arch/CNRS/arch-X64_JEANZAY_DEBUG.fcm

@@ -36,7 +36,7 @@
 #---------------------------------------------------------------------------------------------
 #
 #
-%XIOS_HOME           $WORK/xios-2.5
+%XIOS_HOME           $WORK/xios-trunk
 %OASIS_HOME          
 
 %NCDF_INC            

arch/MERCATOR/arch-X64_AA_GCC_OMPI.fcm

+# compiler options for AA (using GCC compiler)
+#
+#
+# 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            ${NETCDF4_INCLUDE}
+%NCDF_LIB            -L${NETCDF4_DIR}/lib -lnetcdff -lnetcdf -L${HDF5_DIR}/lib -lhdf5_hl -lm
+%XIOS_INC            -I${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 -Dkey_nosignedzero
+%FC                  mpif90 -c -cpp
+# O3 breaks reproduci/restartabi-lity with gcc/12.2.0
+%FCFLAGS             -fdefault-real-8 -O2 -funroll-all-loops -fcray-pointer -ffree-line-length-none -fallow-argument-mismatch -Wno-missing-include-dirs
+%FFLAGS              %FCFLAGS
+%LD                  mpif90
+%LDFLAGS             -Wl,-rpath,${HDF5_DIR}/lib -Wl,-rpath=${NETCDF4_DIR}/lib -Wl,-rpath=${XIOS_DIR}/lib
+%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                  gcc
+%CFLAGS              -O0 -fcommon

arch/MERCATOR/arch-X64_AA_GCC_OMPI_DEBUG.fcm

+# compiler options for AA (using GCC compiler)
+#
+#
+# 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            ${NETCDF4_INCLUDE}
+%NCDF_LIB            -L${NETCDF4_DIR}/lib -lnetcdff -lnetcdf -L${HDF5_DIR}/lib -lhdf5_hl -lm
+%XIOS_INC            -I${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 -Dkey_nosignedzero
+%FC                  mpif90 -c -cpp
+%FCFLAGS       -fdefault-real-8 -Og -g -fbacktrace -funroll-all-loops -fcray-pointer -ffree-line-length-none -fcheck=all,no-array-temps -finit-real=nan -ffpe-trap=invalid,zero,overflow -ffpe-summary=invalid,zero,overflow -fallow-argument-mismatch -Wno-missing-include-dirs
+%FFLAGS              %FCFLAGS
+%LD                  mpif90
+%LDFLAGS             -Wl,-rpath,${HDF5_DIR}/lib -Wl,-rpath=${NETCDF4_DIR}/lib -Wl,-rpath=${XIOS_DIR}/lib
+%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                  gcc
+%CFLAGS              -O0 -fcommon

arch/MERCATOR/arch-X64_AA_INTEL_OMPI.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}/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
+%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_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}/include
+%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

-# compiler options for BELENOS/TARANIS (using INTEL compiler)
+# compiler options for BELENOS/TARANIS (using INTEL compiler + INTEL MPI)
 #
-# INTEL_IMPI (XIOS-2.5)
-# 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 4.0 + 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 (XIOS-TRUNK must be compiled)
-# gcc/9.2.0 intel/2018.5.274 intelmpi/2018.5.274 phdf5/1.8.18 netcdf_par/4.7.1_V2
+# ----------------------------------
+# 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
@@ -44,7 +50,7 @@
 %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

arch/MERCATOR/arch-X64_BELENOS_INTEL_IMPI_DEBUG.fcm

-# compiler options for BELENOS/TARANIS (using INTEL compiler)
+# compiler options for BELENOS/TARANIS (using INTEL compiler + INTEL MPI)
 #
-# INTEL_IMPI (XIOS-2.5)
-# 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 4.0 + 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 (XIOS-TRUNK must be compiled)
-# gcc/9.2.0 intel/2018.5.274 intelmpi/2018.5.274 phdf5/1.8.18 netcdf_par/4.7.1_V2
+# ----------------------------------
+# 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
@@ -44,7 +50,7 @@
 %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

arch/MERCATOR/arch-X64_KARA_GCC_OMPI_DEBUG.fcm

@@ -49,7 +49,7 @@
 
 %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=nan -Wno-missing-include-dirs
+%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/NOC/arch-X86_ARCHER2-Gnu_DEBUG.fcm

