add attempt to render notebook

note that the notebook has bugs (pun intended) so the render
is commented out for now.

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

weave-demos/Dockerfile

@@ -22,13 +22,26 @@ RUN DEBIAN_FRONTEND="noninteractive" apt-get -y install \
     && 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/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
+    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

@@ -66,6 +66,26 @@ $ python /workflow/ball_bounce/./ball_bounce.py output.dsv 45 37 19 -3 3 1 0.5 1
 
 It generated an output.dsv almost immediately. We could likely adjust the simulation parameters for the calculation.
 
+## Quick Start with Flux
+
+We can basically run the workflow to run the simulation, generate a (partial) notebook (note there were bugs with the
+final visualization) and then copy it over to view it locally.
+
+```bash
+$ docker run --entrypoint bash --rm --name demo -it demos 
+$ flux start --test-size=4
+$ maestro run ball_bounce_suite_flux.yaml --pgen pgen.py -y
+```
+
+**Important** the current notebook has bugs (and is commented out) but if someone can fix them,
+we should be able to uncomment the step and copy it over to our local machine as follows:
+
+```bash
+$ docker cp demo:/workflow/ball_bounce/render.ipynb ./scripts/render.ipynb
+```
+
+If we were doing this with the operator, we would copy this result to a bound volume to save (and maybe some of the simulation data).
+
 ## Run with Flux
 
 I then wanted to run with Flux. Start an instance:
@@ -106,9 +126,8 @@ The content of each looks like:
 $(LAUNCHER) python /workflow/ball_bounce/./ball_bounce.py output.dsv 73 48 11 1 4 5 0.5 100 dcb980 9
 ```
 
-I'm not sure I did that correctly  - I saw [an example for LAUNCHER](https://github.com/LLNL/maestrowf/blob/51056ccfe279495a329036597510d1489dd0c1b1/samples/lulesh/lulesh_sample1_unix_flux.yaml#L19)
-and mimicked it, but I'm skeptical because I don't see any jobs in the `flux jobs -a`. To test, I ran the command manually with flux submit, and I saw the jobs! So I changed `${LAUNCHER}`
-in the flux YAML to just be flux submit, and that seemed to (instead) run everything with Flux.
+I saw [an example for LAUNCHER](https://github.com/LLNL/maestrowf/blob/51056ccfe279495a329036597510d1489dd0c1b1/samples/lulesh/lulesh_sample1_unix_flux.yaml#L19)
+and mimicked it to make a variable named launcher that is basically an alias for `flux submit`.
 
 ```bash
 flux jobs -a
@@ -130,24 +149,18 @@ flux jobs -a
    ƒ41BYo11Z root     python     CD      1      1   0.059s 10864fec333d
 ```
 Note that you'll get callback errors because flux is running as root. We can likely get around this running in the operator.
+When everything is done, you'll see an output.sqlite database in the root directory where you ran maestro, and a render.ipynb
+in the output path.
 
 A high level note - given that Maestro doesn't stay attached to the job, if we are running via the operator the "run as a command" single-user
 mode likely won't work - we would need to run via an interactive job, and determine (on our own) when the workflow is done.
-
-
-## Run with Flux + Notebooks
-
-TBA! I need to test this.
+We can likely use the presence of this file.
 
 ```bash
-$ docker run --entrypoint bash -p 8000:8000 -it demos 
+# ls
 ```
-
-Here is a more "quick start" (not tested yet)
-
-```bash
-$ flux start --test-size=4
-$ maestro run ball_bounce_suite_flux.yaml --pgen pgen.py -y
-# Living dangerously!
-$ jupyter notebook --allow-root --no-browser visualization.ipynb
+```console
+01_baseline_simulation   04_manage_data        README.md       ball_bounce_suite.yaml       output         requirements.txt  visualization.ipynb
+02_uncertainty_bounds    05_post-process_data  __pycache__     ball_bounce_suite_flux.yaml  output.sqlite  setup.sh
+03_simulation_ensembles  06_surrogate_model    ball_bounce.py  dsv_to_sina.py               pgen.py        teardown.sh
 ```

weave-demos/ball_bounce_suite_flux.yaml

@@ -8,6 +8,7 @@ env:
         SIM_SCRIPT_PATH: ./ball_bounce.py
         PROCESS_SCRIPT_PATH: ./dsv_to_sina.py
         OUTPUT_DS_PATH: ./output.sqlite
+        LAUNCHER: flux submit
 
 batch:
     type        : flux
@@ -18,11 +19,20 @@ study:
       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: |
-            flux submit 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)
+            $(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: |
-            flux submit python $(SPECROOT)/$(PROCESS_SCRIPT_PATH) ../run-ball-bounce $(SPECROOT)/$(OUTPUT_DS_PATH)
+            $(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]
+