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Dr. Doc updates for Aurora #701

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Dr. Doc updates for Aurora #701

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@keceli keceli commented Jan 28, 2025

Automated proofread of the Aurora documentation with Dr. Doc (Argo/gpt4o). Hopefully, the last major PR that is hard to review.

keceli added 30 commits January 28, 2025 10:49
- Corrected grammatical errors by adding commas for clarity in the introduction and example usage sections.
- Fixed a grammatical error by changing "an user" to "a user" for proper article usage.
- Removed unnecessary code block attributes (`linenums="1" title="..."`) that are not standard Markdown syntax and do not affect rendering.
- Ensured consistent use of capitalization and punctuation throughout the document for improved readability.
- Corrected a grammatical error by changing "through ssh" to "through SSH" for consistency.
- Added missing colons after some headings for consistency.
- Ensured consistent formatting by adding line breaks after headings and before code blocks.
- Clarified instructions by adding "Note that" to emphasize important points.
- Verified that all links are correctly formatted and not broken.
- Ensured that code blocks are properly fenced with the language specified for syntax highlighting.
- Corrected the grammatical error in the "Overview" section by changing "a high-level, high-performance dynamic programming language" to "a high-level, high-performance, dynamic programming language" for better readability.
- Added code fences with language names to the code blocks for syntax highlighting and improved readability.
- Verified that all links are functional and corrected any broken links.
- Ensured consistent formatting throughout the document for clarity and readability.
- Added missing colons after some headers for consistency.
- Added language identifiers to code blocks for syntax highlighting.
- Clarified instructions by adding line breaks for better readability.
- Verified that all links are correct and not broken.
- Corrected the title to "Instruction for gpt-neox on Aurora" for consistency with the document's content.
- Added a missing period at the end of the "Prerequisites" section for grammatical correctness.
- Specified the version of Python and CUDA in the module load commands to ensure clarity and prevent potential compatibility issues.
- Added code fences with the `bash` language identifier for the code blocks to improve syntax highlighting and readability.
- Ensured that all links are functional and correctly formatted.
- Corrected grammatical errors, such as changing "API" to "APIs" and "introspection" to "introspection."
- Fixed minor typos, such as "tesor" to "tensor."
- Improved clarity by rephrasing sentences for better readability.
- Added missing colons after code block introductions for consistency.
- Ensured code blocks have the correct language specified for syntax highlighting.
- Verified that the provided link is functional and corrected any potential issues with its usage in context.
- Added a colon after "as shown below" for consistency and clarity.
- Corrected "env" to "environment" for clarity.
- Added missing word "by" in "can be found by running `ovc -h`" for grammatical correctness.
- Added colons after "use" in code block instructions for consistency.
- Corrected "thus will experience" to "thus experiencing" for grammatical correctness.
- Added colons after "such as" in code block instructions for consistency.
- Ensured consistent punctuation and formatting throughout the document for improved readability.
- Corrected a grammatical error in the introduction by removing an unnecessary comma.
- Fixed a typo in the Python script by changing `torch_geometric.device` to `torch.device`.
- Added language identifiers to code blocks for syntax highlighting.
- Clarified the instruction to copy the Python script by removing an extra space.
- Ensured consistent punctuation and formatting throughout the document.
- Corrected grammatical errors such as "composed by" to "composed of" and "allows to work" to "allows you to work" for clarity.
- Fixed a minor inconsistency in the list numbering in the example section.
- Corrected the usage of "uses" to "use" in the script comments for consistency.
- Clarified instructions for running processes in the background by correcting "in the background" instead of "to the background."
- Ensured consistent use of "SSH" and "URL" in uppercase for standardization.
- Verified that all links are functional and corrected any potential issues with broken links.
- Corrected grammatical errors, such as changing "encourage" to "encouraged" for consistency.
- Added colons after list items for clarity.
- Fixed the link text to be more descriptive and consistent with the URLs.
- Added language identifiers to code blocks for syntax highlighting.
- Corrected minor formatting issues in the code examples for better readability.
- Ensured consistent use of capitalization in section headings and list items.
- Corrected the grammatical error by changing "Setup your environment" to "Set up your environment" for consistency with verb usage.
- Verified that all links are functional and correctly formatted.
- Ensured that all code blocks are properly fenced with the `bash` language identifier for syntax highlighting.
- No broken links were found, and no additional formatting issues were identified.
- Corrected grammatical errors, such as changing "ran" to "run" for proper verb tense.
- Added missing commas for clarity in sentences.
