Kickstart 2023 initial page

Author: rkdarst

training/index.rst

@@ -29,6 +29,7 @@ to suggest a new course, `please take this survey <https://link.webropol.com/s/s
 
    Coderefinery Workshop Spring 2023 (21-23 and 28-30. March) <https://coderefinery.github.io/2023-03-21-workshop/>
    scip/workflows-2023
+   scip/kickstart-2023
    Take the survey! Request a re-run of past courses / new courses <https://link.webropol.com/s/scipod>
    scip/index
 

training/scip/kickstart-2023.rst

@@ -0,0 +1,360 @@
+=====================================================================
+June 2023 / Intro to Scientific Computing /  HPC Summer Kickstart
+=====================================================================
+
+.. important::
+
+   This page mostly has information from 2022.  The page will be
+   updated closer to time.  The dates are confirmed to be 6-8 June
+   2023 (T-Th).  The schedule will be updated based on what we decide
+   to focus on this year - if you have special topic requests, please
+   let us know.
+
+
+Kickstart is a three × half day course for researchers to get
+started with high-performance computing (HPC) clusters.
+**The first day serves as a guide to your career:** a map to the types of
+resources that are available and skills you may need in your career,
+so that you can be prepared when you
+need more in the future.  This part is especially suitable to new researchers or students trying to
+understand computational/data analysis options available to them.  It
+won't go into anything too deep, but will provide you with a good
+background for your next steps: you will know what resources are
+available and know the next steps to use them.
+
+**The second and third days take
+you from being a new user to being competent to run your code at a
+larger scale than you could before.**
+This part is good for any researcher who thinks they may need to
+scale up to larger resources in the next six months, in any field.
+Even if you don't use computing clusters, you will be better prepared
+to understand how computing works on other systems.  If you are a
+student, this is an investment in your skills.  By the end of the course you
+get the hints, ready solutions and
+copy/paste examples on how to find, run and monitor your applications,
+and manage your data.
+
+If you are at Aalto University: the course is obligatory for all new
+Triton users and recommended to all interested in the field.
+
+This course is part of :doc:`Scientific Computing in Practice <index>` lecture series
+at Aalto University, supported by many others outside Aalto, and offered to others as part of `CodeRefinery <https://coderefinery.org>`__.
+
+
+
+Other universities
+------------------
+
+**If you are not at Aalto University**, you can follow along with the
+course and will learn many things anyway.  The course is designed to
+be as useful to people outside of Aalto, but some of the examples
+won't directly work on your cluster (most will, anyway we will give
+hints about adapting).  Known sites partnering with this course:
+
+* Regardless of where you are from, you may register using the
+  registration form below to get emails about the course.
+* Participants from University of Helsinki can follow how to connect
+  to their Kale/Turso cluster by following `their own instructions
+  <https://wiki.helsinki.fi/pages/viewpage.action?pageId=408323613>`__.
+* Participants from University of Oulu: please follow instructions on
+  `how to access the Carpo2 computing cluster <https://ict.oulu.fi/17120/?page&lang=en>`__.
+* Tampere: this course is recommended for all new Narvi users and also all
+  interested in HPC. Most things should work with simply replacing triton
+  -> narvi. Some differences in configuration are listed in
+  `Narvi differences
+  <https://narvi-docs.readthedocs.io/narvi/kickstart-diffs.html>`__
+* `CSC <https://csc.fi>`__ (Finland): Participants with `CSC user
+  account <https://docs.csc.fi/accounts/>`__ can try examples also in
+  CSC supercomputers, see the `overview of CSC supercomputers
+  <https://docs.csc.fi/computing/overview/>`__ for details on
+  connecting, etc.
+
+If you want to get your site listed here and/or help out, contact us
+via the `CodeRefinery chat
+<https://coderefinery.github.io/manuals/chat/>`__ (#workshops stream).
+Our :doc:`hints for other sites' support staff
+</triton/tut/required-cluster-setup>` are available.
+
+
+
+Practical information
+---------------------
+
+This is an online hybrid of MOOC and interactive: everyone may attend
+the **livestream** at https://twitch.tv/coderefinery, no registration
+needed!  This is the primary way to watch all sessions.  **Zoom** is
+used for exercise sessions of partner audiences, and **HackMD** is
