Resolve "add a new "debug" (-d) option to `makenemo` and a specific FCM flag...

Resolve "add a new "debug" (-d) option to `makenemo` and a specific FCM flag to switch more easily in debug mode"

arch/CNRS/arch-X64_IRENE.fcm

@@ -30,7 +30,8 @@
 #  - unix variables "$..." are accpeted and will be evaluated before calling fcm.
 #  - fcm variables are starting with a % (and not a $)
 #
-%XIOS_HOME           $CCCWORKDIR/xios-trunk
+%PROD_XIOS_HOME      $CCCWORKDIR/xios-trunk
+%DEBUG_XIOS_HOME     %{PROD_XIOS_HOME}_debug
 %OASIS_HOME          $CCCWORKDIR/now/models/oa3mct
 
 %NCDF_INC            -I$NETCDFFORTRAN_INCDIR -I$NETCDF_INCDIR
@@ -43,7 +44,8 @@
 
 %CPP	             cpp
 %FC                  mpif90 -c -cpp
-%FCFLAGS             -i4 -r8 -O3 -fp-model strict -xCORE-AVX512 -fno-alias
+%PROD_FCFLAGS        -i4 -r8 -O3 -fp-model strict -xCORE-AVX512 -fno-alias
+%DEBUG_FCFLAGS       -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                  mpif90
 %LDFLAGS             

arch/CNRS/arch-X64_IRENE_DEBUG.fcm

-# Irene BULL at TGCC, http://www-hpc.cea.fr/en/complexe/tgcc-Irene.htm
-#
-# NCDF_HOME   root directory containing lib and include subdirectories for netcdf4
-# HDF5_HOME   root directory containing lib and include subdirectories for HDF5
-# XIOS_HOME   root directory containing lib for XIOS
-# OASIS_HOME  root directory containing lib for OASIS
-#
-# NCDF_INC    netcdf4 include file
-# NCDF_LIB    netcdf4 library
-# XIOS_INC    xios include file    (taken into accound only if key_xios is activated)
-# XIOS_LIB    xios library         (taken into accound only if key_xios is activated)
-# OASIS_INC   oasis include file   (taken into accound only if key_oasis3 is activated)
-# OASIS_LIB   oasis library        (taken into accound only if key_oasis3 is activated)
-#
-# FC          Fortran compiler command
-# FCFLAGS     Fortran compiler flags
-# FFLAGS      Fortran 77 compiler flags
-# LD          linker
-# LDFLAGS     linker flags, e.g. -L<lib dir> if you have libraries
-# FPPFLAGS    pre-processing flags
-# AR          assembler
-# ARFLAGS     assembler flags
-# MK          make
-# USER_INC    complete list of include files
-# USER_LIB    complete list of libraries to pass to the linker
-# CC          C compiler used to compile conv for AGRIF
-# CFLAGS      compiler flags used with CC
-#
-# Note that:
-#  - unix variables "$..." are accpeted and will be evaluated before calling fcm.
-#  - fcm variables are starting with a % (and not a $)
-#
-%XIOS_HOME           $CCCWORKDIR/xios-trunk
-%OASIS_HOME          $CCCWORKDIR/now/models/oa3mct
-
-%NCDF_INC            -I$NETCDFFORTRAN_INCDIR -I$NETCDF_INCDIR
-%NCDF_LIB            -L$NETCDFFORTRAN_LIBDIR -lnetcdff -L$NETCDF_LIBDIR -lnetcdf -L$HDF5_LIBDIR -lhdf5_hl -lhdf5 -lz -lcurl
-
-%XIOS_INC            -I%XIOS_HOME/inc 
-%XIOS_LIB            -L%XIOS_HOME/lib -lxios -lstdc++
-%OASIS_INC           -I%OASIS_HOME/build/lib/mct -I%OASIS_HOME/build/lib/psmile.MPI1
-%OASIS_LIB           -L%OASIS_HOME/lib -lpsmile.MPI1 -lmct -lmpeu -lscrip
-
-%CPP	             cpp
-%FC                  mpif90 -c -cpp
-%FCFLAGS             -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                  mpif90
-%LDFLAGS             
-%FPPFLAGS            -P -traditional
-%AR                  ar
-%ARFLAGS             rs
-%MK                  gmake
-%USER_INC            %XIOS_INC %OASIS_INC %NCDF_INC
-%USER_LIB            %XIOS_LIB %OASIS_LIB %NCDF_LIB
-
-%CC                  cc
-%CFLAGS              -O0

