Useful commands¶

This section contains a collection of useful commands that I don’t use enough to remember.

Bash and general commands¶

On Fujitsu LIFEBOOK E Series use the <F2> key to enter the bios.
Find command:

# Find files or directory with specific name:
find [path] -name [\*part_of_filename*] -type f/d -print

# Find file with specific name **and** which contains a specific string:
find [path] -name [\*part_of_filename*] -type f -exec grep [string] '{}' \; -print

# Remove all files except the ones matching a specific string:
find . ! -name [\*part_of_filename*] -exec rm -rf {} +

Merge different pdf files into a single one:

pdftk in1.pdf in2.pdf cat output out1.pdf

Create symbolic link:

ln -s source_file myfile

Tar compression and extraction:

tar -czvf name-of-archive.tar.gz /path/to/directory-or-file
tar -xzvf name-of-archive.tar.gz

Managing packages:

# update package list:
sudo apt-get update

# upgrade installed package:
sudo apt-get upgrade

# remove unused package:
sudo apt-get autoremove

# install package:
sudo dpkg -i filename.deb

Print the total disk space used inside the current directory:
```
du -sh *
```
Shutdown from command line:
```
sudo /sbin/shutdown -r now
```
To get ID of running jobs (on background):
```
jobs -l
# or better
ps -u pbaudin
```
To produce a diff file between two directories, for example a patch for CPMD:
```
diff -ruN -x '.svn' -x '.git' cpmd_new/ cpmd_ref/ > patch
```

Description of options: -r is for recursive, -u is to add 3 lines of context arround diffs, and -N is to treat absent files as empty. The -x allows to exclude files from the diff and should be repeated as many times as required.

To print fortran code in a pretty format:

a2ps --pretty-print=fortran --pro=color -Ppdf print.F90

Open a file (e.g. .doc or .png) from command line using default application:

gnome-open myfile
# or
xdg-open myfile

It can be convenient to put the following alias in the .bashrc file:

alias open='xdg-open'

Setting the cell dimension in vmd (usefull when plotting g(r)):

pbc set {30.0 30.0 30.0} -all

Set up new computer cluster¶

Copy rc and other configuration files from laptop to cluster:

scp -r ~/.bashrc \
    ~/.git-completion.bash \
    ~/.gitignore_global \
    ~/.gitconfig \
    ~/.vimrc \
    ~/.vim/ \
    ~/.ssh/config \
    cluster:~

Where cluster is the ssh label of the cluster from the ~/.ssh/config file.

Generate ssh key for git:

ssh-keygen -t rsa -C "pablo.baudin@epfl.ch" -b 4096

Go to https://gitlab.com/profile/keys to add the key.

Git set up¶

Note

This is not needed if the gitconfig and other git files have been copied above

Global settings when using git on new station:

# general settings
git config --global user.name "Pablo Baudin"
git config --global user.email "pablo.baudin@epfl.ch"
git config --global core.editor vim
git config --global color.branch auto
git config --global color.diff auto
git config --global color.status auto
git config --global core.excludesfile ~/.gitignore_global

# Tools for merge and diff:
git config --global diff.tool vimdiff
git config --global diff.merge vimdiff
git config --global difftool.prompt false

# Alias (maybe too much?):
git config --global alias.st status
git config --global alias.d difftool

Set the default mode for git push (current, matching or tracking):

git config --global push.default current

Disable fast-forward merges:

git config branch.master.mergeoptions "--no-ff"

Add the .git-completion.bash file to your home.

Git commands¶

Create new branch:

git checkout -b <local-branch-name>
git push -u origin <local-branch-name>

If push.default = current is set then the -u option will track remote branch of same name.

Delete branch:

git push origin --delete <remote-branch-name>
git branch -d <local-branch-name>

Show all branches:

git branch -a

Vim commands¶

In the root directory of a fortran code, run

ctags --fortran-kinds=+i -R *
# or with the bash alias (inside the .bashrc file)
ct

For a python code, run

ctags --exclude=*.pyc --python-kinds=-i -R *
# or with the bash alias (inside the .bashrc file)
ctpy

This will create a tag file that can be used by vim. In your .vimrc file, insert the following lines:

set tags=./tags;/
map <C-h> :split <CR>:exec("tag ".expand("<cword>"))<CR>
map <C-g> :vsp <CR>:exec("tag ".expand("<cword>"))<CR>

It is then possible to navigate inside the code from vim and to use auto-completion of functions and variables when writing code.

For opening the file containing the definition of the function or variable

under the cursor use <Ctrl-G> (vertical split) or <Ctrl-H> (horizontal split).
For auto-completion, use either <Ctrl-N> or <Ctrl-P>.

When pasting already indented code press <F8> to enter paste mode and avoid extra indentation. It works with the line

set pastetoggle=<F8>

in .vimrc.

For spell checking, I have set the following

map <silent> <F7> "<Esc>:silent setlocal spell! spelllang=en<CR>"
map <silent> <F6> "<Esc>:silent setlocal spell! spelllang=fr<CR>"

when spell checl is set, correction suggestions are available by typing z= in command mode.

Create hotspot on linux mint¶

If you have wired connection, then do this:

Go to “Network Connections” from bottom-corner networking icon.
Click on “Add” and choose “Wi-Fi” option.
Give the connection name (to adapter not SSID).
Provide a name of your hotspot in SSID field.
Set mode to Hotspot.
Select the (only?) availeble option under “Device”. wlp2s0 (48:51:B7:71:D4:37)
Go to “Wi-Fi Security” and choose “WPA & WPA2 personal” or any type of security of your preference and set up a good password.
Now, go to “IPv4 Settings” and set the “Mode” to “Shared to other computers”.
Save your settings and connect your hotspot from “Connect to Hidden Network…” and you’re done.