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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.…
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FLOSS for Science
1 EP030 Spack: a package manager for supercomputers 52:26
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Play Later Play Later Lists Like LikedIn 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…
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FLOSS for Science
1 EP029 Distributing Python packages with setuptools 1:07:17
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Play Later Play Later Lists Like LikedIn 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…
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FLOSS for Science
1 EP028 NumFocus: A Nonprofit Supporting Open Source 45:10
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Play Later Play Later Lists Like LikedIn episode 28, we interviewed Leah Silen from the NumFocus organization. She introduced us to the goals and the mission of the organization. We then had a discussion about the different levels of support provided by the organization to its member projects. She informed us about the legal, financial, technological and logistical support that can be provided by NumFocus. Following that, we asked her about the revenue sources of the organization as well as the possible influence from the corporate sponsors over the decisions and governance of the organization. We also discussed of the requirements to become part of NumFocus including details about the application process. We had a brief discussion about the history of the project and the evolution of the scope of projects that are part of the organization. After discussing the governance of the organization, we concluded the interview with our usual questions. 00:00:00 Intro 00:00:18 Introducing Leah Silen 00:02:28 Goals and mission of NumFocus 00:03:06 Examples of supported projects 00:03:39 Status of sponsorded and affiliated projects 00:05:04 Advantages of one status over the other 00:05:48 Legal challenges for open source scientific projects 00:07:19 Financial support for scientific open source projects 00:10:13 Assistance to apply for external grants 00:11:01 Paying developers from outside of US? 00:11:43 Revenue sources for NumFocus 00:12:21 Levels of corporate sponshorships 00:13:14 The influence of corporate sponsors 00:13:56 Motivations of corporate sponsors 00:15:02 Some of the sponsors of the NumFocus organization 00:16:05 Technological support for projects 00:17:03 Events previously supported by the organization 00:18:09 The kind of support that can be provided for events 00:19:22 Requirements for new projects 00:21:10 Clarification about the meaning of being a scientific oriented project 00:23:11 Requirements about the team size and strong governance within projects 00:24:58 The application process 00:26:18 Duration of support 00:26:44 Timeframe to receive a response for an application 00:28:30 Feedback in the case of rejection 00:29:12 Are there downsides of becoming a part of NumFocus? 00:30:32 Additional administrative overhead? 00:32:01 Location of NumFocus staff members 00:33:00 Foudation of NumFocus and initial projects 00:34:05 Opening to projects outside of the Python ecosystem 00:34:54 Favourite project? 00:35:46 Initial role in NumFocus 00:36:53 Term duration for positions at the board of directors 00:37:24 Selection process for the board of directors 00:38:31 Leah's vision about FLOSS and its importance for the openness of science 00:39:04 Negative impacts of FLOSS 00:39:33 Most notable scientific discovery in recent years 00:39:59 Favourite text processing tool 00:40:37 A topic in science about which she changed her mind about 00:41:36 Anything else we forgot to ask about? 00:42:54 How to contact Leah Silen 00:43:14 Outro…
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FLOSS for Science
1 EP027 Scientific Computing with SciPy and NumPy 59:05
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Play Later Play Later Lists Like LikedIn episode 27, we interviewed Ralf Gommers from the NumPy and SciPy projects. We started our discussion by talking about his past research experience as a physicist and his transition to open source software and programming. This led him to get involved in projects such as PyWavelets, NumPy and SciPy. Following that, we had a great discussion about NumPy, its many features, its target audience and its performance. We learned why NumPy is not included in Python's standard library and its overlap with Scipy. We also compared the combination of Matlab to NumPy and Python and how users could transition to this open source solution. We then had a brief discussion about SciPy and the features it provides. Ralf informed us of the positive results from Google's previous Summer of Code and Season of Docs participations. We discussed how to reach the project and the many kinds of contributions that they are looking for. We talked about the importance of FLOSS for science and attribution of research output. We finished the interview with our classic quick questions and a reflection from Ralf about the need for more sustainability in open source software development as volunteer effort may not be sufficient in the future. 