Tag Archives: linux

The Beautiful Nitrux Linux Distro Could Be a Contender | Linux.com


What happens when you take Ubuntu 17.10, a new desktop interface (one that overlays on top of KDE), snap packages, and roll them all up into a pseudo rolling release? You get Nitrux. At first blush, this particular Linux distribution seems more of an experiment than anything else — to show how much the KDE desktop can be tweaked to resemble the likes of the Elementary OS or MacOS desktops. At its heart, however, it’s much more than that.

First and foremost, Nitrux makes use of snap packages; so installing software is handled a bit differently than the norm. Even though Nitrux is based on Ubuntu, apt install isn’t what you want to use (although it is available).

I’m getting ahead of myself. This distro focuses very much on the GUI — so the GUI should be the route you take. Good thing Nitrux includes a GUI software installer tool for that purpose. That Nitrux uses snaps is good and bad, and it’s the bad that will put users off faster than the good.

Again, I’m getting ahead of myself.

Let’s first talk about what Nitrux is. This particular take on the Linux desktop is focused on the portable, universal nature of snap packages and makes use of a unique desktop, called Nomad, which sits atop KDE Plasma 5. It’s minimum requirements are:

  • 2.66 GHz quad-core CPU or better.

  • 4 GB system memory.

  • 256 MB video memory and OpenGL 2.0 support.

  • 4.29 GB of free hard drive space.

On that 4.29GB of free hard drive space, I installed Nitrux as a VirtualBox VM with 10GB of space. Upon installation, I installed the LibreOffice snap package, only to find out I was then out of space. I don’t know about you, but no LibreOffice installation I’ve ever done takes 5GB of space. I say this, only so you’ll be aware, should you opt to text Nitrux via VirtualBox—give that virtual disk about 20GB of space.

The Nomad desktop (Figure 1), will feel instantly familiar.

The desktop includes a dock, a system/notification tray, a quick search tool (Plasma Search), and an app menu. Of all the elements on the desktop, it’s the Plasma Search tool that will appeal to anyone looking for an efficient means to interact with their desktops. With this tool, you can just start typing on a blank desktop to see a list of results. Say, for example, you want to open LibreOffice writer; on the blank desktop, just start typing “libre” and related entries will appear (Figure 2).

The search feature is also capable of enabling/disabling various plugins, to add extra functionality. For example, you can include Bookmarks, web shortcuts, terminal applications, power management, and more to the desktop search (this is done through System Settings > Search > Plasma Search).

Take a step back

Although the Nitrux desktop might well be something every new user (even to Linux) could get up to speed with quickly, getting to the point of usage can be a bit confusing. Why? First off, when booting up the live instance, you are asked for a password, but never told what it is. Said password, for the Live user nitrux, is nitrux. Beyond that, the operating system installer is not what you might be used to. Instead of including an “Install Nitrux” button on the Live desktop, there’s absolutely no indication as to what one should do to install the platform. Turns out, Nitrux uses Systemback for installation. Once you have the live instance up and running, click on the desktop menu and locate the Systemback entry (Figure 3).

The one downfall of using Systemback is it is not nearly as intuitive as many other live distro installers. Once you start the tool up, you must click System install (Figure 4).

The first interactive section of the Systemback System installer is simple: you enter your user information. It’s the the next screen — for disk partitioning — that will trip up most users. Although Systemback will autodetect a partition, you have to delete it and create a new one, because the Mount point drop-down is greyed out. It isn’t until you delete the autodetected partition and create a new partition that you can select the mount point and file system type (Figure 5).

Here’s where we have to dock Systemback another point in user-friendliness. Once you’ve selected a mount point and filesystem type, you then have to click on the left-pointing green arrow to apply the settings. Why not a simple Apply Changes button? With that complete, you’ll then be able to click the Next button, so the installation can continue and complete.

I cannot imagine how many instances of Linux I have installed over the years, dating back to the late 1990s. Even with those early iterations of Linux, I must confess, this one had me dumbfounded. No, it’s not impossible—not even slightly; but with a desktop as user-friendly as Nomad, I wonder why the developers opted to make use of a platform installer that will most likely leave new users scratching their heads and, quite possibly, giving up. That is a shame, as Nitrux is certainly something to be experienced.

