NEMO 安装

# Prerequisites

Suggestion from J Mak^[4]:
Get someone who knows what they are doing to do it for you! Compiling the following from scratch is not the most interesting activity and is actually quite fiddly (especially the HDF5 and NetCDF4 stuff)…if you don’t have access to people who can do that, then try.

Before installing these, run which h5copy and which nc-config to see if hdf5 and netcdf are already available. If so, we can skip installing them and zlib.

# zlib

When I was trying to install Netcdf, I found this requirement in its INSTALL.md file. After downloading packages from server, build it like:

	./configure --prefix=/usr/local/pnetcdf
	make check install

# hdf5

Specifying the location of the zlib library:

	CC=/.../mpicc ./configure --with-zlib=/usr/local/pnetcdf/lib --prefix=/usr/local/pnetcdf --enable-parallel --enable-shared
	make check install

Just add [--{enable-fortran,disable-shared,enable-parallel}] from offical documentation of NEMO^[1] may bring some problems.

# netcdf

After HDF5 is done, build netcdf, specifying the location of the HDF5, zlib, and libraries in the CPPFLAGS and LDFLAGS environment variables. For example:

	CC=/.../mpicc CPPFLAGS=-I/usr/local/pnetcdf/include LDFLAGS=-L/usr/local/pnetcdf/lib ./configure --prefix=/usr/local/pnetcdf --enable-parallel-tests --disable-dap

	make check install

You can check the output or setting file in lib to see whether parallel IO is on. Or use nc-config --all .

Then build netcdf-fortran like:

	CPPFLAGS=-I/usr/local/pnetcdf/include LDFLAGS=-L/usr/local/pnetcdf/lib ./configure --prefix=/usr/local/pnetcdf --enable-parallel-tests
	make
	make install
	make check

Could try adding LIBS='-hdf5 -lhdf5_hl -lz' if something go wrong.

# Errors and fixes

checking for library containing H5Fflush… no

We need to build HDF5 lib as shared, so add flag --enable-shared when building HDF5.

undefined reference to `H5Pset_fapl_mpiposix’

Edit file libsrc4/nc4file.c . See this commit.

# ncview

It is not necessary, but it’s a easy tool to check the nc file.

First install Xaw using sudo yum install libXaw-devel .
Then just following [6].

./configure --prefix=${HOME}/study/software/ncview/ --with-udunits2_incdir=${HOME}/study/software/udunits/include/ --with-udunits2_libdir=${HOME}/study/software/udunits/lib/ --with-png_incdir=${HOME}/study/software/libpng/include/ --with-png_libdir=${HOME}/study/software/libpng/lib/

Or, just run yum install ncview .

# XIOS

Refer to wiki^[2] and J Mak’s notes^[4], first

svn checkout  http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.0 xios-2.0

NEMO has requirements for the XIOS version, remember to check that.

Then modify files arch-GCC_LINUX.* in arch , add the -ldl flag to HDF5_LIB in arch-GCC_local.path if build hdf5 library as a not shareable.

The boost_dir and OASIS_dir are not necessary, just leave them.

Finally, run

./make_xios --arch GCC_LINUX

# NEMO

Copy and rename an configuration file as arch-my_arch.fcm from an architecture similar to our own. Set the following variables:

	%NCDF_HOME /usr/local/path/to/netcdf
	%HDF5_HOME /usr/local/path/to/hdf5
	%XIOS_HOME /home/$( whoami )/path/to/xios-trunk

Compile a reference configuration:

./makenemo –m 'my_arch' –r GYRE_PISCES

And find nemo in cfgs/GYRE_PISCES/EXP00 .

# Good luck!

Hope you can find nemo soon.

	._ ._ ._ ._ ._
	_.-._)`\_.-._)`\_.-._)`\_.-._)`\_.-._)`\_

	o _, _,
	o .' ( .-' /
	o _/..._'. .' /
	( o .-'` ` '-./ _.'
	) ( o) ;= <_ (
	( '-.,\\__ __.-;`\ '. )
	) ) \) \|`\ \) '. \ ( (
	( ( \_/ '-._\ ) )
	) ) jgs ` ( (
	^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

# Reference

NEMO documentation
XIOS wiki
Kunpeng NEMO transplant
J Mak NEMO notes
NEMO Reference configurations inputs
NCVIEW installation