Install dependencies

Install dependencies from package repository

Under Ubuntu 14.04

sudo apt-get install libnetcdf-dev netcdf-bin libopenmpi-dev gfortran build-essential

Install dependencies from source

Intel compilers under Linux in general, and nic4 in particular

• download zlib, szlib, hdf5, netcdf4 and netcdf-fortran libraries
• install them all in the directory of your choice using configure --prefix=/my/directory, then make, then make install.
• I found that parallel compilation (make -j) sometimes fails while a simple make will work.

For hdf5, don't forget to configure using --with-zlib=/my/directory --with-szip=/my/directory --enable-parallel For netcdf4, don't forget to configure using --enable-netcdf-4.

I found that xios-1.0 does NOT like the couple netcdf-4.4.4 -- hdf5 1.10. I had to revert to hdf5 1.8.2, netcdf 4.3.2 and netcdf-fortran 4.4.3. Don't forget to set the environment variables CC, FC, F77, LDFLAGS, CFLAGS, FCFLAGS, FFLAGS. For the 3 last ones, I used -fPIC (for hdf5 AND netcdf4 AND netcdf-fortran). Without fPIC netcdf wouldn't compile.

Still, some netcdf-fortran make check test would NOT pass, but the library works and is used for nco tools, gher tools, gher model, xios and nemo, all without errors.

XIOS 1

cd src
svn co -r 703 http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-1.0 xios-1.0
cd xios-1.0/
./make_xios --arch GCC_LINUX --netcdf_lib netcdf4_seq

If you installed the parallel version of hdf5 and netcdf4, then you don't need the last option in the make_xios command

NEMO

In /home/abarth/src/NEMOGCM/ARCH/OLD/arch-gfortran_linux.fcm

%XIOS_HOME           /home/abarth/src/xios-1.0
%XIOS_INC            -I%XIOS_HOME/inc 
%XIOS_LIB            -L%XIOS_HOME/lib -lxios
%NCDF_INC            -I/usr/include
%NCDF_LIB            -L/usr/lib -lnetcdff -lnetcdf
%FC	             mpif90
%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                  gmake
%USER_INC            %XIOS_INC %NCDF_INC
%USER_LIB            %XIOS_LIB %NCDF_LIB  -lstdc++ -lmpi_cxx
%CPP            cpp
%CC                  cc
%CFLAGS              -O0

Generate the NEMO configuration

The following command creates the NEMO configuration and compiles the code:

cd CONFIG
./makenemo -m gfortran_linux -r GYRE -n MY_GYRE add_key "key_iomput key_mpp_mpi"

Recompilation

If you modify the Fortran sources, you can recompile NEMO with:

./makenemo

Clear configuration

./makenemo -m gfortran_linux -r GYRE -n MY_GYRE clean_config

Run NEMO

cd CONFIG/GYRE/EXP00
mpirun ./opa 

Troubleshooting

• Many Perl warnings:

Use of uninitialized value in uc at /home/abarth/src/NEMOGCM-git/EXTERNAL/fcm/bin/../lib/Fcm/CfgFile.pm line 234.

They do not seem to be of any consequence.

• CPP error message

Can't exec "%CPP": No such file or directory at /home/abarth/src/NEMOGCM/EXTERNAL/fcm/bin/../lib/Fcm/Util.pm line 454.

add the C preprocessor in arch-gfortran_linux.fcm

%CPP            cpp

• Long Fortran lines

4,num_fields), zfoldwk(jpi,4,num_fields), znorthgloio(jpi,4,num_fields,jpni
                                                                           1
Error: Invalid form of array reference at (1)

use -ffree-line-length-none as compiler option

• time_origin key

Error message: $ mpirun ./opa

Error [CAttributeMap::operator[](const StdString& key)] : In file '/home/abarth/src/xios-2.0/src/attribute_map.cpp', line 61 -> [ key = time_origin] key not found !

Use XIOS 1 (not XIOS 2, does not work with NEMO 3.6 or with the provided input files) XIOS 2 xml files have a slightly different syntax, which isn't easily obtained from documentation.

Suggestions

How could be process be simpler?

• Use arch-gfortran_linux.fcm which works with the recommended defaults (i.e. XIOS, long Fortran lines and CPP preprocessor)
• Use _FillValue in resulting NetCDF files for land