+used for a continuous Q&A session.
+
+**Time, date:**  6 -- 8 June (Tue--Thu). 11:50-16:00 EEST
+
+**Place:** Online via public livestream, Zoom exercise sessions for
+partners, and probably in-person discussion/practice rooms at some
+campus.
+
+**Registration:** Please register at this link [TODO]. Attending
+ individual sessions is fine.
+
+**Cost:** Free of charge for FGCI consortium members including Aalto
+employees and students.  Livestream is free to everyone.
+
+**Additional course info at:** scip@aalto.fi
+
+
+
+Schedule
+--------
+
+**All times are EEST (Europe/Helsinki time)!**
+
+The daily schedule will be adjusted based on the audience's questions.
+There will be frequent breaks and continuous questions time going on,
+this is the mass equivalent of an informal help session to get you
+started with the computing resources.
+
+
+.. admonition:: Subject to change
+
+   Schedule may still have minor updates, please check back for
+   the latest.
+
+* **Day #1 (Tue 6.jun):** Basics and background
+
+  * 11:50--12:00: Connecting time, basics, and 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: What is parallel computing?  An analogy with
+    cooking** *Enrico Glerean and Thomas Pfau*
+
+    In workshops such as this, you will hear lots about parallel
+    computing and how you need it, but rarely get a understandable
+    introduction to how they relate and which are right for you.
+    Here, we give a understandable metaphor with preparing large
+    meals.  `Slides <https://docs.google.com/presentation/d/e/2PACX-1vQLTzWkRy7Du3jjPJ6Y9BqKczU_JcSTEL6XsndrNJ7ylzi4RWeEy8lhfWZQu_lpwbAKroh51qqLoPFG/pub>`__
+
+  * **13:00--13:25: Behind the scenes: the humans of scientific
+    computing** *Richard Darst and ???*
+
+    Who are we that provide these services.  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: How you actually install software on the cluster:
+    an example case (Conda and Python)** *Simo Tuomisto and ???*
+
+    Software installation is one of the questions we most often get.
+    Usually, on clusters, this happens via *environments*, which
+    allows you to install specific software per-project.  We'll give a
+    demonstration of how these work in Python. Materials for demo:
+    :doc:`/triton/apps/python-conda`
+
+  - **14:00--14:50: Secure Shell (ssh) tips and tricks** *Thomas Pfau
+    and Enrico Glerean*
+
+    Remembering server address... Another login? Another password prompt? 
+    Again? Wouldn't it be nice to just have a key instead of a keycode that
+    you need to type in? Here, we will show you how to set up your computer
+    to easily connect to the server(s) you need. And we will explain the 
+    process from keys to config.  While useful, this part is skippable if 
+    you are able to connect to Triton (next section).
+    Materials: :doc:`/scicomp/ssh`
+
+  - **15:00--15:45: Connecting to a HPC cluster** *Thomas Pfau and
+    Simo Tuomisto*
+
+    - Required if you are attending the Triton/HPC tutorials the
+      following days, otherwise the day is done.
+    - 15:00--15:20?: Livestream introduction to connecting
+    - 15:??--??: Individual help time in Zoom (links sent to
+      registered participants)
+    - Material: :doc:`/triton/tut/connecting`
+
+  - Preparation for day 2:
+
+    Remember to read/watch the "shell crash course" (see "Preparation"
+    below) if you are not yet confident with the command line.  This
+    will be useful for tomorrow.
+
+* **Day #2 (Wed 7.jun):** Basic use of a cluster *(Richard Darst, Simo
+  Tuomisto)*
+
+  - 11:50--12:00: Connecting time and icebreaker
+
+  - **12:00--12:05: Introduction to days 2-3**
+
+    - :doc:`/triton/tut/intro`
+
+  - **12:05--12:30: What can you do with a computational cluster?**
+
+    Several real examples of how people use the cluster (what you can
+    do at the end of the course).
+
+    - Real example 1: Large-scale computing with array jobs
+    - Real example 2: Large-scale parallel computing
+
+  - **12:30--15:00: Running your first jobs in the queue**
+
+    - :doc:`/triton/tut/interactive`
+    - :doc:`/triton/tut/serial`
+    - :doc:`/triton/tut/monitoring`
+
+  - **15:00--15:30: Other things you should know about the HPC environment**
+
+    - :doc:`/triton/tut/modules`
+    - :doc:`/triton/tut/storage`
+    - :doc:`/triton/tut/remotedata`
+
+  - **15:30--16:00: Q&A**
+
+* **Day #3 (Thu 8.jun):** Advanced cluster use *(Simo Tuomisto, Richard
+  Darst)*
+
+  - 11:50: Joining time/icebreaker
+
+  - **11:50--13:00: Simple parallelization with array jobs:**
+    :doc:`/triton/tut/array`
+
+  - **13:00--14:00: Using more than one CPU at the same time:**
+    :doc:`/triton/tut/parallel`
+
+  - **14:00--14:30: Laptops to Lumi**
