF
     shift
 done
 
-export NEW_CONF=${x_n}
+
+# Variables definition based on options
 NBR_PRC=${x_j}
 CMP_NAM=${x_m}
-NEM_SUBDIR=${x_d}
-REF_CONF=${x_r}
-DEMO_CONF=${x_a}
-export NEMO_DIR=${MAIN_DIR}/${x_s}
 NEMO_DBG=${x_b}
+NEMO_DIR=${MAIN_DIR}/${x_s}
+
+
+# Print available arch files
+[ "${CMP_NAM}" == 'all' ] && ${COMPIL_DIR}/Flist_archfile.sh && exit 0
+
+
+# New config case
+if [ -n "${x_n}" ]; then
+
+  # Look for already-existing new config
+  NEW_CONF=${x_n}
+  if [ -n "${x_t}" ]; then
+    NEW_DIR=$( find -L ${x_t} -maxdepth 1 -type d -name ${x_n} 2>/dev/null )
+  else
+    NEW_DIR=$( find -L ${MAIN_DIR}/cfgs ${MAIN_DIR}/tests -maxdepth 1 -type d -name ${NEW_CONF} 2>/dev/null )
+  fi
+  NEW_NB=$( echo ${NEW_DIR} | wc -w )
+  NEW_CMP=$( grep -l "^${NEW_CONF} " ${MAIN_DIR}/cfgs/*_cfgs.txt ${MAIN_DIR}/tests/*_cfgs.txt | tail -1 )
+
+  # Define if new config needs to be created or not
+  if [[ ${NEW_NB:-0} -eq 0 || -z "${NEW_CMP}" ]]; then
+    DO_NEW=1
+  else
+    DO_NEW=0
+    NEW_SUB="$( grep "^${NEW_CONF} " ${NEW_CMP} | awk '{$1 = ""; print $0}' )"
+    if [[ -n "${x_r}" || -n "${x_a}" ]]; then
+      echo -e "\nWARNING: ${NEW_CONF} configuration is already existing, we ignore \"-r\" & \"-a\" options\n"
+    fi
+  fi
 
