Adventures & experiences in contemporary technology
Having an older PC to upgrade, I decided to install OpenMediaVault on there a few years ago after adding in 6 TB and 4 TB hard drives for storage, a Gigabit network card to speed up backups and a new BeQuiet! power supply to make it quieter. It has been working smoothly since then, and the release of OpenMediaVault 6.x had me wondering how to move to it.
Usefully, I enabled an SSH service for remote logins and set up an account for anything that I needed to do. This includes upgrades, taking backups of what is on my NAS drives, and even shutting down the machine when I am done with what I need to do with it.
Using an SSH session, the first step was to switch to the administrator account and issue the following command to ensure that my OpenMediaVault 6.x installation was as up-to-date as it could be:
omv-update
Once that had completed what it needed to do, the next step was to do the upgrade itself with the following command:
omv-release-upgrade
With that complete, it was time to reboot the system, and I fired up the web administration interface and spotted a kernel update that I applied. Again, the system was restarted, and further updates were noticed and these were applied, again through the web interface. The whole thing is based on Debian 12.x, but I am not complaining since it quietly does exactly what I need of it. There was one slight glitch when doing an update after the changeover, and that was quickly sorted.
My response to changes in the technology stack used in clinical research is to develop some familiarity with programming and scripting platforms that complement and compete with SAS, a system with which I have been programming since 2000. One of these has been R but Python is another that has taken up my attention and I now also have Julia in my sights as well. There may be others to assess in the fullness of time.
While I first started to explore the Data Science world in the autumn of 2017, it was in the autumn of 2019 that I began to complete LinkedIn training courses on the subject. Good though they were, I find that I need to actually use a tool in order to better understand it. At that time, I did get to hear about Python packages like Pandas, NumPy, SciPy, Scikit-learn, Matplotlib, Seaborn and Beautiful Soup though it took until of spring of this year for me to start gaining some hands-on experience with using any of these.
During the summer of 2020, I attended a BCS webinar on the CodeGrades initiative, a programming mentoring scheme inspired by the way classical musicianship is assessed. In fact, one of the main progenitors is a trained classical musician and teacher of classical music who turned to Python programming when starting a family so as to have a more stable income. The approach is that a student selects a project and works their way through it with mentoring and periodic assessments carried out in a gentle and discursive manner. Of course, the project has to be engaging for the learning experience to stay the course and that point came through in the webinar.
That is one lesson that resonates with me with subjects as diverse as web server performance and the ongoing pandemic pandemic supplying data and there are other sources of public data to examine as well before looking through my own personal archive gathered over the decades. Some subjects are uplifting while others are more foreboding but the key thing is that they sustain interest and offer opportunities for new learning. Without being able to dream up new things to try, my knowledge of R and Python would not be as extensive as it is and I hope that it will help with learning Julia too.
In the main, my own learning has been a solo effort with consultation of documentation along with web searches that have brought me to the likes of Real Python, Stack Abuse, Data Viz with Python and R and others for longer tutorials as well as threads on Stack Overflow. Usually, the web searching begins when I need a steer on a particular or a way to resolve a particular error or warning message but books always are worth reading even if that is the slower route. Those from the Dummies series or from O’Reilly have proved must useful so far but I do need to read them more completely than I already have; it is all too tempting to go with the try the “programming and search for solutions as you go” approach instead.
To get going, many choose the Anaconda distribution to get Jupyter notebook functionality but I prefer a more traditional editor so Spyder has been my tool of choice for Python programming and there are others like PyCharm as well. Spyder itself is written in Python so it can be installed using pip from PyPi like other Python packages. It has other dependencies like Pylint for code management activities but these get installed behind the scenes.
The packages that I first met in 2019 may be the mainstays for doing data science but I have discovered others since then. It also seems that there is porosity between the worlds of R an Python so you get some Python packages aping R packages and R has the Reticulate package for executing Python code. There are Python counterparts to such Tidyverse stables as dply and ggplot2 in the form of Siuba and Plotnine, respectively. The syntax of these packages are not direct copies of what is executed in R but they are close enough for there to be enough familiarity for added user friendliness compared to Pandas or Matplotlib. The interoperability does not stop there for there is SQLAlchemy for connecting to MySQL and other databases (PyMySQL is needed as well) and there also is SASPy for interacting with SAS Viya.