00:00:00 Intro 00:00:18 Introduction 00:00:33 Introducing Ralf Gommers 00:02:05 Research during his PhD and and PostDoc 00:03:20 When he started to use open source tools 00:03:52 Learning to code 00:04:39 PyWavelets, another sideproject he likes 00:05:55 His elevator pitch for NumPy 00:06:55 Vector arrays in Python before NumPy 00:07:49 How he got involved in the NumPy project 00:10:13 Traget users for NumPy 00:11:36 NumPy as part of the standard library? 00:13:24 Features provided by NumPy 00:14:22 Major differences between Python built-in list and NumPy's array 00:16:01 Structured data 00:16:45 Why appending a row to an array is made hard 00:18:09 Multithreaded code with NumPy 00:19:48 Distributed array processing 00:20:50 GPU computation with Python and NumPy 00:22:16 Linear algebra functions in NumPy 00:23:25 Overlap between SciPy and NumPy for linear algebra 00:23:55 Python speed as an interpreted language 00:25:43 Python with NumPy compared to Matlab 00:28:07 How easy is the transition between Matlab and Python Numpy 00:29:26 Performance difference between Matlab and Python 00:31:00 Commercial applications of NumPy 00:32:15 Contributions from the industry ans incentives to contribute 00:34:10 Elevator pitch for SciPy 00:35:37 Overview of some of the submodules in SciPy 00:38:11 The size of the communities 00:39:33 Participation in Google Summer of Code 00:40:24 Participation in Google Season of Docs 00:41:48 Communication channels in the project 00:43:25 Where to ask for support? 00:44:48 Possible contributions 00:46:25 Skills usefull to contribute to the NumPy project 00:48:12 Identifying possible contributions 00:48:52 The importance of FLOSS for science 00:52:02 Possible negative impact of FLOSS on science 00:52:49 Crediting contributions in science 00:53:42 Most notable scientific discovery in recent years 00:54:49 His favourite text processing tool 00:55:30 Volunteer effort may not be sufficient anymore 00:56:58 Contact informations for Ralf Gommers 00:57:27 Outro…
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In episode 24, we interviewed Simon Hettrick Professor at the University of Southampton in the UK. We started the discussion with him by asking about his transition from deveoppin high-power lasers to founding the research software engineers (RSE) association and how his experiences got him in his current position. We then discussed about the roles of RSE in research and how funding for RSE evolved over the past. The discussion went on about the RSE association, its growth over time, branches in other countries and local events. We discussed that the relation between FLOSS and more sustainable research software is not always clear and more work is needed in that area. After talking with him about the lack of sufficient preparation that students receives during their undergrad studies in regard to the tools needed to tackle research software development we finished with our usual quick questions. 00:00:00 Intro 00:00:18 Introduction and Simon Hettrick's presentation 00:00:56 His academic status at the University of Southampton 00:01:53 His transition from developping high power compact lasers to RSE 00:03:31 About his PhD and general comments about PhD defenses 00:04:21 Any relations between laser and his current research area? 00:07:57 1 minute elevator pitch for UK RSE 00:08:32 The growing importance of software and the effect on funding 00:14:03 Defining what is a RSE 00:17:35 How many RSE in UK? 00:18:20 The state of preparation of the research community for brexit 00:20:05 When was the RSE association founded? 00:20:16 How to become a member of RSE UK and the growth rate of the association 00:22:44 Other RSE branches 00:24:42 Relations between RSE associations 00:25:40 Regional RSE organizations and RSE groups 00:27:09 Local meetups groups 00:28:00 Crediting research software development 00:31:39 Is FLOSS the norm or the exception for RSE? 00:35:09 Does FLOSS helps providing better and more sustainable research software? 00:38:55 Curriculum for new researchers 00:43:50 The state of research software licensing 00:46:13 Most notable recent scientific discovery 00:48:13 His favourite text processing tool 00:48:58 A topic in science he changed his mind about 00:50:13 How to contact Simon 00:50:37 Conclusion…
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1 EP023 Reproducible Science and Synthetic Datasets Using R 55:36
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Play Later Play Later Lists Like LikedIn episode 23, we interviewed Dan Quintana from the University of Oslo. We started the discussion with him by asking the link between all his subjects of interest and where R fits into his workflow. We then had an extensive discussion about R including his must have R packages and the synthpop package for generating synthetic datasets. We then widened the discussion and talked about the multiple facets of open science and reproducibility. Dan then talked about what he sees as one of the next big challenge of science. We finished the interview with our usual quick questions. 00:00:18 Introduction 00:00:39 Presentation of Dan Quintana 00:01:55 The links between his research interests 00:04:00 Where does R fits in his workflow 00:05:22 His 30 seconds elevator pitch for R 00:06:28 How difficult is it to switch from SPSS to R? 00:08:05 The best time to switch to R 00:08:40 JASP and Jamovi as a gateway to R 00:10:53 Standing on the shoulders of giants with R 00:12:15 R or Python? 