arch/CNRS/arch-X64_IRENE_GCC.fcm

@@ -29,7 +29,8 @@
 
 %CPP	             cpp -Dkey_nosignedzero 
 %FC                  mpif90
-%FCFLAGS             -fdefault-real-8 -O3 -funroll-all-loops -fcray-pointer -ffree-line-length-none -Wno-missing-include-dirs 
+%PROD_FCFLAGS        -fdefault-real-8 -O3 -funroll-all-loops -fcray-pointer -ffree-line-length-none -Wno-missing-include-dirs 
+%DEBUG_FCFLAGS       -fdefault-real-8 -O0 -g -fbacktrace -funroll-all-loops -fcray-pointer -ffree-line-length-none -fcheck=all -finit-real=nan
 %FFLAGS              %FCFLAGS
 %LD                  mpif90
 %LDFLAGS             

arch/CNRS/arch-X64_IRENE_GCC_DEBUG.fcm

-# Irene BULL at TGCC, http://www-hpc.cea.fr/en/complexe/tgcc-Irene.htm
-#
-# list of modules used
-#
-#   module purge
-#   module load gnu/8.3.0
-#   module load flavor/buildcompiler/gcc/8
-#   module load flavor/buildmpi/openmpi/2.0
-#   module load flavor/hdf5/parallel
-#   module load mpi/openmpi/2.0.4
-#   module load hdf5/1.8.20
-#   module load netcdf-c/4.6.0
-#   module load netcdf-fortran/4.4.4
-#
-# Note that:
-#  - unix variables "$..." are accpeted and will be evaluated before calling fcm.
-#  - fcm variables are starting with a % (and not a $)
-#
-%XIOS_HOME           $CCCWORKDIR/xios-trunk_gcc
-%OASIS_HOME          $CCCWORKDIR/now/models/oa3mct
-
-%NCDF_INC            -I$NETCDFFORTRAN_INCDIR -I$NETCDF_INCDIR
-%NCDF_LIB            -L$NETCDFFORTRAN_LIBDIR -lnetcdff -L$NETCDF_LIBDIR -lnetcdf -L$HDF5_LIBDIR -lhdf5_hl -lhdf5 -lz -lcurl
-
-%XIOS_INC            -I%XIOS_HOME/inc 
-%XIOS_LIB            -L%XIOS_HOME/lib -lxios -lstdc++
-%OASIS_INC           -I%OASIS_HOME/build/lib/mct -I%OASIS_HOME/build/lib/psmile.MPI1
-%OASIS_LIB           -L%OASIS_HOME/lib -lpsmile.MPI1 -lmct -lmpeu -lscrip
-
-%CPP	             cpp -Dkey_nosignedzero 
-%FC                  mpif90
-%FCFLAGS             -fdefault-real-8 -O0 -g -fbacktrace -funroll-all-loops -fcray-pointer -ffree-line-length-none -fcheck=all -finit-real=nan
-%FFLAGS              %FCFLAGS
-%LD                  mpif90
-%LDFLAGS             
-%FPPFLAGS            -P -traditional
-%AR                  ar
-%ARFLAGS             rs
-%MK                  make
-%USER_INC            %XIOS_INC %OASIS_INC %NCDF_INC
-%USER_LIB            %XIOS_LIB %OASIS_LIB %NCDF_LIB
-
-%CC                  cc
-%CFLAGS              -O0

arch/CNRS/arch-X64_JEANZAY.fcm

@@ -48,7 +48,8 @@
 
 %CPP	             cpp
 %FC                  mpiifort -c -cpp
-%FCFLAGS             -i4 -r8 -O3 -fp-model strict -xCORE-AVX512 -fno-alias
+%PROD_FCFLAGS        -i4 -r8 -O3 -fp-model strict -xCORE-AVX512 -fno-alias
+%DEBUG_FCFLAGS       -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                  mpiifort
 %LDFLAGS             