A step forward

The idea of making use of snap packages is intriguing, one that would allow for:

  • Developers to deliver the latest version of their app

  • App isolation and confinement, which improves the security and reliability said app

The biggest downfall (for the moment) is that not every Linux package has been rolled into a snap. For instance, my favorite audio player, Clementine, has yet to find its way to a snap package. The über-popular Audacity audio recorder doesn’t have a snap package. The list goes on and on.

The good news is, if there’s a piece of software that doesn’t yet have a snap, it can be installed by way of the usual means (i.e., sudo apt install clementine). That means anyone using Nitrux won’t be severely limited to what software they have available to them. However, that does sort of defeat the purpose of using snap packages. When possible, at least with Nitrux, always install with snap packages.

One other feature of note is the inclusion of Android apps (Figure 6).

From what it seems, users might be able to install and run Android applications. However, on two different installations, I have yet to get this feature to work. Even the pre-installed Android apps never start. What promised to be a really cool out of the box experience, fell flat.

Who is this distro for?

That’s a tough question. New users would feel right at home on the Nomad desktop — getting there, however, could be problematic. Skilled Linux users should have no problem using Nitrux and might find themselves intrigued with the snap-centric Nomad desktop. The one advantage of having a distribution centered around snap packages would be the ease with which you could quickly install and uninstall a package, without causing issues with other applications. However, that can be achieved with any distribution supporting snap packages.

In the end, Nitrux is a beautiful desktop that is incredibly efficient to use — only slightly hampered by an awkward installer and a lack of available snap packages. Give this distribution a bit of time to work out the kinks and it could become a serious contender.

3 Cool Linux Service Monitors | Linux.com


The Linux world abounds in monitoring apps of all kinds. We’re going to look at my three favorite service monitors: Apachetop, Monit, and Supervisor. They’re all small and fairly simple to use. apachetop is a simple real-time Apache monitor. Monit monitors and manages any service, and Supervisor is a nice tool for managing persistent scripts and commands without having to write init scripts for them.

Monit

Monit is my favorite, because provides the perfect blend of simplicity and functionality. To quote man monit:

monit is a utility for managing and monitoring processes, files, directories and filesystems on a Unix system. Monit conducts automatic maintenance and repair and can execute meaningful causal actions in error situations. E.g. Monit can start a process if it does not run, restart a process if it does not respond and stop a process if it uses too much resources. You may use Monit to monitor files, directories and filesystems for changes, such as timestamps changes, checksum changes or size changes.

Monit is a good choice when you’re managing just a few machines, and don’t want to hassle with the complexity of something like Nagios or Chef. It works best as a single-host monitor, but it can also monitor remote services, which is useful when local services depend on them, such as database or file servers. The coolest feature is you can monitor any service, and you will see why in the configuration examples.

Let’s start with its simplest usage. Uncomment these lines in /etc/monit/monitrc:

 set daemon 120
 set httpd port 2812 and
     use address localhost  
     allow localhost        
     allow admin:monit      

Start Monit, and then use its command-line status checker:

$ sudo monit
$ sudo monit status
The Monit daemon 5.16 uptime: 9m 

System 'studio.alrac.net'
  status                  Running
  monitoring status       Monitored
  load average            [0.17] [0.23] [0.14]
  cpu                     0.8%us 0.2%sy 0.5%wa
  memory usage            835.7 MB [5.3%]
  swap usage              0 B [0.0%]
  data collected          Mon, 04 Sep 2017 13:04:59

If you see the message “/etc/monit/monitrc:289: Include failed — Success ‘/etc/monit/conf.d/*'” that is a bug, and you can safely ignore it.

Monit has a built-in HTTP server. Open a Web browser to http://localhost:2812. The default login is admin, monit, which is configured in /etc/monit/monitrc. You should see something like Figure 1 (below).

Click on the system name to see more statistics, including memory, CPU, and uptime.

