Inhomogeneous Cosmologies IV work space

• For general IC IV community organising notes, see InhomCosmIV
• older: 2017: CosmoTorun17Software | 2018: InhomCosmIIISoftware

Basic introduction to UNIX-like shells and programming

• You need a laptop (during the workshop) running a UNIX-like operating system such as GNU/Linux, GNU/kFreeBSD, OSX (UNIX/FreeBSD)
• If you are a newbie to anything numerical (if you don't know what a "terminal" is, and how to use it), please see try one (either) of these introductory tutorials:
  • Lorena Barba tutorial: https://barbagroup.github.io/essential_skills_RRC/nix/setup/
  • Daniel Price pdf for Monash University (Australia) astrophysical computing tutorial (aimed at undergraduates), specifically Section 1 (the other sections may not be used in the numerical sessions, but are useful nonetheless!). Download the PDF here: https://framadrop.org/r/0EmDcryppY#mIAiXtcFz6heFVkLP/n9GuFODMBzT+ZOoarCmWS+VQQ=

• For the afternoon tutorials we assume that you know how to:
  • use a terminal (change directories, rename files/directories, copy and move files around, etc.)
  • use in-terminal text editors (your long-term interest is to learn either emacs or vi)
  • all of which is covered in detail in the above tutorials

Before the numerical sessions

• Before attending the numerical sessions please attempt the following:
  • Intro to UNIX-like shell tutorial (if newbie else continue)
  • Download and compile the latest version of the Einstein Toolkit on your machine: http://einsteintoolkit.org
  • Download and compile gevolution: https://github.com/gevolution-code/gevolution-1.1
  • Download and compile SPLASH (used for visualisation in both the ET and gevolution tutorials): http://users.monash.edu.au/~dprice/splash/
    • compile the Cactus HDF5 capabilities (after compiling according to the instructions on the webpage) using: make SYSTEM=gfortran cactus (from your SPLASH directory)
  • Ensure you have Python installed, including h5py and numpy (both included by default with Anaconda: https://www.anaconda.com/distribution/)
  • See if you can download, compile and run the inhomog reproducibility script - https://bitbucket.org/broukema/1902.09064 - to check the tables and figures in https://arXiv.org/abs/1902.09064.

White paper

elementary usage

• clone or download and compile, without logging in:
  • https://bitbucket.org/broukema/whitepaper_inhomog
• OR download, edit, upload, check history, with overleaf account:
  • git clone https://git.overleaf.com/5c3db40ac41fc0665b938eaf
• OR edit, view, with overleaf/orcid/GAFAM account :
  • https://overleaf.com/16937394rvbwybqsvgjp

full power of git

1. create a bitbucket account (or an account on e.g. gitlab or (github %GAFAM%))
2. log in to your bitbucket account in your browser
3. go to https://bitbucket.org/broukema/whitepaper_inhomog in your browser
4. find "fork" and click and wait a few seconds
5. adjust the parameters of your fork (make it "public" not private)
6. git clone your fork
7. modify things locally
8. git commit --all - this is still only local on your computer
9. git push - this step (if it succeeds) will make your commits public
10. on the web interface, create a "pull request" to boud
11. if boud does not answer quickly, hassle him with an email

git tutorial

• https://git-scm.com/docs/gittutorial

Einstein Toolkit Tutorial

• See InhomCosmIIISoftware for the tutorial from Inhomogeneous Cosmologies III

updates compared to the 2018 notes of InhomCosmIIISoftware

prefer native libraries

• http://cactuscode.org/pipermail/users/2018-September/003634.html
• https://bitbucket.org/einsteintoolkit/tickets/issues/2239/getcomponents-avoid-useless-downloads
  • Try commenting out all the ExternalLibraries lines, and instead install them from your system, e.g.
    • As of 2022-02-03 on Debian/bullseye: aptitude install petsc-dev libopenblas-dev libfftw3-dev libgsl-dev libhdf5-dev libhwloc-dev liblapack-dev libjpeg-dev liblorene-dev mpi-default-dev openssl libpapi-dev python3-dev python3-cffi libudev-dev
      • might also be needed: aptitude install zlib1g
    • As of 2019-07-18 on Debian/stretch: aptitude install petsc-dev libopenblas-dev pciutils-dev libfftw3-dev libgsl-dev libhdf5-dev libhwloc-dev liblapack-dev libjpeg-dev liblorene-dev mpi-default-dev openssl libpapi-dev pciutils-dev zlibc
    • As of 2019-07-18 on Debian/stretch: aptitude install opencl-dev - you will have to choose an implementation, e.g. aptitude install ocl-icd-opencl-dev

optionally use NDS host

• One updated option is to create an account at the "NCSA Nebula and the National (USA) Data Service" using authentication from your university centralised login (https://cilogon.org/) or ORCID or %GAFAM% (github/Google), and then waiting a few working days: https://etkhub.ndslabs.org/hub/login

gevolution hackathon

• See InhomCosmIIISoftware for the hackathon details from Inhomogeneous Cosmologies III
• LATfield2GevolutionTutorial

inhomog/reproducible paper hackathon

1. Browse through the README at https://bitbucket.org/broukema/1902.09064
2. Either git clone the file distribution (search for the "Clone" button for hints) or download it by navigating to the Downloads button and choosing your preferred download method.
3. Read the README more carefully and after a little checking and try installing system-level "native" packages using sudo, either with the main script or by reading the script and doing this by hand
4. Run the main script as described in the README and within about half an hour you should have reproduced statistically equivalent tables and plots to those in https://arXiv.org/abs/1902.09064 , with you in full control of all the software involved.
5. If you have found a bug, then first make notes in a file (using a text editor) to see if the bug is reproducible so that you can provide a useful bug report. The post it as an "Issue" at bitbucket and use face-to-face interaction to encourage others to try to solve the bug.