Advanced Techniques for Scientific Programming and Collaborative Development of Open Source Software Packages at the International Centre for Theoretical Physics (ICTP)

Advanced Techniques for Scientific Programming and Collaborative Development of Open Source Software Packages at the International Centre for Theoretical Physics (ICTP)

Ivan Girotto Axel Kohlmeyer David Grellscheid Shawn T. Brown The Abdus Salam, International Centre for Theoretical Physics (ICTP) Strada Costiera 11, 34014 Trieste, Italy Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, United States Institute for Particle Physics Phenomenology, Durham University, South Rd, Durham DH1 3LE, UK Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, PA, USA
Abstract

A large number of computational scientific research projects make use of open source software packages. However, the development process of such tools frequently differs from conventional software development; partly because of the nature of research, where the problems being addressed are not always fully understood; partly because the majority of the development is often carried out by scientists with limited experience and exposure to best practices of software engineering. Often the software development suffers from the pressure to publish scientific results and that credit for software development is limited in comparison.

Fundamental components of software engineering like modular and reusable design, validation, documentation, and software integration as well as effective maintenance and user support tend to be disregarded due to lack of resources and qualified specialists. Thus innovative developments are often hindered by steep learning curves required to master development for legacy software packages full of ad hoc solutions. The growing complexity of research, however, requires suitable and maintainable computational tools, resulting in a widening gap between the potential users (often growing in number) and contributors to the development of such a package.

In this paper we share our experiences aiming to improve the situation by training young scientists, through disseminating our own experiences at contributing to open source software packages and practicing key components of software engineering adapted for scientists and scientific software development. Specifically we summarize the outcome of the “Workshop in Advanced Techniques for Scientific Programming and Collaborative Development of Open Source Software Packages” run at the Abdus Salam International Centre for Theoretical Physics in March 2013, and discuss our conclusions for future efforts.

keywords:
Modular Software Design, Scientific Programming, Collaborative Software Development, Open Source Scientific Software Packages
journal: arXiv.org

1 Introduction

Since it was founded in 1964 by the late Nobel Laureate Abdus Salam, the International Centre for Theoretical Physics (ICTP) has been a driving force behind global efforts to advance scientific expertise in the developing world. Under the governance of UNESCO and IAEA, ICTP seeks to accomplish its mandate by providing scientists from developing countries with the continuing education and skills that they need to enjoy long and productive careers. One of the means to achieve this goal is to organize workshops where young scientists from both, the developing and the developed world learn side-by-side about state of the art research and methodology.

The current strategic plan of the ICTP contains a particular commitment for building and fostering resources and competences in scientific software development and high-performance computing (HPC). This applies to the infrastructure and staff at the ICTP as well as its educational programs, and has resulted in the formation of a small team specializing in development and execution of educational programs for scientific and high-performance computing.

The complexity of current computational scientific research, especially in scientific domains that require productivity through high-performance computing, favors using flexible software packages or frameworks that provide domain specific scripting, modular software design and code reuse. Often large parts of the work can be implemented in a script language with time critical operations offloaded to compiled language extensions or wrappers to external libraries. This way scientists can realize new projects often without having to write and maintain a complete application, but can focus on small domain specific modules and at the same time leverage improvements to the framework that are contributed by experts in other domains. In step with this, modern multi-core architectures with vectorized floating point units as well as accelerators like GPUs require a much higher level of programming expertise to be effectively utilized for scientific computations.

For about the last 20 years, it was possible to implement efficient scientific applications with just one programming language (often some variant of Fortran) and using a rather minimal subset of the Message Passing Interface (MPI) standard for parallelization. Many scientific applications have matured into packages by adding new features and are used by ever growing user communities. The growing demand for computational resources was easily satisfied through more efficient processors with higher clock rates and faster interconnects, without significant changes to the overall structure of the software.

In light of the current disruptive changes in computer hardware requiring a refactoring if not a complete rewrite of many codes, the challenges to developers of scientific software are manyfold: they need to understand the inner workings of new hardware, need to learn new tools, libraries and programming paradigms to effectively exploit this new hardware, need to embrace and support an ever growing (non-technical) user community, need to handle increasingly complex science and algorithms, and all of this frequently without any formal training or funding for specifically these tasks. Correspondingly, these challenges have to be addressed from multiple directions. In the following we will focus on the aspects of developing suitable training events and raising awareness in the research community for supporting and educating qualified and motivated scientists to become scientific software developers.

