arch/MERCATOR/arch-X64_BELENOS_INTEL_IMPI.fcm

-# compiler options for BELENOS/TARANIS (using INTEL compiler)
-#
-# 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 (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
-#
+# compiler options for BELENOS/TARANIS (using INTEL compiler + Open MPI)
 #
 # NCDF_INC    netcdf4 include file
 # NCDF_LIB    netcdf4 library
@@ -44,12 +37,15 @@
 %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${OASIS_DIR}/build/lib/mct -I${OASIS_DIR}/build/lib/psmile.MPI1
+%OASIS_INC           -I${OASIS_DIR}/build-static/mct -I${OASIS_DIR}/build-static/lib/psmile.MPI1
 %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
+%BASE_FCFLAGS        -march=core-avx2 -i4 -r8 -fp-model strict -fno-alias -align array64byte
+%PROD_FCFLAGS        %BASE_FCFLAGS -O3
+%DEBUG_FCFLAGS       %BASE_FCFLAGS -O0 -g -debug all -traceback -ftrapuv -check all,noarg_temp_created -fpe-all0 -ftz -init=arrays,snan,huge
 %FFLAGS              %FCFLAGS
 %LD                  mpiifort
 %LDFLAGS             
@@ -60,5 +56,5 @@
 %USER_INC            %XIOS_INC %OASIS_INC %NCDF_INC
 %USER_LIB            %XIOS_LIB %OASIS_LIB %NCDF_LIB
 
-%CC                  mpiicc
-%CFLAGS              -O0
+%CC                  gcc
+%CFLAGS              -O0 -fcommon

arch/MERCATOR/arch-X64_BELENOS_INTEL_OMPI.env

+if ! grep -qi xios <<< $(module list 2>&1); then
+  module purge
+  module use /home/ext/mr/smer/samsong/modules
+  module load git/2.27.0 gcc/9.2.0 intel/2018.5.274 openmpi/intel/4.0.2.2 hdf5/1.8.18-ompi netcdf/4.7.1-ompi_V2 xios/trunk/r2515_intel-ompi &> /dev/null
+  export OMPI_CC=icc
+  export OMPI_CXX=icpc
+  export OMPI_FC=ifort
+  export OMPI_F77=ifort
+  export OMPI_F90=ifort
+  if ! grep -qi xios <<< $(module list 2>&1); then echo 'module error'; exit 1; fi
+else
+  echo 'xios module already loaded'
+fi
+module list

arch/MERCATOR/arch-X64_BELENOS_INTEL_OMPI.fcm

-# compiler options for BELENOS/TARANIS (using INTEL compiler)
-#
-# INTEL_OMPI (XIOS-2.5)
-# intel/2018.5.274 openmpi/intel/4.0.2.2 hdf5-1.8.18-ompi netcdf-4.7.1-ompi_V2 xios-2.5_rev1903-ompi
-#
-# INTEL_MVAPICH2 (XIOS-2.5)
-# intel/2018.5.274 mvapich2-2.3.5 hdf5-1.8.18-mvapich2 netcdf-4.7.1-mvapich2 xios-2.5_rev1903-mvapich2
-#
+# compiler options for BELENOS/TARANIS (using INTEL compiler + Open MPI)
 #
 # NCDF_INC    netcdf4 include file
 # NCDF_LIB    netcdf4 library
@@ -44,12 +37,15 @@
 %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${OASIS_DIR}/build/lib/mct -I${OASIS_DIR}/build/lib/psmile.MPI1
+%OASIS_INC           -I${OASIS_DIR}/build-static/mct -I${OASIS_DIR}/build-static/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 -O3 -fp-model strict -fno-alias -align array64byte
+%BASE_FCFLAGS        -march=core-avx2 -i4 -r8 -fp-model strict -fno-alias -align array64byte
+%PROD_FCFLAGS        %BASE_FCFLAGS -O3
+%DEBUG_FCFLAGS       %BASE_FCFLAGS -O0 -g -debug all -traceback -ftrapuv -check all,noarg_temp_created -fpe-all0 -ftz -init=arrays,snan,huge
 %FFLAGS              %FCFLAGS
 %LD                  mpifort
 %LDFLAGS             
@@ -60,5 +56,5 @@
 %USER_INC            %XIOS_INC %OASIS_INC %NCDF_INC
 %USER_LIB            %XIOS_LIB %OASIS_LIB %NCDF_LIB
 
-%CC                  mpicc
-%CFLAGS              -O0
+%CC                  gcc
+%CFLAGS              -O0 -fcommon

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 -O2 -ffp-contract=off -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/NOC/arch-ANEMONE-ifort-xios3.fcm

+# generic ifort compiler options for linux
+#
+# 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           $EBROOTNETCDF
+%HDF5_HOME           $EBROOTHDF5
+%XIOS_HOME           /home/acc/xios3-trunk
+#%OASIS_HOME          /not/defined
+
+%NCDF_INC            -I%NCDF_HOME/include 
+%NCDF_LIB            -L%NCDF_HOME/lib -lnetcdff -lnetcdf -L%HDF5_HOME/lib -lhdf5_hl -lhdf5 -lhdf5
+%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           
+%OASIS_INC           
+#%OASIS_LIB           -L%OASIS_HOME/lib -lpsmile.MPI1 -lmct -lmpeu -lscrip
+
+%CPP	             cpp -Dkey_xios3
+%FC                  mpiifort -c -fpp -fpp-name:/opt/software/eb/software/GCCcore/11.2.0/bin/cpp -Wp,-P,-traditional
+%PROD_FCFLAGS        -i4 -r8 -O3 -fp-model precise -fno-alias
+%DEBUG_FCFLAGS       -i4 -r8 -g -fp-trap=common -traceback  -fp-model precise -fno-alias
+%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 -Wl,--allow-multiple-definition
+%CFLAGS              -O0
+

