CINXE.COM

<!DOCTYPE html> <html class="writer-html5" lang="en"> <head> <meta charset="utf-8" /> <meta property="article:modified_time" content="2024-04-18T10:09:20+02:00" /> <meta name="viewport" content="width=device-width, initial-scale=1.0" /> <title>No.215, April 2024 — Technical Documentation</title> <link rel="stylesheet" type="text/css" href="../_static/pygments.css" /> <link rel="stylesheet" type="text/css" href="../_static/css/theme.css" /> <link rel="stylesheet" type="text/css" href="../_static/copybutton.css" /> <link rel="stylesheet" type="text/css" href="../_static/custom.css" /> <link rel="shortcut icon" href="../_static/favicon.ico"/>  <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script> <script src="../_static/jquery.js"></script> <script src="../_static/underscore.js"></script> <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script> <script src="../_static/doctools.js"></script> <script src="../_static/sphinx_highlight.js"></script> <script src="../_static/clipboard.min.js"></script> <script src="../_static/copybutton.js"></script> <script src="../_static/js/theme.js"></script> <link rel="index" title="Index" href="../genindex.html" /> <link rel="search" title="Search" href="../search.html" /> <link rel="next" title="No.214, December 2023" href="214.html" /> <link rel="prev" title="No.216, August 2024" href="216.html" /> </head> <body class="wy-body-for-nav"> <div class="wy-grid-for-nav"> <nav data-toggle="wy-nav-shift" class="wy-nav-side"> <div class="wy-side-scroll"> <div class="wy-side-nav-search" style="background: #EEEEEE" > <a href="https://www.mpcdf.mpg.de"> <img src="../_static/mpcdflogo.png" class="logo" alt="Logo"/> </a> <div role="search"> <form id="rtd-search-form" class="wy-form" action="../search.html" method="get"> <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" /> <input type="hidden" name="check_keywords" value="yes" /> <input type="hidden" name="area" value="default" /> </form> </div> </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu"> <ul> <li class="toctree-l1"><a class="reference internal" href="../faq/index.html">Frequently Asked Questions</a><ul> <li class="toctree-l2"><a class="reference internal" href="../faq/account.html">Account registration</a></li> <li class="toctree-l2"><a class="reference internal" href="../faq/connecting.html">Connecting</a><ul> <li class="toctree-l3"><a class="reference internal" href="../faq/connecting.html#how-can-i-log-into-the-machines-at-the-mpcdf">How can I log into the machines at the MPCDF?</a><ul> <li class="toctree-l4"><a class="reference internal" href="../faq/connecting.html#what-are-the-gateway-machines-for-ssh-login">What are the gateway machines for SSH login?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/connecting.html#two-factor-authentication-2fa">Two-factor authentication (2FA)</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/connecting.html#are-ssh-keys-supported">Are SSH keys supported?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/connecting.html#can-ssh-scp-sftp-performance-be-improved">Can ssh/scp/sftp performance be improved?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/connecting.html#i-get-a-ssh-security-warning-about-a-host-key-change-when-trying-to-log-in-what-does-this-mean-and-what-should-i-do">I get a SSH security warning about a host key change when trying to log in. What does this mean and what should I do?</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="../faq/connecting.html#how-can-i-run-applications-with-graphical-user-interfaces-on-mpcdf-systems">How can I run applications with graphical user interfaces on MPCDF systems?</a><ul> <li class="toctree-l4"><a class="reference internal" href="../faq/connecting.html#x11-forwarding">X11 forwarding</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/connecting.html#vnc">VNC</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/connecting.html#remote-visualization-service">Remote Visualization Service</a></li> </ul> </li> </ul> </li> <li class="toctree-l2"><a class="reference internal" href="../faq/2fa.html">Two-factor authentication (2FA)</a><ul> <li class="toctree-l3"><a class="reference internal" href="../faq/2fa.html#general-information-about-2fa">General information about 2FA</a><ul> <li class="toctree-l4"><a class="reference internal" href="../faq/2fa.html#do-i-need-to-enable-2fa">Do I need to enable 2FA?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/2fa.html#do-i-already-have-2fa-activated">Do I already have 2FA activated?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/2fa.html#why-is-2fa-enforced">Why is 2FA enforced?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/2fa.html#what-is-a-token-otp-and-seed">What is a token, OTP, and seed?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/2fa.html#what-kinds-of-tokens-are-there">What kinds of tokens are there?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/2fa.html#why-am-i-asked-for-an-otp">Why am I asked for an OTP?</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="../faq/2fa.html#activation-of-2fa">Activation of 2FA</a><ul> <li class="toctree-l4"><a class="reference internal" href="../faq/2fa.html#how-do-i-enable-2fa">How do I enable 2FA?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/2fa.html#how-do-i-enroll-and-use-an-app-token">How do I enroll and use an app token?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/2fa.html#what-app-do-i-need-to-install">What app do I need to install?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/2fa.html#how-do-i-register-my-existing-token">How do I register my existing token?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/2fa.html#how-do-i-enroll-and-use-a-secondary-backup-token">How do I enroll and use a secondary/backup token?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/2fa.html#why-can-t-i-have-both-an-app-token-and-a-hardware-token">Why can’t I have both an app token and a hardware token?</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="../faq/2fa.html#fa-tips-and-tricks">2FA Tips and Tricks</a><ul> <li class="toctree-l4"><a class="reference internal" href="../faq/2fa.html#do-i-have-to-type-in-an-otp-every-time-i-access-the-secured-systems">Do I have to type in an OTP every time I access the secured systems?</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="../faq/2fa.html#fa-troubleshooting">2FA Troubleshooting</a><ul> <li class="toctree-l4"><a class="reference internal" href="../faq/2fa.html#i-need-to-factory-reset-my-phone-how-can-i-preserve-my-app-token">I need to factory-reset my phone. How can I preserve my app token?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/2fa.html#how-do-i-transfer-my-token-to-a-new-phone">How do I transfer my token to a new phone?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/2fa.html#i-can-t-validate-activate-the-token-i-just-scanned-wrong-otp">I can’t validate/activate the token I just scanned (“Wrong OTP”)</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/2fa.html#i-can-t-log-in-to-the-selfservice-anymore">I can’t log in to the SelfService anymore</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/2fa.html#i-can-t-log-in-to-a-gate-machine-via-ssh">I can’t log in to a gate machine via SSH</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/2fa.html#i-can-t-access-the-hpc-clusters-through-vnc-anymore">I can’t access the HPC clusters through VNC anymore</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="../faq/2fa.html#hardware-and-client-support">Hardware and client support</a><ul> <li class="toctree-l4"><a class="reference internal" href="../faq/2fa.html#how-can-i-use-my-sshfs-rsync-scp-sftp-gui-with-2fa">How can I use my sshfs/rsync/scp/sftp GUI with 2FA?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/2fa.html#how-can-i-use-filezilla-with-2fa">How can I use FileZilla with 2FA?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/2fa.html#how-to-use-2fa-on-a-phone-with-a-time-shift">How to use 2FA on a phone with a time shift?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/2fa.html#do-you-or-are-you-planning-to-support-fido2-u2f-yubikeys">Do you or are you planning to support FIDO2/U2F/YubiKeys?</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="../faq/2fa.html#on-security">On security</a><ul> <li class="toctree-l4"><a class="reference internal" href="../faq/2fa.html#if-the-seed-is-stored-on-the-server-how-secure-is-it">If the seed is stored on the server, how secure is it?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/2fa.html#where-do-the-hardware-tokens-come-from-does-the-vendor-know-the-seeds">Where do the hardware tokens come from? Does the vendor know the seeds?</a></li> </ul> </li> </ul> </li> <li class="toctree-l2"><a class="reference internal" href="../faq/hpc_software.html">HPC Software and Applications</a><ul> <li class="toctree-l3"><a class="reference internal" href="../faq/hpc_software.html#general-questions">General questions</a><ul> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_software.html#how-and-where-can-i-install-software-myself">How and where can I install software myself?</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="../faq/hpc_software.html#environment-modules">Environment modules</a><ul> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_software.html#how-can-i-use-environment-modules-interactively">How can I use environment modules interactively?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_software.html#how-can-i-use-environment-modules-in-scripts">How can I use environment modules in scripts?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_software.html#how-can-i-use-environment-modules-to-avoid-absolute-paths-in-my-scripts">How can I use environment modules to avoid absolute paths in my scripts?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_software.html#examples">Examples</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_software.html#how-do-the-hierarchical-environment-modules-work">How do the hierarchical environment modules work?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_software.html#how-do-i-quickly-find-a-module">How do I quickly find a module?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_software.html#how-can-i-disable-the-mpcdf-specific-note-for-module-avail">How can I disable the “MPCDF specific note” for <code class="docutils literal notranslate"><span class="pre">module</span> <span class="pre">avail</span></code>?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_software.html#why-there-are-no-blas-lapack-modules-available-on-the-clusters">Why there are no BLAS/LAPACK modules available on the clusters?</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="../faq/hpc_software.html#compiled-languages">Compiled Languages</a><ul> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_software.html#cmake">CMake</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_software.html#c-c-and-fortran">C/C++ and Fortran</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_software.html#debugging-of-c-c-and-fortran-codes">Debugging of C/C++ and Fortran codes</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="../faq/hpc_software.html#interpreted-languages">Interpreted Languages</a><ul> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_software.html#python">Python</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_software.html#r">R</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_software.html#julia">Julia</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_software.html#jupyter-notebooks">Jupyter Notebooks</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_software.html#matlab">MATLAB</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="../faq/hpc_software.html#message-passing-interface-mpi-libraries-and-runtimes">Message Passing Interface (MPI) Libraries and Runtimes</a><ul> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_software.html#which-mpi-implementations-are-supported">Which MPI implementations are supported?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_software.html#how-can-i-compile-and-link-my-mpi-application">How can I compile and link my MPI application?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_software.html#cmake-cannot-find-mpi-what-can-i-do">CMake cannot find MPI, what can I do?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_software.html#i-cannot-launch-my-mpi-code-using-mpirun-what-am-i-doing-wrong">I cannot launch my MPI code using <code class="docutils literal notranslate"><span class="pre">mpirun</span></code>, what am I doing wrong?</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="../faq/hpc_software.html#visualization">Visualization</a><ul> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_software.html#how-can-i-combine-many-image-files-jpg-png-into-a-movie-mp4">How can I combine many image files (JPG, PNG) into a movie (MP4)?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_software.html#how-can-i-install-additional-packages-for-tex-latex-locally">How can I install additional packages for TeX/LaTeX locally?