# Summer 2021 Kickstart internal document # DAY3 - 12:00 - 12:15 Recap on srun - 12:15 - 12:50 Non-interactive jobs - 12:50 - 13:00 Break - 13:00 - 13:30 Explaining the exercise and doing it - 13:30 - 13:50 Solutions + monitoring - 13:50 - 14:00 Break - 14:00 - 14:30 Modules and brieflyn on array jobs. - No Array jobs exercises - 14:30 - 14:50 GPU start + typealong - 14:50 - 15:00 Break - 15:00 - 15:30 GPU finish + exercises - 15:30 - \infty On parallelization, speed, Q&A --- ## Where to go next? ### 1. Set your next learning goal. Just one goal! With a goal you immediately give a purpose to what you want/need to learn. Not sure what to learn? Come chat with us at garage. **Pick just one, start small, baby steps. Do not aim at the best practices, aim at the "good enough" practices** For inspiration this is worth reading: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005510 Examples: - I want to find the workflow best for my needs - I want to speed up my analysis with parallelization - I want to run deep learning models - I want to keep my code cleaned and versioned with git - I want my research to be reproducible - I want my data and code and project to be tidy and in order, backed up, and versioned - I want to move my code away from my slow laptop - I want to master linux shell - I want to make my code available to the world - ...? ### 2. Find resources to fullfil your goal - Join a code refinery workshop (or do it by yourself with online videos from past workshops) https://coderefinery.org/ - Check more learning materials at https://handsonscicomp.readthedocs.io/en/latest/ - Check some past episodes from Research Software Hour https://researchsoftwarehour.github.io/ - Come and ask if you feel overwhelmed and are not sure where to start your learning path # DAY2 - 12:00 - 12:05 About our tutorials https://scicomp.aalto.fi/triton/#tutorials - Note: We do not need to talk about us or how to ask for help as we covered it on day 1, **so we go immediately to connecting to the cluster** - 12:05 - 12:25 Connecting to the cluster https://scicomp.aalto.fi/triton/tut/connecting/ - 12:25 - 12:35 Exercises from page above + try jupyter or VDI (10 minutes) - This will be critical as surely someone is not able to connect - 12:35 - 12:40 Applications https://scicomp.aalto.fi/triton/tut/applications/ - Applications page can be joined with modules, no exercises for applications IMO - 12:40 - 12:50 Modules part 1 https://scicomp.aalto.fi/triton/tut/modules/ - 12:50 - 13:00 Break - 13:00 - 13:10 Resuming on modules - 13:10 - 13:20 Module exercises - No optional exercises - 13:20 - 13:50 Storage + exercises https://scicomp.aalto.fi/triton/tut/storage/ - 13:50 - 14:00 break - 14:00 - 14:25 Guest talk: Radovan https://cicero.xyz/v3/remark/0.14.0/github.com/bast/help-with-supercomputers/main/talk.md/ (I will do some small tweaks to it) - 14:25 - 14:35 Post talk Q&A + Review exercise from storage and other questions - 14:35 - 14:50 Intro to slurm https://scicomp.aalto.fi/triton/tut/interactive/ - 14:50 - 15:00 Break - 15:00 - 15:40 Slurm type-along - 15:40 - Wrapping up the day and all srun exercises in zoom --- I watched the shell video: yes: o no: o I watched the computing workflows video: yes: o no: o How do you feel about shell/shell scripting?: good: o whatever: o scared: o powerful: o ## useful links Meeting info (star this message): Instructor Zoom: 67660333570 / gitgitgit ( https://aalto.zoom.us/j/67660333570?pwd=VVNjNlpKWklGUGNYWktteU5xUDZmUT09 ) Student Zoom: https://aalto.zoom.us/j/69608324491 Twitch: https://aaltoscicomp.github.io/scip/ or https://twitch.tv/coderefinery Course web page: https://scicomp.aalto.fi/training/scip/summer-kickstart/ Attendee HackMD: https://hackmd.io/@AaltoSciComp/IntroSummer2021 Coordination HackMD: https://hackmd.io/@AaltoSciComp/S15-YcLvd # email to participants Hello! And thank you for registering to “Intro to Scientific Computing - Summer 2021” (Monday 07/06-Wednesday 09/06 11:50). Please read on to prepare. Detailed schedule: https://scicomp.aalto.fi/training/scip/summer-kickstart/ To join the sessions, you need the following three channels: 1. Watch via CodeRefinery Twitch: https://aaltoscicomp.github.io/scip/ 2. Ask questions via HackMD: https://hackmd.io/@AaltoSciComp/IntroSummer2021 3. Session together on Zoom (for exercises and discussions): https://aalto.zoom.us/j/69608324491 **Open the three links on Monday at 11:50 and you are set.