arch/NOC/arch-ANEMONE-ifort.fcm

+# generic ifort compiler options for linux
+#
+# 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           $EBROOTNETCDF
+%HDF5_HOME           $EBROOTHDF5
+%XIOS_HOME           /home/acc/xios-trunk
+#%OASIS_HOME          /not/defined
+
+%NCDF_INC            -I%NCDF_HOME/include 
+%NCDF_LIB            -L%NCDF_HOME/lib -lnetcdff -lnetcdf -L%HDF5_HOME/lib -lhdf5_hl -lhdf5 -lhdf5
+%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           
+%OASIS_INC           
+#%OASIS_LIB           -L%OASIS_HOME/lib -lpsmile.MPI1 -lmct -lmpeu -lscrip
+
+%CPP	             cpp 
+%FC                  mpiifort -c -fpp -fpp-name:/opt/software/eb/software/GCCcore/11.2.0/bin/cpp -Wp,-P,-traditional
+%PROD_FCFLAGS        -i4 -r8 -O3 -fp-model precise -fno-alias
+%DEBUG_FCFLAGS       -i4 -r8 -g -fp-trap=common -traceback  -fp-model precise -fno-alias
+%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 -Wl,--allow-multiple-definition
+%CFLAGS              -O0
+

arch/NOC/arch-X86_ARCHER2-Cray.fcm

@@ -44,8 +44,9 @@
 
 %CPP	             cpp -Dkey_nosignedzero
 %FC                  ftn
-%FCFLAGS             -em -s integer32 -s real64 -O0 -hflex_mp=intolerant -N1023
-%FFLAGS              -em -s integer32 -s real64 -O0 -hflex_mp=intolerant -N1023
+%PROD_FCFLAGS        -em -s integer32 -s real64 -O2 -hvector_classic -hflex_mp=intolerant -N1023 -M878
+%DEBUG_FCFLAGS       -em -s integer32 -s real64 -O0 -hvector_classic -hflex_mp=intolerant -N1023 -M878 -hfp0 -e mCI -G0 -m2 -rl -Rcdsp
+%FFLAGS              %FCFLAGS
 %LD                  CC -Wl,"--allow-multiple-definition"
 %FPPFLAGS            -P -traditional
 %LDFLAGS             -lmpifort_cray

arch/NOC/arch-X86_ARCHER2-Cray_DEBUG.fcm → arch/NOC/arch-X86_ARCHER2-Gnu_DEBUG.fcm

-# compiler options for Archer CRAY XC-30 (using crayftn compiler)
+# 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
@@ -32,7 +32,7 @@
 #
 %NCDF_HOME           $NETCDF_DIR
 %HDF5_HOME           $HDF5_DIR
-%XIOS_HOME           /work/n01/shared/nemo/xios-trunk
+%XIOS_HOME           /work/n01/shared/nemo/xios-trunk-gnu
 #OASIS_HOME          
 
 %NCDF_INC            -I%NCDF_HOME/include -I%HDF5_HOME/include
@@ -44,13 +44,13 @@
 
 %CPP	             cpp -Dkey_nosignedzero
 %FC                  ftn
-%FCFLAGS             -s real64 -s integer32 -Ovector0 -hfp0 -O0 -hflex_mp=intolerant -e mCI -G0 -m2 -rl -Rcdsp -N1023
-%FFLAGS              -s real64 -s integer32 -Ovector0 -hfp0 -O0 -hflex_mp=intolerant -e mCI -G0 -m2 -rl -Rcdsp -N1023
-%LD                  CC -Wl,"--allow-multiple-definition"
+%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             -lmpifort_cray
+%LDFLAGS             -lmpichf90
 %AR                  ar 
-%ARFLAGS             -r
+%ARFLAGS             rs
 %MK                  gmake
 %USER_INC            %XIOS_INC %NCDF_INC
 %USER_LIB            %XIOS_LIB %NCDF_LIB

arch/UKMO/arch-XC40_METO_IFORT_debug.fcm

+# compiler options for Archer CRAY XC-40 (using crayftn 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 $)
+#
+# This arch file depends on loading XIOS-PrgEnv/2.0/24708
+
+%NCDF_HOME           $NETCDF_DIR
+%HDF5_HOME           $HDF5_DIR
+%XIOS_HOME           $xios_path
+%OASIS_HOME          $prism_path
+
+%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 -lstdc++
+
+%OASIS_INC           -I%OASIS_HOME/build/lib/mct -I%OASIS_HOME/build/lib/psmile.MPI1
+%OASIS_LIBDIR        -L%OASIS_HOME/lib
+%OASIS_LIB           -lpsmile.MPI1 -lmct -lmpeu -lscrip
+
+%CPP                 cpp
+%FC                  ftn
+
+%FCFLAGS             -r8 -i4 -init=arrays,snan,huge -traceback -debug all -debug inline-debug-info -g -O0 -fp-model strict -check all,noarg_temp_created -fpe-all0 -ftz -ftrapuv
+%FFLAGS              %FCFLAGS
+%LD                  ftn
+%FPPFLAGS            -P -E -traditional-cpp
+%LDFLAGS             -hbyteswapio
+%AR                  ar
+%ARFLAGS             -r
+%MK                  gmake
+
+%USER_INC            %NCDF_INC %XIOS_INC
+%USER_LIB            %NCDF_LIB %XIOS_LIB 
+
+%CC                  cc
+%CFLAGS              -O0
+

arch/UKMO/arch-vdi_gfortran.fcm

+# generic gfortran compiler options for linux
+#
+# 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 $)
+#
+# =======================================================================================
+# The following envirnment was used to compile NEMO with this arch file on a UKMO VDI:
+#
+# module purge
+# module load libraries/gcc/6.4.0
+# module load gcc/6.4.0
+# module load mpi/mpich/3.2.1/gnu/6.4.0
+# module load hdf5/1.8.20/gnu/6.4.0
+# module load netcdf/4.6.1/gnu/6.4.0
+# module load xios/r1063/gnu/6.4.0
+# module list
+# export xios_path=/project/ukmo/rhel7/fortran/opt/gfortran/packages/gnu/6.4.0/xios/r1063
+# =======================================================================================
+
+%NCDF_HOME           $NETCDF_DIR
+%HDF5_HOME           $HDF5_DIR
+%XIOS_HOME           $xios_path
+
+%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 -c -cpp
+%FCFLAGS             -fdefault-real-8 -O3 -funroll-all-loops -fcray-pointer -ffree-line-length-none
+%FFLAGS              %FCFLAGS
+%LD                  mpif90
+%LDFLAGS             
+%FPPFLAGS            -P -traditional
+%AR                  ar
+%ARFLAGS             rs
+%MK                  make
+%USER_INC            %XIOS_INC %NCDF_INC
+%USER_LIB            %XIOS_LIB %NCDF_LIB
+
+%CC                  cc
+%CFLAGS              -O0

