Aalto Scientific Computing
SciCompAalto@fosstodon.org

On Friday, @rkdarst gave an internal-but-public talk on "simple deployment of web services" (concepts/examples). The target was people (like Research Software Engineers) who might be benefit from simpler deployment of web services and have access to and support of kubernetes.

If you're at , we can support you in this kind of project!

read: hackmd.io/@AaltoSciComp/kubern
watch: youtu.be/WnkGkCoRGnk

November 05, 2023
Aalto Scientific Computing
SciCompAalto@fosstodon.org

Old news by now, but if you want to know the kinds of things we are thinking about for late 2023, you can check out our "development day" blog post from August:

aaltoscicomp.github.io/blog/20

October 30, 2023
SciCompAalto shared a status by rkdarst
Richard Darst
rkdarst@fosstodon.org

Talk by me tomorrow:

We say "email me for data" isn't acceptable for open science. Then is "email me with updates or corrections" ok? Probably not. We talk about how Github can be used, even for small projects and by non-programmers, to synchronize working on projects and what this should mean for . This talk is high-level and aspirational.

Tomorrow 14 EEST; you can still register: aalto.fi/en/events/github-for-

October 11, 2023
Aalto Scientific Computing
SciCompAalto@fosstodon.org

The security vulnerability might affect :s, especially those that make their own environments and process image data (via code or apps). Our blog post discusses what a person might need to know (and if you have corrections or more suggestions, please send them our way)
aaltoscicomp.github.io/blog/20

Screenshot, text is: libwebp security vulnerability and computational scientists Recently, a major security vulnerability (CVE-2023-5129) has been found in libwebp, an image decoding library for the .webp format. This is major, since this library is embedded in many apps and web browsers and allows remote code execution just by opening a file. For computational scientists, there is still some impact - and it’s harder to compensate for. In short, just by processing an image in the .webp format, someone can take over your computer or session. libwebp is the current issue, but the problem is general: computational scientists often create software environments and use them for a long time. These environments aren’t usually browsing the web (the most likely attack vector here), but they do involve lots of code installed from different projects. How does one manage security in this case? Screenshot, text is: How it affects scientists If you use web browsers or apps on your own desktops, laptops, phones, etc. - make sure update them! If you don’t use images in your research, there probably isn’t much impact. If you do, this is what could happen: You make a Python / Anaconda environment which uses libwebp somehow - directly installed through Conda, or some other application. You download a dataset containing images. You process them as part of your research with the old environment. The malicious image runs an exploit. It has access to your whole user account on that computer: extract any data, add SSH keys for remote access, corrupt/delete data (which might not be backed up from the cluster…). Many things have to happen here, but it’s very possible for it to happen. You could lose access to non-backed up data or code or other confidential or sensitive data could be compromised, since code from one project from your user account has access to all projects from your account. One would normally fix things by updating software. But when you are dealing with a research environment that can’t easily be updated, what should you do? This is the real question here.
September 29, 2023
Aalto Scientific Computing
SciCompAalto@fosstodon.org

Since Monday, general Aalto SSH servers require passwords in addition to SSH keys. This isn't our change, but we have extra info and support in case of usability impact of scientific computing. Simplest is to use VPN.
aaltoscicomp.github.io/blog/20

Screenshot, text is: Aalto public servers requiring passwords with SSH keys From 2023-09-25, publicly accessible Aalto server login is changing and will now require a password in addition to SSH keys. This will have a significant usability impact on some users. This post is made as a landing page for users who need immediate, practical help and for whom the aalto.fi page isn’t findable or detailed enough. The official contact is the IT Services service desk The reference page SSH has been updated to include detailed reference information for every common operating system and SSH client. Secure Shell is one of the standard methods of connecting to remote servers and it is important that users of all skill levels are able to use it securely.
September 28, 2023
Aalto Scientific Computing
SciCompAalto@fosstodon.org

@westbynoreaster Soon, it will require a key plus a password. We aren't implementing this so hopefully more details soon.

