trouble compiling and installing cantera python module

Question

I'm attempting to install the Cantera as a python module within Ubuntu linux. For reference I used these instructions: Installing Cantera. After running ./preconfig and make, I get the following error:

fatal error: numarray/arrayobject.h: No such file or directory

According to the preconfig file,

# If numpy was installed using the --home option, set this to the
# home directory for numpy. This will be needed for all numpy installations
# that don't put the include files into python's native include directory.
#NUMPY_HOME=${NUMPY_HOME:="$HOME/python_packages"}

and I'm using the student version of Enthought Python Distribution so I thought maybe I need to change the last line to:

NUMPY_HOME=${NUMPY_HOME:="/usr/local/EPD/lib/python2.7/site-packages/"}

but this is not working. I still get the same error. Thoughts? I've installed python-dev to fix an earlier bug so that's not it.

Answer 1

I found a fix. By following these instructions that I had previously followed, I got it to work. The difference is that the last time, I downloaded the tar.gz file, and this time, I used the subversion repository, which might be more updated I guess. Anyway, it worked, and I did not need to change the default python command either.

Edit: I did need to change this from the default to:

PYTHON_CMD=${PYTHON_CMD:="/usr/local/EPD/bin/python"}

I guess it's a good idea to also post the instructions so they're available here for other users:

First step is to install any dependencies. This is handled by apt-get: sudo apt-get install subversion g++ gfortran python2.6-dev python-numpy libsundials* graphviz
Next step is to get the source for cantera. This can be done by either downloading the cantera-1.8.0-beta-tar.gz from the cantera site our checking the latest version from svn svn checkout http://cantera.googlecode.com/svn/cantera18/trunk/ cantera
Change to the cantera directory (either the svn checkout or the untarred/gunzipped cantera-1.8.0)
Edit the file named preconfig and make sure the following lines are included by commenting/editing
PYTHON_PACKAGE=${PYTHON_PACKAGE:="full"}
USE_NUMPY=${USE_NUMPY:="y"}
SUNDIALS_VERSION=${SUNDIALS_VERSION:='2.3'}

Then in a terminal run the following commands:
./preconfig
make
sudo make install
source ~/setup_cantera
If every thing went well you should be able to import the Cantera module in python:
python
>>>from Cantera import *

Answer 2

You probably have several Python distributions on your Ubuntu box. In order to use EPD to install Cantera you should tell it explicitly which distribution to use:

PYTHON_CMD=${PYTHON_CMD:="/usr/local/EPD/bin/python"}

Every distribution has its own site-packages directory, so by specifying PYTHON_CMD you also specify which site-packages to use. When Numpy is installed, it also installs interfaces to Numarray to site-packages/numpy/core/include/numpy, so there is no need to download Numarray. Also, numpy is installed to site-packages directory of EPD, so NUMPY_HOME (which is used only when numpy is not installed in the default directory) should be left intact. Hope this helps.

Answer 3

We've never gotten it to work by just setting the include variable in pre_config. Instead, we do:

...
USE_NUMPY=${USE_NUMPY:="y"}

if [ "$USE_NUMPY" = "y" ]; then
    export NUMPY_INC_DIR=`python -c 'import numpy; print numpy.get_include()'`
fi

Haven't had any issues since we've started including that.