add weave demos (#23)

* add weave demos

Signed-off-by: vsoch <vsoch@users.noreply.github.com>

weave-demos/Dockerfile

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+ARG tag=jammy
+FROM ubuntu:${tag}
+
+# docker build -t demos .
+# command without flux: maestro run ball_bounce_suite.yaml --autoyes --pgen pgen.py
+# workdir: /workflow
+
+ENV DEBIAN_FRONTEND=noninteractive
+RUN apt-get update
+RUN apt-get -y install \    
+    bwa \
+    git \
+    samtools \
+    bcftools \
+    curl \
+    libbz2-dev \
+    liblzma-dev \
+    libcurl4-openssl-dev \
+    libncurses5-dev \
+    python3-pip \
+    && apt-get clean \
+    && apt-get autoremove \
+    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+# This is needed for the notebook render
+RUN  git clone https://github.com/LLNL/PyDV /tmp/pydv && \
+     cd /tmp/pydv/ && \
+     python3 -m pip install .
+
+# Wrappers to ensure we source the mamba environment!
+RUN git clone --depth 1 https://github.com/LLNL/weave-demos /workflow
+WORKDIR /workflow/CZ/ball_bounce
+COPY ./scripts/setup.sh /setup.sh
+COPY ./ball_bounce_suite_flux.yaml ./ball_bounce_suite_flux.yaml
+RUN /bin/bash /setup.sh && python3 -m pip install -r requirements.txt && \
+    # The workflow expects to find python
+    ln -s /usr/bin/python3 /usr/bin/python && \
+    python3 -m pip install jut && \
+    python3 -m pip install typing-extensions --upgrade && \
+    python3 -m pip install ipympl && \
+    python3 -m pip install pydv
+
+# Temporary fix for
+# https://github.com/LLNL/PyDV/issues/275
+COPY ./scripts/pydvpy.py /usr/local/lib/python3.8/dist-packages/pydv/pydvpy.py 
+COPY ./scripts/visualization.ipynb ./visualization.ipynb
+EXPOSE 8888

weave-demos/README.md

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+# Weave Demos
+
+This is an example container where you can build (optional) and run
+the [weave demos](https://github.com/LLNL/weave-demos), specifically
+to simualte bouncing a ball.
+
+```bash
+$ docker build -t demos .
+```
+
+Then shell inside
+
+```bash
+$ docker run --entrypoint bash -it demos 
+```
+
+## Manual Run
+
+To run the tutorial as is (without Flux) do:
+
+```bash
+# The "y" says yes to prompts
+$ maestro run ball_bounce_suite.yaml --pgen pgen.py -y
+```
+
+Output will appear in "output" and you can dig into the subdirectory to find logs:
+
+```bash
+$ cat output/ball-bounce_20230315-035713/logs/ball-bounce.log 
+```
+```console
+...
+2023-03-15 03:57:22,708 - maestrowf.datastructures.core.executiongraph:_execute_record:584 - INFO - Attempting submission of 'run-ball-bounce_BOX_SIDE_LENGTH.100.GRAVITY.0.5.GROUP_ID.8d0688.RUN_ID.7.X_POS_INITIAL.45.X_VEL_INITIAL.-2.Y_POS_INITIAL.37.Y_VEL_INITIAL.8.Z_POS_INITIAL.19.Z_VEL_INITIAL.-1' (attempt 1 of 1)...
+2023-03-15 03:57:22,775 - maestrowf.interfaces.script.localscriptadapter:submit:151 - INFO - Execution returned status OK.
+```
+The last line should say it returned OK and shouldn't say FAILED! I found the output directories (length!) a little overwhelming to browse, so I installed and used tree:
+
+```bash
+$ apt-get update && apt-get install -y tree
+$ tree output/*/run-ball-bounce/
+```
+```console
+└── BOX_SIDE_LENGTH.100.GRAVITY.0.5.GROUP_ID.8d0688.RUN_ID.9.X_POS_INITIAL.45.X_VEL_INITIAL.7.Y_POS_INITIAL.37.Y_VEL_INITIAL.-6.Z_POS_INITIAL.19.Z_VEL_INITIAL.-2
+    ├── output.dsv
+    ├── run-ball-bounce_BOX_SIDE_LENGTH.100.GRAVITY.0.5.GROUP_ID.8d0688.RUN_ID.9.X_POS_INITIAL.45.X_VEL_INITIAL.7.Y_POS_INITIAL.37.Y_VEL_INITIAL.-6.Z_POS_INITIAL.19.Z_VEL_INITIAL.-2.33.err
+    ├── run-ball-bounce_BOX_SIDE_LENGTH.100.GRAVITY.0.5.GROUP_ID.8d0688.RUN_ID.9.X_POS_INITIAL.45.X_VEL_INITIAL.7.Y_POS_INITIAL.37.Y_VEL_INITIAL.-6.Z_POS_INITIAL.19.Z_VEL_INITIAL.-2.33.out
+    └── run-ball-bounce_BOX_SIDE_LENGTH.100.GRAVITY.0.5.GROUP_ID.8d0688.RUN_ID.9.X_POS_INITIAL.45.X_VEL_INITIAL.7.Y_POS_INITIAL.37.Y_VEL_INITIAL.-6.Z_POS_INITIAL.19.Z_VEL_INITIAL.-2.sh
+```
+It looks like each directory has a script, and output, and an error file. I found the output/error to be empty, but the `output.dsv` is some kind of matric of numbers, and the submit script
+(the shell script) is just a single line:
+
+```
+#!/bin/bash
+
+python /workflow/ball_bounce/./ball_bounce.py output.dsv 45 37 19 -3 3 1 0.5 100 8d0688 2
+```
+
+This is probably what they mean when they say running a single simulation. That command runs one simulation. For
+fun, I tried this on my own:
+
+```bash
+$ mkdir test
+$ cd test
+$ python /workflow/ball_bounce/./ball_bounce.py output.dsv 45 37 19 -3 3 1 0.5 100 8d0688 2
+```
+
+It generated an output.dsv almost immediately. We could likely adjust the simulation parameters for the calculation.