-[ "${CMP_NAM}" == 'all' ] && . ${COMPIL_DIR}/Flist_archfile.sh all && exit
-
-# '-r': reference config ('cfgs' directory)
-if [ -n "${REF_CONF}" ]; then
-    conf_file=ref_cfgs.txt ; export CONFIG_DIR=${CFGS_DIR} ; TML_CONF=${REF_CONF}
-# '-a': testcases ('tests' directory)
-elif [ -n "${DEMO_CONF}" ]; then
-    conf_file=demo_cfgs.txt; export CONFIG_DIR=${TESTS_DIR}; TML_CONF=${DEMO_CONF}
-# '-n': new or already-existing config (any directory)
-elif [[ -n "${NEW_CONF}" && -z "${conf_file}" ]]; then
-    # already-existing config (check work_cfgs.txt)
-    if [ $( grep -l "^${NEW_CONF} " ${CFGS_DIR}/work_cfgs.txt ${TESTS_DIR}/work_cfgs.txt 2> /dev/null | wc -l ) -eq 1 ]; then
-        conf_file=$( 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}
-    # new config (check ref_cfgs.txt & demo_cfgs.txt)
-    elif [ $( grep -l "^${NEW_CONF} " ${CFGS_DIR}/ref_cfgs.txt ${TESTS_DIR}/demo_cfgs.txt 2> /dev/null | wc -l ) -eq 1 ]; then
-        conf_file=$( grep -l "^${NEW_CONF} " ${CFGS_DIR}/ref_cfgs.txt ${TESTS_DIR}/demo_cfgs.txt )
-        export CONFIG_DIR=$( dirname $conf_file ); conf_file=$( basename $conf_file )
-        TML_CONF=${NEW_CONF}
-    # config not found in both cfgs & tests directories
-    else
-        echo -e "\033[0;31m\nUser configuration ${NEW_CONF} not found !"
-        echo -e "Please choose a reference configuration (-r) or a testcase (-a)"
-        echo -e "among this list to create your own configuration (-n):"
-        ${COMPIL_DIR}/Flist_cfgs.sh
-        exit 2
+fi
+
+
+# Define ref config if new config not defined or not existing yet
+if [[ ${DO_NEW:-0} -eq 1 || -z "${NEW_CONF}" ]]; then
+
+  if [[ -n "${x_r}" || -n "${x_a}" ]]; then
+    REF_DIR=$( find ${MAIN_DIR}/cfgs ${MAIN_DIR}/tests -maxdepth 1 -type d -name ${x_r:-""} -o -name ${x_a:-""} 2>/dev/null )
+    REF_NB=$( echo ${REF_DIR} | wc -w )
+    REF_CMP=$( grep -l "^${x_r} \|^${x_a} " ${MAIN_DIR}/cfgs/ref_cfgs.txt ${MAIN_DIR}/tests/demo_cfgs.txt )
+    if [[ ${REF_NB} -eq 1 && -n "${REF_CMP}" ]]; then
+      REF_CONF=$(basename ${REF_DIR})
+      REF_TYPE=$(basename ${REF_DIR%\/*})
+      REF_FILE=$(basename ${REF_CMP})
+      REF_SUB="$( grep "^${REF_CONF} " ${REF_CMP} | awk '{$1 = ""; print $0}' )"
+    elif [ ${REF_NB} -gt 1 ]; then
+      echo -e "Please choose only one reference configuration (-r) or testcase (-a)"; exit 2
+    elif [ ${REF_NB} -eq 0 ]; then
+      echo -e "Please choose at least one reference configuration (-r) or testcase (-a) from:"
+      ${COMPIL_DIR}/Flist_cfgs.sh ${MAIN_DIR}; exit 2
     fi
-# using both '-r' and '-a' options
-elif [[ -n "${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"
-    echo -e "  - Unsupported cases  in ./tests ('-a')\033[0m\n"
-    exit 2
-# config found in both cfgs & tests directories
-elif [ $( grep -l "^${NEW_CONF} " */work_cfgs.txt 2> /dev/null | wc -l ) -gt 1 ]; then
-    echo -e "\033[0;31m\nUser configuration ${NEW_CONF} is present in both"
-    echo -e "cfgs/work_cfgs.txt and tests/work_cfgs.txt files"
-    echo -e "Please choose only one \033[0m"
-    exit 2
-# 'all': list all available configurations
-elif [[ "${REF_CONF}" == 'all' || "${DEMO_CONF}" == 'all' ]]; then
-    ${COMPIL_DIR}/Flist_cfgs.sh
-    exit 0
-# any other case
-else
-    exit 2
+  else
+    echo -e "Please choose at least one reference configuration (-r) or testcase (-a) from:"
+    ${COMPIL_DIR}/Flist_cfgs.sh ${MAIN_DIR}; exit 2
+  fi
+
+  # force config creation if ref config installed outside nemo directory
+  if [[ -n "${x_t}" && ${x_t} != ${REF_DIR%\/*} ]]; then DO_NEW=1; fi
+
 fi
 
-if [ -z "${NEW_CONF}" ]; then NEW_CONF=$TML_CONF; fi
-export NEMO_TDIR=${x_t:-$CONFIG_DIR}
+
+# Current config (new or ref) definition
+CFG_DIR=$( dirname ${NEW_CMP:-${REF_CMP}} )
+CUR_DIR=${NEW_DIR:-${REF_DIR}}
+CUR_CONF=${NEW_CONF:-${REF_CONF}}
+CUR_SUB=${NEW_SUB:-${REF_SUB}}
+NEMO_TDIR=${x_t:-${CUR_DIR%\/*}}
 