September 24, 2023
SciCompAalto shared a status by jsaramak
Jari Saramäki
jsaramak@datasci.social

A new blog post on scientific writing where I discuss how writing the abstract first makes you think more clearly: jarisaramaki.fi/2023/09/19/the

September 19, 2023
Aalto Scientific Computing
SciCompAalto@fosstodon.org

is a standard tool, but it can be tricky to explain setup to people across different operating systems. Our updated SSH reference is designed to help people on all the standard platforms. If you ever needed a place to point people, this might work: scicomp.aalto.fi/scicomp/ssh/

Please help checking and send corrections for all the various operating systems, surely there is more to do still.

Screenshot of attached link, text is: Setup Check the tabs below for your operating system and methods to see which method you want to use. Tabs: Windows with PowerShell, Windows with WSL, Windows with PuTTY, Windows with MobaXterm, Linux, Mac. Tab Linux is selected: --- SSH is built-in to almost any distribution. If it’s not there, try installing the openssh-client package. Start the Terminal application to follow the rest of the instructions. Then, follow the “Command Line” instructions on most of this page. --- This guide uses Aalto University’s HPC cluster as an example, but should be applicable to other remote servers at Aalto as well and many other outsiders as well. Screenshot of table of contest: SSH - Setup Basic use: connect to a server - SSH keys: better than just passwords - ProxyJump - Multiplexing - Config file: don't type so many options - References
September 22, 2023
Aalto Scientific Computing
SciCompAalto@fosstodon.org

Reminder: You can drop by our in-person session for the CodeRefinery workshop any time it's ongoing - please register so you can get info but it's not required. You can also drop by just to say hi, get some snacks, and ask us any non-related questions, too.

U523 Top Lounge
coderefinery.github.io/2023-09

Picture of a nice-looking lounge area with people working around it. (For privacy, this is during a break - most people are behind the camera getting snacks now)
September 18, 2023
Aalto Scientific Computing
SciCompAalto@fosstodon.org

Our "Git the way you need it" cheatsheet has been updated for the conventions of modern Git and distributed to at least the CS department coffee rooms. Please print and distribute to other places, too!

aaltoscicomp.github.io/cheatsh

Screenshot titled "Git the way you need it, the cheatsheet", with some intro text and parts of the sections "Basics", "Info commands", and "Level 0" visible. The text itself is not so important and available from the link, but it's some generic basic information about git.
September 18, 2023
Aalto Scientific Computing
SciCompAalto@fosstodon.org

Blog post: Preparing for new Triton. Sometime in the autumn, our cluster will get an OS upgrade. Unlike most clusters, this happens gradually in-place to minimize disruption and get the most out of existing hardware. It will require changes and awareness from our users to keep your stuff running on the new OS. Read the post to see how to prepare: aaltoscicomp.github.io/blog/20

Screenshot; title: Preparing for new Triton Sometime in autumn of 2023 (e.g. September), we will do a major update of Triton: updating the basic operating system, and thus almost everything else. There are big benefits to this: newer basic operating system software, but also such a basic update affects almost every user. For a short time, this will make a lot of work for almost every user. This post gives advance warning and a chance of feedback of how to make the update most usable. This post is just advance warning and things to prepare already. All actual instructions will come later. What will happen We will update the basic operating system from CentOS 7 to something else (Rocky 9 or Red Hat 9). We’ve ordered all new management hardware to make the backend more reliable and manageable. Along with this comes with an update of the software build system, which should allow us to deploy software to our users even better. We’ll also update our configuration management system for more reproducibility. We also hope to think about the usability of the new system: remove a lot of old options and add in new, simpler ways of doing what people need. All data and storage will remain the same, so there is no big data migration needed.
September 13, 2023
SciCompAalto shared a status by coderefinery
CodeRefinery
coderefinery@fosstodon.org

Our new is ready for use, thanks to @SciCompAalto: aaltoscicomp.github.io/cheatsh

It's designed for beginners/intermediates to introduce things slowly, recognizing that most use is simple, and grouping advanced uses together how they are used. It'll be used in our workshop next week.

September 12, 2023
Aalto Scientific Computing
SciCompAalto@fosstodon.org

Hello scientists in 🇫🇮 and 🌍 - @coderefinery starts next week, and everyone is invited. This isn't a programming course, but extra tools (, , , , etc) needed for a scientist to do programming comfortably. T-Th, Sep 19-21 and 26-28, online.
coderefinery.github.io/2023-09

If you're at Aalto, invite us to your research group to help put these tools into practice - we don't teach and leave you alone!