+# compiler options for Archer2 CRAY XC-30 (using GNU compiler)
+#
+# 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 $)
+#
+%NCDF_HOME           $NETCDF_DIR
+%HDF5_HOME           $HDF5_DIR
+%XIOS_HOME           /work/n01/shared/nemo/xios-trunk-gnu
+#OASIS_HOME          
+
+%NCDF_INC            -I%NCDF_HOME/include -I%HDF5_HOME/include
+%NCDF_LIB            -L%HDF5_HOME/lib -L%NCDF_HOME/lib -lnetcdff -lnetcdf -lhdf5_hl -lhdf5 -lz
+%XIOS_INC            -I%XIOS_HOME/inc 
+%XIOS_LIB            -L%XIOS_HOME/lib -lxios
+#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                  ftn
+%FCFLAGS             -fdefault-real-8 -O0 -g -fallow-argument-mismatch -fbacktrace -funroll-all-loops -fcray-pointer -ffree-line-length-none -fcheck=all -finit-real=nan
+%FFLAGS              %FCFLAGS
+%LD                  CC 
+%FPPFLAGS            -P -traditional
+%LDFLAGS             -lmpichf90
+%AR                  ar 
+%ARFLAGS             rs
+%MK                  gmake
+%USER_INC            %XIOS_INC %NCDF_INC
+%USER_LIB            %XIOS_LIB %NCDF_LIB
+#USER_INC            %XIOS_INC %OASIS_INC %NCDF_INC
+#USER_LIB            %XIOS_LIB %OASIS_LIB %NCDF_LIB
+
+%CC                  cc
+%CFLAGS              -O0
+bld::tool::fc_modsearch -J

arch/arch-linux_gfortran.fcm

@@ -30,32 +30,31 @@
 #  - unix variables "$..." are accpeted and will be evaluated before calling fcm.
 #  - fcm variables are starting with a % (and not a $)
 #
-%NCDF_HOME           /usr/local/netcdf
-%HDF5_HOME           /usr/local/hdf5
-%XIOS_HOME           $HOME/xios-2.5
-%OASIS_HOME          /not/defined
+#%HDF5_HOME           $HOME/MODNUM/util/hdf5-1.8.13
+#%NCDF_C_HOME         $HOME/MODNUM/util/netcdf-c-4.3.3.1
+#%NCDF_F_HOME         $HOME/MODNUM/util/netcdf-fortran-4.4.2
+#%XIOS_HOME           $HOME/MODNUM/xios-trunk
 
-%NCDF_INC            -I%NCDF_HOME/include -I%HDF5_HOME/include
-%NCDF_LIB            -L%NCDF_HOME/lib -lnetcdff -lnetcdf
+%NCDF_INC            -I%NCDF_F_HOME/include -I%NCDF_C_HOME/include -I%HDF5_HOME/include
+%NCDF_LIB            -L%NCDF_F_HOME/lib -lnetcdff -L%NCDF_C_HOME/lib -lnetcdf
 %XIOS_INC            -I%XIOS_HOME/inc 
-%XIOS_LIB            -L%XIOS_HOME/lib -lxios -L/usr/lib/gcc/x86_64-linux-gnu/5 -lstdc++
+%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	             /usr/bin/mpif90 -c -cpp 
+%FC	             mpif90 -c -cpp
 %FCFLAGS             -fdefault-real-8 -O3 -funroll-all-loops -fcray-pointer -ffree-line-length-none
 %FFLAGS              %FCFLAGS
-#%LD                  /usr/bin/mpif90 -Wl,-rpath=$HOME/INSTALL/lib:/usr/lib
-%LD                  /usr/bin/mpif90
+%LD                  mpif90
 %LDFLAGS             
 %FPPFLAGS            -P -C -traditional
 %AR                  ar
 %ARFLAGS             rs
 %MK                  make
-%USER_INC            %XIOS_INC %OASIS_INC %NCDF_INC
-%USER_LIB            %XIOS_LIB %OASIS_LIB %NCDF_LIB
+%USER_INC            %XIOS_INC %NCDF_INC
+%USER_LIB            %XIOS_LIB %NCDF_LIB
 
