Installation

You have two options to install Mocafe:

Currently, Mocafe has been tested on:

  • Linux (Ubuntu 20.04)

  • Windows (using Windows Subsystem for Linux 2.0)

Notice: WSL is available for Windows 10 onwards.

Install with apt and pip

The procedure requires three steps:

  1. Install MPI

  2. Install FEniCS

  3. Install Mocafe

Install MPI

First of all, verify if you have MPI already installed on your system. You can do it easily with:

mpirun --version

If you don’t already have it on your system, it is recommended to install it with:

sudo apt install openmpi-bin

And test it typing:

mpirun --version

If everything worked out well, you should get something like:

mpirun (Open MPI) 4.0.3

Report bugs to http://www.open-mpi.org/community/help/

And you can proceed to the next step.

If you had problems in the procedure above, we recommend you to use the Singularity container of Mocafe (see section Install Singularity container), which already includes MPI. However, you can also use other methods to install MPI, such as sudo apt install mpich.

Install FEniCS

Then, install FEniCS using apt-get:

sudo apt-get install software-properties-common
sudo add-apt-repository ppa:fenics-packages/fenics
sudo apt-get update
sudo apt-get install fenics

Test if FEniCS has been correctly installed trying to import it:

python3 -c "import fenics; print('FEniCS is Installed')"

If everything worked out well, you should get the message:

FEniCS is Installed

If you encounter errors, you can:

Install Mocafe

If FEniCS works, you can proceed to installing Mocafe using pip:

pip3 install git+https://github.com/BioComputingUP/mocafe#egg=mocafe

Test it executing the main script:

python3 -m mocafe

I everything is properly working, the output should be:

Your Mocafe is ready!

Note: FEniCS is transitioning from version “2019” to FEniCSx, so the apt package might not be supported in the future. In that case, consider using the Mocafe container as explained below.

Install Singularity container

Singularity, like Docker, is a container platform which allows you to create and run containers that package up pieces of software in a way that is portable and reproducible. We preferred using Singularity instead of Docker because it is optimized to work on large HPC clusters and take full advantage of MPI.

Install Singularity

If you don’t have Singularity installed, just follow the instructions provided at the official documentation page for SingularityCE.

You can find the SingularityCE documentation at this link. To find the installation instructions, just:

  • find the User Guide for the Last Released Version

  • look for the Quick Installation Steps

  • follow them to install Singularity

Notice that the procedure might take some time and requires the installation of the Singularity dependencies and the go language.

Install and test Mocafe container

If you have Singularity:

  1. Download the definition file mocafe.def from here, or, if you have wget:

    wget https://raw.githubusercontent.com/BioComputingUP/mocafe/main/singularity/mocafe.def

  2. From the terminal, built the container (it might take some time):

    sudo singularity build mocafe.sif mocafe.def

Now you already have a Singularity image with all you need to use Mocafe on your system.

To test the container:

  1. Open a shell inside the container:

    singularity shell mocafe.sif

  2. type:

    python3 -m mocafe

If everything is working properly, you should see the output message:

Your Mocafe is ready!

And now you can run any Mocafe or FEniCS script inside the container.

Notice: by default, Singularity binds the home path of the container with the home of the host system. So, you can find and use any file of your host system inside the container.

Uninstalling

In case you want to remove Mocafe and its dependencies from your system, you just need to follow the instructions provided below. Notice that uninstalling instruction change depending on the installation procedure you followed.

In case you installed Mocafe using apt and pip:

  1. Uninstall Mocafe and its python dependencies using pip uninstall; see section Uninstalling Mocafe

  2. Remove FEniCS using apt autoremove; see section Remove FEniCS with apt

In case you installed Mocafe using Singularity:

  1. Remove the Mocafe container; see section Remove Mocafe container

  2. Remove Singularity (in case you don’t need it anymore); see section Remove Singularity

Uninstalling Mocafe

To do so, you just need to type:

pip uninstall mocafe

Notice that Mocafe has some dependencies, such as tqdm, pandas, and so on, that won’t be automatically removed with the command above. To remove them, you need to tell pip to do so.

This is what you need to type to remove moacfe with all its dependencies:

pip uninstall mocafe numpy pandas pandas-ods-reader tqdm

Of course, if you use any of the packages listed above for other purposes you should not remove them.

Remove FEniCS with apt

In case you installed FEniCS using apt, you can just remove it with all its dependencies using apt autoremove:

sudo apt autoremove fenics -y

Remove Mocafe container

To remove correctly the Mocafe container from your system, you need to remove all the cached data:

singularity cache clean mocafe.sif

Then, you can simply remove the mocafe.sif file:

rm mocafe.sif

Remove Singularity

There is no “out of the box” method to remove Singularity from your system, since the recommended way to install it is to compile it from source. The easier way to remove it is to just remove the following folders from your computer:

sudo rm -rf /usr/local/etc/singularity \
   /usr/local/etc/bash_completion.d/singularity \
   /usr/local/bin/singularity \
   /usr/local/libexec/singularity \
   /usr/local/var/singularity