Jitify compilation errors are not visible in notebooks

[ptheywood]

When running pyflamegpu from a notebook, jitify compile errors are not shown to the user

I.e. all that is seen is:

FLAMEGPURuntimeException: (InvalidAgentFunc) /__w/FLAMEGPU2/FLAMEGPU2/src/flamegpu/util/detail/JitifyCache.cu(342): Error compiling runtime agent function (or function condition) ('grass_growth'): function had compilation errors (see std::cout), in JitifyCache::buildProgram().

This is not the case for running python outside of a notebook

This appears to be resolved by running a more recent version of ipython/jupyter, but a workaround is still required for collab where we cannot update this.

Todo

• [ ] Update instance hub to use a newer jupyter/ipython (@mondus)
  • ipykernel >= 6.0.0a5 outputs the stdout when an exception is thrown
  • Requires python >= 3.7, process will depend on the base AWS image used.
• [ ] Describe this issue in a known issues section of the readme + the solution(s) (update, and/or restart the kernel)
• [ ] Colab branch needs a new cell and section to perform this update, and instructions on how to restart the kernel. Potentially make this opt-in (i.e. comment it out initially unless there is a way to exclude from run_all

Notes

Locally, jupyter lab and jupyter notebook both show stdout on Ubuntu 21.04, python 3.9 with the following jupyter packages:

ipykernel           6.3.1
ipython             7.27.0
ipython-genutils    0.2.0

nbclassic           0.3.1
nbclient            0.5.4
nbconvert           6.1.0

jupyter-client      7.0.2
jupyter-core        4.7.1
jupyter-server      1.10.2
jupyterlab          3.1.10
jupyterlab-pygments 0.1.2
jupyterlab-server   2.8.0

And from About juptyer notebook:

The version of the notebook server is: 6.4.3-86f11a1

Python 3.9.5 (default, May 11 2021, 08:20:37) 
[GCC 10.3.0]

Python 3.9.5 (default, May 11 2021, 08:20:37) 
Type 'copyright', 'credits' or 'license' for more information
IPython 7.27.0 -- An enhanced Interactive Python. Type '?' for help.

The Innstance hub jupyter notebook is running:

ipykernel                     5.5.5
ipython                       7.16.1
ipython-genutils              0.2.0
ipywidgets                    7.6.3

nbclient                      0.5.3
nbconvert                     6.0.7
nbformat                      5.1.3

jupyter                       1.0.0
jupyter-client                6.1.12
jupyter-console               6.4.0
jupyter-core                  4.7.1
jupyterlab-pygments           0.1.2
jupyterlab-widgets            1.0.0

The version of the notebook server is: 6.4.0
The server is running on this version of Python:
Python 3.6.9 (default, Jan 26 2021, 15:33:00) 
[GCC 8.4.0]

Current Kernel Information:
Python 3.6.9 (default, Jan 26 2021, 15:33:00) 
Type 'copyright', 'credits' or 'license' for more information
IPython 7.16.1 -- An enhanced Interactive Python. Type '?' for help.

Installing the exact versions as found on the intancehub hosted copy, the stdout being consumed can be reproduced:

python3 -m pip install ipykernel==5.5.5 ipython==7.16.1 ipython-genutils==0.2.0 ipywidgets==7.6.3 nbclient==0.5.3 nbconvert==6.0.7 nbformat==5.1.3 jupyter==1.0.0 jupyter-client==6.1.12 jupyter-console==6.4.0 jupyter-core==4.7.1 jupyterlab-pygments==0.1.2 jupyterlab-widgets==1.0.0 

Colab is running the following:

ipython                       5.5.0
ipython-genutils              0.2.0
ipython-sql                   0.3.9
jupyter                       1.0.0
jupyter-client                5.3.5
jupyter-console               5.2.0
jupyter-core                  4.7.1
jupyterlab-pygments           0.1.2
jupyterlab-widgets            1.0.0
nbclient                      0.5.4
nbconvert                     5.6.1
nbformat                      5.1.3

Installing differnt versions of ipykernel has identified 6.0.0a5 (Released: Apr 26, 2021) as the first pypi release version which fixes this issue / introduces the change. This may help find a workaround.

The closed issues for milestone 6.0 for the ipykernel project may provide some insight.

The diff between 6.0.0a4 and 6.0.0a5 can also be found: https://github.com/ipython/ipykernel/compare/6.0.0a4...6.0.0a5

https://github.com/ipython/ipykernel/pull/630 is the relevant PR.

[ptheywood]

Older ipython versions will also consume any stdout output from flamegpu, i.e. --timing or --verbose output.

[ptheywood]

Updating ipykernel on colab does work, but requires a kernel restart. Pip also complains due to package incompatibility but it does work. This seems like a very sketchy solution though.

!python -m pip install ipykernel==6.0.0

Runtime > Restart Runtime (or ctrl + M .), then Yes. Variables are then lost, so most cells wil need re-running.

[ptheywood]

Decisions:

• @mondus will tweak the instancehub image to upgrade the version on ipykernel via pip (and dependent packages
  • This may also need the python version upgrading / a new version installing. (ipykern 6.0.0 is python 3.7+)
• The readme will be updated with a known issues section describing this issue, and solutions (update ipykernel, if on colab restart the kernel
• The collab branch will have an (optional?) early cell which will upgrade the packages, and instruct users on how to restart the kernel.

[ptheywood]

This issues is still present, with google collab still running ipykernel 5.3.4

import ipykernel
print(ipykernel.__version__)
5.3.4

I opened an issue about this / requesting an update with googlecollab at the time: https://github.com/googlecolab/colabtools/issues/2230

[ptheywood]

Logs can be viewed by Runtime -> view runtime logs (https://github.com/FLAMEGPU/FLAMEGPU2/discussions/1020#discussioncomment-4410748). We should probably add this to the text.

We could potentially ammend the error message in python land if running in jupyter too, if detection and ipython version detection is possible?