</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="../faq/hpc_software.html#gui-applications">GUI applications</a><ul> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_software.html#visual-studio-code-in-combination-with-the-remote-ssh-extension-does-not-work-any-more-on-certain-hpc-clusters">Visual Studio Code (in combination with the Remote-SSH extension) does not work any more on certain HPC clusters</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_software.html#why-do-certain-gui-applications-not-work-any-more-on-the-login-nodes-of-hpc-clusters-what-are-the-alternatives">Why do certain GUI applications not work (any more) on the login nodes of HPC clusters? What are the alternatives?</a></li> </ul> </li> </ul> </li> <li class="toctree-l2"><a class="reference internal" href="../faq/hpc_systems.html">HPC Systems and Services</a><ul> <li class="toctree-l3"><a class="reference internal" href="../faq/hpc_systems.html#raven">Raven</a><ul> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_systems.html#what-are-the-recommended-compiler-optimization-flags-for-raven">What are the recommended compiler optimization flags for Raven?</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="../faq/hpc_systems.html#slurm-batch-system">Slurm batch system</a><ul> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_systems.html#how-do-i-submit-jobs-to-the-slurm-batch-system">How do I submit jobs to the Slurm batch system?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_systems.html#can-i-submit-jobs-longer-than-24-hours-why-are-job-run-times-limited-to-24-hours">Can I submit jobs longer than 24 hours? Why are job run times limited to 24 hours?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_systems.html#how-do-i-launch-an-mpi-code">How do I launch an MPI code?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_systems.html#what-is-the-correct-order-of-executable-commands-and-sbatch-directives-in-a-slurm-job-script">What is the correct order of executable commands and ‘#SBATCH’ directives in a Slurm job script?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_systems.html#can-i-work-interactively-for-debugging-and-development-work">Can I work interactively for debugging and development work?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_systems.html#how-can-i-query-the-estimated-start-time-of-my-job">How can I query the estimated start time of my job?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_systems.html#how-can-i-get-information-about-my-job-at-runtime">How can I get information about my job at runtime?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_systems.html#how-can-i-get-information-about-my-job-after-it-has-finished">How can I get information about my job after it has finished?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_systems.html#what-happens-when-a-running-job-is-hit-by-a-hardware-failure">What happens when a running job is hit by a hardware failure?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_systems.html#how-do-i-do-pinning-correctly">How do I do pinning correctly?</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="../faq/hpc_systems.html#parallel-file-systems-gpfs">Parallel File Systems (GPFS)</a><ul> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_systems.html#which-file-systems-are-available-and-how-should-i-use-them">Which file systems are available and how should I use them?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_systems.html#i-do-not-get-the-io-performance-i-would-expect-am-i-doing-something-wrong">I do not get the IO performance I would expect. Am I doing something wrong?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_systems.html#how-can-i-grant-other-users-access-to-my-files-how-do-i-use-acls">How can I grant other users access to my files? How do I use ACLs?</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="../faq/hpc_systems.html#how-can-i-transfer-files-to-and-from-the-hpc-systems">How can I transfer files to and from the HPC systems?</a></li> <li class="toctree-l3"><a class="reference internal" href="../faq/hpc_systems.html#performance-monitoring">Performance Monitoring</a><ul> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_systems.html#how-can-i-find-out-about-the-performance-of-my-runs">How can I find out about the performance of my runs?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_systems.html#how-can-i-stop-the-background-performance-monitoring">How can I stop the background performance monitoring?</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="../faq/hpc_systems.html#gpu-computing">GPU Computing</a><ul> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_systems.html#how-can-i-launch-the-nvidia-multi-process-service-mps">How can I launch the NVIDIA Multi-Process Service (MPS)?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_systems.html#how-can-i-profile-my-gpu-code">How can I profile my GPU code?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_systems.html#are-there-dedicated-gpu-resources-available-for-interactive-gpu-development">Are there dedicated GPU resources available for interactive GPU development?</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="../faq/hpc_systems.html#containers">Containers</a><ul> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_systems.html#which-container-solutions-are-supported-can-i-run-docker-containers">Which container solutions are supported? Can I run Docker containers?</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="../faq/hpc_systems.html#remote-visualization">Remote Visualization</a><ul> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_systems.html#how-can-i-run-visualization-tools-or-any-software-that-uses-opengl-on-mpcdf-systems">How can I run visualization tools or any software that uses OpenGL on MPCDF systems?</a></li> <li class="toctree-l4"><a class="reference internal" href="../faq/hpc_systems.html#how-can-i-get-access-to-mpcdf-remote-visualization-services">How can I get access to MPCDF remote visualization services?</a></li> </ul> </li> </ul> </li> <li class="toctree-l2"><a class="reference internal" href="../faq/tricks.html">Hints, Tips, and Tricks</a><ul> <li class="toctree-l3"><a class="reference internal" href="../faq/tricks.html#how-can-i-change-my-default-shell">How can I change my default shell?</a></li> <li class="toctree-l3"><a class="reference internal" href="../faq/tricks.html#how-can-i-launch-ssh-agent-in-a-terminal-session">How can I launch <code class="docutils literal notranslate"><span class="pre">ssh-agent</span></code> in a terminal session?</a></li> <li class="toctree-l3"><a class="reference internal" href="../faq/tricks.html#how-can-i-avoid-having-to-type-my-password-repeatedly-how-can-i-tunnel-through-the-gateway-machines">How can I avoid having to type my password repeatedly? How can I tunnel through the gateway machines?</a></li> <li class="toctree-l3"><a class="reference internal" href="../faq/tricks.html#how-can-i-access-the-clusters-using-a-windows-machine">How can I access the clusters using a Windows machine?</a></li> </ul> </li> <li class="toctree-l2"><a class="reference internal" href="../faq/help.html">Help, Support, and Training</a><ul> <li class="toctree-l3"><a class="reference internal" href="../faq/help.html#how-can-i-get-help-and-support">How can I get Help and Support?</a></li> <li class="toctree-l3"><a class="reference internal" href="../faq/help.html#are-you-offering-trainings-on-how-to-use-mpcdf-resources">Are you offering trainings on how to use MPCDF resources?</a></li> <li class="toctree-l3"><a class="reference internal" href="../faq/help.html#how-to-acknowledge-mpcdf">How to acknowledge MPCDF?</a></li> </ul> </li> </ul> </li> </ul> <ul> <li class="toctree-l1"><a class="reference internal" href="../doc/index.html">Documentation</a><ul> <li class="toctree-l2"><a class="reference internal" href="../doc/computing/index.html">Computing</a><ul> <li class="toctree-l3"><a class="reference internal" href="../doc/computing/overview.html">Introduction</a><ul> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/overview.html#overview">Overview</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/overview.html#compute-facilities">Compute Facilities</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="../doc/computing/application-support.html">Application Support for HPC, AI and HPDA</a></li> <li class="toctree-l3"><a class="reference internal" href="../doc/computing/gateways.html">Gateway machines</a><ul> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/gateways.html#login">Login</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/gateways.html#gssapi-based-logins-to-mpcdf-hosts">GSSAPI-based logins to MPCDF hosts</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/gateways.html#tunneled-access-to-mpcdf-services">Tunneled access to MPCDF services</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="../doc/computing/viper-user-guide.html">Viper User Guide</a><ul> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/viper-user-guide.html#system-overview">System overview</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/viper-user-guide.html#access">Access</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/viper-user-guide.html#hardware-configuration">Hardware configuration</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/viper-user-guide.html#file-systems">File systems</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/viper-user-guide.html#software">Software</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/viper-user-guide.html#slurm-batch-system">Slurm batch system</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/viper-user-guide.html#slurm-example-batch-scripts">Slurm example batch scripts</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/viper-user-guide.html#migration-guide-for-users-coming-from-intel-based-hpc-systems">Migration guide for users coming from Intel-based HPC systems</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="../doc/computing/raven-user-guide.html">Raven User Guide</a><ul> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/raven-user-guide.html#system-overview">System Overview</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/raven-user-guide.html#access">Access</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/raven-user-guide.html#hardware-configuration">Hardware configuration</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/raven-user-guide.html#file-systems">File systems</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/raven-user-guide.html#software">Software</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/raven-user-guide.html#slurm-batch-system">Slurm batch system</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/raven-user-guide.html#slurm-example-batch-scripts">Slurm example batch scripts</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="../doc/computing/clusters/index.html">Dedicated clusters</a><ul> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/clusters/systems/Astronomy.html">Astronomy</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/clusters/systems/Astrophysics.html">Astrophysics</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/clusters/systems/Biochemistry.html">Biochemistry</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/clusters/systems/Biological_Cybernetics.html">Biological Cybernetics</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/clusters/systems/Biological_Intelligence.html">Biological Intelligence</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/clusters/systems/Biophysics.html">Biophysics</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/clusters/systems/Brain_Research.html">Brain Research</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/clusters/systems/Chemical_Physics_Solids.html">Chemical Physics of Solids</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/clusters/systems/Extraterrestrial_Physics.html">Extraterrestrial Physics</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/clusters/systems/FHI_MPIE_MPIP_TALOS.html">FHI / MPIE / MPIP</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/clusters/systems/Gravitational_Physics.html">Gravitational Physics</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/clusters/systems/Gravitational_Physics_ACR.html">Gravitational Physics - ACR</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/clusters/systems/Gravitational_Physics_CRA.html">Gravitational Physics - CRA</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/clusters/systems/Iron_Research.html">Iron Research</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/clusters/systems/MPSD_PKS_ADA.html">MPSD / PKS</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/clusters/systems/Neurobiology_of_Behavior.html">Neurobiology of Behavior – caesar</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/clusters/systems/Physics.html">Physics</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/clusters/systems/Plasma_Physics.html">Plasma Physics</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/clusters/systems/Psychiatry.html">Psychiatry</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/clusters/systems/Quantum_Optics.html">Quantum Optics</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/clusters/systems/Radioastronomy.html">Radioastronomy</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/clusters/systems/Science_of_Light.html">Science of Light</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="../doc/computing/software/index.html">Software</a><ul> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/software/environment-modules.html">Environment Modules</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/software/hpc-application-packages.html">HPC Application Packages</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/software/compilers_languages.html">Compilers and languages</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/software/libraries.html">Libraries</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/software/debugging-tools.html">Debugging tools</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/software/performance-tools.html">Performance tools</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/software/mathematical-tools.html">Mathematical tools</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/software/bioinformatics.html">Bioinformatics</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/software/containers.html">Containers</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/software/data_analytics-machine_learning.html">Data Analytics / Machine Learning</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/software/vnc.html">VNC</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="../doc/computing/hpc-get-started.html">Quickstart guide to HPC</a><ul> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/hpc-get-started.html#software-environment-modules">Software environment (modules)</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/hpc-get-started.html#mpi-parallel-hpc-applications">MPI parallel HPC applications</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/hpc-get-started.html#multithreaded-openmp-or-hybrid-mpi-openmp-hpc-applications">Multithreaded (OpenMP) or hybrid (MPI/OpenMP) HPC applications</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/hpc-get-started.html#execution-of-parallel-programs-via-slurm">Execution of (parallel) programs via Slurm</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="../doc/computing/performance-monitoring.html">Performance Monitoring</a><ul> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/performance-monitoring.html#introduction">Introduction</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/performance-monitoring.html#pdf-performance-reports-for-users">PDF Performance Reports for Users</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/performance-monitoring.html#suspending-the-performance-monitoring-system-for-specific-jobs">Suspending the Performance Monitoring System for Specific Jobs</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/performance-monitoring.html#technical-background">Technical Background</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/performance-monitoring.html#overhead">Overhead</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/performance-monitoring.html#further-information">Further information</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="../doc/computing/training.html">Training</a><ul> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/training.html#courses-and-workshops-arranged-by-or-in-collaboration-with-the-mpcdf">Courses and workshops arranged by or in collaboration with the MPCDF</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/computing/training.html#training-programmes-of-other-institutions">Training programmes of other institutions</a></li> </ul> </li> </ul> </li> <li class="toctree-l2"><a class="reference internal" href="../doc/data/index.html">Data</a><ul> <li class="toctree-l3"><a class="reference internal" href="../doc/data/share/index.html">DataShare: Sync and Share Service</a><ul> <li class="toctree-l4"><a class="reference internal" href="../doc/data/share/datashare.html">DataShare: An Introduction</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/data/share/domainchange.html">Update the domain of the client</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/data/share/faq.html">FAQ</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/data/share/sync-share-clients.html">Desktop and Mobile clients</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="../doc/data/globusonline/index.html">Globus Online: Large-Scale data Transfer and Sharing</a><ul> <li class="toctree-l4"><a class="reference internal" href="../doc/data/globusonline/mpcdf-datahub-and-globus-online.html">MPCDF DataHub and Globus Online</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/data/globusonline/datahub-file-staging.html">Staging Files to HPC systems via Globus Online</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/data/globusonline/datahub-staging-flow.html">Staging data via Flows</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/data/globusonline/go-nexus.html">GO-Nexus</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/data/globusonline/globus-demo-videos.html">Globus Demo Videos - Demonstrating Globus Functionality for end users</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="../doc/data/object-storage/index.html">Nexus-S3: Object Storage for data Transfer and Sharing</a><ul> <li class="toctree-l4"><a class="reference internal" href="../doc/data/object-storage/nexus-s3.html">Nexus-S3</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/data/object-storage/publishing-data-via-s3.html">Publishing Data for public access via S3</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="../doc/data/data-transfer/index.html">Small to Medium Scale Data Transfers</a><ul> <li class="toctree-l4"><a class="reference internal" href="../doc/data/data-transfer/data-transfer.html">Data Transfer: Tools & Tips</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/data/data-transfer/mpcdf-datahub-and-globus-online.html">MPCDF DataHub and Globus Online</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/data/data-transfer/sharing-large-files-with-datashare.html">Sharing Large Files with DataShare</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="../doc/data/gitlab/index.html">GitLab: Software Development</a><ul> <li class="toctree-l4"><a class="reference internal" href="../doc/data/gitlab/gitlab.html">The MPCDF GitLab Instance: an introduction</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/data/gitlab/devop-tutorial.html">Poetry and GitLab: Devops for Python developers</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/data/gitlab/gitlabrunners.html">GitLab Runners for CI/CD</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="../doc/data/publication/index.html">Data Publication and Metadata Management</a><ul> <li class="toctree-l4"><a class="reference internal" href="../doc/data/publication/datapublishing.html">Service: Data Repositories</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/data/publication/mmd.html">The MPCDF Metadata Tools: User Documentation</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/data/publication/mmd-dev.html">The MPCDF Metadata Tools: Developer Documentation</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/data/publication/metastore-documentation.html">MetaStore User Documentation</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="../doc/data/backup-archive/index.html">Backup and Archive</a><ul> <li class="toctree-l4"><a class="reference internal" href="../doc/data/backup-archive/backup-archive-system.html">Backup & Archive Systems</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/data/backup-archive/archives.html">How to archive data</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/data/backup-archive/BA_HPC/index.html">Backup HPC</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/data/backup-archive/BA_Linux_clusters/index.html">Backup Linux Clusters</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/data/backup-archive/BA_AFS/index.html">Backup AFS</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/data/backup-archive/BA_desktops/index.html">Backup Desktops</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="../doc/data/store/index.html">Deprecated: The Andrew File System (AFS)</a><ul> <li class="toctree-l4"><a class="reference internal" href="../doc/data/store/introduction-to-afs.html">Store (AFS)</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/data/store/introduction/index.html">Introduction</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/data/store/specific-technical/index.html">Specific-Technical</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/data/store/glossary/index.html">Glossary</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/data/store/troubleshooting/index.html">Troubleshooting</a></li> </ul> </li> </ul> </li> <li class="toctree-l2"><a class="reference internal" href="../doc/cloud/index.html">HPC-Cloud</a><ul> <li class="toctree-l3"><a class="reference internal" href="../doc/cloud/technical/index.html">Technical and User Documentation</a><ul> <li class="toctree-l4"><a class="reference internal" href="../doc/cloud/technical/quickstart.html">Quick Start</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/cloud/technical/compute.html">Compute</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/cloud/technical/storage.html">Storage</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/cloud/technical/network.html">Network</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/cloud/technical/clients.html">Command Line Interface and Scripting</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/cloud/technical/recipes.html">Recipes</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="../doc/cloud/renting/index.html">Rental Model</a><ul> <li class="toctree-l4"><a class="reference internal" href="../doc/cloud/renting/index.html#introduction">Introduction</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/cloud/renting/index.html#cost-components">Cost components</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/cloud/renting/index.html#setup-procedure-and-billing-procedure">Setup procedure and billing procedure</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/cloud/renting/index.html#available-resources">Available Resources</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/cloud/renting/index.html#compute-resources">Compute resources</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/cloud/renting/index.html#storage-resources">Storage resources</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="../doc/cloud/terms_of_use/index.html">Terms of Use</a><ul> <li class="toctree-l4"><a class="reference internal" href="../doc/cloud/terms_of_use/index.html#general">General</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/cloud/terms_of_use/index.html#backup-and-recovery">Backup and Recovery</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/cloud/terms_of_use/index.html#data-privacy-and-sensitive-data">Data Privacy and Sensitive Data</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/cloud/terms_of_use/index.html#proprietary-software">Proprietary Software</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/cloud/terms_of_use/index.html#service-interventions-and-scheduled-down-times">Service Interventions and Scheduled Down times</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/cloud/terms_of_use/index.html#performance">Performance</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/cloud/terms_of_use/index.html#support">Support</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/cloud/terms_of_use/index.html#potential-sanctions">Potential Sanctions</a></li> </ul> </li> </ul> </li> <li class="toctree-l2"><a class="reference internal" href="../doc/visualization/index.html">Visualization</a><ul> <li class="toctree-l3"><a class="reference internal" href="../doc/visualization/index.html#support-for-the-visualization-of-scientific-data">Support for the Visualization of Scientific Data</a></li> <li class="toctree-l3"><a class="reference internal" href="../doc/visualization/index.html#remote-visualization-and-jupyter-notebook-services">Remote Visualization and Jupyter Notebook Services</a><ul> <li class="toctree-l4"><a class="reference internal" href="../doc/visualization/index.html#web-interface">Web Interface</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/visualization/index.html#command-line-interface">Command line interface</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/visualization/index.html#technical-details">Technical