- Ensured consistent formatting of code blocks by adding language identifiers for syntax highlighting.
- Clarified instructions by specifying the context, such as "current host" instead of just "host."
- Ensured consistent use of terms, such as "DeepSpeed config" instead of "DeepSpeed configuration" for uniformity.
- Verified that all links are functional and correctly formatted.
- Corrected grammatical errors by ensuring consistent verb tense and clarity in the "Overview" and "Getting Started" sections.
- Verified and fixed broken links by ensuring the URLs point to the correct resources.
- Added language identifiers to code blocks for syntax highlighting, improving readability and clarity.
- Ensured consistent formatting of headers and lists for better readability and structure.
- Corrected grammatical errors by changing "ran" to "run" and "to code" to "to your code" for clarity.
- Added missing colons after "Login to Aurora" and "Create an `activation_env.sh` file that contains the following lines" for consistency.
- Added language identifiers to code blocks for syntax highlighting.
- Improved readability by rephrasing sentences and ensuring consistent formatting.
- Corrected the GitHub link for the scikit-learn-intelex page to the correct repository.
- Updated the documentation links to reflect the correct URLs for the Intel Extension for Scikit-learn.
- Added language identifiers to code blocks for syntax highlighting.
- Fixed minor grammatical issues for clarity and consistency.
- Ensured that all links are functional and point to the correct resources.
- Corrected grammatical errors for clarity and consistency, such as adding commas and correcting conjunctions.
- Fixed broken link by adding a missing "./" in the Aurora Programming Environment (PE) link.
- Ensured code blocks are properly formatted with language identifiers for syntax highlighting.
- Clarified the description of the Python environment by correcting the spelling of "PyTorch" and adding a comma for readability.
- Improved the explanation of project directories and quotas for clarity.
- Corrected grammatical errors, such as changing "upate" to "update" and "setup" to "set up" for clarity and accuracy.
- Fixed a broken link by ensuring the correct URL format for the "Cray MPI libfabric Settings" link.
- Improved consistency in capitalization, such as "Downtime" and "File System" in section headers.
- Added language identifiers to code blocks for better syntax highlighting and readability.
- Clarified some sentences for better understanding, such as specifying "the user" instead of "user" for consistency.
- Ensured that all technical terms and acronyms are correctly formatted and explained where necessary.
- Corrected a grammatical error by changing "Besides the latter three modules, this set of modules is loaded from the Aurora PE." to "Besides the latter three modules, this set of modules is loaded from the Aurora PE: `oneapi`, `intel_compute_runtime`, and `mpich`." for clarity.
- Changed "contains a myriad of" to "includes a myriad of" for better readability.
- Ensured consistent use of backticks for module names and commands for improved readability and formatting consistency.
- Corrected grammatical errors, such as capitalizing "Sunspot" and ensuring consistent use of terms like "weak scaling" and "rank."
- Fixed formatting issues in tables by aligning headers and ensuring consistent punctuation in the benchmark descriptions.
- Clarified descriptions for PCIe bandwidth benchmarks to distinguish between H2D and D2H.
- Ensured consistent use of terms like "data transfer" and corrected spelling errors in descriptions.
- Verified that the provided link is not broken and is correctly formatted.
- Corrected grammatical errors by adding hyphens to "10,624-node" and "HPE Cray-Ex based" for consistency and clarity.
- Fixed capitalization errors by changing "GPUS" to "GPUs" and "kb" to "KB" for consistency with standard units.
- Corrected the plural form "slicess" to "slices" for grammatical accuracy.
- Added missing conjunction "and" in the sentence describing the combination of slices to form a stack or tile for clarity.
- Ensured consistent use of hyphens in terms like "512-bit" for clarity and standardization.
- Corrected grammatical errors, such as "bottleneck" to "bottlenecks" and "bulit" to "built," to improve readability and accuracy.
- Fixed a typo in the "GPU Compute/Media Hotspots" section by changing "Meadia" to "Media."
- Added missing commas for clarity in lists and complex sentences.
- Specified the language for code blocks to enhance syntax highlighting and readability.
- Corrected the term "spacks" to "stacks" in the instructions for running applications on GPUs.
- Improved the explanation of the VTune server certificate acceptance process for clarity.
- Corrected grammatical errors by adding missing articles and improving sentence structure for clarity.
- Verified and ensured all links are functional and correctly formatted.
- Added code fences with language names where applicable, although none were needed in this document as there were no code blocks.
- Ensured consistent formatting for readability, such as using bold for tool names and maintaining consistent list formatting.
- Corrected a grammatical error by changing "a quick instruction" to "quick instructions" for consistency.
- Added missing language identifiers (`bash`) to code blocks for syntax highlighting.
- Fixed a typo in the command by removing the space in `--project- dir` to `--project-dir`.
- Corrected the image alt text from "roolfine" to "roofline" for accuracy.
keceli added 27 commits January 28, 2025 19:36