arch/CNRS/arch-X64_JEANZAY_DEBUG.fcm

-# Jean-Zay HPE at IDRIS, http://www.idris.fr/jean-zay
-#
-# XIOS_HOME   root directory containing lib for XIOS
-# OASIS_HOME  root directory containing lib for OASIS
-#
-# NCDF_INC    netcdf4 include file
-# NCDF_LIB    netcdf4 library
-# XIOS_INC    xios include file    (taken into accound only if key_xios is activated)
-# XIOS_LIB    xios library         (taken into accound only if key_xios is activated)
-# OASIS_INC   oasis include file   (taken into accound only if key_oasis3 is activated)
-# OASIS_LIB   oasis library        (taken into accound only if key_oasis3 is activated)
-#
-# FC          Fortran compiler command
-# FCFLAGS     Fortran compiler flags
-# FFLAGS      Fortran 77 compiler flags
-# LD          linker
-# LDFLAGS     linker flags, e.g. -L<lib dir> if you have libraries
-# FPPFLAGS    pre-processing flags
-# AR          assembler
-# ARFLAGS     assembler flags
-# MK          make
-# USER_INC    complete list of include files
-# USER_LIB    complete list of libraries to pass to the linker
-# CC          C compiler used to compile conv for AGRIF
-# CFLAGS      compiler flags used with CC
-#
-# Note that:
-#  - unix variables "$..." are accpeted and will be evaluated before calling fcm.
-#  - fcm variables are starting with a % (and not a $)
-#
-#---------------------------------------------------------------------------------------------
-#---------------------------------------------------------------------------------------------
-# All NETCDF and HDF paths are empty as they are automatically defined through environment
-# variables by the load of modules
-#---------------------------------------------------------------------------------------------
-#---------------------------------------------------------------------------------------------
-#
-#
-%XIOS_HOME           $WORK/xios-trunk
-%OASIS_HOME          
-
-%NCDF_INC            
-%NCDF_LIB            -lnetcdff -lnetcdf
-%XIOS_INC            -I%XIOS_HOME/inc 
-%XIOS_LIB            -L%XIOS_HOME/lib -lxios -lstdc++
-%OASIS_INC           -I%OASIS_HOME/build/lib/mct -I%OASIS_HOME/build/lib/psmile.MPI1
-%OASIS_LIB           -L%OASIS_HOME/lib -lpsmile.MPI1 -lmct -lmpeu -lscrip
-
-%CPP	             cpp
-%FC                  mpiifort -c -cpp
-%FCFLAGS             -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                  mpiifort
-%LDFLAGS             
-%FPPFLAGS            -P -traditional
-%AR                  ar
-%ARFLAGS             rs
-%MK                  gmake
-%USER_INC            %XIOS_INC %OASIS_INC %NCDF_INC
-%USER_LIB            %XIOS_LIB %OASIS_LIB %NCDF_LIB
-
-%CC                  cc
-%CFLAGS              -O0

arch/MERCATOR/arch-X64_AA_INTEL_IMPI.fcm

@@ -41,12 +41,13 @@
 %NCDF_LIB            ${NETCDF4_LIB} ${HDF5_LIB}
 %XIOS_INC            -I${XIOS_INC}
 %XIOS_LIB            -L${XIOS_LIB} -lxios -lstdc++
-%OASIS_INC           -I${OASIS_DIR}/build/lib/mct -I${OASIS_DIR}/build/lib/psmile.MPI1
+%OASIS_INC           -I${OASIS_DIR}/include
 %OASIS_LIB           -L${OASIS_DIR}/lib -lpsmile.MPI1 -lmct -lmpeu -lscrip
 
 %CPP                 cpp
 %FC                  mpiifort -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                  mpiifort
 %LDFLAGS             

