Carol, I don't think anyone is saying, "Tell people not to use notebooks." The questions are about whether they improve the learning experience for beginners. There is also the question of whether use of the GUI somehow defeats the purpose of the shell lesson by contradicting what is often said there; namely, the command line is a powerful tool, you should use it.
One respondent said they review ways to run python -- python, ipython, jupyter -- then go on to use whatever in their workshop. That goes some way toward giving the participants choices. It may not counteract the message that is still implicit or implicit in the shell lesson. Perhaps the shell lesson should be modified so that the shell is treated as a data management tool, and notebooks and Rstudio are treated as development environments? Then the dissonance between advocating the shell in one lesson and abandoning it in another would be lessened? Perhaps all it would take would be a couple of examples of running a notebook from the command line and telling it to start from scratch and run all cells. If a notebook can be run in the same way from a prompt that a .py file can be, then maybe showing that capability solves a whole bunch of problems. The out-of-phase evaluation of things that is possible in notebooks can also lead to irreproducible results, which is not, I think, in keeping with the goals of the Carpentries. Some people will want to keep notebooks, and others will want to forego them; there should be a place for both approaches, and the one that best fits the goal of the particular offering and the expected audience should be chosen. I think it would not be a service to future learners if only one way were available for all circumstances. Perhaps it would help to consider a full two-day workshop as a bundle, and pick the lesson components that leads to the most coherent and clear presentation of the most important points to the targeted audience? That would lesson the dissonance between command-line for shell/git and GUI for R/Python, maybe? Should there be an option to do GUI-only workshops, no shell and a GUI for Git? Similarly, a command-line only option. I think that might be worth considering. On Tue, Aug 28, 2018 at 6:31 PM Carol Willing <willi...@willingconsulting.com> wrote: > > Hi all, > > There's positive discussion that has been started by Joel's talk. While I > liked his talk and there are some good points re: improving support for > software engineering best practices in Jupyter and JupyterLab notebooks, I'm > a bit concerned about the direction that this conversation is going. > > While all are entitled to their personal opinions and the Carpentries will > use notebooks when and if needed, I believe that the Carpentries would be > doing its students a disservice by warning people not to use the notebooks or > conda. > > The notebooks are a popular and effective tool for scientists and data > scientists to have in their toolbox. Project Jupyter won the ACM Software > System Award recently, and the ACM stated "These tools, which include > IPython, the Jupyter Notebook and JupyterHub, have become a de facto standard > for data analysis in research, education, journalism and industry." > https://awards.acm.org/software-system > > While it's great for folks to have different personal perspectives, I want to > make sure that the Carpentries and its lessons do not recommend that the > Jupyter Notebooks, IPython, and JupyterHub should be avoided by scientists > and data scientists. > > Thanks, > > Carol Willing > > > > On 28 Aug 2018, at 11:38, Maxime Boissonneault > > <maxime.boissonnea...@calculquebec.ca> wrote: > > > > These kinds of things are rather hard to track in time, because everything > > is a moving target (conda and other package managers constantly get > > updated, but also version of packages changes), but here is a bit more > > details : > > > > - The 10x performance difference was with a user code, which I > > unfortunately can't share (nor do I still have a copy of it). It was about > > numpy, which may or may not have changed since MKL can now be shipped with > > Anaconda. > > > > - FFTW, 2x performance gain : These slides compare between Conda-provided > > (and those provided by other package managers) FFTW, and one which was > > built on an avx2 cluster, the performance gain is 2x (see slides 28 and 29 : > > https://archive.fosdem.org/2018/schedule/event/installing_software_for_scientists/attachments/slides/2437/export/events/attachments/installing_software_for_scientists/slides/2437/20180204_installing_software_for_scientists.pdf > > > > > > - Tensorflow, 7x gain for CPU version, slide 28 of this talk : > > https://archive.fosdem.org/2018/schedule/event/how_to_make_package_managers_cry/attachments/slides/2297/export/events/attachments/how_to_make_package_managers_cry/slides/2297/how_to_make_package_managers_cry.pdf > > > > This one was not comparing Conda itself, but manylinux python wheels > > provided by the Tensorflow team, but no doubt Conda has the same issue if > > they build for generic architectures. > > > > > > > > Basically, any package that is compiled in a portable manner, such as what > > Conda and manylinux wheels do, will have some degree of speedup if compiled > > for the target architecture instead. This is typically achieved by the team > > of analysts who manage a cluster. > > > > Cheers, > > > > Maxime > > > > > > On 2018-08-28 2:20 PM, Ashwin Srinath wrote: > >> I'm very interested to see these examples? We use and advocate the use > >> of conda environments and I'm happy to be convinced otherwise. > >> > >> Thanks, > >> Ashwin > >> > >> On Tue, Aug 28, 2018 at 2:17 PM, Maxime Boissonneault > >> <maxime.boissonnea...@calculquebec.ca> wrote: > >>> Regarding performance, we have example of code using Anaconda-provided > >>> packages that run 10 times slower than the same code using locally built > >>> packages, optimized for the cluster architectures. That's not *a bit* > >>> slower, that's a lot slower. > >>> > >>> Regarding "cheating on your partner", that analogy is not by me, but the > >>> point he is trying to carry is that Anaconda basically replaces any > >>> cluster > >>> provided versions, which HPC center people are working hard to optimize. > >>> Recent versions of Anaconda are even worse, by packaging things like > >>> compilers and linkers, creating conflicts with cluster-provided system > >>> libraries and tools, and creating a lot of debugging problems for users > >>> and > >>> support people alike. > >>> > >>> Regards, > >>> > >>> Maxime > >>> > >>> > >>> On 2018-08-28 12:48 PM, Rémi Rampin wrote: > >>> > >>> 2018-08-28 12:27 EDT, Maxime Boissonneault > >>> <maxime.boissonnea...@calculquebec.ca>: > >>>> As a side-discussion, I think we should also be wary of using Anaconda, > >>>> and tell users not to use it in a cluster environment. For reasons, see > >>>> here : > >>>> https://twitter.com/mboisso/status/1034476890353020928 > >>> > >>> Hi Maxime, > >>> > >>> All I see in this thread is that "it's like cheating on your partner" > >>> (!!!) > >>> and it's "generically optimized software" that might be a bit slower than > >>> locally-built libs (interesting concern when using Python, an interpreted > >>> scripting language (and on the slow side too)). > >>> > >>> Could you elaborate on those reasons? > >>> > >>> Best > >>> -- > >>> Rémi > >>> > >>> > >>> The Carpentries / discuss / see discussions + participants + delivery > >>> options Permalink > >> ------------------------------------------ > >> The Carpentries: discuss > >> Permalink: > >> https://carpentries.topicbox.com/groups/discuss/T1505f74d7f6e32f8-Mad4fadc6a6da6de2b5f2aeb9 > >> Delivery options: > >> https://carpentries.topicbox.com/groups/discuss/subscription > > > > > > -- > > --------------------------------- > > Maxime Boissonneault > > Analyste de calcul - Calcul Québec, Université Laval > > Président - Comité de coordination du soutien à la recherche de Calcul > > Québec > > Team lead - Research Support National Team, Compute Canada > > Instructeur Software Carpentry > > Ph. 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