HPCC The .bashrc File
The .bashrc file
The .bashrc file is a file in your home directory that sets up your kernel environment every time you log onto the HPCC. In order to be more efficient, we make custom commands aka aliases to make our lives easier. We also need to add specific modules and settings to our local bash environment in order for the DFT programs to run. The .bashrc file is located in your home directory.
Steps to Edit and "Refresh" your .bashrc file
- Use your text editor of choice. The file path is always
~/.bashrc - Add or change the lines of the .bashrc file.
- Save the changes.
- Run the command
source ~/.bashrc- This command will rerun your .bashrc file and apply the changes you made to the linux environment.
- It is also suitable to log out and log back into the terminal to "refresh" your .bashrc file.
Example .bashrc File
This example starter bashrc file shown below is also located here /home/tristfis/AQUINO_COURSE/250825/instructions/EXAMPLE.bashrc.
You can copy this file to be your bashrc file by using this command:
cd; cp /home/tristfis/AQUINO_COURSE/250825/instructions/EXAMPLE.bashrc .bashrc; ln -is .bashrc .profile; source ~/.bashrc
[ -z "$PS1" ] && return
#leave these for parallel computing
ulimit -s unlimited 1>/dev/null 2>/dev/null
ulimit -l unlimited 1>/dev/null 2>/dev/null
#set prompt, optional
PS1='`/bin/hostname -s`:`echo $PWD | sed "s=$HOME=="`$ '
#after creating .bashrc, link this to .profile
#cd;ln -is .bashrc .profile
#R/W Permissions for specific user:
# chmod a+rx $user
# setfacl -R -m u:$user:rX */
##### PathLists ######
LUS=/lustre/scratch/$USER
WRK=/lustre/work/$USER
JERI=/home/jerizamo
TRIS=/home/tristfis
JERE=/home/jerschro
AQUI=/home/aaquino
######################
########## ENVIRONMENTS ##############################################################################
#__________General
export PATH=$PATH:.
export PATH=$HOME/bin:$PATH
#__________Turbomole
export TURBODIR=/home/hlischka/programs/TURBOMOLE-7.5/TURBOMOLE
export PATH=$TURBODIR/scripts:$PATH
export PATH=$TURBODIR/bin/`sysname`:$PATH
#__________Conda
source $HOME/conda/etc/profile.d/conda.sh
export PATH=$HOME/conda/bin:$PATH
#__________gnuPlot
alias gnuplt='module load gcc/10.1.0; module load gnuplot; echo "starting gnuplot."; sleep 2; gnuplot'
#__________Orca
export ORCADIR=/lustre/work/rnieman/orca_5_0_1_linux_x86-64_shared_openmpi411
export PATH=$ORCADIR:$PATH
export LD_LIBRARY_PATH=$ORCADIR:$LD_LIBRARY_PATH
######################################################################################################
############ MODULES ############
#module load intel gnuplot gnu
#module load gcc/9.2.0 molden/6.5
#module load gcc/10.2.0
#module load gnuplot
#################################
#### Scripts & Functions ####
shopt -s cdspell #spelling corrections
shopt -s checkhash
shopt -s checkwinsize
shopt -s no_empty_cmd_completion
shopt -s cmdhist
shopt -s histappend histreedit histverify
shopt -s extglob # Allows boolean completion.
source $HOME/bin/*.sh
#############################
########## Aliases ##########
###_General
alias rm='rm -i'
alias mv='mv -i'
alias grep='grep --color=auto'
alias ll='ls -lahF --color=auto'
alias ls='ls --color=auto'
alias diff='diff -ys --suppress-common-lines --width=$(tput cols)' # USAGE: diff <(echo $string) <(...)
alias src='export PATH="/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/dell/srvadmin/bin"; source ~/.bashrc'
###_Directory Switch
alias lus=' cd /lustre/scratch/$USER '
alias wrk=' cd /lustre/work/$USER '
###_HPCC Jobs
alias myq='qstat'
alias sgeqst='qstat -u "*"'
alias qlist=" qstat -g c"
alias sq='squeue -u $USER'
###_Py-Stuff
alias coa='conda activate'; alias cod='conda deactivate'
###_Misc.
alias vi='vim'
alias ftp_vsc='sftp 172.16.21.58'
#############################
Commands Needed for Turbomole
If you are using Turbomole, you will need to have these lines in your .bashrc file in order for Turbomole to run correctly.
export TURBODIR=/home/hlischka/programs/TURBOMOLE-7.5/TURBOMOLE
source $TURBODIR/Config_turbo_env
export PATH=$TURBODIR/scripts:$PATH
export PATH=$TURBODIR/bin/`sysname`:$PATH
Aliases Recommended for Ease of Use
Replace eraider with your eraider/hpcc account name.