Contents

  1. Linux for Science : or How I set up my Dell laptop
    1. Power management
    2. Problems with Dell XPS touchpad
      1. Multi-touch gestures
      2. libinput settings
    3. Firewall
    4. Printers
      1. CUPs
      2. Samsung printers
    5. Problems with a high-res screen
      1. Gnuplot
    6. Wireless Network
    7. Wired Network
    8. Zotero
    9. One Drive: Syncing with a Windows machine
      1. Old Instructions follow

Navigation:

Linux for Science : or How I set up my Dell laptop

Power management

Installed tlp today using 

  $ sudo apt install tlp tlp-rdw

Still testing to see if power management improves. I was getting about 7-8h of battery life before. That was OK, but the battery could drain rather quickly when sleeping. It once drained almost completely overnight. The laptop was warm when I pulled it out of the case! I am hoping that tlp will be able to stop or reduce the hibernating power draw.

Verdict: No appreciable change in power draw. Sometimes the laptop sleeps well enough without much power draw, but at other times the draw is significant (20-30% per night!).

Problems with Dell XPS touchpad

Basically, the Synaptics driver made my life a mess. The touch pad was excessively sensitive and the cursor would jump places as I typed. This was untenable.

I removed Synaptics and installed libinput. That worked very well. More on this to follow.

Important

Dell has a solution to the problem

See their description on this page as they talk you through the process of removing Synaptics and installing libinput.

Here is a PDF copy of their instructions.

Multi-touch gestures

Not yet tried this but have a look at http://askubuntu.com/questions/789915/ubuntu-16-04-multitouch-gestures. In particular see the Github wiki at https://github.com/bulletmark/libinput-gestures.

libinput settings

This file is in /usr/share/X11/xorg.conf.d/90-libinput.conf 

# Match on all types of devices but tablet devices and joysticks
Section "InputClass"
        Identifier "libinput pointer catchall"
        MatchIsPointer "on"
        MatchDevicePath "/dev/input/event*"
        Driver "libinput"
EndSection

Section "InputClass"
        Identifier "libinput keyboard catchall"
        MatchIsKeyboard "on"
        MatchDevicePath "/dev/input/event*"
        Driver "libinput"
EndSection

Section "InputClass"
        Identifier "libinput touchpad catchall"
        MatchIsTouchpad "on"
        MatchDevicePath "/dev/input/event*"
        Driver "libinput"
        Option "Tapping" "true"
        Option "NaturalScrolling" "true"
        Option "ClickMethod" "clickfinger"
        Option "ScrollMethod" "twofinger"
EndSection

Section "InputClass"
        Identifier "libinput touchscreen catchall"
        MatchIsTouchscreen "on"
        MatchDevicePath "/dev/input/event*"
        Driver "libinput"
EndSection

libinput settings can be changed using:

Firewall

Use ufw. Instructions from https://help.ubuntu.com/lts/serverguide/firewall.html

Printers

CUPs

First you need to add yourself to the lpadmin group. In terminal: 

sudo usermod -aG lpadmin <username>

Next, restart CUPs. This can be done by typing: 

sudo /etc/init.d/cups restart

into the terminal.

To get to the CUPs web interface open up http://localhost:631/ in your web browser. When asked for a user name and password you can use you log-in user-name and password.

If the interface does not open, then CUPs may need to be re/started. First check to see if it is running: 

systemctl status cups.service

If not, restart it 

systemctl enable cups.service

These commands may need to be sudo'd.

Samsung printers

Before trying to install a Samsung printer, install the PPD files and drivers from Samsung:

Problems with a high-res screen

Gnuplot

By default plots were absurdly small and fonts small too. Enlarging the plots was not an option as the graph would get bigger, but line widths, fonts etc. would remain tiny. There is a way of setting up Gnuplot to change defaults so that plots are mostly viewable. You do this by editing the system gnuplotrc file in: 

/usr/share/gnuplot5/gnuplot/5.0/gnuplotrc

to include the line:

The default graph size was something I had to figure out by trial and error. The rest of the settings should be obvious.

