Writing

Notes on Linux, HPC, and DNA simulation

Practical write-ups from setting up clusters and running oxDNA — mostly so future-me doesn't have to remember it twice.

August 25, 20253 min read

SLURM: Commands and Cluster Management

Installing munge and SLURM, everyday queue/partition commands, and setting up slurmdbd accounting from scratch.

August 20, 20254 min read

oxDNA Simulation Guide

A step-by-step guide to relaxing and equilibrating structures in oxDNA, from installation through production simulation.

#oxdna#simulation#hpc

May 23, 20252 min read

Linux System Setup From Scratch

A repeatable script-driven setup for a fresh Linux box: base packages, oh-my-zsh, SSH keys and jump hosts, and handy shell functions.

#linux#zsh#dotfiles

September 15, 20242 min read

Sharing Mouse & Keyboard with Barrier

Generating a self-signed SSL cert for Barrier so one keyboard and mouse can control multiple machines.

#linux#networking#productivity

September 7, 20242 min read

Setting Up an ARM Linux Server

Distro choice, a lightweight desktop environment, and the NVML/CUDA fix needed for SLURM to see GPUs correctly on ARM (aarch64/sbsa).

#arm#linux#slurm#gpu

August 17, 20243 min read

C++ ofstream Tips

What each std::ios flag actually does when opening a file for writing.

#c++#coding

August 17, 20242 min read

Docker Commands Cheatsheet

Running disposable GPU-enabled containers and listing what's running.

#docker#gpu

August 1, 20242 min read

Linux User & Group Management

Creating groups and users, and locking a shared directory like /var/www down to a single group with the right permission bits.

#linux#users#permissions

June 20, 20242 min read

GNUplot Cheatsheet

Plotting a column against its row index, and building normalized histograms from a single-column data file.

#gnuplot#plotting

May 23, 20241 min read

Cogli2 Build Requirements

The Ubuntu and conda dependencies Cogli2 needs, and the CMake snippet for pointing it at a conda environment.

#linux#build#visualization

May 4, 20242 min read

Vim Commands & Neovim C++ Setup

Search-and-replace patterns worth memorizing, plus wiring up NvChad with Mason and clangd for C++ development.

#vim#neovim#editor

April 27, 20243 min read

Bash Automation for HPC Job Management

Scripts for launching oxDNA replicas, auto-resuming jobs that die on a private SLURM queue, and sweeping a parameter before batch-plotting the results.

#bash#slurm#oxdna#hpc

April 18, 20242 min read

Speech-to-Text with Whisper

Installing OpenAI's Whisper and picking the right model size for the VRAM you actually have.

#ml#whisper#audio

April 9, 20242 min read

macOS Network Reset

The file-deletion trick that fixes stubborn Wi-Fi issues on a Mac when toggling Wi-Fi off and on doesn't help.

#macos#networking

April 9, 20241 min read

Windows Time Server Fix

Changing which NTP server Windows syncs its clock against via the registry.

#windows#networking

March 15, 20242 min read

All-Atom MD Simulation Setup for DNA (AMBER)

Building an AMBER-ready system for a DNA duplex with a covalently attached small molecule: antechamber, tleap, and homology modeling for missing residues.

#amber#dna#simulation

March 15, 20242 min read

Pacman Cheatsheet

The four pacman commands I actually use on Arch: install, clean the cache, uninstall completely, and prune orphans.

#arch#linux#pacman

February 27, 20243 min read

Useful Bash Commands & Functions

A grab bag of .bashrc functions I re-add on every new machine: server shortcuts, SLURM/GPU job killers, and VPN login helpers.

#bash#linux#slurm

February 26, 20242 min read

Optimizing Molecular Structures with DFT

Measuring ligand-to-DNA-backbone distances accurately by pre-optimizing structures with a classical force field before handing them to a quantum engine.

#quantum-chemistry#dft#dna

February 12, 20243 min read

CryoSPARC Installation & Management

Licensing, installing, and standing up a CryoSPARC master on a single machine or an HPC cluster node.

#cryo-em#hpc#linux

January 23, 20242 min read

Disk Management with parted

Creating and formatting partitions with parted, verifying mounts, and making them permanent via /etc/fstab.

#linux#disk#parted

January 15, 20242 min read

LVM Partition Management

Extending an LVM partition without downtime: the fdisk/lvs/lvextend/resize2fs sequence, and when to reach for LVM over BTRFS.

#linux#disk#lvm

October 9, 20232 min read

Compiling TensorFlow Natively

Building TensorFlow from source with AVX, cuDNN, and TensorRT support for a real (if modest) speedup over the pip wheel.

#tensorflow#ml#compilation