Accessing Unix/Linux Programming Environments

This guide is meant to inform UMN students on options they have to access a Unix/Linux environment for course work in computer science. This applies to courses that use the C programming language like CSCI 2021 and CSCI 4061 and may be useful for other courses as well.

The first section provides information on UMN Unix computing resources and some links to tutorials on how to install Unix one personal computers. In the latter case, the focus is on the use of Virtual Machines so that a Linux environment can coexist with an existing Windows or Mac OSX installation rather than overwriting these more familiar environments.

Have Several Options

Familiarize yourself with several ways to edit/compile/run code in a Unix environment so that if your primary mechanism fails, you have a backup. Expect your Internet Connection to go down at some point and have a non-networked solution (Virtual Machine or WSL).

All Students

Learn about SSH and SCP to log into remote computers in a terminal. The commands ssh / scp are installed by default on almost all platforms (Windows/Mac/Linux). Read the sections on SSH and SCP for quick introductions.

CSE Labs provides some excellent physical and remote access options to Linux machines on campus.

Most Students

Most students find that using Visual Studio Code with Remote Editing works well for their day-to-day coding for the course. This has some pitfalls but is a good option to explore if you aren't sure of what to try first.

Windows Users

Your are encouraged to use a remote connection to true Unix Machines for coursework. It is possible to set up the Windows Subsystem for Linux (WSL) but this system has proved somewhat unreliable for students in recent years. It is also possible to set up a Virtual Machine to have a local Linux environment.

Mac Users

Your are encouraged to use a remote connection to true Unix Machines for coursework. It is possible to set up a Virtual Machine to work in a local Linux environment but students have reported difficulties with this on Mac in recent years. Apple no longer supports the tools we use for this class running natively.

Linux Users

You're already set for the most part as you're using the same OS as your professor and will reap the benefits thereof.

CSE Labs provides several physical lab locations many of which have Linux computers with a Unix environment. Visiting a lab physically and working on their computers is a plausible way to get work done in courses that require such an environment.

This link lists the lab locations and their usage / hours of operation:

https://cse.umn.edu/cseit/classrooms-labs

Labs that list "Ubuntu" have Linux machines as Ubuntu Linux is a popular "flavor" of Linux. Be mindful of the times these labs are open and which labs have Unix machines listed as Ubuntu 20.04.

If you are reading this guide during a PLAGUE make sure to check which labs are open/closed. Plagues tend to limit lab availability to prevent the spread of disease.

Most UMN resources now require 2-factor authentication, including remote access to CSE Labs machines. You will need to install the Duo App on a mobile device to receive the verification prompts while logging into machines. After entering a username / password in a login sequence, usually one will get a final prompt to use Duo to verify the login. Keep track of your phone for this.

CSE Labs has implemented a web-based remote desktop connection to most Linux lab computers. This technology is referred to as "FASTX" and allows one to connect to lab machines graphically through a web browser.

Aside from individual machine access, CSE Labs provides a pool of Linux Virtual Machines for graphical web access via its VOLE system. Navigate to http://vole.cse.umn.edu, click the Connect to VOLE link and enter your login credentials.

VOLE currently runs on an the older FASTX2 system so may be a bit laggier than the FASTX2 connections to individual machines. Many students notice see this when the system fails to respond for a short time or a single press of the "x" key results in "xxxxxxxxxxxxxxxxxxxxxx" showing up on their screen For these reasons, it is also good to familiar with alternatives to VOLE described later.

Note: unless you are doing dedicated graphics programming, don't use the VOLE 3D nodes. Use normal VOLE. I have received reports that the memory checking program Valgrind can report spurious errors on VOLE3D and should therefore be avoided.

CSE Labs allows you to remotely log into a variety of machines using the secure shell or SSH for short. For this you will need an SSH tool.

• Mac / Linux: Open a terminal and use the ssh command

• Windows: Open cmd.exe and check that the ssh command is present by typing ssh -V then pressing Enter. This should list a version for your ssh client, something like

    >> ssh -V
    OpenSSH_9.1p1, OpenSSL 3.0.7
  

  Most recent Windows installs have it. If ssh is not installed, install PuTTY which is a classic favorite OR explore alternatives.

SSH connections are non-graphical and therefore are much more robust against slow network connections compared to tools like Vole.

Sick of typing your password + doing Duo authentication? Use the following commands to set up a pair of encryption keys that will allow password and Duo-free login.