 
-# check configuration existence & clean it if asked
-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
+# Config cleaning
+if [ -d ${NEMO_TDIR}/${CUR_CONF} ]; then
+
     if [ $x_c_cfg -eq 1 ] ; then
-        . ${COMPIL_DIR}/Fclean_config.sh
+        ${COMPIL_DIR}/Fclean_config.sh ${NEMO_TDIR}/${CUR_CONF}
         exit 0
     elif [ ${#x_c} -ne 0 ]; then
-        #read -p "Are you sure that you want to clean $NEW_CONF configuration ? " -n 1 -r; echo
+
+        #read -p "Are you sure that you want to clean $CUR_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
-            grep key_agrif ${NEMO_TDIR}/BLD/cpp.fcm 2>/dev/null && export AGRIFUSE=1 && export USEBLD=${USEBLD/xag/}
+            # choose & generate fcm cfg file
+            [ $x_nocdf -eq 1 ] && USEBLD=bldxagxcdf.cfg || USEBLD=bldxag.cfg
+            grep key_agrif ${NEMO_TDIR}/${CUR_CONF}/BLD/cpp.fcm 2>/dev/null && USEBLD=${USEBLD/xag/}
+            sed -e "s~MAIN_DIR~${MAIN_DIR}~; s~NEMO_TDIR~${NEMO_TDIR}~; s~CUR_CONF~${CUR_CONF}~; s~COMPIL_DIR~${COMPIL_DIR}~" ${COMPIL_DIR}/${USEBLD} > ${NEMO_TDIR}/${CUR_CONF}/BLD/${USEBLD}
+
             # 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'
+            fcm build ${x_c} --ignore-lock -v ${x_v} -j ${NBR_PRC} ${NEMO_TDIR}/${CUR_CONF}/BLD/${USEBLD} || exit 1
+
+            # remove all build directories
+            echo -e '\nCleaning '${CUR_CONF}' building directories and variables\n'
             for dir in AGRIFLIB BLD LONG NEMOFILES REPRO_* SHORT WORK; do
-               rm -rf ${NEMO_TDIR}/${NEW_CONF}/$dir
+               rm -rf ${NEMO_TDIR}/${CUR_CONF}/$dir
             done
             for file in cpp.history cpp.fcm full_key_list.txt; do
-               rm -f ${NEMO_TDIR}/${NEW_CONF}/BLD/$file
+               rm -f ${NEMO_TDIR}/${CUR_CONF}/BLD/$file
             done
             exit 0
         #else
@@ -320,117 +293,108 @@ if [ $incfg -eq 1 ] ; then
         #    exit 2
         #fi
     fi
-    if [[ -n "$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
+else
     [ $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
 
 
-## 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
+# Create/update config components list
+NEM_SUBDIR=( ${x_d:-${CUR_SUB}} )
+if [ ${DO_NEW:-0} -eq 1 ]; then
+    echo
+    printf "\nYou are installing a new configuration %s from %s " ${CUR_CONF} ${REF_CONF}
+    printf  "with sub-components: %s\n"  "${NEM_SUBDIR[*]}"
+    echo
+else
+    echo
+    printf "\nYou are compiling an existing configuration %s " ${CUR_CONF}
+    printf  "with sub-components: %s\n"  "${NEM_SUBDIR[*]}"
+    echo
 fi
-
-## Update sub-comps if needed
-if [ -z "${NEM_SUBDIR}" ]; then
-    NEM_SUBDIR=$( grep "${TML_CONF} " ${CONFIG_DIR}/${conf_file}  | awk '{$1 = ""; print $0}' )
+if [[ -n "${x_d}" || ${DO_NEW:-0} -eq 1 ]]; then
+    [ -f ${CFG_DIR}/work_cfgs.txt ] && sed -i "/^${CUR_CONF} /d" ${CFG_DIR}/work_cfgs.txt
+    echo ${CUR_CONF} "${NEM_SUBDIR[*]}" >> ${CFG_DIR}/work_cfgs.txt
 fi
 
-export NEM_SUBDIR="${NEM_SUBDIR}" NEW_CONF="${NEW_CONF}"
 
