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pangenome / pggb

the pangenome graph builder
https://doi.org/10.1038/s41592-024-02430-3
MIT License
368 stars 41 forks source link

gcc 11 docker #240

Closed ekg closed 1 year ago

ekg commented 2 years ago

Try to work around build errors with an updated seqwish.

ekg commented 2 years ago

@AndreaGuarracino I was trying to get around -mcx16 because it prevents ARM builds.

AndreaGuarracino commented 2 years ago

I think this post explains what is happening. Indeed, this commit was necessary to be able to build seqwish without the -march=native option. Moreover, also on my laptop, with Ubuntu 22.04 and Intel CPU, I am not able to build the current seqwish's master with the -DCMAKE_BUILD_TYPE=Generic option.

Now, by using this seqwish's commit that forces the -march=haswell option when we build with -DCMAKE_BUILD_TYPE=Generic or -DCMAKE_BUILD_TYPE=Debug (not -DCMAKE_BUILD_TYPE=Release, so without -march=native), we are able to fully build PGGB's Dockerfile with the latest seqwish, but I am not sure if this destroys stuff on ARM systems. I see that with aarch64 ASAN doesn't like the result.

AndreaGuarracino commented 2 years ago

Building seqwish with -DCMAKE_BUILD_TYPE=Release is the only current way to get it on aarch64 (https://github.com/ekg/seqwish/pull/104/commits/6bc8c87ae77ee61c816fe6e56040cac6125d4ffc), so the doubts remain.