details</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/visualization/index.html#troubleshooting">Troubleshooting</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="../doc/visualization/index.html#robin">Robin</a></li> </ul> </li> <li class="toctree-l2"><a class="reference internal" href="../doc/campus/index.html">Campus</a><ul> <li class="toctree-l3"><a class="reference internal" href="../doc/campus/software/index.html">Software</a></li> <li class="toctree-l3"><a class="reference internal" href="../doc/campus/vpn/index.html">VPN</a><ul> <li class="toctree-l4"><a class="reference internal" href="../doc/campus/vpn/index.html#vpn-server-gateway">VPN Server (Gateway)</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/campus/vpn/index.html#connection-profile-group">Connection Profile (Group)</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/campus/vpn/index.html#desktop-and-notebook-windows-mac-os-x-linux">Desktop and Notebook (Windows, Mac OS X, Linux)</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/campus/vpn/index.html#linux-clients">Linux Clients</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/campus/vpn/index.html#mobile-devices-android-and-ios">Mobile Devices (Android and iOS)</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="../doc/campus/wifi/index.html">Wi-Fi</a><ul> <li class="toctree-l4"><a class="reference internal" href="../doc/campus/wifi/index.html#guest-networks">Guest networks</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/campus/wifi/index.html#eduroam">Eduroam</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/campus/wifi/index.html#installation-mpcdf-mpq-staff-only">Installation (<em>MPCDF/MPQ staff only</em>)</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="../doc/campus/email/index.html">Email Configuration</a><ul> <li class="toctree-l4"><a class="reference internal" href="../doc/campus/email/electronic-mail-at-mpcdf.html">Email Service</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/campus/email/email_client_config/config.html">Email Client configuration</a></li> <li class="toctree-l4"><a class="reference internal" href="../doc/campus/email/mailing-lists.html">Mailing Lists</a></li> </ul> </li> </ul> </li> </ul> </li> </ul> <ul class="current"> <li class="toctree-l1 current"><a class="reference internal" href="index.html">Bits and Bytes</a><ul class="current"> <li class="toctree-l2"><a class="reference internal" href="216.html">No.216, August 2024</a><ul> <li class="toctree-l3"><a class="reference internal" href="216.html#high-performance-computing">High-performance Computing</a><ul> <li class="toctree-l4"><a class="reference internal" href="216.html#new-hpc-system-viper-phase-1-cpu">New HPC system <em>Viper</em> (Phase-1: CPU)</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="216.html#hpc-software-news">HPC Software News</a><ul> <li class="toctree-l4"><a class="reference internal" href="216.html#mpcdf-gitlab-module-image-to-be-discontinued-on-october-31">MPCDF GitLab <code class="docutils literal notranslate"><span class="pre">module-image</span></code> to be discontinued on October 31</a></li> <li class="toctree-l4"><a class="reference internal" href="216.html#new-module-images-available-in-mpcdf-gitlab">New module images available in MPCDF GitLab</a></li> <li class="toctree-l4"><a class="reference internal" href="216.html#nvidia-hpc-sdk-version-24-3-available-on-raven">Nvidia HPC SDK version 24.3 available on <em>Raven</em></a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="216.html#major-change-in-the-python-infrastructure-on-the-hpc-clusters">Major Change in the Python Infrastructure on the HPC Clusters</a></li> <li class="toctree-l3"><a class="reference internal" href="216.html#introducing-containerized-applications-as-part-of-the-mpcdf-software-stack">Introducing containerized Applications as Part of the MPCDF Software Stack</a></li> <li class="toctree-l3"><a class="reference internal" href="216.html#nexus-s3-object-storage-in-the-hpc-cloud-and-beyond">Nexus-S3: Object Storage in the HPC-Cloud and beyond</a><ul> <li class="toctree-l4"><a class="reference internal" href="216.html#example-use-case">Example use case</a></li> <li class="toctree-l4"><a class="reference internal" href="216.html#opt-in-via-selfservice">Opt-in via SelfService</a></li> <li class="toctree-l4"><a class="reference internal" href="216.html#object-storage-for-larger-projects">Object storage for larger projects</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="216.html#the-metastore-research-data-publication-platform">The MetaStore Research Data Publication Platform</a><ul> <li class="toctree-l4"><a class="reference internal" href="216.html#managing-data-sets-and-resources-in-metastore">Managing data sets and resources in MetaStore</a></li> <li class="toctree-l4"><a class="reference internal" href="216.html#who-can-use-it">Who can use it</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="216.html#news">News</a><ul> <li class="toctree-l4"><a class="reference internal" href="216.html#password-policy">Password policy</a></li> <li class="toctree-l4"><a class="reference internal" href="216.html#fa-for-datashare-and-gitlab">2FA for DataShare and GitLab</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="216.html#events">Events</a><ul> <li class="toctree-l4"><a class="reference internal" href="216.html#amd-gpu-workshop-hackathon-november-5-7">AMD GPU workshop & hackathon (November 5-7)</a></li> <li class="toctree-l4"><a class="reference internal" href="216.html#introduction-to-mpcdf-services-october-24">Introduction to MPCDF services (October 24)</a></li> <li class="toctree-l4"><a class="reference internal" href="216.html#meet-mpcdf">Meet MPCDF</a></li> <li class="toctree-l4"><a class="reference internal" href="216.html#mpcdf-at-garching-campus-open-doors-october-3">MPCDF at Garching Campus Open Doors (October 3)</a></li> <li class="toctree-l4"><a class="reference internal" href="216.html#hpc-cloud-workshop-september-10-12">HPC-Cloud workshop (September 10-12)</a></li> <li class="toctree-l4"><a class="reference internal" href="216.html#course-on-python-for-hpc-november-26-28">Course on “Python for HPC” (November 26-28)</a></li> </ul> </li> </ul> </li> <li class="toctree-l2 current"><a class="current reference internal" href="#">No.215, April 2024</a><ul> <li class="toctree-l3"><a class="reference internal" href="#high-performance-computing">High-performance computing</a><ul> <li class="toctree-l4"><a class="reference internal" href="#licensed-software-in-slurm-comsol">Licensed software in Slurm (Comsol)</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="#hpc-software-news">HPC Software News</a><ul> <li class="toctree-l4"><a class="reference internal" href="#improved-workflow-for-multimer-predictions-with-alphafold2-on-raven">Improved workflow for multimer predictions with AlphaFold2 on <em>Raven</em></a></li> <li class="toctree-l4"><a class="reference internal" href="#new-version-of-intel-oneapi-with-deprecation-of-ifort-compiler">New version of Intel oneAPI with deprecation of ifort compiler</a></li> <li class="toctree-l4"><a class="reference internal" href="#cuda-modules-on-raven">CUDA modules on <em>Raven</em></a></li> <li class="toctree-l4"><a class="reference internal" href="#new-amd-gpu-elpa-release">New AMD-GPU ELPA release</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="#kubernetes-in-the-hpc-cloud">Kubernetes in the HPC-Cloud</a><ul> <li class="toctree-l4"><a class="reference internal" href="#usage">Usage</a></li> <li class="toctree-l4"><a class="reference internal" href="#function">Function</a></li> <li class="toctree-l4"><a class="reference internal" href="#existing-applications">Existing applications</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="#gitlab-graphs-diagrams">GitLab: Graphs & Diagrams</a><ul> <li class="toctree-l4"><a class="reference internal" href="#alternatives">Alternatives</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="#llms-meet-mpcdf">LLMs meet MPCDF</a></li> <li class="toctree-l3"><a class="reference internal" href="#news-events">News & Events</a><ul> <li class="toctree-l4"><a class="reference internal" href="#introduction-to-mpcdf-services">Introduction to MPCDF services</a></li> <li class="toctree-l4"><a class="reference internal" href="#meet-mpcdf">Meet MPCDF</a></li> </ul> </li> </ul> </li> <li class="toctree-l2"><a class="reference internal" href="214.html">No.214, December 2023</a><ul> <li class="toctree-l3"><a class="reference internal" href="214.html#hpc-software-news">HPC Software News</a><ul> <li class="toctree-l4"><a class="reference internal" href="214.html#cuda-aware-openmpi-on-raven">CUDA-aware OpenMPI on <em>Raven</em></a></li> <li class="toctree-l4"><a class="reference internal" href="214.html#gpu-accelerated-vasp">GPU-accelerated VASP</a></li> <li class="toctree-l4"><a class="reference internal" href="214.html#intel-oneapi-transition-from-ifort-to-ifx">Intel oneAPI: transition from ifort to ifx</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="214.html#module-software-stacks-for-continuous-integration-pipelines-on-mpcdf-gitlab-shared-cloud-runners">Module Software Stacks for Continuous Integration Pipelines on MPCDF GitLab Shared Cloud Runners</a><ul> <li class="toctree-l4"><a class="reference internal" href="214.html#introducing-a-novel-module-enabled-docker-image-infrastructure">Introducing a novel module-enabled Docker image infrastructure</a></li> <li class="toctree-l4"><a class="reference internal" href="214.html#announcing-legacy-status-and-later-discontinuation-of-the-module-image">Announcing legacy status and later discontinuation of the <code class="docutils literal notranslate"><span class="pre">module-image</span></code></a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="214.html#compressed-portable-conda-environments-for-hpc-systems">Compressed Portable Conda Environments for HPC Systems</a><ul> <li class="toctree-l4"><a class="reference internal" href="214.html#introduction-and-motivation">Introduction and Motivation</a></li> <li class="toctree-l4"><a class="reference internal" href="214.html#move-conda-environments-into-compressed-image-files">Move Conda environments into compressed image files</a></li> <li class="toctree-l4"><a class="reference internal" href="214.html#basic-usage-examples">Basic usage examples</a></li> <li class="toctree-l4"><a class="reference internal" href="214.html#limitations">Limitations</a></li> <li class="toctree-l4"><a class="reference internal" href="214.html#availability">Availability</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="214.html#new-features-in-the-hpc-cloud">New Features in the HPC-Cloud</a><ul> <li class="toctree-l4"><a class="reference internal" href="214.html#expanded-menu-of-flavors-and-images">Expanded menu of flavors and images</a></li> <li class="toctree-l4"><a class="reference internal" href="214.html#ssd-based-block-volumes">SSD-based block volumes</a></li> <li class="toctree-l4"><a class="reference internal" href="214.html#automated-domain-name-service">Automated domain name service</a></li> <li class="toctree-l4"><a class="reference internal" href="214.html#shared-filesystem-service">Shared filesystem service</a></li> <li class="toctree-l4"><a class="reference internal" href="214.html#the-robin-cluster">The Robin cluster</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="214.html#news-events">News & Events</a><ul> <li class="toctree-l4"><a class="reference internal" href="214.html#amd-gpu-development-workshop">AMD-GPU development workshop</a></li> <li class="toctree-l4"><a class="reference internal" href="214.html#meet-mpcdf">Meet MPCDF</a></li> <li class="toctree-l4"><a class="reference internal" href="214.html#rda-deutschland-tagung-2024">RDA Deutschland Tagung 2024</a></li> </ul> </li> </ul> </li> <li class="toctree-l2"><a class="reference internal" href="213.html">No.213, August 2023</a><ul> <li class="toctree-l3"><a class="reference internal" href="213.html#high-performance-computing">High-performance Computing</a><ul> <li class="toctree-l4"><a class="reference internal" href="213.html#new-gpu-development-partition-on-raven">New GPU development partition on <em>Raven</em></a></li> <li class="toctree-l4"><a class="reference internal" href="213.html#memory-profiling-with-heaptrack">Memory profiling with heaptrack</a></li> <li class="toctree-l4"><a class="reference internal" href="213.html#new-compilers-and-libraries-intel-oneapi-2023-1">New compilers and libraries: Intel oneAPI 2023.1</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="213.html#using-linters-to-improve-and-maintain-code-quality">Using linters to improve and maintain code quality</a></li> <li class="toctree-l3"><a class="reference internal" href="213.html#hpc-cloud-object-storage">HPC-Cloud Object Storage</a></li> <li class="toctree-l3"><a class="reference internal" href="213.html#jade-automated-slurm-deployments-in-the-hpc-cloud">JADE - Automated Slurm deployments in the HPC-Cloud</a></li> <li class="toctree-l3"><a