From e0005dc8eeeaff2da8418247ed69ae0b67651ca6 Mon Sep 17 00:00:00 2001 From: Jayant Yadav Date: Wed, 8 Jan 2025 10:57:23 +0100 Subject: [PATCH 1/8] adding courses and workshop tab --- mkdocs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mkdocs.yml b/mkdocs.yml index 0abca76b0..b9b81da6b 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -104,8 +104,8 @@ nav: - Simons Genome Diversity Project datasets: databases/simons_genome.md - Other bioinformatics-oriented local data resources: databases/other_local.md -# - Workshops and courses: workshops_courses/workshops_courses.md - Support: support.md + - Workshops and courses: workshops_courses/workshops_courses.md - Back to UPPMAX main page: https://www.uu.se/en/centre/uppmax theme: From 99e901058452ad8e906111c118f0182dbca8a9fb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Claremar?= <70746791+bclaremar@users.noreply.github.com> Date: Wed, 8 Jan 2025 11:10:59 +0100 Subject: [PATCH 2/8] Update workshops_courses.md --- docs/workshops_courses/workshops_courses.md | 16 ++++++++++++++-- 1 file changed, 14 insertions(+), 2 deletions(-) diff --git a/docs/workshops_courses/workshops_courses.md b/docs/workshops_courses/workshops_courses.md index 14ad53405..4ec15a486 100644 --- a/docs/workshops_courses/workshops_courses.md +++ b/docs/workshops_courses/workshops_courses.md @@ -1,13 +1,25 @@ # Workshops and courses -## UPPMAX +## UPPMAX Local - Intro to UPPMAX day 1 - [MkDocs style](https://uppmax.github.io/uppmax_intro_day_1/) - [Sphinx style](https://uppmax.github.io/uppmax_intro/) -- [Intro to Python](https://uppmax.github.io/uppmax_intro_python/) + - [Introduction to Bianca](https://uppmax.github.io/bianca_workshops) + + +## NAISS centre + +## NAISS centre agnostic + +### Programming +#### Python +- [Intro to Python](https://uppmax.github.io/uppmax_intro_python/) + - [HPC-Python](https://uppmax.github.io/HPC-python/index.html) + +#### Other - [Introduction to running R, Python, and Julia in HPC](https://uppmax.github.io/R-python-julia-matlab-HPC/) - [Programming formalisms](https://uppmax.github.io/programming_formalisms_intro/index.html) From 82d99a9480f67a7a984c720d4f99ad043947b557 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Claremar?= <70746791+bclaremar@users.noreply.github.com> Date: Wed, 8 Jan 2025 11:30:50 +0100 Subject: [PATCH 3/8] Create connect_transfer.md --- docs/workshops_courses/connect_transfer.md | 4 ++++ 1 file changed, 4 insertions(+) create mode 100644 docs/workshops_courses/connect_transfer.md diff --git a/docs/workshops_courses/connect_transfer.md b/docs/workshops_courses/connect_transfer.md new file mode 100644 index 000000000..2bec00d7d --- /dev/null +++ b/docs/workshops_courses/connect_transfer.md @@ -0,0 +1,4 @@ +# Connecting to HPC systems & File transfer course + + + From acb9e44370a2149ea57d6169951418ef939e8b19 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Claremar?= <70746791+bclaremar@users.noreply.github.com> Date: Wed, 8 Jan 2025 11:31:22 +0100 Subject: [PATCH 4/8] Rename connect_transfer.md to naiss_connect_transfer.md --- .../{connect_transfer.md => naiss_connect_transfer.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename docs/workshops_courses/{connect_transfer.md => naiss_connect_transfer.md} (100%) diff --git a/docs/workshops_courses/connect_transfer.md b/docs/workshops_courses/naiss_connect_transfer.md similarity index 100% rename from docs/workshops_courses/connect_transfer.md rename to docs/workshops_courses/naiss_connect_transfer.md From 1e78f51d5c31c4a744a84dc49afa487d3a95684f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Claremar?= <70746791+bclaremar@users.noreply.github.com> Date: Wed, 8 Jan 2025 11:32:16 +0100 Subject: [PATCH 5/8] Create bianca_intro.md --- docs/workshops_courses/bianca_intro.md | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 docs/workshops_courses/bianca_intro.md diff --git a/docs/workshops_courses/bianca_intro.md b/docs/workshops_courses/bianca_intro.md new file mode 100644 index 000000000..f02686c8b --- /dev/null +++ b/docs/workshops_courses/bianca_intro.md @@ -0,0 +1,2 @@ +# Bianca introduction workshop + From 96e4a951374f723481d00b5e64620393047c5f8c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Claremar?