 %CC                  cc
 %CFLAGS              -O0

arch/arch-osx_gfortran.fcm

@@ -23,7 +23,7 @@
 #
 %NCDF_HOME           /opt/local
 %HDF5_HOME           /opt/local
-%XIOS_HOME           /Users/$( whoami )/xios-2.5
+%XIOS_HOME           /Users/$( whoami )/xios-trunk
 %OASIS_HOME          /not/defined
 
 %NCDF_INC            -I%NCDF_HOME/include -I%HDF5_HOME/include
@@ -35,7 +35,7 @@
 
 %CPP	             cpp -Dkey_nosignedzero 
 %FC	             mpif90 
-%FCFLAGS             -fdefault-real-8 -O3 -funroll-all-loops -fcray-pointer -ffree-line-length-none
+%FCFLAGS             -fdefault-real-8 -O3 -funroll-all-loops -fcray-pointer -ffree-line-length-none  -fallow-argument-mismatch 
 %FFLAGS              %FCFLAGS
 %LD                  %FC
 %LDFLAGS             

arch/arch-osx_gfortran_debug.fcm

@@ -24,7 +24,7 @@
 #
 %NCDF_HOME           /opt/local
 %HDF5_HOME           /opt/local
-%XIOS_HOME           /Users/$( whoami )/xios-2.5
+%XIOS_HOME           /Users/$( whoami )/xios-trunk
 %OASIS_HOME          /not/defined
 
 %NCDF_INC            -I%NCDF_HOME/include -I%HDF5_HOME/include

cfgs/AGRIF_DEMO/EXPREF/1_context_nemo.xml

@@ -27,7 +27,6 @@
 
 <!-- Files definition -->
     <file_definition src="./file_def_nemo-oce.xml"/>     <!--  NEMO ocean dynamics                     -->
-    <file_definition src="./file_def_nemo-ice.xml"/>     <!--  NEMO ocean sea ice                      -->
     <file_definition src="./file_def_nemo-innerttrc.xml"/> <!--  NEMO ocean inert passive tracer           -->
 
 <!-- Axis definition -->

cfgs/AGRIF_DEMO/EXPREF/1_namelist_cfg

@@ -30,12 +30,13 @@
    ln_linssh   = .false.   !  =T  linear free surface  ==>>  model level are fixed in time
    !
    rn_Dt      = 5400.     !  time step for the dynamics and tracer
+   ln_meshmask = .false.  !  =T create a mesh file
 /
 !-----------------------------------------------------------------------
 &namcfg        !   parameters of the configuration                      (default: user defined GYRE)
 !-----------------------------------------------------------------------
    ln_read_cfg = .true.    !  (=T) read the domain configuration file
-      cn_domcfg = "ORCA_R2_zps_domcfg_agrif"    ! domain configuration filename
+      cn_domcfg = "domain_cfg.nc"    ! domain configuration filename
       !
       ln_closea    = .false.    !  F => suppress closed seas (defined by closea_mask field) 
       !                         !       from the bathymetry at runtime.
@@ -84,7 +85,7 @@
                      ! Type of air-sea fluxes 
    ln_blk      = .true.    !  Bulk formulation                          (T => fill namsbc_blk )
                      ! Sea-ice :
-   nn_ice      = 2         !  =0 no ice boundary condition
+   nn_ice      = 0         !  =0 no ice boundary condition
       !                    !  =1 use observed ice-cover                 (  => fill namsbc_iif )
       !                    !  =2 or 3 for SI3 and CICE, respectively
                      ! Misc. options of sbc : 
@@ -360,6 +361,10 @@
 !-----------------------------------------------------------------------
 &namzdf_tke    !   turbulent eddy kinetic dependent vertical diffusion  (ln_zdftke =T)
 !-----------------------------------------------------------------------
+      nn_mxlice = 0           ! type of scaling under sea-ice
+      !                       !    = 0 no scaling under sea-ice
+      !                       !    = 1 scaling with constant sea-ice thickness
+      !                       !    = 2 scaling with mean sea-ice thickness ( only with SI3 sea-ice model )
 /
 !!======================================================================
 !!                  ***  Diagnostics namelists  ***                   !!

