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mkdocs.yml
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site_name: ALCF User Guides
repo_name: 'argonne-lcf/user-guides'
repo_url: 'https://github.com/argonne-lcf/user-guides'
site_url: 'https://docs.alcf.anl.gov/'
theme:
name: 'material'
custom_dir: overrides
language: 'en'
palette:
scheme: alcf
font:
text: proxima-nova
features:
- tabs
- instant
- search.highlight
- navigation.sections
- navigation.path
- navigation.indexes
- toc.follow
- search.suggest
- content.code.copy
- content.code.annotate
#- content.code.select # experimental
logo: images/logo.svg
favicon: "images/favicon.svg"
extra_css:
- stylesheets/alcf-extra.css
extra_javascript:
- javascripts/alcf-extra.js
markdown_extensions:
- footnotes
- admonition
- codehilite
- tables
- attr_list
- md_in_html
- pymdownx.critic
- pymdownx.inlinehilite
- pymdownx.keys
- pymdownx.caret
- pymdownx.mark
- pymdownx.tilde
- pymdownx.snippets:
base_path: ["."] # for root of repo, default since that is where mkdocs.yml is
# base_path: ["docs"]
dedent_subsections: True # experimental; new in 9.10 (2023-03-05)
check_paths: True
url_download: True
- pymdownx.superfences
- pymdownx.details
- pymdownx.inlinehilite
- pymdownx.highlight:
use_pygments: true
anchor_linenums: true
line_spans: __span
pygments_lang_class: true
- pymdownx.tabbed:
alternate_style: true
- pymdownx.tasklist:
custom_checkbox: true
- pymdownx.blocks.definition
- pymdownx.blocks.caption
validation:
omitted_files: warn
absolute_links: warn
unrecognized_links: warn
anchors: warn
not_found: warn
extra:
social:
- icon: 'fontawesome/brands/github-alt'
link: 'https://github.com/argonne-lcf/user-guides'
analytics:
provider: google
property: G-4M48E2L33R
plugins:
- include-markdown
- codeinclude:
title_mode: pymdownx.tabbed
- search:
lang: en
nav:
- ALCF User Guides:
- index.md
- Account and Project Management:
- Accounts and Access:
- MyALCF: account-project-management/accounts-and-access/MyALCF.md
- User Account: account-project-management/accounts-and-access/user-account-overview.md
- Passcode Tokens: account-project-management/accounts-and-access/alcf-passcode-tokens.md
- Accounts and Access FAQs: account-project-management/accounts-and-access/accounts-and-access-faqs.md
- Project Management:
- Starting Your ALCF Award: account-project-management/project-management/starting-alcf-award.md
- Managing Your Team Members: account-project-management/project-management/team-management.md
- Reporting: account-project-management/project-management/project-reports.md
- Allocations:
- Allocations on ALCF Computing Resources: account-project-management/allocation-management/overview.md
- Managing Your Allocations: account-project-management/allocation-management/allocation-management.md
- sbank Allocation Accounting System: account-project-management/allocation-management/sbank-allocation-accounting-system.md
- Data Management:
- ALCF Community Data Co-Op: data-management/acdc/acdc-overview.md
- Sharing on Eagle Using Globus: data-management/acdc/eagle-data-sharing.md
- Transferring Data to Eagle: data-management/acdc/transferring-data-to-eagle.md
- Data Transfer:
- SFTP and SCP: data-management/data-transfer/sftp-scp.md
- Using Globus: data-management/data-transfer/using-globus.md
- File System & Storage:
- File Systems: data-management/filesystem-and-storage/file-systems.md
- Data Storage: data-management/filesystem-and-storage/data-storage.md
- HPSS: data-management/filesystem-and-storage/hpss.md
