Linux for Scientific Computing Masterclass - 10.5 Hours

Master Linux commands by understanding command structure, options, and inputs, explore the shell path and history, and practice with echo, cal, and date.

Create and customize bash aliases by creating a hidden .bash_aliases file in your home directory using a text editor. Then define aliases like get_dates to simplify long commands.

Learn to create files with touch and content with echo, and to make directories with mkdir, including using -p for paths and brace expansion to generate many folders and files.

Master cp and mv to copy files and folders, rename items, and move content across desktop, home, and documents, using recursion and tilde notation.

Create diary.txt with nano on the desktop, edit content, save with write out, and exit with ctrl+x; use read file, whereis, search, replace, cut, paste, and undo/redo.

Locate searches a system database for patterns like dot com files, using wildcards and regular expressions; apply -i, --limit, --existing, and -L to verify, then sudo update db.

Learn to read, concatenate, and manipulate files using cat, tac, and rev, and to navigate output with less, head, and tail in Linux pipelines for efficient data workflows.

Learn how to create tarballs, archive files with tar (c, v, f), list and test contents, and compress with gzip or bzip2, then extract and verify results.

Master cron tab scheduling by editing crontab in nano, using six fields to run commands, from every minute to weekly backups with script logging.

Explore how software repositories function like libraries, with main, universe, restricted, and multiverse on Ubuntu. See how the apt package manager handles dependencies and updates to keep the system secure.

Learn how the apt cache stores package lists and enables quick searches with apt-cache search and show, using DocX to text and Apache as examples, even offline.

Discover how the apt package manager updates the cache, installs and upgrades software from repositories, and uses purge, auto remove, and clean to keep dependencies and security current.

The lecture demonstrates using lvm to combine two hard drives into a single file system by creating partitions, physical volumes, volume group, and logical volumes mounted at mount point.

Demonstrate practical lvm by adding two drives, creating physical volumes and the Viji Pool volume group, a 3 gb logical volume, formatting, mounting, and extending to 11 gb.

Bonding combines multiple network interfaces into a single logical interface using the Linux bonding driver, boosting throughput and providing redundancy through various load balancing and fault tolerance modes.

install and configure ntp on the central server, disable cronie d, set iburst pool servers, enable and start ntp, adjust firewall, and verify remote stratum, offset, and jitter.

Master linux firewall rules with rich rules (rituals) to configure logging, masquerading, port forwarding, and rate limiting, and understand rule order and sample commands in zone testing.

Explore arithmetic in bash scripts by defining variables A and B, performing sum and difference with double parentheses, and echoing results.

Learn bash loops by scripting a range 1 to 10 with a for loop, employing backticks for command substitution, and building a while-based menu with input and exit handling.

This lesson demonstrates a Bash script that defines functions to fetch the IP address, system time, and the logged-in user and host, then uses a menu to display results.

Submit HPC jobs with a job file to a resource manager, request resources and software environment, and monitor the EQR partition; run interactive or non-interactive tasks and review outputs.

Explore HPC job schedulers, including the Portable Batch System and Slurm, comparing PBS variants and open source options, and learn how these workload managers allocate computing resources on supercomputers.

Master the core Slurm commands for scientific computing, including scontrol, sinfo, squeue, scancel, sacct, and sbatch, to manage state, jobs, accounting, and parallel task submission.

Learn how to use the PBS scheduler on HPC systems by submitting jobs with qsub, monitoring with qstat, modifying resources with qalter, and deleting your own jobs with qdel.

Discover how to write a PBS job script as a bash script with a shebang, including resource requests like walltime, select, and mem.

Configure samba by editing smb.conf, set workgroup and netbios name, and enable the smb service; create an anonymous share with proper permissions, adjust SELinux context, and test with testparm.

Explore the free interactive playground included with the Linux for scientific computing masterclass, a browser-based tool to learn and run scientific code with in-browser comments.