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
+%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
+%USER_INC            %XIOS_INC %NCDF_INC
+%USER_LIB            %XIOS_LIB %NCDF_LIB
 
 %CC                  cc
 %CFLAGS              -O0

arch/arch-linux_ifort.fcm

@@ -48,7 +48,7 @@
 %FFLAGS              %FCFLAGS
 %LD                  ftn
 %LDFLAGS             
-%FPPFLAGS            -P -C -traditional
+%FPPFLAGS            -P -traditional
 %AR                  ar
 %ARFLAGS             rs
 %MK                  gmake

arch/arch-linux_ifort_omp.fcm

@@ -20,7 +20,7 @@
 %FCFLAGS 	         -r8 -O3  -traceback -openmp
 %FFLAGS 	            -r8 -O3  -traceback -openmp
 %LD                  ifort
-%FPPFLAGS            -P -C -traditional
+%FPPFLAGS            -P -traditional
 %LDFLAGS
 %AR                  ar 
 %ARFLAGS             -r

arch/arch-linux_pgf90.fcm

@@ -21,7 +21,7 @@
 %FFLAGS              %FCFLAGS
 %LD                  pgf90
 %LDFLAGS
-%FPPFLAGS            -P -C -traditional
+%FPPFLAGS            -P -traditional
 %AR                  ar
 %ARFLAGS             -rs
 %MK                  gmake

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 +35,8 @@
 
 %CPP	             cpp -Dkey_nosignedzero 
 %FC	             mpif90 
-%FCFLAGS             -fdefault-real-8 -O3 -funroll-all-loops -fcray-pointer -ffree-line-length-none
+%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 -fallow-argument-mismatch 
 %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-2.5
-%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