The ICTP “Workshop in Advanced Techniques for Scientific Programming and Collaborative Development of Open Source Software Packages” was conceived to address those two key issues through sharing experiences of scientists involved in developing scientific software packages and building and practicing fundamental skills in creating, maintaining, and enhancing modular, reusable, and extensible software. Emphasis is also given to practice working in a team with distributed responsibilities and using modern collaborative software development and management tools like distributed source code management, facilities for validation and embedding documentation.

The workshop was planned as a three week activity with two weeks of general training, followed by a third week dedicated to training of (future) developers of a particular software package. Leading expert developers of that software are invited to show how the topics of the first two weeks of the workshop can be translated to real world scientific software development and also to get students to discuss with the expert developers, how they can improve the adoption of the previously practiced methodologies. For the inaugural workshop in 2013, the selected software package was Quantum ESPRESSO (QE) Quantum-Espresso (), since there already exists a strong connection between QE developers, the ICTP and many potential workshop participants, which simplified planning and the content development process.

In the following sections we describe the event and our motivations and observations about the program in detail. Section 2 will cover the generic software development part of the first two weeks and features the Quantum ESPRESSO Developer Training in the third week. The final part of the document presents the authors’ conclusions and raises questions for further discussion.

2 The Workshop Experience

The 2013 “Workshop in Advanced Techniques for Scientific Programming and Collaborative Development of Open Source Software Packages” was held March 11th to 22nd 2013 in Trieste at the ICTP with 43 attendees from 25 countries (11 faculty and 32 participants) with financial support of the ICTP for executing the workshop and supporting scientists from developing countries.

The course was specifically targeted at computational scientists who are already participating or want to participate in the development of scientific software packages or plan to start such a project by themselves. While many of such packages are grounded in HPC, the workshop touched the topics of optimization and parallelization only marginally and focused on software design, software engineering practices, and collaborative development. Through lectures and practical exercises participants were introduced to challenges of complex scientific problems, modern computer hardware architectures, modular software design, and collaborative software tools. This was all done under consideration of the boundary conditions of scientific research, where formal training in programming and software engineering is inconsistent at best, and also skill sets and experience vary significantly between different collaborators on a software project. Since effective use and understanding of such methods and tools requires practice, typical days were scheduled with about 3-4 hours of lectures and 4-5 hours of practical demonstrations and exercises plus additional opportunities for informal presentations and discussions.

The first week of the school focused on concepts and introduction of the tools themselves, whereas the second week was dominated by having groups of 4-6 participants work on small projects requiring the use of tools and software design patterns introduced in the preceding week. These projects comprised either refactoring of a small example code in C or Fortran or developing a small software project from scratch. Key topics of the workshop were: the design of modular and object oriented applications, building applications with multiple levels of abstraction that can use a scripting language like python at the top level which is augmented in time critical parts with C/C++ or Fortran subroutines, efficient use of tools for unit and regression testing, debugging, profiling, documentation and source code management, and building applications with support for accelerators and vectorization. The topics and materials were directed at participants with intermediate level knowledge in programming and physics.

3 The Quantum ESPRESSO Developer Training

Around 37 participants from 18 different countries participated to the Quantum ESPRESSO Developer Training (QE-Dev): 4 directors, 3 additional speakers, and 30 attendees. The QE-Dev was organized within the same budget available for the first two weeks. 20 participants have attended all three weeks of the activity, 10 of which were financially supported by ICTP. The first three days were split into a morning session of direct lectures and an afternoon practical session. The last day was fully dedicated to direct lectures. Directors and speakers were actively participating in the hands-on sessions as teaching assistants to guarantee adequate support.

QE is an integrated suite of Open Source computer codes for electronic structure calculations and materials modeling at the nanoscale. Like the majority of community codes, it has a complex structure that has been incrementally developed for more than two decades. Today the QE distribution is composed of around half a million code lines, mostly written in FORTRAN 90, and it includes a number of different binaries. In spite of such complexity, it is considered a fundamental tool for scientific research within the Condensed Matter community at ICTP. A sizeable number of ICTP activities has been dedicated in the past to the usage of QE. The objective of the QE-Dev is to increase the knowledge in the community of the different aspects of development. For the first three days the morning lectures were aimed at creating the ground needed to face the hands-on sessions. This included methodology and best practice of community development: how to best contribute to both the improvement and the maintenance of the package. Overall the first three days of the workshop targeted fundamental aspects such as:

  1. learning the most commons components (Modules, variables, routines) of the QE package, including an overview of the parallel approach;

  2. learning how to perform standard tasks like wave-function I/O, calculating scalar product of 2 wave-functions, apply the Hamiltonian operator to a wave-function;

  3. learning how to develop a Post-Processing Tool based on existing QE components.