class="reference internal" href="213.html#gitlab-tips-tricks">GitLab: Tips & Tricks</a><ul> <li class="toctree-l4"><a class="reference internal" href="213.html#online-editing-of-source-code-revisited">Online editing of source code revisited</a></li> <li class="toctree-l4"><a class="reference internal" href="213.html#custom-badges">Custom badges</a></li> <li class="toctree-l4"><a class="reference internal" href="213.html#security-warning">Security warning</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="213.html#new-ibm-tape-library-and-tape-drives-installed-at-mpcdf">New IBM tape library and tape drives installed at MPCDF</a></li> <li class="toctree-l3"><a class="reference internal" href="213.html#news-events">News & Events</a><ul> <li class="toctree-l4"><a class="reference internal" href="213.html#open-positions-at-mpcdf">Open positions at MPCDF</a></li> <li class="toctree-l4"><a class="reference internal" href="213.html#meet-mpcdf">Meet MPCDF</a></li> <li class="toctree-l4"><a class="reference internal" href="213.html#amd-gpu-development-workshop">AMD-GPU development workshop</a></li> </ul> </li> </ul> </li> <li class="toctree-l2"><a class="reference internal" href="212.html">No.212, April 2023</a><ul> <li class="toctree-l3"><a class="reference internal" href="212.html#high-performance-computing">High-performance Computing</a><ul> <li class="toctree-l4"><a class="reference internal" href="212.html#new-supercomputer-of-the-mpg-cobra-successor">New Supercomputer of the MPG - <em>Cobra</em> successor</a></li> <li class="toctree-l4"><a class="reference internal" href="212.html#documentation-of-hpc-hardware-characteristics">Documentation of HPC hardware characteristics</a></li> <li class="toctree-l4"><a class="reference internal" href="212.html#cmake-recipes-repository">CMake Recipes Repository</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="212.html#mpcdf-hpc-cloud">MPCDF HPC Cloud</a><ul> <li class="toctree-l4"><a class="reference internal" href="212.html#introduction">Introduction</a></li> <li class="toctree-l4"><a class="reference internal" href="212.html#hardware-resources">Hardware Resources</a></li> <li class="toctree-l4"><a class="reference internal" href="212.html#project-support">Project Support</a></li> <li class="toctree-l4"><a class="reference internal" href="212.html#summary">Summary</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="212.html#news">News</a><ul> <li class="toctree-l4"><a class="reference internal" href="212.html#mpcdf-selfservice">MPCDF SelfService</a></li> <li class="toctree-l4"><a class="reference internal" href="212.html#pushing-fusion-plasma-simulations-towards-exascale">Pushing Fusion-Plasma Simulations Towards Exascale</a></li> <li class="toctree-l4"><a class="reference internal" href="212.html#base4nfdi-creating-nfdi-wide-basic-services-in-a-world-of-specific-domains">Base4NFDI: Creating NFDI-wide basic services in a world of specific domains</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="212.html#events">Events</a><ul> <li class="toctree-l4"><a class="reference internal" href="212.html#meet-mpcdf">Meet MPCDF</a></li> <li class="toctree-l4"><a class="reference internal" href="212.html#introduction-to-mpcdf-services">Introduction to MPCDF services</a></li> <li class="toctree-l4"><a class="reference internal" href="212.html#ai-training-course">AI Training Course</a></li> <li class="toctree-l4"><a class="reference internal" href="212.html#course-on-python-for-hpc">Course on “Python for HPC”</a></li> <li class="toctree-l4"><a class="reference internal" href="212.html#rda-deutschland-conference">RDA-Deutschland Conference</a></li> </ul> </li> </ul> </li> <li class="toctree-l2"><a class="reference internal" href="211.html">No.211, December 2022</a><ul> <li class="toctree-l3"><a class="reference internal" href="211.html#high-performance-computing">High-performance Computing</a><ul> <li class="toctree-l4"><a class="reference internal" href="211.html#anaconda-python-modules">Anaconda Python modules</a></li> <li class="toctree-l4"><a class="reference internal" href="211.html#hints-for-architecture-specific-and-optimized-cuda-compilation">Hints for architecture-specific and optimized CUDA compilation</a></li> <li class="toctree-l4"><a class="reference internal" href="211.html#new-intel-c-c-compilers-and-associated-mpcdf-software-stack">New Intel C/C++ compilers and associated MPCDF software stack</a></li> <li class="toctree-l4"><a class="reference internal" href="211.html#turbomole-license-for-mpg-renewed">Turbomole license for MPG renewed</a></li> <li class="toctree-l4"><a class="reference internal" href="211.html#apptainer-on-hpc-clusters-the-linux-foundation-successor-to-singularity">Apptainer on HPC clusters, the Linux Foundation successor to Singularity</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="211.html#gitlab-tips-tricks-use-of-docker-images-in-gitlab-ci">GitLab Tips & Tricks: Use of Docker Images in GitLab CI</a></li> <li class="toctree-l3"><a class="reference internal" href="211.html#go-nexus">GO-Nexus</a></li> <li class="toctree-l3"><a class="reference internal" href="211.html#news-events">News & Events</a><ul> <li class="toctree-l4"><a class="reference internal" href="211.html#discontinuation-of-general-vpn">Discontinuation of General VPN</a></li> <li class="toctree-l4"><a class="reference internal" href="211.html#meet-mpcdf">Meet MPCDF</a></li> <li class="toctree-l4"><a class="reference internal" href="211.html#python-for-hpc">Python for HPC</a></li> <li class="toctree-l4"><a class="reference internal" href="211.html#advanced-hpc-workshop">Advanced HPC Workshop</a></li> </ul> </li> </ul> </li> <li class="toctree-l2"><a class="reference internal" href="210.html">No.210, August 2022</a><ul> <li class="toctree-l3"><a class="reference internal" href="210.html#high-performance-computing">High-performance Computing</a><ul> <li class="toctree-l4"><a class="reference internal" href="210.html#cobra-successor-procurement">Cobra successor procurement</a></li> <li class="toctree-l4"><a class="reference internal" href="210.html#co-sub-2-sub-footprint-of-mpcdf">CO<sub>2</sub> footprint of MPCDF</a></li> <li class="toctree-l4"><a class="reference internal" href="210.html#software-news">Software news</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="210.html#gitlab-ci-distributed-cache">GitLab CI Distributed Cache</a><ul> <li class="toctree-l4"><a class="reference internal" href="210.html#introduction">Introduction</a></li> <li class="toctree-l4"><a class="reference internal" href="210.html#adding-a-cache-to-your-ci-configuration">Adding a cache to your CI configuration</a></li> <li class="toctree-l4"><a class="reference internal" href="210.html#ci-of-software-that-depends-on-third-party-packages">CI of software that depends on third-party packages</a></li> <li class="toctree-l4"><a class="reference internal" href="210.html#ci-of-a-complex-hpc-code-that-requires-cpu-and-partly-gpu-resources">CI of a complex HPC code that requires CPU and partly GPU resources</a></li> <li class="toctree-l4"><a class="reference internal" href="210.html#concluding-remarks">Concluding remarks</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="210.html#globus-flows">Globus Flows</a><ul> <li class="toctree-l4"><a class="reference internal" href="210.html#id1">Introduction</a></li> <li class="toctree-l4"><a class="reference internal" href="210.html#flows-in-detail">Flows in detail</a></li> <li class="toctree-l4"><a class="reference internal" href="210.html#example">Example</a></li> <li class="toctree-l4"><a class="reference internal" href="210.html#summary">Summary</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="210.html#news-events">News & Events</a><ul> <li class="toctree-l4"><a class="reference internal" href="210.html#introduction-to-mpcdf-services">Introduction to MPCDF services</a></li> <li class="toctree-l4"><a class="reference internal" href="210.html#meet-mpcdf">Meet MPCDF</a></li> <li class="toctree-l4"><a class="reference internal" href="210.html#advanced-hpc-workshop">Advanced HPC workshop</a></li> <li class="toctree-l4"><a class="reference internal" href="210.html#python-for-hpc">Python for HPC</a></li> </ul> </li> </ul> </li> <li class="toctree-l2"><a class="reference internal" href="209.html">No.209, April 2022</a><ul> <li class="toctree-l3"><a class="reference internal" href="209.html#high-performance-computing">High-performance Computing</a><ul> <li class="toctree-l4"><a class="reference internal" href="209.html#alphafold2-on-the-hpc-system-raven">AlphaFold2 on the HPC system <em>Raven</em></a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="209.html#gitlab-ci">GitLab CI</a><ul> <li class="toctree-l4"><a class="reference internal" href="209.html#gitlab-shared-runners-on-gpus">GitLab shared runners on GPUs</a></li> <li class="toctree-l4"><a class="reference internal" href="209.html#continuous-integration-testing-for-hpc-codes-on-mpcdf-gitlab">Continuous integration testing for HPC codes on MPCDF GitLab</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="209.html#globus-online">Globus Online</a><ul> <li class="toctree-l4"><a class="reference internal" href="209.html#datahub-access-via-the-globus-online-portal">DataHub access via the Globus Online Portal</a></li> <li class="toctree-l4"><a class="reference internal" href="209.html#enhanced-functionality">Enhanced functionality</a></li> <li class="toctree-l4"><a class="reference internal" href="209.html#more-information">More information</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="209.html#new-selfservice-features-and-improvements">New SelfService Features and Improvements</a><ul> <li class="toctree-l4"><a class="reference internal" href="209.html#redesign-of-the-login-process">Redesign of the login process</a></li> <li class="toctree-l4"><a class="reference internal" href="209.html#viewing-accounting-data">Viewing accounting data</a></li> <li class="toctree-l4"><a class="reference internal" href="209.html#additional-improvements">Additional improvements</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="209.html#access-to-afs-restricted-for-local-access-only">Access to AFS restricted for local Access only</a></li> <li class="toctree-l3"><a class="reference internal" href="209.html#news-events">News & Events</a><ul> <li class="toctree-l4"><a class="reference internal" href="209.html#ai-bootcamp">AI bootcamp</a></li> <li class="toctree-l4"><a class="reference internal" href="209.html#international-hpc-summer-school-2022">International HPC Summer School 2022</a></li> <li class="toctree-l4"><a class="reference internal" href="209.html#workshop-introduction-to-mpcdf-services-online">Workshop “Introduction to MPCDF services (online)”</a></li> <li class="toctree-l4"><a class="reference internal" href="209.html#meet-mpcdf-new-online-forum-and-lectures-for-mpcdf-users">“Meet MPCDF”: New online forum and lectures for MPCDF users</a></li> <li class="toctree-l4"><a class="reference internal" href="209.html#rda-deutschland-tagung-2022">RDA-Deutschland-Tagung 2022</a></li> </ul> </li> </ul> </li> <li class="toctree-l2"><a class="reference internal" href="208.html">No.208, December 2021</a><ul> <li class="toctree-l3"><a class="reference internal" href="208.html#high-performance-computing">High-performance Computing</a><ul> <li class="toctree-l4"><a class="reference internal" href="208.html#termination-of-general-user-operation-for-draco-login-nodes">Termination of general user operation for <em>Draco</em> login nodes</a></li> <li class="toctree-l4"><a class="reference internal" href="208.html#announcement-of-cuda-no-defaults-on-cobra-and-raven">Announcement of CUDA no-defaults on <em>Cobra</em> and <em>Raven</em></a></li> <li class="toctree-l4"><a class="reference internal" href="208.html#usage-of-tmp-and-dev-shm-on-cobra-and-raven">Usage of /tmp and /dev/shm on <em>Cobra</em> and <em>Raven</em></a></li> <li class="toctree-l4"><a class="reference internal" href="208.html#eigensolver-library-elpa">Eigensolver library ELPA</a></li> <li class="toctree-l4"><a class="reference internal" href="208.html#using-python-based-hybrid-parallel-codes-on-hpc-systems">Using Python-based hybrid-parallel codes on HPC systems</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="208.html#python-bindings-for-c-using-pybind11-and-scikit-build">Python bindings for C++ using pybind11 and scikit-build</a><ul> <li class="toctree-l4"><a class="reference internal" href="208.html#interfacing-python-numpy-with-c-using-pybind11">Interfacing Python/NumPy with C++ using pybind11</a></li> <li class="toctree-l4"><a class="reference internal" href="208.html#build-with-scikit-build">Build with scikit-build</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="208.html#the-gitlab-package-registry">The Gitlab Package Registry</a><ul> <li class="toctree-l4"><a class="reference internal" href="208.html#example-publishing-python-packages">Example: Publishing Python