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Configuring Cantera

Warning

This documentation is for an old version of Cantera. You can find docs for newer versions here.

# Cantera Compilation Guide¶

This guide contains instructions for compiling Cantera on the following operating systems:

• Linux
• Ubuntu 12.04 LTS (Lucid Lynx) or newer
• Debian 6.0 (Squeeze) or newer
• Windows Vista, Windows 7, or Windows 8 (32-bit or 64-bit versions)
• OS X 10.9 (Mavericks) or OS X 10.10 (Yosemite).

In addition to the above operating systems, Cantera should work on any Unix-like system where the necessary prerequisites are available, but some additional configuration may be required.

## Installation Prerequisites¶

### Linux¶

• For Ubuntu or Debian users, the following packages should be installed using your choice of package manager:

g++ python scons libboost-all-dev libsundials-serial-dev

• Building the python module also requires:

cython python-dev python-numpy python-numpy-dev

• Checking out the source code from version control requires Git (install git).

• The minimum compatible Cython version is 0.19. If your distribution does not contain a suitable version, you may be able to install a more recent version using easy_install or pip.

• Building the Fortran interface also requires gfortran or another supported Fortran compiler.

• Users of other distributions should install the equivalent packages, which may have slightly different names.

### Windows¶

There are a number of requirements for the versions of software to install depending on which interfaces (Python, Matlab) you want to build and what architecture (32-bit or 64-bit) you want to use. See Software used by Cantera for the full list of dependencies.

• The build process will produce a Python module compatible with the version of Python used for the compilation. To generate different modules for other versions of Python, you will need to install those versions of Python and recompile.

• If you want to build the Matlab toolbox and you have a 64-bit copy of Windows, by default you will be using a 64-bit copy of Matlab, and therefore you need to compile Cantera in 64-bit mode. For simplicity, it is highly recommended that you use a 64-bit version of Python to handle this automatically.

• There is no 64-bit installer for SCons under Windows, so you will need to download the ZIP version. After extracting it, start a command prompt in the unzipped folder and run:

python setup.py install

• It is generally helpful to have SCons and Python in your PATH. This can usually be accomplished by adding the top-level Python directory (e.g. C:\Python27) to your PATH. This is accessible from:

Control Panel > System and Security > System > Advanced System Settings > Environment Variables

• In order to use SCons to install Cantera to a system folder (e.g. C:\Program Files\Cantera) you must run the scons install command in a command prompt that has been launched by selecting the run as administrator option.

### OS X¶

• From a Terminal, run:

sudo xcode-select --install


and agree to the Xcode license agreement

• If you don’t have numpy version >= 1.4, you can install a recent version with:

sudo easy_install -U numpy

• If you want to build Cantera with Fortran 90 support, download gfortran from:

http://gcc.gnu.org/wiki/GFortranBinaries#MacOS

• Download scons-2.x.y.tar.gz from scons.org and extract the contents. Install with either:

sudo python setup.py install


to install for all users, or:

python setup.py install --user


to install to a location in your home directory.

### Stable Release¶

• Option 1: Download the most recent source tarball from SourceForge and extract the contents.

• Option 2: Check out the code using Git:

git clone https://github.com/Cantera/cantera.git
cd cantera
git checkout 2.2


### Development Version¶

• Check out the code using Git:

git clone https://github.com/Cantera/cantera.git


## Determine configuration options¶

### General¶

• run scons help to see a list all configuration options for Cantera, or see Configuring Cantera.

• Configuration options are specified as additional arguments to the scons command, e.g.:

scons build -j4 blas_lapack_libs=lapack,blas

• If the prerequisites are installed in standard locations, the default values should work.

• If you installed Sundials to a non-standard location (e.g. the libraries aren’t in /usr/lib), you will need to specify the options:

sundials_include=/path/to/sundials/include
sundials_libdir=/path/to/sundials/lib

• If you want to build the Matlab toolbox, you will need to specify the path to the Matlab installation, e.g.:

matlab_path=/opt/MATLAB/R2011a
matlab_path="C:\Program Files\MATLAB\R2011a"
matlab_path=/Applications/MATLAB_R2011a.app


The above paths are typical defaults on Linux, Windows, and OS X, respectively.

• SCons saves configuration options specified on the command line in the file cantera.conf in the root directory of the source tree, so generally it is not necessary to respecify configuration options when rebuilding Cantera. To unset a previously set configuration option, either remove the corresponding line from cantera.conf or use the syntax:

option_name=

• Sometimes, changes in your environment can cause SCons’s configuration tests (e.g. checking for libraries or compiler capabilities) to unexpectedly fail. To force SCons to re-run these tests rather than trusting the cached results, run scons with the option --config=force.