The last day was entirely dedicated to direct talks with particular focus on advanced topic such as: the LDA+U Implementation and Atomic Wavefunctions LDA+U (), the Phonon package, the QE version for hybrid systems equipped with NVIDIA GPUs QE-GPU () and a vision in depth of the levels of parallelism, including a detailed introduction on how to perform large-scale simulation QE-Userguide (); QE-EXX () .

4 Conclusions

Taking into consideration that the concept of the workshop was new and significantly different from previous activities organized and executed by the directors and staff, the directors are unanimous in the appraisal of the event as extremely successful. We attribute this to the following reasons:

  1. Our excellent and dedicated workshop staff, all of whom performed admirably during a long and demanding event. Their efforts and time commitment far exceeded our requirements and expectations and were absolutely critical for making the event as successful as it was.

  2. Efficient, professional, and prompt services provided by ICTP staff of the Adriatico Guest House along with the extensive help from the workshop secretary.

  3. Careful selection of the participants. The selection was based primarily on answers to a provided self-evaluation questionnaire, which was rated on a demonstrated need for the course, scientific accomplishments (relative to their experience), recommendations and the appropriate skill level. This resulted in a very motivated group of participants, most of whom were very actively involved in both practical exercises and lectures. As a result, the morale of the workshop was very high despite the fact that the programming covered 12 hours each day for both weeks and included Saturday morning.

The co-scheduling with the QE-Dev resulted in a bias toward participants with a background of condensed matter physics, nevertheless other areas of computational physics were well represented. The school proceeded without any disruptions and due to the advanced level of experience, participants quickly managed to adjust to the tasks of the practical sessions and actively participated in lectures with competent and useful questions. We see the largest accomplishment of the workshop in the successful execution of the group projects. It quickly became visible, that scientists are in general not prepared for collaborative software development and thus their experience of their own difficulties and successes while working on the group project is likely to significantly improve their ability to collaborate; a skill that is becoming highly important in computational sciences. The fact that all groups managed to present tangible achievements at the end of the workshop and were highly engaged in their respective projects demonstrated that we found a good balance between the complexity of the project (medium) and the difficulty of the physics.

While this workshop benefits from experiences made during previous schools and workshops on high-performance computing, it contained a significant amount of new teaching material and a different conceptual focus and as a result, the program and topics will have to be refined for future events of a similar kind. To that end, an evaluation of the workshop was performed through an online form. Overall the responses indicate a high approval rating and indicate some areas that the directors also identified as needing improvement and are indicative of the range of pre-existing skills. While requiring a minimum level of experience to participate, the overall level of difficulty was aimed a bit more toward the lower end of the distribution of skills explaining some of the less favorable comments. On the other hand directors could take advantage of the skill set distribution in the group project phase by assigning participants to groups so that the diversity of skills was represented in each group and added to the challenge and learning experience.

The large number of applicants coming on their own funding and the large number of applicants that were interested in co-scheduled QE-Dev indicate that the workshop as such is addressing a need that is not easily satisfied and that for future installments the co-scheduling should be expanded into other large application packages with relevance to the ICTP and affiliated communities. A successful event of this kind requires a large degree of commitment from the staff, which must not only be knowledgeable, but also care about teaching and handing their own skills to the developing world. The positive feedback in this respect from participants as well as from tutors and lecturers is an extremely gratifying experience. For the teaching assistants who were at or close to the graduate student level, the workshop provided an opportunity to hone their skills in managing a small group of scientists, an experience that cannot be easily had otherwise until much later in their career. Any future version of this workshop should continue in this tradition.

The QE-Dev was a new initiative not only for ICTP but also for the world-wide scientific community behind this package. Despite several years of experience by both directors and speakers, gathered during the activity of code development, a significant effort was requested to teach how a given problem is coded and structured within the package. Only a small amount of teaching material was available for such a purpose, especially for the hands-on sections where an entire program had to be developed from scratch.

The directors of the QE-Dev consider the outcome of the training school as the starting point on which it is possible to base and build similar Developer Training world-wide, in analogy to the already established users’ schools of QE. An on-line evaluation form was proposed for evaluation of the QE-Dev, too. The answers received about the relevance of most of the topic presented were extremely positive. On the other hand, lower enthusiasm has been expressed in regards to how those topic were presented. This experience suggests that the following actions be taken for the preparation of a similar tutorial in the future: more carefully prepared lectures; longer hands-on sessions; distribution of a written text with the supporting documentation; the selection of a more homogeneous group of participants. In conclusion, we report of a successful event that definitely allows scientist to meet together for a common and challenging purpose: the development of a scientific community code.

