becoming a krome developerkromepackage.org/bootcamp/2014/talks/19_09_2014.pdf · 7 bitbucket and...

Becoming a KROME developerand more...

September 19, 2014

Stefano BovinoKROME school 2014

Historische Sternwarte-Göttingen

Institute for AstrophysicsGeorg-August Universität Göttingen

Germany

1News from the world

People happy because of the last KROME release!?

Stefano Bovino KROME school 2014 Historische Sternwarte-Göttingen | Becoming a KROME developer

2News from the world


3

First: a quick summaryon how to include KROME in your simulations

which microphysics?

includedin

KROME?

join the dev

luckyenough?

run KROME

obtain acompact file

x(:),Tgas,hydro_dt

no

yes

no

yes


4

Simple scheme of an hydro codewhere to include KROME

e-

OPAC I T Y

T

A+B C+Dk(T)

A

COOLING

ad

HYDRO

DUST

E

F J

I

HG

RAD+CR

HEATING

nH nH2

nH+ nenHCO

B

DC


5

First: a quick summaryon how to include KROME in your simulations

I enable options you needI run KROME

I inlcude the krome modulesI use kromeI use krome_user

I call krome_init()I once and for all

I be sure to have initialized thespecies (make use of krome_nmolsand other common arrays)

I change your Makefile accordinglyI solver files (opkd*.F)I krome routine (krome_all)


6

Bitbucket and KROMEa happy marriage

KROME is developed and maintained on Bitbucket

What is bitbucket?Bitbucket is a web-based hosting service for projects that usedistributed version control system (DVCS)

I GitI Mercurial

Main advantagesI it is not a centralized system (there is no central server)I it is a peer-to-peer networkI you can work without being connected to a network


7

Bitbucket and KROMEa happy marriage

To be part of the Bitbucket community you needI to register and create an accountI create your own repository (project) or start to follow an existing

repoI learn the basics of git

I git cloneI git addI git statusI git commitI git pushI git pull


8Follow a repository


9Git clone

I the most common way for users to obtain a development copyI makes a copy of an existing repository into your machine

basic usage$ git clone <repo>$ git clone <repo> <directory>

I once cloned everything is managed through your local repository.

I a central repo does not existI push or pull commits from

one repository to another


10Git clone


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Git cloneoutput

$ git clone https://bitbucket.org/tgrassi/krome.gitCloning 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), 16.81 MiB | 673.00 KiB/s, done.Resolving deltas: 100% (2675/2675), done.Checking connectivity... done.

I you will generate a folder named "krome"I note that you’re downloading the "dev" version


12

Git push and Git pullsharing the code

I once cloned the users can start to modify their local repositoryI Git is designed to give each developer an entirely isolated

development environment.I users typically need to share a series of commits (modifications)

before to push any modificationsPlease commit your modifications ("git commit -m "comment")Please update your repository

$ git pull origin

I it’s an easy way to synchronize your local repository withupstream changes


13

Pulling processupdate the code

I master → local branch/repoI origin/master → remote repo


14

Git pushPush your modification

Now that you are in line with the remote repo you can "push" yourmodifications.

I This has the potential to overwrite changes, so you need to becareful how you use it.


15

Git pushbasic steps

1. you prepared your modifications2. you updated to the latest version of the remote repo3. you are ready to push your commits

$ git add .$ git status$ git commit -m "name_of_the_commit"$ git push origin master


16

Become a KROME developerwe need help!

KROME is centralized

Centralized Workflow uses a central repository to serve as the singlepoint-of-entry for all changes to the project.


17

Become a KROME developerwe need help!

1. create a branch or fork the KROME repo2. a branch represents an independent line of development3. branches serve as an abstraction for the edit/stage/commit

process discussed in Git Basics


18

Create a branchdevelopment

I once created the branch, clone itI then you can modify the code

(python and fortran)I push your commits


19

Fork the central repodevelopment


20Fork or branch?

