mkdocs.yml

site_name: ALCF User Guides
nav:
  - Home: index.md
  - Account and Project Management:
    - Accounts and Access: 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
  - 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
  - Aurora:
      - Getting Started: aurora/getting-started-on-aurora.md
      - Aurora PE: aurora/aurora-pe.md
      - Sunspot to Aurora: aurora/sunspot-to-aurora.md
      - Known Issues: aurora/known-issues.md
      - Hardware 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
      - Data Science:
        #- Julia: aurora/data-science/julia.md
        - Python: aurora/data-science/python.md
        #- Applications:
          #- gpt-neox: aurora/data-science/applications/gpt-neox.md
        - Containers: aurora/data-science/containers/containers.md
        - Frameworks:
          #- DeepSpeed: aurora/data-science/frameworks/deepspeed.md
          #- JAX: aurora/data-science/frameworks/jax.md
          - PyTorch: aurora/data-science/frameworks/pytorch.md
          - TensorFlow: aurora/data-science/frameworks/tensorflow.md
          - LibTorch: aurora/data-science/frameworks/libtorch.md
          - OpenVINO: aurora/data-science/frameworks/openvino.md
          - oneCCL: aurora/data-science/frameworks/oneCCL.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-aurora.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:
        # - 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
  - Polaris:
    - Getting Started: polaris/getting-started.md
    - System Updates: polaris/system-updates.md
    - Known Issues: polaris/known-issues.md
    - Hardware Overview:
      - 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
        - 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
        - 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
  - 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
  - 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
  - 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
  - Docs Questions/Issues: issues.md
not_in_nav: |
  not_in_nav/
  unused/
  todo.md
  TODO.md
  notes.md
  account-project-management/index.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/applications-and-libraries/libraries/onedal.md
  aurora/data-science/julia.md
  aurora/data-science/applications/gpt-neox.md
  aurora/data-science/frameworks/deepspeed.md
  aurora/data-science/frameworks/jax.md
  aurora/programming-models/raja-aurora.md
  aurora/debugging/gdb-oneapi-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
  aurora/workflows/parsl.md

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