Setting up my scientific computing environment

posted in: Research | 0

I use macs at work due to their fluid interface with the unix environment, and their ability to run unix/linux programs.  I’ve recently bought a new mac, which has required that I get it set up for my scientific computing.  Below are the pieces of software I’ve needed, which help streamline your own computational workflows.

 

I start with most of Alejandro Soto’s instructions here (http://alejandrosoto.net/blog/2016/08/16/setting-up-my-mac-for-climate-research/), including iTerm, the XCode developer tools, XQuartz, Homebrew, and Anaconda (for Python).

Obspy for working with seismic data (https://github.com/obspy/obspy/wiki/Installation-via-Anaconda)

ffmpeg for working with video files and making timelapse movies – I used

brew install ffmpeg --with-fdk-aac --with-ffplay --with-freetype --with-libass --with-libquvi --with-libvorbis --with-libvpx --with-opus --with-x265

(https://trac.ffmpeg.org/wiki/CompilationGuide/MacOSX)

Octave, for my legacy Matlab code.  Octave is a free substitute for Matlab, with most of the same functionality.  I’m pleased to learn that it has a new GUI that also reproduces the Matlab GUI.  At the terminal:

brew install octave

BasicTex from Mactex-2016 for latex typesetting (because I think the full MacTex download of 2.8 Gb is obscene) (https://tug.org/mactex/morepackages.html) and then also TeXShop and LaTeXIt, from the same page

Cyberduck to have an easy to use GUI for transferring files between different computers/servers  (https://cyberduck.io/?l=en)

The Microsoft Office Suite, available through the University of Idaho

Google Earth Pro, available as a free download, for quickly learning about field sites (https://www.google.com/earth/download/gep/agree.html)

Dropbox, Google Drive, and OneDrive, for my online file storage.

The “Be Focused” app, from the App Store, which has a timer I use to keep targeted during my days.  It’s based on the pomodoro technique.