arch/MERCATOR/arch-X64_AA_INTEL_OMPI.fcm

@@ -47,7 +47,8 @@
 
 %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             

arch/MERCATOR/arch-X64_AA_INTEL_OMPI_DEBUG.fcm

-# compiler options for AA (using INTEL compiler & OpenMPI)
-#
-# module purge
-# module use /home/ar0s/modules
-# module load prgenv/intel intel/2021.4.0 openmpi/4.1.1.1 hdf5-parallel/1.10.6 netcdf4-parallel/4.7.4 xios/trunk/rev2320-nmpi
-#
-#
-# NCDF_INC    netcdf4 include file
-# NCDF_LIB    netcdf4 library
-# XIOS_INC    xios include file    (taken into accound only if key_xios is activated)
-# XIOS_LIB    xios library         (taken into accound only if key_xios is activated)
-# OASIS_INC   oasis include file   (taken into accound only if key_oasis3 is activated)
-# OASIS_LIB   oasis library        (taken into accound only if key_oasis3 is activated)
-#
-# FC          Fortran compiler command
-# FCFLAGS     Fortran compiler flags
-# FFLAGS      Fortran 77 compiler flags
-# LD          linker
-# LDFLAGS     linker flags, e.g. -L<lib dir> if you have libraries
-# FPPFLAGS    pre-processing flags
-# AR          assembler
-# ARFLAGS     assembler flags
-# MK          make
-# USER_INC    complete list of include files
-# USER_LIB    complete list of libraries to pass to the linker
-# CC          C compiler used to compile conv for AGRIF
-# CFLAGS      compiler flags used with CC
-#
-# Note that:
-#  - unix variables "$..." are accpeted and will be evaluated before calling fcm.
-#  - fcm variables are starting with a % (and not a $)
-#
-#---------------------------------------------------------------------------------------------
-#---------------------------------------------------------------------------------------------
-# All NETCDF and HDF paths are empty as they are automatically defined through environment
-# variables by the load of modules
-#---------------------------------------------------------------------------------------------
-#---------------------------------------------------------------------------------------------
-#
-#
-%NCDF_INC            ${NETCDF4_INCLUDE}
-%NCDF_LIB            ${NETCDF4_LIB} -L${HDF5_DIR}/lib -Wl,-rpath,${HDF5_DIR}/lib -lhdf5_hl -lhdf5 -lz
-%XIOS_INC            -I${XIOS_INC}
-%XIOS_LIB            -L${XIOS_LIB} -lxios -lstdc++
-%OASIS_INC           -I${OASIS_DIR}/build/lib/mct -I${OASIS_DIR}/build/lib/psmile.MPI1
-%OASIS_LIB           -L${OASIS_DIR}/lib -lpsmile.MPI1 -lmct -lmpeu -lscrip
-
-%CPP                 cpp
-%FC                  mpifort -c -cpp
-%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             
-%FPPFLAGS            -P -traditional
-%AR                  ar
-%ARFLAGS             rs
-%MK                  gmake
-%USER_INC            %XIOS_INC %OASIS_INC %NCDF_INC
-%USER_LIB            %XIOS_LIB %OASIS_LIB %NCDF_LIB
-
-%CC                  mpicc
-%CFLAGS              -O0

arch/MERCATOR/arch-X64_BELENOS_INTEL_IMPI.fcm

@@ -55,7 +55,8 @@
 
 %CPP                 cpp
 %FC                  mpiifort -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                  mpiifort
 %LDFLAGS             

arch/MERCATOR/arch-X64_BELENOS_INTEL_IMPI_DEBUG.fcm

-# compiler options for BELENOS/TARANIS (using INTEL compiler)
-#
-# --------------------------------
-# INTEL_IMPI (NEMO 4.0 + XIOS-2.5)
-# --------------------------------
-# module use /home/ext/mr/smer/samsong/modules
-# module load intel/2018.5.274 intelmpi/2018.5.274 phdf5/1.8.18 netcdf_par/4.7.1_V2 xios/2.5/rev1903
-#
-# ----------------------------------
-# INTEL_IMPI (NEMO 4.2 + XIOS-TRUNK)
-# ----------------------------------
-# module use /home/ext/mr/smer/samsong/modules
-# module load gcc/9.2.0 intel/2018.5.274 intelmpi/2018.5.274 phdf5/1.8.18 netcdf_par/4.7.1_V2 xios/trunk/rev2134
-#
-#
-# NCDF_INC    netcdf4 include file
-# NCDF_LIB    netcdf4 library
-# XIOS_INC    xios include file    (taken into accound only if key_xios is activated)
-# XIOS_LIB    xios library         (taken into accound only if key_xios is activated)
-# OASIS_INC   oasis include file   (taken into accound only if key_oasis3 is activated)
-# OASIS_LIB   oasis library        (taken into accound only if key_oasis3 is activated)
-#
-# FC          Fortran compiler command
-# FCFLAGS     Fortran compiler flags
-# FFLAGS      Fortran 77 compiler flags
-# LD          linker
-# LDFLAGS     linker flags, e.g. -L<lib dir> if you have libraries
-# FPPFLAGS    pre-processing flags
-# AR          assembler
-# ARFLAGS     assembler flags
-# MK          make
-# USER_INC    complete list of include files
-# USER_LIB    complete list of libraries to pass to the linker
-# CC          C compiler used to compile conv for AGRIF
-# CFLAGS      compiler flags used with CC
-#
-# Note that:
-#  - unix variables "$..." are accpeted and will be evaluated before calling fcm.
-#  - fcm variables are starting with a % (and not a $)
-#
-#---------------------------------------------------------------------------------------------
-#---------------------------------------------------------------------------------------------
-# All NETCDF and HDF paths are empty as they are automatically defined through environment
-# variables by the load of modules
-#---------------------------------------------------------------------------------------------
-#---------------------------------------------------------------------------------------------
-#
-#
-%NCDF_INC            -I${NETCDF_INC}
-%NCDF_LIB            -L${NETCDF_LIB} -lnetcdff -lnetcdf -L${PHDF5_LIB_DIR} -lhdf5_hl -lhdf5
-%XIOS_INC            -I${XIOS_INC}
-%XIOS_LIB            -L${XIOS_LIB} -lxios -lstdc++
-%OASIS_INC           -I${OASIS_DIR}/include
-%OASIS_LIB           -L${OASIS_DIR}/lib -lpsmile.MPI1 -lmct -lmpeu -lscrip
-
-%CPP                 cpp
-%FC                  mpiifort -c -cpp
-%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                  mpiifort
-%LDFLAGS             
-%FPPFLAGS            -P -traditional
-%AR                  ar
-%ARFLAGS             rs
-%MK                  gmake
-%USER_INC            %XIOS_INC %OASIS_INC %NCDF_INC
-%USER_LIB            %XIOS_LIB %OASIS_LIB %NCDF_LIB
-
-%CC                  mpiicc
-%CFLAGS              -O0

