Hi Olaf
how are you installing ipython? I add ipython as a python extension in my
main python easyconfig because I want it automatically loaded when loading
python and I don't want an extra module for ipython
What I have in my extensions section is this, and it's working fine for me
('ipython', '1.2.0', {
'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'
],
#workaround for sanity checking
'modulename': 'os',
}),
pablo
2014-03-13 14:56 GMT+01:00 Kenneth Hoste <[email protected]>:
> Hi Olaf,
>
> On 13/03/14 14:50, Olaf Walter wrote:
> > Hi Kenneth,
> >
> >> So, it seems like somehow telling Python to also link with "-lncurses"
> >> should resolve the issue.
> > How can I do this? Just mentioning ncurses in the dependencies seems not
> to be enough.
> I'm working on a proper fix.
>
> Python automagically tries to link to libreadline as follows:
>
> checking how to link readline libs... -lreadline -lncursesw
>
> Right now, the libncurses built with EasyBuild doesn't provide
> libncursesw.so (or .a).
>
> I'm trying to see whether making sure that they are there fixes the
> problem.
>
> I'll let you know once I've figured things out, and we'll enhance the
> sanity checks included in the Python easyblock to capture this problem
> earlier. It's easy to check: if "import readline" doesn't work, stuff is
> broken...
>
>
> regards,
>
> Kenneth
>
>
> >
> > I tried Pablo's approach using the RPMs and it solves the issue in
> Python, but not in IPython. I would prefer to solve this within easybuild,
> but it's too puzzling.
> >
> > The IPython build fails, with a similar error message:
> >
> > == 2014-03-13 14:16:30,691 main.run INFO parse_log_for_error msg:
> Command used: iptest
> > == 2014-03-13 14:16:30,692 main.run INFO parse_log_for_error (some may
> be harmless) regExp (?<![(,-]|\w)(?:error|segmentation
> fault|failed)(?![(,-]|\.?\w) found:
> > ERROR: Test we're not loading modules on startup that we shouldn't.
> > ValueError: Running file '/tmp/easybuild-9LI3g5/tmpvba19N.py' produced
> error: 'WARNING: Readline services not available or not loaded.\nWARNING:
> The auto-indent feature requires the readline library\n'
> >
> > Did anybody get IPython working with readline?
> >
> > Best regards,
> > Olaf
> >
> > -----Ursprüngliche Nachricht-----
> > Von: [email protected] [mailto:
> [email protected]] Im Auftrag von Kenneth Hoste
> > Gesendet: Donnerstag, 13. März 2014 11:03
> > An: [email protected]
> > Betreff: Re: [easybuild] Python and readline
> >
> >
> > On 13/03/14 10:54, Fotis Georgatos wrote:
> >> Hello *,
> >>
> >> On Mar 13, 2014, at 9:34 AM, Kenneth Hoste wrote:
> >>> *** WARNING: renaming "readline" since importing it failed:
> /path/to/software/libreadline/6.2-goolf-1.4.10/lib/libreadline.so.6:
> undefined symbol: PC
> >> hey, that rings a bell:
> >> * ncurses is an -optional- dependency of libreadline;
> >> and when not explicitly declared the above message appears.
> >>
> >> I have noticed at least two round of discussions over the last 12
> months as regards the matter;
> >> fi. last summer's EB-provided libreadline builds are supposed to have
> the dep defined (July 2013);
> >> *plenty* of software sits atop libreadline so that has far-reaching
> (and build-silent) effects;
> >> In fact, this is a prime example why having *buildsets* to fight sw
> temporal divergence is a MUST.
> >>
> >> I hope others can confirm that the above is on-topic hint.
> > I've been looking into this a bit more, and it's indeed ncurses who's to
> > blame.
> >
> > It's even worse... As far as I can tell, libreadline never links to
> > ncurses itself, even though the libreadline.so|a libraries use symbols
> > provided by ncurses.
> >
> > The idea is that users are left free to chose whether they use ncurses
> > or termcap to provide the symbols.
> >
> > Result: if you don't link with "-lreadline -lncurses", and e.g. use
> > "-lreadline", you can run into problems like this.
> > So, it seems like somehow telling Python to also link with "-lncurses"
> > should resolve the issue.
> >
> > Now, what really puzzles me is:
> >
> > 1) Why does this problem only occur with Python 2.7.5 and 2.7.6? Python
> > 2.7.3 seems to be fine...
> >
> > 2) Why didn't we notice this earlier? :(
> >
> >
> > regards,
> >
> > Kenneth
>
>
--
Pablo Escobar López
HPC systems engineer
Biozentrum, University of Basel
Swiss Institute of Bioinformatics SIB
Email: [email protected]
Phone: +41 61 267 15 82
http://www.biozentrum.unibas.ch
