<div dir="ltr">Hi Jan,<div><br></div><div>Do you need to build cctbx from scratch? The cctbx has been available for Python 3 for a while now, but is using conda packages (<a href="https://docs.conda.io/en/latest/">https://docs.conda.io/en/latest/</a>) for managing dependencies. Building the dependencies from scratch for multiple versions of Python 3 for multiple platforms was getting too complicated.</div><div><br></div><div>You can install cctbx as a conda package for Python 3.6 through 3.9 with support for macOS (Intel and Apple Silicon), linux, and Windows. Instructions can be found here (<a href="https://github.com/cctbx/cctbx_project#installation">https://github.com/cctbx/cctbx_project#installation</a>), but essentially it is just</div><div><br></div><div><font face="monospace">conda install -c conda-forge cctbx-base </font></div><div><br></div><div>to get it into an existing environment. The smtbx module will be available, but not fast_linalg yet.</div><div><br></div><div>Note that with a conda environment, you do not need to run any of the "setpaths" scripts to set it up. Just activate the environment and cctbx will be available in python.</div><div><br></div><div>There are also nightly builds of the conda packages on a separate channel (<a href="https://github.com/cctbx/cctbx_project#nightly-builds">https://github.com/cctbx/cctbx_project#nightly-builds</a>). The command above becomes</div><div><br></div><div><font face="monospace">conda install -c cctbx-nightly -c conda-forge cctbx-base </font><br></div><div><br></div><div>You can also build cctbx with Python 3 using conda packages as dependencies (<a href="https://github.com/cctbx/cctbx_project#building-a-development-version">https://github.com/cctbx/cctbx_project#building-a-development-version</a>). The bootstrap.py command becomes</div><div><br></div><div><font face="monospace">python bootstrap.py --use-conda --python 38</font></div><div><br></div><div>This will install miniconda if conda is not already available on your system.</div><div><br></div><div>You can run</div><div><br></div><div><font face="monospace">python bootstrap.py --help</font></div><div><br></div><div>to see more options.</div><div><br></div><div>There are monthly releases and I will make announcements on this bulletin board from now on to help spread the word.</div><div><br></div><div><div><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></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Jul 9, 2021 at 4:57 AM Jan M. Simons <<a href="mailto:marten@ifk.rwth-aachen.de">marten@ifk.rwth-aachen.de</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">Hi Oleg,<br>
<br>
Am 09.07.21 um 13:16 schrieb Oleg Dolomanov:<br>
> Hi Jan,<br>
><br>
> which way have you been using to build cctbx?<br>
<br>
I've been following <a href="https://cctbx.github.io/installation.html" rel="noreferrer" target="_blank">https://cctbx.github.io/installation.html</a><br>
<br>
(as <a href="https://cci.lbl.gov/cctbx_docs/installation.html" rel="noreferrer" target="_blank">https://cci.lbl.gov/cctbx_docs/installation.html</a> seems to be the<br>
older/outdated documentation which should perhaps redirect to the newer<br>
one instead.)<br>
<br>
Is this not the right documentation on how to build it on a bare bones<br>
linux distribution? (I'm using sabayon, a gentoo derivative)<br>
<br>
So right now I've re-tried to execute an up-to-date bootstrap.py with my<br>
system supplied python3.7 and on first attempt it still built python2.7<br>
and then failed with<br>
<br>
Installing h5py 2.10.0...<br>
Read and write HDF5 files from Python<br>
log file is /home/jan/Arbeit/cctbx-dev/base_tmp/h5py_install_log<br>
Traceback (most recent call last):<br>
File<br>
"modules/cctbx_project/libtbx/auto_build/install_base_packages.py", line<br>
1682, in <module><br>
installer(args=sys.argv, log=sys.stdout)<br>
File<br>
"modules/cctbx_project/libtbx/auto_build/install_base_packages.py", line<br>
256, in __init__<br>
self.build_dependencies(packages=packages)<br>
File<br>
"modules/cctbx_project/libtbx/auto_build/install_base_packages.py", line<br>
782, in build_dependencies<br>
getattr(self, 'build_%s'%i)()<br>
File<br>
"modules/cctbx_project/libtbx/auto_build/install_base_packages.py", line<br>
1220, in build_h5py<br>
confirm_import_module='h5py', extra_options=["--no-binary=h5py"])<br>
File<br>
"modules/cctbx_project/libtbx/auto_build/install_base_packages.py", line<br>
694, in build_python_module_pip<br>
log=log)<br>
File<br>
"modules/cctbx_project/libtbx/auto_build/install_base_packages.py", line<br>
359, in call<br>
return call(args, log=log, verbose=self.verbose, **kwargs)<br>
File<br>
"/home/jan/Arbeit/cctbx-dev/modules/cctbx_project/libtbx/auto_build/installer_utils.py",<br>
line 55, in call<br>
raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc))<br>
RuntimeError: Call to '/home/jan/Arbeit/cctbx-dev/base/bin/python -m pip<br>
install "h5py==2.10.0" --no-binary=h5py' failed with exit code 1<br>
Process failed with return code 1<br>
<br>
Then calling<br>
$ python3 ./bootstrap.py<br>
again it is still compiling, but from the paths I suppose that it's<br>
continuing to only build the python2.7 version (like before).<br>
<br>
<br>
So, I suppose I'm missing some bit of documentation on how to get it<br>
working with python3.<br>
<br>
Thanks for your support<br>
Jan<br>
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</blockquote></div>