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Combined display of all available logs of HPCwiki. You can narrow down the view by selecting a log type, the username (case-sensitive), or the affected page (also case-sensitive).

• 14:19, 24 August 2026 Honfi001 talk contribs created page Uv (Created page with "{{DISPLAYTITLE:uv}} uv is a tool for installing Python packages and for managing the environments they live in. It does the same work as <code>pip</code> and <code>venv</code>, and it does it a great deal faster. This page explains what uv is, how to load it on Anunna, where it keeps your files, and how to use it for everyday work. It also explains what uv is '''not''' the right tool for: the packages it installs are not built for our hardware, so when the speed of you...")
• 10:25, 24 August 2026 Honfi001 talk contribs created page FrequentlyAskedQuestions (Created page with "{{DISPLAYTITLE:Frequently Asked Questions}}")
• 14:51, 19 August 2026 Honfi001 talk contribs created page Best-Practices (Created page with "==Best Practices==")
• 14:27, 18 August 2026 Honfi001 talk contribs created page Python/uv (Created page with "{{DISPLAYTITLE:uv}} uv is a tool for installing Python packages and for managing the environments they live in. It does the same work as <code>pip</code> and <code>venv</code>, and it does it a great deal faster. This page explains what uv is, how to load it on Anunna, where it keeps your files, and how to use it for everyday work. It also explains what uv is '''not''' the right tool for: the packages it installs are not built for our hardware, so when the speed of you...")
• 15:09, 17 August 2026 Honfi001 talk contribs created page Tutorials/Apptainer-Conda (Created page with "{{DISPLAYTITLE:Totorial: Conda in an Apptainer Container}} = Running a Conda Environment in a Container = Sometimes a piece of software is published only as a conda package, with no module, no Python-only equivalent and no ready-made image. Building it into a container is the cleanest way to run it on Anunna: the environment is created once, on a compute node, and afterwards it is a single file that behaves the same way every time you use it. Read Python/Conda firs...")
• 13:42, 17 August 2026 Honfi001 talk contribs created page Python/Conda (Created page with "Conda is a tool for installing scientific software and keeping it in self-contained folders called environments. You will meet it most often in bioinformatics, data science and machine learning, where a great deal of software is published this way. This page explains what Anaconda and Mamba are, why we do not recommend them on Anunna, what to use instead, and — if you have no alternative — how to use conda here with the least trouble. == Introduction == === What i...")
• 11:52, 12 August 2026 Honfi001 talk contribs created page Python/Modules (Created page with "= Modules = Anunna provides one Python version per module bucket, plus bundle modules that carry a curated set of common extensions. Load a bucket, then the Python module: * '''2023''': <code>Python/3.11.3</code> * '''2024''': <code>Python/3.12.3</code> * '''2024''': <code>Python/3.13.1</code> <syntaxhighlight lang="bash"> module load 2024 module load Python/3.12.3 </syntaxhighlight> The bundle module <code>Python-bundle-PyPI</code> adds ma...")
• 14:40, 5 August 2026 Honfi001 talk contribs created page IntelMPI (Created page with "'''Intel MPI''' is the other MPI implementation available on Anunna, alongside OpenMPI. It arrives as part of the Intel toolchain, together with the Intel compilers and the Intel Math Kernel Library (MKL). Everything general about MPI — that it runs one program as many cooperating processes, that it has to be built into the program, and when it is the right tool at all — is covered on Multi-Process Workflows. This page is the Intel-sp...")
• 13:43, 5 August 2026 Honfi001 talk contribs created page OpenMPI (Created page with "'''OpenMPI''' is the MPI library Anunna is built around. MPI — the Message Passing Interface — is how a single program runs as many cooperating processes at once, each with its own private memory, passing messages between themselves as the calculation proceeds. It is what lets one job use more than one node. This page is the practical side: which OpenMPI modules exist here, how to launch a job on one node and across several, and how to choose the network transport,...")