That is fun and easy, and so is adding more services to monitor, like this example for the Apache HTTP server on Ubuntu.

check process apache with pidfile /var/run/apache2/apache2.pid
    start program = "service apache2 start" with timeout 60 seconds
    stop program  = "service apache2 stop"
    if cpu > 80% for 5 cycles then restart
    if totalmem > 200.0 MB for 5 cycles then restart
    if children > 250 then restart
    if loadavg(5min) greater than 10 for 8 cycles then stop
    depends on apache2.conf, apache2
    group server    

Use the appropriate commands for your Linux distribution. Find your PID file with this command:

echo $(. /etc/apache2/envvars && echo $APACHE_PID_FILE)

The various distros package Apache differently. For example, on Centos 7 use systemctl start/stop httpd.

After saving your changes, run the syntax checker, and then reload:

$ sudo monit -t
Control file syntax OK
$ sudo monit reload
Reinitializing monit daemon

This example shows how to monitor key files and alert you to changes. The Apache binary should not change, except when you upgrade.

    check file apache2
    with path /usr/sbin/apache2
    if failed checksum then exec "/watch/dog"
       else if recovered then alert

This example configures email alerting by adding my mailserver:

set mailserver smtp.alrac.net

monitrc includes a default email template, which you can tweak however you like.

man monit is well-written and thorough, and tells you everything you need to know, including command-line operation, reserved keywords, and complete syntax description.

apachetop

apachetop is a simple live monitor for Apache servers. It reads your Apache logs and displays updates in realtime. I use it as a fast easy debugging tool. You can test different URLs and see the results immediately: files requested, hits, and response times.

$ apachetop
last hit: 20:56:39         atop runtime:  0 days, 00:01:00             20:56:56
All:           12 reqs (   0.5/sec)         22.4K (  883.2B/sec)    1913.7B/req
2xx:       6 (50.0%) 3xx:       4 (33.3%) 4xx:     2 (16.7%) 5xx:     0 ( 0.0%)
R ( 30s):      12 reqs (   0.4/sec)         22.4K (  765.5B/sec)    1913.7B/req
2xx:       6 (50.0%) 3xx:       4 (33.3%) 4xx:     2 (16.7%) 5xx:     0 ( 0.0%)

 REQS REQ/S    KB KB/S URL
    5  0.19  17.2  0.7*/
    5  0.19   4.2  0.2 /icons/ubuntu-logo.png
    2  0.08   1.0  0.0 /favicon.ico

You can specify a particular logfile with the -f option, or multiple logfiles like this: apachetop -f logfile1 -f logfile2. Another useful option is -l, which makes all URLs lowercase. If the same URL appears as both uppercase and lowercase it will be counted as two different URLs.

Supervisor

Supervisor is a slick tool for managing scripts and commands that don’t have init scripts. It saves you from having to write your own, and it’s much easier to use than systemd.

On Debian/Ubuntu, Supervisor starts automatically after installation. Verify with ps:

$ ps ax|grep supervisord
 7306 ?        Ss     0:00 /usr/bin/python 
   /usr/bin/supervisord -n -c /etc/supervisor/supervisord.conf

Let’s take our Python hello world script from last week to practice with. Set it up in /etc/supervisor/conf.d/helloworld.conf:

[program:helloworld.py]
command=/bin/helloworld.py
autostart=true
autorestart=true
stderr_logfile=/var/log/hello/err.log
stdout_logfile=/var/log/hello/hello.log

Now Supervisor needs to re-read the conf.d/ directory, and then apply the changes:

$ sudo supervisorctl reread
$ sudo supervisorctl update

Check your new logfiles to verify that it’s running:

$ sudo supervisorctl reread
helloworld.py: available
carla@studio:~$ sudo supervisorctl update
helloworld.py: added process group
carla@studio:~$ tail /var/log/hello/hello.log
Hello World!
Hello World!
Hello World!
Hello World!

See? Easy.

Visit Supervisor for complete and excellent documentation.

Largest Open Source Summit to Date Around the C… » Linux Magazine


The Linux Foundation is organizing the first Open Source Summit (OSS) North America in Los Angeles on September 11-14.

