### Install and Clone AdaptiveCpp Examples Source: https://doku.lrz.de/operation-of-supermuc-ng-phase-2-403079197.html?showLanguage=en_GB Install the github-clone utility using pip and then clone the AdaptiveCpp examples repository. Navigate to the desired example directory. ```bash > pip install --user github-clone > ghclone https://github.com/AdaptiveCpp/AdaptiveCpp/tree/a1647a832ce81eed6d5b5972b7bbd76a45473150/examples > cd examples/bruteforce_nbody ``` -------------------------------- ### Install and clone AdaptiveCpp examples Source: https://doku.lrz.de/operation-of-supermuc-ng-phase-2-403079197.html Install the 'github-clone' utility and clone AdaptiveCpp examples. Navigate to the 'bruteforce_nbody' example directory. ```bash > pip install --user github-clone > ghclone https://github.com/AdaptiveCpp/AdaptiveCpp/tree/a1647a832ce81eed6d5b5972b7bbd76a45473150/examples > cd examples/bruteforce_nbody ``` -------------------------------- ### Spack Install Procedure Example Source: https://doku.lrz.de/openfoam-on-hpc-systems-10746499.html?showLanguage=de_DE Demonstrates the typical workflow for installing OpenFOAM using spack, from loading the module to specifying installation options and verifying the installation. ```bash ~> module load user_spack ~> spack list openfoam ~> spack info openfoam ~> spack spec -lINt openfoam%gcc@7.5.0 ~> spack install -j 40 openfoam%gcc@7.5.0+int64+kahip+metis+mgridgen ``` ```bash ~> module use ~/user_spack/23.1.0/modules/x86_avx512 ~> module av openfoam ~> module load openfoam ``` ```bash ~> blockMesh -help ``` ```bash ~> module load user_spack ~> spack find -pl openfoam -- linux-sles15-x86_64 / gcc@7.5.0 ~> spack load openfoam ~> spack find --loaded -- linux-sles15-x86_64 / gcc@7.5.0 ``` -------------------------------- ### Start R and Install Packages Source: https://doku.lrz.de/faq-r-problems-10746040.html?showLanguage=de_DE Initiates an R session and demonstrates the command to install a package from a repository. Ensure R is installed and accessible in your environment. ```bash $ R R version 2.10.1 (2009-12-14) Copyright (C) 2009 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > install.packages("XML") ``` -------------------------------- ### Load PETSc module and run example Source: https://doku.lrz.de/operation-of-supermuc-ng-phase-2-403079197.html Load the installed PETSc module and Python environment, set necessary environment variables for SYCL offloading and tracing, then run a PETSc example application. ```bash > module load py-petsc4py > module load python/3.10.12-extended # > export I_MPI_HYDRA_BOOTSTRAP=fork I_MPI_FABRICS=shm # on login nodes; otherwise salloc > export ONEAPI_DEVICE_SELECTOR=level_zero:gpu # for offload to the GPU > export SYCL_UR_TRACE=2 # to see L0 offload; ontrace can also be used > python poisson2d.py # lot of L0 output # or >>> from petsc4py import PETSc ``` -------------------------------- ### Install MED from Source Source: https://doku.lrz.de/telemac-on-hpc-systems-opentelemac-telemac-mascaret-2497709101.html?showLanguage=de_DE Initiates the download and installation process for the MED library, a data format for simulation results. The snippet shows the start of the download command. ```bash install_med() { if [ ! -f $THIRD_PARTY_INSTALL_DIR/lib/libmed.so ]; then wget --user-agent="Mozilla/5.0 (Windows NT 10.0; Win64; x64) C ``` -------------------------------- ### Select Installation Steps Source: https://doku.lrz.de/spaces/TUMdocs/pages/1241598632/ACME-DNS%2BServer?showLanguage=de_DE Choose the desired installation steps for the certificate. Options include IIS bindings, external scripts, or no additional steps. ```text 1: Create or update bindings in IIS 2: Start external script or program 3: No (additional) installation steps Add another installation step?: 3 ``` -------------------------------- ### Install NumPy and Start Python 3.8 Session with Conda Source: https://doku.lrz.de/faq-python-problems-10746039.html?showLanguage=de_DE After activating a conda environment, you can install packages like NumPy using 'conda install' and then launch a Python interpreter. This example shows installing