** All sessions will be recorded and shared online without any attendee video or voice. #### BEFORE #### ## THE EVENT ## ################ Please watch these videos before day 2: - [Basic Linux shell and scripting](https://www.youtube.com/watch?v=ESXLbtaxpdI&list=PLZLVmS9rf3nN_tMPgqoUQac9bTjZw8JYc&index=3) ([companion page](https://scicomp.aalto.fi/scicomp/shell/)) - [Scientific computing workflows](https://www.youtube.com/watch?v=ExFbc5EikU0) We will discuss them together on day 1. In particular **the shell course is very important to be able to work on days 2-3**. If you have not used the command line/Linux shell before, you must watch this video, or you won't be prepared. ##### Monday 07/06 ####### # Intro to HPC with FCCI # ## Linux Shell and Git ## ########################## You don’t need anything pre-installed if you just watch, but if you install the Git version control system, you can follow along with the Git demo. These CodeRefinery installation instructions work well: https://coderefinery.github.io/installation/shell-and-git/ #### Tuesday 08/06 #### #### Wednesday 09/06 #### #### H.P.C.Kickstart #### https://scicomp.aalto.fi/training/scip/summer-kickstart/ For this part of the course you need an account on a computer cluster. On Monday we will test that your account works. See the course page for information on who to contact depending on where you are. You may attend via Twitch (watch only) and ask questions via HackMD. If you would like breakout rooms to do exercises with other participants, join Zoom as well. General While the material is developed and tested with the Aalto Triton HPC cluster, most of the examples we are showing will also work in your institution cluster. - People from Helsinki University can follow more instructions at: https://wiki.helsinki.fi/display/it4sci/HPC+SUMMER+KICKSTART+2021 - People from Tampere University can check: https://narvi-docs.readthedocs.io/narvi/tut/connecting.html - People from Oulu: your contact person is pekka.sodervall@oulu.fi See you tomorrow! Enrico and Richard, on behalf of Aalto Scientific Computing / Science IT https://scicomp.aalto.fi --- For your future career: * coderefinery * research software hour * nordic RSE and aalto RSE * continue learning * hands on sci comp with Aplus * garage * usergroups * zulip, chat in general ## EMAIL TO SENIORS Dear senior Triton users, (professors, postdocs, lecturers, etc...) If you have a junior collaborator who has just started (summer worker, new doctoral student, etc...), could you please forward the invitation below to them? In our kickstart event we cover Triton HPC, basics of Linux terminal, git, data analysis workflows at Aalto and resources at CSC. The event is open for any school at Aalto, as well as other collaborating universities in Finland. If you need to be sure that your group is efficient, this is a good resource. Have a nice summer! Enrico =EMAIL_TO_SUMMER_WORKERS_AND_NEW_COLLABORATORS== hello! We (Science IT / Aalto Scientific Computing) are organizing an introductory course for all on how to do data science using Aalto computing facilities from remote. It can be intimidating to make the transition from small projects to using some of the best computational resources in Finland, with so many different options. Come to this course to learn both what the options are (intro material and day 1), and how to use some of the more high-performance computing resources (days 2-3). Last year we had 200+ summer workers attending, and we are happy to get even more this year! Please register since we need to prepare your accounts so that you can access remote computing resources. Link for the event and prerequisites: https://www.aalto.fi/en/events/intro-to-scientific-computing-7-9-june-2021-fgci-kickstart If you want to know more about what is available and see our standard starting page for researchers, see here: https://scicomp.aalto.fi/aalto/welcomeresearchers/ Best regards Enrico Glerean on behalf of Science IT / Aalto Scientific Computing http://scicomp.aalto.fi/ ## EMAIL FOR EVERYONE hello! We are organizing an introductory course for all on how to do computing/data science using facilities from remote in collaboration with Aalto University, CSC, University of Helsinki, Tampere University, University of Oulu. We will cover what the options are (intro material and day 1), and how to use some of the more high-performance computing resources (days 2-3). This course is especially targeted to research assistant who are starting their research (for example summer interns), but of course everyone else is welcome. Examples