- Disk Quota: data-management/filesystem-and-storage/disk-quota.md
- Facility Policies:
- Overview of Policies: policies/facility-policies.md
- ALCF Acknowledgement Policy: policies/alcf-acknowledgement-policy.md
- Account Policies:
- Accounts Policy: policies/accounts/accounts-policy.md
- Account Sponsorship & Retention Policy: policies/accounts/account-sponsorship-retention-policy.md
- User Authentication Policy: policies/accounts/user-authentication-policy.md
- Queue and Scheduling Policies:
- Queue and Scheduling Policy: policies/queue-scheduling/queue-and-scheduling-policy.md
- Refund Policy: policies/queue-scheduling/refund-policy.md
- Pullback Policy: policies/queue-scheduling/pullback-policy.md
- Data and Software Policies:
- Data Policy: policies/data-and-software-policies/data-policy.md
- Software Policy: policies/data-and-software-policies/software-policy.md
- Machines:
- AI Testbed:
- Getting Started: ai-testbed/getting-started.md
- Cerebras:
- System Overview: ai-testbed/cerebras/system-overview.md
- Getting Started: ai-testbed/cerebras/getting-started.md
- Running a Model/Program: ai-testbed/cerebras/running-a-model-or-program.md
- Customizing Environments: ai-testbed/cerebras/customizing-environment.md
- Job Queuing and Submission: ai-testbed/cerebras/job-queuing-and-submission.md
- Example Programs: ai-testbed/cerebras/example-programs.md
#- Performance Tools: ai-testbed/cerebras/performance-tools.md
- Tunneling and Forwarding Ports: ai-testbed/cerebras/tunneling-and-forwarding-ports.md
- Miscellaneous: ai-testbed/cerebras/miscellaneous.md
- Graphcore:
- System Overview: ai-testbed/graphcore/system-overview.md
- Getting Started: ai-testbed/graphcore/getting-started.md
- Virtual Environment: ai-testbed/graphcore/virtual-environments.md
- Running a Model/Program: ai-testbed/graphcore/running-a-model-or-program.md
- Job Queuing and Submission: ai-testbed/graphcore/job-queuing-and-submission.md
- Example Programs: ai-testbed/graphcore/example-programs.md
- Miscellaneous: ai-testbed/graphcore/miscellaneous.md
- Documentation: ai-testbed/graphcore/documentation.md
- Groq:
- System Overview: ai-testbed/groq/system-overview.md
- Getting Started: ai-testbed/groq/getting-started.md
- Running a Model/Program: ai-testbed/groq/running-a-model-or-program.md
#- Example Programs: ai-testbed/groq/example-programs.md
- Virtual Environments: ai-testbed/groq/virtual-environments.md
- Job Queueing and Submission: ai-testbed/groq/job-queuing-and-submission.md
- Profiling with GroqView: ai-testbed/groq/groqview.md
- SambaNova:
- System Overview: ai-testbed/sambanova/system-overview.md
- Getting Started: ai-testbed/sambanova/getting-started.md
- Virtual Environment: ai-testbed/sambanova/virtual-environment.md
- Running a Model/Program: ai-testbed/sambanova/running-a-model-or-program.md
- Job Queuing and Submission: ai-testbed/sambanova/job-queuing-and-submission.md
- Example Programs: ai-testbed/sambanova/example-programs.md
- Example Multi-Node Programs: ai-testbed/sambanova/example-multi-node-programs.md
# - Running BERT Large on Sambanova DataScale SN30-8: ai-testbed/sambanova/running-bert-large-on-sn30.md
- Modelzoo Samples: ai-testbed/sambanova/example-modelzoo-programs.md
- Tunneling and Forwarding Ports: ai-testbed/sambanova/tunneling-and-forwarding-ports.md
- SambaTune for profiling and performance tuning: ai-testbed/sambanova/sambatune.md
- Miscellaneous: ai-testbed/sambanova/miscellaneous.md
- SambaNova Documentation: ai-testbed/sambanova/documentation.md
