Environment¶

Note

This page outlines tips on managing user shell environment and startup scripts for Cori system.

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.

No more .ext dotfiles at NERSC since February 21, 2020.

NERSC used to reserve the standard dotfiles (~/.bashrc, ~/.bash_profile, ~/.cshrc, ~/.login, etc.) for system use so that users had to use the corresponding .ext files (e.g., ~/.bashrc.ext, ~/.bash_profile.ext, etc.) for their shell modifications. This is not the case anymore! You can modify those standard dotfiles for your personal use now.

The actual dotfile transition occurred during the center maintenance on February 21-25, 2020. To mitigate the interruptions to existing workloads, we have preserved shell environments by replacing dotfiles with template dotfiles that source .ext files. For example, if you are an existing user at NERSC, here is how your ~/.bashrc file would look like,

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

You are recommended to move the contents of your ~/.bashrc.ext file into your ~/.bashrc file after the transition (and remove the .ext files afterwards).

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.

Note

On Cori ~/.bash_profile and ~/.profile are sourced by login shells, while ~/.bashrc is sourced by most of the shell invocations including the login shells. In general you can put the environment variables, such as PATH, which are inheritable to subshells in ~/.bash_profile or ~/.profile and functions and aliases in the ~/.bashrc file in order to make them available in subshells.

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.

Example

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.