Wireless Network

This worked from the start, but would occasionally not show known networks I had previously connected to. This can be resolved by rescanning for available networks using:

rescan_netowrk.bash 

sudo iwlist wlp58s0 scan

Wired Network

I have been using a Cable Matters USB-C to multiport dongle that supports an ethernet port. Some issues:

Zotero

I downloaded and installed the code in $HOME/bin/ and start it from there and leave it running.

One Drive: Syncing with a Windows machine

The information below is now old and things seem to have got much better. Here are new instructions from https://www.maketecheasier.com/sync-onedrive-linux/.

For Ubuntu:

If you are using Ubuntu 18.04 or newer, use snap to install dmd:

If not:

After installing the dependencies, fetch the files with git:

And compile and install it:

After you have done this, now you need to authorize onedrive with Microsoft so it can access your account. Simply enter the following in the Terminal:

And it will prompt you to visit the URL to get authorization. Log in to your OneDrive account, and grant the app permission to access your account.

Once this is done, you will be presented with a blank white page. Copy the URL and paste it into the Terminal at the prompt.

This will complete the setting up.

To start synchronizing OneDrive to your local folder, run

Onedrive will start downloading all your files in the cloud to your local folder.

Alternatively, you can run:

to get it to monitor your local folder for changes.

Configuration You can find the “config” file at the onedrive git folder. To make it active, move it to the “~/.config/onedrive/” folder.

Open the config file. There are three options that you can configure: “sync_dir” and “skip_files.”

sync_dir: the location to store your OneDrive files. All files placed in/removed from this folder will be synced to the cloud. skip_files: the file type (or file pattern) that won’t be synced. monitor_interval: the time interval between sync operations. Once you have made the changes, save and restart onedrive.

At any time, you can check your configuration with the command:

Old Instructions follow

I have a Surface tablet and use OneDrive a lot. Luckily you can get OneDrive to sync on a Linux machine too. Here's information about OneDrive on Linux:

The first step to installing onedrive-d is to open a terminal window and clone the source code from git using the following command:

If you don’t have “git” installed, you can install it with the command: 

sudo apt-get install git
Now change directory into the onedrive-d folder:
{{{
cd onedrive-d
And run the install script:
{{{
./inst install
Enter your Ubuntu password if prompted. The installation script will download and install any dependencies via “apt-get”. Accept the list of packages to install.

You will then be asked to accept the permissions for onedrive-d so that it can “Access and edit your OneDrive” and “Access your info anytime.” These are necessary for onedrive-d to perform the sync operations.

Next click on “(None)” in the dropdown box just below where it says “The local folder to sync with your OneDrive.” Click “Other…” and use “Create Folder” on the file open dialog to create a new folder called “OneDrive.” Select the “OneDrive” directory as the sync folder.

To finish, click on “Close” and then on “Yes” to confirm that you want to save your preferences. The onedrive-d daemon doesn’t run automatically at system boot, so you need to start it manually by typing the following in a terminal window:
{{{
onedrive-d
  
There is more information and screen-captures at the link above.

== Setting up Compiz ==
=== Multiple desktops/workspaces ===
By default Ubuntu gives you 4 desktops/workspaces. I wanted six. Install Compiz Config setting manager
{{{
sudo apt-get install compizconfig-settings-manage
See the site [[http://askubuntu.com/questions/764625/how-to-set-6-workspaces-in-ubuntu-mate-16-04-using-compiz|for details of setting up more than 4 desktops]]. This site [[https://www.maketecheasier.com/tweak-number-workspaces-unity/|tells you more about the Unity Tweak Tool]] that I may have tried.

=== Stopping the screen flicker on display wake-up ===
The screen, or some windows in the screen, flickers when the display wakes up. This happens often and is irritating even though it can be stopped by moving between desktops. There is a compiz setting that fixes this issue:

Make sure you have Compiz installed and enable "Don't wait for video sync" and "Force complete redraw on initial damage"

Compiz -> Utility -> Workarounds -> Don't wait for video sync

Compiz -> Utility -> Workarounds -> Force complete redraw on initial damage

Taken from [[https://askubuntu.com/questions/883067/ubuntu-16-10-screen-flicker-after-monitor-wake-up|the discussion here.]]

