The core of the Cyclus nuclear fuel cycle code from the University of Wisconsin, Madison
C++ Python CMake Shell
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Updating to 1.3.1

README.rst

Cyclus Core

The core of the Cyclus nuclear fuel cycle simulator from the University of Wisconsin - Madison is intended to be a simulation framework upon which to develop innovative fuel cycle simulations.

To see user and developer documentation for this code, please visit the Cyclus Homepage.

Quick Start

If you want to get up and running as quickly as possible:

  1. Install VirtualBox
  2. Download the environment
  3. Open the .ova file using VirtualBox (File->Import Appliance).
  4. Login with the username ubuntu and pw reverse
  5. Skip to "Installing Cyclus"

Note that the Cyclus source code exists already on the virtual machine. You can update it with

$ cd cyclus
    $ git pull origin cyclus

Dependencies

In order to facilitate future compatibility with multiple platforms, Cyclus is built using `CMake`_. A full list of the Cyclus package dependencies is shown below:

Package Minimum Version
CMake 2.8
boost 1.46.1
libxml2 2
libxml++ 2.36
python 2.7 or 3.3+
sqlite3 3.7.10
HDF5 1.8.4
Coin-Cbc 2.5

On some platforms, such as Ubuntu 14.04, the following are also necessary:

Package Minimum Version
g++ 4.8.2
libblas-dev 1.2
liblapack-dev 3.5.0

And a few optional dependencies:

Package Minimum Version
doxygen (for docs) 1.7.6.1
tcmalloc (for speed) any?

Note that the Debian/Ubuntu package `libtcmalloc` is NOT discovered correctly by our build system. Instead use `libgoogle-perftools-dev`.

Installing Dependencies

Cyclus dependencies can either be installed via an operating system's package manager or via Conda.

Via Conda

Note, at present, Conda dependency downloading is only supported for Linux

A Conda installation may be the most straightforward for a new developer. These instructions will be similar to those shown for Cyclus users conda installation.

  1. Download the appropriate miniconda installer

  2. Install miniconda

    $ bash Miniconda-3.5.2-Linux-x86_64.sh -b -p ~/miniconda
  3. Add the following line to your .bashrc (.bash_profile for Mac users):

    export PATH-"${HOME}/miniconda/bin:${PATH}"

  4. Install the dependencies

    $ conda install cyclus-deps

Installing Dependencies (Linux and Unix)

This guide assumes that the user has root access (to issue sudo commands) and access to a package manager or has some other suitable method of automatically installing established libraries. This process was tested using a fresh install of Ubuntu 12.10 using apt-get as the package manager (scroll down further for Mac OSX instructions).

The command to install a dependency takes the form of:

sudo apt-get install package

where "package" is replaced by the correct package name. The minimal list of required library package names is:

  1. make
  2. cmake
  3. libboost-all-dev (see note below)
  4. libxml2-dev
  5. libxml++2.6-dev
  6. libsqlite3-dev
  7. libhdf5-serial-dev
  8. libbz2-dev
  9. coinor-libcbc-dev
  10. coinor-libcoinutils-dev
  11. coinor-libosi-dev
  12. coinor-libclp-dev
  13. coinor-libcgl-dev

and (optionally):

  1. doxygen
  2. g++
  3. libblas-dev
  4. liblapack-dev
  5. libgoogle-perftools-dev

For example, in order to install libxml++ (and libxml2) on your system, type:

sudo apt-get install libxml++2.6-dev

If you'd prefer to copy/paste, the following line will install all Cyclus dependencies:

sudo apt-get install -y cmake make libboost-all-dev libxml2-dev libxml++2.6-dev libsqlite3-dev libhdf5-serial-dev libbz2-dev coinor-libcbc-dev coinor-libcoinutils-dev coinor-libosi-dev coinor-libclp-dev coinor-libcgl-dev libblas-dev liblapack-dev g++ libgoogle-perftools-dev
Boost Note

The libboost-all-dev used above will install the entire Boost library, which is not strictly needed. We currently depend on a small subset of the Boost libraries:

  1. libboost-program-options-dev
  2. libboost-system-dev
  3. libboost-filesystem-dev

However, it is possible (likely) that additional Boost libraries will be used because they are an industry standard. Accordingly, we suggest simply installing libboost-all-dev to limit any headaches due to possible dependency additions in the future.

