All public logs

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

• 14:08, 6 December 2023 User account Tberlok talk contribs was created by Haugboel talk contribs and password was sent by email
• 09:39, 29 November 2023 User account Christian talk contribs was created by Haugboel talk contribs and password was sent by email
• 07:27, 29 November 2023 User account Michael talk contribs was created by Haugboel talk contribs and password was sent by email
• 14:39, 15 November 2023 Philip talk contribs created page Running batch jobs (Created page with "<h1> Submit Jobs Via The SLURM Queueing System </h1> This is the preferred method of submitting batch jobs to the cluster queueing system and to run jobs interactively. <h2> Most Important Queue Commands: </h2> Here we list the most commonly used queueing commands. If you are migrating from a different scheduling system, this cheat sheet may be useful for you. There also exists a compact two-page overview of the most important commands. <h3> Use The <code>'Sinfo'</code...")
• 14:27, 15 November 2023 David.oneill talk contribs created page FAQs (Created page with "* How do I access the HPC Cluster? Enter the following in the command terminal SSH username@astroXX.hpc.ku.dk You can remotely access the frontend machines astro06-09 via SSH to submit jobs or to analyze data. It may be a good idea to check the load factor after logging in, using "top", and choose a different frontend if the CPU or memory use is already high (use "<" or ">" in top to temporarily change from sorting on CPU to memory / virtiual memory). Login You can lo...")
• 14:24, 15 November 2023 David.oneill talk contribs created page MPI Libraries (Created page with "Normally, the choice of MPI-libraries does not need to be made explicitly, but is instead chosen by selecting a specific mpi module (see "Software->Modules"). Notice that the MPI module has to match the compiler. The default setup is to use the Intel compiler suite together with the Intel MPI library. With the default setup, the program is automatically linking against the SLURM process manager, and it is easy to get optimal performance when running batch jobs (see "Ru...")
• 14:18, 15 November 2023 Philip talk contribs created page Examples of SLURM scripts (Created page with "Here is examples of simple SLURM scripts for running serial, OpenMP and MPI jobs. Note that a very nice introduction to running SLURM scripts exist at https://hpc.ku.dk/documentation/slurm.html. <h2> Simple Batch Script For Running Serial Programs </h2> Submission scripts are really just shell scripts (here we use bash syntax) with a few additional variable specifications at the beginning. These are prefixed with "#SBATCH" and otherwise use the same keywords and syn...")
• 14:14, 15 November 2023 Haugboel talk contribs created page Acknowledging the use of Tycho in articles and presentations (Created page with "Tycho is a group effort and we rely entirely on external funding to maintain the hardware. Users are strongly encouraged to acknowledge Tycho in all publications that describe results obtained using Tycho resources. Users shall use the following wording in such acknowledgement in all papers and other publications. Having a standard formulation helps when assessing the impact of Tycho in e.g. future grant applications, and benefit all of us. ====Acknowledging Tycho in a...")
• 14:10, 15 November 2023 Jredondo talk contribs created page Module system (Created page with "Tycho makes use of the Module system to manage dependencies and load common compilers and software. Environment modules modify the users environment via modulefiles. They are typically used to manage different versions of applications, by e.g. modifying the PATH system variable, using one module file per application version. To ensure consistency, we recommend that you put relevant module commands in a file (e.g. ~/.modules), and source it from relevant startup files...")
• 13:56, 15 November 2023 Jredondo talk contribs created page Adding a second IP Address (Created page with "Once you are logged in to the front-end, write: <pre> hpc-setup-firewall.sh </pre> There, you can add up to 3 total IP addresses. One useful tip is to add the ERDA IP address, so that you can always log in to the cluster even if you are travelling.")
• 13:49, 15 November 2023 Jredondo talk contribs created page Setting up One-Time-Password Access before travelling (Created page with "If you are going to travel, but want to continue working on Tycho while you are travelling, you need to set up a One Time Password access '''before''' travelling. You can do so by following the detailed instructions [https://hpc.ku.dk/documentation/otp.html: here]")
• 13:42, 15 November 2023 Jredondo talk contribs created page GRChombo (Created page with "[GRChombo](https://www.grchombo.org/) is an open-source, AMR-based code for Numerical Relativity. Here are some instructions on how to set up GRChombo in Tycho. === Step 1. Compile Chombo === Go to [Chombo](https://github.com/GRTLCollaboration/Chombo) and clone the repository in the cluster: <pre> >>git clone https://github.com/GRTLCollaboration/Chombo.git </pre> Then we need to make a new file that will set up the compilation details, specifically tweaked for our cl...")
• 13:38, 15 November 2023 Jredondo talk contribs created page Running Mathematica on compute nodes (Created page with "Here are some instructions on how to run Mathematica on the cluster. === Step 1. === Load the mathematica module: <pre> >>module load astro >>module load mathematica </pre> === Step 2. === Prepare our test script. You can make mathematica scripts in different ways, but .wls files are good option. Here is an example script, you can make it into a file called <code>test.wls</code>: <pre> #!/usr/bin/env wolframscript outdir = "Data/"; fn1 = outdir<>"test.dat"; values...")
• 13:38, 15 November 2023 David.oneill talk contribs created page Erda (Created page with "## ERDA Is A File System Provided By The University Of Copenhagen. It can be accessed through your webbrowser at http://erda.ku.dk/. It is very easy to create an account using your KU credentials (Swedish number plate). The full documentation for ERDA is currently located here.")
