[phenixbb] Running phenix into a M1 apple processor

[Billy Poon]

Hi Florian,

Great!

Yes, the conda_base directory is Intel because it would probably take a lot
of effort to get everything to natively compile on Apple Silicon. We do
have environments defined for Apple Silicon for Python 3. You can see them
in <installation directory>/modules/phenix/conda_envs. These files are just
standard text files created by conda for recreating environments exactly.
I'm currently in the process of updating them for the next 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 Wed, Jun 22, 2022 at 3:48 PM Florian Nachon <mailinglist at nachon.net>
wrote:

>
> Hi Billy,
>
> Thanx for the instructions!
> I tried both the binary installer and the source installer as suggested,
> with the "—use-conda" flag and the installation worked well in both cases
> without messing up with /usr/bin.
>
> The full installation was completed in 15 min on my M1 Max
>
> Also, I installed arm64 anaconda with brew, but I noticed that conda_base
> was still Intel. And the generated Mac app is also Intel.
> I guess the explanation is that the default conda environment in the
> install script is osx-64 instead of osx-arm64?
>
> 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
>>
>>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20220624/cb84ab7c/attachment.htm>