• 09:54, 5 August 2026 Honfi001 talk contribs created page Workflows/Multi-Process (Created page with "Multi-threaded work gave one process many arms, and then ran into a wall: threads share memory, and shared memory stops at the edge of the machine. This page is how a single calculation gets past that wall — not by growing one process, but by running '''many separate processes''', each with its own private memory, that send messages to each other as the calculation proceeds. The standard way to do that is '''MPI''', the Message Passing Inte...")
• 07:31, 5 August 2026 Honfi001 talk contribs created page Workflows/Embarassinly-Parallel (Created page with "This tutorial is a gentle, hands-on introduction to '''parallel computing on Anunna'''. Instead of a heavy scientific code, it uses one friendly problem — estimating the number π by throwing random darts — and runs the ''same'' calculation across every kind of parallelism the cluster offers: a single core, many threads, many processes, multiple nodes, and a GPU. Because the problem stays the same, you can see exactly what each step up the ladder buys you. You do no...")
• 19:15, 28 July 2026 Honfi001 talk contribs created page Workflows/Multi-threaded (Created page with "Serial ran one program on one core. This page takes that same job and lets the program spread its work across '''many''' cores on the '''same''' machine — still one process, but now with several ''threads'' inside it, all sharing the same memory. It is the gentlest real step up the ladder, because for most tools someone else already did the hard part: the program already knows how to use extra cores. Your job is only to give it some, and...")
• 10:36, 27 July 2026 Honfi001 talk contribs moved page Workflows/Serial-Workflows to Workflows/Serial without leaving a redirect
• 10:35, 27 July 2026 Honfi001 talk contribs created page Workflows/Serial-Workflows (Created page with "Every other page in this section describes a way of splitting work across many cores. This one describes ''not'' doing that — one program, running on a single core, from start to finish. It is the baseline, and, to be honest up front, it is not a parallel workflow at all. It earns a page anyway, for two reasons. Most software you did not ''specifically'' choose for its parallelism runs this way, so this is where many jobs on Anunna may actually belong. And every othe...")
• 15:22, 23 July 2026 Honfi001 talk contribs moved page Workflows/Paralle-Computing to Workflows/Parallel-Computing without leaving a redirect
• 15:18, 23 July 2026 Honfi001 talk contribs created page Workflows/Paralle-Computing (Created page with "Your analysis runs. It just runs for too long, or it no longer fits on one machine. '''Parallel computing''' is the answer to both, and this page is the map: what it actually means on Anunna, and which of the six workflow types below is yours. Each section is a short paragraph and a link. Read them, recognise your own problem in one of them, and follow it. If you would rather learn by doing, the π estimation tutorial walks the sa...")
• 11:48, 23 July 2026 Honfi001 talk contribs deleted page Conda for teaching (content was: "{{Warning|This page describes the older cluster setup: the <code>/cm/shared/...</code> paths and the tcl modulefiles below are from the previous (Bright) cluster and do '''not''' match current Anunna, which uses the Lustre filesystem and EasyBuild buckets. The general approach — a shared conda environment registered as a Jupyter kernel — still applies, but the paths and commands need updating. For the current way to set up course kernels, see Steps for courses and Pyt...")
• 09:15, 24 June 2026 Honfi001 talk contribs created page File:Pi-tutorial-speedup-vs-cores.png (Speedup against the serial baseline. The dashed line is perfect (linear) speedup; real runs sit just below it.)
• 09:15, 24 June 2026 Honfi001 talk contribs uploaded File:Pi-tutorial-speedup-vs-cores.png (Speedup against the serial baseline. The dashed line is perfect (linear) speedup; real runs sit just below it.)
• 09:14, 24 June 2026 Honfi001 talk contribs created page File:Pi-tutorial-walltime-vs-cores.png (Wall time falls as cores are added. Note both axes are logarithmic; a straight line here means near-ideal scaling.)
• 09:14, 24 June 2026 Honfi001 talk contribs uploaded File:Pi-tutorial-walltime-vs-cores.png (Wall time falls as cores are added. Note both axes are logarithmic; a straight line here means near-ideal scaling.)