= <70746791+bclaremar@users.noreply.github.com> Date: Wed, 8 Jan 2025 11:35:09 +0100 Subject: [PATCH 6/8] Create julia_R_matlab.md --- docs/workshops_courses/julia_R_matlab.md | 10 ++++++++++ 1 file changed, 10 insertions(+) create mode 100644 docs/workshops_courses/julia_R_matlab.md diff --git a/docs/workshops_courses/julia_R_matlab.md b/docs/workshops_courses/julia_R_matlab.md new file mode 100644 index 000000000..c84f005db --- /dev/null +++ b/docs/workshops_courses/julia_R_matlab.md @@ -0,0 +1,10 @@ +# Introduction to running Julia, R, and Matlab in HPC + +Learn how to run Julia, R, and Matlab at Swedish HPC centres. We will show you how to find and load the needed modules, how to write a batch script, as well as how to install and use your own packages, and more. +The course will consist of lectures interspersed with hands-on sessions where you get to try out what you have just learned. + +We will mainly use Tetralith at NSC for the examples for the course, but there is little difference in how you use the various HPC centres in Sweden and you should have no problems applying the knowledge to the other systems. + +This course will consist of three days (9:00-16:00), one for each language. It is a cooperation between HPC2N, LUNARC, and UPPMAX. + +Dates: 24-26 March 2025. From 1c7c3b2bff43ec6845e9f04b937d25c8e4b366cd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Claremar?= <70746791+bclaremar@users.noreply.github.com> Date: Wed, 8 Jan 2025 11:42:05 +0100 Subject: [PATCH 7/8] Update bianca_intro.md --- docs/workshops_courses/bianca_intro.md | 30 +++++++++++++++++++++++++- 1 file changed, 29 insertions(+), 1 deletion(-) diff --git a/docs/workshops_courses/bianca_intro.md b/docs/workshops_courses/bianca_intro.md index f02686c8b..05274d160 100644 --- a/docs/workshops_courses/bianca_intro.md +++ b/docs/workshops_courses/bianca_intro.md @@ -1,2 +1,30 @@ -# Bianca introduction workshop +# Introduction to Bianca: Handling Sensitive Research Data +## Overview and schedule +Are you just beginning to work with sensitive data in your research? If yes, welcome to a 1-day introduction to handling sensitive data on the UPPMAX cluster, Bianca. We will tell you about NAISS-SENS, how to login to Bianca, transfer files via wharf, basics of the SLURM workload manager and the module system. + +This is a workshop is intended for beginner users of Bianca. + +You do not need to be a member of a NAISS-SENS project in order to join the workshop. A SUPR course project will be available to all participants. The workshop will consist of both lectures and exercise sessions. + +**Prerequisites**: none. + +**When:** Wednesday, March 19, 2024. +**Time:** 09:00 - 12:00, and 13:00 - 16:00. +**Where:** online via Zoom. Connection details will be sent to registered participants. + +**Login help session:** TBD. + +Registration form (soon open) + +- Introduction +- Intro to NAISS-Sens +- Login: Thinlinc +- Command line intro specific to Bianca +- Module system +- Intro to transfering files to and from Bianca +- Compute nodes and slurm +- Summary +- Q/A + + From cf99adeee3ccea075ec2cd4ca31847e4c58a98d3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Rich=C3=A8l=20Bilderbeek?= Date: Wed, 8 Jan 2025 13:41:15 +0100 Subject: [PATCH 8/8] Update vscode_on_rackham.md --- docs/software/vscode_on_rackham.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/software/vscode_on_rackham.md b/docs/software/vscode_on_rackham.md index d524b1cd2..98ae054de 100644 --- a/docs/software/vscode_on_rackham.md +++ b/docs/software/vscode_on_rackham.md @@ -26,7 +26,8 @@ to work with your files on Rackham. ## Procedure to start VSCode Below is a step-by-step procedure to start VSCode. -This procedure is also demonstrated in [this YouTube video](https://youtu.be/RG2FWA8yoUs). +This procedure is also demonstrated in [this YouTube video]([https://youtu.be/RG2FWA8yoUs](https://youtu.be/MkrKi5oU_po)). +An older version of this procedure is demonstrated in [this YouTube video](https://youtu.be/RG2FWA8yoUs). ### 1. Install VSCode on your local computer