-## Create new config
-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"  "${NEM_SUBDIR}"; fi
-    echo
-fi
-${COMPIL_DIR}/Fmake_config.sh ${NEMO_TDIR}/${NEW_CONF} ${CONFIG_DIR}/${TML_CONF}  # must be called for existing config to create EXP00 if not existing
+# Create config directories
+${COMPIL_DIR}/Fmake_config.sh ${NEMO_TDIR}/${CUR_CONF} ${REF_DIR:-${NEMO_TDIR}/${CUR_CONF}}
 
-## 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
 
-#- Create the WORK ---
-#- Clean links and librairies ---
-#- Creating the good links, at first on OCE ---
-. ${COMPIL_DIR}/Fmake_WORK.sh ${x_e[@]} || exit 3
+# Create/update WORK directory
+${COMPIL_DIR}/Fmake_WORK.sh "${NEM_SUBDIR[*]/#/${NEMO_DIR}/}" "${x_e:-"MY_SRC"}" ${NEMO_TDIR}/${CUR_CONF} || exit 3
 
-. ${COMPIL_DIR}/Fmake_bld.sh ${CONFIG_DIR} ${NEW_CONF} ${NEMO_TDIR} || exit 3
 
-# build the complete list of the cpp keys of this configuration
+# 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_" ${NEMO_TDIR}/${NEW_CONF}/WORK/* ); do
-	echo $i | grep key_ | sed -e "s/=.*//"
-    done \
-	| sort -d | uniq > ${NEMO_TDIR}/${NEW_CONF}/BLD/full_key_list.txt
-    
-    [ ${list_key} -eq 1 ] && echo && cat ${NEMO_TDIR}/${NEW_CONF}/BLD/full_key_list.txt && exit 0
+    grep -h "^#.*defined.*" ${NEMO_TDIR}/${CUR_CONF}/WORK/* | \
+    grep -o "key_[[:alnum:]]\+\|key_[[:alnum:]]\+_[[:alnum:]]\+\|iso_[[:alnum:]]\+_[[:alnum:]]\+" | \
+    sort | uniq > ${NEMO_TDIR}/${CUR_CONF}/BLD/full_key_list.txt
+    [ ${list_key} -eq 1 ] && echo && cat ${NEMO_TDIR}/${CUR_CONF}/BLD/full_key_list.txt && exit 0
 fi
 
-#- At this stage new configuration has been added, we add or remove keys
-[ ! -z "${list_add_key}" ] && { . ${COMPIL_DIR}/Fadd_keys.sh ${NEW_CONF} add_key ${list_add_key}; }
-[ ! -z "${list_def_key}" ] && { . ${COMPIL_DIR}/Fdef_keys.sh ${NEW_CONF} def_key ${list_def_key}; }
-[ ! -z "${list_del_key}" ] && { . ${COMPIL_DIR}/Fdel_keys.sh ${NEW_CONF} del_key ${list_del_key}; }
 
-#- check that all keys are really existing...
+# CPP keys addition/removal
+[ -n "${list_add_key}" ] && ${COMPIL_DIR}/Fadd_keys.sh ${NEMO_TDIR}/${CUR_CONF} ${list_add_key}
+[ -n "${list_def_key}" ] && ${COMPIL_DIR}/Fdef_keys.sh ${NEMO_TDIR}/${CUR_CONF} ${list_def_key}
+[ -n "${list_del_key}" ] && ${COMPIL_DIR}/Fdel_keys.sh ${NEMO_TDIR}/${CUR_CONF} ${list_del_key}
+
+
+# CPP keys check
 if [ $chk_key -eq 1 ] ; then
-    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 ${NEMO_TDIR}/${NEW_CONF}/BLD/full_key_list.txt ) ]; then
-		echo
-		echo "E R R O R : key "$kk" is not found in ${NEMO_TDIR}/${NEW_CONF}/WORK routines..."
-		echo "we stop..."
-		echo
-		exit 1
-	    fi
-	fi
+    for kk in $( sed -n "s/bld::tool::fppkeys \+//p" ${NEMO_TDIR}/${CUR_CONF}/cpp_${CUR_CONF}.fcm ); do
+        if ! grep -q $kk ${NEMO_TDIR}/${CUR_CONF}/BLD/full_key_list.txt; then
+	    echo
+	    echo "E R R O R : key "$kk" is not found in ${NEMO_TDIR}/${CUR_CONF}/WORK routines..."
+	    echo "we stop..."
+	    echo
+	    exit 1
+        fi
     done  
 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
-#-
-#_ END OF CONFIGURATION PHASE
-#_
 