packages</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="208.html#using-application-tokens-instead-of-passwords">Using Application Tokens instead of Passwords</a><ul> <li class="toctree-l4"><a class="reference internal" href="208.html#datashare">DataShare</a></li> <li class="toctree-l4"><a class="reference internal" href="208.html#gitlab">GitLab</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="208.html#software-publishing">Software Publishing</a><ul> <li class="toctree-l4"><a class="reference internal" href="208.html#do-it-yourself">Do it yourself</a></li> <li class="toctree-l4"><a class="reference internal" href="208.html#publish-via-a-data-archiving-site">Publish via a data archiving site</a></li> <li class="toctree-l4"><a class="reference internal" href="208.html#software-heritage">Software Heritage</a></li> <li class="toctree-l4"><a class="reference internal" href="208.html#final-remarks">Final remarks</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="208.html#news-events">News & Events</a><ul> <li class="toctree-l4"><a class="reference internal" href="208.html#international-hpc-summer-school-2022">International HPC Summer School 2022</a></li> <li class="toctree-l4"><a class="reference internal" href="208.html#advanced-hpc-workshop-2021">Advanced HPC workshop 2021</a></li> <li class="toctree-l4"><a class="reference internal" href="208.html#years-max-planck-computing-centre-in-garching">60 Years Max Planck Computing Centre in Garching</a></li> </ul> </li> </ul> </li> <li class="toctree-l2"><a class="reference internal" href="207.html">No.207, August 2021</a><ul> <li class="toctree-l3"><a class="reference internal" href="207.html#high-performance-computing">High-performance Computing</a><ul> <li class="toctree-l4"><a class="reference internal" href="207.html#hpc-system-raven-fully-operational">HPC system <em>Raven</em> fully operational</a></li> <li class="toctree-l4"><a class="reference internal" href="207.html#gpu-computing-on-raven">GPU Computing on <em>Raven</em></a></li> <li class="toctree-l4"><a class="reference internal" href="207.html#hpc-system-cobra-module-system-to-be-aligned-with-raven">HPC system <em>Cobra</em> - Module system to be aligned with <em>Raven</em></a></li> <li class="toctree-l4"><a class="reference internal" href="207.html#decommissioning-of-draco">Decommissioning of <em>Draco</em></a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="207.html#hpc-cloud">HPC Cloud</a></li> <li class="toctree-l3"><a class="reference internal" href="207.html#poetry-packaging-and-dependency-management-for-python">Poetry: Packaging and Dependency Management for Python</a><ul> <li class="toctree-l4"><a class="reference internal" href="207.html#introduction">Introduction</a></li> <li class="toctree-l4"><a class="reference internal" href="207.html#a-poetry-project-and-initial-configuration">A Poetry project and initial configuration</a></li> <li class="toctree-l4"><a class="reference internal" href="207.html#dependency-management">Dependency Management</a></li> <li class="toctree-l4"><a class="reference internal" href="207.html#running-your-code">Running your code</a></li> <li class="toctree-l4"><a class="reference internal" href="207.html#package-creation-and-publishing">Package creation and publishing</a></li> <li class="toctree-l4"><a class="reference internal" href="207.html#conclusion">Conclusion</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="207.html#more-functionality-for-the-selfservice-call-to-action-for-2fa-users">More functionality for the SelfService - Call to action for 2FA users</a><ul> <li class="toctree-l4"><a class="reference internal" href="207.html#migration-of-mympcdf-functionality">Migration of MyMPCDF functionality</a></li> <li class="toctree-l4"><a class="reference internal" href="207.html#updated-password-policy">Updated password policy</a></li> <li class="toctree-l4"><a class="reference internal" href="207.html#two-factor-authentication-2fa-call-to-action">Two-Factor Authentication (2FA) - Call to action</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="207.html#news-events">News & Events</a><ul> <li class="toctree-l4"><a class="reference internal" href="207.html#brochure-high-performance-computing-and-data-science-in-the-mpg">Brochure “High-Performance Computing and Data Science in the MPG”</a></li> <li class="toctree-l4"><a class="reference internal" href="207.html#gpu-bootcamp">GPU bootcamp</a></li> <li class="toctree-l4"><a class="reference internal" href="207.html#introductory-course-for-new-users-of-mpcdf">Introductory course for new users of MPCDF</a></li> <li class="toctree-l4"><a class="reference internal" href="207.html#advanced-hpc-workshop">Advanced HPC workshop</a></li> <li class="toctree-l4"><a class="reference internal" href="207.html#python-for-hpc">Python for HPC</a></li> </ul> </li> </ul> </li> <li class="toctree-l2"><a class="reference internal" href="206.html">No.206, April 2021</a><ul> <li class="toctree-l3"><a class="reference internal" href="206.html#high-performance-computing">High-performance Computing</a><ul> <li class="toctree-l4"><a class="reference internal" href="206.html#hpc-system-raven-deployment-of-the-final-system">HPC System <em>Raven</em>: deployment of the final system</a></li> <li class="toctree-l4"><a class="reference internal" href="206.html#charliecloud-and-singularity-containers-supported-on-cobra-and-raven">Charliecloud and Singularity containers supported on <em>Cobra</em> and <em>Raven</em></a></li> <li class="toctree-l4"><a class="reference internal" href="206.html#control-and-verification-of-the-cpu-affinity-of-processes-and-threads">Control and verification of the CPU affinity of processes and threads</a></li> </ul> </li> <li class="toctree-l3"><a class="reference internal" href="206.html#high-performance-data-analytics-and-ai-software-stack-at-mpcdf">High-performance data analytics and AI software stack at MPCDF</a></li> <li class="toctree-l3"><a class="reference internal" href="206.html#decommissioning-of-afs">Decommissioning of AFS</a></li> <li class="toctree-l3"><a class="reference internal" href="206.html#relaunch-of-mpcdf-website-and-new-technical-documentation-platform">Relaunch of MPCDF website and new technical documentation platform</a></li> <li class="toctree-l3"><a class="reference internal" href="206.html#events">Events</a><ul> <li class="toctree-l4"><a class="reference internal" href="206.html#new-online-introductory-course-for-new-users-of-mpcdf">New online introductory course for new users of MPCDF</a></li> <li class="toctree-l4"><a class="reference internal" href="206.html#advanced-hpc-workshop-save-the-date">Advanced HPC workshop: save the date</a></li> </ul> </li> </ul> </li> <li class="toctree-l2"><a class="reference internal" href="previous.html">Previous Editions</a></li> </ul> </li> </ul> </div> </div> </nav> <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" style="background: #EEEEEE" > <i data-toggle="wy-nav-top" class="fa fa-bars"></i> <a href="../index.html">Technical Documentation</a> </nav> <div class="wy-nav-content"> <div class="rst-content style-external-links"> <div role="navigation" aria-label="Page navigation"> <ul class="wy-breadcrumbs"> <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li> <li class="breadcrumb-item"><a href="index.html">Bits and Bytes</a></li> <li class="breadcrumb-item active">No.215, April 2024</li> <li class="wy-breadcrumbs-aside"> </li> </ul> <hr/> </div> <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article"> <div itemprop="articleBody"> <img src="_static/bblogo.jpg" alt="Bits and Bytes Logo" width="25%" height="25%" style="float:right"><div class="section" id="no-215-april-2024"> <h1>No.215, April 2024<a class="headerlink" href="#no-215-april-2024" title="Permalink to this heading"></a></h1> <div class="contents local topic" id="contents"> <p class="topic-title">Contents</p> <ul class="simple"> <li><p><a class="reference internal" href="#high-performance-computing" id="id1">High-performance computing</a></p> <ul> <li><p><a class="reference internal" href="#licensed-software-in-slurm-comsol" id="id2">Licensed software in Slurm (Comsol)</a></p></li> </ul> </li> <li><p><a class="reference internal" href="#hpc-software-news" id="id3">HPC Software News</a></p> <ul> <li><p><a class="reference internal" href="#improved-workflow-for-multimer-predictions-with-alphafold2-on-raven" id="id4">Improved workflow for multimer predictions with AlphaFold2 on <em>Raven</em></a></p></li> <li><p><a class="reference internal" href="#new-version-of-intel-oneapi-with-deprecation-of-ifort-compiler" id="id5">New version of Intel oneAPI with deprecation of ifort compiler</a></p></li> <li><p><a class="reference internal" href="#cuda-modules-on-raven" id="id6">CUDA modules on <em>Raven</em></a></p></li> <li><p><a class="reference internal" href="#new-amd-gpu-elpa-release" id="id7">New AMD-GPU ELPA release</a></p></li> </ul> </li> <li><p><a class="reference internal" href="#kubernetes-in-the-hpc-cloud" id="id8">Kubernetes in the HPC-Cloud</a></p> <ul> <li><p><a class="reference internal" href="#usage" id="id9">Usage</a></p></li> <li><p><a class="reference internal" href="#function" id="id10">Function</a></p></li> <li><p><a class="reference internal" href="#existing-applications" id="id11">Existing applications</a></p></li> </ul> </li> <li><p><a class="reference internal" href="#gitlab-graphs-diagrams" id="id12">GitLab: Graphs & Diagrams</a></p> <ul> <li><p><a class="reference internal" href="#alternatives" id="id13">Alternatives</a></p></li> </ul> </li> <li><p><a class="reference internal" href="#llms-meet-mpcdf" id="id14">LLMs meet MPCDF</a></p></li> <li><p><a class="reference internal" href="#news-events" id="id15">News & Events</a></p> <ul> <li><p><a class="reference internal" href="#introduction-to-mpcdf-services" id="id16">Introduction to MPCDF services</a></p></li> <li><p><a class="reference internal" href="#meet-mpcdf" id="id17">Meet MPCDF</a></p></li> </ul> </li> </ul> </div> <p><a class="reference external" href="./pdf/bits_and_bytes_issue_215.pdf">PDF version</a></p> <div class="section" id="high-performance-computing"> <h2><a class="toc-backref" href="#id1">High-performance computing</a><a class="headerlink" href="#high-performance-computing" title="Permalink to this heading"></a></h2> <div class="section" id="licensed-software-in-slurm-comsol"> <h3><a class="toc-backref" href="#id2">Licensed software in Slurm (Comsol)</a><a class="headerlink" href="#licensed-software-in-slurm-comsol" title="Permalink to this heading"></a></h3> <p>The Slurm workload manager can handle licensed software by assigning available licenses to jobs at scheduling time. If licenses are not available, jobs are kept pending until specified licenses become available, rather than failing at runtime due to a lack of available licenses. This can be particularly useful for software that only has a few licenses. For example, for the Comsol software, MPCDF currently maintains only two licenses for each Comsol module for batch use. In order to use this feature, you need to add the <code class="docutils literal notranslate"><span class="pre">-L,</span> <span class="pre">--licenses</span></code> option to the batch job scripts with a comma-separated list of required license names. To find out which licenses the <code class="docutils literal notranslate"><span class="pre">mph</span></code> comsol file requires, you can check it in the comsol GUI or simply run the <code class="docutils literal notranslate"><span class="pre">mphlicenses</span></code> command after loading the comsol module on HPC <em>Cobra</em> or <em>Raven</em> systems:</p> <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">~></span> <span class="n">module</span> <span class="n">load</span> <span class="n">comsol</span><span class="o">/</span><span class="mf">6.2</span> <span class="o">~></span> <span class="n">mphlicenses</span> <span class="n">test_file</span><span class="o">.