training-hpc issueshttps://gricad-gitlab.univ-grenoble-alpes.fr/python-uga/training-hpc/-/issues2019-07-03T09:29:57+02:00https://gricad-gitlab.univ-grenoble-alpes.fr/python-uga/training-hpc/-/issues/12Remarks / todo after 1st session2019-07-03T09:29:57+02:00Pierre AugierRemarks / todo after 1st session## Think about what is important (and has to be presented) and what is not so important and should not be presented
It is a very general remark but I think it was a problem of this session.
An example: in my point of view, it is not u...## Think about what is important (and has to be presented) and what is not so important and should not be presented
It is a very general remark but I think it was a problem of this session.
An example: in my point of view, it is not useful to present `pipenv` in such training on Python HPC.
## Change the README to tell participants that they have to install the virtual box.
- Add a file explaining how to setup the virtual box (for example the potential problems with the BIOS configuration) and even how to create the virtual box from nothing
## dtw_cort_dist
- Add Julia
- Add a function using high level Numpy functions
- time the 3 functions
- change the structure to avoid using runpy + a directory per case only when needed...
- plots to show the speed up
- use pytest for checking
- write a nice blog post to summarize the results
## Simple decorators
Should be introduced at the end of the presentation on functions
- user perspective
- how to create decorators
- `functools.wraps`
## Simple generators
When should it be presented? After loops, functions and list comprehensions.
- Generator Expressions https://www.python.org/dev/peps/pep-0289/
- `yield` keyword
## Standardize presentations (all using ipynb and all included in the main web page)
- Merge the 2 presentations on packaging (with a little bit more on pytest)
## Put the presentations on the web!
## A good presentation of pip, virtualenv, pyenv (show how to use PyPy), conda
## Change order of the presentations: (wrapping, accelerators, parallel) to (parallel, wrapping, accelerators)
- We need to present the GIL before wrapping and accelerators.
- We don't need extensions to present parallelism
- We can come back to parallelism once accelerators are presented (OpenMP with Pythran, parallel loops with Numba / Cython, Dask + Numba(?))
## Improve the presentation on parallelism
See also https://github.com/fchuffar/practicle_sessions
- a little bit more on the architecture of the computers
- concepts of distributed and shared memories
- concepts of processes, threads, processors, cores, CPU
## A little bit more on GPU ?
## A little bit more on the statistic ecosystem (pandas, statsmodels, seaborn, ...), especially if there are R usershttps://gricad-gitlab.univ-grenoble-alpes.fr/python-uga/training-hpc/-/issues/11cython: remove call to min func2019-06-19T10:54:18+02:00Franck Thollardcython: remove call to min funcusing if elseusing if elseFranck ThollardFranck Thollardhttps://gricad-gitlab.univ-grenoble-alpes.fr/python-uga/training-hpc/-/issues/10parallelism: add future2019-06-19T10:36:08+02:00Franck Thollardparallelism: add futurehttps://gricad-gitlab.univ-grenoble-alpes.fr/python-uga/training-hpc/-/issues/9dtw_cort : unify setup.py (remove makes)2019-06-24T12:02:12+02:00Franck Thollarddtw_cort : unify setup.py (remove makes)https://gricad-gitlab.univ-grenoble-alpes.fr/python-uga/training-hpc/-/issues/8rework testing (adding a ipynb)2019-06-24T11:52:02+02:00Franck Thollardrework testing (adding a ipynb)https://gricad-gitlab.univ-grenoble-alpes.fr/python-uga/training-hpc/-/issues/7add dask ?2019-06-19T10:34:28+02:00Franck Thollardadd dask ?https://gricad-gitlab.univ-grenoble-alpes.fr/python-uga/training-hpc/-/issues/6add pres decorateurs2019-06-19T10:34:11+02:00Franck Thollardadd pres decorateurshttps://gricad-gitlab.univ-grenoble-alpes.fr/python-uga/training-hpc/-/issues/5pres generateurs2019-06-19T10:33:57+02:00Franck Thollardpres generateursFranck ThollardFranck Thollardhttps://gricad-gitlab.univ-grenoble-alpes.fr/python-uga/training-hpc/-/issues/4Improve pres complexity - O def2019-06-19T10:33:33+02:00Franck ThollardImprove pres complexity - O defFranck ThollardFranck Thollardhttps://gricad-gitlab.univ-grenoble-alpes.fr/python-uga/training-hpc/-/issues/3Improve pres dtw2019-06-19T10:33:02+02:00Franck ThollardImprove pres dtwFranck ThollardFranck Thollardhttps://gricad-gitlab.univ-grenoble-alpes.fr/python-uga/training-hpc/-/issues/2Fail installing Mercurial and clone the training repository2019-06-19T07:59:34+02:00Ghost UserFail installing Mercurial and clone the training repositoryHi there!