Pyhton may not have the speed of Julia but there are plenty of packages for working with larger workloads. Of these, Dask, Modin and RAPIDS all have there uses for dealing with data volumes that make Pandas code crawl. As if to prove that there are plenty of libraries for various forms of data analytics, data science, artificial intelligence and machine learning, there also are the likes of Keras, TensorFlow and NetworkX. These are just a selection of what is available and there is no need not to check out more. It may be tempting to stick with the most popular packages all the time, especially when they do so much, but it never hurst to keep an open mind either.
One should not do a new PC build in the middle of a heatwave if you do not want to be concerned about how fast fans are spinning and how hot things are getting. Yet, that is what I did last month after delaying the act for numerous months.
My efforts mean that I have a system built around an AMD Ryzen 9 5950X CPU and a Gigabyte X570 Aorus Pro with 64 GB of memory and things are settling down after the initial upheaval. That also meant some adjustments to the CPU fan profile in the BIOS for quieter running while the the use of Be Quiet! Dark Rock 4 cooler also helps as does a Be Quiet! Silent Wings 3 case fan. All are components from trusted brands though I wonder how much abuse they got during their installation and subsequent running in.
Fan noise is a non-quantitative indicator of heat levels as much as touch so more quantitative means are in order. Aside from using a thermocouple device, there are in-built sensors too. My using Linux Mint means that I have the sensors command from the lm-sensors package for checking on CPU and other temperatures though hddtemp is what you need for checking on the same for hard drives. The latter can be used as follows:
sudo hddtemp /dev/sda /dev/sdb
This has to happen using administrator access and a list of drives needs to be provided because it cannot find them by itself. In my case, I have no mechanical hard drives installed in non-NAS systems and I even got to replacing a 6 TB Western Digital Green disk with an 8 TB SSD but I got the following when I tried checking on things with hddtemp:
WARNING: Drive /dev/sda doesn't seem to have a temperature sensor.
WARNING: This doesn't mean it hasn't got one.
WARNING: If you are sure it has one, please contact me ([email protected]).
WARNING: See --help, --debug and --drivebase options.
/dev/sda: Samsung SSD 870 QVO 8TB: no sensor
The cause of the message for me was that there is no entry for Samsung SSD 870 QVO 8TB in /etc/hddtemp.db so that needed to be added there. Before that could be rectified, I needed to get some additional information using smartmontools and these needed to be installed using the following command:
sudo apt-get install smartmontools
What I needed to do was check the drive’s SMART data output for extra information and that was achieved using the following command:
sudo smartctl /dev/sda -a | grep -i Temp
What this does is to look for the temperature information from smartctl output using the grep command with output from the first being passed to the second through a pipe. This yielded the following:
190 Airflow_Temperature_Cel 0x0032 072 050 000 Old_age Always - 28
The first number in the above (190) is the thermal sensor’s attribute identifier and that was needed in what got added to /etc/hddtemp.db. The following command added the necessary data to the aforementioned file:
echo \"Samsung SSD 870 QVO 8TB\" 190 C \"Samsung SSD 870 QVO 8TB\" | sudo tee -a /etc/hddtemp.db
Here, the output of the echo command was passed to the tee command for adding to the end of the file. In the echo command output, the first part is the name of the drive, the second is the heat sensor identifier, the third is the temperature scale (C for Celsius or F for Fahrenheit) and the last part is the label (it can be anything that you like but I kept it the same as the name). On re-running the hddtemp command, I got output like the following so all was as I needed it to be.
/dev/sda: Samsung SSD 870 QVO 8TB: 28°C
Since then, temperatures may have cooled and the weather become more like what we usually get but I am still keeping an eye on things, especially when the system is put under load using Perl, R, Python or SAS. There may be further modifications such as changing the case or even adding water cooling, not least to have a cooler power supply unit, but nothing is being rushed as I monitor things to my satisfaction.
Like Fedora, Manjaro also installs a package for VirtualBox Guest Additions when you install the Linux distro in a VirtualBox virtual machine. However, it does have certain expectations when doing this. On many systems and my own is one of these, Linux guests are forced to use the VMSVGA virtual graphics controller while Windows guests are allowed to use the VBoxSVGA one. It is the latter that Manjaro expects so you get a message like the following appearing when the desktop environment has loaded:
Windows Resizing
Set your VirtualBox Graphics Controller to enable windows resizing
After ensuring that gcc, make, perl and kernel headers are installed, I usually install VirtualBox Guest Additions myself from the included ISO image and so I did the same with Manjaro. Doing that and restarting the virtual machine got me extra functionality like screen resizing and being able to copy and paste between the VM and elsewhere after choosing the Bidirectional setting in the menus under Devices > Shared Clipboard.