00:14:00 Dan's must have R packages 00:15:59 Ressources to learn R 00:17:21 Introduction to synthetic datasets 00:21:54 Synthetic datasets for privacy and their limitations 00:24:52 How much time should be spent to publish datasets and code 00:26:58 Dan's view on open science practices 00:28:27 FLOSS and open science practices 00:30:49 The licence he uses for sharing code and data 00:32:06 Obtaining a DOI with the Open Science Framework 00:32:21 Journal of Open Source Software 00:34:15 The importance of publishing in open access journals 00:37:28 Publishig in open access journals and plan S 00:39:09 The lack of affordability for open access publishing 00:40:22 Preprints as a solution? 00:43:04 How to publish a perfectly reproducible paper 00:46:02 How to convince other scientists to share their data and code 00:46:42 The next big challenge of science 00:48:55 The most notable discovery in recent years 00:51:20 Favourite text processing tool 00:51:43 A topic in science he recently changed his mind about 00:52:49 Anything else? 00:53:34 How to contact Dan Quintana 00:53:56 Conclusion…
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In episode 22, we interviewed Robert Dodier from the Maxima project. After a brief introduction and a presentation of Robert's current uses for Maxima he introduced what is Maxima and what can be achieved with it. We discussed some core concepts of Maxima's language as well as how to access the documentation within the software to help users. Then discussion went on about the interesting origin story of Maxima and its origin as a tool for AI. We then talked about the current state of the project and how can someone provide help. As well as our usual quick questions, we had an interesting discussion about the social aspects within FLOSS and other self-organized projects. 00:00:17 Introduction 00:00:26 Presentation of Robert Dodier 00:02:01 The scope of Maxima and its application for Bayesian inferences 00:02:57 Why not use R or another programming language for Bayesian inferences? 00:05:03 When did he discover Maxima? 00:05:29 Maxima's core features stability since 2003 00:06:04 His 30 seconds elevator pitchfor Maxima 00:06:43 Reference manual and Maxima's documentation 00:07:52 Accessing Maxima's documentation 00:08:41 Comparison with Maple and Mathematica 00:10:50 The concept of "code equal data"? 00:12:54 Maxima's language complexity/simplicity 00:15:13 User interfaces for Maxima 00:16:24 Console interface for Maxima 00:17:12 Presentation of the resulting equations or results 00:17:46 Integrating Maxima and LaTeX 00:19:08 The origin story of Maxima 00:25:17 Licensing status before the relicensing to GPL 00:26:00 Maxima for undergrad students and researchers 00:28:33 Robert's contributions to the project and its self-organized structure 00:31:39 How many people are involved in the project 00:32:13 Communication channels for the project 00:32:52 Underlying technologies in Maxima 00:34:27 Ressources for newcomers 00:35:47 Robert's vision about FLOSS in science 00:36:26 Negative impacts of FLOSS on science 00:37:25 The most notable scientific discovery in recent years 00:39:22 Robert's favourite text processing tool 00:40:04 The social aspect of FLOSS 00:42:34 Anything else he wanted to share with us? 00:43:39 How to contact Robert 00:43:57 Outro…
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1 EP021 High-level Scientific Computing with GNU Octave 46:30
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Play Later Play Later Lists Like LikedIn episode 21, we interviewed Juan Pablo Carbajal, an Argentinian physicist currently working as a postdoctoral researcher in the Department of Urban Water Management at the ETH domain in Switzerland. We had a great discussion about GNU Octave and how it can help scientists. We compared its core functions and its expandability through packages to its commercial equivalent Matlab and its toolboxes. An interesting feature of GNU Octave that we explored with Juan is the possibility to migrate code from Matlab directly to GNU Octave and to a certain point maintain code compatible with both. Juan shared with us that since the introduction of an integrated GUI in 2015, he noticed a continuous growth in popularity for the project. We then discussed about a few of the reasons why companies are interested by GNU Octave and why universities should teach using free/libre software. Before asking our usual quick questions, Juan talked with us about the reasons why FLOSS is important for science and the importance of exposing non-FLOSS users to the benefits of FLOSS. 00:00:00 Message to our listeners 00:00:29 Intro 00:00:45 Introducing Juan Pablo Carbajal 00:01:32 30 seconds elevator pitch for GNU Octave 00:02:20 How does the Octave programming language compares to other common programming languages 00:03:23 Compatibility between GNU Octave and Matlab 00:06:29 Matlab's toolboxes compared to GNU Octave packages 00:07:31 Simulink models with GNU Octave 00:09:06 Parallel processing with GNU Octave 00:10:40 The issue with CUDA in GNU Octave 00:11:48 How GNU Octaves differs rom other open source Matlab equivalents 00:13:34 Syntax compatibility to ease transition and reusing code from Matlab 00:15:11 Resources to start using GNU Octave 00:16:40 GNU Octave's graphical user interface and the old QT Octave GUI 00:20:14 GNU Octave's graphical user interface compared to Matlab 00:22:11 Why GNU Octave and not simply Octave 00:23:06 GNU Octave licence 00:24:01 How often he uses GNU Octave 00:24:18 Juan's numerous contributions to the project 00:25:27 GNU octave for companies 00:27:45 Arguments for teaching with GNU Octave instead of Matlab 00:29:32 How many are involved in the project? 