EN.540.635 - Software Carpentry The Linux Kernel and Associated Operating Systems

What’s in an Operating System? Bootloader Kernel Daemons Shell/Command Line/Terminal Graphical Server Desktop & File Browser Applications (Excel, Chrome, VLC, …) EVERYTHING TOGETHER IS THE OPERATING SYSTEM! This is what starts your operating system. The most fundamental part of an OS is the ability to manage the “brain” (CPU), memory, and devices attached to the system. One Kernel can’t rule it all. That is, one kernel is unable to run all the processes directly, so it calls helpers (Daemons) to run them (sshd, sysloggerd…) We need a fundamental interface to our OS, allowing us to use the computer. This is done via a command line. Note, original MSDOS was just that! Not all functionality can be done in a command line! What if we want to watch something? Or… make life easier and not use the command line? Well, we can have a graphical server to handle that. … For more information, lookie here! https://en.wikipedia.org/wiki/Comparison_of_operating_system_kernels

MS-DOS Source Code

What is Linux? An Open-Source Kernel, released by Linus Torvalds on September 17th, 1991 Note, Linux is not an Operating System! Common “Linux” operating systems: Ubuntu CentOS Fedora Debian Arch Linux

The Maryland Advanced Research Computing Center MARCC The Maryland Advanced Research Computing Center https://www.marcc.jhu.edu

MARCC 676 Compute “Nodes” 50 “Large memory Nodes” 48 “GPU Nodes” Each “Node” has 24 cores of the Intel Haswell processors (2.4 GHz) Each “Node” has 128 GB of RAM A total of 16,224 cores! 50 “Large memory Nodes” Each with 48 cores and 1024 GB of RAM A total of 2,400 cores! 48 “GPU Nodes” Each with 2 Nvidia K80 GPUs Each with 24 CPU cores https://www.marcc.jhu.edu

How do we access MARCC?

What is SSH? Secure SHell Secure, Encrypted connection to Server (Port 22)

What is SFTP? Secure File Transfer Protocol Secure, Encrypted connection to Server (Port 21)

Connecting to MARCC via Mac/Linux Open up a terminal Use the SSH or SFTP command as follows: Enter Second Factor Authentication Information followed by your password Now you’re logged in! Call the SSH or SFTP command Specify you want to forward your display (not needed in SFTP) Specify your username Specify what to connect to

Connecting to MARCC via Windows Most easily accomplished via Third-Party Software MobaXTerm Alternatively, using Windows Subsystem for Linux (WSL). If so, then instructions are the same as the previous slide!

Linux Command Line (Terminal) ls cd mkdir cat <FPTR> head <FPTR> tail <FPTR> rm <FPTR> mkdir –p test/this/out touch test/this/file ls –l test/this

Let’s Get Ready! Ensure you are able to login to MARCC (Necessary for class on Thursday, Feb 7th) Ensure you have python 2.7 setup on your laptops (Necessary for class on Tues, Feb 12th) Have some sort of workflow ready (Necessary for class on Tues, Feb 12th)