Last year, the Linux Foundation changed the name of the event from LinuxCon to Open Source Summit. The name change reflects the growing trend toward the open source development model as the de facto standard in software development, at least in the infrastructure and enterprise space.

This year the event will co-host many other open source events, including Hacking for Humanity – A Social Innovation Hackathon with Girls in Tech; the How to Build Habit-Forming Products Workshop; Kubernetes Core Concepts Live Training; Linux Security Summit; Moby Summit; and the Open Source Entrepreneur Network Symposium.

A major highlight of this year’s summit is a keynote speech by Hollywood actor Joseph Gordon-Levitt, who played the character of Edward Snowden in Oliver Stone’s movie “Snowden.” Gordon-Levitt has also founded a company called hitREC●rd that has produced TV shows, books, and DVDs using an online collaboration platform.

As usual, a keynote discussion will take place between Linus Torvalds and Jim Zemlin, the executive director of the Linux Foundation.

A full day of Kids Workshop will expose school-aged children to lower level basic coding and computers. The event also provides a daycare program, so working parents can leave their kids at daycare and participate in the events.



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Reddit Closing Doors to Open Source » Linux Magazine


Reddit, the peanut gallery of the Internet, reported in a blog post that it is shutting down their open source repository on GitHub: “We’re archiving reddit/reddit and reddit/reddit-mobile which are playing an increasingly small role in day to day development at Reddit. We’d like to thank everyone who has been involved in this over the years.”

Reddit was open source in 2008, roughly 10 years ago, when it was a new company, because they wanted the source code of their product to be available as open source.

However, as the company grew, they found it difficult to keep up with their open source code, and their GitHub repo had not been updated for a long time. The company provided many reasons behind “doing a bad job of keeping their open-source product repos up to date.”

Some reasons are legit and many others not. One such reason given by the company is that “Open-source makes it hard for us to develop some features ‘in the clear’ (like our recent video launch) without leaking our plans too far in advance. As Reddit is now a larger player on the web, it is hard for us to be strategic in our planning when everyone can see what code we are committing.”

Companies like Red Hat, SUSE, Google, CoreOS, Docker, and others continue to innovate, yet all of their code is available as open source. The company has given many other reasons, but all fall flat compared with the way the larger open source world functions. Reddit will continue to open source some of their tools.

The good news is that Reddit is not a platform that’s used by others to build their Reddit-like services, so Reddit source code might not be missed by the larger open source communities.



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Linux Distros That Serve Scientific and Medical Communities | Linux.com


Linux serves — of that there is no doubt — literally and figuratively. The open source platform serves up websites across the globe, it serves educational systems in numerous ways, and it also serves the medical and scientific communities and has done so for quite some time.

I remember, back in my early days of Linux usage (I first adopted Linux as my OS of choice in 1997), how every Linux distribution included so many tools I would personally never use. Tools used for plotting and calculating on levels I’d not even heard of before. I cannot remember the names of those tools, but I know they were opened once and never again. I didn’t understand their purpose. Why? Because I wasn’t knee-deep in studying such science.

Modern Linux is a far cry from those early days. Not only is it much more user-friendly, it doesn’t include that plethora of science-centric tools. There are, however, still Linux distributions for that very purpose — serving the scientific and medical communities.

Let’s take a look at a few of these distributions. Maybe one of them will suit your needs.

Scientific Linux

You can’t start a listing of science-specific Linux distributions without first mentioning Scientific Linux. This particular take on Linux was developed by Fermilab. Based on Red Hat Enterprise Linux, Scientific Linux aims to offer a common Linux distribution for various labs and universities around the world, in order to reduce duplication of effort. The goal of Scientific Linux is to have a distribution that is compatible with Red Hat Enterprise Linux, that:

  • Provides a stable, scalable, and extensible operating system for scientific computing.

  • Supports scientific research by providing the necessary methods and procedures to enable the integration of scientific applications with the operating environment.

  • Uses the free exchange of ideas, designs, and implementations in order to prepare a computing platform for the next generation of scientific computing.

  • Includes all the necessary tools to enable users to create their own Scientific Linux spins.

Because Scientific Linux is based on Red Hat Enterprise Linux, you can select a Security Policy for the platform during installation (Figure 1).