arch/MERCATOR/arch-X64_BELENOS_INTEL_MVAP.fcm

@@ -50,14 +50,15 @@
 %NCDF_LIB            -L${NETCDF_LIB} -lnetcdff -lnetcdf -L${PHDF5_LIB_DIR} -lhdf5_hl -lhdf5
 %XIOS_INC            -I${XIOS_INC}
 %XIOS_LIB            -L${XIOS_LIB} -lxios -lstdc++
-%OASIS_INC           -I${OASIS_DIR}/build/lib/mct -I${OASIS_DIR}/build/lib/psmile.MPI1
+%OASIS_INC           -I${OASIS_DIR}/include
 %OASIS_LIB           -L${OASIS_DIR}/lib -lpsmile.MPI1 -lmct -lmpeu -lscrip
 
 %CPP                 cpp
-%FC                  mpifort -c -cpp
-%FCFLAGS             -march=core-avx2 -i4 -r8 -O3 -fp-model strict -fno-alias -align array64byte
+%FC                  mpiifort -c -cpp
+%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
+%LD                  mpiifort
 %LDFLAGS             
 %FPPFLAGS            -P -traditional
 %AR                  ar
@@ -66,5 +67,5 @@
 %USER_INC            %XIOS_INC %OASIS_INC %NCDF_INC
 %USER_LIB            %XIOS_LIB %OASIS_LIB %NCDF_LIB
 
-%CC                  mpicc
+%CC                  mpiicc
 %CFLAGS              -O0

arch/MERCATOR/arch-X64_BELENOS_INTEL_MVAP_DEBUG.fcm

-# compiler options for BELENOS/TARANIS (using INTEL compiler + Intel MPI)
-#
-# --------------------------------
-# INTEL_IMPI (NEMO 4.0 + XIOS-2.5)
-# --------------------------------
-# module use /home/ext/mr/smer/samsong/modules
-# module load intel/2018.5.274 intelmpi/2018.5.274 phdf5/1.8.18 netcdf_par/4.7.1_V2 xios/2.5/rev1903
-#
-# ----------------------------------
-# INTEL_IMPI (NEMO 4.2 + XIOS-TRUNK)
-# ----------------------------------
-# module use /home/ext/mr/smer/samsong/modules
-# module load gcc/9.2.0 intel/2018.5.274 intelmpi/2018.5.274 phdf5/1.8.18 netcdf_par/4.7.1_V2 xios/trunk/rev2134
-#
-#
-# NCDF_INC    netcdf4 include file
-# NCDF_LIB    netcdf4 library
-# XIOS_INC    xios include file    (taken into accound only if key_xios is activated)
-# XIOS_LIB    xios library         (taken into accound only if key_xios is activated)
-# OASIS_INC   oasis include file   (taken into accound only if key_oasis3 is activated)
-# OASIS_LIB   oasis library        (taken into accound only if key_oasis3 is activated)
-#
-# FC          Fortran compiler command
-# FCFLAGS     Fortran compiler flags
-# FFLAGS      Fortran 77 compiler flags
-# LD          linker
-# LDFLAGS     linker flags, e.g. -L<lib dir> if you have libraries
-# FPPFLAGS    pre-processing flags
-# AR          assembler
-# ARFLAGS     assembler flags
-# MK          make
-# USER_INC    complete list of include files
-# USER_LIB    complete list of libraries to pass to the linker
-# CC          C compiler used to compile conv for AGRIF
-# CFLAGS      compiler flags used with CC
-#
-# Note that:
-#  - unix variables "$..." are accpeted and will be evaluated before calling fcm.
-#  - fcm variables are starting with a % (and not a $)
-#
-#---------------------------------------------------------------------------------------------
-#---------------------------------------------------------------------------------------------
-# All NETCDF and HDF paths are empty as they are automatically defined through environment
-# variables by the load of modules
-#---------------------------------------------------------------------------------------------
-#---------------------------------------------------------------------------------------------
-#
-#
-%NCDF_INC            -I${NETCDF_INC}
-%NCDF_LIB            -L${NETCDF_LIB} -lnetcdff -lnetcdf -L${PHDF5_LIB_DIR} -lhdf5_hl -lhdf5
-%XIOS_INC            -I${XIOS_INC}
-%XIOS_LIB            -L${XIOS_LIB} -lxios -lstdc++
-%OASIS_INC           -I${OASIS_DIR}/include
-%OASIS_LIB           -L${OASIS_DIR}/lib -lpsmile.MPI1 -lmct -lmpeu -lscrip
-
-%CPP                 cpp
-%FC                  mpiifort -c -cpp
-%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                  mpiifort
-%LDFLAGS             
-%FPPFLAGS            -P -traditional
-%AR                  ar
-%ARFLAGS             rs
-%MK                  gmake
-%USER_INC            %XIOS_INC %OASIS_INC %NCDF_INC
-%USER_LIB            %XIOS_LIB %OASIS_LIB %NCDF_LIB
-
-%CC                  mpiicc
-%CFLAGS              -O0