NumPy and starting Python 3.8. ```bash (py38) $ conda install -c numpy (py38) $ python Python 3.8.0 (default, Nov 6 2019, 21:49:08) [GCC 7.3.0] :: Anaconda, Inc. on linux Type "help", "copyright", "credits" or "license" for more information. ``` -------------------------------- ### Install NumPy using Conda and Start Python Interpreter Source: https://doku.lrz.de/faq-python-problems-10746039.html Within an activated conda environment (e.g., 'py38'), install the NumPy library using conda. Then, start the Python interpreter. This example assumes the 'py38' environment is already active. ```bash (py38) $ conda install -c numpy (py38) $ python Python 3.8.0 (default, Nov 6 2019, 21:49:08) [GCC 7.3.0] :: Anaconda, Inc. on linux Type "help", "copyright", "credits" or "license" for more information. ``` -------------------------------- ### Setup Local HTTP Proxy Source: https://doku.lrz.de/julia-for-hpc-10746035.html Installs and starts a local HTTP proxy using Python. This is a prerequisite for installing Julia packages on SuperMUC-NG due to internet restrictions. ```bash local> pip install --upgrade --user proxy.py local> ~/.local/bin/proxy --port 3128 # the port number is arbitrary 1024 < port < 64k, but you must remember it! ``` -------------------------------- ### List Job Overview with sacct Source: https://doku.lrz.de/slurm-command-examples-on-the-linux-cluster-1894257007.html?showLanguage=en_US Use sacct to get a compact overview of jobs, including finished ones. This example lists jobs on a specific cluster and partition started after a given date. ```bash sacct --clusters=cm4 --partition=cm4_tiny -X --starttime=2025-08-01T00:00:00 ``` ```text JobID JobName Partition Account AllocCPUS State ExitCode ------------ ---------- ---------- ---------- ---------- ---------- -------- 7919001 job-name cm4_tiny lxcusers 224 TIMEOUT 0:0 7919002 job-name cm4_tiny lxcusers 112 RUNNING 0:0 7919000 job-name cm4_tiny lxcusers 224 COMPLETED 0:0 7919004 job-name cm4_tiny lxcusers 112 PENDING 0:0 7919005 job-name cm4_tiny lxcusers 224 FAILED 1:0 7919003 job-name cm4_tiny lxcusers 224 OUT_OF_ME+ 0:125 ``` -------------------------------- ### Navigate to Download Directory Source: https://doku.lrz.de/einrichten-des-netzzugangs-fuer-mwn-events-unter-linux-1578117658.html?showLanguage=en_US Before executing the setup script, navigate to your download directory in the terminal. This ensures the script can be found and executed correctly. ```bash cd ~/Downloads ``` -------------------------------- ### Initialize Windows Setup Key Source: https://doku.lrz.de/key-management-service-kms-aktivierung-11475966.html?showLanguage=en_US Set the product key for your Windows client before switching to KMS activation. Replace '' with the appropriate key from the provided list. ```batch cscript \windows\system32\slmgr.vbs /ipk ``` -------------------------------- ### Create and Navigate to Tools Directory Source: https://doku.lrz.de/picrust22-10746430.html?showLanguage=de_DE Create a directory for placement tools and change into it. ```bash mkdir ~/DIR/placement_tools cd placement_tools ``` -------------------------------- ### Start Local HTTP Proxy (pip installed) Source: https://doku.lrz.de/faq-installing-your-own-applications-on-supermug-ng-10746066.html?showLanguage=en_GB Alternative command to start the proxy.py server if installed via pip. This is used for enabling internet access from SuperMUC-NG via a reverse SSH tunnel. ```bash local> .local/bin/proxy --port 1234 ``` -------------------------------- ### Configure, Make, and Install Software Source: https://doku.lrz.de/faq-installing-your-own-applications-on-supermug-ng-10746066.html?showLanguage=de_DE Use this command sequence to compile and install self-developed software or packages with small dependency trees. Ensure all dependencies are resolved beforehand and load necessary environment modules. ```bash sng> ./configure --prefix=/home///mydir sng> make sng> make install ``` -------------------------------- ### Get Job Start Time with squeue --start Source: https://doku.lrz.de/slurm-command-examples-on-the-linux-cluster-1894257007.html?showLanguage=en_US