NEMO 3.6 (stable) + XIOS 1.0

Tested with

• gcc4.9, gcc5.4 on a linux system

• gcc4.8 on a Mac (El Capitan OSX 10.11)

The assumption here is that the compiler is fixed and the packages (e.g., NetCDF4 and a MPI bindings) are configured to be consistent with the compilers. See here to check whether the binaries exist, where they are, and how they might be installed separately if need be. All the #CHANGE ME highlighted below needs be modified to point to the appropriate paths or binaries (soft links with ln -s are ok).

The instructions below uses gcc4.9 for demonstration (modifications with gcc5.4 as appropriate). I defined some extra variables on a Linux machine:

export $BD=/home/julian/testing/gcc4.9-builds # CHANGE ME

export C_INCLUDE_PATH=$BD/install/include:$C_INCLUDE_PATH
export CPLUS_INCLUDE_PATH=$BD/install/include:$CPLUS_INCLUDE_PATH
export LIBRARY_PATH=$BD/install/lib:$LIBRARY_PATH
export LD_LIBRARY_PATH=$BD/install/lib:$LD_LIBRARY_PATH

You shouldn’t need to do the above if the packages are forced to look at the right place (e.g. via -L and/or -I flags with path to libraries and include files respectively). Not all of these are necessary depending on whether you choose to build/have static or dynamic libraries, and the LD_LIBRARY_PATH seems to sort out a lot of problems with linking libraries.

On a Mac done through anaconda the above was not necessary. My understanding is that setting these variables might not actually do anything unless an option is specifically enabled in Xcode.

XIOS 1.0 (svn v703)

To use NEMO you probably do need XIOS to do the I/O. The instructions here follow the one given in the XIOS instructions with any errors that arise. A useful site to search for XIOS related errors may be found on the XIOS user mailing list.

Here XIOS1.0 is used with NEMO3.6 for compatibility reasons. For the purposes here I created a folder called XIOS and used svn to get XIOS1.0 (which is going to be XIOS/xios1.0):

mkdir XIOS
cd XIOS
svn checkout -r 703 http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-1.0 xios-1.0

To get XIOS to compile, the compilers and packages need to be pointed to first, via modifying files in arch. Since I am using gcc, I did the following just to make a fresh copy:

cd xios1.0/arch
cp arch-GCC_LINUX.env arch-GCC_local.env
cp arch-GCC_LINUX.fcm arch-GCC_local.fcm
cp arch-GCC_LINUX.path arch-GCC_local.path

The *.env file specifies where HDF5 and NetCDF4 libraries live. The *.fcm file specifies which compilers and options to use. The *.path file specifies which paths and options to include. My files look like the following:

# arch-GCC_local.env

export HDF5_INC_DIR=/usr/local/include       # CHANGE ME
export HDF5_LIB_DIR=/usr/local/lib           # CHANGE ME

export NETCDF_INC_DIR=/usr/local/include     # CHANGE ME
export NETCDF_LIB_DIR=/usr/local/lib         # CHANGE ME

You could get an idea where the HDF5 and NetCDF4 directories are by doing which h5copy and which nc-config (assuming these are on $PATH), which should give you a directory/bin, and it is the directory part you want. If you did install the libraries somewhere else as in other packages, say, then make sure the which commands are pointing to the right place.

# arch-GCC_local.fcm

################################################################################
###################                Projet XIOS               ###################
################################################################################

%CCOMPILER      /usr/local/bin/mpicc                # CHANGE ME
%FCOMPILER      /usr/local/bin/mpif90               # CHANGE ME
%LINKER         /usr/local/bin/mpif90               # CHANGE ME

%BASE_CFLAGS    -ansi -w
%PROD_CFLAGS    -O3 -DBOOST_DISABLE_ASSERTS
%DEV_CFLAGS     -g -O2
%DEBUG_CFLAGS   -g

%BASE_FFLAGS    -D__NONE__
%PROD_FFLAGS    -O3
%DEV_FFLAGS     -g -O2
%DEBUG_FFLAGS   -g

%BASE_INC       -D__NONE__
%BASE_LD        -lstdc++

%CPP            cpp-4.9                             # CHANGE ME
%FPP            cpp-4.9 -P                          # CHANGE ME
%MAKE           make

Check the MPI locations and versions by doing which mpicc and mpicc --version say. If they are the right ones you could just have mpicc instead of the full path as given above. MPI bindings are used here to avoid a possible error that may pop up in relation to the build trying to find mpi.h. The gmake command was swapped out by the make command (I don’t have cmake on the laptop).