# - Performance Tools: ai-testbed/sambanova/performance-tools.md
- Data Management: ai-testbed/data-management/data-management-overview.md
- Aurora:
- Getting Started: aurora/getting-started-on-aurora.md
- Aurora Programming Environment: aurora/aurora-pe.md
- Early User Notes and Known Issues: aurora/known-issues.md
- Machine Overview: aurora/hardware-overview/machine-overview.md
- Node Performance Overview: aurora/node-performance-overview/node-performance-overview.md
- Compiling and Linking:
- Compiling and Linking Overview: aurora/compiling-and-linking/compiling-and-linking-overview.md
- Programming Models: aurora/compiling-and-linking/aurora-programming-models.md
- Example Program and Makefile: aurora/compiling-and-linking/aurora-example-program-makefile.md
# - LLVM Compilers: aurora/compiling-and-linking/llvm-compilers-aurora.md
# - GNU Compilers: aurora/compiling-and-linking/gnu-compilers-aurora.md
# - CCE Compilers: aurora/compiling-and-linking/cce-compilers-aurora.md
# - Continuous Integration: aurora/compiling-and-linking/continuous-integration-aurora.md
- Build Tools:
- CMake: aurora/build-tools/cmake-aurora.md
- Running Jobs: aurora/running-jobs-aurora.md
- Data Management:
- Copper: aurora/data-management/copper/copper.md
- DAOS: aurora/data-management/daos/daos-overview.md
- Lustre (Flare): aurora/data-management/lustre/flare.md
- Moving data to Aurora:
- DAOS Data Mover: aurora/data-management/moving_data_to_aurora/daos_datamover.md
- Globus: aurora/data-management/moving_data_to_aurora/globus.md
- SCP: aurora/data-management/moving_data_to_aurora/scp.md
- Applications and Libraries:
- Libraries:
- Cabana: aurora/applications-and-libraries/libraries/cabana-aurora.md
#- Math Libraries: aurora/applications-and-libraries/libraries/math-libraries.md
#- MKL: aurora/applications-and-libraries/libraries/mkl.md
#- MPI: aurora/applications-and-libraries/libraries/mpi.md
- oneDAL: aurora/applications-and-libraries/libraries/onedal.md
- Spack PE: aurora/applications-and-libraries/libraries/spack-pe.md
- Containers: aurora/containers/containers.md
- Data Science:
#- Julia: aurora/data-science/julia.md
- Python: aurora/data-science/python.md
- Jupyter: aurora/data-science/jupyter.md
#- Applications:
#- gpt-neox: aurora/data-science/applications/gpt-neox.md
- Profiling: aurora/data-science/profiling_dl.md
- Frameworks:
- DeepSpeed: aurora/data-science/frameworks/deepspeed.md
- Megatron-DeepSpeed: aurora/data-science/frameworks/megatron-deepspeed.md
#- JAX: aurora/data-science/frameworks/jax.md
- PyTorch: aurora/data-science/frameworks/pytorch.md
- TensorFlow: aurora/data-science/frameworks/tensorflow.md
- Dask: aurora/data-science/frameworks/dask.md
- oneCCL: aurora/data-science/frameworks/oneCCL.md
- scikit-learn: aurora/data-science/frameworks/scikit-learn.md
- oneDAL: aurora/applications-and-libraries/libraries/onedal.md
- GPyTorch: aurora/data-science/frameworks/gpytorch.md
- PyTorch Geometric (PyG): aurora/data-science/frameworks/pyg.md
- AI Inference:
- LibTorch: aurora/data-science/inference/libtorch.md
- OpenVINO: aurora/data-science/inference/openvino.md
- Programming Models:
- Kokkos: aurora/programming-models/kokkos-aurora.md
- Level Zero: aurora/programming-models/level-0.md
- OpenCL: aurora/programming-models/opencl-aurora.md
- OpenMP: aurora/programming-models/openmp-aurora.md
#- RAJA: aurora/programming-models/raja-aurora.md
- SYCL: aurora/programming-models/sycl-aurora.md
- Debugging Tools:
- Overview: aurora/debugging/debugging-overview.md
- gdb-oneapi: aurora/debugging/gdb-oneapi.md