September 12, 2023
Aalto Scientific Computing
SciCompAalto@fosstodon.org

Videos from "Linux Shell Basics" are now available on YouTube (CC-BY):
scicomp.aalto.fi/training/scip

Rapid production thanks to , , and , and a whole lot of work from our staff. Please enjoy! (3/?)

September 01, 2023
Aalto Scientific Computing
SciCompAalto@fosstodon.org

Linux Shell Basics (see replied-to message for description) starts in 10 minutes, if you register now you get an auto-reply with attendance information. Visitors from 🌍 welcome, target audience is researchers who wish to be more comfortable with command-line computational tools.

scicomp.aalto.fi/training/scip

August 29, 2023
Aalto Scientific Computing
SciCompAalto@fosstodon.org

Course announcement:
Need to use more computer power, but this " " thing holding you back? Come learn the basics of being comfortable with a for basic science and data management ( actually, but applies to other things like and . Course is hosted for , but we welcome others, too.

Online, Next week, 29-31 August (T-Th), EU afternoons: scicomp.aalto.fi/training/scip

Screenshot from the link, text is: Audience: Scientists, researchers, and others looking for an extensive intro into Linux shell / terminal. Primary audience is academics in Finland, outsiders are welcome to register and are accepted if there is space (there always is space). About the course: The Linux shell lets you work efficiently on remote computers and automate bigger projects - whether you are managing a lot of data or running programs on a computer cluster. Without it, you are often stuck when you need to do move beyond basic tools like Jupyter notebooks. This course covers the Bash shell, but the principles apply to other shells such as zsh. This course will cover the basics so that you’ll know what the shell is, are comfortable using it for your own projects, and are able to attend other courses with the shell as a prerequisite. We’ll get familiar with the command line, files and directories, and other things you often find in shell environments. We will unleash the power of that blinking cursor in the terminal window. Windows/Mac/Linux users are warmly welcome - regardless of what you use on your desktop, you’ll need this when using more powerful remote computers. We will start with somewhat basics like files and processes and go up to command line magic like redirections and pipes. This should be enough to get started with the Linux terminal.
August 23, 2023
Aalto Scientific Computing
SciCompAalto@fosstodon.org

Interested in moving from an focus to Research Software Engineering? Our new blog post discusses how to successfully apply to a job working with us:
aaltoscicomp.github.io/blog/20

(every place is different, but this might give you some inspiration for applying to other places, too! If you think we might have a position opening soon... you'd be right!)

Screenshot of link's first paragraph: The Aalto RSE hiring process This post describes the hiring process of Aalto RSE. The goal is to make hiring more equitable by providing the background information so that everyone can apply successfully. For those not applying to us, it might still provide some valuable insight about how to market your skills as a PhD making a sideways career move. What’s said here may not apply to every organization, but it might give you some things to think about.
August 21, 2023
Aalto Scientific Computing
SciCompAalto@fosstodon.org

Do you use our cluster (Triton)? (the audio transcription tool) is now easily available for your use. This is just the first step in making various AI tools available.

aaltoscicomp.github.io/blog/20

Installing Whisper (and similar) isn't the easiest, since they try to be too clever and do a lot automatically - the post also discusses the challenges and solutions.

Screenshot: Luckily, we have a cluster with GPUs and a way to provide software for researchers. We’ve made Whisper available on the cluster as a module, so it’s trivial to use it for any audio data you may have. All one needs to do is: [code block] $ module load whisper (help gets printed out) $ srun --mem=6G singularity_wrapper run YOUR_FILE.wav --model_directory $medium --local_files_only True --language en [This uses pre-downloaded models, which makes it faster, saves storage space, and ensures the model matches with the code now and in the future.]
August 08, 2023
SciCompAalto shared a status by coderefinery
CodeRefinery
coderefinery@fosstodon.org

We have started preparing our next CodeRefinery workshop September 19-21 and 26-28, 2023.

Registration is now open: coderefinery.github.io/2023-09

July 21, 2023
Aalto Scientific Computing
SciCompAalto@fosstodon.org

Our / kickstart course finished, all videos are already available. This is an overwhelming amount of information which not everyone can absorb, so hopefully the videos will help our participants far into the future.

scicomp.aalto.fi/training/scip

June 10, 2023