Retrieve the estimated start time and state of specific jobs using squeue with the --start option. Note that start times are estimations and may vary. ```bash squeue --clusters=cm4 --job=7918670 --start ``` ```text CLUSTER: cm4 JOBID PARTITION NAME USER ST START_TIME NODES SCHEDNODES NODELIST(REASON) 7918670 cm4_tiny job-name ab01xyz2 PD 2025-08-15T10:13:00 1 node_name (Priority) ``` -------------------------------- ### Initialize Office Setup Key Source: https://doku.lrz.de/key-management-service-kms-aktivierung-11475966.html?showLanguage=en_US Set the product key for your Office client when switching to KMS activation. Replace '' with the relevant key and '' with the correct Office directory. ```batch cscript "«P»\Microsoft Office\\ospp.vbs" /inpkey: ``` -------------------------------- ### Install Bioperl Module using CPAN Source: https://doku.lrz.de/faq-perl-problems-10746065.html Example of installing a specific Perl module, Bioperl, from within the CPAN shell. It shows how to search for distributions and force installation. ```perl cpan> d /bioperl/ CPAN: Storable loaded ok Going to read /home/bosborne/.cpan/Metadata Database was generated on Mon, 20 Nov 2006 05:24:36 GMT .... Distribution B/BI/BIRNEY/bioperl-1.2.tar.gz Distribution B/BI/BIRNEY/bioperl-1.4.tar.gz Distribution C/CJ/CJFIELDS/BioPerl-1.6.0.tar.gz Now install: cpan> force install C/CJ/CJFIELDS/BioPerl-1.6.0.tar.gz ``` -------------------------------- ### Initialize Local Spack Instance Source: https://doku.lrz.de/faq-installing-your-own-applications-on-supermug-ng-10746066.html?showLanguage=de_DE Set up a local Spack environment on your machine by cloning the Spack repository and checking out a specific version. This is the first step in creating a Spack mirror for offline installation. ```bash local> git clone https://github.com/spack/spack ~/spack local> cd spack local> git checkout v0.22.0 # check versions locally and remotely to agree! local> source ~/spack/share/spack/setup-env.sh ``` -------------------------------- ### Aleph Installation: Execute User Mode Source: https://doku.lrz.de/citrix-fuer-bibliotheken-im-bvb-10333067.html?showLanguage=en_US After installation, run this command in the DOS box to finalize the user mode setup for Aleph. ```bash chgusr /execute ``` -------------------------------- ### Set Up Local Spack Instance and Mirror Source: https://doku.lrz.de/faq-installing-your-own-applications-on-supermug-ng-10746066.html This sequence details creating a local Spack environment, adding a package, concretizing dependencies, and creating a mirror for later transfer to SuperMUC-NG. Ensure local and remote Spack versions match. ```bash local> git clone https://github.com/spack/spack ~/spack local> cd spack local> git checkout v0.22.0 # check versions locally and remotely to agree! local> source ~/spack/share/spack/setup-env.sh ``` ```bash local> spack env create -d cache-env local> spacktivate -p cache-env [cache-env] local> spack add cmake@master # add your desired package [cache-env] local> spack find -c # check [cache-env] local> spack concretize # concretize to resolve dependencies [cache-env] local> spack mirror create -d ~/mirror -a # create the mirror ``` -------------------------------- ### LAMMPS Job Script (Local Install) Source: https://doku.lrz.de/operation-of-supermuc-ng-phase-2-403079197.html Example SLURM job script for running a locally installed LAMMPS executable. Ensure environment variables for the installation path and GPU-aware MPI are set correctly. ```bash #!