-#-
-#- Compile ---
+# CPP & arch files check
+ln -sf ${NEMO_TDIR}/${CUR_CONF}/cpp_${CUR_CONF}.fcm ${NEMO_TDIR}/${CUR_CONF}/BLD/cpp.fcm
+${COMPIL_DIR}/Fcheck_archfile.sh ${NEMO_TDIR}/${CUR_CONF}/BLD/arch_nemo.fcm ${NEMO_TDIR}/${CUR_CONF}/BLD/cpp.fcm ${MAIN_DIR}/arch/arch-${CMP_NAM}.fcm ${NEMO_DBG} || exit 3
 
+
+# Compilation
 if [ "${NBR_PRC}" -gt 0 ]; then
 
-    # We coose the default light file
-    [ $x_nocdf -eq 1 ] && export USEBLD=bldxagxcdf.cfg || export USEBLD=bldxag.cfg
+    # choose & generate fcm cfg file
+    [ $x_nocdf -eq 1 ] && USEBLD=bldxagxcdf.cfg || 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
-	echo ''
+    # AGRIF preprocessing
+    grep key_agrif ${NEMO_TDIR}/${CUR_CONF}/BLD/cpp.fcm 2>/dev/null && USEBLD=${USEBLD/xag/}
+    if [[ ! ${USEBLD} =~ "xag" ]]; then
+        ${COMPIL_DIR}/Fprep_agrif.sh ${MAIN_DIR} ${NEMO_TDIR}/${CUR_CONF} || exit 3
+
+        # compile & copy conv
+        sed -e "s~MAIN_DIR~${MAIN_DIR}~; s~NEMO_TDIR~${NEMO_TDIR}~; s~CUR_CONF~${CUR_CONF}~; s~COMPIL_DIR~${COMPIL_DIR}~" ${COMPIL_DIR}/conv.cfg > ${NEMO_TDIR}/${CUR_CONF}/BLD/conv.cfg
+        fcm build ${NEMO_TDIR}/${CUR_CONF}/BLD/conv.cfg || exit 1
+        ln -sfv ${MAIN_DIR}/ext/AGRIF/agrif_oce.in ${NEMO_TDIR}/${CUR_CONF}/AGRIFLIB/bin/conv ${NEMO_TDIR}/${CUR_CONF}/NEMOFILES/.
+
+        sed -e "s~MAIN_DIR~${MAIN_DIR}~; s~NEMO_TDIR~${NEMO_TDIR}~; s~CUR_CONF~${CUR_CONF}~; s~COMPIL_DIR~${COMPIL_DIR}~" ${COMPIL_DIR}/bld_preproagr.cfg > ${NEMO_TDIR}/${CUR_CONF}/BLD/bld_preproagr.cfg
+	fcm build --ignore-lock -j 1 ${NEMO_TDIR}/${CUR_CONF}/BLD/bld_preproagr.cfg || exit 1
+	echo
 	echo "---------------------------------"
 	echo "CONV preprocessing successfull !!"
 	echo "---------------------------------"
-	echo ''
+	echo
     fi
 
-    fcm build ${x_c} --ignore-lock -v ${x_v} -j ${NBR_PRC} ${COMPIL_DIR}/$USEBLD || exit 1
+    sed -e "s~MAIN_DIR~${MAIN_DIR}~; s~NEMO_TDIR~${NEMO_TDIR}~; s~CUR_CONF~${CUR_CONF}~; s~COMPIL_DIR~${COMPIL_DIR}~" ${COMPIL_DIR}/${USEBLD} > ${NEMO_TDIR}/${CUR_CONF}/BLD/${USEBLD}
+    fcm build --ignore-lock -v ${x_v} -j ${NBR_PRC} ${NEMO_TDIR}/${CUR_CONF}/BLD/${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
+    if [ -f ${NEMO_TDIR}/${CUR_CONF}/BLD/bin/nemo.exe ]; then
+	(cd ${NEMO_TDIR}/${CUR_CONF}/EXP00; ln -sfv ../BLD/bin/nemo.exe ./nemo)
+    else
+        exit 1
     fi
-
     
