NERSC User Enviroment¶
Home Directories, Shells and Dotfiles¶
All NERSC systems use global home directories, which are are pre-populated with shell initialization files (also known as dotfiles) for all available shells. NERSC supports
tcsh as login shells. Other shells (
zsh) are also available. The default shell at NERSC is bash.
The standard dotfiles are symbolic links to read-only files that NERSC controls. For each standard dotfile, there is a user-writeable ".ext" file.
~/.cshrc are read-only. Customizations should be put in
Occasionally, a user will accidentally delete the symbolic links to the standard dotfiles, or otherwise damage the dotfiles to the point that it becomes difficult to do anything. In this case, the user should run the command
fixdots. This will recreate the original dotfile configuration, after first saving the current configuration in the directory
$HOME/KeepDots.timestamp is a string that includes the current date and time. After running
fixdots, the user should carefully incorporate the saved customizations into the newly-created .ext files.
Changing Default Login Shell¶
Use NIM to change your default login shell. Login, then select Change Shell from the Actions pull-down menu.
NERSC Modules Environment¶
NERSC uses the module utility to manage nearly all software. There are two huge advantages of the module approach:
- NERSC can provide many different versions and/or installations of a single software package on a given machine, including a default version as well as several older and newer version.
- Users can easily switch to different versions or installations without having to explicitly specify different paths. With modules, the
MANPATHand related environment variables are automatically managed.
The following is a list of commands available in the Modules Environment tool available on Cori.
To get a usage list of module options type the following (listing is abbreviated):
module help Available Commands and Usage: + add|unload modulefile [modulefile …] + rm|unload modulefile [modulefile …] + switch modulefile1 modulefile2 + display modulefile [modulefile …] + avail path [path] + list + help modulefile [modulefile …]
# To get all available packages module avail # To know the availability of a specific software module avail netcdf # To know all packages that contain a substring, use -S flag. module avail -S netcdf
To see what changes are made to your environment when a module is loaded:
module display [modulefile]
module show [modulefile]
This command will add one or more modulefiles to your current environment. It does so silently, but will throw errors if there are any problems with the modulefile. If you load the generic name of a module, you will get the default version. To load a specific version, load the modulefile using the full specification.
module load [modulefile1][modulefile2] # Load visit module load visit # Load visit version 2.1.2 module load visit/2.1.2
Unloads the specified modulefile from the user's environment. This command will fail silently if the modulefile you specify is not already loaded.
module unload [modulefile]
The modules environment allows you to swap between versions of packages
module swap [old modulefile] [new modulefile]
Accessing old Cray PE Software¶
Old Cray Developer Toolkits (CDT's) are removed after they are made available on the system for one year. We encourage users to use the new CDT's available on the system. However, if your workload depends on a specific old CDT version, you can continuously access these older CDT's from the archived copy at
/global/common by doing the following:
module load pe_archive
Creating a Custom Environment¶
You can modify your environment so that certain modules are loaded whenever you log in. Put changes in one of the following files, depending on your shell:
Users may have certain customizations that are appropriate for one NERSC platform, but not for others. This can be accomplished by testing the value of the environment variable
$NERSC_HOST. For example, on Cori the default programming environment is Intel (PrgEnv-Intel). A C-shell user who wants to use the
GNU programming environment should include the following module command in their
if ($NERSC_HOST == "cori") then module swap PrgEnv-intel PrgEnv-gnu endif
Install Your Own Customized Modules¶
You can create and install your own modules for your convenience or for sharing software among collaborators. The module definition files can be placed in the following locations:
- project directory
- your home directory
- available file system.
Make sure the UNIX file permissions grant access to all users who want to use the software.
Do not give write permissions to your home directory to anyone else.
As an example, we have modulefile named myzlib located in
To register this modulefile with our modules environment we run the following commands:
nersc$ module use /global/project/projectdirs/mpccc/usg/modulefiles/cori nersc$ module load myzlib/1.2.7
module use command adds this new directory before other module search paths (defined as
$MODULEPATH), so modules defined in this custom directory will have precedence if there are other modules with the same name in the module search paths. If you prefer to have the new directory added at the end of
module use -a instead of