Editing CommunityData:Klone (section)

== Setting up your Environment == 
The recommended way to manage software for your research projects on Klone is to use [https://apptainer.org/docs/user/main/quick_start.html Apptainer containers] (formerly known as Singularity). At first, you probably do not need to know much about containers because we maintain a shared setup described below.  However, before getting to work on Klone, you'll need to set up an environment that provides our containerized commands and a few other conveniences. You do this by creating the following <code>.bashrc</code> file in your home directory (i.e., <code>/mmfs1/home/{your_username}</code>) where you land when you connect to klone.

=== Initial .Bashrc ===
Before we get started using our apptainer package on klone, we need to start with a <code>.bashrc</code>.  Using a text editor (nano is a good choice if you don't already have a preference), create your <code>.bashrc</code> by pasting in the following code. Then run the command <code>source ~/.bashrc</code> to run the .bashrc and enable the environment. 

<syntaxhighlight language='bash'>
# .bashrc

export LOGIN_NODE=$(hostname | grep -q '^klone-login01' ; echo $?)
export SBATCH_EXPORT=BASH_ENV='~/.bashrc'
export SLURM_EXPORT_ENV=BASH_ENV='~/.bashrc'
export SLURM_EXPORT_ENV=BASH_ENV='~/.bashrc'

if [ -f ~/.bash_aliases ]; then
    . ~/.bash_aliases
fi

# User specific environment
if ! [[ "$PATH" =~ "$HOME/.local/bin:$HOME/bin:" ]]
then
    PATH="$HOME/.local/bin:$HOME/bin:$PATH"
fi

export PATH

# Source global definitions
if [ -f /etc/bashrc ]; then
	. /etc/bashrc
fi

source "/gscratch/comdata/env/cdsc_klone_bashrc"

if [[ "$LOGIN_NODE" == 0 ]]; then
:
else

# Uncomment the following line if you don't like systemctl's auto-paging feature:
# export SYSTEMD_PAGER=

# User specific aliases and functions
umask 007
export APPTAINER_BIND="/gscratch:/gscratch,/mmfs1:/mmfs1,/gpfs:/gpfs,/sw:/sw,/usr:/kloneusr,/bin:/klonebin"

export OMP_THREAD_LIMIT=40
export OMP_NUM_THREADS=40
                                                                                                              
export PATH="$PATH:/gscratch/comdata/users/$(whoami)/bin:/gscratch/comdata/local/spark:/gscratch/comdata/local/bin"
source "/gscratch/comdata/users/nathante/spark_env.sh"
export _JAVA_OPTIONS="-Xmx362g"
fi
</syntaxhighlight>