Warwick SCRTP

Basics

  • Log into my machine vega1.astro.warwick.ac.uk (not the gateway machine godzilla) using x2go, instructions on CSC wiki here (use your CSC user/password).
  • Basic information on how to use the Linux OS here. Most important is how to use a terminal (i.e. the “Linux command line”).
  • To get stuff from github, copy the clone link and then do “git clone https://github.com/someone/repo_link.git”

Machine choice

Don’t run stuff on godzilla (the machine you first connect to with x2go). If you’re working with me use vega1.astro.warwick.ac.uk; ssh to it in a terminal with “ssh -X vega1.astro.warwick.ac.uk”.

Loading CSC modules

When logging in to CSC machines, run the command below in a terminal to get access to python and some necessary modules. This will allow you to run a jupyter notebook too.

module load GCC/8.3.0  OpenMPI/3.1.4 Python/3.7.4 IPython/7.9.0-Python-3.7.4 matplotlib astropy

module load GCC/6.4.0-2.28 OpenMPI/2.1.1 Python/3.6.3 IPython/6.2.1-Python-3.6.3 matplotlib astropy

If you then type “module save”, you can restore the configuration next time with “module restore” (rather than pasting the whole command in each time).

Python

If you need python modules that don’t exist in CSC, you can install these with something like “pip install –user kplr”. This puts them in a hidden folder in your home space.

Having loaded the modules, open a jupyter notebook by typing “jupyter notebook”. This will open a browser window with the jupyter file browser, use this to find and then run your notebook.

Mac setup

My list of software to get a new mac up to speed. Latest was el Capitan.

  • Run software update
  • Sign into iCloud, turn everything but Notes off
  • Check shell is zsh in System Preferences (apparently default?)
  • Various finder preferences, e.g. filename extensions
  • Turn on FileVault, Firewall
  • Chrome
  • Office
  • Xcode (also xcode-select --install)
  • Slack
  • x2go
  • MacTex and BibDesk (use TeX Live Utility to do updates and check paper size )
  • XQuartz
  • homebrew (this involved cloning homebrew-core on a different machine with institutional internet and copying it into place)
  • web server, system httpd, homebrew php, mysql
    • copy tables using mysqldump, mysql -uuser -ppass -N -e “show databases like ‘%’;” |grep -v -F mysql |grep -v -F _schema|grep -v -F sys |xargs mysqldump -uuser -ppass –databases > alldb.sql, and read back in with –force option if version related errors.
    • there is a signing issue with homebrew php, the fix looks like a pain so use system php for now (but this will disappear sometime)
  • Sequel Pro (buggy, latest test build seems fine)
  • iObserve
  • Sublime Text
  • Topcat and the stilts script
  • cdsclient (had to compile and place wwwget to /usr/local/bin by hand)
  • ads2bibdesk (and ads)
    • comment line ~287 in python script to use bibcodes as cite key
    • service doesn’t work, but terminal OK
  • (py)multinest
    • may need to do: export FCFLAGS="-w -fallow-argument-mismatch -O2" and export FFLAGS="-w -fallow-argument-mismatch -O2" for make to work
  • galario
  • DS9

Installing galario

  • Import modules, e.g. module load GCC/8.3.0 OpenMPI/3.1.4 Python/3.7.4 FFTW/3.3.8 CMake/3.15.3 IPython/7.9.0-Python-3.7.4
  • Follow instructions here, including python binding
  • Find python site-packages, create galario directory, and copy contents of galario/build/python/galario (single, double, __init__.py) into it.
module load GCC/8.3.0  OpenMPI/3.1.4 Python/3.7.4 FFTW/3.3.8 CMake/3.15.3 IPython/7.9.0-Python-3.7.4
git clone https://github.com/mtazzari/galario.git
cd galario
mkdir build
cd build
cmake -DPython_ADDITIONAL_VERSIONS=3.7 ..
make
cp -r python/galario/* ~/.local/lib/python3.7/site-packages/galario/

These instructions seem to work on a Mac too, though I needed to remove the galario folder and start from scratch when upgrading the python version.

To use galario with emcee, set the number of galario threads to 1 with galario.double.threads(num=1). It won’t work otherwise.