• 08:59, 24 June 2026 Honfi001 talk contribs created page File:Pi-tutorial-best-per-approach.png (Plot of comparing the performance of different parallelization strategies for the MonteCarlo Pi Tutorial)
• 08:59, 24 June 2026 Honfi001 talk contribs uploaded File:Pi-tutorial-best-per-approach.png (Plot of comparing the performance of different parallelization strategies for the MonteCarlo Pi Tutorial)
• 08:40, 24 June 2026 Honfi001 talk contribs created page Tutorials/Parallelism-Estimating-Pi (Created page with "This tutorial is a gentle, hands-on introduction to '''parallel computing on Anunna'''. Instead of a heavy scientific code, it uses one friendly problem — estimating the number π by throwing random darts — and runs the ''same'' calculation across every kind of parallelism the cluster offers: a single core, many threads, many processes, multiple nodes, and a GPU. Because the problem stays the same, you can see exactly what each step up the ladder buys you. You do no...")
• 13:48, 16 June 2026 Honfi001 talk contribs created page HPC Advanced/Preparation Exercise (Created page with "= HPC Basics Refresher — Weather Data Analyser = {{Note|'''Who is this for?''' This is a self-paced preparation exercise for people who are attending the '''HPC Advanced''' course but did '''not''' attend '''HPC Basics'''. Working through it end to end means you arrive at the advanced course already comfortable with environment variables, virtual environments, launcher scripts, interactive jobs, and SLURM batch submission on '''Anunna'''.}} '''The application:''' a s...")
• 09:17, 11 June 2026 Honfi001 talk contribs created page Linux Basic/Linux Self Assessment (Created page with "= Linux Basics — Self-Assessment = This page lets you verify that you have mastered the material from the Linux Basics Course. Work through the parts in order on '''Anunna'''. The final challenge produces a report file that proves you completed every step — submit (or keep) that file as evidence. '''Prerequisites:''' an Anunna account and the course data at <code>/lustre/shared/hpcCourses/shell-lesson-data.zip</code>. '''Rules:''' * Do everything from the comm...")
• 09:42, 25 March 2026 Honfi001 talk contribs created page Tutorials/Apptainer-GPUs (Created page with "= Running Apptainer with GPUs = Apptainer can pass through GPU hardware from the host into a container, allowing you to run GPU-accelerated workloads (such as deep learning inference or training) inside a fully contained environment. This page covers how to use both NVIDIA and AMD GPUs on the Anunna cluster. '''Important:''' Before you begin, make sure the following are in place: * Your <code>.sif</code> image files should be stored on '''Lustre''' (e.g. in your scrat...")
• 09:18, 25 March 2026 Honfi001 talk contribs created page Tutorials/Apptainer-Introduction (Created page with "= Introduction to Apptainer = == What is Apptainer? == Apptainer (formerly known as Singularity) is a container platform designed for High Performance Computing (HPC) environments. If you have heard of Docker, Apptainer solves a similar problem — it lets you package an application together with all of its dependencies (libraries, tools, configuration) into a single portable unit called a '''container'''. The key difference is that Apptainer was built from the ground...")
• 12:32, 12 March 2026 Honfi001 talk contribs created page Tutorials/Apptainer-DefinitionFiles (Created page with "= Apptainer Definition Files: Building Containers from a Recipe = '''Important:''' Before you begin, make sure the following are in place: * You are running on a '''compute node''', not a login node. Request an interactive session first (e.g. via <code>srun</code> or your scheduler). * Your <code>.sif</code> image files should be stored on '''Lustre''' (e.g. in your scratch space), not in your home directory. SIF files can be large and will eat through your home quota...")
• 12:22, 12 March 2026 Honfi001 talk contribs created page Tutorials/Apptainer-FakerootAndSandbox (Created page with "= Apptainer Sandbox: Modifying Containers Interactively = '''Important:''' Before you begin, make sure the following are in place: * You are running on a '''compute node''', not a login node. Request an interactive session first (e.g. via <code>srun</code> or your scheduler). * Your <code>.sif</code> image files should be stored on '''Lustre''' (e.g. in your scratch space), not in your home directory. SIF files can be large and will eat through your home quota fast. *...")
