Monitoring directory growth is essential for tracking logs, temporary files, and catching runaway disk usage before it becomes a problem. Linux offers several approaches depending on whether you need simple periodic checks, interactive exploration, or event-driven monitoring. Simple periodic monitoring The watch command repeatedly runs a command at set intervals: watch -n 1 du -sh…
Merging SAM files is a common task in bioinformatics workflows, and while samtools merge works directly with BAM files, you need a different approach for SAM files. The most efficient method leverages the SAM format structure: headers start with @, and alignment records don’t. Why not convert to BAM first? Converting SAM to BAM, merging…
Writing a master thesis means protecting years of work. You need to handle three core concerns: preventing data loss from hardware failure or malware, ensuring 24/7 access to your work, and keeping it private until publication. The solution is version control with remote backup. Git provides local history and recovery, while a private remote repository…
When pushing to GitHub over HTTPS, you’ll see: error: The requested URL returned error: 403 Forbidden while accessing https://github.com/username/repo.git fatal: HTTP request failed This means Git connected to GitHub successfully, but your credentials were rejected. Common causes: Expired or revoked Personal Access Token (PAT) Using a password instead of a PAT (GitHub disabled password auth…
When you’re processing text with varying amounts of whitespace between fields, the standard cut command falls short. Given input like this: a b c d You need a way to reliably extract fields regardless of how many spaces separate them. Here are the practical approaches. Using tr with cut The tr command can normalize whitespace…
When your Node.js application encounters a fatal error or needs to terminate, you need a reliable way to shut it down. Understanding how to exit gracefully—or forcefully when necessary—is essential for production applications. Using process.exit() The most direct method is process.exit(), which immediately terminates the Node.js process: process.exit(); This is a global method that doesn’t…
The simplest way to detect whether your Linux system booted in UEFI or BIOS (Legacy) mode is to check for the existence of the EFI firmware directory. Check for EFI Directory The /sys/firmware/efi/ directory only exists when the system has booted in UEFI mode. If it’s absent, the system is running in BIOS/Legacy mode. […
When you need the commit hash of the latest commit, there are several ways to get it. The most direct approach is using git log with format options rather than parsing output with grep. Using git log with –format The cleanest method is to use git log with the –format option: git log -1 –format=”%H”…
When troubleshooting email delivery or verifying mail server configuration, you need to look up the MX (Mail Exchange) records for a domain. On Linux, two tools handle this: host and dig. Both are reliable, though dig is generally preferred for its flexibility and cleaner output format. Using dig to query MX records The dig command…
When an NFS server goes down or becomes unreachable, client mounts can end up in a “Stale NFS file handle” state. Standard umount and umount -f commands fail, leaving you stuck with an unusable mount point and no clean way to recover without rebooting. The solution is to use umount -l (lazy unmount), which immediately…
When you have multiple static libraries (.a files) and need to combine them into a single archive, GNU ar provides several approaches. The most straightforward method uses ar‘s MRI mode for clarity and maintainability. Using ar MRI Mode The cleanest approach is to use ar -M with an MRI script. This method is explicit and…
Fedora uses systemd-tmpfiles to automatically clean up temporary files and directories. By default, this includes volatile files in /tmp/, which can cause problems for applications that rely on files persisting there — like HDFS DataNodes that store their PID files as hadoop-hadoop-datanode.pid. How systemd-tmpfiles Works The systemd-tmpfiles service runs periodically (typically daily and at boot)…
Vim supports Xterm 256-color codes on Linux and modern terminals. Understanding the color palette and how to use it in your configuration is essential for building readable syntax highlighting schemes and custom colorschemes. The 256-Color Palette Xterm’s 256-color mode consists of: Colors 0-15: Standard ANSI colors (black, red, green, yellow, blue, magenta, cyan, white, and…
When you run a curl GET request with spaces in the query string, the shell interprets the space as a separator and truncates the URL: curl “http://example.com/send?msg=hello world” The space causes the shell to treat world as a separate argument, so only hello gets sent. You need to properly URL-encode the space (and other special…
When you compile or run screen on a remote host where you lack root privileges, you’ll often hit this error: Cannot make directory ‘/var/run/screen’: Permission denied This happens because screen needs a socket directory to manage sessions, and /var/run/screen is owned by root. If screen isn’t already installed system-wide, you can’t create this directory without…
When sending POST requests through a Squid proxy with curl, you may encounter a proxy error that blocks the request, even though the same request works fine with GET. The issue typically appears as: ERROR The requested URL could not be retrieved The root cause is the Expect: 100-continue header that curl automatically adds to…
When you need to verify the current link speed of a network interface — whether it’s running at 10Mbps, 100Mbps, 1Gbps, or higher — ethtool is the standard tool for the job. Using ethtool to check interface speed The basic command is straightforward: ethtool eth0 Replace eth0 with your actual interface name. Here’s sample output:…
When troubleshooting wireless performance, you need to know both the negotiated link speed and actual throughput. ethtool won’t help here — it’s for wired interfaces. For wireless adapters, you’ll need different tools depending on what information you’re after. Using iwconfig for link speed The iwconfig command shows the currently negotiated link rate between your adapter…
After installing Xen on AMD systems, you may see continuous “powernow-k8 transition frequency failed” messages on the console. This happens because the powernow_k8 driver (AMD CPU power management) is incompatible with Xen’s CPU handling and tries to manage frequencies that Xen controls. Quick Fix The simplest solution is to unload the conflicting module: sudo rmmod…
When processing delimited data in Bash, you often need to drop the last N fields from each line without knowing the total field count. The naive cut -d’.’ -f1 approach fails immediately when field counts vary. Given input like: systemd.3.gz systemd.mount.3.gz systemd.mount.f.3.gz You want to remove the last 2 fields (.3.gz) to get: systemd systemd.mount…