That still left an unwanted message popping up on startup. To get rid of that, I just needed to remove /etc/xdg/autostart/mhwd-vmsvga-alert.desktop. It can be deleted but I just moved it somewhere else and a restart proved that the message was gone as needed. Now everything is working as I wanted.
While some Linux distros like Fedora install VirtualBox drivers during installation time, I prefer to install the VirtualBox Guest Additions themselves. Before doing this, it is best to remove the virtualbox-guest-additions package from Fedora to avoid conflicts. After that, execute the following command to ensure that all prerequisites for the VirtualBox Guest Additions are in place prior to mounting the VirtualBox Guest Additions ISO image and installing from there:
sudo dnf -y install gcc automake make kernel-headers dkms bzip2 libxcrypt-compat kernel-devel perl
During the installation, you may encounter a message like the following:
ValueError: File context for /opt/VBoxGuestAdditions-<VERSION>/other/mount.vboxsf already defined
This is generated by SELinux so the following commands need executing before the VirtualBox Guest Additions installation is repeated:
sudo semanage fcontext -d /opt/VBoxGuestAdditions-<VERSION>/other/mount.vboxsf
sudo restorecon /opt/VBoxGuestAdditions-<VERSION>/other/mount.vboxsf
Without doing the above step and fixing the preceding error message, I had an issue with mounting of Shared Folders whereby the mount point was set up but no folder contents were displayed. This happened even when my user account was added to the vboxsf group and it proved to be the SELinux context issue that was the cause.
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 lesson 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.
Much of the past weekend was spent getting a working Debian 10 installation up and running in a VirtualBox virtual machine. Because I chose the Cinnamon desktop environment, the process was not as smooth as I would have liked so a minimal installation was performed before I started to embellish as I liked. Along the way, I got to wondering if I could create virtual hard drives using the command line and I found that something like the following did what was needed:
VBoxManage createmedium disk --filename <full path including file name without extension> -size <size in MiB> --format VDI --variant Standard
Most of the options are self-explanatory part from the one named variant. This defines whether the VDI file expands to the maximum size specified using the size parameter or is reserved with the size defined in that parameter. Two VDI files were created in this way and I used these to replace their Debian 8 predecessors and even to save a bit of space too. If you want, you can find out more in the user documentation but this post hopefully gets you started anyway.
Recent curiosity about Java programming and Groovy scripting got me trying to start up the Eclipse IDE that I had install on my main machine. What I got instead of a successful application startup was a message that included the following:
!MESSAGE Exception launching the Eclipse Platform:
!STACK
java.lang.ClassNotFoundException: org.eclipse.core.runtime.adaptor.EclipseStarter
at java.base/java.net.URLClassLoader.findClass(URLClassLoader.java:466)
at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:566)
at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:499)
at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:626)
at org.eclipse.equinox.launcher.Main.basicRun(Main.java:584)
at org.eclipse.equinox.launcher.Main.run(Main.java:1438)
at org.eclipse.equinox.launcher.Main.main(Main.java:1414)
The cause was a mismatch between Eclipse and the installed version of Java that it needed in order to run. After all, the software itself is written in the Java language and the installed version from the usual software repositories was too old for Java 11. The solution turned out to be installing a newer version as a Snap (Ubuntu’s answer to Flatpak). The following command did the needful since Snapd already was running on my machine:
sudo snap install eclipse --classic
The only part of the command that warrants extra comment is the --classic switch since that is needed for a tool like Eclipse that needs to access a host file system. On executing, the software was downloaded from Snapcraft and then installed within its own bundle of dependencies. The latter adds a certain detachment from the underlying Linux installation and ensures that no messages appear because of incompatibilities like the one near the start of this post.
It is amazing how the Windows folder manages to grow on your C drive and on in a Windows 7 installation was the cause of my needing to expand the VirtualBox virtual machine VDI disk on which it was installed. After trying various ways to cut down the size, an enlargement could not be avoided. In all of this, it was handy that I had a recent backup for restoration after any damage.
The same thing meant that I could resort to enlarging the VDI file with more peace of mind than otherwise might have been the case. This needed use of the command line once the VM was shut down. The form of the command that I used was the following:
VBoxManage modifyhd <filepath/filename>.vdi --resize 102400
It appears that this also would work on a Windows host but mine was Linux and it did what I needed. The next step was to attach it to an Ubuntu VM and use GParted to expand the main partition to fill the newly available space. That does not mean that it takes up 100 GiB on my system just yet because these things can be left to grow over time and there is a way to shrink them too if you ever need to do just that. As ever, having a backup made before any such operation may have its uses if anything goes awry.
