Installation

The easiest way to install chemreac (on linux) is to use conda:

$ conda install -c chemreac chemreac pytest

and you’re done! To check if chemreac is installed correctly you may run:

$ pytest --pyargs chemreac

which should run the test suite (all tests should pass or xfail). If you are using a special platform with non-standard math libraries you may need to compile your own pacakges. The “recipes” for the conda packages are kept here.

If you are not using the conda package manager you can still install chemreac from source. You will find the instructions for doing so below.

Building from source

Below you will find instructions for installation by building chemreac from source. You may also look in scripts/ folder for automated install scripts used on the continuous integration servers.

Prerequisites

Version numbers of dependencies indicate what has been tested:

  • C++ compiler with C++11 support (e.g. GCC >= 4.8)

  • LAPACK (provided by e.g. OpenBLAS)

  • Sundials 2.6.2

  • Python (2.7 or >=3.4)

In addition to the standard library provided by Python, a number of python packages are required (see setup.py), they are found on PyPI and are automatically installed when using pip.

For rendering the documentation you also need:

to run all the tests you also need these tools:

  • valgrind

  • graphviz

  • dot2tex

  • pdflatex

Building and installing

Once non-python prerequisites are in installed, you may procede e.g. as:

$ git clone https://github.com/chemreac/chemreac.git
$ cd chemreac
$ pip install --user -e .[all]
$ ./scripts/run_tests.sh

the above procedure works on Ubuntu 14.04 for example.

To specify an alternative LAPACK lib, set the environment variable LLAPACK, e.g.:

$ LLAPACK=openblas python setup.py build_ext --inplace

The following environment variables are also supported by setup.py (defaults to “0”, enable by setting them to “1”):

Environament variable

Default

Action

WITH_OPENMP

0

Enable parallell evaluation of rhs and jac.

WITH_BLOCK_DIAG_ILU_DGETRF

0

Use unblocked version of dgetrf instead of LAPACK

WITH_BLOCK_DIAG_ILU_OPENMP

0

Evaluate LU decomposition of blocks in parallel

WITH_DATA_DUMPING

0

For debugging purposes only

WITH_DEBUG

0

For debugging purposes only

Enabling the first three is known to provide significant speed up for some scenarios (performance is system dependent, hence recommendations are not possible to give without benchmarking).

Tests

If you have py.test installed you may run the test suite on the installed package:

$ py.test --pyargs chemreac

All tests should pass (or xfail). If they do not, please file an issue.