== Python ==
The basic python modules I need are:
  * matplotlib
  * numpy
  * scipy
  * ipython
  * These (and others) are needed for python2 and python3

Also needed are:
  * Jupyter (for python notebooks) 

=== Jupyter ===
Information from:
  - [[https://www.digitalocean.com/community/tutorials/how-to-set-up-a-jupyter-notebook-to-run-ipython-on-ubuntu-16-04|Jupyter installation and tutorial]]
  - [[http://stackoverflow.com/questions/28831854/how-do-i-add-python3-kernel-to-jupyter-ipython|Versions of Python]]


Install Python 2.7, Python Pip, and Python Development:
{{{
sudo apt-get -y install python2.7 python-pip python-dev
Something similar will need to be done for python3.x

Installing python2.7 will update to the latest version of Python 2.7, and python-pip will install Pip which allows us to manage Python packages we would like to use. Some of Jupyter’s dependencies may require compilation, in which case you would need the ability to compile Python C-extensions, so we are installing python-dev as well.

To verify that you have python installed:
{{{
python2 --version
and, for pip use
{{{
pip2 --version

Now install iPython 
{{{
sudo apt-get -y install ipython ipython-notebook
Now we can move on to installing Jupyter Notebook:
{{{
sudo -H pip install jupyter

=== Python kernel to Jupyter ===
Jupyter will need a kernel for python2 and python3. 
This information is from [[http://stackoverflow.com/questions/28831854/how-do-i-add-python3-kernel-to-jupyter-ipython|Versions of Python]].

Make sure you have ipykernel installed and use ipython kernel install to drop the kernelspec in the right location for python2. Then ipython3 kernel install for Python3. Now you should be able to chose between the 2 kernels regardless of whether you use jupyter notebook, ipython notebook or ipython3 notebook (the later two are deprecated).

Note that if you want to install for a specific Python executable you can use the following trick:

path/to/python -m ipykernel install <options>
This works when using environments (venv,conda,...) and the <options> let you name your kernel (see --help). So you can do

conda create -n py36-test python=3.6
source activate py36-test
python -m ipykernel install --name py36-test
source deactivate
And now you get a kernel named py36-test in your dropdown menus, along the other ones.

See [[http://stackoverflow.com/questions/30492623/using-both-python-2-x-and-python-3-x-in-ipython-notebook|Using both Python 2.x and Python 3.x in IPython Notebook]] which has more recent information.

Information from the above link follows:

=== Python kernels ===
The idea here is to install multiple ipython kernels. Here are instructions for anaconda. If you are not using anaconda, I recently added instructions using pure virtualenvs.

'''Anaconda 4.1.0'''

Since version 4.1.0, anaconda includes a special package ''nb_conda_kernels'' that detects conda environments with notebook kernels and automatically registers them. This makes using a new python version as easy as creating new conda environments:

{{{
conda create -n py27 python=2.7 ipykernel
{{{
conda create -n py36 python=3.6 ipykernel
After a restart of jupyter notebook, the new kernels are available over the graphical interface. Please note that new packages have to be explicitly installed into the new enviroments. The Managing environments section in conda's docs provides further information.

'''Manually registering kernels'''

Users who do not want to use nb_conda_kernels or still use older versions of anaconda can use following steps to manually register ipython kernels.

configure the python2.7 environment:
{{{
conda create -n py27 python=2.7
{{{
source activate py27
{{{
conda install notebook ipykernel
{{{
ipython kernel install --user
configure the python3.6 environment:
{{{
conda create -n py36 python=3.6
{{{
source activate py36
{{{
conda install notebook ipykernel
{{{
ipython kernel install --user
After that you should be able to choose between python2
and python3 when creating a new notebook in the interface.

Additionally you can pass the --name and --display-name options to ipython kernel install if you want to change the names of your kernels. See ipython kernel install --help for more informations.


=== Some more kernel suggestions ===
This worked for me on Ubuntu 16.04:

{{{
python2 -m pip install ipykernel

python2 -m ipykernel install --user