arch/MERCATOR/arch-X64_BELENOS_INTEL_OMPI_DEBUG.fcm

-arch-X64_BELENOS_INTEL_IMPI_DEBUG.fcm
\ No newline at end of file

arch/MERCATOR/arch-X64_KARA_GCC_OMPI.fcm

@@ -49,8 +49,9 @@
 
 %CPP                 cpp -Dkey_nosignedzero
 %FC                  mpif90 -c -cpp
-#%FCFLAGS             -fdefault-real-8 -O2 -ftree-vectorize -funroll-all-loops -march=skylake-avx512 -ffree-line-length-none -Wno-missing-include-dirs
-%FCFLAGS             -fdefault-real-8 -O1 -march=skylake-avx512 -ffree-line-length-none -Wno-missing-include-dirs
+#%PROD_FCFLAGS       -fdefault-real-8 -O2 -ftree-vectorize -funroll-all-loops -march=skylake-avx512 -ffree-line-length-none -Wno-missing-include-dirs
+%PROD_FCFLAGS        -fdefault-real-8 -O1 -march=skylake-avx512 -ffree-line-length-none -Wno-missing-include-dirs
+%DEBUG_FCFLAGS       -fdefault-real-8 -O0 -g -fbacktrace -ftree-vectorize -funroll-all-loops -march=skylake-avx512 -ffree-line-length-none -fcheck=all -finit-real=snan -Wno-missing-include-dirs -ffpe-trap=invalid,zero,overflow
 %FFLAGS              %FCFLAGS
 %LD                  mpif90
 %LDFLAGS             -lstdc++

arch/MERCATOR/arch-X64_KARA_GCC_OMPI_DEBUG.fcm

-# compiler options for KARA (using GNU compiler)
-#
-# GNU_OMPI (NEMO-4.0 + XIOS-2.5)
-# 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/2.5_rev1903_gcc9.3.0
-#
-# GNU_OMPI (NEMO-4.2 + XIOS-TRUNK)
-# 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
-#
-#
-# NCDF_INC    netcdf4 include file
-# NCDF_LIB    netcdf4 library
-# XIOS_INC    xios include file    (taken into accound only if key_xios is activated)
-# XIOS_LIB    xios library         (taken into accound only if key_xios is activated)
-# OASIS_INC   oasis include file   (taken into accound only if key_oasis3 is activated)
-# OASIS_LIB   oasis library        (taken into accound only if key_oasis3 is activated)
-#
-# FC          Fortran compiler command
-# FCFLAGS     Fortran compiler flags
-# FFLAGS      Fortran 77 compiler flags
-# LD          linker
-# LDFLAGS     linker flags, e.g. -L<lib dir> if you have libraries
-# FPPFLAGS    pre-processing flags
-# AR          assembler
-# ARFLAGS     assembler flags
-# MK          make
-# USER_INC    complete list of include files
-# USER_LIB    complete list of libraries to pass to the linker
-# CC          C compiler used to compile conv for AGRIF
-# CFLAGS      compiler flags used with CC
-#
-# Note that:
-#  - unix variables "$..." are accpeted and will be evaluated before calling fcm.
-#  - fcm variables are starting with a % (and not a $)
-#
-#---------------------------------------------------------------------------------------------
-#---------------------------------------------------------------------------------------------
-# All NETCDF and HDF paths are empty as they are automatically defined through environment
-# variables by the load of modules
-#---------------------------------------------------------------------------------------------
-#---------------------------------------------------------------------------------------------
-#
-#
-%NCDF_INC            -I${NETCDF_INC}
-%NCDF_LIB            -L${NETCDF_LIB} -lnetcdff -lnetcdf -L${HDF5_LIB} -lhdf5_hl -lhdf5
-%XIOS_INC            -I${XIOS_INC}
-%XIOS_LIB            -L${XIOS_LIB} -lxios
-%OASIS_INC           -I${OASIS_DIR}/build/lib/mct -I${OASIS_DIR}/build/lib/psmile.MPI1
-%OASIS_LIB           -L${OASIS_DIR}/lib -lpsmile.MPI1 -lmct -lmpeu -lscrip
-
-%CPP                 cpp -Dkey_nosignedzero
-%FC                  mpif90 -c -cpp
-%FCFLAGS             -fdefault-real-8 -O0 -g -fbacktrace -ftree-vectorize -funroll-all-loops -march=skylake-avx512 -ffree-line-length-none -fcheck=all -finit-real=snan -Wno-missing-include-dirs -ffpe-trap=invalid,zero,overflow
-%FFLAGS              %FCFLAGS
-%LD                  mpif90
-%LDFLAGS             -lstdc++
-%FPPFLAGS            -P -traditional
-%AR                  ar
-%ARFLAGS             rs
-%MK                  gmake
-%USER_INC            %XIOS_INC %OASIS_INC %NCDF_INC
-%USER_LIB            %XIOS_LIB %OASIS_LIB %NCDF_LIB
-
-%CC                  gcc
-%CFLAGS              -O0

