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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

Softenv Keys for netcdf on oliver
Machine Version Softenv Key
None Available N/A N/A
▶ Softenv FAQ?

The information here is applicable to LSU HPC and LONI systems.


A user may choose between using /bin/bash and /bin/tcsh. Details about each shell follows.


System resource file: /etc/profile

When one access the shell, the following user files are read in if they exist (in order):

  1. ~/.bash_profile (anything sent to STDOUT or STDERR will cause things like rsync to break)
  2. ~/.bashrc (interactive login only)
  3. ~/.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.


The file ~/.cshrc is used to customize the user's environment if his login shell is /bin/tcsh.


SoftEnv is a utility that is supposed to help users manage complex user environments with potentially conflicting application versions and libraries.

System Default Path

When a user logs in, the system /etc/profile or /etc/csh.cshrc (depending on login shell, and mirrored from csm:/cfmroot/etc/profile) calls /usr/local/packages/softenv-1.6.2/bin/ to set up the default path via the SoftEnv database.

SoftEnv looks for a user's ~/.soft file and updates the variables and paths accordingly.

Viewing Available Packages

The command softenv will provide a list of available packages. The listing will look something like:

$ softenv
These are the macros available:
*   @default
These are the keywords explicitly available:
+amber-8                       Applications: 'Amber', version: 8 Amber is a
+apache-ant-1.6.5              Ant, Java based XML make system version: 1.6.
+charm-5.9                     Applications: 'Charm++', version: 5.9 Charm++
+default                       this is the default environment...nukes /etc/
+essl-4.2                      Libraries: 'ESSL', version: 4.2 ESSL is a sta
+gaussian-03                   Applications: 'Gaussian', version: 03 Gaussia
... some stuff deleted ...
Managing SoftEnv

The file ~/.soft in the user's home directory is where the different packages are managed. Add the +keyword into your .soft file. For instance, ff one wants to add the Amber Molecular Dynamics package into their environment, the end of the .soft file should look like this:



To update the environment after modifying this file, one simply uses the resoft command:

% resoft

The command soft can be used to manipulate the environment from the command line. It takes the form:

$ soft add/delete +keyword

Using this method of adding or removing keywords requires the user to pay attention to possible order dependencies. That is, best results require the user to remove keywords in the reverse order in which they were added. It is handy to test out individual keys, but can lead to trouble if changing multiple keys. Changing the .soft file and issuing the resoft is the recommended way of dealing with multiple changes.


Softenv or Module defines some variables which point at the library home directory.

For clusters using softenv, use soft-dbq to determine it's name, then use it to add a link option to your build. You may see something like this (the output has been edited for brevity):

$ soft-dbq  +netcdf-4.1.3-Intel-13.0.0

. . .

Name: +netcdf-4.1.3-Intel-13.0.0
Description: @types: Library/IO @name: netcdf @version: 4.1.3 @build:
Intel-13.0.0 @internal: @external: @about: NetCDF is a set of
software libraries and self-describing, machine-independent data
formats that support the creation, access, and sharing of
array-oriented scientific data.
Flags: none
Groups: none
Exists on: Linux
. . .
    PATH = ${PATH}:/usr/local/packages/netcdf/4.1.3/Intel-13.0.0/bin
    netcdf_HOME = /usr/local/packages/netcdf/4.1.3/Intel-13.0.0
. . .
$ ls /usr/local/packages/netcdf/4.1.3/Intel-13.0.0/lib
libnetcdf.a        pkgconfig

The libraries are used at link time by the compiler, so the following options could be used:

   -L${netcdf_HOME}/lib -lnetcdf

For clusters using module, use the module disp command to determine the location of the netcdf path and then add it to your build options:

$ module disp netcdf/
. . .
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:
  conflict         netcdf
  module           load hdf5/1.8.12/INTEL-140-MVAPICH2-2.0
  prepend-path     LIBRARY_PATH /usr/local/packages/netcdf/
  prepend-path     MANPATH /usr/local/packages/netcdf/
  prepend-path     PATH /usr/local/packages/netcdf/
  prepend-path     PKG_CONFIG_PATH /usr/local/packages/netcdf/
  setenv           LHPC_ROOTNETCDF /usr/local/packages/netcdf/
  setenv           LHPC_VERSIONNETCDF
. . .
libnetcdf.a  pkgconfig

The libraries are used at link time by the compiler, so the following options could be used:

   -L${LHPC_ROOTNETCDF}/lib -lnetcdf

Please refer to the documentation in Resources for a discussion of the API and how to choose the correct library.


Last modified: June 19 2015 11:15:08.