Reproducible large-scale neuroimaging studies with the OpenMOLE workflow management system
File(s)fninf-11-00021.pdf (2.42 MB)
Published version
Author(s)
Type
Journal Article
Abstract
OpenMOLE is a scientific workflow engine with a strong emphasis on workload distribution.
Workflows are designed using a high level Domain Specific Language (DSL) built on top of Scala. It exposes natural parallelism constructs to easily delegate the workload resulting from a workflow to a wide range of distributed computing environments.
OpenMOLE hides the complexity of designing complex experiments thanks to its DSL. Users can embed their own applications and scale their pipelines from a small prototype running on their desktop computer to a large-scale study harnessing distributed computing infrastructures, simply by changing a single line in the pipeline definition.
The construction of the pipeline itself is decoupled from the execution context. The high-level DSL abstracts the underlying execution environment, contrary to classic shell-script based pipelines. These two aspects allow pipelines to be shared and studies to be replicated across different computing environments.
Workflows can be run as traditional batch pipelines or coupled with OpenMOLE's advanced exploration methods in order to study the behaviour of an application, or perform automatic parameter tuning.
In this work, we briefly present the strong assets of OpenMOLE and detail recent improvements targeting re-executability of workflows across various Linux platforms. We have tightly coupled OpenMOLE with CARE, a standalone containerisation solution that allows re-executing on a Linux host any application that has been packaged on another Linux host previously.
The solution is evaluated against a Python-based pipeline involving packages such as scikit-learn as well as binary dependencies. All were packaged and re-executed successfully on various HPC environments, with identical numerical results (here prediction scores) obtained on each environment. Our results show that the pair formed by OpenMOLE and CARE is a reliable solution to generate reproducible results and re-executable pipelines.
A demonstration of the flexibility of our solution showcases three neuroimaging pipelines harnessing distributed computing environments as heterogeneous as local clusters or the European Grid Infrastructure (EGI).
Workflows are designed using a high level Domain Specific Language (DSL) built on top of Scala. It exposes natural parallelism constructs to easily delegate the workload resulting from a workflow to a wide range of distributed computing environments.
OpenMOLE hides the complexity of designing complex experiments thanks to its DSL. Users can embed their own applications and scale their pipelines from a small prototype running on their desktop computer to a large-scale study harnessing distributed computing infrastructures, simply by changing a single line in the pipeline definition.
The construction of the pipeline itself is decoupled from the execution context. The high-level DSL abstracts the underlying execution environment, contrary to classic shell-script based pipelines. These two aspects allow pipelines to be shared and studies to be replicated across different computing environments.
Workflows can be run as traditional batch pipelines or coupled with OpenMOLE's advanced exploration methods in order to study the behaviour of an application, or perform automatic parameter tuning.
In this work, we briefly present the strong assets of OpenMOLE and detail recent improvements targeting re-executability of workflows across various Linux platforms. We have tightly coupled OpenMOLE with CARE, a standalone containerisation solution that allows re-executing on a Linux host any application that has been packaged on another Linux host previously.
The solution is evaluated against a Python-based pipeline involving packages such as scikit-learn as well as binary dependencies. All were packaged and re-executed successfully on various HPC environments, with identical numerical results (here prediction scores) obtained on each environment. Our results show that the pair formed by OpenMOLE and CARE is a reliable solution to generate reproducible results and re-executable pipelines.
A demonstration of the flexibility of our solution showcases three neuroimaging pipelines harnessing distributed computing environments as heterogeneous as local clusters or the European Grid Infrastructure (EGI).
Date Issued
2017-03-22
Date Acceptance
2017-03-01
Citation
Frontiers in Neuroinformatics, 2017, 11
ISSN
1662-5196
Publisher
Frontiers Media
Journal / Book Title
Frontiers in Neuroinformatics
Volume
11
Copyright Statement
© 2017 Passerat-Palmbach, Reuillon, Leclaire, Makropoulos, Robinson,
Parisot and Rueckert. This is an open-access article distributed under the terms
of the Creative Commons Attribution License (CC BY). The use, distribution or
reproduction in other forums is permitted, provided the original author(s) or licensor
are credited and that the original publication in this journal is cited, in accordance
with accepted academic practice. No use, distribution or reproduction is permitted
which does not comply with these terms.
Parisot and Rueckert. This is an open-access article distributed under the terms
of the Creative Commons Attribution License (CC BY). The use, distribution or
reproduction in other forums is permitted, provided the original author(s) or licensor
are credited and that the original publication in this journal is cited, in accordance
with accepted academic practice. No use, distribution or reproduction is permitted
which does not comply with these terms.
License URL
Sponsor
Commission of the European Communities
Identifier
http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2017.00021/abstract
Grant Number
319456
Subjects
high performance computing
reproducibility
pipeline
large datasets
parameter exploration
neuroimaging
workflow systems
Publication Status
Published
Article Number
21