Archive for December, 2018

Installing Debian on Lenovo Thinkpad Carbon X-1 (Gen 6)

Posted December 17, 2018 By grigoris

It is exciting to have a new machine, such the Lenovo Thinkpad X-1, but the process for setting it up can be a bit tedious. So this is a small guide what worked or didn’t through my small experience in installing Debian linux. [Just for the fun of it I proceeded with the installation of Win which was really easy with all vocal commands! But they wouldn’t live long … ]

BIOS boot

I started by downloading the net/CD image for Debian 9 (‘stretch’) and putting it to a USB key. I plugged the key at the laptop and started the booting process. First problem: even though it could see the USB and it showed the Debian distro it wouldn’t start. I couldn’t figure out at all why up to the point that I noticed that the new hardware has new BIOS technology called UEFI (yes … I hadn’t installed anything for a looong time!). I went to BIOS > Startup > UEFI/Legacy Boot which was ‘UEFI only’ and I changed the CSM Support to ‘Yes’. But this alone was not enough. So, I changed the UEFI/Legacy Boot from ‘UEFI only’ to ‘Both’ [where I think it should be also to put ‘Legacy only’ if you plan to run on Linux only, but if Win are necessary then leave both].

Debian installation

Then the USB key would finally load and the installation could start. With the graphical installation of Debian the screen goes blank after some time of inactivity, which you can correct with a small movement of the mouse. But since I didn’t have any mouse connected I though that something was wrong. It took me a few iterations before I understand that, which I find ridiculous when you install an operating system. I think that the monitor should be on at all times! The installation went on without any other issues. After logging in the new system, I updated all packages.

Trackpoint/Trackpad issue

At the beginning the trackpad (touchpad) could work with some lag. The trackpoint didn’t work at all but I didn’t pay any serious attention to that. I installed the wifi driver (firmware-iwlwifi, for Intel chips) and after that the touchpad wouldn’t work at all. This is a known problem and many solutions are offered (updating to latest kernel 4.18 and to Debian testing didn’t work). However (and after some iterations of the installation process) I finally went to BIOS > Config > Keyboard/Mouse > Trackpoint and I ‘Disabled’ it. That way the touchpad works without any issue. [At this point it is not so urgent for me to fix this, but I will come back in the future].

Suspend mode

There is a know issue that certain BIOS version have serious problems to recover when suspending the laptop. I learned that the hard way: after suspending the laptop when I was trying to put my password over and over again, as every time it would accept only a few characters before it accepted that raised errors of incorrect password. I had to brutally shut it down (pressing the power button) but for whatever reason the x-server would start. So I had only text access and I couldn’t restarted it (of course I may have missed some more appropriate approaches). Anyway, I re-install Debian from scratch. In order to solve that I needed to update the BIOS.

BIOS update with fwupd

There is a new easy way to update firmware and BIOS through Linux by using the fwupd. After the fresh installation I set this as my first target before I install anything else. fwupd was at Debian repository so it was simply to install it. And the instruction are really easy to follow. Only do ‘fwupdmgr refresh’ to get the latest metadata for you firmware. But at this point it was failing to connect to the webpage (error message: “Failed to download Not Found”). The issue (Debian bug #912414) was simply a wrong site, which was easy to fix by going to the config file “/etc/fwupd.conf” and replace: “DownloadURI=” with the new site: “DownloadURI=”. That should do the work, right? NO! Because the version of fwupd installed in Debian 9 is 0.7 and according to Richard Hughsie: “LVFS will block old versions of fwupd for some firmware […] The ability to restrict firmware to specific versions of fwupd and the existing firmware version was added to fwupd in version 0.8.0. This functionality was added so that you could prevent the firmware being deployed if the upgrade was going to fail, either because: i. The old version of fwupd did not support the new hardware quirks, ii. If the upgraded-from firmware had broken upgrade functionality. Then, let’s upgrade fwupd by upgrading (at the same time it would be nice to have a fully fresh new system) and I switched the repositories to Debian 10 (testing, named ‘buster’), upgrading also the Linux kernel from 4.9 to 4.18. And indeed the fwupd now was working! Almost…

BIOS update with USB key

I run fwupd to get the latest BIOS version but it refused. The installed version was 1.25 while only those >1.27 are upgradable with fwupd. Now the only solution is the classic one, i.e. download the last Thinkpad BIOS update (bootable, for Windows) and install it directly from a USB. After having downloaded the .iso image I followed the instructions by Vivek Gite (with most important part the video showing what to do during the actual BIOS installation).

[In brief, using the El Torito boot image extractor (debian package name: genisoimage) do the following:
geteltorito -o bios.img n23ur13w.iso
sudo dd if=bios.img of=/dev/sdb1 bs=1M

Take care that you know exactly which device is the USB key you are going to write to, else you are going to delete data!
Then reboot and enter BIOS and boot from the USB. Select option 3 to verify that you have the right model (in case you press something and you cannot cancel just retype the model number) and then press 2 to start the actual BIOS update. This will run some things now and then when you reboot it will continue before it shows the booting screen.]

