[cctbxbb] Revisiting cctbx/iotbx/dxtbx dependencies

Aaron Brewster asbrewster at lbl.gov
Fri Feb 9 16:58:13 PST 2018

Hi folks, you can now run python bootstrap.py --builder=cctbxlite to get a
lite version of cctbx.  It will follow the steps listed above, skipping
hdf5, cbflib and dxtbx.

I'd like to close issues 125 and 126 unless someone objects.


On Thu, Feb 8, 2018 at 8:50 PM, Asmit Bhowmick <abhowmick at lbl.gov> wrote:

> For the 2nd step that Aaron mentioned, if certain packages are to be
> skipped during the base step, you can also run bootstrap.py with the flag
> --skip-base-packages and specify the packages to be skipped separated by a
> comma. For example
> python bootstrap.py base --builder=cctbx --skip-base-packages
> hdf5,lz4_plugin
> Best Wishes
> Asmit
> On Wed, Feb 7, 2018 at 3:08 PM, Aaron Brewster <asbrewster at lbl.gov> wrote:
>> Hey folks, especially Rob and Luc.  So after a quick change to
>> iotbx/libtbx_config, it turns out there's a way to get a super minimum
>> version of cctbx, without configuring dxtbx, and it takes advantage of
>> existing mechanisms:
>>    - python bootstrap.py --builder=cctbx hot update
>>    - python modules/cctbx_project/libtbx/auto_build/install_base_packages.py
>>    openssl python python_compatibility certifi numpy cython png libsvm pytest
>>    pythonextra jinja2 junitxml biopython docutils sphinx pyopengl misc
>>    freetype matplotlib pillow gettext glib expat fontconfig render pixman tiff
>>    cairo gtk fonts wxpython
>>    - mkdir build; cd build
>>    - ../base/bin/python ../modules/cctbx_project/libtbx/configure.py
>>    cctbx iotbx
>>    - make
>> Now, some details as to why this works.  First, the cctbx builder in
>> boostrap.py doesn't download cbflib so cbflib is never configured.  Next,
>> the base step of bootstrap.py is simply a call to install_base_packages.py
>> with a list of required packages.  You can just run it standalone and get
>> the packages you need.  Here, I ran "python bootstrap.py --builder=cctbx
>> base", killed it after I saw the list of packages it was going to install,
>> then ran install_base_packages manually after removing hdf5 and lz4 (which
>> depends on hdf5) from the list.  One could imagine removing other packages
>> depending on your use case.  With that, I could run configure.py directly.
>> I can't use cctbx by itself as the cctbx/maptbx/SConscript file has a
>> dependency on iotbx, but configuring cctbx and iotbx together seems to work.
>> The key trick was to make iotbx only depend on dxtbx if dxtbx is
>> explicitly configured.  I used a keyword in libtbx_configure added by Luc a
>> bit ago: optional_modules_only_if_explicit_request.  I committed that
>> change just now.
>> Outstanding questions:
>>    1. Is there interest in making this a builder? It would be
>>    straightforward to add a builder named cctbx_minimal which would just do
>>    the above steps
>>    2. Is there further need for making cbflib and hdf5 optional in
>>    dxtbx?  I purport there is not as the above procedure seems to satisfy the
>>    use case, but I can be persuaded otherwise.
>> Thanks,
>> -Aaron
>> _______________________________________________
>> cctbxbb mailing list
>> cctbxbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/cctbxbb
> --
> Asmit Bhowmick, Ph.D
> Molecular Biophysics & Integrated Bioimaging Division
> Lawrence Berkeley National Laboratory
> 1 Cyclotron Rd., Bldg. 33, Room 349B
> <https://maps.google.com/?q=1+Cyclotron+Rd.,+Bldg.+33,+Room+349B&entry=gmail&source=g>
> Berkeley, CA 94720
> Cell: 510.684.6011 <(510)%20684-6011>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/cctbxbb/attachments/20180209/dfe3664c/attachment.htm>

More information about the cctbxbb mailing list