This year has seen some optimisation being applied to my web presences guided by the results of GTMetrix scans. It was then that I realised how slow things were, so server loads were reduced. Anything that slowed response times, such as WordPress plugins, got removed. Usage of Matomo also was curtailed in favour of Google Analytics while HTML, CSS and JS minification followed. What had yet to happen was a search for a faster server. Now, another website has been moved onto a virtual private server (VPS) to see how that would go.
Speed was not the only consideration since security was a factor too. After all, a VPS is more locked away from other users than a folder on a shared server. There also is the added sense of control, so Let’s Encrypt SSL certificates can be added using the Electronic Frontier Foundation’s Certbot. That avoids the expense of using an SSL certificate provided through my shared hosting provider and a successful transition for my travel website may mean that this one undergoes the same move.
For the VPS, I chose Ubuntu 18.04 as its operating system and it came with the LAMP stack already in place. Have offload development websites, the mix of Apache, MySQL and PHP is more familiar to me than anything using Nginx or Python. It also means that .htaccess files become more useful than they were on my previous Nginx-based platform. Having full access to the operating system by means of SSH helps too and should mean that I have fewer calls on technical support since I can do more for myself. Any extra tinkering should not affect others either, since this type of setup is well known to me and having an offline counterpart means that anything riskier is tried there beforehand.
Naturally, there were niggles to overcome with the move. The first to fix was to make the MySQL instance accept calls from outside the server so that I could migrate data there from elsewhere and I even got my shared hosting setup to start using the new database to see what performance boost it might give. To make all this happen, I first found the location of the relevant my.cnf configuration file using the following command:
find / -name my.cnf
Once I had the right file, I commented out the following line that it contained and restarted the database service afterwards using another command to stop the appearance of any error 111 messages:
bind-address 127.0.0.1
service mysql restart
After that, things worked as required and I moved onto another matter: uploading the requisite files. That meant installing an FTP server so I chose proftpd since I knew that well from previous tinkering. Once that was in place, file transfer commenced.
When that was done, I could do some testing to see if I had an active web server that loaded the website. Along the way, I also instated some Apache modules like mod-rewrite using the a2enmod command, restarting Apache each time I enabled another module.
Then, I discovered that Textpattern needed php-7.2-xml installed, so the following command was executed to do this:
apt install php7.2-xml
Then, the following line was uncommented in the correct php.ini configuration file that I found using the same method as that described already for the my.cnf configuration and that was followed by yet another Apache restart:
extension=php_xmlrpc.dll
Addressing the above issues yielded enough success for me to change the IP address in my Cloudflare dashboard so it pointed at the VPS and not the shared server. The changeover happened seamlessly without having to await DNS updates as once would have been the case. It had the added advantage of making both WordPress and Textpattern work fully.
With everything working to my satisfaction, I then followed the instructions on Certbot to set up my new Let’s Encrypt SSL certificate. Aside from a tweak to a configuration file and another Apache restart, the process was more automated than I had expected so I was ready to embark on some fine-tuning to embed the new security arrangements. That meant updating .htaccess files and Textpattern has its own, so the following addition was needed there:
RewriteCond %{HTTPS} !=on
RewriteRule ^ https://%{HTTP_HOST}%{REQUEST_URI} [R=301,L]
This complemented what was already in the main .htaccess file and WordPress allows you to include http(s) in the address it uses, so that was another task completed. The general .htaccess only needed the following lines to be added:
RewriteCond %{SERVER_PORT} 80
RewriteRule ^(.*)$ https://www.assortedexplorations.com/$1 [R,L]
What all these achieve is to redirect insecure connections to secure ones for every visitor to the website. After that, internal hyperlinks without https needed updating along with any forms so that a padlock sign could be shown for all pages.
With the main work completed, it was time to sort out a lingering niggle regarding the appearance of an FTP login page every time a WordPress installation or update was requested. The main solution was to make the web server account the owner of the files and directories, but the following line was added to wp-config.php as part of the fix even if it probably is not necessary:
define('FS_METHOD', 'direct');
There also was the non-operation of WP Cron and that was addressed using WP-CLI and a script from Bjorn Johansen. To make double sure of its effectiveness, the following was added to wp-config.php to turn off the usual WP-Cron behaviour:
define('DISABLE_WP_CRON', true);
Intriguingly, WP-CLI offers a long list of possible commands that are worth investigating. A few have been examined but more await attention.
Before those, I still need to get my new VPS to send emails. So far, sendmail has been installed, the hostname changed from localhost and the server restarted. More investigations are needed but what I have not is faster than what was there before, so the effort has been rewarded already.