### Python Module¶

Cantera 2.1 introduces a new Python module implemented using Cython. This new module provides support for both Python 2.x and Python 3.x. It also features a redesigned API that simplifies many operations and aims to provide a more “Pythonic” interface to Cantera.

Building the new Python module requires the Cython package for Python.

The Cython module is compatible with the following Python versions: 2.6, 2.7, 3.1, 3.2, and 3.3. Support for Python 2.6 and Python 3.1 requires the scipy and unittest2 packages to be installed as well (see Software used by Cantera) to provide certain features that are included in the standard library in more recent versions.

#### Building for Python 2¶

By default, SCons will attempt to build the Cython-based Python module for Python 2, if both Numpy and Cython are installed.

#### Building for Python 3¶

If SCons detects a Python 3 interpreter installed in a default location (i.e. python3 is on the path), it will try to build the new Python module for Python 3. The following SCons options control how the Python 3 module is built:

python3_package=[y|n]
python3_cmd=/path/to/python3/interpreter
python3_array_home=/path/to/numpy
python3_prefix=/path/to/cantera/module


Note that even when building the Python 3 Cantera module, you should still use Python 2 with SCons, as SCons does not currently support Python 3.

### Windows (MSVC)¶

• In Windows there aren’t any proper default locations for many of the packages that Cantera depends on, so you will need to specify these paths explicitly.
• Remember to put double quotes around any paths with spaces in them, e.g. “C:Program Files”.
• By default, SCons attempts to use the same architecture as the copy of Python that is running SCons, and the most recent installed version of the Visual Studio compiler. If you aren’t building the Python module, you can override this with the configuration options target_arch and msvc_version.

Note

The cantera.conf file uses the backslash character \ as an escape character. When modifying this file, backslashes in paths need to be escaped like this: boost_inc_dir = 'C:\\Program Files (x86)\\boost\\include' This does not apply to paths specified on the command line. Alternatively, you can use forward slashes in paths.

### Windows (MinGW)¶

• To compile with MinGW, use the SCons command line option:

toolchain=mingw

• The version of MinGW from http://www.mingw.org is 32-bit only, and therefore cannot be used to build a 64-bit Python module. Versions of MinGW that provide a 64-bit compiler are available from http://mingw-w64.sourceforge.net/ .

### OS X¶

• The Accelerate framework is automatically used to provide optimized versions of BLAS and LAPACK, so the blas_lapack_libs option should generally be left unspecified.

### Intel Compilers¶

• Before compiling Cantera, you may need to set up the appropriate environment variables for the Intel compiler suite, e.g.:

source /opt/intel/bin/compilervars.sh intel64

• For the Intel compiler to work with SCons, these environment variables need to be passed through SCons by using the command line option:

env_vars=all

• If you want to use the Intel MKL versions of BLAS and LAPACK, you will need to provide additional options. The following are typically correct on 64-bit Linux systems:

blas_lapack_libs=mkl_rt blas_lapack_dir=$(MKLROOT)/lib/intel64  Your final SCons call might then look something like: scons build env_vars=all CC=icc CXX=icpc F90=ifort F77=ifort blas_lapack_libs=mkl_rt blas_lapack_dir=$(MKLROOT)/lib/intel64


When installing Cantera after building with the Intel compiler, the normal method of using sudo to install Cantera will not work because sudo does not pass the environment variables needed by the Intel compiler. Instead, you will need to do something like:

scons build ...
sudo -s
source /path/to/compilervars.sh intel64
scons install
exit


## Compile Cantera & Test¶

• Run scons with the list of desired configuration options, e.g.:

scons build optimize=n blas_lapack_libs=blas,lapack prefix=/opt/cantera

• If Cantera compiles successfully, you should see a message that looks like:

*******************************************************
Compilation completed successfully.

- To run the test suite, type 'scons test'.
- To install, type '[sudo] scons install'.
*******************************************************

• If you do not see this message, check the output for errors to see what went wrong.

• Cantera has a series of tests that can be run with the command:

scons test

• When the tests finish, you should see a summary indicating the number of tests that passed and failed.

