set up odyssey HPC dot files

dot files

Those files are originally got from Samir Amin, my labmate in Roel Verhaak’s lab. Thanks for sharing!

.screenrc
.bashrc
.bash_profile

and inside .profile.d folder, there is a file named 01_odyssey_config.sh. It was executed when you login the shell.

You can grab my dot files in my github repo.

Inside the .bash_profile:

if [ -d $HOME/.profile.d ]; then
  for i in $HOME/.profile.d/*.sh; do
    if [ -r $i ]; then
          if [ "${-#*i}" != "$-" ]; then
            . "$i" >/dev/null 2>&1
        else
            . "$i" >/dev/null 2>&1
        fi
    fi
  done
  unset i
fi

add or remove path in the 01_odyssey_config.sh file. load modules in this file as well.

install conda

install conda to my home directory /n/home02/mtang

After finishing installing, it will ask

Do you wish the installer to initialize Anaconda3
in your /n/home02/mtang/.bashrc ? [yes|no]

I chosed no. It showed me

You may wish to edit your /n/home02/mtang/.bashrc to setup Anaconda3:

source /n/home02/mtang/anaconda3/etc/profile.d/conda.sh

Thank you for installing Anaconda3!

I guess I got why Samir set up the dot files (has a .profile.d folder) like this. conda is doing similar with source /n/home02/mtang/anaconda3/etc/profile.d/conda.sh

add conda to PATH:

In the ~/.profiled.d/01_odyssey_config.sh, add one line:

mypathmunge ${HOME}/anaconda3/bin

mypathmunge is a function inside the .bash_profile

mypathmunge () {
    case ":${PATH}:" in
        *:"$1":*)
            ;;
        *)
            if [ "$2" = "after" ] ; then
                PATH=$PATH:$1
            else
                PATH=$1:$PATH
            fi
    esac
}

it will add the ${HOME}/anaconda3/bin in front of the $PATH. If you want to append it to $PATH, do mypathmunge ${HOME}/anaconda3/bin after

source .bash_profile
which conda
~/anaconda3/bin/conda

A side note. see here for the difference between .bashrc and .bash_profile.

.bash_profile is executed for login shells, while .bashrc is executed for interactive non-login shells.

When you login (type username and password) via console, either sitting at the machine, or remotely via ssh: .bash_profile is executed to configure your shell before the initial command prompt.

But, if you’ve already logged into your machine and open a new terminal window (xterm) then .bashrc is executed before the window command prompt. .bashrc is also run when you start a new bash instance by typing /bin/bash in a terminal.

On OS X, Terminal by default runs a login shell every time, so this is a little different to most other systems, but you can configure that in the preferences.

This is a very helpful blog post to understand the differences.

Dedicating a folder for installing tools

usually, install tools with conda. If there is no recipe in conda. I will downlad the source to ~/apps and compile there.

Then in the ~/.profiled.d/01_odyssey_config.sh file, add the executable to the PATH.

e.g. I want to install ncdu to check disk usage

mkdir apps
cd apps
mkdir ncdu; cd ncdu
wget https://dev.yorhel.nl/download/ncdu-1.13.tar.gz
tar xvzf  ncdu-1.13.tar.gz
cd ncdu-1.13

./configure --prefix=${HOME}/apps/ncdu/ncdu-1.13
make 
make install

In the ~/.profiled.d/01_odyssey_config.sh file, add two lines:

export ODYAPPS="${HOME}/apps
mypathmunge $ODYPPS/ncdu/ncdu-1.13/bin after

source ~/.bash_profile
# now ready to go
ncdu