- DDT: aurora/debugging/ddt-aurora.md
- gdb4hpc: aurora/debugging/gdb4hpc.md
- Performance Tools:
# - Overview: aurora/performance-tools/performance-overview.md
- Advisor: aurora/performance-tools/advisor.md
- VTune: aurora/performance-tools/vtune.md
# - Visualization:
# - ParaView: aurora/visualization/paraview.md
- Services:
- GitLab: aurora/services/gitlab-ci.md
#- JupyterHub: aurora/services/jupyterhub.md
- Workflows:
- ADIOS2: aurora/workflows/adios.md
- Balsam: aurora/workflows/balsam.md
# - DeepHyper: aurora/workflows/deephyper.md
# - libEnsemble: aurora/workflows/libensemble.md
- Parsl: aurora/workflows/parsl.md
- SmartSim: aurora/workflows/smartsim.md
- Crux:
- Machine Overview: crux/hardware-overview/machine-overview.md
- Getting Started: crux/getting-started.md
- Running Jobs: crux/queueing-and-running-jobs/running-jobs.md
- Compiling and Linking: crux/compiling-and-linking/compiling-and-linking-overview.md
- Containers: crux/containers/containers.md
- Data Science:
- Python: crux/data-science/python.md
#- Visualization:
#- Visualization on Crux: crux/visualization/visualization.md
#- ParaView (Launch from Client): crux/visualization/paraview.md
- Polaris:
- Getting Started: polaris/getting-started.md
- System Updates: polaris/system-updates.md
- Contacting Support and Software Requests: polaris/contacting-support.md
- Known Issues: polaris/known-issues.md
- Machine Overview: polaris/hardware-overview/machine-overview.md
# - Polaris Machine Overview: polaris/hardware-overview/machine-overview.md
- Compiling and Linking:
- Compiling and Linking Overview: polaris/compiling-and-linking/compiling-and-linking-overview.md
- Programming Models: polaris/compiling-and-linking/polaris-programming-models.md
- Example Program and Makefile: polaris/compiling-and-linking/polaris-example-program-makefile.md
- CCE Compilers: polaris/compiling-and-linking/cce-compilers-polaris.md
- GNU Compilers: polaris/compiling-and-linking/gnu-compilers-polaris.md
- NVIDIA Compilers: polaris/compiling-and-linking/nvidia-compiler-polaris.md
- LLVM Compilers: polaris/compiling-and-linking/llvm-compilers-polaris.md
- oneAPI Toolkit: polaris/compiling-and-linking/oneapi-compiler.md
- Build Tools:
- CMake: polaris/build-tools/cmake-polaris.md
- Running Jobs: polaris/running-jobs.md
- Applications and Libraries:
- Applications:
- Amber: polaris/applications-and-libraries/applications/amber.md
- GROMACS: polaris/applications-and-libraries/applications/gromacs.md
- LAMMPS: polaris/applications-and-libraries/applications/lammps.md
- NAMD: polaris/applications-and-libraries/applications/namd.md
- NekRS: polaris/applications-and-libraries/applications/nekrs.md
- OpenMM: polaris/applications-and-libraries/applications/openmm.md
- QMCPACK: polaris/applications-and-libraries/applications/QMCPACK.md
- Quantum ESPRESSO: polaris/applications-and-libraries/applications/QuantumESPRESSO.md
- VASP: polaris/applications-and-libraries/applications/vasp.md
- Libraries:
- Math Libraries: polaris/applications-and-libraries/libraries/math-libraries.md
- Cabana: polaris/applications-and-libraries/libraries/cabana-polaris.md
- Spack PE: polaris/applications-and-libraries/libraries/spack-pe.md
- NCCL: polaris/applications-and-libraries/libraries/nccl.md
- XALT: polaris/applications-and-libraries/libraries/xalt.md
- Containers: polaris/containers/containers.md
- Data Science:
- Julia: polaris/data-science/julia.md
- Python: polaris/data-science/python.md
- Profiling: polaris/data-science/profiling_dl.md
- Frameworks:
- TensorFlow: polaris/data-science/frameworks/tensorflow.md
- PyTorch: polaris/data-science/frameworks/pytorch.md
- JAX: polaris/data-science/frameworks/jax.md
- DeepSpeed: polaris/data-science/frameworks/deepspeed.md
- LibTorch: polaris/data-science/frameworks/libtorch.md
- GPyTorch: polaris/data-science/frameworks/gpytorch.md
- Applications:
- Megatron-DeepSpeed: polaris/data-science/applications/megatron-deepspeed.md
- gpt-neox: polaris/data-science/applications/gpt-neox.md
- Programming Models:
- OpenMP: polaris/programming-models/openmp-polaris.md
- SYCL: polaris/programming-models/sycl-polaris.md
- Kokkos: polaris/programming-models/kokkos-polaris.md
- Debugging Tools:
- CUDA-GDB: polaris/debugging-tools/CUDA-GDB.md
- Performance Tools:
- NVIDIA-Nsight: polaris/performance-tools/NVIDIA-Nsight.md
- Visualization:
- Visualization on Polaris: polaris/visualization/visualization.md
- ParaView (Launch from Client): polaris/visualization/paraview.md
- ParaView (Manual Launch): polaris/visualization/paraview-manual-launch.md
- VisIt: polaris/visualization/visit.md
- FFmpeg: polaris/visualization/ffmpeg.md
- ImageMagick: polaris/visualization/imagemagick.md
- ParaView Tutorial: polaris/visualization/paraview-tutorial.md
- VNC: polaris/visualization/vnc.md
- Workflows:
- Multi-Instance GPU (MIG) mode: polaris/workflows/mig-compute.md
- Balsam: polaris/workflows/balsam.md
- Parsl: polaris/workflows/parsl.md
- libEnsemble: polaris/workflows/libensemble.md
- SmartSim: polaris/workflows/smartsim.md
- Sophia:
- Machine Overview: sophia/hardware-overview/machine-overview.md
- Getting Started: sophia/getting-started.md
- Running Jobs: sophia/queueing-and-running-jobs/running-jobs.md
- Compiling and Linking: sophia/compiling-and-linking/compiling-and-linking-overview.md
- Containers: sophia/containers/containers.md
- Data Science:
- Python: sophia/data-science/python.md
- Fine-tuning with Autotrain: sophia/data-science/fine-tune-LLM-with-Autotrain.md
- Visualization:
- Visualization on Sophia: sophia/visualization/visualization.md
- ParaView (Launch from Client): sophia/visualization/paraview.md
- Services: # services/index.md # Cant directly link to this in the nav sidebar, since
# it is a dropdown. Only linked to in base docs/index.md
- Getting Started: services/getting-started.md
- JupyterHub: services/jupyter-hub.md
- Continuous Integration:
- General: services/continuous-integration.md
- Gitlab-CI: services/gitlab-ci.md
- Running Jobs with PBS at the ALCF:
- Job Scheduling and Execution: running-jobs/job-and-queue-scheduling.md
- Example Job Scripts: running-jobs/example-job-scripts.md
- Machine Reservations: running-jobs/machine-reservations.md
- Cobalt to PBS option Comparison: running-jobs/pbs-qsub-options-table.md
- Questions / Issues: issues.md
not_in_nav: |
not_in_nav/
unused/
todo.md
TODO.md
notes.md
# TODO: complete or remove Aurora placeholder pages
llvm-compilers-aurora.md
gnu-compilers-aurora.md
cce-compilers-aurora.md
continuous-integration-aurora.md
aurora/applications-and-libraries/libraries/math-libraries.md
aurora/applications-and-libraries/libraries/mkl.md
aurora/applications-and-libraries/libraries/mpi.md
aurora/data-science/julia.md
aurora/data-science/applications/gpt-neox.md
aurora/data-science/frameworks/jax.md
aurora/programming-models/raja-aurora.md
aurora/performance-tools/performance-overview.md
aurora/visualization/paraview.md
aurora/services/jupyterhub.md
aurora/workflows/balsam.md
aurora/workflows/deephyper.md
aurora/workflows/libensemble.md