Great, all working now. It seemed I didn't need to mess with libtbx.list_modules after all, I could just rebuild the foundations without the house falling down. So, for reference I did this: rm -rf base cd base_tmp find . -maxdepth 1 -mindepth 1 -type d -print0 | xargs -0 -n 1 -- rm -rf cd .. python bootstrap.py --builder=dials base cd build source setpaths.sh make reconf -- David On 8 June 2017 at 14:15, David Waterman wrote:

Thanks, I did this, currently churning through the base build. Checking the latest Python_install_log I see hopeful-looking things like "building 'bz2' extension". I can only assume I've installed a few more packages since I did the original build. Will report back if there are any new problems, otherwise I think this might be fixed :)

Cheers

-- David

On 8 June 2017 at 13:08, wrote:

...

Hi David,

You’ll have to look into the python setup.py script to figure that one out.

https://github.com/python/cpython/blob/2.7/setup.py#L1463

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.

-Markus

*From:* [email protected] [mailto:cctbxbb-bounces@phenix -online.org] *On Behalf Of *David Waterman *Sent:* 08 June 2017 12:58 *To:* cctbx mailing list *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

sunaudiodev

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

make

Cheers

-- David

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