• 09:59, 12 March 2026 Honfi001 talk contribs created page Tutorials/Apptainer-FakerootAndOverlays (Created page with "= Apptainer Overlays: Modifying Container Images = '''Important:''' Before you begin, make sure the following are in place: * You are running on a '''compute node''', not a login node. Request an interactive session first (e.g. via <code>srun</code> or your scheduler). * Your <code>.sif</code> image files should be stored on '''Lustre''' (e.g. in your scratch space), not in your home directory. SIF files can be large and will eat through your home quota fast. * Set you...")
• 09:09, 12 March 2026 Honfi001 talk contribs created page Tutorials/Apptainer-PullingImages (Add message about storing image in lustre) Tag: Visual edit
• 13:55, 11 March 2026 Honfi001 talk contribs created page Main Page/Tutorials/Apptainer (Created page with "This page contains a list of tutorials related to the usage of apptainer in Anunna.")
• 13:55, 11 March 2026 Honfi001 talk contribs created page Main Page/Tutorials (Created page with " =Tutorials= This page contains an index of various tutorials specific to the Anunna supercomputer.")
• 18:01, 25 February 2026 Honfi001 talk contribs created page File:Jupyter-form-20260225.png
• 18:01, 25 February 2026 Honfi001 talk contribs uploaded File:Jupyter-form-20260225.png
• 14:23, 25 February 2026 Honfi001 talk contribs created page Anunna Shell Access (Created page with "Anunna Shell Access is a web based bash shell terminal emulator available at the Anunna apps portal. This application provides quick access to a bash session in one of the login nodes. User's are able to select a theme for their terminal session on the top right corner of the screen. When a session times out, just refresh your browser tab and it should reconnect. Since this runs in a browser, users should mind that some keyboard shortcuts may not work properly, e...") Tag: Visual edit
• 12:15, 25 February 2026 Honfi001 talk contribs created page File:RStudio-connect-20260225.png
• 12:15, 25 February 2026 Honfi001 talk contribs uploaded File:RStudio-connect-20260225.png
• 11:59, 25 February 2026 Honfi001 talk contribs created page File:RStudio-form-20260225.png
• 11:59, 25 February 2026 Honfi001 talk contribs uploaded File:RStudio-form-20260225.png
• 11:42, 25 February 2026 Honfi001 talk contribs created page File:OOD20260225.png
• 11:42, 25 February 2026 Honfi001 talk contribs uploaded File:OOD20260225.png
• 09:50, 25 February 2026 Honfi001 talk contribs created page File:WUR Linux Basics Course 2026 Feb.pdf (Latest Linux Basics slides from the Feb/26 session)
• 09:50, 25 February 2026 Honfi001 talk contribs uploaded File:WUR Linux Basics Course 2026 Feb.pdf (Latest Linux Basics slides from the Feb/26 session)
• 09:40, 25 February 2026 Honfi001 talk contribs created page File:WUR Linux Basics Course.pdf
• 09:40, 25 February 2026 Honfi001 talk contribs uploaded File:WUR Linux Basics Course.pdf
• 17:13, 20 November 2025 Honfi001 talk contribs created page Tutorials (Tutorials Page) Tag: Visual edit
• 11:23, 3 July 2025 Honfi001 talk contribs created page Template:Tip (Created page with "<div style="border: 2px solid #1c873b; background-color: #e8f8ee; padding: 10px 15px; border-radius: 6px; margin: 1em 0;"> <strong>💡 Tip:</strong> {{{1}}} </div>")
• 11:22, 3 July 2025 Honfi001 talk contribs created page Template:Note (Created page with "<div style="border: 2px solid #4e7cc7; background-color: #eef4fa; padding: 10px 15px; border-radius: 6px; margin: 1em 0;"> <strong>ℹ️ Note:</strong> {{{1}}} </div>")