Becoming a KROME developer

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Dominic Bishop
5 years ago
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1 Becoming a KROME developer and more... September 19, 2014 Stefano Bovino K R O M E school 2014 Historische Sternwarte-Göttingen Institute for Astrophysics Georg-August Universität Göttingen Germany

2 News from the world 1 People happy because of the last KROME release!?

3 News from the world 2

4 First: a quick summary on how to include KROME in your simulations 3 which microphysics? run KROME obtain a compact file yes included in KROME? yes lucky enough? x(:),tgas,hydro_dt no no join the dev

5 Simple scheme of an hydro code where to include KROME 4 k(t) A+B C+D E G H HYDRO F A B D C J I RAD+CR ad e - DUST n H + n e n nhco H n H2 HEATING COOLING T OPACITY

First: a quick summary on how to include KROME in your simulations 5 enable options you need run KROME inlcude the krome modules use krome use krome_user call krome_init() once

6 First: a quick summary on how to include KROME in your simulations 5 enable options you need run KROME inlcude the krome modules use krome use krome_user call krome_init() once and for all be sure to have initialized the species (make use of krome_nmols and other common arrays) change your Makefile accordingly solver files (opkd*.f) krome routine (krome_all)

Bitbucket is a web-based hosting service for projects that use distributed version control

7 Bitbucket and KROME a happy marriage 6 KROME is developed and maintained on Bitbucket What is bitbucket? Bitbucket is a web-based hosting service for projects that use distributed version control system (DVCS) Git Mercurial Main advantages it is not a centralized system (there is no central server) it is a peer-to-peer network you can work without being connected to a network

repository (project) or start to follow an existing repo learn the

8 Bitbucket and KROME a happy marriage 7 To be part of the Bitbucket community you need to register and create an account create your own repository (project) or start to follow an existing repo learn the basics of git git clone git add git status git commit git push git pull

9 Follow a repository 8

Git clone 9 the most common way for users to obtain a development copy makes a copy of an existing repository into your machine basic usage $ git clone <repo> $ git

10 Git clone 9 the most common way for users to obtain a development copy makes a copy of an existing repository into your machine basic usage $ git clone <repo> $ git clone <repo> <directory> once cloned everything is managed through your local repository. a central repo does not exist push or pull commits from one repository to another

11 Git clone 10

12 Git clone output 11 $ git clone Cloning into krome... remote: Counting objects: 4193, done. remote: Compressing objects: 100% (2063/2063), done. remote: Total 4193 (delta 2675), reused 3278 (delta 2094 Receiving objects: 100% (4193/4193), MiB Resolving deltas: 100% (2675/2675), done. Checking connectivity... done. you will generate a folder named "krome" note that you re downloading the "dev" version

13 Git push and Git pull sharing the code 12 once cloned the users can start to modify their local repository Git is designed to give each developer an entirely isolated development environment. users typically need to share a series of commits (modifications) before to push any modifications Please commit your modifications ("git commit -m "comment") Please update your repository $ git pull origin it s an easy way to synchronize your local repository with upstream changes

14 Pulling process update the code 13 master local branch/repo origin/master remote repo

15 Git push Push your modification 14 Now that you are in line with the remote repo you can "push" your modifications. This has the potential to overwrite changes, so you need to be careful how you use it.

16 Git push basic steps you prepared your modifications 2. you updated to the latest version of the remote repo 3. you are ready to push your commits $ git add. $ git status $ git commit -m "name_of_the_commit" $ git push origin master

17 Become a KROME developer we need help! 16 KROME is centralized Centralized Workflow uses a central repository to serve as the single point-of-entry for all changes to the project.

18 Become a KROME developer we need help! create a branch or fork the KROME repo 2. a branch represents an independent line of development 3. branches serve as an abstraction for the edit/stage/commit process discussed in Git Basics

19 Create a branch development 18 once created the branch, clone it then you can modify the code (python and fortran) push your commits

20 Fork the central repo development 19

21 Fork or branch? 20 Branches remain part of the original repository the branch knows and relies on the main code (and viceversa) Fork it means a copy of the original code is independent from the original repository if the original repository is deleted, the fork remains In KROME we suggest to fork the central repository

Pull request dev process 21 Now you have your own branch/fork with new features To add your modifications to the central repo (KROME) you need to create a "pull request" pull requests

22 Pull request dev process 21 Now you have your own branch/fork with new features To add your modifications to the central repo (KROME) you need to create a "pull request" pull requests are a mechanism for a developer to notify team members that they have completed a feature everybody involved know that they need to review the code and merge it into the master branch

23 Become a KROME developer a clear example step by step fork or create a branch of the KROME main repo 2. clone your own repo wit "git clone"

24 Become a KROME developer (cont d) a clear example step by step modify KROME adding your features 4. push your commits on your remote branch ("git commit"& "git push")

25 Become a KROME developer (cont d) a clear example step by step create a pull request to KROME

Become a KROME developer (cont d) a clear example step by step 22 6.

26 Become a KROME developer (cont d) a clear example step by step the community will see and review your request if you prepare a nice feature after the review process the feautre can be included or not in the original KROME repo i.e. become part of the package

27 Become a KROME developer requirements 23 to become a KROME developer know fortran and/or python be motivated have the good attitude to share code how you can contribute preparing fortran functions/subroutines carefully modify the heart of KROME, i.e. the python pre-processor simply create or discuss issues

28 What should be clear at this stage 24 KROME is a package which help users to build their own microphysics KROME is open source KROME is a pre-processor a chemical network is compulsory to run KROME KROME is flexible and can be customized KROME allow users to choose between efficiency and accuracy to embed KROME into an external code requires a simple call call krome(x(:), Tgas, dt) BUT there are caveats the community is very important! KROME saves your days (as Tommaso stated)

29 What we learned 25 how to prepare a chemical network the use of some to change the format in the network to add a common to define variables in the network to define block of CR to define block how to run KROME and the pre-built tests how to call KROME from a framework code how to use the krome_user module how to initialize common variables how to initialize and rescale a radiation spectrum some of the KROME flags -n, -usen, -pedantic, -noexample, -cooling=h2,ci, -heating=cr, -PhotoBins

30 Acknowledgements 26 Invited speakers Daniele Galli Troels Haugboelle Muhammad Latif Dominik Schleicher Daniel Seifried Svitlana Zhukovska "you got the weight on your shoulders That s breaking your back." Participants! Users is always the best source of improvement! for your curiosity on the package for the nice and fruitful discussions for the nice (and hard) time during the practical sessions

31 Urgent development anyone interested? 27 the solver is the most important part of the package low-order and simple solver only useful for very small network and a few physical cases (as discussed by Dominik) accurate but efficient not too computational expansive for a good solver capability to work with stiff problems high-enough and variable order good definition of the time-step and a variable time-step computational optimization (e.g. on the matrix inversions) accurate evaluation of the Jacobian matrix (in particular temperature, as mentioned by Tommaso) now in KROME the well-established DLOSDES solver accurate and stable time-step and order variable not so efficient but still fast (extensively proved by Troels) not very well optimized very general (for a broad range of problems)

32 Urgent development 28 Anyone interested in developing a new solver with the above features? First, solve the problem. Then, write the code. - John Johnson -

33 Where are you? the picture will be available online 29

34 Thank you for your attention!

Version control system (VCS)

Version control system (VCS) Remember that you are required to keep a process-log-book of the whole development solutions with just one commit or with incomplete process-log-book (where it is not possible