 fi
 
-#- Unset variables
-${COMPIL_DIR}/Fclean_var.sh
+
+exit 0

mk/Fadd_keys.sh

@@ -62,16 +62,14 @@ set -o posix
 #   * creation
 #
 #-
- echo "Adding keys in : ${NEW_CONF}" 
- for i in ${list_add_key} ; do
-	if [ "$(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}/"  ${NEMO_TDIR}/${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
- 
- unset -v list_add_key
 
+echo "Adding keys ${2} in : ${1}"
+
+for i in ${2} ; do
+    if [ "$(cat ${1}/cpp_$(basename ${1}).fcm | grep -c "\<$i\>" )" -ne 0 ] ; then
+        echo "key $i already present in cpp_$(basename ${1}).fcm"
+    else
+        sed -i "s/$/ ${i}/" ${1}/cpp_$(basename ${1}).fcm
+        echo "added key $i in $(basename ${1})"
+    fi
+done

mk/Fcheck_archfile.sh

@@ -118,7 +118,7 @@ if [ ${#3} -eq 0 ]; then # arch not specified
 	fi
     fi
 else 
-    nb=$( find ${MAIN_DIR}/arch -name arch-${3}.fcm -print | wc -l )
+    nb=$( find $(dirname ${3}) -name $(basename ${3}) -print | wc -l )
     if [ $nb -eq 0 ]; then # no arch file found
 	echo "Warning !!!"
 	echo "Compiler not existing"
@@ -129,12 +129,12 @@ else
     if [ $nb -gt 1 ]; then # more than 1 arch file found
 	echo "Warning !!!"
 	echo "more than 1 arch file for the same compiler have been found"
-	find ${MAIN_DIR}/arch -name arch-${3}.fcm -print
+	find $(dirname ${3}) -name $(basename ${3}) -print
 	echo "keep only 1"
 	echo "EXITING..."
 	exit 1       
     fi
-    myarch=$( find ${MAIN_DIR}/arch -name arch-${3}.fcm -print )
+    myarch=$( find $(dirname ${3}) -name $(basename ${3}) -print )
     # we were already using this arch file ?
     if [ "$myarch" == "$( cat $(dirname $1)/arch.history 2>/dev/null)" ]; then 
 	if [ -f $1 ]; then
@@ -151,7 +151,7 @@ else
 		[ ${#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 $(basename $1) -name arch-${3}.fcm -print )
+	    myarch=$( find -L $(dirname ${3}) -cnewer $(basename $1) -name $(basename ${3}) -print )
 	    [ ${#myarch} -ne 0 ] && cpeval ${myarch} $1
 	else
 	    cpeval ${myarch} $1
@@ -185,7 +185,7 @@ then
     fi
 #- in TOOLS directory looking for USE xios
 else
-    use_iom=$( egrep --exclude-dir=.svn -r USE ${MAIN_DIR}/src/* | grep -c xios )
+    use_iom=$( egrep --exclude-dir=.svn -r USE $(dirname ${3})/../src/* | grep -c xios )
     have_lxios=$( sed -e "s/#.*$//" $1 | grep -c "\-lxios" )
     if [[ ( $use_iom -eq 0 ) || ( $have_lxios != 1 ) ]]
     then 
@@ -216,7 +216,7 @@ do
 done
 