Crossing fingers and … booting again! phew… everything is working and indeed I have now the latest version (1.34).

As a (much) later version of the BIOS it should have fixed the issue with suspending mode. Did it work? So far I have experienced any critical issues. What I did noticed though is that that I could feel it a bit hot when suspending. I was going through the BIOS setting and I discovered that there is an option now with respect to the sleep state (I don’t know if it was present in the previous version): Config > Power > Sleep State, which has two options ‘Windows 10’ and ‘Linux’. I obviously picked the last one to optimize the performance and I think it is working now.

Python pip

Finally, the time that I would actually install what I need to start working has arrived! Since Python2.x and 3.x exist I was going to use pip only to install all necessary packages. I installed pip for both Python versions from the distro repositories. Checking the pip site I saw the following recommendation: “Ensure pip, setuptools, and wheel are up to date, by doing: python -m pip install –upgrade pip setuptools wheel”.

Well, first of all … DON’T DO IT! I missed the obvious warning sign above:

Be cautious if you’re using a Python install that’s managed by your operating system or another package manager. does not coordinate with those tools, and may leave your system in an inconsistent state. You can use python –prefix=/usr/local/ to install in /usr/local which is designed for locally-installed software.

By default the pip version provided by the Debian repositories is 9.x. When I did this upgrade I got the latest version of 18.x and I went on to install numpy, scipy, matplotlib. But when I started python to try out the installation nothing was working! Even worse:

pip install astropy
Traceback (most recent call last):
File "/usr/bin/pip3", line 9, in from pip import main
ImportError: cannot import name 'main'

What is going on now? Apparently is it not a good idea to upgrade with pip a system installation of pip, as then pip gets confused of which version to use exactly and, even worse, some scripts managed by apt may break (see e.g. the discussion in github issues #5447 and #5221). So the two important advice here are:
1. upgrade/install under user (with –user)
2. avoid running pip with sudo (which may affect root accessed files)

I found various ways to fix this over the internet, but I opted for a more … brutal way. I noticed that when installing Python packages from the repositories of the distribution everything is installed under the /usr/lib/python*.*/dist-packages/ while pip puts everything under /home/user/.local/lib/site-packages/. So, the idea was to remove (manually delete) everything under these directories. Then I could re-install pip and the Python packages and it should be clean from all errors. I did that but I continued to get errors, but probably that was because I didn’t re-source the terminal (so paths to the previous packages and scripts were still active). After a reboot I found everything working fine. [One note: after a fresh installation everything is new, such as the content of $PATH. When I installed jupyter and tried to run it I got an error “command not found”, obviously because I forgot to update the $PATH to include the ~/.local/bin/ directory, where binaries from pip are stored.]


Other resources

The above is a personal (certainly not the wisest) experience to install Debian 9/10 (stable/testing) to Thinkpad X-1. There are also more thorough and knowledgeable guides out there (which I have to check also for other issues), such as:
–> Installing Debian On Thinkpad X1 Carbon 5th Gen (previous generation)
–> Lenovo ThinkPad X1 Carbon (Gen 6) by Arch linux

New paper on rho Cas and its recent outburst in 2013

Posted December 11, 2018 By grigoris

A new outburst of the yellow hypergiant star Rho Cas

Michaela Kraus, Indrek Kolka, Anna Aret, Dieter H. Nickeler, Grigoris Maravelias, Tõnis Eenmäe, Alex Lobel, Valentina G. Klochkova

Yellow hypergiants are evolved massive stars that were suggested to be in post-red supergiant stage. Post-red supergiants that evolve back to the blue, hot side of the Hertzsprung-Russell diagram can intersect a temperature domain in which their atmospheres become unstable against pulsations (the Yellow Void or Yellow Wall), and the stars can experience outbursts with short, but violent mass eruptions. The yellow hypergiant Rho Cas is famous for its historical and recent outbursts, during which the star develops a cool, optically thick wind with a very brief but high mass-loss rate, causing a sudden drop in the light curve. Here we report on a new outburst of Rho Cas which occurred in 2013, accompanied by a temperature decrease of ~3000 K and a brightness drop of 0.6 mag. During the outburst TiO bands appear, together with many low excitation metallic atmospheric lines characteristic for a later spectral type. With this new outburst, it appears that the time interval between individual events decreases, which might indicate that Rho Cas is preparing for a major eruption that could help the star to pass through the Yellow Void. We also analysed the emission features that appear during phases of maximum brightness and find that they vary synchronous with the emission in the prominent [CaII] lines. We conclude that the occasionally detected emission in the spectra of Rho Cas, as well as certain asymmetries seen in the absorption lines of low to medium-excitation potential, are circumstellar in nature, and we discuss the possible origin of this material. 1812.03065