00:30:37 Communication channels within the project 00:31:34 Is the project actively looking for developers? 00:32:11 Skills required to contribute 00:33:14 The two-level language dilemma 00:34:59 Juan's vision about FLOSS and its importance for science 00:37:09 Possible negative impacts of FLOSS and converting non-FLOSS users 00:40:17 The most notable scientific discovery in recent years 00:41:46 Juan's favourite text processing tools 00:42:38 Things we forgot to ask about 00:43:57 Anything else to share? 00:44:25 How to contact Juan 00:44:50 Outro…
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FLOSS for Science
1 EP020 Peer-reviewed Publication of Research Software 1:03:24
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Play Later Play Later Lists Like LikedIn episode 20, we interviewed Arfon Smith, Editor-in-chief of the Journal of Open Source Software (JOSS) and Head of Data Science at the Space Telescope Science Institute. We talked with him about the creation of JOSS and its role in peer reviewed publications of research software. He described to us how to start a peer reviewed scientific journal and the challenges and competition that he faces. We chatted about how, by using automation, reusing existing tools and staying nimble, JOSS manages to publish with low operational costs. We also discussed about the submission process and what is reviewed during the peer review. Finally, we had a discussion about the importance of FLOSS and in science and how science and FLOSS could inspire each other.…
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FLOSS for Science
In episode 19, we interviewed Glenn Cooper the Head of experiment computing department at Fermilab about the history and future of the linux distribution Scientific Linux. The discussion started with a brief overview of current research activities at Fermilab. When then extensively talked about Scientific Linux, its goals, the reason why it was started and what made it successful. Glenn made a good argument about the need for a stable software platform in science. We then switched topics and discussed about the recent announcement in regard to the end of the project and the motivations for that. We then talked about the transition to CentOS at Fermilab and CERN and the upgrade path for current users. We concluded the interview with our usual quick questions.…
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FLOSS for Science
In episode 18, we interviewed Jesse Allison an Associate Professor of Experimental Music and Digital Media at Louisiana State University. We had a great discussion about his work to expand the experience and interactivy of music and sounds. He shared with us his view on how sciences and arts intersect in his projects. He listed some of the tools he uses to create sounds and how these can be applied to create sonic intervention. We had a chat about his past experiences regarding open source software and running a business based on it. We also questioned him whether or not anyone could or even should start creating music. The episode concludes with a small audio sample from his 2013 TEDx talk.…
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FLOSS for Science
1 EP017 HPX: A cure for performance impaired parallel applications 46:36
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Play Later Play Later Lists Like LikedIn episode 17, we interviewed Adrian Serio the Scientific Program Coordinator of the STELLAR group about the C++ Standard Library for Concurrency and Parallelism (HPX). We started with a general discussion about parallel computing, where it comes from, where it is going and what can we still expect to gain. We then clarified what are C++ standards and how HPX is developed to be standard compliant. HPX was compared to other parallelism libraries such as MPI and we learned that HPX is a foundation to develop other software for domain specific applications. Adrian informed us how HPX can be used to take advantage of hardware accelerators such as Intel Xeon Phi or GPUs. We looked at the inception of the project and the sources of contributions to the project…
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The Talk Show With John Gruber
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The Talk Show With John Gruber
Daring Fireball / John Gruber
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The director’s commentary track for Daring Fireball. Long digressions on Apple, technology, design, movies, and more.
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On The Bike Shed, hosts Joël Quenneville and Stephanie Minn discuss development experiences and challenges at thoughtbot with Ruby, Rails, JavaScript, and whatever else is drawing their attention, admiration, or ire this week.
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