BUG: _sysconfigdata__linux_aarch64-linux-gnu.py contains invalid compiler options in CFLAGS

[geoffreyblake]

Checklist

• I added a descriptive title.
• I searched through existing issues and couldn't find a solution or duplicate issue.
• I searched on the web (e.g. Google) and didn't find any helpful information.
• I searched the Anaconda documentation and didn't find any helpful information.

Impacted product

• A conda package (built by Anaconda)
• Anaconda Distribution (formerly Anaconda Individual Edition)
• Miniconda
• Anaconda.org

What happened?

Downloaded and installed Miniconda3-latest-Linux-aarch64.sh on an Ubuntu 20.04 VM on Graviton2 and discovered that certain Python packages with binary dependencies will not install properly due to bad CFLAGS directives causing compiler errors in the distribution's lib/_sysconfigdata__linux_aarch64-linux-gnu.py file that is used by setuptools and distutils to compile python modules from source.

Inspecting this file I see mal-formed compiler directives for AWS Graviton instances:

• -n1 -> -mcpu=neoverse-n1
• .2-a+fp16+rcpc+dotprod+crypto -> -march=armv8.2-a+fp16+rcpc+dotprod+crypto

Others have seen this behavior: https://stackoverflow.com/questions/74739356/python-cant-install-ta-lib-in-oracle-arm64-vm-ubuntu-20-04

The workaround is use the system python.

Expected behavior or outcome

The vended Miniconda and Anaconda distributions should come with well formed information in lib/_sysconfigdata__linux_aarch64-linux-gnu.py so it can used in the same way as any python distribution.

Conda info

active environment : base
    active env location : /home/ubuntu/miniconda3
            shell level : 1
       user config file : /home/ubuntu/.condarc
 populated config files :
          conda version : 4.12.0
    conda-build version : not installed
         python version : 3.9.12.final.0
       virtual packages : __linux=5.15.0=0
                          __glibc=2.31=0
                          __unix=0=0
                          __archspec=1=aarch64
       base environment : /home/ubuntu/miniconda3  (writable)
      conda av data dir : /home/ubuntu/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://repo.anaconda.com/pkgs/main/linux-aarch64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-aarch64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /home/ubuntu/miniconda3/pkgs
                          /home/ubuntu/.conda/pkgs
       envs directories : /home/ubuntu/miniconda3/envs
                          /home/ubuntu/.conda/envs
               platform : linux-aarch64
             user-agent : conda/4.12.0 requests/2.27.1 CPython/3.9.12 Linux/5.15.0-1026-aws ubuntu/20.04.5 glibc/2.31
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False

### Conda config

```shell
I get no output

Conda list

# packages in environment at /home/ubuntu/miniconda3:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main    defaults
_openmp_mutex             5.1                      51_gnu    defaults
brotlipy                  0.7.0           py39hfd63f10_1002    defaults
ca-certificates           2022.3.29            hd43f75c_1    defaults
certifi                   2021.10.8        py39hd43f75c_2    defaults
cffi                      1.15.0           py39h9a3cfec_1    defaults
charset-normalizer        2.0.4              pyhd3eb1b0_0    defaults
colorama                  0.4.4              pyhd3eb1b0_0    defaults
conda                     4.12.0           py39hd43f75c_0    defaults
conda-content-trust       0.1.1              pyhd3eb1b0_0    defaults
conda-package-handling    1.8.1            py39h2f4d8fa_0    defaults
cryptography              36.0.0           py39h3d58568_0    defaults
idna                      3.3                pyhd3eb1b0_0    defaults
ld_impl_linux-aarch64     2.36.1               h0ab8de2_3    defaults
libffi                    3.3                  h7c1a80f_2    defaults
libgcc-ng                 10.2.0              h1234567_51    defaults
libgomp                   10.2.0              h1234567_51    defaults
libstdcxx-ng              10.2.0              h1234567_51    defaults
ncurses                   6.3                  h2f4d8fa_2    defaults
openssl                   1.1.1n               h2f4d8fa_0    defaults
pip                       22.3.1                   pypi_0    pypi
pycosat                   0.6.3            py39hfd63f10_2    defaults
pycparser                 2.21               pyhd3eb1b0_0    defaults
pyopenssl                 22.0.0             pyhd3eb1b0_0    defaults
pysocks                   1.7.1            py39hd43f75c_0    defaults
python                    3.9.12               hc137634_0    defaults
readline                  8.1.2                h2f4d8fa_1    defaults
requests                  2.27.1             pyhd3eb1b0_0    defaults
ruamel_yaml               0.15.100         py39h2f4d8fa_0    defaults
setuptools                65.6.3                   pypi_0    pypi
six                       1.16.0             pyhd3eb1b0_1    defaults
sqlite                    3.38.2               h6632b73_0    defaults
tk                        8.6.11               h241ca14_0    defaults
tqdm                      4.63.0             pyhd3eb1b0_0    defaults
tzdata                    2022a                hda174b7_0    defaults
urllib3                   1.26.8             pyhd3eb1b0_0    defaults
wheel                     0.37.1             pyhd3eb1b0_0    defaults
xz                        5.2.5                hfd63f10_1    defaults
yaml                      0.2.5                hfd63f10_0    defaults
zlib                      1.2.12               h2f4d8fa_1    defaults

Additional information

No response

[geoffreyblake]

There is a _sysconfigdata__linux_aarch64-linux-gnu.py.orig in the same directory as the bad _sysconfigdata__linux_aarch64-linux-gnu.py file and that appears to have properly formed compiler directives. Why is there an .orig file in the release build? Was there a bad merge?

[AndrewVallette]

Thank you for reporting this issue, Geoffrey. We are investigating.

[AndrewVallette]

There was indeed an issue with a previous python 3.9.12 package (build hc137634_0) for linux-aarch64, which was included in older Miniconda installers.

To resolve this issue, you can upgrade to the latest Miniconda release (22.11.1-1), which can be downloaded here: https://docs.conda.io/en/latest/miniconda.html

You can then install the new Miniconda with the following command:
bash Miniconda3-latest-Linux-aarch64.sh

Alternatively, if you wish to stay with an existing Miniconda installation, you can upgrade python with conda update python, and this should also resolve the issue. The latest python version for linux-aarch64 is currently 3.9.15 build h89984f6_2.

[geoffreyblake]

Thanks @AndrewVallette for the speedy work, the problem is fixed.