Update readme #506
Update readme #506
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WalkthroughThe changes in this pull request focus on enhancing the documentation for the Changes
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🧹 Outside diff range and nitpick comments (4)
README.md (1)
26-31: Improve text formatting around hyperlinksThe text formatting around the hyperlinks could be improved for better readability. There are unnecessary spaces and dashes around some links.
Apply this diff:
-submitting each function as individual job to the HPC job scheduler - [HPC Submission Mode](https://executorlib.readthedocs.io/en/latest/2-hpc-submission.html) - +submitting each function as individual job to the HPC job scheduler ([HPC Submission Mode](https://executorlib.readthedocs.io/en/latest/2-hpc-submission.html)) -or by requesting a compute allocation of multiple nodes and then distribute the Python functions within this - allocation - -[HPC Allocation Mode](https://executorlib.readthedocs.io/en/latest/3-hpc-allocation.html). Finally, to accelerate the +or by requesting a compute allocation of multiple nodes and then distribute the Python functions within this allocation +([HPC Allocation Mode](https://executorlib.readthedocs.io/en/latest/3-hpc-allocation.html)). Finally, to accelerate the -development process executorlib also provides a - [Local Mode](https://executorlib.readthedocs.io/en/latest/1-local.html) - +development process executorlib also provides a [Local Mode](https://executorlib.readthedocs.io/en/latest/1-local.html)docs/installation.md (3)
36-42: Consider reducing redundant hyperlinksThe hyperlink to [HPC Submission Mode] is repeated in consecutive sentences (lines 38-39). Consider combining these sentences to improve readability while maintaining the same information.
-This is required as in [HPC Submission Mode](https://executorlib.readthedocs.io/en/latest/2-hpc-submission.html) the -Python function is stored on the file system until the requested computing resources become available. +The Python function is stored on the file system until the requested computing resources become available.
71-75: Reduce repetitive references to flux frameworkThe text mentions "flux framework" with its hyperlink 4 times in 5 lines. Consider restructuring to maintain readability while reducing repetition.
-For optimal performance in [HPC Allocation Mode](https://executorlib.readthedocs.io/en/latest/3-hpc-allocation.html) the -[flux framework](https://flux-framework.org) is recommended as job scheduler. Even when the [Simple Linux Utility for Resource Management (SLURM)](https://slurm.schedmd.com) -or any other job scheduler is already installed on the HPC cluster. [flux framework](https://flux-framework.org) can be -installed as a secondary job scheduler to leverage [flux framework](https://flux-framework.org) for the distribution of -resources within a given allocation of the primary scheduler. +For optimal performance in [HPC Allocation Mode](https://executorlib.readthedocs.io/en/latest/3-hpc-allocation.html) the +[flux framework](https://flux-framework.org) is recommended as job scheduler. Even when [SLURM](https://slurm.schedmd.com) +or any other job scheduler is already installed on the HPC cluster, flux can be installed as a secondary scheduler to +leverage its capabilities for resource distribution within a given allocation of the primary scheduler.
77-81: Enhance clarity and add documentation linksConsider improving the technical explanation and adding relevant documentation links:
- Add hyperlinks to
libhwlocandpmidocumentation- Clarify the relationship between MPI implementation and PMI compatibility
-The [flux framework](https://flux-framework.org) uses `libhwloc` and `pmi` to understand the hardware it is running on -and to booststrap MPI. `libhwloc` not only assigns CPU cores but also GPUs. This requires `libhwloc` to be compiled with -support for GPUs from your vendor. In the same way the version of `pmi` for your queuing system has to be compatible -with the version installed via conda. As `pmi` is typically distributed with the implementation of the Message Passing -Interface (MPI), it is required to install the compatible MPI library in your conda environment as well. +The [flux framework](https://flux-framework.org) uses [libhwloc](https://www.open-mpi.org/projects/hwloc/) for hardware +topology discovery and [PMI](https://www.mpich.org/documentation/guides/pmi/) for MPI bootstrapping. While libhwloc handles +both CPU cores and GPU assignments, it requires vendor-specific GPU support during compilation. Similarly, the PMI version +must be compatible between your queuing system and conda installation. Since PMI typically comes with your MPI +implementation, you'll need to install the corresponding MPI library in your conda environment.
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README.md
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README.md
[duplication] ~139-~139: Possible typo: you repeated a word
Context: ...o/en/latest/3-hpc-allocation.html) * SLURM * [SLURM with Flux](https://executorlib.readthed...