 # Nemo debug ?
-if [ -n "${NEMO_DBG}" ]; then
+if [ -n "${4}" ]; 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

mk/Fcheck_config.sh

@@ -69,18 +69,18 @@ declare -a ZTAB
 if [ ${#2} -eq 0 ]; then
    tail -1  ${CONFIG_DIR}/$1	> ${CONFIG_DIR}/cfg.tmp
    read -a ZTAB < ${CONFIG_DIR}/cfg.tmp
-   NEW_CONF=${ZTAB[0]} ; TAB=( ${ZTAB[@]:1} )
+   CUR_CONF=${ZTAB[0]} ; TAB=( ${ZTAB[@]:1} )
    \rm ${CONFIG_DIR}/cfg.tmp
    echo "Warning !!!"
    echo "No configuration specified"
    echo "Use makenemo -n MYCONFIG"
    echo "or  makenemo -h for help"
-   echo "Using default configuration : ${NEW_CONF}"
+   echo "Using default configuration : ${CUR_CONF}"
 fi
 if [ "$1" == cfg.txt ]; then
-   cat ${CONFIG_DIR}/$1 | grep "${NEW_CONF} " > ${CONFIG_DIR}/cfg.tmp
+   cat ${CONFIG_DIR}/$1 | grep "${CUR_CONF} " > ${CONFIG_DIR}/cfg.tmp
    read -a ZTAB < ${CONFIG_DIR}/cfg.tmp
-   NEW_CONF=${ZTAB[0]} ; TAB=( ${ZTAB[@]:1} )
+   CUR_CONF=${ZTAB[0]} ; TAB=( ${ZTAB[@]:1} )
    \rm ${CONFIG_DIR}/cfg.tmp
 fi
 

mk/Fclean_config.sh

@@ -63,31 +63,23 @@ set -o posix
 #
 #-
 
-NEW_CONF=${x_n}
+CONF=$(basename ${1})
+CONFIG_DIR=$(dirname ${1})
 
-if [ ${#NEW_CONF} -eq 0 ] ; then
+if [ ${#CONF} -eq 0 ] ; then
 	echo " "
 	echo "No configuration specified, please use makenemo -n CONFIG clean_config "
 else
 	echo " "
-	echo "Are you sure that you want to remove this directory $NEW_CONF? [y/n] "
+	echo "Are you sure that you want to remove this directory $CONF? [y/n] "
 	read answer
 	answer=`echo $answer | sed 's/^[y].*$/y/'`
 
 	if [  -z "$answer" -o "x$answer" = "xy" ]; then
 
-		## testing if configuration exists
-		if [[ ! $( grep "${NEW_CONF} " */work_cfgs.txt ) ]] ; then
-			echo "The configuration ${NEW_CONF} does not exist in file work_cfgs.txt"     
-			echo "No removing configuration"
-			echo " "
-		else
-			CONFIG_DIR=${MAIN_DIR}/$( grep -l "${NEW_CONF} " */work_cfgs.txt | cut -d/ -f1 )
-			rm -rf ${CONFIG_DIR}/${NEW_CONF}
-			sed -e "/${NEW_CONF} /d"  ${CONFIG_DIR}/work_cfgs.txt >  ${CONFIG_DIR}/work_cfgs.tmp
-			mv  ${CONFIG_DIR}/work_cfgs.tmp  ${CONFIG_DIR}/work_cfgs.txt
-			echo "${NEW_CONF} configuration REMOVED" 
-		fi
+		rm -rf ${CONFIG_DIR}/${CONF}
+		sed -i "/^${CONF} /d"  ${CONFIG_DIR}/work_cfgs.txt >  ${CONFIG_DIR}/work_cfgs.tmp
+		echo "${CONF} configuration REMOVED" 
 
