<div dir="ltr">Hi Florian,<div><br></div><div>Great!</div><div><br></div><div>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.</div><div><br clear="all"><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><div>--</div><div><span style="font-size:12.8000001907349px">Billy K. Poon</span><br></div></div><div>Research Scientist, Molecular Biophysics and Integrated Bioimaging</div><div>Lawrence Berkeley National Laboratory</div><div>1 Cyclotron Road, M/S 33R0345</div><div>Berkeley, CA 94720</div><div>Fax: (510) 486-5909</div><div>Web: <a href="https://phenix-online.org" target="_blank">https://phenix-online.org</a></div></div></div></div></div></div></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Jun 22, 2022 at 3:48 PM Florian Nachon <<a href="mailto:mailinglist@nachon.net">mailinglist@nachon.net</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div style="word-wrap:break-word;line-break:after-white-space"><div><br></div><div>Hi Billy,</div><div><br></div><div>Thanx for the instructions!</div><div>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.</div><div><br></div><div>The full installation was completed in 15 min on my M1 Max </div><div><br></div><div>Also, I installed arm64 anaconda with brew, but I noticed that conda_base was still Intel. And the generated Mac app is also Intel.</div><div>I guess the explanation is that the default conda environment in the install script is osx-64 instead of osx-arm64?</div><div><br></div><div>Florian</div><div><br><br><blockquote type="cite"><div><div dir="ltr"><div>It looks like you are using the source tarball.</div></div></div></blockquote><blockquote type="cite"><div><div dir="ltr"><div>Please use the binary installers for macOS. The install script will then use the python that we provide in the "conda_base" directory.</div><div><br></div><div>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 <a href="https://docs.conda.io/en/latest/miniconda.html" target="_blank">https://docs.conda.io/en/latest/miniconda.html</a> 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</div><div><br></div><div>./install --prefix <prefix> --try-unsupported --use-conda --nproc <nproc></div><div><br></div><div>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 <a href="https://github.com/cctbx/cctbx_project" target="_blank">https://github.com/cctbx/cctbx_project</a>.</div><div><br></div><div>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.</div><div><br clear="all"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><div>--</div><div><span style="font-size:12.8000001907349px">Billy K. Poon</span><br></div></div><div>Research Scientist, Molecular Biophysics and Integrated Bioimaging</div><div>Lawrence Berkeley National Laboratory</div><div>1 Cyclotron Road, M/S 33R0345</div><div>Berkeley, CA 94720</div><div>Fax: (510) 486-5909</div><div>Web: <a href="https://phenix-online.org/" target="_blank">https://phenix-online.org</a></div></div></div></div></div></div></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Jun 21, 2022 at 4:19 PM Florian Nachon <<a href="mailto:mailinglist@nachon.net" target="_blank">mailinglist@nachon.net</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div style="word-wrap:break-word;line-break:after-white-space"><br><div><br><blockquote type="cite"><div>On 22 Jun 2022, at 00:55, Billy Poon <<a href="mailto:BKPoon@lbl.gov" target="_blank">BKPoon@lbl.gov</a>> wrote:</div><br><div><span style="font-family:Calibri;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">We ship our own python and 1.20.1 is the last Python 2 release. The next release will be in Python 3.</span></div></blockquote></div><br><div>If I run <span style="color:rgb(242,242,242);font-family:Monaco;font-size:12px;background-color:rgba(0,0,0,0.82)">sudo ./install --prefix=/Applications --try-unsupported</span><span style="color:rgb(242,242,242);font-family:Monaco;font-size:12px;background-color:rgba(0,0,0,0.82)"> </span></div><div>then I get right away <span style="color:rgb(242,242,242);font-family:Monaco;font-size:12px;background-color:rgba(0,0,0,0.82)">./install: line 15: /usr/bin/python: No such file or directory</span></div><div><br></div><div>Obviously because there is no /usr/bin/python in Monterey but /usr/bin/python3… </div><div>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’</div><div><br></div><div><div style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:Monaco;color:rgb(242,242,242);background-color:rgba(0,0,0,0.82)"><span style="font-variant-ligatures:no-common-ligatures">Source installation specified.</span></div><div style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:Monaco;color:rgb(242,242,242);background-color:rgba(0,0,0,0.82)"><span style="font-variant-ligatures:no-common-ligatures">/bin/sh: python: command not found</span></div><div style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:Monaco;color:rgb(242,242,242);background-color:rgba(0,0,0,0.82)"><span style="font-variant-ligatures:no-common-ligatures">Traceback (most recent call last):</span></div><div style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:Monaco;color:rgb(242,242,242);background-color:rgba(0,0,0,0.82)"><span style="font-variant-ligatures:no-common-ligatures"> File "./bin/install.py", line 268, in <module></span></div><div style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:Monaco;color:rgb(242,242,242);background-color:rgba(0,0,0,0.82)"><span style="font-variant-ligatures:no-common-ligatures"> installer(sys.argv[1:]).install()</span></div><div style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:Monaco;color:rgb(242,242,242);background-color:rgba(0,0,0,0.82)"><span style="font-variant-ligatures:no-common-ligatures"> File "/Users/florian/Downloads/phenix-installer-1.20.1-4487-source/lib/libtbx/auto_build/install_distribution.py", line 198, in install</span></div><div style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:Monaco;color:rgb(242,242,242);background-color:rgba(0,0,0,0.82)"><span style="font-variant-ligatures:no-common-ligatures"> self.install_from_source()</span></div><div style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:Monaco;color:rgb(242,242,242);background-color:rgba(0,0,0,0.82)"><span style="font-variant-ligatures:no-common-ligatures"> File "/Users/florian/Downloads/phenix-installer-1.20.1-4487-source/lib/libtbx/auto_build/install_distribution.py", line 367, in install_from_source</span></div><div style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:Monaco;color:rgb(242,242,242);background-color:rgba(0,0,0,0.82)"><span style="font-variant-ligatures:no-common-ligatures"> call(cmd, log=log)</span></div><div style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:Monaco;color:rgb(242,242,242);background-color:rgba(0,0,0,0.82)"><span style="font-variant-ligatures:no-common-ligatures"> File "/Users/florian/Downloads/phenix-installer-1.20.1-4487-source/lib/libtbx/auto_build/installer_utils.py", line 55, in call</span></div><div style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:Monaco;color:rgb(242,242,242);background-color:rgba(0,0,0,0.82)"><span style="font-variant-ligatures:no-common-ligatures"> raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc))</span></div><div style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:Monaco;color:rgb(242,242,242);background-color:rgba(0,0,0,0.82)"><span style="font-variant-ligatures:no-common-ligatures">RuntimeError: Call to 'python modules/cctbx_project/libtbx/auto_build/bootstrap.py base build --builder phenix --nproc 10' failed with exit code 127</span></div></div><div><br></div><div><div>And an alias does not do the trick either.</div><div><br></div></div><div>So what should I do?</div><div><br></div><div>Florian</div><div><br></div><div><span style="color:rgb(242,242,242);font-family:Monaco;font-size:12px;background-color:rgba(0,0,0,0.82)"><br></span></div></div></blockquote></div>
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