Technology Tales

Accessing Julia REPL command history

In the BASH shell used on Linux and UNIX, the history command calls up a list of recent commands used and has many uses. There is a .bash_history file in the root of the user folder that logs and provides all this information, so there are times when you need to exclude some commands from there, but that is another story.

The Julia REPL environment works similarly to many operating system command line interfaces, so I wondered if there was a way to recall or refer to the history of commands issued. So far, I have not come across an equivalent to the BASH history command for the REPL itself, but there the command history is retained in a file like .bash_history. The location varies on different operating systems, though. On Linux, it is ~/.julia/logs/repl_history.jl while it is %USERPROFILE%\.julia\logs\repl_history.jl on Windows. While I tend to use scripts that I have written in VSCode rather than entering pieces of code in the REPL, the history retains its uses. Thus, I am sharing it here for others. In the past, the location changed, but these are the ones with Julia 1.8.2, the version that I have at the time of writing.

Removing obsolete libraries from Flatpak

Along with various pieces of software, Flatpak also installs KDE and GNOME libraries needed to support them. However, it does not always remove obsolete versions of those libraries whenever software gets updated. One result is that messages regarding obsolete versions of GNOME may be issued and this has been known to cause confusion because there is the GNOME instance that is part of a Linux distro like Ubuntu and using Flatpak adds another one for its software packages to use. My use of Linux Mint may lessen the chances of misunderstanding.

Thankfully, executing a single command will remove any obsolete Flatpak libraries so the messages no longer appear and there then is no need to touch your actual Linux installation. This then is the command that sorted it for me:

flatpak uninstall --unused && sudo flatpak repair

The first part that removes any unused libraries is run as a normal user, so there is no error in the above command. Administrative privileges are needed for the second section that does any repairs that are needed. It might be better if Flatpak did all this for you using the update command, but that is not how the thing works. At least, there is a quick way to address this state of affairs and there might be some good reasons for having things work as they do.

Lightening of desktop background images on Linux Mint Debian Edition running in Virtualbox

After a recent upgrade to Linux Mint Debian Edition 3 in a VirtualBox virtual machine that I had running its predecessor, I began to notice that background images were being loaded with more washed out or faded colours. This happened at startup, so selecting another background image worked as intended until the same thing happened to that after a system restart.

This problem is not new and has affected the Cinnamon desktop in the main Linux Mint variant (the one that is based on Ubuntu) and issuing the following command in a terminal session is a suggested solution:

gsettings set org.cinnamon.muffin background-transition fade-in

In my case, that solved the problem and the desktop background image display is as it should be since I executed the above. All it took was a change to a system setting.

Sorting out sluggish start-up and shutdown times in Linux Mint 19

The Linux Mint team never forces users to upgrade to the latest version of their distribution, but curiosity often provides a strong enough impulse for me to do so. When I encounter rough edges, the wisdom of leaving things unchanged becomes apparent. Nevertheless, the process brings learning opportunities, which I am sharing in this post. It also allows me to collect various useful titbits that might help others.

Again, I went with the in-situ upgrade option, though the addition of the Timeshift backup tool means that it is less frowned upon than once would have been the case. It worked well too, apart from slow start-up and shutdown times, so I set about tracking down the causes on the two machines that I have running Linux Mint. As it happens, the cause was different on each machine.

On one PC, it was networking that holding up things. The cause was my specifying a fixed IP address in /etc/network/interfaces instead of using the Network Settings GUI tool. Resetting the configuration file back to its defaults and using the Cinnamon settings interface took away the delays. It was inspecting /var/log/boot.log that highlighted problem, so that is worth checking if I ever encounter slow start times again.

As I mentioned earlier, the second PC had a very different problem, though it also involved a configuration file. What had happened was that /etc/initramfs-tools/conf.d/resume contained the wrong UUID for my system's swap drive, so I was seeing messages like the following:

W: initramfs-tools configuration sets RESUME=UUID=<specified UUID for swap partition>
W: but no matching swap device is available.
I: The initramfs will attempt to resume from <specified file system location>
I: (UUID=<specified UUID for swap partition>)
I: Set the RESUME variable to override this.

Correcting the file and executing the following command resolved the issue by updating the affected initramfs image for all installed kernels and speeded up PC start-up times:

sudo update-initramfs -u -k all

Though it was not a cause of system sluggishness, I also sorted another message that I kept seeing during kernel updates and removals on both machines. This has been there for a while and causes warning messages about my system locale not being recognised. The problem has been described elsewhere as follows: /usr/share/initramfs-tools/hooks/root_locale is expecting to see individual locale directories in /usr/lib/locale, but locale-gen is configured to generate an archive file by default.  Issuing the following command sorted that:

sudo locale-gen --purge --no-archive

Following these, my new Linux Mint 19 installations have stabilised with more speedy start-up and shutdown times. That allows me to look at what is on Flathub to see what applications and if they get updated to the latest version on an ongoing basis. That may be a topic for another entry on here, but the applications that I have tried work well so far.

