[phenixbb] Running phenix into a M1 apple processor

[Billy Poon]

Hi Florian,

It looks like you are using the source tarball. Please use the binary
installers for macOS. The install script will then use the python that we
provide in the "conda_base" directory.

If you want to use the source installer, you can modify the ./install and
./lib/libtbx/auto_build/install_distribution.py scripts to use
/usr/bin/python3 instead of /usr/bin/python. You will still need a "python"
somewhere in your path and the easiest way would be to install miniconda
from https://docs.conda.io/en/latest/miniconda.html and create a new conda
environment with any python version ("conda create -n new_env python" will
use Python 3.10). Activate the new environment ("conda activate new_env")
and then you will have a "python" in your path. Then you can run

./install --prefix <prefix> --try-unsupported --use-conda --nproc <nproc>

It is recommended that you add the "--use-conda" flag since it is not
likely that all the dependencies will compile from source. We have moved
our dependencies to use conda so that we can more easily test different
versions of Python 3. You can see that in our continuous integration output
of cctbx at https://github.com/cctbx/cctbx_project.

We have conda packages for cctbx that are built to run natively on Apple
Silicon and we will be doing the same for the next Phenix release.

--
Billy K. Poon
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Fax: (510) 486-5909
Web: https://phenix-online.org


On Tue, Jun 21, 2022 at 4:19 PM Florian Nachon <mailinglist at nachon.net>
wrote:

>
>
> On 22 Jun 2022, at 00:55, Billy Poon <BKPoon at lbl.gov> wrote:
>
> We ship our own python and 1.20.1 is the last Python 2 release. The next
> release will be in Python 3.
>
>
> If I run sudo ./install --prefix=/Applications --try-unsupported
> then I get right away ./install: line 15: /usr/bin/python: No such file
> or directory
>
> Obviously because there is no /usr/bin/python in Monterey but
> /usr/bin/python3…
> I can change ‘python' by ‘python3’ in the install script to go one step
> further, but it fails later because the install scripts always call
> ‘python’ instead of ‘python3’
>
> Source installation specified.
> /bin/sh: python: command not found
> Traceback (most recent call last):
>   File "./bin/install.py", line 268, in <module>
>     installer(sys.argv[1:]).install()
>   File
> "/Users/florian/Downloads/phenix-installer-1.20.1-4487-source/lib/libtbx/auto_build/install_distribution.py",
> line 198, in install
>     self.install_from_source()
>   File
> "/Users/florian/Downloads/phenix-installer-1.20.1-4487-source/lib/libtbx/auto_build/install_distribution.py",
> line 367, in install_from_source
>     call(cmd, log=log)
>   File
> "/Users/florian/Downloads/phenix-installer-1.20.1-4487-source/lib/libtbx/auto_build/installer_utils.py",
> line 55, in call
>     raise RuntimeError("Call to '%s' failed with exit code %d" % (args,
> rc))
> RuntimeError: Call to 'python
> modules/cctbx_project/libtbx/auto_build/bootstrap.py base build --builder
> phenix --nproc 10' failed with exit code 127
>
> And an alias does not do the trick either.
>
> So what should I do?
>
> Florian
>
>
>
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