Installing Dependencies (Mac OSX)

Cyclus archetype development is not fully supported on Mac. Nonetheless, because there are some use cases which require installation from source, we have compiled a list of instructions that should be successful. (Note that the HDF5 interface is not working on Yosemite as of 1-Apr-2015. Ignore related warnings when building cyclus). Use a Mac platform at your own risk, we strongly recommend sticking to Linux for development.

This guide assumes that the user has root access (to issue sudo commands) and access to a package manager or has some other suitable method of automatically installing established libraries. This process was tested using a fresh install of Yosemite 10.10.2 using macports as the package manager. Macports installs packages in /opt/local. If installing to a different location, (i.e. /usr/local) change paths in the following instructions accordingly. If you use homebrew, try the following instructions with brew commands in place of the port commands.

The command to install a dependency takes the form of:

sudo port install package

where "package" is replaced by the correct package name. The minimal list of required library package names is:

  1. cmake
  2. boost
  3. libxml2
  4. libxmlxx2
  5. sqlite3
  6. doxygen
  7. glibmm

Then install Coin-Cbc and HDF5 from source. They can be downloaded to any directory on your computer:

Coin-Cbc: Download and build using the svn command in the terminal:

svn co https://projects.coin-or.org/svn/Cbc/stable/2.8 Coin-Cbc
cd Coin-Cbc/
mkdir build
cd build/
../configure --prefix=/opt/local
make
sudo make install

HDF5: The 1.8.13 version appears to work better than 1.8.14. Do not use the macports distribution, it is definitely broken. Download and build using the gzip Linux/Unix distribution of HDF5. (For Safari users - the file will be automatically unzipped so change the mv command in the the following codeblock to mv hdf5-1.8.13.tar hdf5/ ).

mkdir hdf5/
mv hdf5-1.8.13.tar.gz hdf5/
cd hdf5/
mkdir build
cd build/
../configure --prefix=/opt/local
make
sudo make install

Finally, update your path and the following environment variables in your ~/.profile (or ~/.bashrc ) file:

export DYLD_FALLBACK_LIBRARY_PATH=/opt/local/lib:/opt/local:$DYLD_FALLBACK_LIBRARY_PATH

export CMAKE_MODULE_PATH=/opt/local/include:$CMAKE_MODULE_PATH
export CMAKE_PREFIX_PATH=/opt/local:$CMAKE_PREFIX_PATH

export HDF5_DIR=/opt/local/hdf5/lib
export HDF5_ROOT=/opt/local/hdf5

# add to PATH:
export PATH=${HDF5_DIR}:/opt/local/bin:${HOME}/.local/bin:$PATH

Installing Cyclus (Linux, Unix, and Mac OSX)

Assuming you have the dependencies installed correctly, installing Cyclus is fairly straightforward.

We make the following assumptions in this guide:

  1. there is some master directory in which you're placing all Cyclus-related files called .../cyclus
  2. you want to install cyclus locally (in ~/.local)
  3. you have acquired the Cyclus source code from the Cyclus repo
  4. you have placed the Cyclus repository in .../cyclus/cyclus

Under these assumptions and if you used a package manager to install coin-Cbc (i.e. it's installed in a standard location), the Cyclus building and installation process will look like:

.../cyclus/cyclus$ python install.py

If you have installed coin-Cbc from source or otherwise have it installed in a non-standard location, you should make use of the coinRoot installation flag. The otherwise identical process would look like:

.../cyclus/cyclus$  python install.py --coin_root=path/to/coin

Additionally, if you have installed Boost in a non-standard location you should make use of the boostRoot installation flag.

.../cyclus/cyclus$ python install.py --coin_root=/path/to/coin --boost_root=/path/to/boost

There are additional options which can be inspected via install.py's help:

.../cyclus/cyclus$ python install.py -h

Finally, add the following line to the bottom your ~/.bashrc file (~/.bash_profile on Macs):

export PATH="$HOME/.local/bin:$PATH"

Then update your environment

$ source ~/.bashrc

Running Tests

Installing Cyclus will also install a test driver (i.e., an executable of all of our tests). You can run the tests yourself via:

$ cyclus_unit_tests

Running Cyclus

You can find instructions for writing an input file for cyclus from Cyclus User Guide or use sample input files from Cycamore Repo. Assuming you have some file input.xml, you can run Cyclus via:

$ cyclus path/to/input.xml

For a more detailed explanation, checkout the user guide.

