[cctbxbb] bz2 support on Ubuntu

markus.gerstel at diamond.ac.uk markus.gerstel at diamond.ac.uk
Thu Jun 8 05:08:03 PDT 2017

Hi David,

You’ll have to look into the python setup.py script to figure that one out.
Python expects the library to be in some fixed place, and If it’s not there support is disabled.

Regarding your rebuild question. I would keep the base_tmp directory, you then don’t have to redownload and recompile everything. Stuff should still recompile if anything changed, and if versions are updated etc.
If you definitely want to recompile everything you can still save time by running  this *in the base_tmp directory*:
    find . -maxdepth 1 -mindepth 1 -type d -print0 | xargs -0 -n 1 -- rm –rf
This removes all subdirectories, leaving the files intact, so you don’t have to redownload everything.

I would expect the steps export, rm -rf base, python bootstrap.py base, cd build, setpaths, libtbx.configure, make to suffice.


From: cctbxbb-bounces at phenix-online.org [mailto:cctbxbb-bounces at phenix-online.org] On Behalf Of David Waterman
Sent: 08 June 2017 12:58
To: cctbx mailing list <cctbxbb at phenix-online.org>
Subject: [cctbxbb] bz2 support on Ubuntu

Hi folks,

My bootstrap build of cctbx/DIALS on Ubuntu 16.04.2 LTS produces a base Python that does not have bz2 support. This is despite the fact that the package "libbz2-dev is already the newest version (1.0.6-8)." Looking in Python_install_log I see

Python build finished, but the necessary bits to build these modules were not found:
_bsddb             _curses            _curses_panel
_sqlite3           _tkinter           bsddb185
bz2                dbm                dl
gdbm               imageop            readline

Has anyone got any ideas? Anyone done a boostrap build on Ubuntu where bz2 can be imported in Python?

Also, what's the procedure to rebuild from base, recovering all the currently configured modules? My guess is that something like this would do it, but is there a better way?

export MYMODULES=$(libtbx.list_modules | tr '\n' ' ')
rm -rf base_tmp/ base/ build/
python bootstrap.py --builder=dials base
python bootstrap.py --builder=dials build
cd build
source setpaths.sh
libtbx.configure $MYMODULES


-- David

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