Introductory Notes

For linux I currently use Ubuntu. For Mac, the default compiler is clang, but I like to use gcc, so there are sometimes two sets of OS X instructions, one for clang ("OSX") and one for gcc ("OSX-gcc"). These notes are designed so that one installs software near the top of the list before software near the bottom of the list. I read somewhere that you ought to put aliases in .bashrc and environment variables in .bash_profile, but I haven't run across many cases where that matters.

bash

(Because redirection is so much better than in csh and variants.)

I like to set CC, CXX, and FC in .bash_profile to the compiler set (gcc, g++, gfortran) in Ubuntu or OSX with clang and (gcc-8, g++-8, and gfortran-8) for OSX-gcc.

To change the shell on OSX to bash, use chsh -s /bin/bash

Brave, Firefox

Directly from mozilla.org and brave.com (I've had trouble with brave on Ubuntu. The brave snap might be the best to use.)

OSX and OSX-gcc: Karabiner-elements, Homebrew

Karabiner-elements, from pqrs.org: Simple modification from key "fn" : to key "left_control"

Homebrew default install command:
ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

OSX-gcc: gcc, autoconf, automake

From homebrew, using brew install gcc automake libtool

gfortran

Ubuntu and OSX-gcc: automatically included by previous installation steps above

OSX: from here

Emacs

OSX: from http://emacsformacosx.com/

Also, aspell from "brew install aspell"

Latex

OSX: From http://tug.org/mactex/

Ubuntu: The texlive distribution, including texlive-fonts-extra, texlive-fonts-recommended, texlive-lang-greek, texlive-luatex, texlive-latex-recommended, texlive-pictures, texlive-sicence, and texlive-xetex

X11

OSX: from Xquartz at http://xquartz.macosforge.org/trac

Boost

Ubuntu: From package

OSX: From homebrew (make sure to use --c++11 in installation)

OSX-gcc: From homebrew

GSL, HDF5, open-mpi

Ubuntu: From packages (libgsl-dev, libhdf5-dev, libhdf5-openmpi-dev, libopenmpi-dev)

OSX: From homebrew; For HDF5, make sure to use --c++11 --with-mpi

OSX-gcc: from homebrew

O₂scl

Ubuntu: from source using ./configure or using snap

OSX and OSX-gcc: Using homebrew or from source

Thunderbird, VLC, and Gimp

From their respective websites. I used to install GIMP for OSX from this site because it has ufraw automatically included, but that link appears stale. Currently, I install gimp from the main website and ufraw is a homebrew package. VLC from here.

snapcraft

From ubuntu package.

FFTW

From ubuntu package and homebrew (called fftw)

Brews for OSX-gcc

curl, youtube-dl, ufraw, ffmpeg, git-lfs, imagemagick, wget, gsl, hdf5, doxygen, eigen, armadillo, subversion, aspell, fftw, openssl, pkg-config, gnupg, cmake, youtube-dl

Ubuntu packages

libeigen3-dev, libarmadillo-dev, libreadline-dev, libncurses-dev

Python packages

OSX and OSX-gcc: Using pip3 install: sphinx, breathe, yt, sympy, twine, mpi4py, matplotlib, jupyter, scipy, astropy

Ubuntu: Using sudo pip3 install

List of aliased files

.bashrc, .bash_profile, .emacs, wcs/makefile, bin, todos.rst