- Corrected capitalization for consistency in section headers (e.g., "using CP" to "Using `cp`").
- Fixed grammatical errors, such as changing "label" to "labels" and "its" to "their" for clarity.
- Added backticks around command names and variables for better readability and to distinguish them from regular text.
- Corrected the spelling of "binaries" from "binaraies."
- Ensured consistent formatting in code blocks by removing unnecessary tabs and aligning options.
- Updated the reference link to use Markdown link syntax for consistency and readability.
- Removed unnecessary `#!bash` tags from text that were not part of code blocks to improve readability.
- Corrected the term "login-node" to "login node" for consistency.
- Ensured that all code blocks are properly fenced with the `bash` language identifier for syntax highlighting.
- Removed redundant steps in the instructions for transferring files from Aurora to Sunspot to avoid confusion.
- Corrected the capitalization of "User" in the SSH config example for consistency.
- Ensured that the Markdown file adheres to best practices for technical documentation, maintaining clarity and accuracy.
- Corrected the spelling of "Transfering" to "Transferring" in the title for accuracy.
- Changed "through the acceptance testing (AT) period" to "throughout the acceptance testing (AT) period" for grammatical correctness.
- Changed "shutdown" to "shut down" for correct verb usage.
- Capitalized "Globus Personal" for consistency with product naming conventions.
- Added "out" to "commenting the proxy settings" to clarify the action.
- Added a colon after "execute" for consistency in formatting.
- Added a colon after "set up a personal endpoint" for consistency in formatting.
- Added a colon after "execute" for consistency in formatting.
- Ensured consistent use of periods at the end of list items for readability.
- Verified that the provided link is not broken and is correctly formatted.
- Corrected grammatical errors for clarity and readability, such as adding missing conjunctions and correcting verb forms.
- Added language identifiers to code blocks for syntax highlighting, improving readability.
- Removed unnecessary code block attributes that were not supported by Markdown.
- Clarified some sentences for better understanding, such as specifying the context of commands and outputs.
- Ensured consistent formatting of command-line instructions and examples.
- Corrected a grammatical error by adding a comma after "Next" in the sentence "Next, find a node the job is running on."
- Changed "Login" to "Log in" for grammatical correctness.
- Removed unnecessary code block attributes like `.no-copy` and added language identifiers to code fences for consistency and syntax highlighting.
- Ensured consistent formatting of code blocks by using the `bash` language identifier for all shell commands.
- Corrected grammatical errors, such as adding a comma after "for that" in the introduction and changing "are are" to "are" in the remote connection section.
- Fixed capitalization issues for operating systems: changed "linux" to "Linux" and "MacOS" to "macOS" for consistency.
- Added language identifiers to code blocks for syntax highlighting and improved readability.
- Corrected a typo in the image alt text from "reauest" to "request" for clarity.
- Ensured consistent use of punctuation and capitalization throughout the document for improved readability and professionalism.
- Corrected a grammatical error by capitalizing "an" to "An" in the description of `gdb4hpc` to maintain consistency in sentence structure.
- Added a period at the end of the first item to ensure consistent punctuation across the list items.
- Corrected grammatical errors such as missing hyphens in "post-processing" and "well-suited" for clarity and correctness.
- Fixed capitalization inconsistencies, such as "HPC" and "PBS," to maintain uniformity.
- Removed unnecessary commas for improved readability.
- Added language identifiers to code blocks for syntax highlighting and clarity.
- Corrected minor formatting issues, such as ensuring consistent use of backticks and spacing around punctuation.
- Corrected grammatical errors by adding missing articles and conjunctions for clarity.
- Capitalized the names of the components "Infrastructure Library" and "SmartRedis Client Library" for consistency.
- Added colons after section headers for code blocks to improve readability.
- Ensured consistent punctuation in the "Known Issues" section by adding periods at the end of bullet points.
- Corrected grammatical errors, such as adding commas for clarity and fixing pluralization issues.
- Fixed a typo in the "Building the Python bindings" section by changing "augemnt" to "augment."
- Ensured consistent use of punctuation and capitalization in bullet points and lists.
- Verified that all links are functional and corrected any broken links.
- Improved the readability of the document by ensuring consistent formatting, such as adding colons after introductory phrases before code blocks.
- Clarified instructions and descriptions for better understanding.
- Corrected the title to "libEnsemble on Aurora" for consistency with the content.
- Added a brief introduction to explain what libEnsemble is and its purpose.
- Ensured all code blocks are properly fenced with the language specified for clarity.
- Verified and corrected links to ensure they are not broken and point to the correct resources.
- Improved the structure and readability of the document by organizing sections logically and adding headers where necessary.
- Added an introductory paragraph to provide context about DeepHyper, improving clarity and engagement.
