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Commit b551b4cf authored by Blaas-Schenner, Claudia's avatar Blaas-Schenner, Claudia
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Add README.md

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# MPI # MPI
## Getting started
To make it easy for you to get started with GitLab, here's a list of recommended next steps.
Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)!
## Add your files
- [ ] [Create](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#create-a-file) or [upload](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#upload-a-file) files
- [ ] [Add files using the command line](https://docs.gitlab.com/ee/gitlab-basics/add-file.html#add-a-file-using-the-command-line) or push an existing Git repository with the following command:
```
cd existing_repo
git remote add origin https://gitlab.tuwien.ac.at/vsc-public/training/mpi.git
git branch -M main
git push -uf origin main
```
## Integrate with your tools
- [ ] [Set up project integrations](https://gitlab.tuwien.ac.at/vsc-public/training/mpi/-/settings/integrations)
## Collaborate with your team
- [ ] [Invite team members and collaborators](https://docs.gitlab.com/ee/user/project/members/)
- [ ] [Create a new merge request](https://docs.gitlab.com/ee/user/project/merge_requests/creating_merge_requests.html)
- [ ] [Automatically close issues from merge requests](https://docs.gitlab.com/ee/user/project/issues/managing_issues.html#closing-issues-automatically)
- [ ] [Enable merge request approvals](https://docs.gitlab.com/ee/user/project/merge_requests/approvals/)
- [ ] [Set auto-merge](https://docs.gitlab.com/ee/user/project/merge_requests/merge_when_pipeline_succeeds.html)
## Test and Deploy
Use the built-in continuous integration in GitLab.
- [ ] [Get started with GitLab CI/CD](https://docs.gitlab.com/ee/ci/quick_start/index.html)
- [ ] [Analyze your code for known vulnerabilities with Static Application Security Testing (SAST)](https://docs.gitlab.com/ee/user/application_security/sast/)
- [ ] [Deploy to Kubernetes, Amazon EC2, or Amazon ECS using Auto Deploy](https://docs.gitlab.com/ee/topics/autodevops/requirements.html)
- [ ] [Use pull-based deployments for improved Kubernetes management](https://docs.gitlab.com/ee/user/clusters/agent/)
- [ ] [Set up protected environments](https://docs.gitlab.com/ee/ci/environments/protected_environments.html)
***
# Editing this README
When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thanks to [makeareadme.com](https://www.makeareadme.com/) for this template.
## Suggestions for a good README
Every project is different, so consider which of these sections apply to yours. The sections used in the template are suggestions for most open source projects. Also keep in mind that while a README can be too long and detailed, too long is better than too short. If you think your README is too long, consider utilizing another form of documentation rather than cutting out information.
## Name
Choose a self-explaining name for your project.
## Description ## Description
Let people know what your project can do specifically. Provide context and add a link to any reference visitors might be unfamiliar with. A list of Features or a Background subsection can also be added here. If there are alternatives to your project, this is a good place to list differentiating factors. Jupyter Notebooks in C, Fortran, and Python for the hands-on labs of the [MPI courses of the VSC Research Center, TU Wien](https://vsc.ac.at/training/courses/MPI).
## Badges
On some READMEs, you may see small images that convey metadata, such as whether or not all the tests are passing for the project. You can use Shields to add some to your README. Many services also have instructions for adding a badge.
## Visuals
Depending on what you are making, it can be a good idea to include screenshots or even a video (you'll frequently see GIFs rather than actual videos). Tools like ttygif can help, but check out Asciinema for a more sophisticated method.
## Installation The Jupyter Notebooks were written and tested on the VSC clusters, but apart from the job submission sections (that are specific for VSC-5 and the VSC Jupyterhub) they should work in other environments as well.
Within a particular ecosystem, there may be a common way of installing things, such as using Yarn, NuGet, or Homebrew. However, consider the possibility that whoever is reading your README is a novice and would like more guidance. Listing specific steps helps remove ambiguity and gets people to using your project as quickly as possible. If it only runs in a specific context like a particular programming language version or operating system or has dependencies that have to be installed manually, also add a Requirements subsection.