Note

For gcc5.4 and maybe newer versions, doing just the above when compiling leads to a whole load of errors about clashing in C++:

.../include/boost/functional/hash/extensions.hpp:69:33: error: ‘template<class T, class A> std::size_t boost::hash_value’ conflicts with a previous declaration
 std::size_t hash_value(std::list<T, A> const& v)
                             ^

Adding -D_GLIBCXX_USE_CXX11_ABI=0 to %BASE_CFLAGS fixes these.

# arch-GCC_local.path

NETCDF_INCDIR="-I$NETCDF_INC_DIR"
NETCDF_LIBDIR="-Wl,'--allow-multiple-definition' -L$NETCDF_LIB_DIR"
NETCDF_LIB="-lnetcdff -lnetcdf"

MPI_INCDIR=""
MPI_LIBDIR=""
MPI_LIB=""

HDF5_INCDIR="-I$HDF5_INC_DIR"
HDF5_LIBDIR="-L$HDF5_LIB_DIR"
HDF5_LIB="-lhdf5_hl -lhdf5 -lhdf5 -lz"

The above has all the OASIS (the atmosphere / ocean coupler) keys removed. I added the -Wl,'--allow-multiple-definition' key for reasons I don’t remember anymore…

Now it should be ready to compile. Assuming the current directory is xios1.0/arch:

cd ../
./make_xios --full --prod --arch GCC_local -j2 |& tee compile_log.txt

The -j2 option uses two processors to build. The tee command is to keep logs of potential errors (the |& is short for 2>&1 |) for debugging errors that may arise.

Note

If you get something like

/home/julian/testing/nemo-6800/xios-703/xios-1.0/inc/netcdf.hpp:20:26: fatal error: netcdf_par.h: No such file or directory
 #  include <netcdf_par.h>
                          ^
compilation terminated.
fcm_internal compile failed (256)
/home/julian/testing/nemo-6800/xios-703/xios-1.0/Makefile:1620: recipe for target 'inetcdf4.o' failed

then it is probably because NetCDF4 was not built as parallel. There is a actually a copy of the file in ./extern/src_netcdf4/netcdf_par.h, and it could be pointed to by looking into bld.cfg:

bld::tool::cflags    %CFLAGS %CBASE_INC -I${PWD}/extern/src_netcdf -I${PWD}/extern/boost/include -I${PWD}/extern/rapidxml/include -I${PWD}/extern/blitz/include

where src_netcdf should be changed to src_netcdf4.

Note

If you get something like

libhdf5.a(H5PL.o): undefined reference to symbol 'dlclose@@GLIBC_2.2.5'

then this suggests that the HDF5 library that is being called is built as a static and/or not shareable library. In this case adding the -ldl flag to HDF5_LIB in arch-GCC_local.path should work. Or if you want to you can recompile HDF5 as a shareable library; see other packages on how you might go about doing this.

It should work and takes around 5 mins to compile for me. The main end result is are binaries in xios1.0/bin/ which NEMO will call.

Note

Do ldd bin/xios_server.exe (or wherever xios_server.exe lives) to make sure the libraries linked to it are the intended libraries. XIOS may still work if the NetCDF versions are ok, but if not, go back and define LD_LIBRARY_PATH and other variables accordingly; see above.

xios_server.exe is one of the other binaries built from compiling but is not required for small runs on a laptop. For its use on a cluster see for example the instructions on the NOCL ARCHER guide.

NEMO 3.6 (svn v6800)

Check out a version of NEMO. I have another folder separate to the XIOS folders to contain the NEMO codes and binaries:

mkdir NEMO
cd NEMO
svn checkout -r 6800 http://forge.ipsl.jussieu.fr/nemo/svn/NEMO/trunk nemo3.6-6800

This checks out version 6800 (NEMO 3.6) and dumps it into a folder called nemo3.6-6800 (change the target path to whatever you like).

Note

svn checkout https://forge.ipsl.jussieu.fr/nemo/svn/NEMO/releases/release-3.6 nemo3.6 would pull the official version

A similar procedure to specify compilers and where XIOS lives needs to be done for NEMO. Again, because of the compilers I am using:

cd nemo3.6-6800/NEMOGCM/ARCH
cp OLD/arch-gfortran_linux.fcm ./arch-gfortran_local.fcm

None of the fcm files associated with gfortran actually worked for me out of the box so here is my build of it (click HERE for a detailed log of how I got to the following):

# gfortran_local.fcm

# generic gfortran compiler options for linux
# NCDF_INC    netcdf include file
# NCDF_LIB    netcdf library
# 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 in a
# FPPFLAGS    pre-processing flags
# AR          assembler
# ARFLAGS     assembler flags
# MK          make
# USER_INC    additional include files for the compiler,  e.g. -I<include dir>
# USER_LIB    additional libraries to pass to the linker, e.g. -l<library>

