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Running ESPResSo in the web browser

From: Jean-Noël Grad
Subject: Running ESPResSo in the web browser
Date: Thu, 14 Jul 2022 17:52:56 +0200
User-agent: Roundcube Webmail/1.4.13

Dear users,

The ESPResSo team is pleased to announce that two cloud-based solutions were developed to make the software more accessible. ESPResSo now runs directly in the web browser, in a single click, for free.

Binder gives you access to a Jupyter Notebook environment that runs tutorials out-of-the-box with ESPResSo 4.2.0 [2]. Gitpod gives you access to a web IDE and a terminal that automatically builds ESPResSo from the python branch [3].

Please find below detailed instructions on how to use these services. Feel free to contact us on the mailing list or on the GitHub Discussions if you need more information or have suggestions for improvement.

Best regards,
Jean-Noël Grad
Institute for Computational Physics
University of Stuttgart, Germany

Running a Gitpod instance

The Gitpod platform offers a free plan limited to 1 core per workspace and 50 core hours per month [4]. This cloud service requires a user account. The python branch of ESPResSo provides a YAML file to automatically build ESPResSo in the default configuration. Here is the direct link:

The workspace automatically pulls dependencies and builds the source code. This usually takes 15 min. Once the build has completed, use the terminal to run simulation scripts:

$ ./pypresso ../samples/

or start a JupyterLab session:

$ cd ${GITPOD_REPO_ROOT}/build/doc/tutorials
$ ../../ipypresso lab --NotebookApp.allow_origin="$(gp url 8888)" \
    --port=8888 --no-browser

In the bottom-right corner of the IDE, a notification will appear in a box to mention port 8888 is now active. Click the orange button "Make public" to open that port and then Ctrl+click one of the urls in the terminal output to open JupyterLab in a pop-up window. Some web browsers may block the pop-up and ask you to confirm opening an url that starts with `https://8888-espressomd-espresso-`, if that's the case, click on "Allow" to open JupyterLab in a new browser tab.

JupyterLab is the preferred way to run tutorials in Gitpod. Although tutorials can be executed in the IDE directly too, it requires the pypresso kernel, which is not visible the first time the IDE starts. To make it available, quit the Gitpod workspace by closing the tab in your web browser, then open the url again and select the old workspace. The pypresso kernel should now be available in the VS Code Jupyter environment. More details can be found in the user guide [6].

It is also possible to access a Gitpod workspace via SSH from any operating system [7].

Running a Binder instance

The Binder platform offers free spot instances limited to 1 core and 2 GB of RAM. No user account is needed. Here is the direct link:

The workspace automatically pulls a Docker image containing a pre-built version of ESPResSo 4.2.0 in its default configuration, and then pip installs its python dependencies. This usually takes less than 4 min. In the main Launcher window, you can open a terminal to run simulation scripts:

$ python samples/

Note how `python` is used instead of `pypresso`. To run tutorials, navigate to the `tutorials/exercises` folder and open one of the notebooks. The solutions are hidden but can be revealed by clicking on the "Show solutions" buttons. The other folder `tutorials/solutions` contains the same notebooks with the solutions already copy-pasted in the code cells.

If the JupyterLab interface is too confusing, it is possible to switch to the classic Jupyter Notebook interface by clicking on the `Help` tab and then on the `Launch Classic Notebook` item.

To share your session with a coworker, open a python terminal in the JupyterLab environment and run the following code to print the url and session token:

import subprocess
out =["jupyter", "notebook", "list"], capture_output=True)
url = out.stdout.decode("utf-8").split("\n")[1].split()[0]
url = url.replace("";, "";)

Users who open this link will be able to see and edit your files, but editing the same file at the same time won't work properly, because the file won't synchronize in real time. Live collaborative editing is therefore not possible yet, although a solution is currently being developed by the Jupyter Project [8]; if you have experience setting up this feature, we would welcome your input (the ESPResSo Binder git repository is available at [5]). People who use your link should leave your session with `File / Log Out`, and not with `File / Shut Down`, otherwise your session will be terminated too.


Running the last two ESPResSo summer schools as hybrid events helped us reach out to a wider audience who could not necessarily make travel arrangements to Europe. By providing recordings of the summer school lectures on YouTube [9] and making the hands-on sessions run in web browsers, we want to give everyone a chance to learn ESPResSo at their own pace, all year round.

Another application for these could services is the creation of reproducible execution environments that can be shared with your peers [10]. By storing simulation scripts together with a list of versioned dependencies in a git repository or on Zenodo, anyone can reproduce your scientific results in a web browser in a single click.

Remote research code execution in Jupyter environments is well established in academia, both for teaching and scientific research. We developed these two cloud-based solutions to satisfy slightly different needs: Gitpod is better suited to developers thanks to its IDE and git integration, while Binder is more suitable in a learning environment, since it provides a simpler interface and doesn't require subscription to online services.

How to help

Spread the word. This mailing list reaches people who are already comfortable building ESPResSo. If you know coworkers or students who would benefit from ESPResSo but had a bad experience installing the software, consider sharing this e-mail with them.

Tinker with the tools. The Gitpod [11] and Binder [5] configuration files are available online and are easy to adapt. Tell us how you made these cloud-based solutions more relevant to your research or teaching duties.

Give feedback. If these cloud-based solutions have been useful to you, please let us know and we will allocate more resources to their continued improvement. Gitpod is now part of the ESPResSo code, but it is currently not tested in CI. The Binder solution relies on a feature that is still in Beta [12] and we are currently not storing it in the official ESPResSo organization.

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