## Usage The [tasks/](tasks/) folder contains all tasks with descriptions, skeleton files, and solutions for all exercises. Normally this folder is not needed, but serves as an alternative way of doing the very same exercises if no JupyterHub is available.
Use examples liberally, and show the expected output if you can. It's helpful to have inline the smallest example of usage that you can demonstrate, while providing links to more sophisticated examples if they are too long to reasonably include in the README.
## Support
Tell people where they can go to for help. It can be any combination of an issue tracker, a chat room, an email address, etc.
## Roadmap
If you have ideas for releases in the future, it is a good idea to list them in the README.
## Contributing
State if you are open to contributions and what your requirements are for accepting them.
For people who want to make changes to your project, it's helpful to have some documentation on how to get started. Perhaps there is a script that they should run or some environment variables that they need to set. Make these steps explicit. These instructions could also be useful to your future self.
You can also document commands to lint the code or run tests. These steps help to ensure high code quality and reduce the likelihood that the changes inadvertently break something. Having instructions for running tests is especially helpful if it requires external setup, such as starting a Selenium server for testing in a browser.
## Authors and acknowledgment ## Authors and acknowledgment
Show your appreciation to those who have contributed to the project. The Jupyter Notebooks are written by [Claudia Blaas-Schenner (VSC Research Center, TU Wien)](mailto:training@vsc.ac.at).
The material in this repository is based on the [MPI course developed by Rolf Rabenseifner, HLRS](https://www.hlrs.de/training/self-study-materials/mpi-course-material) that is under a quite restrictive copyright by Rolf Rabenseifner and HLRS. The copyrighted material (some images, some exercise descriptions, some code snippets) is used with permission. Some partstaken from the HLRS material are modified and the Jupyter Notebooks are extended with own material of the Notebook authors.
## License ## License
For open source projects, say how it is licensed. [CC BY-SA 4.0 (Attribution-ShareAlike)](https://creativecommons.org/licenses/by-sa/4.0/)
## Roadmap and project status
We have just started with this repository, it will be continually expanded and updated, usually before and after the [MPI courses of the VSC Research Center, TU Wien](https://vsc.ac.at/training/courses/MPI), that run at least twice a year.
## Project status ## Contributing and error reporting
If you have run out of energy or time for your project, put a note at the top of the README saying that development has slowed down or stopped completely. Someone may choose to fork your project or volunteer to step in as a maintainer or owner, allowing your project to keep going. You can also make an explicit request for maintainers. Please contact [training@vsc.ac.at](mailto:training@vsc.ac.at) if you would like to contribute or found any issues.
#!/usr/bin/env bash
##
# source this script from a jupyter terminal or notebook cell
# to unset all jupyter related env variables and functions
##
if conda -V >/dev/null 2>&1; then
eval "$(conda shell.bash hook)"
for i in $(seq ${CONDA_SHLVL}); do
conda deactivate
done
echo "deactivated all conda envs ..."
else
echo "no conda found."
fi
PREVIOUS_IFS="$IFS"
IFS=$'\n'
SLURM_VARS=$( env | sort | grep -E "^SLURM_.*=" | sed "s/=.*//g" )
for var in $SLURM_VARS; do
unset $var
done
echo "unset all SLURM_* env variables ..."
IFS="$PREVIOUS_IFS"
spack unload
echo "unloaded all spack packages ..."
module purge
echo "unloaded all modules ..."
# sanitize LD_LIBRARY_PATH by removing all paths from spack base
spack_base=$( readlink -f "$( dirname $( which spack ) )/../" )
library_path=${LD_LIBRARY_PATH//:/ }
new_library_path=
for path in $library_path; do
if [[ $path =~ $spack_base ]]; then
continue
fi
if [[ $new_library_path =~ $path ]]; then
continue
fi
if [ -z "$new_library_path" ]; then
new_library_path="$path"
else
new_library_path="$new_library_path:$path"
fi
done
export LD_LIBRARY_PATH="$new_library_path"
export LIBRARY_PATH=
echo "removed all spack library paths ..."
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