• If you have tests that fail, try looking at the following to determine the source of the error:

• Messages printed to the console while running scons test
• Output files generated by the tests

### Building Documentation¶

• To build the Cantera HTML documentation, run the commands:

scons doxygen
scons sphinx


or append the options sphinx_docs=y and doxygen_docs=y to the build command, e.g.:

scons build doxygen_docs=y sphinx_docs=y


### MinGW Compilation problems¶

• If you get a compiler error while compiling some of the “f2c” code, then your version of MinGW has a problem with the order of its internal include paths, such that it sees the GCC float.h before its own special version. To fix this problem edit the GCC float.h located at (roughly):

c:\MinGW\lib\gcc\mingw32\4.6.1\include\float.h


and add the following just before the end (before the final #endif)

#ifndef _MINGW_FLOAT_H_
#include_next <float.h>
#endif


## Software used by Cantera¶

This section lists the versions of third-party software that are required to build and use Cantera.

### Compilers¶

You must have one of the following C++ compilers installed on your system. A Fortran compiler is required only if you plan to use Cantera from a Fortran program.

• GNU compilers (C/C++/Fortran)
• Known to work with version 4.8; Expected to work with version >= 4.4
• Clang/LLVM (C/C++)
• Known to work with versions 3.3 through 3.5. Expected to work with version >= 2.9.
• Works with the versions included with Xcode 5.1 and Xcode 6.1.
• Intel compilers (C/C++/Fortran)
• Known to work with version 11.0 and 12.1; Expected to work with versions >= 11.0
• Microsoft compilers (C/C++)
• MinGW (C/C++/Fortran)

### Other Required Software¶

• SCons:
• Known to work with SCons 2.3.0; Expected to work with versions >= 1.0.0
• Version 2.3.2 or newer is required to use Visual Studio 2013.
• Python:
• Known to work with 2.6 and 2.7; Expected to work with versions >= 2.6.
• The Cython module supports Python 2.x and 3.x. However, SCons requires Python 2.x, so compilation of the Python 3 module requires two Python installations.
• Boost
• Known to work with version 1.54; Expected to work with versions >= 1.41
• Only the “header-only” portions of Boost are required. Cantera does not currently depend on any of the compiled Boost libraries.
• The compiled Boost.Thread library is required to build a thread-safe version of Cantera (using the build_thread_safe option to SCons.
• Pre-built Binaries for Windows are available from http://boost.teeks99.com/ . Make sure to download the file corresponding to your architecture and Visual Studio version.

### Optional Programs¶

• Numpy

• Required to build the Cantera Python module, and to run significant portions of the test suite.
• http://sourceforge.net/projects/numpy/
• Known to work with versions 1.7-1.9; Expected to work with version >= 1.4
• Cython

• Required version >=0.19 to build the Python module
• Known to work with versions 0.19 and 0.20.
• Tested with Python 2.7, 3.3, and 3.4. Expected to work with versions 2.6 and 3.1+ as well.
• 3to2

• Used to convert Cython examples to Python 2 syntax.
• Known to work with version 1.0
• Scipy

• Required in order to use the Python module with Python 2.6 or 3.1.
• Unittest2

• Matlab

• Required to build the Cantera Matlab toolbox.
• Known to work with 2009a and 2014b. Expected to work with versions >= 2009a.
• Sundials

• Required to enable some features such as sensitivity analysis.

• Strongly recommended if using reactor network or 1D simulation capabilities.

• Known to work with versions 2.4, 2.5 and 2.6.

• To use Sundials with Cantera on a Linux/Unix system, it must be compiled with the -fPIC flag. You can specify this flag when configuring Sundials (2.4 or 2.5):

configure --with-cflags=-fPIC


or Sundials 2.6:

cmake -DCMAKE_C_FLAGS=-fPIC <other command-line options>


Note

If you are compiling Sundials 2.5.0 on Windows using CMake, you need to edit the CMakeLists.txt file first and change the lines:

SET(PACKAGE_STRING "SUNDIALS 2.4.0")
SET(PACKAGE_VERSION "2.4.0")


SET(PACKAGE_STRING "SUNDIALS 2.5.0")
SET(PACKAGE_VERSION "2.5.0")


instead, so that Cantera can correctly identify the version of Sundials.

• Windows Installer XML (WiX) toolset

• Required to build MSI installers on Windows.
• Known to work with versions 3.5 and 3.8.
• Distribute (Python)

• Provides the easy_install command which can be used to install most of the other Python modules.
• Packages required for building Sphinx documentation

• Sphinx (install with easy_install -U Sphinx)
• Pygments (install with easy_install -U pygments)
• pyparsing (install with easy_install -U pyparsing)