%NCDF_HOME           /usr/local                                       # CHANGE ME

%XIOS_HOME           /home/julian/testing/gcc4.9-builds/XIOS/xios-1.0 # CHANGE ME

%CPP                 cpp-4.9                                          # CHANGE ME
%CPPFLAGS            -P -traditional

%XIOS_INC            -I%XIOS_HOME/inc
%XIOS_LIB            -L%XIOS_HOME/lib -lxios

%NCDF_INC            -I%NCDF_HOME/include
%NCDF_LIB            -L%NCDF_HOME/lib -lnetcdf -lnetcdff -lstdc++
%FC                  mpif90                                           # CHANGE ME
%FCFLAGS             -fdefault-real-8 -O3 -funroll-all-loops -fcray-pointer -cpp -ffree-line-length-none
%FFLAGS              %FCFLAGS
%LD                  %FC
%LDFLAGS
%FPPFLAGS            -P -C -traditional
%AR                  ar
%ARFLAGS             -rs
%MK                  make
%USER_INC            %XIOS_INC %NCDF_INC
%USER_LIB            %XIOS_LIB %NCDF_LIB

The main changes are (see here for an attempt at the reasoning and a log of errors that motivates the changes):

• added %NCDF_HOME to point to where NetCDF lives

• added %XIOS_* keys to point to where XIOS lives

• added %CPP and flags, consistent with using gcc4.9

• added the -lnetcdff and -lstdc++ flags to NetCDF flags

• using mpif90 which is a MPI binding of gfortran-4.9

• added -cpp and -ffree-line-length-none to Fortran flags

• swapped out gmake with make

Note

It might be worthwhile doing the following first:

cd ../CONFIG/
./makenemo -j0 -r GYRE -n GYRE_testing -m gfortran_local

Then, add key_nosignedzero to the end of /GYRE_testing/cpp_GYRE_testing.fcm (see note at the bottom of the page). -j0 does all the folder creation and copying but not the compile step.

To compile a configuration (using the GYRE config):

cd ../CONFIG/
./makenemo -j2 -r GYRE -n GYRE_testing -m gfortran_local |& tee compile_log.txt

This uses two processors, with GYRE as a reference, builds a new folder called GYRE_testing, with the specified architecture file, and outputs a log.

Note

The -r GYRE flag here only needs to be done once to create an extra folder and add GYRE_testing to cfg.txt. The subsequent compilations should then read, e.g., ./makenemo -n GYRE_testing -m gfortran_local.

Check that it does run with the following:

cd GYRE_testing/EXP00
mpiexec -n 1 ./opa

This may be mpirun instead of mpiexec, and -n 1 just runs it as a single core process. Change nn_itend = 4320 in nn_itend = 120 to only run it for 10 days (rdt = 7200 which is 2 hours). With all the defaults as is, there should be some GYRE_5d_*.nc data in the folder. You can read this with ncview (see the ncview page or, if you have sudo access, you can install it through sudo apt-get install ncview), bearing in mind that this is actually a rotated gyre configuration (see the following NEMO forge page or search for gyre in the NEMO book).

Note

My run actually crashed immediately. Looking into ocean.output and searching for E R R O R shows that key_nosignedzero needed to be added to /GYRE_testing/cpp_GYRE_testing.fcm. Rebuilding with the key then works fine.

Note

If your installation compiles but does not run with the following error

dyld: Library not loaded: @rpath/libnetcdff.6.dylib
Referenced from: /paths/./nemo
Reason: no suitable image found.  Did find:
/usr/local/lib/libnetcdff.6.dylib: stat() failed with errno=13

then it is not finding the right libraries. These could be fixed by adding the -Wl,-rpath,/fill me in/lib flag to the relevant flags bit in the *.fcm files (or possibly in XIOS the path and/or env ) to specify exactly where the libraries live. This can happen for example on a Mac or if the libraries are installed not at the usual place.

Note

One infuriating problem I had specifically with a Mac (though it might be a gcc4.8 issue) is that the run does not get beyond the initialisation stage. Going into ocean.output and searching for E R R O R shows that it complained about a misspelled namelist item (in my case it was in the namberg namelist). If you go into output.namelist.dyn and look for the offending namelist is that it might be reading in nonsense. This may happen if the comment character ! is right next to a variable, e.g.

ln_icebergs = .true.!this is a comment

Fix this by adding a white space, i.e.

ln_icebergs = .true. !this is a comment