Installation

We recommend the conda installation for beginning users. The conda installation will install the Cassandra executable and also provide the library_setup.py and mcfgen.py auxillary scripts. If you wish to contribute to Cassandra or have access to an Intel compiler, you may wish to install from source.

Note

The Intel compiler offers substantial performance improvements compared to gfortran. If you are running a large number of production calculations and have access to the Intel compiler you may want to take the time to install from source.

Installing with conda

If you already have conda installed, you can create a new conda environment and install Cassandra with a single command:

conda create --name mc -c conda-forge cassandra

The command creates a new conda environment (mc) and installs cassandra. The -c flag specifies the conda channels that is used to install cassandra. To use the environment, run conda activate mc.

After activating the environment, you can test your installation by checking that the required executables are on your PATH with the following commands:

which cassandra.exe
which mcfgen.py
which library_setup.py

The version of cassandra installed through conda uses OpenMP parallelization. The number of parallel threads is controlled through the OMP_NUM_THREADS environment variable. For example, to use eight threads with a bash terminal you would run:

export OMP_NUM_THREADS=8

Installing from source

Cassandra may alternatively be installed from source. There are two methods for obtaining the source code: (1) downloading the tarball of the latest release from our GitHub releases page, or (2) cloning the GitHub repository. The command to clone the repository is:

git clone https://github.com/maginngroup/cassandra.git

If you download the tarball from the GitHub releases page, you will need to unpack it:

tar -xzvf Cassandra-1.2.4.tar.gz

In either case, after obtaining the source code, go into the Src directory and run the following:

make -f Makefile.gfortran.openMP
cd ../
mkdir bin/
mv Src/cassandra_gfortran_openMP.exe ./bin/cassandra.exe
cp Scripts/Frag_Library_Setup/library_setup.py ./bin/.
cp Scripts/MCF_Generation/mcfgen.py ./bin/.

Note

There are several different Makefiles in the Src directory. The Makefiles with the .openMP extension use OpenMP parallelization.

Finally, if you wish, you can add Cassandra-1.2.4/bin to your PATH:

export PATH=path_to_install/Cassandra-1.2.4/bin:${PATH}

Unless you add the preceding line to your .bashrc you will need to run it every time you open a new terminal window.