cfgs/AGRIF_DEMO/EXPREF/2_namelist_cfg

@@ -31,12 +31,13 @@
    ln_linssh   = .false.   !  =T  linear free surface  ==>>  model level are fixed in time
    !
    rn_Dt      = 1350.     !  time step for the dynamics (and tracer if nn_acc=0)
+   ln_meshmask = .false.  !  =T create a mesh file
 /
 !-----------------------------------------------------------------------
 &namcfg        !   parameters of the configuration                      (default: user defined GYRE)
 !-----------------------------------------------------------------------
    ln_read_cfg = .true.    !  (=T) read the domain configuration file
-      cn_domcfg = "ORCA_R05_zps_domcfg_agrif"    ! domain configuration filename
+      cn_domcfg = "domain_cfg.nc"    ! domain configuration filename
 /
 !-----------------------------------------------------------------------
 &namtile        !   parameters of the tiling
@@ -297,6 +298,10 @@
 !-----------------------------------------------------------------------
 &namzdf_tke    !   turbulent eddy kinetic dependent vertical diffusion  (ln_zdftke =T)
 !-----------------------------------------------------------------------
+      nn_mxlice = 2           ! type of scaling under sea-ice
+      !                       !    = 0 no scaling under sea-ice
+      !                       !    = 1 scaling with constant sea-ice thickness
+      !                       !    = 2 scaling with mean sea-ice thickness ( only with SI3 sea-ice model )
 /
 !!======================================================================
 !!                  ***  Diagnostics namelists  ***                   !!

cfgs/AGRIF_DEMO/EXPREF/3_namelist_cfg

@@ -30,13 +30,14 @@
 !-----------------------------------------------------------------------
    ln_linssh   = .false.   !  =T  linear free surface  ==>>  model level are fixed in time
    !
-   rn_Dt      = 450.     !  time step for the dynamics (and tracer if nn_acc=0)
+   rn_Dt      = 450.       !  time step for the dynamics (and tracer if nn_acc=0)
+   ln_meshmask = .false.   !  =T create a mesh file
 /
 !-----------------------------------------------------------------------
 &namcfg        !   parameters of the configuration                      (default: user defined GYRE)
 !-----------------------------------------------------------------------
    ln_read_cfg = .true.    !  (=T) read the domain configuration file
-      cn_domcfg = "ORCA_R017_zps_domcfg_agrif"    ! domain configuration filename
+      cn_domcfg = "domain_cfg.nc"    ! domain configuration filename
 /
 !-----------------------------------------------------------------------
 &namtile        !   parameters of the tiling
@@ -154,6 +155,7 @@
 &namagrif      !  AGRIF zoom                                            ("key_agrif")
 !-----------------------------------------------------------------------
    ln_init_chfrpar = .true. !  initialize child grids from parent
+   ln_vert_remap   = .true. !  vertical remapping
 /
 !-----------------------------------------------------------------------
 &namdrg        !   top/bottom drag coefficient                          (default: NO selection)
@@ -297,6 +299,10 @@
 !-----------------------------------------------------------------------
 &namzdf_tke    !   turbulent eddy kinetic dependent vertical diffusion  (ln_zdftke =T)
 !-----------------------------------------------------------------------
+      nn_mxlice = 2           ! type of scaling under sea-ice
+      !                       !    = 0 no scaling under sea-ice
+      !                       !    = 1 scaling with constant sea-ice thickness
+      !                       !    = 2 scaling with mean sea-ice thickness ( only with SI3 sea-ice model )
 /
 !!======================================================================
 !!                  ***  Diagnostics namelists  ***                   !!