I have a MacbookPro with El Capitan (OSX 10.11.6).
A year ago, I intalled Anaconda, with Python 3.6.7. So, I do not need to install Miniconda, since conda commands are already included, do I?
Today, I updated Conda ("conda uda...Hi there!
I have a MacbookPro with El Capitan (OSX 10.11.6).
A year ago, I intalled Anaconda, with Python 3.6.7. So, I do not need to install Miniconda, since conda commands are already included, do I?
Today, I updated Conda ("conda udate conda"), but I didn't have an upgrade to Python 3.7. Is there a way to do it with a command in the Terminal?
- I intalled VS Code.
- conda channel was already activated (Message: "Warning: 'conda-forge' already in 'channels' list, moving to the top").
- Jupyter and Pyder are already included in Anaconda
- Mercurial: I did "pip intall conda-app" (ok), and "conda-app install mercurial", with the following messages:
Create conda environment _env_mercurial with package mercurial-app... warning: json.decoder.JSONDecodeError
done
Install hg-git with pip... done
mercurial should now be installed in
/Users/sophiedarfeuil/anaconda3/envs/_env_mercurial
Open a new terminal and the command(s) ['hg'] should be available.
Traceback (most recent call last):
File "/Users/sophiedarfeuil/anaconda3/bin/conda-app", line 11, in <module>
sys.exit(main())
File "/Users/sophiedarfeuil/anaconda3/lib/python3.6/site-packages/conda_app.py", line 316, in main
install_app(args.package_spec)
File "/Users/sophiedarfeuil/anaconda3/lib/python3.6/site-packages/conda_app.py", line 224, in install_app
add_to_app_list(app_name)
File "/Users/sophiedarfeuil/anaconda3/lib/python3.6/site-packages/conda_app.py", line 247, in add_to_app_list
with open(path_data, "w") as file:
FileNotFoundError: [Errno 2] No such file or directory: '/Users/sophiedarfeuil/.local/share/conda-app.json'
Then, the command "hg" doesn't work in a new Terminal window ("-bash hg: command not found"), and I cannot verify Mercurial configration nor clone the training repository . Any idea how to fix this issue?
Should I install Miniconda anyway and do the installing process from the beginning?
Thanks in advance for your help!
Sophiehttps://gricad-gitlab.univ-grenoble-alpes.fr/python-uga/training-hpc/-/issues/1failing installing spyder and jupyterlab2019-06-24T11:11:04+02:00Sophie Rousseauxfailing installing spyder and jupyterlabHello,
Following your instructions I started installing Python and utilities
I have a mac OSX and installed Miniconda3-latest-MacOSX-x86_64.pkg, then activated the conda channel `conda-forge` then tried to install Spyder and Jupyter wit...Hello,
Following your instructions I started installing Python and utilities
I have a mac OSX and installed Miniconda3-latest-MacOSX-x86_64.pkg, then activated the conda channel `conda-forge` then tried to install Spyder and Jupyter with the command `conda install spyder jupyterlab`
It thinks for a few minutes then I get this error message. Tried it several times :/
Is this because I am trying to do it from home and not from the Institute?
What do you suggest
Thanks
Sophie
ERROR MESSAGE
Collecting package metadata: failed
CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://repo.anaconda.com/pkgs/free/osx-64/repodata.json.bz2>
Elapsed: -
An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.
If your current network has https://www.anaconda.com blocked, please file
a support request with your network engineering team.
ConnectTimeout(MaxRetryError("HTTPSConnectionPool(host='repo.anaconda.com', port=443): Max retries exceeded with url: /pkgs/free/osx-64/repodata.json.bz2 (Caused by ConnectTimeoutError(<urllib3.connection.VerifiedHTTPSConnection object at 0x102921128>, 'Connection to www-cache.ujf-grenoble.fr timed out. (connect timeout=9.15)'))"))