arch/arch-osx_gfortran.fcm

@@ -35,7 +35,8 @@
 
 %CPP	             cpp -Dkey_nosignedzero 
 %FC	             mpif90 
-%FCFLAGS             -fdefault-real-8 -O3 -funroll-all-loops -fcray-pointer -ffree-line-length-none  -fallow-argument-mismatch 
+%PROD_FCFLAGS        -fdefault-real-8 -O3 -funroll-all-loops -fcray-pointer -ffree-line-length-none  -fallow-argument-mismatch 
+%DEBUG_FCFLAGS       -fdefault-real-8 -O0 -g -fbacktrace -funroll-all-loops -fcray-pointer -ffree-line-length-none -fcheck=all -finit-real=nan
 %FFLAGS              %FCFLAGS
 %LD                  %FC
 %LDFLAGS             

arch/arch-osx_gfortran_debug.fcm

-# generic gfortran compiler options for OSX installed with macport, http://www.macports.org/
-#
-#   Prerequisite softwares installed with MacPorts :
-#   Prerequisite softwares installed with MacPorts :
-#     sudo port install gcc9
-#     sudo port install gcc_select
-#     sudo port select --set gcc mp-gcc9
-#     sudo port install mpich-gcc9
-#     sudo port install mpi_select
-#     sudo port select --set mpi mpich-gcc9-fortran
-#     sudo port install hdf5 +gcc9 +mpich +szip
-#     sudo port install netcdf +gcc9 +mpich
-#     sudo port install netcdf-fortran +gcc9 +mpich
-#     sudo port install p5.30-uri
-#
-#     $ port select --show mpi
-#     The currently selected version for 'mpi' is 'mpich-gcc9-fortran'.
-#     $ port select --show gcc
-#     The currently selected version for 'gcc' is 'mp-gcc9'.
-#
-# Note that:
-#  - unix variables "$..." are accpeted and will be evaluated before calling fcm.
-#  - fcm variables are starting with a % (and not a $)
-#
-%NCDF_HOME           /opt/local
-%HDF5_HOME           /opt/local
-%XIOS_HOME           /Users/$( whoami )/xios-trunk
-%OASIS_HOME          /not/defined
-
-%NCDF_INC            -I%NCDF_HOME/include -I%HDF5_HOME/include
-%NCDF_LIB            -L%NCDF_HOME/lib -lnetcdff -lnetcdf
-%XIOS_INC            -I%XIOS_HOME/inc 
-%XIOS_LIB            -L%XIOS_HOME/lib -lxios -lstdc++
-%OASIS_INC           -I%OASIS_HOME/build/lib/mct -I%OASIS_HOME/build/lib/psmile.MPI1
-%OASIS_LIB           -L%OASIS_HOME/lib -lpsmile.MPI1 -lmct -lmpeu -lscrip
-
-%CPP	             cpp -Dkey_nosignedzero 
-%FC	             mpif90 
-%FCFLAGS             -fdefault-real-8 -O0 -g -fbacktrace -funroll-all-loops -fcray-pointer -ffree-line-length-none -fcheck=all -finit-real=nan
-%FFLAGS              %FCFLAGS
-%LD                  %FC
-%LDFLAGS             
-%FPPFLAGS            -P -traditional
-%AR                  ar
-%ARFLAGS             rs
-%MK                  make
-%USER_INC            %XIOS_INC %OASIS_INC %NCDF_INC
-%USER_LIB            %XIOS_LIB %OASIS_LIB %NCDF_LIB
-
-%CC                  cc
-%CFLAGS              -O0

