8000 Docker build on Apple M1 Pro fails · Issue #17 · nvictus/pybbi · GitHub
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pkerpedjiev opened this issue Dec 26, 2021 · 5 comments · Fixed by #18
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Docker build on Apple M1 Pro fails #17

pkerpedjiev opened this issue Dec 26, 2021 · 5 comments · Fixed by #18

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@pkerpedjiev
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pkerpedjiev commented Dec 26, 2021 •
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This can be reproduced using the following Dockerfile:

FROM python:3.10-buster


RUN git clone --depth 1 --branch v0.3.0 https://github.com/nvictus/pybbi.git
WORKDIR /pybbi

RUN python setup.py develop

Which yields the following error:

#6 35.22     gcc -pthread -shared -Wl,--no-as-needed build/temp.linux-aarch64-3.10/tmp/pip-install-9qwissbi/pybbi_a9b215e7b84842eeb5602c22e3022feb/bbi/cbbi.o -L/tmp/pip-install-9qwissbi/pybbi_a9b215e7b84842eeb5602c22e3022feb/src/x86_64 -L/usr/local/lib -lkent -lssl -lcrypto -lpng16 -lz -o build/lib.linux-aarch64-3.10/bbi/cbbi.cpython-310-aarch64-linux-gnu.so
#6 35.22     /usr/bin/ld: cannot find -lkent
#6 35.22     collect2: error: ld returned 1 exit status
#6 35.22     error: command '/usr/bin/gcc' failed with exit code 1

Running python setup.py develop finishes without error.

Edit:

I think it might be because the libkent library gets built in aarch64/libkent.a but gcc expects it to be in x86_64/libkent.a:

Library being built:

ar rcus aarch64/libkent.a aliType.o annoAssembly.o ...

and pybbi being built:

gcc -pthread -shared -Wl,--no-as-needed build/temp.linux-aarch64-3.10/pybbi/bbi/cbbi.o -L/pybbi/src/x86_64

Looks like $(MACHTYPE) in ./Makefile doesn't match $(MACHTYPE) in src/Makefile.

Interesting... if I change the Dockerfile to:

FROM python:3.10-buster


COPY src src
COPY bbi bbi
COPY setup.py setup.py
COPY README.md README.md
COPY Makefile Makefile
COPY include include

RUN python setup.py develop

It runs successfully.

Edit 2:

I think this has something to do with Rosetta running on my mac. uname -m outputs x86_64 on my terminal. Now the question is why the first Makefile is using aarch64 🤔

Edit 3:

The second Dockerfile ran successfully because I had previously built the library outside of the Docker and the COPY src src line included the already built libkent. If I remove that file and run the second Dockerfile above, it fails like the first one.
@pkerpedjiev pkerpedjiev mentioned this issue Dec 26, 2021
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@pkerpedjiev
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Found the issue. Here's a fix:

#18

@pkerpedjiev
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Would be great to get a new release with this PR 🙏

@TkhiienLok TkhiienLok mentioned this issue Dec 27, 2021
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@nvictus
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nvictus commented Dec 27, 2021

Thanks for the fix and sorry for the delay. The source dist is now up on PyPI: https://pypi.org/project/pybbi/0.3.1/#files

@nvictus
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nvictus commented Dec 28, 2021

So, I cavalierly dropped the six dependency without checking that it was actually eliminated... Use this release instead https://pypi.org/project/pybbi/0.3.2/#files

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nvictus commented Dec 28, 2021

I was also able to generate a dual-architecture universal2 wheel for cp310 on Mac OS. You may want to try it too.

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