arch/build_arch-auto.sh

+#!/bin/bash
+#
+set -u
+#
+#- Choice of the options ---
+#
+while [ $# -gt 0 ]
+do
+    case $( echo $1 | tr '[:upper:]' '[:lower:]' ) in
+	-h|--help) cat <<'EOF'
+
+Usage:
+------
+./build_arch-auto.sh
+
+
+build_arch-auto.sh should automatically find all necessary information by itself...
+However the following environment variables or their corresponding optional arguments can be used
+to force the default and automatic definition of the variables used by build_arch-auto.sh
+
+Environment variables that can be defined
+-----------------------------------------
+
+  NETCDF_C_prefix : prefix of the NetCDF-C library ($NCDF_F_PREFIX/lib) and include ($NCDF_C_PREFIX/include)
+	     - set it to "no" if you don't want to use NetCDF library
+	     - if not defined : we use "nc-config --prefix"
+  	     Can also be specified with the optional argument --NETCDF_C_prefix
+
+  NETCDF_F_prefix : prefix of the NetCDF-Fortran library ($NCDF_F_PREFIX/lib) and include ($NCDF_F_PREFIX/include)
+	     - if not defined : we use "nf-config --prefix"
+	     - if nf-config not found : we use "nc-config  --flibs" to find it
+	     - not used if NETCDF_C_prefix="no"
+  	     Can also be specified with the optional argument --NETCDF_F_prefix
+
+  HDF5_prefix : prefix of the HFD5 library ($HDF5_PREFIX/lib)
+	     - if not defined : we use "nc-config  --cflags" and "h5pcc -showconfig" to find it
+	     - not used if NETCDF_C_prefix="no"
+  	     Can also be specified with the optional argument --HDF5_prefix
+
+  XIOS_prefix : prefix of the XIOS library ($XIOS_PREFIX/lib) and include ($XIOS_PREFIX/inc)
+  	     Can also be specified with the optional argument --XIOS_prefix
+
+  OASIS_prefix : prefix of the OASIS library ($OASIS_PREFIX/lib) and
+	     include ($OASIS_PREFIX/build/lib/mct and $OASIS_PREFIX/build/lib/psmile.MPI1)
+  	     Can also be specified with the optional argument --OASIS_prefix
+
+  PSYCLONE_prefix : path to a PSyclone installation; also configurable with argument '--PSYCLONE_prefix <path>'
+
+  LIBMpath : path of the m library (standard C library of basic mathematical functions)
+  	     Can also be specified with the optional argument --LIBMpath
+
+  CURLpath : path of the curl library
+  	     Can also be specified with the optional argument --CURLpath
+
+  ZLIBpath : path of the z library
+  	     Can also be specified with the optional argument --ZLIBpath
+
+  FCnemo : fortran compiler
+  	   Can also be specified with the optional argument --FCnemo
+
+  CCnemo : C compiler (used only for AGRIF conv)
+  	   Can also be specified with the optional argument --CCnemo
+
+  CPPnemo : cpp compiler
+  	    Can also be specified with the optional argument --CPPnemo
+
+  MKnemo : make 
+  	   Can also be specified with the optional argument --MKnemo
+
+  ARnemo : archiver
+           Can also be specified with the optional argument --ARnemo
+
+EOF
+	   exit 0 ;;
+
+	--netcdf_c_prefix) NETCDF_C_prefix=${2} ; shift ;;
+	--netcdf_f_prefix) NETCDF_F_prefix=${2} ; shift ;;
+	--hdf5_prefix)     HDF5_prefix=${2}     ; shift ;;
+	--xios_prefix)     XIOS_prefix=${2}     ; shift ;;
+	--oasis_prefix)    OASIS_prefix=${2}    ; shift ;;
+	--psyclone_prefix) PSYCLONE_prefix=${2} ; shift ;;
+	--libmpath)        LIBMpath=${2}        ; shift ;;
+	--curlpath)        CURLpath=${2}        ; shift ;;
+	--zlibpath)        ZLIBpath=${2}        ; shift ;;
+	--fcnemo)          FCnemo=${2}          ; shift ;;
+	--ccnemo)          CCnemo=${2}          ; shift ;;
+	--cppnemo)         CPPnemo=${2}         ; shift ;;
+	--mknemo)          MKnemo=${2}          ; shift ;;
+	--arnemo)          ARnemo=${2}          ; shift ;;
+	
+	*) echo -e "\033[0;31m\nERROR: \"$1\" BAD OPTION\033[0m\n"
+	   exit 2 ;;
+    esac
+    
+    shift
+done
+#
+#-----------------------------------------------------
+#
+echo_red () {
+    echo
+    while [ $# -gt 0 ] ; do echo -e "\033[0;31m$1\033[0m" ; shift ; done
+}
+
+echo_green () {
+    echo
+    while [ $# -gt 0 ] ; do echo -e "\033[0;32m$1\033[0m" ; shift ; done
+}
+#
+echo_orange () {
+    echo
+    while [ $# -gt 0 ] ; do echo -e "\033[0;33m$1\033[0m" ; shift ; done
+}
+#
+# check the exit status of which 
+err_which () { which ${1} > /dev/null 2>&1 ; echo $? ; }
+#
+# call err_which and print and error message
+chk_which () {
+    if [ $( err_which ${!1} ) -ne 0 ]
+    then
+	echo_red "ERROR: ${2^} ${!1} not found." \
+		 "       please define your ${2,} path with 'export $1=...'"
+	exit 1
+    fi
+}
+#
+# find fortran wrapper
+find_fortran_wrapper () {
+    if   [ $( err_which mpiifort ) -eq 0 ] ; then FCnemo=mpiifort
+    elif [ $( err_which mpif90   ) -eq 0 ] ; then FCnemo=mpif90
+    elif [ $( err_which ftn      ) -eq 0 ] ; then FCnemo=ftn
+    else
+	echo_red "ERROR: we found neither \"mpiifort\" nor \"mpif90\" nor \"ftn\"." \
+		 "       please define your fortran compiler path with 'export FCnemo=...'"
+	exit 1
+    fi
+}
+# find the fortran compiler associated with the fortran wrapper $FCnemo
+find_fortran_compiler () {
+    if   [ $( $FCnemo --version | head -n 1 | grep -ci "\(gcc\|gnu\)" ) -eq 1 ] ; then ftncomp="gnu"
+    elif [ $( $FCnemo --version | head -n 1 | grep -ci        "ifort" ) -eq 1 ] ; then ftncomp="intel"
+    elif [ $( $FCnemo --version | head -n 1 | grep -ci "Cray Fortran" ) -eq 1 ] ; then ftncomp="cray"
+    else
+	echo_red "ERROR: the fortran wrapper $FCnemo does not correspond to the gnu, the intel or the cray compiler" \
+		 "       please use one of these compilers or add your compiler in $0"
+	exit 1
+    fi
+}
+#
+#-----------------------------------------------------
+# NetCDF
+#-----------------------------------------------------
+#
+NETCDF_C_prefix=${NETCDF_C_prefix:-notdef}
+NETCDF_F_prefix=${NETCDF_F_prefix:-notdef}
+if [ "$NETCDF_C_prefix" == "no" ]
+then