NOTE: Doing these steps in a terminal will also alleviate password prompts in VS Code Remote Editing.

mylaptop>> ssh-keygen -t rsa   
# press enter a few times for default options

# ON SOME PLATFORMS 
mylaptop>> ssh-copy-id myx500@atlas.cselabs.umn.edu 
# enter password and Duo verify

# IF ERRORS LIKE 'ssh-copy-id not found' (likely on Windows/Mac) use
# the following instead:
mylaptop>> scp .ssh/id_rsa.pub myx500@atlas.cselabs.umn.edu:.ssh/authorized_keys
# copys public key to remote machine as authorized

# IF ERRORS LIKE 
scp: dest open ".ssh/authorized_keys": No such file or directory
scp: failed to upload file .ssh/id_rsa.pub to .ssh/authorized_keys
# Create .ssh on remote directory via
mylaptop>> ssh kauffman@atlas.cselabs.umn.edu
password: ....
Duo Authenticate: 1
atlas>> mkdir .ssh
atlas>> exit

# Then run same command again
mylaptop>> scp .ssh/id_rsa.pub myx500@atlas.cselabs.umn.edu:.ssh/authorized_keys

# WHEN SUCCESSFUL...

mylaptop>> ssh myx500@atlas.cselabs.umn.edu
...
# no password prompt required, no Duo verify required
atlas>> 

If you have access to ssh in a terminal on your home computer, you very likely have access to scp which uses the same secure connection protocol but to transfer files rather than set up an interactive shell. It has a syntax that combines ssh and the Unix cp (copy) program.

Transferring files using newer FASTX 3 graphical connections is a breeze.

Mouse over the small menu at the top of the screen FASTX3 browser tab which sometimes automatically collapses. Click the "Folder" icon.

This will open a file browser for the remote machine. Click the small "Cloud/Up Arrow Icon" which is to initiate an upload.

This will open a file browser for your local files (those on your personal machine). Select a file and confirm with "Okay/Open" and it will be uploaded to the remote machine, usually to your Home Directory.

The uploaded file will appear in the FASTX 3 file browser and can be accessed normal tools on the remote machine like the Terminal or a graphical file browser.

Files can also be downloaded from the FASTX 3 file browser by clicking on them which will prompt for a location on the local machine to download the remote file.

CSE Labs has some information on mapping a local folder/drive to a CSE Labs account location. This can make transfers much easier as they become drag/drop rather than command line interactions.

https://cse.umn.edu/cseit/self-help-guides/mount-unix-directory-mac-or-pc

NOTE: Remote mounts may require use of a VPN to the University. Instructions from the University are here:

https://it.umn.edu/services-technologies/virtual-private-network-vpn

Some systems support a way to "mount" a remote machine filesystem through an SSH connection. The net effect of this is that copying files into what looks like a local folder actually transfers them to a remote machine and copying them from that folder transfers from that machine. This behavior is often not present by default but is incredibly useful and has saved me countless hours of toil. You can investigate these for your system of choice

• Mac OSX FUSE / sshfs: https://osxfuse.github.io/
• SSHFS on Linux: Most Distributions have a package for SSHFS
  • Ubuntu: https://help.ubuntu.com/community/SSHFS
  • Mint: https://community.linuxmint.com/software/view/sshfs
  • Arch Linux: https://wiki.archlinux.org/index.php/SSHFS
  • etc.
• Windows: best achieved through the Windows Subsystem for Linux

TA Mohamed Aboushanab constructed an excellent setup tutorial for VS code which is specifically tailored to CSCI 2021 students but is likely useful for anyone setting up VS Code for Remote Editing.

https://youtu.be/wi4iqKoRRfo

Professor Kauffman also constructed a somewhat less "professional" demonstration of how to set up VS Code.

TA Tien Dinh constructed a guide during the Fall 2020 semester on setting up remote editing in VS Code which is comprehensive and has been vetted by the teaching staff. The direct link is here: https://tienpdinh.com/posts/remote-vscode

As long as you have access to your labs account, your credentials should work via SSH. Instructions on how to set-up SSH for VSCode can be found here, however my set-up was a little different.

1. You do need to ensure you have an ssh client installed.

2. You will need the plug-ins below. I believe the first three may be already installed for you, but "Remote Development" is the important one.

   

3. After installing the plug-ins, you will need to reload the editor.

4. Open up the "Remote Explorer" panel.

   

5. Change the drop-down to "SSH Targets"
6. Click the "+" directly underneath to add a new connection.

7. The window will ask you for your ssh command. You need the full command and be sure to include the -A option otherwise the connection won't complete. Example:

   ssh -A stude028@atlas.cselabs.umn.edu
   

   This will connect to machine atlas. Other possible lab computers are here.

1. Click on the option to save the command in your personal files, not your program files.
2. Click the connection and enter your password in the new window.
3. This will allow you you work in an interactive IDE through the school's environment. The connection is faster since all the rendering is done client-side and not being transmitted through a web browser. You also have access to the terminal directly through the "Terminal" menu.