</span><span class="n">mph</span> <span class="n">comsol_nonlinearstructmaterialsbatch</span><span class="nd">@lserv</span><span class="p">,</span><span class="n">comsol_comsolbatch</span><span class="nd">@lserv</span><span class="p">,</span><span class="n">comsol_structuralmechanicsbatch</span><span class="nd">@lserv</span><span class="p">,</span><span class="n">comsol_clusternode</span><span class="nd">@lserv</span><span class="p">,</span><span class="n">comsol_comsoluser</span><span class="nd">@lserv</span> </pre></div> </div> <p>The complete Slurm #SBATCH directive to run this comsol test_file on the clusters then reads</p> <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1">#SBATCH -L comsol_nonlinearstructmaterialsbatch@lserv,comsol_comsolbatch@lserv,comsol_structuralmechanicsbatch@lserv,comsol_clusternode@lserv,comsol_comsoluser@lserv</span> </pre></div> </div> <p>In order to get a list of all available comsol licenses on HPC systems, run the command:</p> <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">scontrol</span> <span class="n">show</span> <span class="n">licenses</span> </pre></div> </div> <p><em>Mykola Petrov</em></p> </div> </div> <div class="section" id="hpc-software-news"> <h2><a class="toc-backref" href="#id3">HPC Software News</a><a class="headerlink" href="#hpc-software-news" title="Permalink to this heading"></a></h2> <div class="section" id="improved-workflow-for-multimer-predictions-with-alphafold2-on-raven"> <h3><a class="toc-backref" href="#id4">Improved workflow for multimer predictions with AlphaFold2 on <em>Raven</em></a><a class="headerlink" href="#improved-workflow-for-multimer-predictions-with-alphafold2-on-raven" title="Permalink to this heading"></a></h3> <p>AlphaFold2 (AF2) is an artificial-intelligence program released by Google DeepMind which performs predictions of protein structure based on the sequence of amino acids. AF2 has been provided by MPCDF since summer 2021 on <em>Raven</em> and on several institute clusters, and is regularly updated and customized to achieve optimal performance on the MPCDF systems.</p> <p>Initially, the prediction of the structure of single proteins (monomers) has been a main application of AF2, however more recently the users’ focus shifted towards predicting protein-protein complexes (multimers). As the prediction of multimers is considerably more expensive than most monomer cases, users sometimes hit the 24-hour job time limit on <em>Raven</em> with the original AF2 program, which internally loops over multiple models and random seeds.</p> <p>To overcome this limitation, MPCDF has refactored the internal double loop over the models and predictions into individual Slurm jobs. In particular, individual Slurm array jobs are now used for each model, each array containing a configurable number of tasks calculating individual predictions using individual random seeds. As a result, each individual prediction task now has a maximum wall clock time of 24 hours.</p> <p>On <em>Raven</em>, run <code class="docutils literal notranslate"><span class="pre">module</span> <span class="pre">help</span> <span class="pre">alphafold/2.3.2-2024</span></code> to get further instructions. For multimer cases, copy, adapt and run the script <code class="docutils literal notranslate"><span class="pre">submit_alphafold_jobs.sh</span></code> to submit the job-array-based predictions. Users are encouraged to approach us via the helpdesk with their feedback, which is valuable to further improve this service.</p> <p><em>Klaus Reuter</em></p> </div> <div class="section" id="new-version-of-intel-oneapi-with-deprecation-of-ifort-compiler"> <h3><a class="toc-backref" href="#id5">New version of Intel oneAPI with deprecation of ifort compiler</a><a class="headerlink" href="#new-version-of-intel-oneapi-with-deprecation-of-ifort-compiler" title="Permalink to this heading"></a></h3> <p>Intel oneAPI version 2024.0 has been installed on <em>Raven</em> and other HPC clusters recently. With this installation, we drop the <code class="docutils literal notranslate"><span class="pre">.x</span></code> suffix and the patch-level version from the compiler module name. Thus, the Intel compiler module is now called <code class="docutils literal notranslate"><span class="pre">intel/2024.0</span></code>. Bugfixes provided by Intel incrementing the patch level number will be installed under the hood without further notification. Run <code class="docutils literal notranslate"><span class="pre">module</span> <span class="pre">show</span> <span class="pre">intel/2024.0</span></code> in order to see which exact compiler version is present. The corresponding MPI module is <code class="docutils literal notranslate"><span class="pre">impi/2021.11</span></code>, and the latest MKL module is <code class="docutils literal notranslate"><span class="pre">mkl/2024.0</span></code>. As <a class="reference external" href="https://docs.mpcdf.mpg.de/bnb/214.html#intel-oneapi-transition-from-ifort-to-ifx">announced previously</a>, MPCDF, starting with <code class="docutils literal notranslate"><span class="pre">intel/2024.0</span></code>, is using <code class="docutils literal notranslate"><span class="pre">ifx</span></code> as the default Intel Fortran compiler, together with its MPI wrapper <code class="docutils literal notranslate"><span class="pre">mpiifx</span></code>. The “classic” Fortran compiler <code class="docutils literal notranslate"><span class="pre">ifort</span></code> is still present, but is now formally tagged as deprecated by Intel.</p> <p><em>Tobias Melson</em></p> </div> <div class="section" id="cuda-modules-on-raven"> <h3><a class="toc-backref" href="#id6">CUDA modules on <em>Raven</em></a><a class="headerlink" href="#cuda-modules-on-raven" title="Permalink to this heading"></a></h3> <p>MPCDF offers various CUDA modules on <em>Raven</em>. It depends on the desired compiler, which of these modules should be picked. If an application code is compiled with the GNU compiler (<code class="docutils literal notranslate"><span class="pre">gcc/11</span></code> or <code class="docutils literal notranslate"><span class="pre">gcc/12</span></code>), the CUDA modules <code class="docutils literal notranslate"><span class="pre">cuda/*</span></code> are suitable. In case the code is compiled with the Nvidia compiler (<code class="docutils literal notranslate"><span class="pre">nvhpcsdk/23</span></code>), the matching CUDA modules are named <code class="docutils literal notranslate"><span class="pre">cuda/*-nvhpcsdk</span></code> (note the suffix here). The following table lists the compatible CUDA modules for the recent GNU and Nvidia compilers:</p> <table border="1" class="docutils"> <thead> <tr> <th>Compiler</th> <th>Compatible CUDA modules</th> </tr> </thead> <tbody> <tr> <td>gcc/11</td> <td>cuda/11.4, cuda/11.6</td> </tr> <tr> <td>gcc/12</td> <td>cuda/12.1, cuda/12.2</td> </tr> <tr> <td>nvhpcsdk/23</td> <td>cuda/11.8-nvhpcsdk, cuda/12.3-nvhpcsdk</td> </tr> </tbody> </table><p>As <a class="reference external" href="https://docs.mpcdf.mpg.de/bnb/214.html#cuda-aware-openmpi-on-raven">announced previously</a>, CUDA-aware OpenMPI (<code class="docutils literal notranslate"><span class="pre">openmpi_gpu/4.1</span></code>) is available after having loaded one valid combination of compiler and CUDA modules.</p> <p><em>Tobias Melson, Tilman Dannert</em></p> </div> <div class="section" id="new-amd-gpu-elpa-release"> <h3><a class="toc-backref" href="#id7">New AMD-GPU ELPA release</a><a class="headerlink" href="#new-amd-gpu-elpa-release" title="Permalink to this heading"></a></h3> <p>The <a class="reference external" href="https://elpa.mpcdf.mpg.de">ELPA library</a> provides highly optimized, scalable solvers for generalized and standard, dense symmetric (Hermitian) eigenproblems. Since 2022, the ELPA library supports AMD GPUs and on Europe’s first pre-exascale system <em>LUMI</em> (CSC, Finland) ELPA was successfully employed for solving huge standard eigenvalue problems with a matrix size of up to 3.2 million (leading dimension) on more than 8000 AMD MI250x GPUs. In preparation for the new HPC system <em>Viper</em> at the MPCDF we have released a new version 2024.03.001 of the ELPA library which has been further extensively optimized for AMD GPUs. Among others, support of the GPU-to-GPU collective communications library RCCL (the equivalent to Nvidia’s NCCL library) has been implemented. In addition, the GPU implementation of the routines for the generalized eigenvalue problem has been reworked and speedups of up to a factor of 10 have been achieved. The latest version of ELPA is available to all users as a pre-built software package in the module environment of the MPCDF software stack.</p> <p><em>Andreas Marek</em></p> </div> </div> <div class="section" id="kubernetes-in-the-hpc-cloud"> <h2><a class="toc-backref" href="#id8">Kubernetes in the HPC-Cloud</a><a class="headerlink" href="#kubernetes-in-the-hpc-cloud" title="Permalink to this heading"></a></h2> <p>Containers have been widely adopted as a way to develop, distribute, and deploy applications. Kubernetes provides a framework to run containerized applications in a reliable and scalable fashion. Kubernetes is based on cluster management technology developed at Google (<a class="reference external" href="https://dl.acm.org/doi/abs/10.1145/2741948.2741964">cf. Verma, Abhishek, et al.: “Large-scale cluster management at Google with Borg”, Proceedings of the tenth European conference on computer systems, 2015</a>) and donated to the Linux Foundation in 2015. It has enjoyed wide adoption since.</p> <p>At MPCDF projects can deploy Kubernetes clusters hosted in the HPC-Cloud based on an <a class="reference external" href="https://docs.openstack.org/heat/latest/template_guide/hot_guide.html">OpenStack Heat Orchestration Template</a> as <a class="reference external" href="https://gitlab.mpcdf.mpg.de/mpcdf/cloud/kubernetes/">provided by the MPCDF Cloud enabling team</a>. The team maintains two templates: one for a small and simple cluster aimed at projects that wish to test and evaluate Kubernetes, and the second providing a production-grade cluster aimed at projects looking to deploy their services and applications using Kubernetes.</p> <div class="section" id="usage"> <h3><a class="toc-backref" href="#id9">Usage</a><a class="headerlink" href="#usage" title="Permalink to this heading"></a></h3> <p>The canonical way to control a Kubernetes cluster is with <a class="reference external" href="https://kubernetes.io/docs/reference/kubectl/"><code class="docutils literal notranslate"><span class="pre">kubectl</span></code></a>. The credentials required to connect to the cluster are provided on the control plane nodes set up by the template. The most important feature is that users define desired states for pods executing their containers and any peripheral resources in configuration files.</p> <p>Many software projects publish the configuration states required to run their products using <a class="reference external" href="https://helm.sh"><code class="docutils literal notranslate"><span class="pre">Helm</span></code></a>, the package manager for Kubernetes. Helm charts define the desired state of many interacting Kubernetes components. Users can configure charts by setting desired values of chart variables defining the specific features of their deployment.</p> <p>In productive deployments, it is imperative to store and track the configuration files of the services orchestrated in Kubernetes. This can be accomplished, for example, using GitLab. In addition, GitLab offers integrations for Kubernetes that deploy the state defined in the configuration files stored in a repository to Kubernetes as defined in the GitLab CI/CD pipelines. Taking advantage of this feature of GitLab provides a concise way to manage applications for teams of administrators and developers.</p> </div> <div class="section" id="function"> <h3><a class="toc-backref" href="#id10">Function</a><a class="headerlink" href="#function" title="Permalink to this heading"></a></h3> <p>Kubernetes is best suited for orchestrating long-running services that are implemented as many inter-dependent microservices. It is also possible to run applications on a schedule, or execute single commands in their containers.</p> <div class="section" id="deploying-a-web-service"> <h4>Deploying a web service<a class="headerlink" href="#deploying-a-web-service" title="Permalink to this heading"></a></h4> <p>Here is a configuration file you can apply with <code class="docutils literal notranslate"><span class="pre">kubectl</span> <span class="pre">create</span> <span class="pre">-f</span> <span class="pre"><filename>.yaml</span></code></p> <div class="highlight-yaml! notranslate"><div class="highlight"><pre><span></span>--- apiVersion: apps/v1 kind: Deployment metadata: name: svc-demo-deployment labels: app: svc-demo-app spec: replicas: 2 selector: matchLabels: app: svc-demo-app template: metadata: labels: app: svc-demo-app spec: containers: - name: svc-demo-container image: jmalloc/echo-server ports: - containerPort: 8080 --- apiVersion: v1 kind: Service metadata: name: svc-demo spec: selector: app: svc-demo-app type: LoadBalancer ports: - port: 80 targetPort: 8080 protocol: TCP </pre></div> </div> <p>The first section defines a deployment with a container image that runs the application, in this case a server that parrots your HTTP requests. The second section defines a service, exposing the application using a load balancer. Now running <code class="docutils literal notranslate"><span class="pre">kubectl</span> <span class="pre">get</span> <span class="pre">all</span></code> will give you:</p> <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">NAME</span> <span class="n">READY</span> <span class="n">STATUS</span> <span class="n">RESTARTS</span> <span class="n">AGE</span> <span class="n">pod</span><span class="o">/</span><span class="n">svc</span><span class="o">-</span><span class="n">demo</span><span class="o">-</span><span class="n">deployment</span><span class="o">-</span><span class="mi">587</span><span class="n">b7c9974</span><span class="o">-</span><span class="mi">4</span><span class="n">z5wn</span> <span class="mi">1</span><span class="o">/</span><span class="mi">1</span> <span class="n">Running</span> <span class="mi">0</span> <span class="mi">66</span><span class="n">s</span> <span class="n">pod</span><span class="o">/</span><span class="n">svc</span><span class="o">-</span><span class="n">demo</span><span class="o">-</span><span class="n">deployment</span><span class="o">-</span><span class="mi">587</span><span class="n">b7c9974</span><span class="o">-</span><span class="n">lz7pp</span> <span class="mi">1</span><span class="o">/</span><span class="mi">1</span> <span class="n">Running</span> <span class="mi">0</span> <span class="mi">66</span><span class="n">s</span> <span class="n">NAME</span> <span class="n">TYPE</span> <span class="n">CLUSTER</span><span class="o">-</span><span class="n">IP</span> <span class="n">EXTERNAL</span><span class="o">-</span><span class="n">IP</span> <span class="n">PORT</span><span class="p">(</span><span class="n">S</span><span class="p">)</span> <span class="n">AGE</span> <span class="n">service</span><span class="o">/</span><span class="n">svc</span><span class="o">-</span><span class="n">demo</span> <span class="n">LoadBalancer</span> <span class="mf">10.101.113.187</span> <span class="n">XXX</span><span class="o">.