BranchesI remain part of the original repositoryI the branch knows and relies on the main code (and viceversa)

ForkI it means a copy of the original codeI is independent from the original repositoryI if the original repository is deleted, the fork remains

In KROME we suggest to fork the central repository


21

Pull requestdev process

I Now you have your own branch/fork with new featuresI To add your modifications to the central repo (KROME) you need

to create a "pull request"I pull requests are a mechanism for a developer to notify team

members that they have completed a featureI everybody involved know that they need to review the code and

merge it into the master branch


22

Become a KROME developera clear example step by step

1. fork or create a branch of theKROME main repo

2. clone your own repo wit "gitclone"


22

Become a KROME developer (cont’d)a clear example step by step

3. modify KROME adding yourfeatures

4. push your commits on yourremote branch("git commit"& "git push")


22


5. create a pull request to KROME


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6. the community will see andreview your request

if you prepare a nice featureafter the review process the feautre can be included or not in theoriginal KROME repo → i.e. become part of the package


23

Become a KROME developerrequirements

to become a KROME developerI know fortran and/or pythonI be motivatedI have the good attitude to share code

how you can contributeI preparing fortran functions/subroutinesI carefully modify the heart of KROME, i.e. the python

pre-processorI simply create or discuss issues


24What should be clear at this stage

I KROME is a package which help users to build their ownmicrophysics

I KROME is open sourceI KROME is a pre-processorI a chemical network is compulsory to run KROME

I KROME is flexible and can be customizedI KROME allow users to choose between efficiency and accuracyI to embed KROME into an external code requires a simple call

I call krome(x(:), Tgas, dt)I BUT there are caveats

I the community is very important!I KROME saves your days (as Tommaso stated)


25What we learned

I how to prepare a chemical networkI the use of some tokens

I @format→ to change the format in the network fileI @common→ to add a common variableI @var→ to define variables in the network fileI @CR_begin/@CR_stop→ to define block of CR recationsI @photo_begin/@photo_stop→ to define block of

photo-recationsI @cooling_start, @cooling_stop, and @cooling

I how to run KROME and the pre-built testsI how to call KROME from a framework codeI how to use the krome_user module

I how to initialize common variablesI how to initialize and rescale a radiation spectrum

I some of the KROME flagsI -n, -useN, -pedantic, -noExample, -cooling=H2,CI, -heating=CR,

-PhotoBinsStefano Bovino KROME school 2014 Historische Sternwarte-Göttingen | Becoming a KROME developer

26Acknowledgements

Invited speakersI Daniele GalliI Troels HaugboelleI Muhammad LatifI Dominik SchleicherI Daniel SeifriedI Svitlana Zhukovska

"you gotthe weight on your shouldersThat’s breaking your back."

Participants! Users is always the best source of improvement!I for your curiosity on the packageI for the nice and fruitful discussionsI for the nice (and hard) time during the practical sessions


27

Urgent developmentanyone interested?

I the solver is the most important part of the packageI low-order and simple solver only useful for very small network

and a few physical cases (as discussed by Dominik)I accurate but efficient → not too computational expansiveI for a good solver

I capability to work with stiff problemsI high-enough and variable orderI good definition of the time-stepI and a variable time-stepI computational optimization (e.g. on the matrix inversions)I accurate evaluation of the Jacobian matrix

(in particular temperature, as mentioned by Tommaso)I now in KROME the well-established DLOSDES solver

I accurate and stableI time-step and order variableI not so efficient but still fast (extensively proved by Troels)I not very well optimizedI very general (for a broad range of problems)


28Urgent development

Anyone interested in developing a new solver with theabove features?

“First, solve the problem. Then, write the code.”- John Johnson -


29

Where are you?the picture will be available online


Thank you for your attention!

becoming a krome developerkromepackage.org/bootcamp/2014/talks/19_09_2014.pdf · 7 bitbucket and...

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