+    echo_orange "WARNING: You chose to compile without any NetCDF Library" \
+		"     1)  You must use --nonetcdf when calling makenemo" \
+		"     2)  You won't be able to read/write any input/output file when running nemo" \
+		"         -> You can run only the BENCH test" \
+		"     3)  You can neither use XIOS nor OASIS" \
+    
+    NETCDF_F_prefix=no
+    HDF5_prefix=no
+    XIOS_prefix=no
+    OASIS_prefix=no
+    NCDF_INC=""
+    NCDF_LIB=""
+    XIOS_INC=""
+    XIOS_LIB=""    
+    OASIS_INC=""
+    OASIS_LIB=""
+else
+    # find NETCDF_C_prefix and NC_CONFIG
+    if [ "$NETCDF_C_prefix" == "notdef" ]              # use nc-config to define NETCDF_C_prefix
+    then
+	if [ $( err_which nc-config ) -ne 0 ]          # nc-config not found in $PATH
+	then
+	    echo_red "ERROR: nc-config not found." \
+		     "       please define either your path to the NetCDF-C library with 'export NETCDF_C_prefix=...'" \
+		     "       or specify you don't want to use NetCDF with 'export NETCDF_C_prefix=no'" \
+	    exit 2
+	fi    
+       	NC_CONFIG=nc-config
+	NETCDF_C_prefix=$( $NC_CONFIG --prefix  )
+    else                                               # use NETCDF_C_prefix to define NC_CONFIG
+	NC_CONFIG=$NETCDF_C_prefix/bin/nc-config       # assume that nc-config is in $NETCDF_C_prefix/bin
+	nbok=$( ls $NC_CONFIG 2>/dev/null | wc -l )    # check if we have nc-config
+	if [ $nbok -eq 0 ]
+	then
+	    echo_red "ERROR: nc-config not found in $NETCDF_C_prefix/bin" ; exit 2
+	fi
+    fi
+
+    # find NETCDF_F_prefix and NF_CONFIG
+    if [ "$NETCDF_F_prefix" == "notdef" ]              # use nf-config to define NETCDF_F_prefix
+    then
+	if [ $( err_which nf-config ) -ne 0 ]          # nf-config not found in $PATH
+	then
+	    NF_CONFIG=${NC_CONFIG/nc-config/nf-config} # try to find nf-config at the same place than nc-config
+	    if [ $( err_which $NF_CONFIG ) -ne 0 ]     # nf-config not located at the same place than nc-config
+	    then
+		if [ "$( $NC_CONFIG --all | grep -c "has-fortran" )" -gt 0 ]  # we can use nc-config instead of nf-config?
+		then
+		    # do we have NetCDF-Fortran?
+		    if [ "$( $NC_CONFIG --has-fortran )" != "yes" ]
+		    then
+			echo_red "ERROR: no netcdf-fortran " ; exit 2
+		    fi
+		    NF_CONFIG=$NC_CONFIG   # use nc-config instead of nf-config
+		    #                        define NETCDF_F_prefix with nc-config
+		    NETCDF_F_prefix=$( $NF_CONFIG --flibs | sed -e "s/.*\(-L\|-rpath,\)\([^ ]*\)\/lib  *-lnetcdff.*/\2/" )
+		    [ -z $NETCDF_F_prefix ] && NETCDF_F_prefix=$NETCDF_C_prefix   # empty -> we try NETCDF_C_prefix
+		else
+		    echo_red "ERROR: nf-config not found." \
+			     "       please define either your path to the NetCDF-Fortran library with 'export NETCDF_F_prefix=...'" \
+			     "       or specify you don't want to use NetCDF with 'export NETCDF_C_prefix=no'" \
+			     exit 2
+		fi
+	    else
+		NETCDF_F_prefix=$( $NF_CONFIG --prefix  )   # use nf-config to define NETCDF_F_prefix
+	    fi
+	else
+       	    NF_CONFIG=nf-config
+	    NETCDF_F_prefix=$( $NF_CONFIG --prefix  )   # use nf-config to define NETCDF_F_prefix
+	fi
+    else
+	NF_CONFIG=$NETCDF_F_prefix/bin/nf-config   # assume that nf-config is in $NETCDF_F_prefix/bin
+	nbok=$( ls $NF_CONFIG 2>/dev/null | wc -l )   # check if we have nf-config
+	if [ $nbok -eq 0 ]
+	then
+	    echo_red "ERROR: nf-config not found in $NETCDF_F_prefix/bin" ; exit 2
+	fi
+    fi
+
+    # do we have the proper path to the netcdf library?
+    nbok=$( ls $NETCDF_C_prefix/lib/libnetcdf* 2>/dev/null | wc -l )
+    if [ $nbok -eq 0 ]
+    then
+	echo_red "ERROR: netcdf library not found in $NETCDF_C_prefix/lib" ; exit 2
+    else
+	echo_green "NETCDF_C_prefix=$NETCDF_C_prefix"
+    fi
+
+    # do we have NetCDF-F90 interface?
+    if [ "$( $NF_CONFIG --has-f03 )" != "yes" ]
+    then
+	if [ "$( $NF_CONFIG --has-f90 )" != "yes" ]
+	then
+	    echo_red "ERROR: no netcdf-fortran F90 interface" ; exit 2
+	fi
+    fi
+  
+    # do we have the proper path to the netcdff library?
+    nbok=$( ls $NETCDF_F_prefix/lib/libnetcdff* 2>/dev/null | wc -l )
+    if [ $nbok -eq 0 ]
+    then
+	echo_red "ERROR: netcdff library not found in $NETCDF_F_prefix/lib" ; exit 2
+    else
+        echo_green "NETCDF_F_prefix=$NETCDF_F_prefix"
+    fi
+
+    # do we have nc4?
+    if [ "$( $NC_CONFIG --has-nc4 )" != "yes" ]
+    then
+	echo_red "ERROR: no nc4 interface in your netcdf library" ; exit 2
+    fi
+    
+    # do we have hdf5?
+    if [ "$( $NC_CONFIG --has-hdf5 )" != "yes" ]
+    then
+	echo_red "ERROR: no hdf5 interface in your netcdf library" ; exit 2
+    fi
+    
+    HDF5_prefix=${HDF5_prefix:-notdef}
+    if [ "$HDF5_prefix" == "notdef" ]
+    then
+	# look for libhdf5 in the paths found in nc-config --cflags
+	for dd in $( $NC_CONFIG --cflags | sed -e "s/-I//g" )
+	do
+	    nbok=$( ls $dd/../lib/libhdf5* 2>/dev/null | wc -l )
+	    [ $nbok -gt 0 ] && HDF5_prefix=$( dirname $dd )
+	done
+    fi
+    if [ "$HDF5_prefix" == "notdef" ]   # not found any libhdf5 file... try "h5pcc -showconfig"
+    then
+	if [ $( err_which h5pcc ) -eq 0 ]   # do we have h5pcc?
+	then
+	    HDF5_prefix=$( h5pcc -showconfig | grep "Installation point" | sed -e "s/.*: //" )
+	    [ -z $HDF5_prefix ] && HDF5_prefix=notdef # empty -> back to "notdef"
+	fi
+    fi
+    if [ "$HDF5_prefix" == "notdef" ]   # still not found any libhdf5 file... try $NETCDF_C_prefix
+    then
+	nbok=$( ls $NETCDF_C_prefix/lib/libhdf5* 2>/dev/null | wc -l )
+	[ $nbok -gt 0 ] && HDF5_prefix=$NETCDF_C_prefix
+    fi
+    if [ "$HDF5_prefix" == "notdef" ]   # still not found any libhdf5 file...
+    then
+	echo_red "ERROR: HDF5_prefix not found." \
+		 "       please define it with 'export HDF5_prefix=...'" ; exit 2
+    fi
+    
+    # do we have the proper path to the hdf5 library?