Trying out a new way to upgrade Linux Mint in situ while going from 17.3 to 18.1

There was a time when the only recommended way to upgrade Linux Mint from one version to another was to do a fresh installation with back-ups of data and a list of the installed applications created from a special tool.

Even so, it never stopped me doing my own style of in situ upgrade, though some might see that as a risky option. More often than not, that actually worked without causing major problems in a time when Linux Mint releases were more tightly tied to Ubuntu's own six-monthly cycle.

Linux Mint releases now align with Ubuntu's Long Term Support (LTS) editions. This means major changes occur only every two years, with minor releases in between. These minor updates are delivered through Linux Mint's Update Manager, making the process simple. Upgrades are not forced, so you can decide when to upgrade, as all main and interim versions receive the same extended support. The recommendation is to avoid upgrading unless something is broken on your installation.

For a number of reasons, I stuck with that advice by sticking on my main machine with Linux Mint 17.3 instead of upgrading to Linux Mint 18. The fact that I broke things on another machine using an older method of upgrading provided even more encouragement.

However, I subsequently discovered another means of upgrading between major versions of Linux Mint that had some endorsement from the project. There still are warnings about testing a live DVD version of Linux Mint on your PC first and backing up your data beforehand. Another task is ensuring that you are upgraded from a fully up-to-date Linux Mint 17.3 installation.

When you are ready, you can install mintupgrade using the following command:

sudo apt-get install mintupgrade

When that is installed, there is a sequence of tasks that you need to do. The first of these is to simulate an upgrade to test for the appearance of untoward messages and resolve them. Repeating any checking, until all is well, gets a recommendation. The command is as follows:

mintupgrade check

Once you are happy that the system is ready, the next step is to download the updated packages so they are on your machine ahead of their installation. Only then should you begin the upgrade process. The two commands that you need to execute are below:

mintupgrade download
mintupgrade upgrade

After these complete, restart your system. In my case, the process worked well, with only my PHP installation requiring attention. I resolved a clash between different versions of the scripting interpreter by removing the older one, as PHP 7 is best kept for testing. Apart from reinstalling VMware Player and upgrading from version 18 to 18.1, I had almost nothing else to do and experienced minimal disruption. This is fortunate as I rely heavily on my main PC. The alternative of a full installation would have left me sorting things out for several days afterwards because I use a customised selection of software.

Updating Piwik using the Linux Command Line

Because updating Piwik using its web interface has proved tempestuous, I have decided to update the self-hosted analytics application on an SSH session. The production web servers that I use are hosted on Linux systems, so that is why any commands apply to the Linux or UNIX command line only. What is needed for Windows servers may differ.

The first step is to down the required ZIP file with this command:

wget https://builds.piwik.org/piwik.zip

Once the download is complete, the contents of the ZIP archive are extracted into a new subfolder. This is a process that I carry out in a separate folder to that where the website files are kept before copying everything from the extraction folder in there. Here is the unzip command, and the -o switch turns on overwriting of any previously existing files:

unzip -o piwik.zip

Without the required folder in the web server area to be updated, the next step is to do the actual system update that includes any updates to the Piwik database that you are using. There are two commands that you can use once you have specified the location of your Piwik installation. The second is needed when the first option cannot find where the PHP executable is stored. My systems had something more specific than these because both PHP 5.6 and PHP 7.0 are installed. Looking in /usr/bin was enough to find what I needed to execute in place of PHP below. Otherwise, the command was the same.

./[path to piwik]/console core:update

php [path to piwik]/console core:update

While the upgrade is ongoing, it prompts you to permit it to continue before it goes and modifies the database. This did not take long on my systems, but that depends on how much data there is. Once, the process has completed, you can delete any extraneous files using the rm command.

Reloading .bashrc within a BASH terminal session

BASH is a command-line interpreter that is commonly used by Linux and UNIX operating systems. Chances are that you will find yourself in a BASH session if you start up a terminal emulator in many of these, though there are others like KSH and SSH too.

BASH comes with its own configuration files and one of these is located in your own home directory, .bashrc. Among other things, it can become a place to store command shortcuts or aliases. Here is an example:

alias us='sudo apt-get update && sudo apt-get upgrade'

Such a definition needs there to be no spaces around the equals sign, and the actual command to be declared in single quotes. Doing anything other than this will not work, as I have found. Also, there are times when you want to update or add one of these and use it without shutting down a terminal emulator and restarting it.

