Create Docker wheel builder by bdevans · Pull Request #592 · genn-team/genn

bdevans · 2023-07-05T16:31:19Z

This adds Dockerfile.builder and a Makefile target (make wheel) to cleanly build python wheels within a Docker container. The versions of CUDA and Python can be specified by passing build arguments.

… 3.10

bdevans · 2023-07-18T12:24:28Z

You may also want to consolidate GENN_DIR and GENN_PATH into one argument throughout the project, as they appear to refer to the same path but have different names in the Dockerfile and Makefile.

neworderofjamie · 2023-07-25T16:37:04Z

This is very cool - would it be possible to build them on manylinux2014 (https://github.com/pypa/manylinux) for compatibility across linuxes? https://github.com/ameli/manylinux-cuda has some docker files for installing CUDA on top of many linux

bdevans · 2023-07-26T11:23:57Z

I can have a go at basing it on manylinux2014. Those docker images don't have the cuDNN libraries though - does the wheel need them?

neworderofjamie · 2023-07-26T11:25:31Z

That'd be awesome - GeNN doesn't need cuDNN at all, just cuRAND

bdevans · 2023-07-27T18:03:23Z

Here you go! I've renamed the previous target (use it with: make ubuntu_wheel) and added a new one make wheels which will build a wheel for each of the installed python versions for a given CUDA version.

Note that building against python 3.12 currently fails (probably to do with it still being in beta) so I included a clause to skip it which will eventually need to be removed. Also the build process still uses the double python setup.py bdist_wheel craziness, so the second one will need to be removed when a new release is made with the fix.

neworderofjamie

Very cool! manylinux wheels will be an excellent feature for GeNN 5.0.0

neworderofjamie · 2023-07-28T10:46:59Z

Dockerfile

-LABEL org.opencontainers.image.documentation="https://genn-team.github.io/"
-LABEL org.opencontainers.image.source="https://github.com/genn-team/genn"
-LABEL org.opencontainers.image.title="GeNN Docker image"
+LABEL maintainer="J.C.Knight@sussex.ac.uk" \


thank you for the tidying here - I didn't realise just how directly dockerfile lines mapped to layers and thus massive disk wastage when I wrote this

neworderofjamie · 2023-07-28T10:48:12Z

Dockerfile.ubuntu_builder

@@ -0,0 +1,46 @@
+# syntax=docker/dockerfile:1


What's the point of keeping (and maintaining) this one? if you have manylinux wheels you can use them on all the ubunti

Well you can ignore it for now but it might be a more robust alternative for Ubuntu users and it's a little simpler so might also be a useful reference for when the build system changes.

neworderofjamie · 2023-07-28T10:50:25Z

Dockerfile.ubuntu_builder

+WORKDIR ${GENN_PATH}
+
+# Install GeNN and PyGeNN
+RUN make install -j `lscpu -p | egrep -v '^#' | sort -u -t, -k 2,4 | wc -l`


there is no need to make install when all you're doing is build PyGeNN - that's only if you want a system-wide installation to use GeNN from C++

Ok I'll remove it.

neworderofjamie · 2023-07-28T10:50:37Z

build-wheels.sh

+    # "${PYBIN}/pip" install -r /io/dev-requirements.txt
+    "${PYBIN}/pip" install numpy swig
+    # "${PYBIN}/pip" wheel /opt/genn/ --no-deps -w dist/
+    make install -j `lscpu -p | egrep -v '^#' | sort -u -t, -k 2,4 | wc -l`


Again, no need to make install

neworderofjamie · 2023-07-28T10:50:56Z

build-wheels.sh

+    "${PYBIN}/pip" install numpy swig
+    # "${PYBIN}/pip" wheel /opt/genn/ --no-deps -w dist/
+    make install -j `lscpu -p | egrep -v '^#' | sort -u -t, -k 2,4 | wc -l`
+    make DYNAMIC=1 LIBRARY_DIRECTORY=${GENN_PATH}/pygenn/genn_wrapper/ -j `lscpu -p | egrep -v '^#' | sort -u -t, -k 2,4 | wc -l`


this doesn't link against python so could be done once outside of the loop

I must have misunderstood something then. The packages need to be installed within the loop still though don't they? Since GeNN uses them for bindings, doesn't that also mean it should be built within the loop?

the stuff you're installing with pip definitely need to be done within the loop but make DYNAMICS=1 etc etc isn't Python-specific, it just builds GeNN as shared libraries and sticks them where the python build system expects them to be so can move it outside the loop (it probably won't do anything after the first iteration anyway cos nothing will have changed)

neworderofjamie · 2023-07-28T10:53:25Z

Makefile

+		--build-arg CUDA=$(CUDA) \
+		--target=output --output type=local,dest=dist/ .
+
+# TODO: Consider build with docker run instead of docker build


What would the advantages of that be?

I'm not sure yet, beyond saving a bit of time in image building. It was the method used in the example but I'd need to investigate a bit more.

neworderofjamie · 2023-07-28T10:55:38Z

Dockerfile

 FROM nvidia/cuda:${BASE}

-LABEL maintainer="J.C.Knight@sussex.ac.uk"
-LABEL version="4.8.0"


Do you know if there's any way to read this from the version.txt? I've managed to convince setuptools and doxygen to do this but couldn't figure it out for docker

Well passing it as a build-arg is simple and explicit but I expect you could also do it with the right cat / sed incantation.

Dockerfile.builder

bdevans added 12 commits July 5, 2023 12:30

Tidy up Dockerfile

59821ad

Use best practice for pip

4c5232b

Implement wheel builder

62be93d

Fix missing numpy and build command

36695b5

Fix broken variable expansion with relative path

453584d

Generalise to choose python version

535c158

Try to fix missing pip

9ecfb1d

Enable use of python not python3

2b2fcba

Fix pip version problem although it may still be using pip for python…

df13a92

… 3.10

Update labels

777fddf

Remove cruft

650ea5f

More tidying

7173468

bdevans added 14 commits July 26, 2023 12:37

Rename Dockerfile.builder

aa1517c

Revise target

006dc8a

Add syntax metadata

75a8104

Change maintainer

2a0e322

Fix typo

7d7aff3

Install swig with pip

45eab7e

Create manylinux builder with script

0bbbc1e

Add Makefile wheel target

03ce5a7

Rename and set execute permissions

e5afcf9

Fix path

6c65327

Rename target

467df85

Fix python path

6b89724

Skip python 3.12 (still in beta)

454588d

Tidy up and add notes

4964c4c

neworderofjamie self-requested a review July 28, 2023 10:46

neworderofjamie reviewed Jul 28, 2023

View reviewed changes

neworderofjamie added enhancement linux docker labels Jul 28, 2023

neworderofjamie added this to the GeNN 5.0.0 milestone Jul 28, 2023

bdevans added 12 commits July 28, 2023 12:56

Skip pypy builds

0cb7461

No need to make install

340e5b8

Move make command outside of python loop

52d1114

Update default base image

0faac71

Get versions and save as labels with build-arg

198c5bc

Restrict wheels to current python versions

5f0bbcc

Create all_wheels to build for all supported CUDA versions

bd4027b

Fix syntax

ed4a23f

Make all_wheels phony

dc90abc

Add link to supported Python versions

412ca02

Output to subdirectory named after CUDA version

06c85f3

Merge branch 'genn-team:master' into master

e28b84c

neworderofjamie mentioned this pull request Oct 11, 2023

Docker improvements #601

Merged

neworderofjamie merged commit d1e97e1 into genn-team:master Oct 11, 2023

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bdevans commented Jul 27, 2023 •

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