Open Source software in Science
FLOSS for Science
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31 episodes
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Podcast Overview
Open Source software in Science
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Publishing Since
1/12/2018
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Recent Episodes
April 27, 2021
EP031 GNU licenses
Note : This interview was recorded in the summer of 2020. However, due to the pandemic we could not release the episode timely. Therefore, the current status of FSF and recent events are not discussed in this episode. In episode 31, we interviewed Craig Topham from the Licensing and Compliance Team of the GNU Project about GNU software licenses. We started by discussing about his involvment in the compliance team at the Free Software Foundation (FSF) and what got him interested in the topic of free software. The portion of the interview centered around the GNU project with an emphasis on the GNU software licenses. We went through the GPL, LGPL, AGPL and GFDL licenses to explain some of their differences and why you may want to use one instead of another. We asked questions about the specificities of licensing your code in the context of scientific software and the issue with licenses proliferation. Some of the differences between the different versions of the GPL were presented later in the discussion to show the improvements brought in the version 3 in regard to the compliance and patent sections. We asked him about his take on the philosophical differences between GNU style licenses and the MIT/BSD licenses in regard to the debate between user and developper freedom. We followed by going through some myths surrounding the GNU licenses and a general discussion about freedom and privacy. We finished the interview with our usual quick questions.
September 3, 2020
EP030 Spack: a package manager for supercomputers
In episode 30, we interviewed Todd Gamblin from the Lawrence Livermore National Laboratory about the Spack project. We discussed his current research project along with his involvement in Spack. We widely discussed the philosophy of Spack, some usage patterns, its capabilities for managing package management in HPC clusters as well as standalone computers and which operating systems it supports at the moment. Todd shared with us his opinion on the trend for containerized workloads to achieve reproducible science and why it may not be the goal we need to set. He highlighted for us the similarities and differences between EasyBuild and Spack as well as the origin of those differences. We finished the interview with our usual quick questions. 00:00:00 Intro music 00:00:17 Introduction 00:00:36 Introducing Todd Gamblin 00:00:58 His current research topics 00:01:23 Spack as official duties 00:01:43 Spack usage at Lawrence Livermore National Laboratory 00:02:01 Other research projects 00:02:47 Profiling in HPC 00:04:24 His role as leader of software packaging technology for the exascale computing project 00:04:58 One-minute elevator pitch for Spack 00:05:34 Spack's usage philosophy compared to other package managers 00:06:59 Installation from source code or binary? 00:07:28 Spack's usage in the top500 super computers 00:07:49 Geographical distribution of users 00:08:18 Number of packages in the repo and some examples 00:09:05 Managing computer clusters with Spack's automation capabilities 00:11:04 Module files in Spack 00:12:32 Syntax of a Spack package file 00:13:43 Configuration of compiler flags 00:15:00 Importing python libraries in the Spack files 00:15:48 The procedure to submit a package 00:16:27 Review process for new packages 00:17:34 Reasons for rejection of Spack packages 00:18:01 Operating systems supported by Spack 00:18:23 WSL and Spack 00:18:58 Restricting packages to certain hardware and software configurations 00:20:04 Build testing and nightly builds 00:21:28 Working with containers in a Spack environment 00:22:25 Deploying prebuilt containers 00:23:05 About the "universality" of containers 00:24:16 His opinion on containerized applications for reproducible science 00:26:17 Spack's log file to document reproducibility 00:27:13 Reproducing older results 00:28:10 Specifying requirements on compilers 00:30:39 Post-installation verification test 00:31:10 Using Spack on a standalone computer instead of HPC systems 00:32:56 Differences between EasyBuild and Spack 00:34:24 EasyBuild in the top500 00:34:49 Transitionning between EasyBuild and Spack 00:35:38 Other alternatives 00:36:23 Using EasyBuild and Spack on the same system 00:38:36 When did the project start? 00:39:53 External contributions to Spack 00:40:53 How many core developpers? 00:41:30 Organization of the community and governance model 00:43:06 Who decides which package is accepted in the repo? 00:44:38 Spack's choice of software license 00:47:09 Todd's vision about the importance of FLOSS for the openness of science 00:48:13 Possible negative impacts of FLOSS 00:48:58 Most notable recent scientific discovery 00:49:14 Favourite text processing tool 00:49:25 A topic in science about which he recently changed his mind about 00:49:58 Anything else we forgot to ask? 00:50:09 How to contact Todd 00:50:46 Conclusion
July 1, 2020
EP029 Distributing Python packages with setuptools
In episode 29, we interviewed Jason R Coombs from the setuptools project. We started with a discussion about his background and his interest for Python and other programming languages. Following that, we had a thorough discussion about setuptools. We covered topics such as how he got involved in the project, the nature and composition of a Python package, why packaging your code can be important even for small projects, the hidden complexity of binary packages in the Python Package Index and how to maintain compatibility between Python versions. We also had a brief segment about the security aspects of Python packages. He informed us about how you could start contributing to the project and where to discuss Python packaging. We then followed with a general discussion about FLOSS in science and the problem of long-term maintenance in academia. We concluded the interview with our usual quick questions. 00:00:00.000 Intro 00:00:23 Introducing Jason R. Coombs 00:01:28 The first programming languages he learned and how he got into Python 00:03:46 New interesting programming languages 00:05:07 His favourite past Python projects 00:06:53 His one minute elevator pitch for setuptools 00:08:00 The relation between setuptools, PIP and Anaconda 00:10:43 How he got involved with the setuptools project 00:14:43 What is a Python package ? 00:16:07 What can be included in a package? 00:16:36 At which point is it beneficial to create a package ? 00:18:04 Managing compatibility with multiple versions of Python 00:20:33 Advantages of packages for small projects 00:22:46 How much work is required to create a package ? 00:25:05 Files required to create a Python package 00:27:45 Licenses and readme for Python packages 00:30:51 The nature of distribution archives 00:31:27 Compatibility of binary archives 00:32:39 Eggs and wheel files 00:34:32 Dealing with non portable packages in the Python Package Index across multiple operating systems 00:37:49 Uploading packages to the Python Package Index 00:39:12 Review for broken or malicious code 00:40:08 Vulneraility from package removal in the Python Package Index 00:43:24 Package name collisions 00:45:13 How many packages are in the Python Package Index 00:45:25 Alternatives to the main Python Package Index 00:46:35 Other packaging tools 00:47:39 How many developpers are involved in the project 00:48:31 Communication channels and discussions about Python packaging 00:49:53 Openings for new contributors 00:50:59 Skills required to contribute 00:52:24 The challenge of long term maintenance of packages in academia 00:55:43 His vision about the importance of FLOSS for the openess of science 00:59:18 Disadvantage of using FLOSS 01:01:24 The most notable scientific discovery in recent years 01:02:13 Favourite text processing tool 01:03:23 A topic in science about which he recently changed his mind 01:04:50 Contact informations 01:05:23 Conclusion
31 total episodes available
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