Enzo v2.1 documentation

Introduction to Enzo Modification

Note

This is not a comprehensive document, but it does cover some of the grounds of modifying Enzo. Please don’t hesitate to email the users’ mailing list with any further questions about Enzo, Mercurial, or how to write and execute new test problems.

If this is the first time you’ve opened the hood to Enzo, welcome. If you’re an old hand and have already added new physics to it, welcome back.

Enzo is an extremely powerful piece of software, but by no means a complete representation of the observable universe. It’s quite likely that there will be some piece of physics that you’ll want to model, and these span a broad range of software complexities. In all cases, whether it’s a mildly invasive change such as a new background heating model or extremely invasive like adding relativistic non-neutral multi-fluid plasma physics, we strongly recommend taking advantage of some basic tools. These are outlined in the sections that follow. These tools prevent the developer from breaking existing features (which is far easier than one would expect), keeping track of your changes, and sharing those changes with others. We strongly recommend you start with getting LCATest running before you start programming, so mistakes can be caught early.

Additionally in the Tutorials section you’ll see a pair of flow chart tools that are intended as educational tools, and several descriptions on how to actually add various components to the code. It is intended that these will be at least read in order, as doing complex things with the code require the ability to do the simpler things.

We are very happy to accept patches, features, and bugfixes from any member of the community! Enzo is developed using mercurial, primarily because it enables very easy and straightforward submission of changesets. We’re eager to hear from you, and if you are developing Enzo, please subscribe to the users’ mailing list:

http://groups.google.com/group/enzo-users

This document describes how to use Mercurial to make changes to Enzo, how to send those changes upstream, and how to navigate the Enzo source tree.

Mercurial Introduction

If you’re new to Mercurial, these three resources are pretty great for learning the ins and outs:

The major difference between Mercurial (and other distributed version control systems) and centralized version control systems (like CVS, RCS, SVN) is that of the directed acyclic graph (DAG). Rather than having a single timeline of modifications, Mercurial (or “hg”) can have multiple, independent streams of development.

There are a few concepts in Mercurial to take note of:

Changesets
Every point in the history of the code is referred to as a changeset. These are specific states of the code, which can be recovered at any time in any checkout of the repository. These are analagous to revisions in Subversion.
Children
If a changeset has changesets that were created from its state, those are called children. A changeset can have many children; this is how the graph of development branches.
Heads
Every changeset that has no children is called a head.
Branches
Every time the DAG branches, these are branches. Enzo also uses “named branches,” where the branches have specific identifiers that refer to the feature under development or some other characteristic of a line of development.

On the Google Code wiki there is a list of active branches.

When you check out the Enzo repository, you receive a full and complete copy of the entire history of that repository; you can update between revisions at will without ever touching the network again. This allows not only for network-disconnected development, but it also means that if you are creating some new feature on top of Enzo you can (and should!) conduct local version control on your development. Until you choose explicitly to share changes, they will remain private to your checkout of the repository.

Enzo Source Trees

Enzo has two primary repositories, the “stable” repository which is curated and carefully modified, and the “development” repository which is where active development occurs. Please note that while we test and verify the results of the “stable” repository, the “unstable” repository is not guaranteed to be tested, verified, or even to provide correct answers.

Note

The “stable” Enzo source tree is not for general development. If you want to contribute to Enzo, make your changes to a fork of the development repository!

To conceptually – and technically! – separate these two repositories, they also live in different places. We keep the stable repository at Google Code, and the development repository at BitBucket. Enzo is (as of 2.1) developed in a relatively simple fashion:

  1. On BitBucket, developers “fork” the primary development repository.
  2. When a piece of work is ready to be shared, a “pull request” is issued. This notifies the current set of Enzo curators that a new feature has been suggested for inclusion.
  3. These features
  4. When a new patch release is issued, the current development branch is pushed to the “stable” branch on Google Code.

The idea here is that there is a double firewall: the development repository is very high-cadence and with high-turnover, but the stable repository is much slower, more carefully curated, and inclusions in it are well-tested.

How To Share Changes

Sharing your changes to Enzo is easy with Mercurial and the BitBucket repository.

Go here:

http://bitbucket.org/enzo/enzo-dev/fork

Now, clone your new repository. Make your changes there. Now go back and issue a pull request. For instance, you might do something like this:

  1. Clone Enzo, make a few changes, commit them, and decide you want to share.
  2. Fork the main enzo repository at that link.
  3. Now, edit .hg/hgrc to add a new path, and push to that path.
  4. Go to the BitBucket URL for your new repository and click “Pull Request”. Fill it out, including a summary of your changes, and then submit. It will get evaluted – and it might not get accepted right away, but the response will definitely include comments and suggestions.

That’s it! If you run into any problems, drop us a line on the Enzo Users’ Mailing List.

How To Use Branching

Warning

In most cases, you do not need to make a new named branch! Do so with care, as it lives forever.

If you are planning on making a large change to the code base that may not be ready for many, many commits, or if you are planning on breaking some functionality and rewriting it, you can create a new named branch. You can mark the current repository as a new named branch by executing:

$ hg branch new_feature_name

The next commit and all subsequent commits will be contained within that named branch. At this point, add your branch here:

http://code.google.com/p/enzo/wiki/ActiveBranches

To merge changes in from another branch, you would execute:

$ hg merge some_other_branch

Note also that you can use revision specifiers instead of “some_other_branch”. When you are ready to merge back into the main branch, execute this process:

$ hg merge name_of_main_branch
$ hg commit --close-branch
$ hg up -C name_of_main_branch
$ hg merge name_of_feature_branch
$ hg commit

When you execute the merge you may have to resolve conflicts. Once you resolve conflicts in a file, you can mark it as resolved by doing:

$ hg resolve -m path/to/conflicting/file.py

Please be careful when resolving conflicts in files.

Once your branch has been merged in, mark it as closed on the wiki page.

The Patch Directory

If you are experimenting with a code change or just debugging, then the patch directory, found in the top level of your Enzo directory, may be of use. Files put in here are compiled in preference to those in /src/enzo, so you can implement changes without overwriting the original code. To use this feature, run make from inside /patch. You may need to add -I../src/enzo to the MACH_INCLUDES line of your machine makefile (e.g. Make.mach.triton) to ensure the .h files are found when compiling.

As an example, suppose you wish to check the first few values of the acceleration field as Enzo runs through EvolveLevel.C. Copy EvolveLevel.C from /src/enzo into /patch and put the appropriate print statements throughout that copy of the routine. Then recompile Enzo from inside the patch directory. When you no longer want those changes, simply delete EvolveLevel.C from /patch and the next compile of the code will revert to using the original /src/enzo/EvolveLevel.C. If you make adjustments you wish to keep, just copy the patch version of the code into /src/enzo to replace the original.

How To Include Tests

If you have added any new functionality, you should add it as a test in the directory tree run/ under the (possibly new!) appropriate directory. Your test file should consist of:

  • A parameter file, ending in the extension .enzo
  • A file of notes.txt, describing the problem file, the expected results, and how to verify correctness
  • A test file, using the yt extension enzo_test, which verifies correctness. (For more information on this, see some of the example test files.)
  • (optional) Scripts to plot the output of the new parameter file.

Please drop a line to the mailing list if you run into any problems!