<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class=""><br class=""></div><div>Hi Billy,</div><div><br class=""></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 class=""></div><div>The full installation was completed in 15 min on my M1 Max </div><div><br class=""></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 class=""></div><div>Florian</div><div><br class=""><br class=""><blockquote type="cite" class=""><div class=""><div dir="ltr" class=""><div class="">It looks like you are using the source tarball.</div></div></div></blockquote><blockquote type="cite" class=""><div class=""><div dir="ltr" class=""><div class="">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 class=""><br class=""></div><div class="">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" class="">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 class=""><br class=""></div><div class="">./install --prefix <prefix> --try-unsupported --use-conda --nproc <nproc></div><div class=""><br class=""></div><div class="">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" class="">https://github.com/cctbx/cctbx_project</a>.</div><div class=""><br class=""></div><div class="">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 class=""><br clear="all" class=""><div class=""><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div class=""><div class="">--</div><div class=""><span style="font-size:12.8000001907349px" class="">Billy K. Poon</span><br class=""></div></div><div class="">Research Scientist, Molecular Biophysics and Integrated Bioimaging</div><div class="">Lawrence Berkeley National Laboratory</div><div class="">1 Cyclotron Road, M/S 33R0345</div><div class="">Berkeley, CA 94720</div><div class="">Fax: (510) 486-5909</div><div class="">Web: <a href="https://phenix-online.org/" target="_blank" class="">https://phenix-online.org</a></div></div></div></div></div></div></div></div></div></div><br class=""></div></div><br class=""><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" class="">mailinglist@nachon.net</a>> wrote:<br class=""></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" class=""><br class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">On 22 Jun 2022, at 00:55, Billy Poon <<a href="mailto:BKPoon@lbl.gov" target="_blank" class="">BKPoon@lbl.gov</a>> wrote:</div><br class=""><div class=""><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" class="">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 class=""><div class="">If I run <span style="color:rgb(242,242,242);font-family:Monaco;font-size:12px;background-color:rgba(0,0,0,0.82)" class="">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)" class=""> </span></div><div class="">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)" class="">./install: line 15: /usr/bin/python: No such file or directory</span></div><div class=""><br class=""></div><div class="">Obviously because there is no /usr/bin/python in Monterey but /usr/bin/python3… </div><div class="">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 class=""><br class=""></div><div class=""><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)" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">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)" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">/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)" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">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)" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> 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)" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> 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)" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> 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)" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> 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)" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> 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)" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> 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)" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> 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)" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> 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)" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">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 class=""><br class=""></div><div class=""><div class="">And an alias does not do the trick either.</div><div class=""><br class=""></div></div><div class="">So what should I do?</div><div class=""><br class=""></div><div class="">Florian</div><div class=""><br class=""></div><div class=""><span style="color:rgb(242,242,242);font-family:Monaco;font-size:12px;background-color:rgba(0,0,0,0.82)" class=""><br class=""></span></div></div></blockquote></div>
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