 	else
 		echo " "
@@ -95,5 +87,3 @@ else
 	fi
 
 fi 
-
-unset -v answer

mk/Fclean_var.sh

-#!/bin/bash
-#set -x
-set -o posix
-#set -u
-#set -e
-#+
-#
-# =============
-# Fclean_var.sh
-# =============
-#
-# ----------------------------
-# Clean environment variables
-# ----------------------------
-#
-# SYNOPSIS
-# ========
-#
-# ::
-#
-#  $ Fclean_var.sh
-#
-#
-# DESCRIPTION
-# ===========
-#
-#
-# Clean environment variables
-#
-# EXAMPLES
-# ========
-#
-# ::
-#
-#  $ ./Fclean_var.sh
-#
-#
-# TODO
-# ====
-#
-# option debug
-#
-#
-# EVOLUTIONS
-# ==========
-#
-# $Id: Fclean_var.sh 4990 2014-12-15 16:42:49Z timgraham $
-#
-#
-#
-#   * creation
-#
-#-
-#- Unset variables
-
-unset -v NSTOP
-unset -v TAB
-unset -v NEW_CONF
-unset -v REF_CONF
-unset -v CMP_NAM
-unset -v NBR_PRC
-unset -v NEM_SUBDIR
-unset -v MAIN_DIR
-unset -v CONFIG_DIR
-unset -v TOOLS_DIR
-unset -v COMPIL_DIR
-unset -v NEMO_DIR
-unset -v USEBLD

mk/Fdef_keys.sh

@@ -56,8 +56,5 @@ set -o posix
 #
 #-
 
-echo "Defining keys in : ${NEW_CONF}"
-
-echo " bld::tool::fppkeys ${list_def_key}" > ${NEMO_TDIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm
-
-unset -v list_def_key
+echo "Defining keys in : $(dirname ${1})"
+echo " bld::tool::fppkeys ${2}" > ${1}/cpp_$(basename ${1}).fcm

mk/Fdel_keys.sh

@@ -60,22 +60,13 @@ set -o posix
 #
 #-
 
-echo "Removing keys in : ${NEW_CONF}"
+echo "Removing keys ${2} in : ${1}"
 
-for i in ${list_del_key} ; do
-
-     if [ "$(echo ${i} | grep -c key_nproc )" -ne 0                                      ]; then
-        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 ${NEMO_TDIR}/${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}"
+for i in ${2} ; do
+     if [ "$(echo ${i} | grep -c key_nproc )" -gt 0 ]; then
+        sed -i "s/key_nproc[ij]=.* //" ${1}/cpp_$(basename ${1}).fcm
+     elif [ "$(cat ${1}/cpp_$(basename ${1}).fcm | grep -c "$i")" -gt 0 ]; then
+         sed -i "s/\b${i}\b//" ${1}/cpp_$(basename ${1}).fcm
+         echo "deleted key $i in $(basename ${1})"
      fi
-
 done
-
-unset -v list_del_key

mk/Flist_archfile.sh

@@ -67,11 +67,11 @@ archfile_loop() {
 
 echo -e "\n  ¤ Generic computing architectures"
 
-archfile_loop ${MAIN_DIR}/arch
+archfile_loop ${1}/arch
 
-for dir in $( ls ${MAIN_DIR}/arch | grep -v "fcm$" ); do
-	echo -e "\n  ¤ Specific HPC architectures for "${dir}
-	archfile_loop ${MAIN_DIR}/arch/$dir
+for dir in $( ls ${1}/arch | grep -v "fcm$" ); do
+    echo -e "\n  ¤ Specific HPC architectures for "${dir}
+    archfile_loop ${1}/arch/$dir
 done
 
 echo

mk/Flist_cfgs.sh

 #!/bin/bash
 
 echo -e "\n  ¤ Reference configurations with default sub-components (can be updated by a new set)"
-cat ${MAIN_DIR}/cfgs/ref_cfgs.txt \
+cat ${1}/cfgs/ref_cfgs.txt \
 | awk '{printf "%-20s", $1}{$1 = ""; printf "%s\n", $0}'
 
 echo -e "\n  ¤ Demonstrations cases (see https://github.com/sflavoni/NEMO-test-cases for more)"
-cat ${MAIN_DIR}/tests/demo_cfgs.txt \
+cat ${1}/tests/demo_cfgs.txt \
 | awk '{printf "%-20s", $1}{$1 = ""; printf "%s\n", $0}'
 
 echo -e "\n  ¤ Available sub-components ('OCE' is mandatory in any set)"
-ls  ${MAIN_DIR}/src | awk -F/ '{ print $NF }' | column
+ls ${1}/src | awk -F/ '{ print $NF }' | column
 
 echo