Environment¶

NERSC User Environment¶

Home Directories, Shells and Dotfiles¶

All NERSC systems use global home directories. NERSC supports bash, csh, and tcsh as login shells. Other shells (ksh, sh, and zsh) are also available. The default login shell at NERSC is bash. NERSC does not populate shell initialization files (also known as dotfiles) on users' home directories. You can create dotfiles (e.g., ~/.bashrc, ~/.bash_profile, etc.) as needed to put your personal shell modifications.

# begin .bashrc
if [ -z "$SHIFTER_RUNTIME" ]
then
    . $HOME/.bashrc.ext
fi
# end .bashrc

Changing Default Login Shell¶

Use Iris to change your default login shell. Log in, then under the "Details" tab look for the "Server Logins" section. Click on "Edit" under the "Actions" column.

Customizing Shell Environment¶

You can create dotfiles (e.g., .bashrc, .bash_profile, or .profile, etc) in your $HOME directory to put your personal shell modifications.

System specific customizations¶

All NERSC systems share the Global HOME; the same $HOME is available regardless of the platform. To make system specific customizations use the pre-defined environment variable NERSC_HOST.

case $NERSC_HOST in
    "cori")
        : # settings for Cori
        export MYVARIABLE="value-for-cori"
        ;;
    "datatran")
        : # settings for DTN nodes
        export MYVARIABLE="value-for-dtn"
        ;;
    *)
        : # default value for other nodes
        export MYVARIABLE="default-value"
        ;;
esac

darshan and altd¶

NERSC loads a light I/O profiling tool, darshan, and altd (a library tracking tool) on Cori by default. If you encounter any problems with them, you can unload them in your ~/.bash_profile, or ~/.login file:

module unload darshan
module unload altd

shifter¶

If you run shifter applications, you may want to skip the dotfiles. You can use the following if block in your dotfiles:

if [ -z "$SHIFTER_RUNTIME" ]; then
    : # Settings for when *not* in shifter
fi

missing NERSC variables¶

If any of the NERSC defined environment variables such as $SCRATCH, are missing in your shell invocations, you can add them in your ~/.bashrc file as follows:

if [ -z "$SCRATCH" ]; then
    export SCRATCH=/global/cscratch1/sd/$USER
fi

crontabs¶

If you run bash scripts in crontabs, you may want to invoke a login shell (#!/bin/bash -l) in order to get the NERSC defined environment variables, such as NERSC_HOST, SCRATCH, CSCRATCH, and to get the module command defined.

NERSC Modules Environment¶

NERSC uses the module utility to manage nearly all software. There are two advantages of the module approach:

1. 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.
2. Users can easily switch to different versions or installations without having to explicitly specify different paths. With modules, the MANPATH and related environment variables are automatically managed.

Module Commands¶

General usage:

nersc$ module [ switches ] [ subcommand ] [subcommand-args ]

Further reading:

• module help
• man module
• man modulefile
• Online manual (note: some features may only be available in later versions than what is installed on NERSC systems)

Common commands¶

List currently loaded modules:

module list

List all available modules:

module avail

Show availability of specific module:

module avail <module-name>

Show availability of all modules containing a substring:

module avail -S <substring>

Display what changes are made when a module is loaded:

module display <module-name>

Add a module to your current environment:

module load <module-name>

module load gcc

module load gcc/8.1.0

Remove module from the current environment:

module unload <module-name>

Switch currently loaded module with a new module:

module swap <old-module> <new-module>

Creating a Custom Module Environment¶

You can modify your environment so that certain modules are loaded whenever you log in.

The first option is to use shell commands in ~/.bash_profile (or ~/.login for csh/tcsh users).

module swap PrgEnv-${PE_ENV,,} PrgEnv-gnu

The second option is to use the "snapshot" feature of modules.

1. swap and load modules to your desired configuration
2. save a "snapshot" with module snapshot <snapshot-filename>

Then at any time later restore the environment with module restore <snapshot-filename>.

Install Your Own Customized Modules¶

You can create and install your own modules for your convenience or for sharing software among collaborators. See the man modulefile or the modulefile documentation for details of the required format and available commands. These custom modulefiles can be made visible to the module command by module use /path/to/the/custom/modulefiles.