/bin/bash #SBATCH --job-name=your_chosen_name #SBATCH --output=path/to/output/your_job_name_%j.out #SBATCH --error=path/to/error/your_job_name_%j.err #SBATCH --export=NONE #SBATCH --get-user-env #SBATCH --partition=general #SBATCH --account=your_project_id #SBATCH --nodes=n #SBATCH --ntasks-per-node=4 #keep 4 for best performance #SBATCH --time=01:00:00 # modify depending on your required time export FI_PSM3_UUID=$(uuidgen) export OMP_PROC_BIND=spread export OMP_PLACES=threads export ONEAPI_DEVICE_SELECTOR=level_zero:gpu export LD_LIBRARY_PATH=path/to/lammps/install/dir/lib64:$LD_LIBRARY_PATH export PATH=path/to/lammps/install/dir/bin:$PATH export I_MPI_OFFLOAD=1 #activation of gpu-aware mpi export MPICH_GPU_SUPPORT_ENABLED=1 #keep intelmpi gpu-aware. When eqauls to 0 mpich is activated and performance drops. export I_MPI_OFFLOAD_IPC=1 export I_MPI_OFFLOAD_L0_D2D_ENGINE_TYPE=1 export I_MPI_OFFLOAD_RDMA=1 module load intel-toolkit/2024.1.0 #every mpi rank connects with one full gpu. mpirun -np n*4 lmp -sf kk -k on g 4 -pk kokkos newton off neigh half gpu/aware on -in path/to/in.you_script ``` -------------------------------- ### Start Sophos Antivirus Installation Source: https://doku.lrz.de/linux-installation-und-aktualisierung-von-sophos-anti-virus-10615304.html Execute this script to begin the Sophos Antivirus installation process after extracting the files. Ensure you are in the directory where the files were extracted. ```bash ./sophos-av/install.sh ``` -------------------------------- ### Setup and Use Julia with oneAPI Source: https://doku.lrz.de/operation-of-supermuc-ng-phase-2-403079197.html?showLanguage=de_DE Load the Intel toolkit and Julia module, then add and use the 'oneAPI' package within Julia. This example demonstrates checking the oneAPI version and its binary dependencies. ```bash > module load intel-toolkit > module load julia/1.10.5 > julia julia> import Pkg; Pkg.add("oneAPI") # internet access necessary ... julia> using oneAPI julia> oneAPI.versioninfo() Binary dependencies: - NEO: 23.17.26241+3 - libigc: 1.0.13822+0 - gmmlib: 22.3.0+0 - SPIRV_LLVM_Translator_unified: 0.3.0+0 - SPIRV_Tools: 2023.2.0+0 Toolchain: - Julia: 1.10.5 - LLVM: 15.0.7 1 driver: - 00000000-0000-0000-17ac-a75001036681 (v1.3.26241, API v1.3.0) 4 devices: - Intel(R) Data Center GPU Max 1550 - Intel(R) Data Center GPU Max 1550 - Intel(R) Data Center GPU Max 1550 - Intel(R) Data Center GPU Max 1550 ``` -------------------------------- ### Import NumPy in Python Interpreter Source: https://doku.lrz.de/faq-python-problems-10746039.html After starting the Python interpreter within a conda environment where NumPy has been installed, this command verifies the installation by importing the library. ```python >>> import numpy ``` -------------------------------- ### Create Directory for Placement Tools Source: https://doku.lrz.de/picrust2-10746445.html?showLanguage=de_DE Create a directory to store placement tools and navigate into it. ```bash $ mkdir ~/DIR/placement_tools $ cd placement_tools ``` -------------------------------- ### Create and Activate Python Virtual Environment Source: https://doku.lrz.de/faq-conda-mamba-and-python-virtual-environment-on-lrz-hpc-clusters-41616204.html?showLanguage=en_GB This example demonstrates loading a Python module, creating a virtual environment using `venv`, activating it, and verifying the Python executable path. It also shows how to upgrade pip within the environment. ```bash > module av python ------ /lrz/sys/spack/release/22.2.1/modules/x86_64/linux-sles15-x86_64 ------- python/3.7.11-base python/3.8.11-base python/3.7.11-extended python/3.8.11-extended > module load python/3.8.11-base # whatever you want > which python /lrz/sys/spack/release/22.2.1/views/python/3.8.11-base/bin/python > python -m venv my_py_env/ > source my_py_env/bin/activate (my_py_env)> which python /home/user/bin/python (my_py_env)> pip list Package Version ---------- ------- pip 21.1.1 setuptools 56.0.0 WARNING: You are using pip version 21.1.1; however, version 23.2 is available. You should consider upgrading via the '/home/user/my_py_env/bin/python -m pip install --upgrade pip' command. (my_py_env)> python -m pip install --upgrade pip ... (my_py_env)> pip list Package Version ---------- ------- pip 23.2 setuptools 56.0.0 (my_py_env)> pip install numpy scipy ... (my_py_env)> pip list Package Version ---------- ------- numpy 1.24.4 pip 23.2 scipy 1.10.1 setuptools 56.0.0 (my_py_env)> python Python 3.8.11 (default, Jan 26 2022, 17:51:41) [GCC 11.2.0] on linux Type "help", "copyright", "credits" or "license" for more information. >>> import scipy # noticeable ... no errors >>> ... # and so on (my_py_env)> deactivate # deactivate python virtual environment> ```