cfgs/AGRIF_DEMO/EXPREF/namelist_cfg

@@ -30,12 +30,13 @@
    ln_linssh   = .false.   !  =T  linear free surface  ==>>  model level are fixed in time
    !
    rn_Dt      = 5400.     !  time step for the dynamics and tracer
+   ln_meshmask = .false.  !  =T create a mesh file
 /
 !-----------------------------------------------------------------------
 &namcfg        !   parameters of the configuration                      (default: use namusr_def in namelist_cfg)
 !-----------------------------------------------------------------------
    ln_read_cfg = .true.    !  (=T) read the domain configuration file
-      cn_domcfg = "ORCA_R2_zps_domcfg_agrif"    ! domain configuration filename
+      cn_domcfg = "domain_cfg.nc"    ! domain configuration filename
       !
       ln_closea    = .false.    !  F => suppress closed seas (defined by closea_mask field) 
       !                         !       from the bathymetry at runtime.
@@ -356,6 +357,10 @@
 !-----------------------------------------------------------------------
 &namzdf_tke    !   turbulent eddy kinetic dependent vertical diffusion  (ln_zdftke =T)
 !-----------------------------------------------------------------------
+      nn_mxlice = 2           ! type of scaling under sea-ice
+      !                       !    = 0 no scaling under sea-ice
+      !                       !    = 1 scaling with constant sea-ice thickness
+      !                       !    = 2 scaling with mean sea-ice thickness ( only with SI3 sea-ice model ) 
 /
 !!======================================================================
 !!                  ***  Diagnostics namelists  ***                   !!

cfgs/AMM12/EXPREF/namelist_cfg

@@ -24,6 +24,7 @@
    nn_itend    =    1296   !  last  time step (std 1 day = 144)
    nn_date0    =  20120102 !  date at nit_0000 (format yyyymmdd) used if ln_rstart=F or (ln_rstart=T and nn_rstctl=0 or 1)
    nn_leapy    =       1   !  Leap year calendar (1) or not (0)
+   ln_rstart   = .true.    !  start from rest (F) or from a restart file (T)
    cn_ocerst_in   = "amm12_restart_oce"   !  suffix of ocean restart name (input)
    cn_ocerst_out  = "restart"             !  suffix of ocean restart name (input)
    nn_stock    =    1296   !  frequency of creation of a restart file (modulo referenced to 1)

cfgs/GYRE_BFM/EXPREF/context_nemo.xml

@@ -19,12 +19,13 @@
     </variable_definition>
 
 <!-- Fields definition -->
-    <field_definition src="./field_def_nemo-oce.xml"/>      <!--  NEMO ocean dynamics                     -->
-    <field_definition src="./field_def_nemo-pisces.xml"/>   <!--  NEMO ocean dynamics                     -->
+    <field_definition src="./field_def_nemo-oce.xml"/>    <!--  NEMO ocean dynamics    -->
+    <field_definition src="./field_def_bfm.xml"/>         <!--  BFM BGC  dynamics      -->
 
 
 <!-- Files definition -->
-    <file_definition src="./file_def_nemo.xml"/>     <!--  NEMO ocean dynamics                     -->
+    <file_definition src="./file_def_nemo.xml"/>          <!--  NEMO ocean dynamics    -->
+    <file_definition src="./file_def_bfm.xml"/>           <!-- BFM BGC dynamics        -->
 
 <!-- Axis definition -->
     <axis_definition src="./axis_def_nemo.xml"/>