+
+    You now know of basics of using a computing cluster.  What if you
+    need more than what a university can provide?  CSC (and other
+    national computing centers) have even more resources, and this is
+    a tour of them. `Slides here <https://github.com/AaltoSciComp/scicomp-docs/raw/master/training/scip/CSC-services_062022.pdf>`__.
+
+  - **14:40--15:30: Running jobs that can utilize GPU hardware:** :doc:`/triton/tut/gpu`
+
+  - **15:30--16:00: Q&A**
+
+
+
+Preparation
+-----------
+
+We strongly recommend you are familiar with the Linux command line.
+Browsing the following material is sufficient:
+
+* `Basic Linux shell and scripting
+  <https://www.youtube.com/watch?v=ESXLbtaxpdI&list=PLZLVmS9rf3nN_tMPgqoUQac9bTjZw8JYc&index=3>`__
+  (important) (or read/watch the shorter :doc:`crash course
+  </scicomp/shell>` / `video <https://youtu.be/56p6xX0aToI>`__)
+
+**How to attend:** Online workshops can be a productive format, but it
+takes some effort to get ready.  Browse these resources:
+
+* `Attending a livestream workshop
+  <https://coderefinery.github.io/manuals/how-to-attend-stream/>`__,
+  good to read in detail (ignore the CodeRefinery-specific parts).
+* `How to use HackMD to take answer questions and hold discussions <https://coderefinery.github.io/manuals/hackmd-mechanics/>`__.
+
+
+
+
+Technical prerequisites
+-----------------------
+
+**Software installation**
+
+* SSH client to connect to the cluster (+ be able to connect, see next
+  point)
+* `Zoom <https://coderefinery.github.io/installation/zoom/>`__ (if
+  attending breakout rooms)
+
+
+**Cluster account and connection verification:**
+
+* Access to your computer cluster.
+
+  * Aalto: if you do not yet have access to Triton, :doc:`request an account
+    </triton/accounts>` in advance.
+
+* Then, connect and get it working
+
+  * Aalto (and possibly useful to others): try to :doc:`connect to
+    Triton </triton/tut/connecting>` to be ready.  Come to the
+    Wednesday session for help connecting (required).
+
+
+
+Next steps / follow-up courses
+------------------------------
+
+Keep the :doc:`Triton quick reference </triton/ref/index>` close (or
+equivalent for your cluster).
+
+Each year the first day has varying topics presented.  We don't repeat
+these every year, but we strongly recommend that you watch some of
+these videos yourself as preparation.
+
+Very strongly recommended:
+
+* `When and how to ask for help
+  <https://www.youtube.com/watch?v=5fgXXz3fzdM>`__ (very useful)
+* `Git intro
+  <https://www.youtube.com/watch?v=r9AT7MqmLrU&list=PLZLVmS9rf3nOaNzGrzPwLtkvFLu35kVF4&index=5>`__ (useful)
+
+Other useful material in previous versions of this course:
+
+* Scientific Computing workflows at Aalto - concepts apply to other
+  sites, too (optional): `lecture notes
+  <https://hackmd.io/@AaltoSciComp/SciCompIntro>`__ and `video
+  <https://www.youtube.com/watch?v=Oz37XAzWFhk>`__, :doc:`reference
+  material </triton/usage/workflows>`.
+* Tools of scientific computing (optional): `lecture notes
+  <https://hackmd.io/@AaltoSciComp/ToolsOfScientificComputing>`__ and
+  `video <https://www.youtube.com/watch?v=kXYfxXEb0Go>`__
+
+While not an official part of this course, we suggest these videos
+(co-produced by our staff) as a follow-up perspective:
+
+* Attend a `CodeRefinery workshop <https://coderefinery.org>`__,
+  which teaches more useful tools for scientific software
+  development.
+* Look at `Hands-on Scientific Computing
+  <https://hands-on.coderefinery.org>`__ for an online course to
+  either browse or take for credits.
+* `Cluster Etiquette (in Research Software Hour)
+  <https://www.youtube.com/watch?v=NIW9mqDwnJE&list=PLpLblYHCzJAB6blBBa0O2BEYadVZV3JYf>`__:
+  The Summer Kickstart teaches what you *can* do from this course,
+  but what *should* you do to be a good user.
+* `How to tame the cluster (in Research Software Hour)
+  <https://www.youtube.com/watch?v=5HN9-MW7Tw8&list=PLpLblYHCzJAB6blBBa0O2BEYadVZV3JYf>`__.
+  This mostly repeats the contents of this course, with a bit more
+  discussion, and working one example from start to parallel.
+
+
+
+Community standards
+-------------------
+
+We hope to make a good learning environment for everyone, and expect
+everyone to do their part for this.  If there is anything we can do to
+support that, let us know.
+
+If there is anything wrong, *tell us right away* - if you need to
+contact us privately, you can message the host on Zoom or
+:doc:`contact us outside the course </help/index>`.  This could be as
+simple as "speak louder / text on screen is unreadable / go slower" or
+as complex as "someone is distracting our group by discussing too
+advanced things".
+
+
+
+Material
+--------
+
+See the schedule