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podio

linux ubuntu coverity

Documentation

Prerequisites

If you are on lxplus, all the necessary software is preinstalled if you use a recent LCG or Key4hep stack release.

On Mac OS or Ubuntu, you need to install the following software.

ROOT 6.08.06

Install ROOT 6.08.06 (or later) and set up your ROOT environment:

source <root_path>/bin/thisroot.sh

Catch2 v3 (optional)

Podio uses Catch2 v3 for some unittests. By default it will look for a suitable external version of this library already installed (an available on the CMAKE_PREFIX_PATH) and use that if possible. In case no suitable version is found podio will fetch a copmatible version and build that automatically. This behavior is controlled via the USE_EXTERNAL_CATCH2 cmake variable. It defaults to AUTO but can also be set to ON or OFF to fully control the desired behavior.

Python > 3.6

Check your Python version by doing:

python --version

or

python3 --version

depending on your used system.

python packages

Podio requires the yaml and jinja2 python modules. Check that the yaml and jinja2 python modules are available

python
>>> import yaml
>>> import jinja2

If the import goes fine (no message), you're all set. If not, the necessary modules need to be installed. This is most easily done via (first install pip if you don't have it yet)

pip install -r requirements.txt

In order for the yaml module to be working it might also be necessary to install the C++ yaml library. On Mac OS, The easiest way to do that is to use homebrew (install homebrew if you don't have it yet):

brew install libyaml

Check that you can now import the yaml and jinja2 modules in python.

Some tools have additional dependencies that are not required for code generation or library use

  • graphviz is required for podio-vis
  • tabulate is required for podio-dump

Preparing the environment

Full use of PODIO requires you to set the PODIO environment variable and modify LD_LIBRARY_PATH and PYTHONPATH. Some convenience scripts are provided:

# Set PODIO install area to `./install` and setup environment accordingly
source ./init.sh

or

# Setup environment based on current value of `PODIO`
source ./env.sh

Or you can setup the environment entirely under your control: see init.sh and env.sh.

Compiling

If you are using the easy setup from init.sh then create separate build and install areas, and trigger the build:

mkdir build
mkdir install
cd build
cmake -DCMAKE_INSTALL_PREFIX=../install ..
make -j 4 install

To see a list of options, do this in the build-directory:

cmake -LH ..

Running tests

After compilation you can run unit tests as well as some integration level tests that check the full I/O circle via

ctest --output-on-failure

These tests also create some example files and read them back.

Installing using SPACK

A recipe for building podio is included with the spack package manager, so podio can also installed with:

spack install podio

Note that if you do not have any previous installations or registered system packages, this will compile ROOT and all its dependencies, which may be time-consuming.

Modifying the data model

Podio features an example event data model, fully described in the yaml file tests/datalayout.yaml. The C++ in tests/datamodel/ has been fully generated by a code generation script, python/podio_class_generator.py.

To run the code generation script, do

python ../python/podio_class_generator.py ../tests/datalayout.yaml ../Tmp data ROOT

The generation script has the following additional options:

  • --clangformat (-c): Apply clang-format after file creation (uses option -style=file with llvm as backup style), needs clang-format in $PATH.
  • --quiet (-q): Suppress all print out to STDOUT
  • --dryrun (-d): Only run the generation logic and validate yaml, do not write files to disk
  • --lang (-l): Specify the programming language (default: cpp), choices: cpp, julia

Running workflows

To run workflows manually (for example, when working on your own fork) go to Actions then click on the workflow that you want to run (for example edm4hep). Then if the workflow has the workflow_dispatch trigger you will be able to run it by clicking Run workflow and selecting on which branch it will run.

Advanced build topics

It is possible to instrument the complete podio build with sanitizers using the USE_SANITIZER cmake option. Currently Address, Memory[WithOrigin], Undefined and Thread are available. Given the sanitizers limitations they are more or less mutually exclusive, with the exception of Address;Undefined. Currently some of the tests will fail with sanitizers enabled (issue). In order to allow for a smoother development experience with sanitizers enabled, these failing tests are labelled (e.g. [ASAN-FAIL] or [THREAD-FAIL]) and will not be run by default if the corresponding sanitizer is enabled. It is possible to force all tests to be run via the FORCE_RUN_ALL_TESTS cmake option.

Model visualization

There is a tool to generate a diagram of the relationships between the elements in a model. To generate a diagram run python python/tools/podio-vis model.yaml and use --help for checking the possible options. In particular there is the option --graph-conf that can be used to pass a configuration file defining groups that will be clustered together in the diagram, like it is shown in. The syntax is

group label:
  - datatype1
  - datatype2
another group label:
  - datatype3
  - datatype4

Additionally, it is possible to remove from the diagram any data type (let's call it removed_datatype) by adding to this configuration file:

Filter:
  - removed_datatype