scine-puffin 2.0.1

Calculation handler for SCINE Chemoton

Introduction

SCINE Puffin is a calculation handler for SCINE Chemoton. Thus, it bridges the gap between high level exploration jobs for reaction networks and basic quantum chemical calculations. Making use of the abstractions defined the SCINE Core and SCINE Utilities modules it provides the means to define and execute jobs that generate new data for reaction networks. SCINE Puffin is designed as an instanced runner that, once bootstrapped, continuously processes requested jobs. It is built to work in containerized environments (Docker, Apptainer/Singularity).

License and Copyright Information

For license and copyright information, see the file LICENSE.txt in this directory.

Installation

Prerequisites

Basic Requirements

Thus far Puffin is expected to run on Linux systems and possibly on OSX systems, Windows-based architectures are not specifically supported. Using containers and the integrated subsystem feature of Windows 10 it should be possible to toy around with it nonetheless. This is, however, not a case we would recommend for inexperienced users.

Puffin collects a variety of programs to run calculations. In order to get a minimal working version of Puffin to run on a given system, the following programs/packages are required:

• Python3

• CMake >= v3.12

• Git

• GCC >= v7.0.0, CLang >= v6.0.0 (Unix), ICC >= v2017.01

• Boost >= v1.64.0

• A MongoDB including the C++ bindings

Puffin Python Package

The main Python package Puffin requires the several additional packages, which will be automatically installed when installing Puffin using pip. These packages are listed in the file requirements.txt.

For development work, a few extra packages are needed; these are listed in the file requirements-dev.txt.

Puffin Instance

A usable Puffin instance will require at least a minimal set of additional C++ components. These components do not need to be compiled by the user, but instead they will be compiled when bootstrapping the instance. These components are:

• SCINE Database

• SCINE Molassembler

• SCINE ReaDuct

• SCINE Utilities

Installation

Puffin can be installed using pip (pip3) once the repository has been cloned:

git clone <puffin-repo>
pip install ./puffin

A non super user can install the package using a virtual environment, or the --user flag.

It is also possible to run/install a dockerized version of Puffin. For more details on this please see the Usage->Docker section of this documentation.

The documentation can be found online, or it can be built using:

cd puffin
make -C docs html

It is then available at:

<browser name> docs/build/html/index.html

In order to build the documentation, you need a few extra Python packages wich are not installed automatically together with Puffin. In order to install them, run

cd puffin
pip install -r requirements-dev.txt

Usage

Basic Usage

In order to use Puffin, at least one Puffin instance has to be generated. Each instance will then separately accept and run jobs later on. In order to setup a first instance, prepare a folder:

mkdir puffin_instance
cd puffin_instance

and generate the default configuration file for an instance inside it:

python3 -m scine_puffin configure
vi puffin.yaml

Afterwards it is possible to configure the instance to your liking, by editing the generated puffin.yaml file.

It is also possible to enter configurations via environment variables. The environment variables override the variables given in the configure file. Any configuration option can be given via the environment as:

export PUFFIN_<key1>_<key2>_<key3>=<value>

or as a concrete example:

export PUFFIN_DATABASE_PORT=27019

The settings for each program are explained in the documentation of that particular program. The general settings pertaining to the daemon and Puffin in general are explained separately in a section below.

After (if desired) editing the settings it is possible to bootstrap Puffin and thus install all programs that have to be installed in order to run the instance.

python3 -m scine_puffin -c puffin.yaml bootstrap

All programs that will be installed are marked in the configuration as available and have a source path given. Bootstrapping the instance will generate a source file called puffin.sh. It contains all environment variables that have to be set in order to make the instance find all installed programs. Hence, source the installed programs using:

source puffin.sh

The Puffin instance is now ready to be used. Start and stop the actual daemon by using

python3 -m scine_puffin -c puffin.yaml start

and

python3 -m scine_puffin -c puffin.yaml stop

If the puffin.yaml is not given, the default options will be used. Once again, any environment variables precede the loaded file.

Docker

It is possible to generate a containerized version of Puffin using Docker or Podman. The Dockerfile is present in the directory container/docker of this repository. The generated Docker image includes all packages required to run Puffin with the default set of programs. When running the image it is possible to configure the options of the Puffin instance. We recommend mounting a scratch directory e.g. /scratch/puffin into the Docker.

Furthermore, it is possible to dry-run (without a database) a version of the image which will still execute the bootstrap stage of Puffin. It is then possible to copy the clean /scratch/puffin folder and then shorten (skip) the bootstrap step in other instances of the image by pasting this copied folder into the /scratch folder mounted into the other instances. However, for this to properly work we advise caution when bootstrapping with -march=native flags for the programs in the initial instance.

Command Line Setup

In order to build the image, execute

sudo docker build -t <image name>

The image will bootstrap and start running a Puffin instance as soon as the image is run with:

docker run -it --mount src=<path to local folder>,target=/scratch,type=bind <image name>

Any configuration can be done by adding environment variables in the run command.

Docker Compose Setup

A minimal version of docker-compose input starting an instance of Puffin is deposited in the docker folder located in the top directory of this repository.

Basic Settings and Configuration

The full list of all options to be set is given in the online documentation in the Settings section. Furthermore, this documentation can be read directly from the doc-string of the scine_puffin.config.Configuration class. The settings of each program can be read from the documentation of the respective class interfacing the program, e.g. scine_puffin.programs.sparrow.Sparrow.

How to Cite

When publishing results obtained with Puffin, please cite the corresponding release as archived on Zenodo (DOI 10.5281/zenodo.6695461; please use the DOI of the respective release).

In addition, we kindly request you to cite the following article when using Puffin: J. P. Unsleber, S. A. Grimmel, M. Reiher, “Chemoton 2.0: Autonomous Exploration of Chemical Reaction Networks”, J. Chem. Theory Comput., 2022, 18, 5393.

Furthermore, when publishing results obtained with any SCINE module, please cite the following paper:

T. Weymuth, J. P. Unsleber, P. L. Türtscher, M. Steiner, J.-G. Sobez, C. H. Müller, M. Mörchen, V. Klasovita, S. A. Grimmel, M. Eckhoff, K.-S. Csizi, F. Bosia, M. Bensberg, M. Reiher, “SCINE—Software for chemical interaction networks”, J. Chem. Phys., 2024, 160, 222501 (DOI 10.1063/5.0206974).

Support and Contact

In case you should encounter problems or bugs, please write a short message to [e-mail].