FRE-NCtools is a collection of tools to help with the creation and manipulation of netCDF files used or written by the climate models developed at the Geophysical Fluid Dynamics Laboratory (GFDL). These tools were primarily written by members of the GFDL Modeling Systems Group to be used in the Flexible Modeling System (FMS) Runtime Environment (FRE).
The tools available in FRE-NCtools are:
- combine_blobs -- Combine the MOM5 Lagrangian Blobs netCDF files
- combine_restarts -- Combine restart files generated by a FMS enabled model
- iceberg_comb -- Combine iceberg history files
- combine-ncc -- Combine distributed unstructured FMS grid netCDF files
- decompress-ncc -- Convert an unstructured FMS grid file to a standard lat-lon grid
- mppnccombine -- Combine destributed FMS netCDF files
- is-compressed -- Determine if a netCDF file has an unstructured FMS grid
- scatter-ncc -- Distribute an unstructured FMS grid netCDF file for initializing a FMS climate model
- mppncscatter -- Distribute FMS netCDF file for initializing a FMS climate model
- list_ncvars -- List the variables in a netCDF file
- plevel -- Interpolates data from model levels to pressure levels
- split_ncvars -- Write the variables in a FMS netCDF file into multiple netCDF files, one file per netCDf field
- timavg -- Create a time average netCDF file
- ncexists -- Checks for variables and attributes in a netCDF file
- check_mask -- Configure the processors which contains all land points to be masked out for ocean model
- fregrid -- Convert from one grid resolution to another
- make_coupler_mosaic -- Generates three exchange grids for the FMS coupler
- make_hgrid -- Generate different types of horizontal grids
- make_land_domain -- Generate a land domain file
- make_quick_mosaic -- Generate a complete grid file for the FMS coupler
- make_regional_mosaic -- Generate horizontal grid and solo mosaic to regrid regional output onto a regular lat-lon grid
- make_solo_mosaic -- Generates Mosaic information between tiles
- make_topog -- Generate the topography for any Mosaic
- make_vgrid -- Generate a vertical grid for a FMS model
- remap_land -- Remap land restart file from one mosaic grid to another mosaic grid
- river_regrid -- Remap river network data from global regular lat-lon grid onto any other grid
- runoff_regrid -- Regrid land runoff data to the nearest ocean point
- transfer_to_mosaic_grid -- Convert older style grids to newer mosaic grid
FRE-NCtools has a collection of C and Fortran sources. Within GFDL, FRE-NCtools is built using a recent version of the Intel C and Fortran compilers. Using other compilers (GCC/GFortran) is possible, but is not tested by the Modeling Systems group at GFDL.
FRE-NCtools is built using the GNU Build System. If you received this as a package, the standard:
configure
make
make install
should be sufficient. If you cloned the git repository, you must first run
the autoreconf command with the --install option to copy in the missing
autoconf files:
autoreconf -i
./configure
make
make install
Additionally, you will probably need to set the environment variable CONFIG_SITE and set the recommended environment (modules):
export CONFIG_SITE=/path/to/package/site-configs/<site>/config.site
source /path/to/package/site-configs/<site>/env.sh
The above steps may need to be augmented depending upon your user evironment setup. For example, if autoreconfig is in /home/MyUsername/FRE-NCtools, it will create the configure command in this directory. You may tell the bash shell, for example, the location of both by this command:
export PATH=/home/MyUsername/FRE-NCtools:$PATH
Additionally, installing into a non-default directory may be desired or neccesary. For example, if the target directory is /home/MyUsername/bin, then FRE-NCtools building is configured by:
autoreconf -i ./configure --prefix=/home/MyUsername/bin
Finally compile and install the tools as usual:
make make install
Some FRE-NCtools applications can be run in parallel using MPI. If the
--with-mpi option is given to configure, the MPI version of those
applications will be built.
A few site configurations, for GFDL managed systems, are available in the
site-config directory. These can be used by setting the
CONFIG_SITE environment variable prior to running configure.
An embarrassingly small number of the commands have man pages. These man pages are written using AsciiDoc format. If AsciiDoc is found on the system, the man pages will be built and installed automatically.
Most commands support either a -h or --help options. In some cases, this
should be enough to get you started using the commands. We are in the process
of collecting more information on the tools available in this package. These
will be added when available.
Commonly, to combine restart and history files, one should run is-compressed on the candidate file first.
If it returns 0, it's land compressed file that needs:
- combine-ncc inputfile1 inputfile2 outputfile
- decompress-ncc inputfile outputfile
If is-compressed returns non-zero, it's a regular distributed file that gets:
- mppnccombine outputfile inputfile1 inputfile2 ...
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This project code is made available through GitHub but is managed by NOAA-GFDL at https://www.gfdl.noaa.gov.