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<< Cosmo.WebHome %TOC% ---- ---+ 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 [[WikipediaEn:emacs][emacs]] or [[WikipediaEn:vi][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 [[Wikipedia:Anaconda_(Python_distribution)][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_ * 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#Gevolution_hackathon 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 [[https://www.chiark.greenend.org.uk/~sgtatham/bugs.html][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.
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Topic revision: r17 - 03 Mar 2022,
BoudRoukema
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