installation.rst

Installation

Installation of the European XFEL Offline Calibration tools is best done into an anaconda/3 environment using Maxwell cluster. However, there are no explicit dependencies, so any Python3 environment is capable of running the tool.

A more detailed step-by-step instruction can be found in the :ref:`tutorial`.

Package Requirements

Requirements can be categorized into three types:

1. Those required to run the the general tool chain,
2. Those required by the notebooks themselves,
3. Those required to run notebooks concurrently on a HPC cluster.

Categories 1+2 are usually Python modules, as given in the requirements.txt file found in the root directory. Additionally, PyDetLib is required. It can be installed either as a Karabo dependency or manually.

Parallel execution is currently supported in a SLURM_ environment. However, sequential execution is available using the --no-cluster-job parameter when executing xfel-calibrate.

Installation using Anaconda

First you need to load the anaconda/3 environment through:

1. module load anaconda/3

If installing into other python enviroments, this step can be skipped.

Then the package for the offline calibration can be obtained from the git repository:

2. git clone https://git.xfel.eu/gitlab/detectors/pycalibration.git

Home directory

You can then install all requirements of this tool chain in your home directory by running:

3. pip install -r requirements.txt . --user

in pycalibration's root directory.

After installation, you should make sure that the home directory is in the PATH environment variable:

4. PATH=/home/<username>/.local/bin:$PATH

Preferred directory

Alternatively, you can install all requirements in a directory of your preference by:

3. mkdir /gpfs/exfel/data/scratch/<username>/<directory-name>
   pip install --target=/gpfs/exfel/data/scratch/<username>/<directory-name> -r requirements.txt .

and it is important to make sure that the installed requirements are in the PATH environment:

4. PATH=/gpfs/exfel/data/scratch/<username>/<directory-name>/bin:$PATH

After this make sure that you adjust the :ref:`configuration` and settings in the xfel-calibrate folder to match your environment.

The tool-chain is then available via the:

xfel-calibrate

command.

Installation using karabo

If required, one can install into karabo environment. The difference would be to first source activate the karabo envrionment:

1. source karabo/activate

then after cloning the offline calibration package from git, the requirements can be installed through:

3. pip install -r requirements.txt .

Development Installation

For a development installation in your home directory, which automatically picks up (most) changes, first install the dependencies as above, but then install the tool-chain separately in development mode:

pip install -e . --user

Note

Using "- -target" for development installation in a preferred directory can lead to errors.

Note

For development installation in karabo environment "- -user" is not needed.

Installation of New Notebooks

To install new, previously untracked notebooks in the home directory, repeat the installation of the the tool-chain, without requirments, from the package base directory:

pip install --upgrade . --user

Or, in case you are actively developing:

pip install -e . --user