+    nbok=$( ls $HDF5_prefix/lib/libhdf5* 2>/dev/null | wc -l )
+    if [ $nbok -eq 0 ]
+    then
+	echo_red "ERROR: hdf5 library not found in $HDF5_prefix/lib" ; exit 2
+    else
+	echo_green "HDF5_prefix=$HDF5_prefix"
+    fi
+    
+    # do we have netcdf parallel?
+    if [ "$( $NC_CONFIG --has-parallel )" != "yes" ]
+    then
+	echo_orange "WARNING: your netcdf library cannot write in parallel" \
+		    "         you can use only 'the one_file' mode in XOS"
+    fi
+    if [ $( err_which h5pcc ) -eq 0 ]
+    then
+	if [ $( h5pcc -showconfig | grep "Parallel HDF5" | grep -c yes ) -ne 1 ]
+	then
+	    echo_orange "WARNING: your hdf5 library was configured without --enable-parallel" \
+			"         you cannot use only the 'one_file' mode in XOS"
+	fi
+    fi
+    
+    # curl
+    CURLpath=${CURLpath:-notdef}
+    if [ "$( $NC_CONFIG --dap )" == "yes" ]
+    then
+	if [ "$CURLpath" == "notdef" ]
+	then
+	    if [ $( err_which curl ) -eq 0 ]
+	    then
+		CURLpath="-L$( dirname $( ls -1 $( dirname $( dirname $( which curl ) ) )/*/libcurl* | head -n 1 ) )"
+		echo_green "CURLpath=$CURLpath"
+	    else
+		CURLpath=""
+	    fi    
+	fi
+	CURLlib="${CURLpath:-""} -lcurl"
+    else
+	CURLlib=""
+    fi
+    
+    # Zlib: compression library
+    Zlib="${ZLIBpath:-""} -lz"
+
+    # libM: standard C library of basic mathematical functions
+    libM="${LIBMpath:-""} -lm"
+    
+    # NCDF_INC and NCDF_LIB
+    NCDF_INC="-I%NCDF_F_PREFIX/include -I%NCDF_C_PREFIX/include"
+    #NCDF_LIB="-L%NCDF_F_PREFIX/lib -lnetcdff -L%NCDF_C_PREFIX/lib -lnetcdf -Wl,-rpath,%NCDF_F_PREFIX/lib -L%HDF5_PREFIX/lib -lhdf5_hl -lhdf5 $CURLlib $Zlib $libM -Wl,-rpath,%HDF5_PREFIX/lib"
+    NCDF_LIB="-L%NCDF_F_PREFIX/lib -lnetcdff -L%NCDF_C_PREFIX/lib -lnetcdf -L%HDF5_PREFIX/lib -lhdf5_hl -lhdf5 $CURLlib $Zlib $libM"
+
+fi
+#
+#-----------------------------------------------------
+# fortran Compileur
+#-----------------------------------------------------
+#
+nompi=0 # default
+FCnemo=${FCnemo:-notdef}
+if [ "$FCnemo" == "notdef" ]
+then
+    if [ "$NETCDF_C_prefix" == "no" ]
+    then
+	find_fortran_wrapper
+    else
+	FCnemo=$( $NF_CONFIG --fc ) # use nf-config to find the fortran compiler
+	[ -z $FCnemo ] && find_fortran_wrapper # if $FCnemo is empty try to find it...
+	chk_which FCnemo "fortran compiler"
+
+	# does the fortran compiler start with the 3 letters mpi or ftn
+	ismpi=$( basename $FCnemo | cut -c 1-3 | grep -Ec 'mpi|ftn' )
+	if [ $ismpi -eq 0 ]
+	then
+	    echo_orange "WARNING: the fortran compiler provided by $( basename $NF_CONFIG ), \"$FCnemo\", is not starting with \"mpi\" or \"ftn\"." \
+			"         we look for mpiifort, mpif90 or ftn..."
+	    FCnemo_org=$FCnemo
+	    find_fortran_compiler
+	    ftncomp_org=$ftncomp
+	    find_fortran_wrapper
+	    find_fortran_compiler
+	    if [ "$ftncomp" != "$ftncomp_org" ]
+	    then
+		echo_red "ERROR: \"$FCnemo\" and \"$FCnemo_org\" are refering to different compilers: \"$ftncomp\" and \"$ftncomp_org\"" \
+			 "       please define your fortran compiler path with 'export FCnemo=...'"
+		exit 1
+	    fi
+	fi
+    fi
+else
+    ismpi=$( basename $FCnemo | cut -c 1-3 | grep -Ec 'mpi|ftn' ) # the fortran compiler does not start with mpi or ftn...
+    if [ $ismpi -eq 0 ]
+    then
+	echo_orange "WARNING: the fortran compiler you provided does not start with mpi or ftn." \
+		    "         you must compile nemo with key_mpi_off and you cannot run nemo in parallel"
+	nompi=1
+    fi
+fi
+echo_green "FCnemo=$FCnemo"
+
+find_fortran_compiler
+#
+#-----------------------------------------------------
+# C Compileur (not critical, needed only for the conv of AGRIF)
+#-----------------------------------------------------
+#
+# first guess
+case "$ftncomp" in
+    intel) guess=${CCnemo:-icc}	;;
+    gnu)   guess=${CCnemo:-gcc}	;;
+    cray)  guess=${CCnemo:-cc}	;;
+    *)     guess=${CCnemo:-""}	;;
+esac
+listcc="$guess gcc cc icc"  # try $guess and other usuals C compilers... 
+CCnemo="notfound"
+for ii in $listcc
+do
+    [ $( err_which $ii ) -eq 0 ] && [ "$CCnemo" == "notfound" ] && CCnemo=$ii
+done
+if [ "$CCnemo" == "notfound" ]
+then
+    echo_red "ERROR: we found neither \"gcc\" nor \"icc\" nor \"cc\"." \
+	     "       please define your C compiler with 'export CCnemo=...'"
+    exit 1
+fi
+#
+#-----------------------------------------------------
+# CPP
+#-----------------------------------------------------
+#
+CPPnemo=${CPPnemo:-cpp}
+chk_which CPPnemo "pre-compiler"
+echo_green "CPPnemo=$CPPnemo"
+
+[ "$ftncomp" == "gnu" ] || [ "$ftncomp" == "cray" ] && CPPnemo="$CPPnemo -Dkey_nosignedzero"
+[ $nompi     -eq  1   ] && CPPnemo="$CPPnemo -Dkey_mpi_off"
+#
+#-----------------------------------------------------
+# FCFLAGS
+#-----------------------------------------------------
+#
+case "$ftncomp" in
+    intel)
+	PROD_FCFLAGS="-i4 -r8 -O3 -fp-model strict -xHost -fno-alias"
+	DEBUG_FCFLAGS="-i4 -r8 -g -O0 -debug all -traceback -fp-model strict -ftrapuv -check all,noarg_temp_created -fpe-all0 -ftz -init=arrays,snan,huge"
+	echo_orange "WARNING: We assume you will execute NEMO on the same machine you compiled it. " \
+		    "         If it is not the case, replace -xHost by the appropiate option in PROD_FCFLAGS"
+	;;
+    gnu)
+	PROD_FCFLAGS="-fdefault-real-8 -march=native -O2 -fno-expensive-optimizations -funroll-all-loops -fcray-pointer -ffree-line-length-none"
+	DEBUG_FCFLAGS="-fdefault-real-8 -Og -g -fbacktrace -funroll-all-loops -fcray-pointer -ffree-line-length-none -fcheck=all -finit-real=nan -ffpe-trap=invalid,zero,overflow -ffpe-summary=invalid,zero,overflow"
+	rev=$( $FCnemo --version | head -n 1 | sed -e "s/.* \([0-9]*\).*/\1/" )
+	# if gfortran version >= 10 : add -fallow-argument-mismatch 
+	if [ $rev -ge 10 ]
+	then
+	    PROD_FCFLAGS="$PROD_FCFLAGS -fallow-argument-mismatch" 
+	    DEBUG_FCFLAGS="$DEBUG_FCFLAGS -fallow-argument-mismatch"