The Developer Workflow

General Notes

  • The terminology we use is based on the Integrator Workflow
  • Use a branching workflow similar to the one described at http://progit.org/book/ch3-4.html.
  • Keep your own "master" and "develop" branches in sync with the blessed repository's "master" and "develop" branches. Specifically, do not push your own commits directly to your "master" and "develop" branches.
  • Any commit should pass all tests (see Running Tests).
  • See the An Example section below for a full walk through

Issuing a Pull Request

  • When you are ready to move changes from one of your topic branches into the "develop" branch, it must be reviewed and accepted by another developer.
  • You may want to review this tutorial before you make a pull request to the develop branch.

Reviewing a Pull Request

  • Look over the code.
  • Wait for the Continuous Integration service to show full test passage
  • Click the green "Merge Pull Request" button
    • Note: if the button is not available, the requester needs to merge or rebase from the current HEAD of the blessed's "develop" (or "master") branch

Cautions

  • NEVER merge the "master" branch into the "develop" branch. Changes should only flow to the "master" branch from the "develop" branch.
  • DO NOT rebase any commits that have been pulled/pushed anywhere else other than your own fork (especially if those commits have been integrated into the blessed repository. You should NEVER rebase commits that are a part of the 'master' branch. If you do, we will never, ever accept your pull request.

An Example

Introduction

As this type of workflow can be complicated to converts from SVN and very complicated for brand new programmers, an example is provided.

For the sake of simplicity, let us assume that we want a single "sandbox" branch in which we would like to work, i.e. where we can store all of our work that may not yet pass tests or even compile, but where we also want to save our progress. Let us call this branch "Work". So, when all is said and done, in our fork there will be three branches: "Master", "Develop", and "Work".

Acquiring Cyclus and Workflow

We begin with a fork of the main ("blessed") Cyclus repository. After initially forking the repo, we will have two branches in our fork: "Master" and "Develop".

Acquiring a Fork of the Cyclus Repository

A fork is your copy of Cyclus. Github offers an excellent tutorial on how to set one up. The rest of this example assumes you have set up the "upstream" repository as cyclus/core. Note that git refers to your fork as "origin".

First, let's make our "work" branch:

.../cyclus_dir/$ git branch work
.../cyclus_dir/$ git push origin work

We now have the following situation: there exists the "blessed" copy of the Master and Develop branches, there exists your fork's copy of the Master, Develop, and Work branches, AND there exists your local copy of the Master, Develop, and Work branches. It is important now to note that you may wish to work from home or the office. If you keep your fork's branches up to date (i.e., "push" your changes before you leave), only your local copies of your branches may be different when you next sit down at the other location.

Workflow: The Beginning

Now, for the workflow! This is by no means the only way to perform this type of workflow, but I assume that you wish to handle conflicts as often as possible (so as to keep their total number small). Let us imagine that you have been at work, finished, and successfully pushed your changes to your Origin repository. You are now at home and want to continue working a bit. To begin, let's update our home's local branches.

.../cyclus_dir/$ git checkout develop
.../cyclus_dir/$ git pull upstream develop
.../cyclus_dir/$ git push origin develop

.../cyclus_dir/$ git checkout work
.../cyclus_dir/$ git pull origin work
.../cyclus_dir/$ git rebase develop
.../cyclus_dir/$ git push origin work

Perhaps a little explanation is required. We first want to make sure that this new local copy of the develop branch is up-to-date with respect to the remote origin's branch and remote upstream's branch. If there was a change from the remote upstream's branch, we want to push that to origin. We then follow the same process to update the work branch, except:

  1. we don't need to worry about the upstream repo because it doesn't have a work branch, and
  2. we want to incorporate any changes which may have been introduced in the develop branch update.
Workflow: The End

As time passes, you make some changes to files, and you commit those changes (to your local work branch). Eventually (hopefully) you come to a stopping point where you have finished your project on your work branch AND it compiles AND it runs input files correctly AND it passes all tests! Perhaps you have found Nirvana. In any case, you've performed the final commit to your work branch, so it's time to make a pull request online and wait for our developer friends to review and accept it.

Sometimes, your pull request will be closed by the reviewer until further changes are made to appease the reviewer's concerns. This may be frustrating, but please act rationally, discuss the issues on the GitHub space made for your pull request, consult the style guide, email the developer listhost for further advice, and make changes to your topic branch accordingly. The pull request will be updated with those changes when you push them to your fork. When you think your request is ready for another review, you can reopen the review yourself with the button made available to you.

See also

A good description of a git workflow with good graphics is available at http://nvie.com/posts/a-successful-git-branching-model/

Releases

If you are going through a release of Cyclus and Cycamore, check out the release procedure notes here and on the website.