are based at Aalto, but the general topics will be helpful to people anywhere, and even advanced users will probably learn a few new tricks. Please register in advance since we need to prepare your accounts so that you can access remote computing resources at your university, although we welcome people watching passively or attending only part of the course. Link for the event and prerequisites: https://scicomp.aalto.fi/training/scip/summer-kickstart/ Best regards Enrico Glerean on behalf of Science IT / Aalto Scientific Computing http://scicomp.aalto.fi/ ## EMAIL TO SUMMER WORKERS hello! We (Science IT / Aalto Scientific Computing) are organizing an introductory course for all summer workers on how to do data science using Aalto computing facilities from remote. It can be intimidating to make the transition from small projects to using some of the best computational resources in finland, with so many different options. Come to this course to learn both what the options are (intro material and day 1), and how to use some of the more high-performance computing resources (days 2-3). Last year we had 200+ summer workers attending, and we are happy to get even more this year! Please register since we need to prepare your accounts so that you can access remote computing resources. Link for the event and prerequisites: https://www.aalto.fi/en/events/intro-to-scientific-computing-7-9-june-2021-fgci-kickstart If you want to know more about what is available and see our standard starting page for researchers, see here: https://scicomp.aalto.fi/aalto/welcomeresearchers/ Best regards Enrico Glerean on behalf of Science IT / Aalto Scientific Computing http://scicomp.aalto.fi/ # Planning Look at https://hackmd.io/AWsF8hxGSPmFKOKY6iTJ1A for possible reusable email templates etc. Registration form for edits: https://docs.google.com/forms/d/1GrtvHDRoij9fYW-loLZXfj1QwwcrF9G83ZNd9hLV5EM/edit Zoom room: :::spoiler Zoom link can be the one used for teaching this spring: Enrico Glerean is inviting you to a scheduled Zoom meeting. Topic: Course Room - Scientific Computing in Practice Time: This is a recurring meeting Meet anytime Join Zoom Meeting https://aalto.zoom.us/j/69608324491?pwd=Y1BRV290TzVNZm5OL0xlalExTzZLQT09 Meeting ID: 696 0832 4491 Passcode: scicomp One tap mobile +496938079883,,69608324491# Germany +496950502596,,69608324491# Germany Dial by your location +49 69 3807 9883 Germany +49 695 050 2596 Germany +49 69 7104 9922 Germany +49 30 5679 5800 Germany Meeting ID: 696 0832 4491 Find your local number: https://aalto.zoom.us/u/ckBndjLhd Join by SIP 69608324491@109.105.112.236 69608324491@109.105.112.235 Join by H.323 109.105.112.236 109.105.112.235 Meeting ID: 696 0832 4491 Passcode: 4609228 ::: ## Rethinking the schedule Goals: - take into account past comments - More time for exercises - More time in breakout rooms - We can also do demos in the main room - take into account what is of interests of few having in mind the most common issues we face - people running things in the login node (= interactive usage) - people asking for wrong amount of resources - people filling in their home quota with conda env - anything else? ## Production strategy - Mainly done like winter kickstart (Twitch + Zoom for exercises) - Common schedule, instructors sign up for being in the instructor room. Plus whoever else wants to help teach ## Proposed sessions and examples Please add proposed sessions here. Vote ("+1") if you would like it - Q&A from winter kickstart day 0 (workflows, shell), ask people to watch the videos first - 1-hour git crash course - Ivan's Crash course presentation? Give real-life problems we can use as examples here: - ## Registration link Editable form https://docs.google.com/forms/d/1GrtvHDRoij9fYW-loLZXfj1QwwcrF9G83ZNd9hLV5EM/edit ## Timetable for the days Will it be 12-16 like last year? Too long? - Day 0 - 10m Icebreaker (before start time) - 15m General intro - 30m Discussion and Q&A about "Workflows" and "Shell intro" videos (watched separately) - 15m break - -- - 45m HPC intro (Ivan) - 15m break - -- - 45m One-hour git intro - 15m break - -- - 15m Future of sciencific computing / this course - 30m Getting connected to the cluster - Day 1 - connecting - Demo: SSH config - Demo: JupyterHub - data storage - Demo: can we get someone to show a nice data organization? - interactive jobs - serial jobs - Day 2 - array jobs - applications (day 2 to keep day1 more active) - modules - gpu computing - parallel ## OLD PAGE HERE BELOW :::spoiler :::