# Wrapup Hello! (**even if you did not attend, please read below**) Hopefully the learning experience from this week's "Intro to scientific computing and HPC" was great! Would you mind answering a few questions so that we can improve our course? Course feedback -> https://forms.gle/pxrMDFprvMo3L3sz8 **Please take the questionnaire even if you couldn't join us, so that we know why you couldn't make it.** (for example, if you registered just to get the links and info, that's OK: please let us know). So where to go from here? We are happy to help you learn more about hands-on scientific computing. Here some starting points: - All materials remain online indefinitely, and you should continue to use them. We couldn't teach you everything in this course, but we could set you on the right track. - Aalto Scientific Computing YouTube channel: you find all recordings from this course and our past courses, including the one from last week https://www.youtube.com/channel/UCNErdFO1_GzSkDx0bLKWXOA - Other courses you might want to check out: - CodeRefinery workshop is the best way to learn git and reproducible computational research. The next workshop is in September 2024. Subscribe to the newsletter to stay up to date https://coderefinery.org/#newsletter - Hands-on Scientific Computing https://handsonscicomp.readthedocs.io/en/latest/ Explore the map of all the skills needed in computational research. The course is part of the FITech platform for those who also need the extra credits https://fitech.io/en/studies/hands-on-scientific-computing/ - Check out CSC upcoming training events and other self-learning materials https://www.csc.fi/training#training-calendar - Subscribe to our Aalto Scientific Computing email list to stay up to date on our upcoming courses next Fall https://list.aalto.fi/mailman/listinfo/scicomp-announcements - Request a course from us! https://link.webropol.com/s/scipod There are many thing that go into HPC/scientific computing, far more than most people can know themselves. Do ask for help if you need it. - If you are unsure on where to go next, just ask us! scip@aalto.fi - If you are at Aalto University, we have extensive support available: https://scicomp.aalto.fi/help/ - If you are at other locations, search there or ask that support be created in our model. Have a great Summer! Aalto Scientific Computing # Content for the webpage (in RST) * **Day #1 (Tue 4.jun):** Basics and background * 11:50--12:00: Joining time/icebreaker * **12:00--12:10 Introduction, about the course** *Richard Darst and other staff* Materials: :doc:`../../training/kickstart/intro` * **12:10--12:25: From data storage to your science** *Enrico Glerean and Simo Tuomisto* - Data is how most computational work starts, whether it is externally collected, simulation code, or generated. And these days, you can work on data even remotely, and these workflows aren't obvious. We discuss how data storage choices lead to computational workflows. Materials: `SciComp Intro <https://hackmd.io/@AaltoSciComp/SciCompIntro>`__ * **12:25--12:50: (Computational) reproducibility and open science** *Enrico Glerean and Samantha Wittke* - Transparency in science is one of the core principles in research integrity. Did you know that half of published studies are actually not reproducible? Here we give an overview of CodeRefinery learning materials for those who want to start picking up good enough practices like git version control, clear project folder structure, conda environments, containers. Materials: `Reproducible research (CodeRefinery) <https://coderefinery.github.io/reproducible-research/>`__ * **12:50--13:00: Break** * **13:00--13:25: Behind the scenes: the humans of scientific computing** *Richard Darst and a special guest* - Who are we that teach this course and provide SciComp support? What makes it such a fascinating career? Learn about what goes on behind the scenes and how you could join us. * **13:25--13:50: What can you do with a computational cluster?