makenemo

@@ -84,9 +84,8 @@ set -o posix
 
 #-
 ##- Initialization of the options ---
-x_d=''; x_h=''; x_n=''; x_r='';
-x_u=''; x_a=''; x_m=''; x_t='';
-x_c='';
+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'
 
 ##- Local variables ---
@@ -112,7 +111,7 @@ export PATH=${MAIN_DIR}/ext/FCM/bin:$PATH
 
 #-
 #- Choice of the options ---
-while getopts :hd:n:r:u:a:m:j:e:s:v:t:k: option; do
+while getopts :hd:n:r:u:a:m:j:e:s:v:t:k:b option; do
 
 	case $option in
 		('h') cat <<EOF
@@ -132,6 +131,7 @@ Mandatory
 
 Optional
    -d    New set of sub-components (subfolders from ./src directory)
+   -b    Compile Nemo in debug mode (if %DEBUG_FCFLAGS is defined in arch file)
    -e    Path for alter patch  location (default: 'MY_SRC' in configuration folder)
    -h    Print this help
    -j    Number of processes to compile (0: dry run with no build)
@@ -151,12 +151,12 @@ Examples
         Removal        : ./makenemo -n ... clean_config
 EOF
 				exit 0       ;;
-	  	('d') x_d=${OPTARG};; ('n') x_n=${OPTARG};; ('r') x_r=${OPTARG};; ('u') x_u=${OPTARG};;
-		('a') x_a=${OPTARG};; ('m') x_m=${OPTARG};; ('j') x_j=${OPTARG};; ('t') x_t=${OPTARG};;
-		('e') x_e=(${OPTARG});; ('s') x_s=${OPTARG};; ('v') x_v=${OPTARG}                      ;;
-		('k') chk_key=${OPTARG}                                                              ;;
-		(':') echo ${b_n}" : -"${OPTARG}" option : missing value" 1>&2;	exit 2             ;;
-		('?') echo ${b_n}" : -"${OPTARG}" option : not supported" 1>&2;	exit 2             ;;
+		('b') x_b="True"   ;;   ('n') x_n=${OPTARG};; ('r') x_r=${OPTARG};; ('u') x_u=${OPTARG};;
+		('a') x_a=${OPTARG};;   ('m') x_m=${OPTARG};; ('j') x_j=${OPTARG};; ('t') x_t=${OPTARG};;
+		('e') x_e=(${OPTARG});; ('s') x_s=${OPTARG};; ('v') x_v=${OPTARG};; ('d') x_d=${OPTARG};;
+		('k') chk_key=${OPTARG}                                                                ;;
+		(':') echo ${b_n}" : -"${OPTARG}" option : missing value" 1>&2;	exit 2                 ;;
+		('?') echo ${b_n}" : -"${OPTARG}" option : not supported" 1>&2;	exit 2                 ;;
 	esac
 
 done
@@ -189,6 +189,7 @@ DEMO_CONF=${x_a}
 RMT_CONF=${x_u}
 TML_CONF=${REF_CONF}
 export NEMO_DIR=${MAIN_DIR}/${x_s}
+NEMO_DBG=${x_b}
 
 [ "${CMP_NAM}" == 'all' ] && . ${COMPIL_DIR}/Flist_archfile.sh all && exit
 

mk/Fcheck_archfile.sh

@@ -74,7 +74,8 @@ EOF
     done < $1
 }
 # cleaning related to the old version
-rm -f $( find ${COMPIL_DIR} -type l -name $1 -print )
+rm -f $( find ${COMPIL_DIR} -type f -name $1 -print )
+
 #
 if [ ${#3} -eq 0 ]; then # arch not specified
     if [ ! -f ${COMPIL_DIR}/arch.history ]; then
@@ -213,3 +214,18 @@ do
     fi
 done
 
+# Nemo debug ?
+if [ -n "${NEMO_DBG}" ]; then
+    if [ $( grep -c "^%DEBUG_FCFLAGS" ${COMPIL_DIR}/$1 ) -eq 0 ]; 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
+else
+    if [ $( grep -q "^%PROD_FCFLAGS" ${COMPIL_DIR}/$1 ) -eq 0 ]; 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
+fi