+	fi
+	echo_orange "WARNING: We assume you will execute NEMO on the same machine you compiled it. " \
+		    "         If it is not the case, replace -march=native by the appropiate option in PROD_FCFLAGS"
+	;;
+    cray)
+	PROD_FCFLAGS="-em -s real64 -s integer32 -O2 -hvector_classic -hflex_mp=intolerant -N1023 -M878"
+	DEBUG_FCFLAGS="-s real64 -s integer32 -O0 -hvector_classic -hflex_mp=intolerant -N1023 -M878 -hfp0 -e mCI -G0 -m2 -rl -Rcdsp"
+	;;
+    *)
+	echo_red "ERROR: compilation options for $ftncomp are not defined..."
+	exit 1
+	;;
+esac
+#
+#-----------------------------------------------------
+# CFLAGS
+#-----------------------------------------------------
+#
+case "${ftncomp}" in
+    gnu)
+        PROD_CFLAGS="-O0 -fcommon"
+        ;;
+    *)
+        PROD_CFLAGS="-O0"
+        ;;
+esac
+#
+#-----------------------------------------------------
+# XIOS and OASIS
+#-----------------------------------------------------
+#
+if [ "$NETCDF_C_prefix" != "no" ]
+then
+
+    # XIOS
+    XIOS_prefix=${XIOS_prefix:-notdef}
+    if [ "$XIOS_prefix" == "notdef" ]
+    then
+	echo_orange "WARNING: XIOS_prefix not specified" \
+		    "         either define it with 'export XIOS_prefix=...'" \
+ 		    "         or don't use key_xios when compiling nemo (-> you will not be able to use XIOS)."
+	XIOS_INC=""
+	XIOS_LIB=""
+    else
+	XIOS_INC="-I%XIOS_PREFIX/inc"
+	#XIOS_LIB="-L%XIOS_PREFIX/lib -lxios -lstdc++ -Wl,-rpath,%XIOS_PREFIX/lib"
+	XIOS_LIB="-L%XIOS_PREFIX/lib -lxios -lstdc++"
+    fi
+
+    # OASIS
+    OASIS_prefix=${OASIS_prefix:-notdef}
+    if [ "$OASIS_prefix" == "notdef" ]
+    then
+	echo_orange "WARNING: OASIS_prefix not specified" \
+		    "         either define it with 'export OASIS_prefix=...'" \
+		    "         or don't use key_oasis3 when compiling nemo (-> you will not be able to run coupled simulations)."
+	OASIS_INC=""
+	OASIS_LIB=""
+    else
+	OASIS_INC="-I%OASIS_PREFIX/build/lib/mct -I%OASIS_PREFIX/build/lib/psmile.MPI1"
+	OASIS_LIB="-L%OASIS_PREFIX/lib -lpsmile.MPI1 -lmct -lmpeu -lscrip"    
+    fi
+fi
+#
+#-----------------------------------------------------
+# PSyclone
+#-----------------------------------------------------
+#
+PSYCLONE_prefix=${PSYCLONE_prefix:-notdef}
+if [ "${PSYCLONE_prefix}" == "notdef" ]; then
+    if [ $( err_which psyclone ) -eq 0 ]; then
+        PSYCLONE_cmd=`which psyclone`
+        PSYCLONE_prefix=${PSYCLONE_cmd%/bin/psyclone}
+        if [ "${PSYCLONE_prefix}/bin/psyclone" == "${PSYCLONE_cmd}" ]; then
+            echo_green "PSYCLONE_prefix=${PSYCLONE_prefix}"
+        else
+            PSYCLONE_prefix="notdef"
+        fi
+    fi
+fi
+if [ "${PSYCLONE_prefix}" == "notdef" ]; then
+    echo_orange "WARNING: PSYCLONE_prefix is not specified (only required for PSyclone processing)"
+fi
+#
+#-----------------------------------------------------
+#   make
+#-----------------------------------------------------
+#
+MKnemo=${MKnemo:-make}
+mkerr=$( err_which make )
+gmkerr=$( err_which gmake )
+
+if [ $( err_which $MKnemo ) -ne 0 ]   # no make found
+then
+    if [ $mkerr -eq 0 ]   # make found
+    then
+	echo_orange "WARNING: $MKnemo not found, we switch to make"
+	MKnemo=make
+    else
+	if [ $gmkerr -ne 0 ]   # gmake found
+	then
+	    echo_orange "WARNING: $MKnemo not found, we switch to gmake"
+	    MKnemo=gmake
+	else
+	    echo_red "ERROR: gnu make not found, please define its path with 'export MKnemo=...'"
+	    exit 1
+	fi
+    fi
+fi
+#
+isgnu=$( $MKnemo --version | head -n 1 | grep -ic gnu )   # make is gmake
+if [ $isgnu -ne 1 ]
+then
+    if [ $gmkerr -ne 0 ]   # gmake found
+    then
+	echo_orange "WARNING: $MKnemo is not gnu make, we switch to gmake"
+	MKnemo=gmake
+    else
+	echo_red "ERROR: $MKnemo is not gnu make and gmake not found." \
+		 "       please define gnu make path with 'export MKnemo=...'"
+	exit 1
+    fi
+fi
+echo_green "MKnemo=$MKnemo"
+#
+#-----------------------------------------------------
+# ar command
+#-----------------------------------------------------
+#
+ARnemo=${ARnemo:-ar}
+chk_which ARnemo "archiver"
+echo_green "ARnemo=$ARnemo"
+#
+#
+#-----------------------------------------------------
+#-----------------------------------------------------
+# write arch file
+#-----------------------------------------------------
+#-----------------------------------------------------
+#
+#
+archname=arch-auto.fcm
+cat > $archname << EOF
+#
+# This arch file was automatically created by $0
+# $( date ) 
+#
+%NCDF_C_PREFIX       $NETCDF_C_prefix
+%NCDF_F_PREFIX       $NETCDF_F_prefix
+%HDF5_PREFIX         $HDF5_prefix
+%XIOS_PREFIX         $XIOS_prefix
+%OASIS_PREFIX        $OASIS_prefix
+%PSYCLONE_HOME       $PSYCLONE_prefix
+
+%NCDF_INC            $NCDF_INC
+%NCDF_LIB            $NCDF_LIB
+%XIOS_INC            $XIOS_INC
+%XIOS_LIB            $XIOS_LIB
+%OASIS_INC           $OASIS_INC
+%OASIS_LIB           $OASIS_LIB
+
+%CPP	             $CPPnemo
+%FC                  $FCnemo 
+%PROD_FCFLAGS        $PROD_FCFLAGS
+%DEBUG_FCFLAGS       $DEBUG_FCFLAGS
+%FFLAGS              %FCFLAGS
+%LD                  %FC
+%LDFLAGS             -Wl,-rpath,%HDF5_PREFIX/lib -Wl,-rpath,%NCDF_F_PREFIX/lib -Wl,-rpath,%XIOS_PREFIX/lib
+%FPPFLAGS            -P -traditional
+%AR                  $ARnemo
+%ARFLAGS             rs
+%MK                  $MKnemo
+%USER_INC            %XIOS_INC %OASIS_INC %NCDF_INC
+%USER_LIB            %XIOS_LIB %OASIS_LIB %NCDF_LIB
+
+%CC                  $CCnemo
+%CFLAGS              $PROD_CFLAGS
+EOF
+#
+# Additional module search command for Cray Fortran to enable successful parallel builds
+if [ $ftncomp == "cray" ] ; then
+    echo "bld::tool::fc_modsearch -J" >> $archname
+fi
+#
+echo
+echo "Content of the created $archname:"
+echo "-------------------------------------"
+echo
+cat $archname
+echo