• 13:31, 15 November 2023 User account Philip talk contribs was created by Haugboel talk contribs and password was sent by email
• 13:30, 15 November 2023 User account David.oneill talk contribs was created by Haugboel talk contribs and password was sent by email
• 13:18, 15 November 2023 Ricolo talk contribs created page Visual Studio Remote Development (Created page with "[https://github.com/Microsoft/vscode-remote-release#readme Remote development ] is a set of extensions for Visual Studio Code that allows you to interact with a remote server on VSCode as if it is running on your local computer. == Installing the Remote Development extension pack == == Configuring Visual Studio Code == == Installing even more extensions for extra features == === for python === === for julia === === for jupyter notebook ===")
• 13:10, 15 November 2023 User account Gaia.Fabj talk contribs was created by Haugboel talk contribs and password was sent by email
• 12:52, 15 November 2023 Haugboel talk contribs created page Mattermost discussion forum (Created page with "We have a dedicated user forum for the cluster where you can contact other users, and get more instantaneous community feedback. This is also a good place to discuss usage or installation of scientific software. To get an account, please sign up here: [https://mattermost.nbi.ku.dk/signup_user_complete/?id=d5nueent1tbb7knj6esiw7hp9h] Signup is restricted based on the e-mail account you submit, so please use your work e-mail. If you are an external user of Tycho (e.g. n...")
• 12:49, 15 November 2023 Ricolo talk contribs created page Using GPUs (Created page with "Here is a detailed guide on how to leverage the GPUs on the NBI cluster. == Preparation work: making sure that your software is GPU-aware == Before proceeding, it is recommended to have your local installation of (ana-/mini-)conda with newer python version (preferably 3.10+). === Installing CUDA === Normally, you would/should use the system-wide CUDA installation to make sure that it is compatible with the GPUs. In fact, there are environment modules for CUDA (e.g....")
• 12:47, 15 November 2023 Haugboel talk contribs created page Getting Help (Created page with "* Account renewal: If you need to renew your account, you should first get the renewal approved by your sponsor (e.g. your supervisor, mentor etc), and then forward that confirmation to your group representative, Troels Haugbølle ([haugboel@nbi.ku.dk]), who will sign-off on the renewal and ask the admins to renew your account. * Contact support: Tycho is a cluster installed at the HPC center at the faculty of SCIENCE. The administrators can be contacted by e-mail: [supp...")
• 12:46, 15 November 2023 Haugboel talk contribs created page First steps (Created page with "===Getting help=== * ''Account renewal'': If you need to renew your account, you should first get the renewal approved by your sponsor (e.g. your supervisor, mentor etc), and then forward that confirmation to your group representative, Troels Haugbølle ([haugboel@nbi.ku.dk]), who will sign-off on the renewal and ask the admins to renew your account. * ''Contact support'': Tycho is a cluster installed at the HPC center at the faculty of SCIENCE. The administrators can...")
• 12:33, 15 November 2023 Jredondo talk contribs created page Accessing Tycho (Created page with "After getting an account (following the instructions [https://hpc.ku.dk/account.html](here)), you can now log into Tycho using [https://en.wikipedia.org/wiki/Secure_Shell](ssh). == SSH into the frontends == Open your terminal, and type: <pre> >>ssh username@astro06.hpc.ku.dk </pre> In "username", replace it with your username. You will be prompted to type your password. Do so, press enter, and then you will be in the frontend. You should see something like this: <p...")
• 12:32, 15 November 2023 User account Ricolo talk contribs was created by Haugboel talk contribs and password was sent by email
• 12:30, 15 November 2023 Liz talk contribs created page Using Jupyter notebooks on the frontends (Created page with "Remote data analysis, compilations, and short test runs is possible by using Jupyter notebooks. To configure a Jupyter server do (after loading the python module):")
• 12:27, 15 November 2023 Haugboel talk contribs created page Compilers (Created page with "We recommend using the Intel ifort, icc, and icpc (fortran, C, C++) compilers for production, because of their superior speed optimization. Compiling for MPI is done with mpiifort, mpiicc, mpiicpc (note the double ii), which are wrapper scripts around the compilers that link in the correct MPI libraries. However, using gfortran for development and testing can be a very good idea, especially if / when problems arise, and are difficult to locate. Compiling the same cod...")
• 12:16, 15 November 2023 User account Jredondo talk contribs was created by Haugboel talk contribs and password was sent by email
• 12:08, 15 November 2023 User account Liz talk contribs was created by Haugboel talk contribs and password was sent by email
• 12:24, 14 November 2023 Haugboel talk contribs created page Hardware (Created page with "Tycho contains both frontends that are accessible from the outside and which can be used for interactive work, such as development and analysis, and compute nodes that are only accessible through the SLURM queue systems. {| class="wikitable" style="margin:auto" |+ Analysis Hardware |- ! Name !! CPUs !! RAM !! GPUs !! Scratch !! Notes |- | astro01.hpc.ku.dk || 2 x 24 cores Epyc Rome 7F72 @ 3.2 GHz || 1 TB DDR4-3200 MHz - 21 GB / core || 4x A100 || 11 TB || L2: 512 KB /...")
• 07:49, 14 November 2023 Haugboel talk contribs moved page Main Page to Tycho Technical Documentation
• 07:47, 14 November 2023 Haugboel talk contribs created page MediaWiki:Mainpage-title (Created page with "Tycho Technical Documentation")
• 14:20, 20 October 2023 Waananen talk contribs changed group membership for Haugboel from (none) to administrator and bureaucrat
• 14:16, 20 October 2023 User account Haugboel talk contribs was created by Waananen talk contribs and password was sent by email
• 13:41, 20 October 2023 MediaWiki default talk contribs created page Main Page