** *(Simo Tuomisto and Enrico Glerean)* - A couple of real examples of how people use the cluster (what you can do at the end of the course): 1) Multi-cpu-node computations with LAMMPS, 2) Suprise demo. * **13:50--14:00: break** * **14:00--15:00: Connecting to a HPC cluster** *Thomas Pfau and Jarno Rantaharju* - Required if you are attending the Triton/HPC tutorials the following days, otherwise the day is done. - 14:00--14:20: Livestream introduction to connecting (ssh, openondemand) - 14:20--14:50: Individual help time in Zoom (links sent to registered participants for the affiliated HPC clusters) - Break until 15:00 once you get connected. - Material: :doc:`/triton/tut/connecting` * **15:00--15:25: How to ask for help with (super)computers** *Radovan Bast and Richard Darst* - It’s dangerous to go alone, take us! Don’t waste time struggling, there are plenty of people here for you. Materials: `Slides <https://zenodo.org/records/8392763>`__. * **15:25--15:50: Editors and local/remote workflows** *Hossein Firooz and Richard Darst* - One can use clusters also without the shell, but it comes with some extra care. Materials: `VSCode on HPC <https://coderefinery.github.io/TTT4HPC_Interactive/VSCode/>`__ * **15:50--16:00: Wrapping-up and getting ready for day 2** *Richard Darst* ---- # OLD STUFF HERE BELOW ## Day 1 (audience are beginners) * 12:00 Intro, about the course * link: https://scicomp.aalto.fi/training/kickstart/intro/ * 12:10 From data storgato your science * link: https://hackmd.io/@AaltoSciComp/SciCompIntro * 12:25 ~~What is parallel computing? An analogy with cooking~~ Compressed code refinery * something about (computational) reproducibility in general + open science (open code+methods)? (git, conda, containers, FAIR, github, zenodo) * (basically a 25 minutes compressed overview of coderefinery, EG can make pages + talk) * 12:50 break * 13:00 Humans of Scientific Computing * RD: I always thought this was good for knowing about us / future career prospects. * 13:50 break * 14:00 Connecting to a HPC Cluster * here ssh connection (and some might want to try ood? or should we mention ood later and just give a demo?) * RD: we should mention/demo all options to some degree so people know * ???? help in zoom * 15:00 Using the cluster from the shell * about typing commands in whatever shell you get * +1 * 13:00 Editors and (remote) workflows (local and remote) * 15:25 What can you do with a computational cluster? * last time was a practical demo of mpi and array job ## Day 2 (audience are users who needs HPC but don't need to go full scale) * 12:00 Intro to day 2-3 * 12:05 structure of a cluster and slurm + how big is my calc * https://scicomp.aalto.fi/triton/tut/slurm/ * https://scicomp.aalto.fi/triton/usage/program-size/ * 12:30 Running your first job in the queue: interactive serial, monitoring * 13:00 Break * 13:10 Continues with more interactive, serial monitoring * 14:00 Break * ==ENRICO TO CHECK TIMINGS HERE FROM LAST YEAR VIDEOS== * All timings can be found here: https://github.com/AaltoSciComp/video-editlists-asc/blob/master/kickstart-2023.yaml Or from this playlist: https://piped.video/playlist?list=PLZLVmS9rf3nMKR2jMglaN4su3ojWtWMVw * 15:00 Other things you should know (applications, modules, data storage, remote data) * Should we have a session about conda here? * +1, and exercise with module load mamba (or download micromamba if you don't have mamba, or miniforge) * we can do it for one python and one R environment (and more tabs) * 15:30 Q&A ## Day 3 (audience are people who will truly need parallelisation, gpus etc) * 12:00 what does parallel mean? * also here the italian and a german cooking pasta * gpu as in power grill * 12:30 Forms of parallelism (parallel tutorials) * 14:00 laptops to lumi * 14:40 GPU jobs * 15:30 Ask us anything ## Notes ### Day 1 Samantha + Enrico - Enrico will introduce Samantha and will ask "What is CodeRefinery?", she can tell about herself and about coderefinery - Enrico will start talking about reproducibilty in general using https://coderefinery.github.io/reproducible-research/motivation/ then Enrico will ask Samantha "how does it all connect in the coderefinery workshop?" and we can switch to https://coderefinery.github.io/reproducible-research/intro/ and Samantha could present that figure - Enrico then gives a short overview of the rest of the lesson and tell that people can read and learn by themselves or watch the recordings. - Samantha can tell about next CR workshop, follow CodeRefinery in social media, become an ambassador