arch/misc/arch-X64_BULL.fcm

@@ -20,7 +20,7 @@
 %FFLAGS              %FCFLAGS
 %LD                  scorep-mpiifort
 %LDFLAGS             -lstdc++
-%FPPFLAGS            -P -C -traditional -std=c99
+%FPPFLAGS            -P -traditional -std=c99
 %AR                  ar
 %ARFLAGS             rs
 %MK                  gmake

cfgs/AGRIF_DEMO/EXPREF/1_context_nemo.xml

@@ -4,7 +4,7 @@
 ============================================================================================== 
 -->
 <context id="nemo">
-    <!-- $id$ -->
+
     <variable_definition>
        <!-- Year/Month/Day of time origin for NetCDF files; defaults to 1800-01-01 -->
        <variable id="ref_year"  type="int"> 1900 </variable>
@@ -24,10 +24,8 @@
     <field_definition src="./field_def_nemo-pisces.xml"/>   <!--  NEMO ocean biogeochemical                      -->
     <field_definition src="./field_def_nemo-innerttrc.xml"/> <!--  NEMO ocean inert passive tracer           -->
 
-
 <!-- 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 -->
@@ -38,6 +36,5 @@
 
 <!-- Grids definition -->
     <grid_definition   src="./grid_def_nemo.xml"/>
-  
 
 </context>

cfgs/AGRIF_DEMO/EXPREF/1_namelist_cfg

@@ -10,7 +10,6 @@
 !!   namcfg       parameters of the configuration                       (default: user defined GYRE)
 !!   namwad       Wetting and drying                                    (default: OFF)
 !!   namtsd       data: temperature & salinity                          (default: OFF)
-!!   namcrs       coarsened grid (for outputs and/or TOP)               (ln_crs =T)
 !!   namc1d       1D configuration options                              (ln_c1d =T)
 !!   namc1d_dyndmp 1D newtonian damping applied on currents             (ln_c1d =T)
 !!   namc1d_uvd   1D data (currents)                                    (ln_c1d =T)
@@ -27,9 +26,8 @@
 !-----------------------------------------------------------------------
 &namdom        !   time and space domain
 !-----------------------------------------------------------------------
-   ln_linssh   = .false.   !  =T  linear free surface  ==>>  model level are fixed in time
-   !
-   rn_Dt      = 5400.     !  time step for the dynamics and tracer
+!MLF   rn_Dt      = 5400.     !  time step for the dynamics and tracer
+   rn_Dt      = 10800.    !  time step for the dynamics and tracer
    ln_meshmask = .false.  !  =T create a mesh file
 /
 !-----------------------------------------------------------------------
@@ -85,7 +83,7 @@
                      ! 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 : 
@@ -273,8 +271,6 @@
       !                           !  time invariant coefficients:  aei0 = 1/2  Ue*Le 
       rn_Ue        = 0.03              !  lateral diffusive velocity [m/s] (nn_aht_ijk_t= 0, 10, 20, 30)
       rn_Le        = 200.e+3           !  lateral diffusive length   [m]   (nn_aht_ijk_t= 0, 10)
-      !
-      ln_ldfeiv_dia =.true.   ! diagnose eiv stream function and velocities
 /
 !-----------------------------------------------------------------------
 &namtra_dmp    !   tracer: T & S newtonian damping                      (default: OFF)
@@ -318,6 +314,10 @@
 &namdyn_spg    !   surface pressure gradient                            (default: NO selection)
 !-----------------------------------------------------------------------
    ln_dynspg_ts  = .true.  !  split-explicit free surface
+!MLF      nn_bt_flt     = 1          ! Time filtering with nn_e width boxcar averaging
+!MLF      rn_bt_alpha   = 0.         ! Dissipative Forward Backward parameter
+      nn_bt_flt     = 3          ! Time filtering with dissipative Forward Backward
+      rn_bt_alpha   = 0.09       ! Dissipative Forward Backward parameter
 /
 !-----------------------------------------------------------------------
 &namdyn_ldf    !   lateral diffusion on momentum                        (default: NO selection)
@@ -361,17 +361,18 @@
 !-----------------------------------------------------------------------
 &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  ***                   !!
 !!                                                                    !!
 !!   namtrd       dynamics and/or tracer trends                         (default: OFF)
-!!   namhsb       Heat and salt budgets                                 (default: OFF)
 !!   namdiu       Cool skin and warm layer models                       (default: OFF)
 !!   namdiu       Cool skin and warm layer models                       (default: OFF)
-!!   namflo       float parameters                                      (default: OFF)
 !!   nam_diadct   transports through some sections                      (default: OFF)
-!!   nam_dia25h   25h Mean Output                                       (default: OFF)
 !!   namnc4       netcdf4 chunking and compression settings             ("key_netcdf4")
 !!======================================================================
 !