Downloading and Installing CHAP

CHAP is written in C++ and is developed and tested on Ubuntu Linux. It is expected to be portable to other Unix-like operating systems, although this has not been tested. The following installation guide will assume that you are using Ubuntu and that you are reasonably experienced in using the command line.

Downloading CHAP

To obtain a copy of CHAP, visit the Releases Section on GitHub and download the archive corresponding to the desired version. Alternatively, you can download the code directly from the command line via:

wget https://github.com/channotation/chap/archive/version_0_8_0.tar.gz

As CHAP is still a young project with new features and bug fixes being added continuously, you will usually want to download the latest version.

Prerequisites

Prior to installing CHAP, make sure that you have the following libraries and tools installed:

  1. The CMake tool in version 3.2 or higher. This will typically be available through your system’s package manager. For example, on Ubuntu you can install CMake by typing sudo apt-get install cmake. CMake is used to check the availability of libraries and compilers on your system and will ensure that CHAP is installed properly.
  2. A C++ compiler that supports the C++11 standard. A popular choice is the GNU Compiler Collection, which on Ubuntu can be obtained by typing sudo apt-get install gcc
  3. The Boost C++ libraries, which on Ubuntu can be installed using sudo apt-get install libboost-all-dev. Boost algorithms are used in CHAP to solve some root finding and optimisation problems.
  4. The CBLAS and LAPACKE linear algebra libraries. On Ubuntu, the easiest way to obtain these is by typing sudo apt-get install libblas-dev liblapacke-dev libatlas-base-dev. The linear algebra libraries are used in CHAP’s spline interpolation.
  5. The libgromacs library of the Gromacs molecular dynamics engine in version 2016 or higher. Comprehensive installation instructions for Gromacs can be found here. Please note that for using Gromacs as a library, the underlying FFTW libray may not be installed automatically, i.e. you need to set -DGMX_BUILD_OWN_FFTW=OFF when running CMake during the Gromacs installation.

CHAP also depends on RapidJSON, but this is included as a header-only library, and on GTest, but this is downloaded and installed automatically by CMake, so you don’t need to do anything about either of these (you will however need Internet access when installing CHAP).

Compiling and Installing CHAP

To install CHAP, unpack the source, create a build directory parallel to the source tree and from there run cmake, make, make check, and make install.

tar -xvzf version_0_8_0.tar.gz
cd chap-version_0_8_0
mkdir build
cd build
cmake ..
make
make check
sudo make install

CMake will automatically find all dependencies (and inform you of missing ones), make will compile the code (you can use the make -j flag to speed this up on multicore machines), make check runs a suite of unit tests, and make install will place the binary in /usr/local/chap/bin (so you will need sudo rights for this last step). To check if CHAP has been installed properly, you can type

chap -h

which should bring up an online help for using CHAP.


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