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mkdocs.yml
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site_name: UL HPC Tutorials
nav:
- Home: 'index.md'
- Latest HPC School: 'hpc-school.md'
- Setup:
- Overview: 'setup/index.md'
- Pre-Requisites: 'setup/preliminaries.md'
- Clone and setup ULHPC Tutorials: 'setup/install.md'
- First interactions with ULHPC:
- The UNIX/Linux Shell: 'linux-shell/index.md'
- SSH and OpenOnDemand: 'preliminaries/index.md'
- Getting started:
- Overview: 'beginners/index.md'
- Job scheduling with SLURM: 'basic/scheduling/index.md'
- Using software modules: 'tools/cli/modules.md'
- Tools / Software management:
- Easybuild: 'tools/easybuild/index.md'
- Spack: 'tools/spack/index.md'
- Conda: 'tools/conda/index.md'
# - RESIF: 'tools/resif/index.md'
- Data Management: 'data/index.md'
- Scheduling:
- Advanced job scheduling with SLURM: 'scheduling/advanced/index.md'
- Debugging and Profiling:
- Monitoring and profiling: 'basic/monitoring/index.md'
- Efficient Debugging: 'debugging/basics/index.md'
- Performance engineering: 'debugging/advanced/index.md'
- Sequential/Embarrassingly parallel jobs:
- Introduction to GNU Parallel: 'sequential/manytasks-manynodes2/index.md'
- GNU Parallel on a Single Node: 'sequential/gnu-parallel/index.md'
- GNU Parallel on Multiple Nodes: 'sequential/manytasks-manynodes/index.md'
- Choosing between Parallel-Slurm and GNU Parallel: 'sequential/basics/index.md'
- Serial Tasks in Action:
- Overview: 'sequential/examples/index.md'
- Example/Object Recognition: 'sequential/examples/object_recognition.md'
- Example/Watermarking Images: 'sequential/examples/watermarking.md'
- Example/JCell (GA in Java): 'sequential/examples/jcell.md'
- Parallel MPI and/or OpenMP:
- Overview: 'parallel/basics/index.md'
- OSU Micro-benchmarks: 'parallel/mpi/OSU_MicroBenchmarks/index.md'
- High Perf. Linpack (HPL): 'parallel/mpi/HPL/index.md'
- High Perf. Conjugate Gradient (HPCG): 'parallel/hybrid/HPCG/index.md'
- Python:
- Prototyping with Python: 'python/basics/index.md'
- Jupyter: 'python/advanced/jupyter/index.md'
- Celery: 'python/advanced/celery/index.md'
- Ipyparallel-Scikit-learn: 'python/advanced/scikit-learn/index.md'
- Scoop-Deap: 'python/advanced/scoop-deap/index.md'
- Dask-ML: 'python/advanced/dask-ml/index.md'
- GPU Programming:
- Introduction to CUDA C/C++ (2023): 'gpu/cuda2023/index.md'
- Accelerating Applications with CUDA C/C++: 'cuda/index.md'
- CUDA Convolution using GPU: 'cuda/exercises/convolution/index.md'
- Introduction to OpenCL Programming: 'gpu/opencl/index.md'
- Introduction to OpenACC: 'gpu/openacc/basics/index.md'
- Solving Laplace Equation on GPU with OpenACC: 'gpu/openacc/laplace/index.md'
- Mathematics:
- MATLAB: 'maths/matlab/basics/index.md'
- MATLAB (advanced): 'maths/matlab/advanced/index.md'
- R - statistical computing: 'maths/R/index.md'
- Cplex - Gurobi: 'maths/Cplex-Gurobi/index.md'
- An introduction to numerical methods with BLAS: 'maths/BLAS/index.md'
- Bioinformatics:
- Running bioinformatics software: 'bio/basics/index.md'
- Bioinformatics workflows with snakemake and conda: 'bio/snakemake/index.md'
- Galaxy: 'bio/galaxy/index.md'
- CFD/MD/Chemistry:
- Advanced Parallel execution: 'multiphysics/index.md'
- Big Data:
- Big Data Application Over Hadoop and Spark: 'bigdata/index.md'
- Machine and Deep Learning:
- Machine and Deep Learning workflows: 'deep_learning/basics/index.md'
- Scalable Deep Learning: 'deep_learning/scalable/index.md'
- Distributed Deep Learning with Horovod: 'deep_learning/horovod/index.md'
- Large Language Model with HuggingFace/DeepSpeed: 'deep_learning/huggingface/index.md'
- Containers:
- Reproducibility and HPC Containers : 'containers/ULHPC-containers/index.md'
- Singularity: 'containers/singularity/index.md'
- Singularity-Infiniband: 'containers/singularity-inf/index.md'
- Virtualization:
- Vagrant: 'virtualization/vagrant/index.md'
- Graphcore IPU:
- Machine Learning: 'experimental_hardware/graphcore_ipu/machine_learning/index.md'
- Misc:
- Reproducible Research: 'misc/reproducible-research/index.md'
# - Advanced topics:
# - Advanced workflows on sequential jobs management: 'advanced/advanced_workflows/README.md'
- Documentation (RTFD): 'rtfd.md'
- Contributing: 'contributing.md'
- Contacts: 'contacts.md'
theme: readthedocs
# See https://github.com/mkdocs/mkdocs/issues/253
markdown_extensions:
- pymdownx.arithmatex:
- pymdownx.snippets:
- markdown.extensions.abbr:
- markdown.extensions.toc:
- markdown.extensions.tables:
- markdown.extensions.attr_list:
# - markdown_include.include:
# base_path: docs
extra_javascript:
# other extra java script
- mathjax-config.js
- https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML