Accessing Anaconda Channels from Mamba

Question

I am building my Python environment around micromamba.
I was wondering how can I use the Anaconda channels to download packages as described in conda channels: https://docs.conda.io/projects/conda/en/latest/user-guide/concepts/channels.html.

By default micromamba is configured to work with conda-forge yet I'd like to access the numpy and scipy packages of Anaconda (Which are compiled using MKL).

Motivation

I am asking since when I install from conda-forge by looking at the configuration of numpy I get:

python -c "import numpy as np; np.show_config()"
blas_info:
    libraries = ['cblas', 'blas', 'cblas', 'blas', 'cblas', 'blas']
    library_dirs = ['C:/Applications/Python\\Library\\lib']
    include_dirs = ['C:/Applications/Python\\Library\\include']
    language = f77
    define_macros = [('HAVE_CBLAS', None)]
blas_opt_info:
    define_macros = [('NO_ATLAS_INFO', 1), ('HAVE_CBLAS', None)]
    libraries = ['cblas', 'blas', 'cblas', 'blas', 'cblas', 'blas']
    library_dirs = ['C:/Applications/Python\\Library\\lib']
    include_dirs = ['C:/Applications/Python\\Library\\include']
    language = f77
lapack_info:
    libraries = ['lapack', 'blas', 'lapack', 'blas']
    library_dirs = ['C:/Applications/Python\\Library\\lib']
    language = f77
lapack_opt_info:
    libraries = ['lapack', 'blas', 'lapack', 'blas', 'cblas', 'blas', 'cblas', 'blas', 'cblas', 'blas']
    library_dirs = ['C:/Applications/Python\\Library\\lib']
    language = f77
    define_macros = [('NO_ATLAS_INFO', 1), ('HAVE_CBLAS', None)]
    include_dirs = ['C:/Applications/Python\\Library\\include']
Supported SIMD extensions in this NumPy install:
    baseline = SSE,SSE2,SSE3
    found = SSSE3,SSE41,POPCNT,SSE42,AVX,F16C,FMA3,AVX2,AVX512F,AVX512CD,AVX512_SKX,AVX512_CLX
    not found = AVX512_CNL

Which doesn't seem to be linked to MKL.

merv · Answer 1 · 2022-10-03T14:21:27.090

2

You don't need to use the Anaconda builds to use MKL. Conda Forge uses a different strategy for integrating BLAS/LAPACK implementations, which can mask the info shown from np.show_config() (some details here). Adding the specification

'blas=*=*mkl'

to your package specifications (either in YAML or in conda install) will ensure Conda Forge NumPy, etc. will use MKL.

Otherwise, one can switch to using Anaconda packages by adding the anaconda channel, as in this answer¹. Just be aware that channel mixing can be messy. Personally, I would just stick to Conda Forge.

_{[1]: While I previously recommended using anaconda channel in the other answer, I have since read up more the Conda Forge strategy.}

edited Oct 03 '22 at 14:21

answered Sep 08 '22 at 18:45

merv

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What's the default if one didn't do anything? What to write in the `yaml` file to define the environment? – Mark Sep 09 '22 at 10:05
good day dear Merv - thanks this is very heplful. Well i am new to Python and i want to install a environment - ihave read this here: https://stackoverflow.com/questions/45421163/anaconda-vs-miniconda well should i take mamba instead - plz advice – thannen Oct 02 '22 at 23:01
@Thomas there is no explicit default, which means that the solver will try to take whatever has been updated most recently. Most often I see`openblas` installed on **osx-64** platform when I don't specify. There is [documentation on how to define a YAML](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#create-env-file-manually). The `blas=*=*mkl` specification would go under the `dependencies` section. – merv Oct 03 '22 at 14:22
1

@thannen Mamba is an add-on - it can be added to any **base** installation. That other thread is a better place to discuss installers. Personally, I recommend MambaForge to professional practitioners (e.g., bioinformaticians). – merv Oct 03 '22 at 14:34

Accessing Anaconda Channels from Mamba

Motivation

1 Answers1