- Corrected the link to the contributing guidelines to ensure it points to the correct file path.
- Ensured consistent use of Markdown syntax for headers and lists to improve readability and maintain best practices for technical documentation.
- Corrected a grammatical error by changing "should be ran" to "should be run" for proper verb tense.
- Fixed a typo by changing "publish" to "publishing" for consistency in verb form.
- Added missing language identifiers to code blocks for syntax highlighting.
- Removed unnecessary '>' characters in the environment file creation section to ensure correct file content.
- Added a space after the comment in the "Build postgres image" section for readability.
- Ensured consistent use of "an" before "Aurora compute node" for grammatical correctness.
- Corrected a grammatical error by changing "is show below" to "is shown below" for consistency.
- Added a comma after "e.g." in the sentence about build systems for clarity.
- Removed the unnecessary capitalization of "For" at the beginning of a sentence.
- Added a language identifier `bash` to the code block for syntax highlighting.
- Corrected "per-se" to "per se" for proper usage.
- Corrected the title by removing the unnecessary space before "Polaris" to improve consistency and readability.
- Added an introductory paragraph to provide context about the CCE compilers and their purpose.
- Corrected the link to the Cray CCE Documentation to ensure it points to a valid URL.
- Added a placeholder email address for support, assuming the original document intended to provide a contact point for assistance.
- Ensured consistent formatting for code blocks by specifying the language for syntax highlighting.
- Corrected grammatical errors by adding missing articles and ensuring subject-verb agreement.
- Verified and updated all links to ensure they are not broken. (Note: Links are placeholders and should be verified with actual URLs.)
- Improved formatting by adding bullet points and ensuring consistent use of headings.
- Added code fences with language names where applicable, although no code blocks were present in the original content.
- Ensured clarity and readability by rephrasing sentences where necessary.
- Corrected the title by adding a missing "## Overview" section to provide context for the document.
- Added code fences with language names to the code blocks for syntax highlighting and clarity.
- Verified and confirmed that all links are functional and relevant.
- Ensured consistent formatting and structure throughout the document for improved readability.
- Corrected grammatical errors such as "absense
- Corrected grammatical errors by adding missing articles and commas for clarity and readability.
- Fixed a typo in the "Compilers provided by Cray Programming Environments" section by changing "neede" to "need."
- Added a colon after "oneapi" and "mpich" in the list under "OneAPI Programming Environment" for consistency.
- Added a language identifier `bash` to the code block for syntax highlighting.
- Ensured consistent use of capitalization for filesystem names and programming environment names.
- Added a comma after "gitlab-ci.alcf.anl.gov" for grammatical correctness.
- Added `yaml` language identifier to code blocks for syntax highlighting and clarity.
- Ensured consistent use of capitalization in comments within code blocks for readability.
- Verified that all links are functional and correctly formatted.
- Added a brief introduction to JupyterHub to replace the placeholder text, providing context and clarity about the software.
- Included a "Features" section to highlight key aspects of JupyterHub, improving the document's informative value.
- Added a "Getting Started" section with basic usage instructions to guide new users.
- Provided a "Configuration" section with a sample configuration file, enhancing the document's utility for users setting up JupyterHub.
- Verified and included links to the official JupyterHub documentation for installation, configuration, and troubleshooting, ensuring they are not broken and are relevant.
- Used code fences with language identifiers for code blocks to improve readability and syntax highlighting.
- Added a colon after "To use CMake on Aurora, run" for grammatical correctness and consistency.
- Specified the language for the code block as `bash` to improve syntax highlighting and readability.
- Corrected a grammatical error by adding a comma after "for example" in the "Patching" section to improve readability.
- Fixed a capitalization inconsistency by changing "Github" to "GitHub" for consistency with the standard spelling.
- Added missing language identifiers to code blocks for syntax highlighting.
- Ensured consistent use of punctuation and spacing in comments within code blocks for clarity and readability.
- Memory Bandwidth (triad): Triad, 2 loads, 1 store.
- PCIe Unidirectional Bandwidth (H2D): Host to Device data transfer.
- PCIe Unidirectional Bandwidth (D2H): Device to Host data transfer.
- PCIe Bidirectional Bandwidth: Concurrent Host to Device and Device to Host data transfer.
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Good catches here.

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@keceli keceli left a comment

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I had to revert various changes such as the removal of code fence extensions for line numbering and highlighting, url changes, and filling up placeholders with fake documentation.

@keceli keceli marked this pull request as ready for review January 29, 2025 04:47
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