(ENGLISH_WORD_REPEAT_RULE)
[duplication] ~140-~140: Possible typo: you repeated a word
Context: ...-allocation.html#slurm) * SLURM with Flux * [Flux](https://executorlib.readthedocs.io/en/...
(ENGLISH_WORD_REPEAT_RULE)
🔇 Additional comments (1)
README.md (1)
124-154: Documentation structure looks good!
The new documentation structure with detailed sections and proper hyperlinks improves navigation and accessibility. The hierarchy is well-organized and covers all important aspects of the library.
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[duplication] ~139-~139: Possible typo: you repeated a word
Context: ...o/en/latest/3-hpc-allocation.html) * SLURM * [SLURM with Flux](https://executorlib.readthed...
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[duplication] ~140-~140: Possible typo: you repeated a word
Context: ...-allocation.html#slurm) * SLURM with Flux * [Flux](https://executorlib.readthedocs.io/en/...
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| @@ -60,8 +61,7 @@ Python function. In addition to the compute cores `cores`, the resource dictiona | |||
| as `threads_per_core`, the GPUs per core as `gpus_per_core`, the working directory with `cwd`, the option to use the | |||
| OpenMPI oversubscribe feature with `openmpi_oversubscribe` and finally for the [Simple Linux Utility for Resource | |||
| Management (SLURM)](https://slurm.schedmd.com) queuing system the option to provide additional command line arguments | |||
| with the `slurm_cmd_args` parameter - [resource dictionary](). | |||
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| with the `slurm_cmd_args` parameter - [resource dictionary](https://executorlib.readthedocs.io/en/latest/trouble_shooting.html#resource-dictionary | |||
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Fix incomplete URL
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-with the `slurm_cmd_args` parameter - [resource dictionary](https://executorlib.readthedocs.io/en/latest/trouble_shooting.html#resource-dictionary
+with the `slurm_cmd_args` parameter - [resource dictionary](https://executorlib.readthedocs.io/en/latest/trouble_shooting.html#resource-dictionary).📝 Committable suggestion
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| with the `slurm_cmd_args` parameter - [resource dictionary](https://executorlib.readthedocs.io/en/latest/trouble_shooting.html#resource-dictionary | |
| with the `slurm_cmd_args` parameter - [resource dictionary](https://executorlib.readthedocs.io/en/latest/trouble_shooting.html#resource-dictionary). |
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (11)
docs/trouble_shooting.md (2)
23-25: Consider minor text refinement for better flow.The links are well-placed and valuable. Consider this minor refinement for better readability:
-Additional features like [caching](https://executorlib.readthedocs.io/en/latest/installation.html#caching), [HPC submission mode](https://executorlib.readthedocs.io/en/latest/installation.html#hpc-submission-mode) -and [HPC allocation mode](https://executorlib.readthedocs.io/en/latest/installation.html#hpc-allocation-mode) require additional dependencies. The dependencies are explained in more detail in the -[installation section](https://executorlib.readthedocs.io/en/latest/installation.html#). +Additional features such as [caching](https://executorlib.readthedocs.io/en/latest/installation.html#caching), [HPC submission mode](https://executorlib.readthedocs.io/en/latest/installation.html#hpc-submission-mode), +and [HPC allocation mode](https://executorlib.readthedocs.io/en/latest/installation.html#hpc-allocation-mode) require additional dependencies. These dependencies are explained in detail in the +[installation section](https://executorlib.readthedocs.io/en/latest/installation.html#).
