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training/scip/winter-kickstart-2025.rst

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+===============================================================
+February 2025 / Intro to Triton and HPC /  HPC Winter Kickstart
+===============================================================
+
+.. admonition:: Quick links
+   :class: important
+
+   * News and important links (20/02/2025):
+
+     * Link to register: https://link.webropol.com/ep/hpcwinter25
+     * See the time-line below
+     * Livestream (morning): https://twitch.tv/coderefinery
+     * Exercises (afternoon): *Link sent to registered participants*
+     * Notes document: *Link sent to registered participants*
+
+
+
+For winter 2025, we are running an intensive version (one-day-only) of our **Kickstart course**.
+The longer version of the course will be held on the first week of June and will last for 3 half days
+
+Learning goals
+--------------
+
+* Learn the basics of High Performance Computing with slurm
+* Watch a step-by-step example of the typical data analysis workflow with Aalto Triton HPC cluster
+* Engage with hands-on exercises to make sure you are able to run your analysis on Triton
+
+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>`__.
+
+
+
+Practical information
+---------------------
+
+The course happens on Wed 26 February 2025 and is divided in two parts:
+
+**Morning lectures** (9:45 - 12:00 EET): This is the **livestream demo** part of the course. Everyone may attend the **livestream** at
+https://twitch.tv/coderefinery, no registration needed. This is done so that we get a higher quality recording without any personal data from course participants
+
+**Lunch** (12:00 - 13:00 EET): Lunch on your own
+
+**Afternoon hands-on session** (13:00 - 16:00): This is the practical part of the course. We will be connected to the same zoom room and do the exercises together.
+
+**Cost:** Free!
+
+**Language:** English
+
+**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 as it happens.
+
+  * 09:45--10:00: Joining time/icebreaker
+
+  * **10:00--10:15 Introduction, about the course** *Enrico Glerean and
+    other staff* Materials: :doc:`../../training/kickstart/intro`
+
+  * **10:15--11:45: A day in the life of an HPC user** *Richard Darst and Simo Tuomisto*
+
+    - 1. Check your connection to the cluster [[ref.](https://scicomp.aalto.fi/triton/tut/connecting/)]
+    - 2. Moving data to the cluster [[ref.](https://scicomp.aalto.fi/triton/tut/storage/)]
+    - 3. Datasets/projects that could be used for the demo:
+        - ["Ngrams example"](https://github.com/AaltoSciComp/hpc-examples/tree/master/ngrams) 
+    - 4. Loading an application? Not needed but good to remeber (e.g. python env) [[ref.](
+https://scicomp.aalto.fi/triton/tut/modules/)]
+    - 5. Analysing data with slurm [[ref.](https://scicomp.aalto.fi/triton/#running-calculations)]
+        - 5.1 Getting an interactive session [[ref.](https://scicomp.aalto.fi/triton/tut/interactive/)]
+        - 5.2 Non-interactive serial job [[ref.](https://scicomp.aalto.fi/triton/tut/interactive/)]
+        - 5.3 Parralelisation and array jobs [[ref1](https://scicomp.aalto.fi/triton/tut/parallel/), [ref2](https://scicomp.aalto.fi/triton/tut/array/)]
+        - 5.4 More advanced parallelisation - discussion only - ([multithreading/multiprocessing](https://scicomp.aalto.fi/triton/tut/parallel-shared/), [MPI](https://scicomp.aalto.fi/triton/tut/parallel-mpi/), [GPUs](https://scicomp.aalto.fi/triton/tut/gpu/))
+    - 6. Visualising the results (e.g OOD)
+    - 7. Moving the data away from the cluster
+
+
+
+  * **11:45--12:00: Where to go from here and how to ask for help (Susanne Merz and Enrico Glerean)
+
+  * **12:00--13:00: Lunch break (on your own)**
+
+  * **13:00--16:00: Hands-on exercises with Triton HPC cluster
+
+    - Main room: Lobby and Generic questions (SM)
+    - Room 1: Hands-on with exercises from the morning, Slurm and Triton basics (RD)
+    - Room 2: Connecting questions? (TP)
+    - Room 3: GPUs (ST)
+    - Room 4: Advanced parallelization
+    - Room 5: AI / LLMs (YT)
+    - Room 6: Speech2Text (TR)
+
+Preparation
+-----------
+
+We strongly recommend you are familiar with the Linux command line.
+Browsing the following material is sufficient:
+
+* Command line/shell basics [[ref](https://scicomp.aalto.fi/triton/tut/cluster-shell/)] [[video](https://youtu.be/bJMmz5-svJo?t=7&list=PLZLVmS9rf3nMKR2jMglaN4su3ojWtWMVw&index=8)]
+  - **Important background knowledge which we won't go over again.**
+
+  - A more detailed version of the above, for those who automate a lot of analysis, is [Basic Linux shell and scripting](https://www.youtube.com/watch?v=ESXLbtaxpdI&list=PLZLVmS9rf3nN_tMPgqoUQac9bTjZw8JYc&index=3)
+  - Or read/watch the shorter :doc:`crash course
+    </scicomp/shell>` / `video <https://youtu.be/56p6xX0aToI>`__.
+
+
+* Watch `this background info about why we use computer clusters <https://www.youtube.com/playlist?list=PLZLVmS9rf3nNDHRo1Baz_JVQWDI0mTYyB>`__.  This is important information for *why* we are in this course, which we *won't cover directly*.  The most important videos are the `intro (what is a cluster and why?) <https://www.youtube.com/watch?v=yqGtnA7CUtU&list=PLZLVmS9rf3nNDHRo1Baz_JVQWDI0mTYyB&index=1&pp=gAQBiAQB>`, `storage hierarchy (how the data looks) <https://www.youtube.com/watch?v=JAR9xyy5rcE&list=PLZLVmS9rf3nNDHRo1Baz_JVQWDI0mTYyB&index=2&pp=gAQBiAQB>`, and `the Slurm job scheduler (how the cluster runs things) <https://www.youtube.com/watch?v=Y73A7lXISxU&list=PLZLVmS9rf3nNDHRo1Baz_JVQWDI0mTYyB&index=5&pp=gAQBiAQB>`.
+
+
+
+**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), or print `this cheatsheet
+<https://aaltoscicomp.github.io/cheatsheets/triton-cheatsheet.pdf>`__
+if that's your thing.
+
+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:
+
+* `Installing Python packages with Conda
+  <https://youtu.be/dmTlNh3MWx8>`__ (Note that conda on new-Triton has changed.  See :doc:`/triton/apps/python-conda` for details)
+* `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