Tom White
Tom White
> 80 cores on 2 machines, totally 320 GB memory, running 16 workers, each with 5 threads I would try doubling the amount of memory that each worker has until...
See https://github.com/pystatgen/sgkit/issues/448#issuecomment-780655217 for the best chunk size found so far
@jeromekelleher you were right about pip! Numpy installs fine, but scipy has a build error (https://github.com/scipy/scipy/issues/13409), and there are no llvmlite wheels yet (needed for numba, https://pypi.org/project/llvmlite/#files). There is progress...
Thanks @jeromekelleher
That's great! I just successfully ran the sgkit popgen tests on Mac Mini.
There are now macos arm64 packages for cyvcf2 on [PyPi](https://pypi.org/project/cyvcf2/#files) (since release 0.30.12). I was able to run all tests (except bgen and plink) using the environment file in this...
Numba wheels should be available in the next release according to https://github.com/numba/numba/issues/7951#issuecomment-1126043337
I updated my branch at https://github.com/tomwhite/sgkit/tree/apple-m1. I can now successfully run the bgen tests now that there is a cbgen build for osx-arm64 on https://anaconda.org/conda-forge/cbgen. The only package missing now...
Can this be closed now that #870 is in?
Hi @AlksIDo - thanks for the question. In the case of multiple VCF files, they are expected to have the same samples (in fact, the same headers), so using `vcf_to_zarr`...