To reload the .bashrc file to use the updates contained in there, one of the following commands can be issued:

source ~/.bashrc

. ~/.bashrc

Both will read the file and execute its contents so you get those updates made available so you can continue what you are doing. There appears to be a tendency for this kind of thing in the world of Linux and UNIX because it also applies to remounting drives after a change to /etc/fstab and restarting system services like Apache, MySQL or Nginx. The command for the former is below:

sudo mount -a

Often, the means for applying the sorts of in-situ changes that you make are simple ones too, and anything that avoids system reboots has to be good since you have less work interruptions.

Compressing a VirtualBox VDI file for a Linux guest

In a previous posting, I talked about compressing a virtual hard disk for a Windows guest system running in VirtualBox on a Linux system. Since then, I have needed to do the same for a Linux guest following some housekeeping. Because the Linux distribution used is Debian, the instructions are relevant to that and maybe its derivatives such as Ubuntu, Linux Mint and their like.

While there are other alternatives like dd, I am going to stick with a utility named zerofree to overwrite the newly freed up disk space with zeroes to aid compression later on in the process for this and the first step is to install it using the following command:

apt-get install zerofree

Once that has been completed, the next step is to unmount the relevant disk partition. Luckily for me, what I needed to compress was an area that I reserved for synchronisation with Dropbox. If it was the root area where the operating system files are kept, a live distro would be needed instead. In any event, the required command takes the following form, with the mount point being whatever it is on your system (/home, for instance):

sudo umount [mount point]

With the disk partition unmounted, zerofree can be run by issuing a command that looks like this:

zerofree -v /dev/sdxN

Above, the -v switch tells zerofree to display its progress and a continually updating percentage count tells you how it is going. The /dev/sdxN piece is generic with the x corresponding to the letter assigned to the disk on which the partition resides (a, b, c or whatever) and the N is the partition number (1, 2, 3 or whatever; before GPT, the maximum was 4). Putting all this together, we get an example like /dev/sdb2.

Once, that had completed, the next step is to shut down the VM and execute a command like the following on the host Linux system ([file location/file name] needs to be replaced with whatever applies on your system):

VBoxManage modifyhd [file location/file name].vdi --compact

With the zero filling in place, there was a lot of space released when I tried this. While it would be nice for dynamic virtual disks to reduce in size automatically, I accept that there may be data integrity risks with those, so the manual process will suffice for now. It has not been needed that often anyway.

Killing Windows processes from the command line

During my days at work, I often hear about the need to restart a server because something has gone awry with it. This makes me wonder if you can kill processes from the command line, like you do in Linux and UNIX. A recent need to reset Windows Update on a Windows 10 machine gave me enough reason to answer the question.

Because I already knew the names of the services, I had no need to look at the Services tab in the Task Manager like you otherwise would. Then, it was a matter of opening up a command line session with Administrator privileges and issuing a command like the following (replacing [service name] with the name of the service):

sc queryex [service name]

From the output of the above command, you can find the process identifier, or PID. With that information, you can execute a command like the following in the same command line session (replacing [PID] with the actual numeric value of the PID):

taskkill /f /pid [PID]

After the above, the process no longer exists and the service can be restarted. With any system, you need to find the service that is stuck to kill it, but that would be the subject of another posting. What I have not got to testing is whether these work in PowerShell, since I used them with the legacy command line instead. Along with processes belonging to software applications (think Word, Excel, Firefox, etc.), that may be something else to try should the occasion arise.

Three handy Linux commands, one each for navigation, system Information and upgrades

Here are some Linux commands that I encountered in a feature article in the current issue of Linux User & Developer that I had not met before:

cd -

This returns you to the previous directory where you were before with having to go back through the folder hierarchy to get there and is handy if you are jumping around a file system and any other means is far from speedy.

lsb_release -a

It can be useful to uncover what version of a distro you have from the command line and the above works for distros as diverse as Linux Mint, Debian, Fedora (it automatically installs in Fedora 22 if it is not installed already, a more advanced approach than showing you the command like in Linux Mint or Ubuntu), openSUSE and Manjaro. These days, the version may not change too often, but it still is good to uncover what you have.

yum install fedora-upgrade

This one can be run either with sudo or in a root session started with su and it is specific to Fedora. The command performs an upgrade of the Fedora distro itself, and I wonder if the functionality has been ported to the dnf command that has taken over from yum. My experiences with that in Fedora 22 so far suggest that it should be the case, though I need to check that further with the VirtualBox VM that I have created.