Tykky is a set of tools which wrap installations inside an Apptainer/Singularity container to improve startup times, reduce IO load, and lessen the number of files on large parallel filesystems.
Additionally, Tykky will generate wrappers so that installed software can be used (almost) as if it were not containerized. Depending on tool selection and settings, either the whole host filesystem or a limited subset is visible during execution and installation. This means that it's possible to wrap installation using e.g mpi4py relying on the host provided mpi installation.
This documentation covers a subset of the functionality and focuses on conda and Python, a large part of the advanced use-cases are not covered here yet.
As Tykky is still under development some of the more advanced features might change in exact usage and API.
Basic conda installation
To access the tools provided by Tykky, simply load the module,
module load tykky
Then we can run:
conda-containerize new --prefix <install_dir> env.yml
Where env.yml is a conda environment file. This file can be written manually, e.g:
channels: - conda-forge dependencies: - python=3.8.8 - scipy - nglview
Or generate them from an existing environment
conda env export -n <target_env_name> > env.yaml
--from-historyflag to the export command
conda list -n <target_env_name> --explicit > env.txt
--explicitoption only works if the existing environment is on a Linux machine with x86 CPU architecture. Otherwise the result will not be transferable to Lumi
After the installation is done you simply need to add
the bin directory
<install_dir>/bin to the path.
If you also need to install some additional pip packages you can do so by supplying
-r <req_file> argument e.g:
conda-containerize new -r req.txt --prefix <install_dir> env.yml
The tool also supports using mamba
for installing packages. Enable this feature by adding the
conda-containerize new --mamba ...
Make sure that you have read and understood the license terms for miniconda and any used channels before using the command.
- Miniconda end user license agreement
- Anaconda terms of service
- A blog entry on Anaconda commercial edition
Using the previous
mkdir MyEnv conda-containerize new --prefix MyEnv env.yml
$ export PATH="$PWD/MyEnv/bin:$PATH" $ python --version 3.8.8 $ python3 Python 3.8.8 | packaged by conda-forge | (default, Feb 20 2021, 16:22:27) [GCC 9.3.0] on linux Type "help", "copyright", "credits" or "license" for more information. >>> import scipy >>> import nglview >>>
Modifying a conda installation
As Tykky installed software resides in a container, it can not be directly modified.
Small python packages can be added normally using
pip, but then the python packages are
sitting on the parallel filesystem so this is not recommended for any larger installations.
To actually modify the installation we can use the
together with the
--post-install <file> option which specifies a bash script
with commands to run to update the installation. The commands are executed
with the conda environment activated.
conda-containerize update <existing installation> --post-install <file>
<file> could e.g contain:
conda install -y numpy conda remove -y pyyaml pip install requests
In this mode the whole host system is available including all software and modules.
Plain pip installations
Sometimes you don't need a full blown conda environment or you might prefer pip to manage python installations. For this case we can use:
pip-containerize new --prefix <install_dir> req.txt
req.txtis a standard pip requirements file. The notes and options for modifying a conda installation apply here as well.
Note that the python version used by
pip-containerize is the first python executable found in the path, so it's affected by loading modules.
Important: This python can not be itself container-based as nesting is not possible.
An additional flag
--slim argument exists, which will instead use a pre-built minimal python
container with a much newer version of python as a base. Without the
--slim flag, the whole host system is available,
and with the flag the system installations (i.e /usr, /lib64 ...) are no longer taken from the host, instead
coming from within container.
Tykky also provides a tool to generate wrappers for existing containers, so that they can be used
transparently (no need to prepend
singularity exec ..., or modify scripts if switching between containerized versions of tools).
wrap-container -w </path/inside/container> <container> --prefix <install_dir>
<container>can be a filepath or any url accepted by singularity (e.g
oras//:or any other singularity accepted format)
-wneeds to be an absolute path (or comma separated list) inside the container. Wrappers will then be automatically created for the executables in the target directories / for the target path.
More complicated example
How it works
See the README in the source code repository. The source code can be found in the GitHub repository
Last edited Thu Mar 31 2022