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PyTorch Geometric Setup on DGX

Steps

1. Create a Python virtual enviroment and activate it

[user@hal-dgx]$ pyenv virtualenv 3.9.6 pytorch-geometric-example
[user@hal-dgx]$ pyenv activate pytorch-geometric-example
(pytorch-geometric-example) [user@hal-dgx]$ python -m pip install --upgrade pip setuptools wheel

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Simple cProfile example with snakeviz

Environment Setup

Make a Python virtual environment and install the dependencies

python -m pip install --upgrade pip setuptools wheel
python -m pip install -r requirements.txt

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If you enclose a regex in parentheses () whatever is enclosed can be used in a search and replace by a number that is indexed starting with 1. So for example

\section{\sc Research Interests}

can be found with the regex

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Understanding Python virtual environments

High Level Introductions

• Is UV the FUTURE of Python PACKAGING? 🐍📦, by Hynek Schlawack
• Which Python Package Manager Should You Use?

Articles

• How virtual environments work by Brett Cannon

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X11 Forwarding to Docker

Examples of X11 forwarding to Docker for Linux and macOS. In both situations:

• xhost is used to set the host and/or user names allowed to make connections to the X server
• The DISPLAY Docker environment variable must be set
• The directory /tmp/.X11-unix/ directory must be volume mounted into the container at /tmp/.X11-unix/

Linux

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# Use the generator .next method to quickly get the first non-None item in a list

if __name__ == "__main__":
    item_list = [None, None, "non-None-A", "non-None-B", None]
    item = next(item for item in item_list if item is not None)
    assert item == "non-None-A"
    print(item)

# -            axes = next(
# -                artist

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Examples of non-interactive matplotlib backends with or without GUIs

It is first worth reading about backends in the matplotlib Usage Guide.

Non-interactive with GUI

Running

$ python with_gui.py

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.ipynb_checkpoints/

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Stacked Bar Plot Example

Summary

This is an example of how to create a stacked bar plot with percent family from a fish data set. Using this example you will be able to take a full data set and compute the family proportions just before plotting without the need to save a new dataframe.

Dependencies

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.ipynb_checkpoints/
example.root