We are extremely pleased with the way the overall ‘Workshop in Advanced Techniques for Scientific Programming and Collaborative Development of Open Source Software Packages” has worked out. The very high dedication of the participants, the majority of whom were very attentive and motivated to learn, was an extremely rewarding experience.

The first experience fed enthusiasm to directors and stakeholders for pursuing such activities in the future while changing the target of the scientific community for what concerns the last week. For 2014, LAMMPS LAMMPS () is the selected software package. We aim to promote initiatives that can further motivate the participation of scientists that see the potential for opportunities in new software developments. The presented model of the workshop will be extended, and more open to fresh developers. To complete the event a symposium will be organized. The main topic for the symposium is intended to be the presentation of research works that are based on either usage or new development for the LAMMPS software package or similar. The extension to less restricted sessions should aid in reducing the distance between scientists and what we consider an important component in the future of scientific research: a collaborative software development. We aim to further export the model introduced in ICTP by this workshop, while extending it to a co-organized event outside of ICTP, with particular interest to developing countries.

We aim to build the ground to attract possible contributors from developing countries to the development of open source scientific packages. The relatively small cost for investments needed to create such conditions can increase possibilities for scientists from developing countries to leverage their research work within the world-wide scientific community. In step with the ICTP strategic mission, scientists from developed countries can be attracted to participate in such unique events aiding the possibility of contact with local scientific communities.

Following up on the previous development training organized in early 2013 at ICTP, scientists from the QE community have organized an advanced training for the December 2013. The event is aimed at a selected group of developers that will undertake an (on-line) pre-course to guarantee an adequate preparation to both theoretical and practical aspects of the workshop. The main part of the laboratory session will see participants working closely with world-class experts with the final goal of implementing additional new features into the official distribution of Quantum ESPRESSO.

Acknowledgments

We thank the ICTP for providing an excellent venue and the opportunity to conduct this type of event. We thank ICTP and the Quantum ESPRESSO Foundation for providing the ground to make such event possible. Especially, we would like to thank Prof. Stefano De Gironcoli (SISSA/DEMOCRITOS), Prof. Paolo Giannozzi (University of Udine), Dr. Paolo Umari (University of Padova), Dr. Carlo Cavazzoni (CINECA) as well as Prof. Andrea dal Corso (SISSA) for their availability and Dr. Emine Kucukbenli (EPFL) for the essential contribution and scientific support for the QE-Dev. Ms. Rosa del Rio, secretary of the workshop, made organizing the workshop straightforward and gave the directors the much needed freedom to focus on the program.

References

  • (1) P. Giannozzi, S. Baroni, N. Bonini, M. Calandra, R. Car, C. Cavazzoni, D. Ceresoli, G. L. Chiarotti, M. Cococcioni, I. Dabo, A. Dal Corso, S. de Gironcoli, S. Fabris, G. Fratesi, R. Gebauer, U. Gertsmann, C. Gougoussis, A. Kokalj, M. Lazzeri, L. Martin-Samos, N. Marzari, F. Mauri, R. Mazzarello, S. Paolini, A. Pasquarello, L. Paulatto, C. Sbraccia, S. Scandolo, G. Sclauzero, A. P. Seitsonen, A. Smogunov, P. Umari and R. M. Wentzcovitch, J. Phys.: Condens. Matter 21, 395502 (2009); http://www.quantum-espresso.org
  • (2) M. Cococcioni and Stefano de Gironcoli, ”Linear response approach to the calculation of the effective interaction parameters in the LDA+U method”, Physical Review B 71, 035105 (2005)
  • (3) Spiga, F. & Girotto, I. phiGEMM: A CPU-GPU Library for Porting Quantum ESPRESSO on Hybrid Systems, 2012 20th Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP), doi: 10.1109/PDP.2012.72 Publication Year: 2012 , Page(s): 368 - 375. IEEE Conference Publications
  • (4) Quantum ESPRESSO user guide. [Online]. Available:http://www.quantum-espresso.org/users-manual/
  • (5) N. Varini, D. Ceresoli, L. Martin-Samos, I. Girotto, C. Cavazzoni, ”Enhancement of DFT-calculations at petascale: Nuclear Magnetic Resonance, Hybrid Density Functional Theory and Car-Parrinello calculations”, 2013, Comp. Phys. Comm, doi: 10.1016/j.cpc.2013.03.003, Volume 184, Issue 8, August 2013, Pages 1827-1833
  • (6) S. Plimpton, Fast Parallel Algorithms for Short-Range Molecular Dynamics, J Comp Phys, 117, 1-19 (1995)
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