41-43: Fix typo in parameter description.The added context and link are helpful. There's a minor typo to fix:
-the resource dictionary parameter `resource_dict` can also include additional parameters define in the submission script +the resource dictionary parameter `resource_dict` can also include additional parameters defined in the submission scriptnotebooks/4-developer.ipynb (6)
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1-24: Consider enhancing the documentation headerThe documentation is well-structured, but consider:
- Making the warning about unofficial support more prominent, perhaps in a separate "Warning" or "Note" block
- Adding brief explanations for technical terms like "thread based parallelism" and "MPI based parallelism" for developers who might be new to these concepts
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47-54: Add error handling to execute_shell_command()The function should handle subprocess failures gracefully. Consider adding try-except blocks to catch
subprocess.CalledProcessErrorand other potential exceptions.def execute_shell_command( command: list, universal_newlines: bool = True, shell: bool = False ): import subprocess - - return subprocess.check_output( - command, universal_newlines=universal_newlines, shell=shell - ) + try: + return subprocess.check_output( + command, universal_newlines=universal_newlines, shell=shell + ) + except subprocess.CalledProcessError as e: + raise RuntimeError(f"Command failed with exit status {e.returncode}: {e.output}") + except Exception as e: + raise RuntimeError(f"Failed to execute command: {str(e)}")
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147-157: Enhance process initialization with proper error handlingThe
init_process()function should handle process creation failures and implement proper resource cleanup.def init_process(): import subprocess + import atexit - return { - "process": subprocess.Popen( - ["python", "count.py"], - stdin=subprocess.PIPE, - stdout=subprocess.PIPE, - universal_newlines=True, - shell=False, - ) - } + try: + process = subprocess.Popen( + ["python", "count.py"], + stdin=subprocess.PIPE, + stdout=subprocess.PIPE, + universal_newlines=True, + shell=False, + ) + + def cleanup(): + if process.poll() is None: + process.terminate() + process.wait(timeout=5) + + atexit.register(cleanup) + return {"process": process} + except Exception as e: + raise RuntimeError(f"Failed to initialize process: {str(e)}")
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176-191: Add timeout mechanism to interact()The
interact()function could potentially hang if the expected output is never received. Consider adding a timeout parameter.-def interact(shell_input, process, lines_to_read=None, stop_read_pattern=None): +def interact(shell_input, process, lines_to_read=None, stop_read_pattern=None, timeout=30): + import time + + start_time = time.time() process.stdin.write(shell_input) process.stdin.flush() lines_count = 0 output = "" while True: + if time.time() - start_time > timeout: + raise TimeoutError("Process interaction timed out") + output_current = process.stdout.readline() output += output_current lines_count += 1 if stop_read_pattern is not None and stop_read_pattern in output_current: break elif lines_to_read is not None and lines_to_read == lines_count: break return output
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211-214: Enhance shutdown() with verificationThe
shutdown()function should verify successful process termination and handle hanging processes.-def shutdown(process): +def shutdown(process, timeout=5): process.stdin.write("shutdown\n") process.stdin.flush() + try: + process.wait(timeout=timeout) + except subprocess.TimeoutExpired: + process.terminate() + try: + process.wait(timeout=timeout) + except subprocess.TimeoutExpired: + process.kill() + process.wait()
314-316: Enhance module documentation with version informationConsider adding:
- Version requirements for external dependencies (h5py, cloudpickle, etc.)
- More specific guidance on which standalone components are considered stable for external use
notebooks/1-local.ipynb (3)
233-233: Fix formatting in markdown textThere's a missing space in "Resource \nManagement".
-Management (SLURM)](https://slurm.schedmd.com) +Management (SLURM)](https://slurm.schedmd.com)
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19-19: Improve error handling specificityThe bare try-except block could be more specific about which exceptions it catches. Consider catching specific exceptions like
PermissionErrororFileNotFoundErrorinstead of the generalOSError.- except OSError: + except (PermissionError, FileNotFoundError) as e: + print(f"Failed to remove cache directory: {e}")
328-328: Comprehensive performance optimization guidanceThe documentation provides excellent coverage of performance optimization strategies, including block allocation, caching, and resource management. The warnings about cache usage in production environments are particularly valuable.
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🔇 Additional comments (8)
docs/trouble_shooting.md (1)
19-19: LGTM! Good addition of installation link.
The link to the MPI installation section provides helpful navigation for users seeking setup instructions.
notebooks/3-hpc-allocation.ipynb (6)
9-14: Documentation enhancement looks good!
The added hyperlinks improve navigation and provide clear references to related documentation sections. The links are well-organized and contextually relevant.
25-25: Clear and informative SLURM documentation!
The added explanation about SLURM and flux integration provides valuable context and properly references the documentation.
71-71: Well-documented resource assignment explanation!
The explanation clearly outlines how resource assignment works consistently across different modes, with appropriate links to relevant documentation sections.
125-125: Clear block allocation documentation!
The explanation effectively describes the block allocation functionality and properly references the local mode documentation.
192-192: Well-explained dependencies handling!
The documentation clearly explains how dependencies are handled across different backends, with appropriate reference to the local mode documentation.
234-234: Comprehensive caching documentation!
The explanation effectively describes the caching functionality, includes important performance considerations, and properly references the local mode documentation.
notebooks/1-local.ipynb (1)
Line range hint 1-700: Well-structured and comprehensive code examples
The code examples effectively demonstrate the library's features with a clear progression from basic to advanced concepts. They include proper error handling and resource cleanup.
Summary by CodeRabbit
README.mdwith added hyperlinks to key sections.docs/installation.mdwith updated installation instructions and links to relevant documentation.