</span><span class="n">XXX</span><span class="o">.</span><span class="n">XXX</span><span class="o">.</span><span class="n">XXX</span> <span class="mi">80</span><span class="p">:</span><span class="mi">32260</span><span class="o">/</span><span class="n">TCP</span> <span class="mi">66</span><span class="n">s</span> <span class="n">NAME</span> <span class="n">READY</span> <span class="n">UP</span><span class="o">-</span><span class="n">TO</span><span class="o">-</span><span class="n">DATE</span> <span class="n">AVAILABLE</span> <span class="n">AGE</span> <span class="n">deployment</span><span class="o">.</span><span class="n">apps</span><span class="o">/</span><span class="n">svc</span><span class="o">-</span><span class="n">demo</span><span class="o">-</span><span class="n">deployment</span> <span class="mi">2</span><span class="o">/</span><span class="mi">2</span> <span class="mi">2</span> <span class="mi">2</span> <span class="mi">66</span><span class="n">s</span> <span class="n">NAME</span> <span class="n">DESIRED</span> <span class="n">CURRENT</span> <span class="n">READY</span> <span class="n">AGE</span> <span class="n">replicaset</span><span class="o">.</span><span class="n">apps</span><span class="o">/</span><span class="n">svc</span><span class="o">-</span><span class="n">demo</span><span class="o">-</span><span class="n">deployment</span><span class="o">-</span><span class="mi">587</span><span class="n">b7c9974</span> <span class="mi">2</span> <span class="mi">2</span> <span class="mi">2</span> <span class="mi">66</span><span class="n">s</span> </pre></div> </div> <p>You can see two pods running the application and the service making the application available at <code class="docutils literal notranslate"><span class="pre">http://XXX.XXX.XXX.XXX:80</span></code>. The application can be removed with <code class="docutils literal notranslate"><span class="pre">kubectl</span> <span class="pre">delete</span> <span class="pre">-f</span> <span class="pre"><filename>.yaml</span></code>.</p> </div> </div> <div class="section" id="existing-applications"> <h3><a class="toc-backref" href="#id11">Existing applications</a><a class="headerlink" href="#existing-applications" title="Permalink to this heading"></a></h3> <p>Kubernetes on the HPC-Cloud is already used at MPCDF to host a number of prominent applications, for example <a class="reference external" href="https://www.moveapps.org/">MoveApps</a>, <a class="reference external" href="https://nomad-lab.eu/nomad-lab/">NOMAD</a>, or <a class="reference external" href="https://dioscuri-biophysics.pages.mpcdf.de/glycoshield-md/">GlycoSHIELD</a>.</p> <p><em>Frank Berghaus</em></p> </div> </div> <div class="section" id="gitlab-graphs-diagrams"> <h2><a class="toc-backref" href="#id12">GitLab: Graphs & Diagrams</a><a class="headerlink" href="#gitlab-graphs-diagrams" title="Permalink to this heading"></a></h2> <p>In addition to classic Git functionality, MPCDF’s GitLab instance offers a wide range of capabilities around code organisation and project management. In many of these scopes, for example Wiki pages or issues, the user can enter formatted text in Markdown format. After saving, GitLab will render the Markdown annotations which results in a nicely formatted human readable document. Beside standard Markdown annotations, GitLab integrates out-of-the-box libraries for rendering graph structures and diagrams in Markdown texts. In this article, the creation of graphs and diagrams with the help of the Mermaid library is introduced.</p> <p>Inside any Markdown-formatted document in GitLab, the following code fragment encapsulates a Mermaid sub document:</p> <div class="highlight-default notranslate"><div class="highlight"><pre><span></span>```mermaid graph TD A --> B A --> C C --> D C --> E E --> A ``` </pre></div> </div> <p>After saving the Markdown document, GitLab would create the following graph from the code above:</p> <p><img alt="../_images/215_gitlab_01.png" src="../_images/215_gitlab_01.png" /></p> <p>The Mermaid library supports different types of graphs and diagrams. The image below shows some examples, top to bottom: a timeline, a mindmap, a pie chart and - maybe particularly relevant for GitLab users - a Git graph, showing the branch and commit structure of a Git repository:</p> <p><img alt="../_images/215_gitlab_02_hochkant.png" src="../_images/215_gitlab_02_hochkant.png" /></p> <p>The Markdown and Mermaid code of the examples examples can be found <a class="reference external" href="https://gitlab.mpcdf.mpg.de/thomz/graphs-and-diagrams">here</a>. Further information about supported graph and diagram types can be found in the <a class="reference external" href="https://mermaid.js.org/intro/">Mermaid Documentation</a>.</p> <div class="section" id="alternatives"> <h3><a class="toc-backref" href="#id13">Alternatives</a><a class="headerlink" href="#alternatives" title="Permalink to this heading"></a></h3> <p>In the same way GitLab supports the Mermaid library, also <a class="reference external" href="https://plantuml.com/en/">PlantUML</a> for UML diagrams and <a class="reference external" href="https://kroki.io/">Kroki</a> are supported. And if you don’t want to dive into another descriptive language, GitLab allows you to insert manually drawn diagrams via the external service <a class="reference external" href="https://draw.io">draw.io</a>. You can find this function as “Insert or edit diagram” button in the Markdown editor (red circle):</p> <p><img alt="../_images/215_gitlab_03.png" src="../_images/215_gitlab_03.png" /></p> <p><em>Thomas Zastrow</em></p> </div> </div> <div class="section" id="llms-meet-mpcdf"> <h2><a class="toc-backref" href="#id14">LLMs meet MPCDF</a><a class="headerlink" href="#llms-meet-mpcdf" title="Permalink to this heading"></a></h2> <p><img alt="A GPT4 interpretation of Max Planck using LLMs at the MPCDF" src="../_images/llms_meet_mpcdf.png" /></p> <p>The term “Large Language Model” (LLM), has been part of public discourse since at least the end of 2022, following the release of OpenAI’s ChatGPT. The general-purpose capabilities of these large AI models to process and store unstructured data have ignited a wave of new applications, also in the world of science (cf. <a class="reference external" href="https://arxiv.org/pdf/2311.07361.pdf"><em>The Impact of Large Language Models on Scientific Discovery: a Preliminary Study using GPT-4</em>. Microsoft Research</a>). However, most state-of-the-art models are provided by major tech companies and are accessible only through paid APIs. This paywall, along with the requirement to transfer research data to third parties, often hinders the use of so-called “closed” LLMs. In contrast, “open” LLMs, which can be downloaded and used on-premise, are rapidly narrowing the gap in capabilities compared to their closed counterparts (cf. <a class="reference external" href="https://huggingface.co/spaces/HuggingFaceH4/open_llm_leaderboard"><em>Open LLM Leaderboard</em>. Hugging Face</a>). However, the immense size and complexity of LLMs require significant computational resources and pose technical challenges for less experienced users, both in terms of operation and training.</p> <p>Given the computational resources and expertise at the MPCDF, an increasing number of scientists from the Max Planck Society are seeking our advice and support on utilizing LLMs. The inquiries come from a wide range of scientific domains, from natural sciences to the humanities, underscoring the broad impact these models have on the scientific community. The AI group at the MPCDF is actively enhancing its expertise in large language models and expanding its support for various use cases. To this end, we have created the <a class="reference external" href="https://gitlab.mpcdf.mpg.de/dcfidalgo/llms-meet-mpcdf">“LLMs Meet MPCDF” GitLab repository</a>, where we start offering examples and guidance on deploying and fine-tuning LLMs on our HPC systems. For now we showcase how to set up an inference server for open models with <a class="reference external" href="https://github.com/huggingface/text-generation-inference">TGI</a>, and how to supervise-fine-tune a 70B Llama2 model by means of <a class="reference external" href="https://pytorch.org/tutorials/intermediate/FSDP_tutorial.html">FSDP</a>.</p> <p>If you have unaddressed use cases or projects involving LLMs, please don’t hesitate to reach out to us, we would be more than happy to hear from and collaborate with you.</p> <p><em>David Carreto Fidalgo, Andreas Marek</em></p> </div> <div class="section" id="news-events"> <h2><a class="toc-backref" href="#id15">News & Events</a><a class="headerlink" href="#news-events" title="Permalink to this heading"></a></h2> <div class="section" id="introduction-to-mpcdf-services"> <h3><a class="toc-backref" href="#id16">Introduction to MPCDF services</a><a class="headerlink" href="#introduction-to-mpcdf-services" title="Permalink to this heading"></a></h3> <p>The next issue of our semi-annual online course “Introduction to MPCDF services” will be held on April 25th, 14:00-16:30 via Zoom. Topics comprise login, file systems, HPC systems, the Slurm batch system, and the MPCDF services remote visualization, Jupyter notebooks and datashare, together with a concluding question & answer session. Basic knowledge of Linux is required. No registration is required, just connect at the time of the workshop via the <a class="reference external" href="https://mpcdf-mpg-de.zoom-x.de/j/69488919156?pwd=T256S1dXSjhXcU1hNGhZNExkeVVsQT09">zoom link</a>.</p> </div> <div class="section" id="meet-mpcdf"> <h3><a class="toc-backref" href="#id17">Meet MPCDF</a><a class="headerlink" href="#meet-mpcdf" title="Permalink to this heading"></a></h3> <p>The next editions of our monthly online-seminar series “Meet MPCDF” are scheduled for</p> <ul class="simple"> <li><p>May 2nd, 15:30 “CMake - Cross-supercomputer Make” by Vedran Miletic (MPCDF)</p></li> <li><p>June 6th, tba</p></li> </ul> <p>All announcements and material can be found on our <a class="reference external" href="https://www.mpcdf.mpg.de/services/training">training webpage</a>.</p> <p>We encourage our users to propose further topics of their interest, e.g. in the fields of high-performance computing, data management, artificial intelligence or high-performance data analytics. Please send an E-mail to <a class="reference external" href="mailto:training%40mpcdf.mpg.de">training<span>@</span>mpcdf<span>.</span>mpg<span>.</span>de</a>.</p> <p><em>Tilman Dannert</em></p> </div> </div> </div> </div> </div> <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer"> <a href="216.html" class="btn btn-neutral float-left" title="No.216, August 2024" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a> <a href="214.html" class="btn btn-neutral float-right" title="No.214, December 2023" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a> </div> <hr/> <div role="contentinfo"> <p> <span class="lastupdated">Last updated on Apr 18, 2024. </span></p> </div> <p> © Copyright <a href="https://www.mpcdf.mpg.de/">Max Planck Computing and Data Facility</a> | <a href="https://www.mpcdf.mpg.de/imprint">Imprint</a> | <a href="https://www.mpcdf.mpg.de/privacy-policy">Privacy Policy</a> </p> <p> Built with <a href="https://www.sphinx-doc.org">Sphinx</a> using a <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. </p> </footer> </div> </div> </section> </div> <script> jQuery(function () { SphinxRtdTheme.Navigation.enable(true); }); </script> </body> </html>