netcdf_fortran
Table of Content
About
NetCDF (Network Common Data Format) is a set of software libraries supporting machine-independent data file formats that are useful for accessing and sharing array-oriented scientific data.
Versions and Availability
Module Names for netcdf_fortran on qb
| Machine | Version | Module Name |
|---|---|---|
| qb2 | 4.2 | netcdf_fortran/4.2/INTEL-140-MVAPICH2-2 |
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The information here is applicable to LSU HPC and LONI systems.
Shells
A user may choose between using /bin/bash and /bin/tcsh. Details about each shell follows.
/bin/bash
System resource file: /etc/profile
When one access the shell, the following user files are read in if they exist (in order):
- ~/.bash_profile (anything sent to STDOUT or STDERR will cause things like rsync to break)
- ~/.bashrc (interactive login only)
- ~/.profile
When a user logs out of an interactive session, the file ~/.bash_logout is executed if it exists.
The default value of the environmental variable, PATH, is set automatically using SoftEnv. See below for more information.
/bin/tcsh
The file ~/.cshrc is used to customize the user's environment if his login shell is /bin/tcsh.
Modules
Modules is a utility which helps users manage the complex business of setting up their shell environment in the face of potentially conflicting application versions and libraries.
Default Setup
When a user logs in, the system looks for a file named .modules in their home directory. This file contains module commands to set up the initial shell environment.
Viewing Available Modules
The command
$ module avail
displays a list of all the modules available. The list will look something like:
--- some stuff deleted --- velvet/1.2.10/INTEL-14.0.2 vmatch/2.2.2 ---------------- /usr/local/packages/Modules/modulefiles/admin ----------------- EasyBuild/1.11.1 GCC/4.9.0 INTEL-140-MPICH/3.1.1 EasyBuild/1.13.0 INTEL/14.0.2 INTEL-140-MVAPICH2/2.0 --- some stuff deleted ---
The module names take the form appname/version/compiler, providing the application name, the version, and information about how it was compiled (if needed).
Managing Modules
Besides avail, there are other basic module commands to use for manipulating the environment. These include:
add/load mod1 mod2 ... modn . . . Add modules rm/unload mod1 mod2 ... modn . . Remove modules switch/swap mod . . . . . . . . . Switch or swap one module for another display/show . . . . . . . . . . List modules loaded in the environment avail . . . . . . . . . . . . . . List available module names whatis mod1 mod2 ... modn . . . . Describe listed modules
The -h option to module will list all available commands.
Module is currently available only on SuperMIC.
Usage
For clusters using module, use the module disp command to determine the location of the netcdf_fortran path and then add it to your build options:
$ module disp netcdf_fortran/4.2/INTEL-140-MVAPICH2-2.0 ------------------------------------------------------------------- /usr/local/packages/Modules/modulefiles/apps/netcdf_fortran/4.2/INTEL-140-MVAPICH2-2.0: module-whatis Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. - Homepage: http://www.unidata.ucar.edu/software/netcdf/ conflict netcdf_fortran . . . setenv LHPC_ROOTNETCDF_FORTRAN /usr/local/packages/netcdf_fortran/4.2/INTEL-140-MVAPICH2-2.0 setenv LHPC_VERSIONNETCDF_FORTRAN 4.2 setenv LHPC_DEVELNETCDF_FORTRAN /usr/local/packages/netcdf_fortran/4.2/INTEL-140-MVAPICH2-2.0/easybuild/netcdf_fortran-4.2-INTEL-140-MVAPICH2-2.0-easybuild-devel ------------------------------------------------------------------- . . . $ ls $LHPC_ROOTNETCDF_FORTRAN/lib libnetcdff.a libnetcdff.la libnetcdff.so libnetcdff.so.5 libnetcdff.so.5.3.1 pkgconfig
The libraries are used at link time by the compiler, so the following options could be used:
-L${LHPC_ROOTNETCDF}/lib -lnetcdff
Please refer to the documentation in Resources for a discussion of the API and how to choose the correct library.
Resources
Last modified: August 21 2017 10:47:37.