weave-demos/ball_bounce_suite_flux.yaml

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+description:
+    name: ball-bounce 
+    description: A workflow that simulates a ball bouncing in a box over several input sets.
+
+env:
+    variables:
+        OUTPUT_PATH: ./output
+        SIM_SCRIPT_PATH: ./ball_bounce.py
+        PROCESS_SCRIPT_PATH: ./dsv_to_sina.py
+        OUTPUT_DS_PATH: ./output.sqlite
+        LAUNCHER: flux submit
+
+batch:
+    type        : flux
+
+study:
+    - name: run-ball-bounce
+      description: Run a family of simulations of a ball in a box. 
+      run:
+          # Note that flux submit before (should be?) $(LAUNCHER) but I didn't see that worked - I think likely it needs a different submit command / setup
+          cmd: |
+            $(LAUNCHER) python $(SPECROOT)/$(SIM_SCRIPT_PATH) output.dsv $(X_POS_INITIAL) $(Y_POS_INITIAL) $(Z_POS_INITIAL) $(X_VEL_INITIAL) $(Y_VEL_INITIAL) $(Z_VEL_INITIAL) $(GRAVITY) $(BOX_SIDE_LENGTH) $(GROUP_ID) $(RUN_ID)
+    - name: ingest-ball-bounce
+      description: Ingest the outputs from the previous step
+      run:
+          cmd: |
+            $(LAUNCHER) python $(SPECROOT)/$(PROCESS_SCRIPT_PATH) ../run-ball-bounce $(SPECROOT)/$(OUTPUT_DS_PATH)
+          depends: [run-ball-bounce_*]
+
+# This notebook has bugs - but when fixed this will work
+#    - name: plot-ball-bounce
+#      description: Generate the notebook that shows something interesting!
+#      run:
+          # I hard coded the path because I was lazy - not ideal
+#          cmd: |
+#            $(LAUNCHER) jupyter nbconvert --to notebook --execute /workflow/ball_bounce/visualization.ipynb --output=/workflow/ball_bounce/render.ipynb --ExecutePreprocessor.timeout=-1
+#          depends: [ingest-ball-bounce]
+