The NcdfUtilities package
The NcdfUtilities package contains Fortran modules that you can use to write data to and read data from netCDF files. This package is contained within GEOS-Chem (in the NcdfUtil/ folder, but may also be downloaded as a separate standalone package.
- 1 List of modules
- 2 NcdfUtilities within GEOS-Chem
- 3 NcdfUtilities as a standalone distribution
- 3.1 Standalone directory structure
- 3.2 System requirements for using NcdfUtilities
- 3.3 Setting enviroment variables for the standalone NcdfUtilities package
- 3.4 Compiling the NcdfUtilities Library
- 3.5 Testing the NcdfUtilities Library
List of modules
NcdfUtilities within GEOS-Chem
Setting environment variables for GEOS-Chem
NcdfUtilities as a standalone distribution
The following sections describe
=== ties Directory Structure:
Standalone directory structure
If you download the NcdfUtilities as a standalone package, the root-level directory will contain the following sub-directories:
|Code/||The Fortran source code files (*.F </tt>*.F90</tt>) reside here.|
|bin/||The TestNcdfUtilities.x executable will be created here.|
|doc/||The NcdfUtilities documentation will be created here.|
|lib/||The NetCdfUtilities library file (libNcUtils.a) will be created here.|
|mod/||Compiled module files (*.mod) will be created here.|
|perl/||Several perl scripts that can be useful in creating netCDF files are contained here.|
System requirements for using NcdfUtilities
In order to use NcdfUtilities, you will first have to check to see if the netCDF library is installed on your system. You may find that there are several netCDF library versions to select from. Or you can ask your IT staff to build you a version.
In order to build the reference documents (described below), you must have the LaTeX utilities (i.e. latex, dvips, dvipdf) installed on your system.
Setting enviroment variables for the standalone NcdfUtilities package
The NcdfUtilities library requires that you set the following environment variables in your system startup file (e.g. .bashrc or .cshrc):
|NETCDF_BIN||The bin/ folder of the netCDF installation, where utilities such as nc-config, ncdump, etc. are stored.|
|NETCDF_INCLUDE||The include/ folder of the netCDF installation, where the netcdf.inc and netcdf_mod.F90 are found.|
|NETCDF_LIB||The lib/ or lib64/ folder of the netCDF installation, where the netCDF library files (e.g. libnetcdf.a) are found.|
NOTE: In netCDF-4.2 and higher versions, the netCDF Fortran libraries are built from a separate distribution. If on your system, the netCDF-Fortran libraries have been installed into a different folder than the rest of the netCDF libaries, you will also need to set these environment variables in your system startup file:
|NETCDF_FORTRAN_BIN||The bin/ folder of the netCDF-Fortran installation, where utilities such as nf-config is stored.|
|NETCDF_FORTRAN_INCLUDE||The include/ folder of the netCDF-Fortran installation, where the netcdf.inc and netcdf_mod.F90 are found.|
|NETCDF_FORTRAN_LIB||The lib/ or lib64/ folder of the netCDF-Fortran installation, where the netCDF-Fortran library files (e.g. libnetcdff.a) are found.|
You can set these variables in your .bashrc or .cshrc startup file. If you load a netCDF library into your Unix environment with the module command, then very often the root path to the netCDF library will be automatically set for you (which you can use to define the variables listed above). Ask your IT staff for more information.
--Bob Yantosca (talk) 18:39, 8 March 2017 (UTC)
Compiling the NcdfUtilities Library
The NcdfUtilities/Code directory contains the Fortran source code modules as well as two Makefiles (named Makefile and Makefile_header.mk).
The file "Makefile_header.mk" is a sub-makefile which is used to define the compilation options for different compilers. At present, the ifort, gfortran, and pgfortran compilers are supported.
Once you have set the proper environment variables for your system (as described above), you are ready to build the executable. Make sure you are in the Code/ subdirectory and type:
This should start building the source code and create a library file named "libNcUtils.a" in the lib/ subdirectory.
Testing the NcdfUtilities Library
Once the "libNcUtils.a" file has been created in the lib/ subdirectory, you can test to see if the library was created (and can link to) the netCDF library correctly. Type:
This will create an executable file named "TestNcdfUtilities.x" in the bin subdirectory, and will also execute the file. If the libNcUtils.a library was installed correctly you should see the following output:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%% Testing libNcdfUtilities.a %%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% === Begin netCDF file creation test === Writing XDim (# lons) to netCDF file Writing YDim (# lats) to netCDF file Writing ZDim (# alts) to netCDF file Writing LON (1D array) to netCDF file Writing LAT (1D array) to netCDF file Writing PLEV (1D array) to netCDF file Writing PS (2D array) to netCDF file Writing T (3D array) to netCDF file === End netCDF file creation test === === Begin netCDF file reading test === Reading XDim back from netCDF file...........PASSED Reading YDim back read from netCDF...........PASSED Reading ZDim back from netCDF file...........PASSED Reading LON back from netCDF file...........PASSED Reading LAT back from netCDF file...........PASSED Reading PLEV back from netCDF file...........PASSED Reading PS back from netCDF file...........PASSED Reading T back from netCDF file...........PASSED === End of netCDF file read test! ===
If all of the tests return with "PASSED" then the libNcUtils.a file was created correctly and you have
Building the NcdfUtilities Reference Documentation:
The NcdfUtilities Fortran source code and Makefiles use the ProTeX automatic documentation system. This enables you to create reference documents in
- .pdf and *.ps format from the comments in the subroutine headers.
To build the reference documents, make sure you are in the doc/ subdirectory, then type:
This will create the following documents in the doc/ subdirectory:
NcdfUtilities.pdf NcdfUtilities.ps NcdfUtilities.tex
-- Reference document for the NcdfUtilities Fortran code
in *.pdf, *.ps, and LaTeX formats
NcdfUtilities_Makefiles.pdf NcdfUtilities_Makefiles.ps NcdfUtilities_Makefiles.tex
-- Reference document for the NcdfUtilities Makefiles
in *.pdf, *.ps, and LaTeX formats
The reference documents contain a description of each subroutine and function, the variables that are passed to it as input & output arguments, and the revision history. The Makefile reference document displays the full text of the Makefiles. These documents will come in handy if you need to modify or update the Fortran code or Makefiles.
If you wish to remove the NcdfUtilities reference documentation files, then make sure you are in the doc directory and type:
To remove all of the *.o, *.mod and executable file in the Code subdirectory only, type:
However, if you wish to also remove the contents of the bin/ and lib/ subdirectories (as well as removing the *.ps, *.pdf, and *.txt files from the doc/ subdirectory), then type:
That's it. Good luck and contact me if you have any questions:
Bob Yantosca firstname.lastname@example.org