Running Virtual Machine software allows you to have a "guest" operating system, likely free Linux, which has separate software from the "host" OS. A great option for this is running VirtualBox on your Host OS (Windows or Mac) with a Linux distribution as the "Guest" OS.

In almost all cases, compiling and running code on a Linux VM (virtual machine) will behave identically to a "native" Linux. However, students, especially those on MacOS, indicate setting up VMs to be difficult. If these paths prove difficult, consider using the zero-cost FASTX remote desktop options.

Below are a list of beginner tutorials on installing VirtualBox and a Linux VM.

• How to Install Linux on Windows or Mac with VirtualBox - Beginner Video by IT Career Questions (YouTube)
  • ~15min video
  • Install Ubuntu Linux for easiest experience, NOT Kali Linux
  • No need to make any monetary contributions when downloading anything
  • Mac OSX users will need to adjsut their security settings to allow VirtualBox to work, see the guide How to Fix VirtualBox’s “Kernel Driver Not Installed (rc=-1908)” Error on a Mac.
  • WINDOWS USERS ARE NOT recommended to use Virtualbox, use the Windows Subsystem for Linux instead
• How to set up VirtualBox and Install Ubuntu OS (Mac) by ISOM Suffolk (YouTube)
  • ~22min video
  • Mac OSX install of Ubuntu Linux Guest
  • Mac OSX users will need to adjsut their security settings to allow VirtualBox to work, see the guide How to Fix VirtualBox’s “Kernel Driver Not Installed (rc=-1908)” Error on a Mac.
• Create Shared Folder Between Mac OS X and Ubuntu Linux via VirtualBox by Abanoub Hanna (YouTube)
  • ~4min video
  • Allows files to be accessed both between both Host (Mac) and Guest (Linux)
  • Setup is very short and easy

After installing Linux, you are likely to need some tools. The names for these vary but on Ubuntu they are usually as follows

• build-essential: compiler toolchain based on gcc
• valgrind: memory checker
• gdb: debugger

Usually performing the following command in an Ubuntu Linux terminal will update the package lists and install all of these:

> sudo apt update
> sudo apt install build-essential valgrind gdb zip unzip

While Windows does not have Unix tools by default, Windows 10 supports the Windows Subsystem for Linux on Windows 10. This allows a Linux system to be installed with very little effort complete with compiler and debugging tools.

• Install a flavor of Linux such as Ubuntu (Video Tutorial, highly recommended)
• Start a linux command line via the bash program
• Follow the Linux installation instructions appropriate to the distro (see Linux/Unix instructions)

• After installing Linux, you are likely to need some tools. The names for these vary but on Ubuntu they are usually as follows

  • build-essential: compiler toolchain based on gcc
  • valgrind: memory checker
  • gdb: debugger

  Usually performing the following command will update the package lists and install all of these:

    > sudo apt update
    > sudo apt install build-essential valgrind gdb zip unzip
  

NOTE: Assembly produced by gcc will target the Windows architecture and is not likely to work on lab Linux machines where we will grade. Make sure to verify your code works in those environments as well.

NOTE: Older options for getting a Unix environment include Cygwin and MinGW but these are discouraged as they will not be fully compatible with the tools used in the course.

Unfortunately, Mac OSX no longer has good support for the tools used in this course.

To get a local working environment, Mac OSX users are encouraged to install a virtual machine software like Virtual Box and Ubuntu Linux. The earlier section on Virtual Machines gives some tutorials on how to perform the install.

Historically Mac OSX had better support for native Unix development but changes over the last few years to the default configuration of OSX has made it unlikely to be able to work use tools that are central the course. These are as follows.

• gcc: Most OSX installations come with a command called gcc BUT it is not actually the GNU Compiler Collection. It is usually the CLANG compiler. This is not compatible with our tools and it is not straightforward to get a real GCC installed.
• gdb: A learning goal for this course is to understand the basic utility of debuggers. We will focus on gdb. Unfortunately OSX does not come with this tool by default and installing it is a HUGE headache.
• valgrind: Testing C programs is not easy and the Valgrind memory checker makes it a lot easier. However, the most recent versions of OSX are not compatible with this tool. This is regrettable and there is no known solution at this time.
• Assembly produced by any compiler on Macs will target the OSX architecture and is not likely to work on lab Linux machines where we will grade. This can lead to loss of credit.

Linux is a Unix-like OS. Installing Linux natively on your own computer is NOT required but can be quite useful. For those new to Linux, good beginner distributions (flavors) of Linux include.

• Ubuntu
• Linux Mint
• Debian

The site DistroWatch maintains an up-to-date list of popular Linux distributions and various properties of them.