Two famous experiments that work with Scientific Linux are:

  • Collider Detector at Fermilab — experimental collaboration that studies high energy particle collisions at the Tevatron (a circular particle accelerator)

  • DØ experiment — a worldwide collaboration of scientists that conducts research on the fundamental nature of matter.

What you might find interesting about Scientific Linux is that it doesn’t actually include all the science-y goodness you might expect. There is no Matlab equivalent pre-installed, or other such tools. The good news is that there are plenty of repositories available that allow you to install everything you need to create a distribution that perfectly suits your needs.

Scientific Linux is available to use for free and can be downloaded from the official download page.

Bio-Linux

Now we’re venturing into territory that should make at least one cross section of scientists very happy. Bio-Linux is a distribution aimed specifically at bioinformatics (the science of collecting and analyzing complex biological data such as genetic codes). This very green-looking take on Linux (Figure 2) was developed at the Environmental Omics Synthesis Centre and the Natural Environment for Ecology & Hydrology and includes hundreds of bioinformatics tools, including:

  • abyss — de novo, parallel, sequence assembler for short reads

  • Artemis — DNA sequence viewer and annotation tool

  • bamtools — toolkit for manipulating BAM (genome alignment) files

  • Big-blast — The big-blast script for annotation of long sequence

  • Galaxy — browser-based biomedical research platform

  • Fasta — tool for searching DNA and protein databases

  • Mesquite — used for evolutionary biology

  • njplot — tool for drawing phylogenetic trees

  • Rasmo — tool for visualizing macromolecules

There are plenty of command line and graphical tools to be found in this niche platform. For a complete list, check out the included software page here.

Bio-Linux is based on Ubuntu and is available for free download.

Poseidon Linux

This particular Ubuntu-based Linux distribution originally started as a desktop, based on open source software, aimed at the international scientific community. Back in 2010, the platform switched directions to focus solely on bathymetry (the measurement of depth of water in oceans, seas, or lakes), seafloor mapping, GIS, and 3D visualization.

Poseidon Linux (Figure 3) is, effectively, Ubuntu 16.04 (complete with Ubuntu Unity, at the moment) with the addition of GMT (a collection of about 80 command-line tools for manipulating geographic and Cartesian data sets), PROJ (a standard UNIX filter function which converts geographic longitude and latitude coordinates into Cartesian coordinates), and MB System (seafloor mapping software).

Yes, Poseidon Linux is a very niche distribution, but if you need to measure the depth of water in oceans, seas, and lakes, you’ll be glad it’s available.

Download Poseidon Linux for free from the official download site.

NHSbuntu

A group of British IT specialists took on the task to tailor Ubuntu Linux to be used as a desktop distribution by the UK National Health Service. NHSbuntu was first released, as an alpha, on April 27, 2017. The goal was to create a PC operating system that could deliver security, speed, and cost-effectiveness and to create a desktop distribution that would conform to the needs of the NHS — not insist the NHS conform to the needs of the software. NHSbuntu was set up for full disk encryption to safeguard the privacy of sensitive data.

NHSbuntu includes LibreOffice, NHSMail2 (a version of the Evolution groupware suite, capable of connecting to NHSmail2 and Trust email), and Chat (a messenger app able to work with NHSmail2). This spin on Ubuntu can:

The specific customizations of NHSbuntu are:

  • NHSbuntu wallpaper (Figure 4)

  • A look and feel similar to a well-known desktop

  • NHSmail2 compatibility

  • Email, calendar, address book

  • Messager, with file sharing

  • N3 VPN compatibility

  • RSA token supported

  • Removal of games

  • Inclusion of Remmina (Remote Desktop client for VDI)

NHSbuntu can be downloaded, for free, for either 32- or 64-bit hardware.

The tip of the scientific iceberg

Even if you cannot find a Linux distribution geared toward your specific branch of science or medicine, chances are you will find software perfectly capable of serving your needs. There are even organizations (such as the Open Science Project and Neurodebian) dedicated to writing and releasing open source software for the scientific community.

Learn more about Linux through the free “Introduction to Linux” course from The Linux Foundation and edX.