Hi Olaf,
On 22/03/14 17:22, Olaf Walter wrote:
Hi Kenneth,
THANKS for guiding my through! I guess I have to learn how to handle git. My
brain is hardwired to subversion.
** Python and IPython compiled, passed their tests and sanity checks, and both
work nicely with readline and ncurses! **
This confirms that the fix works in our environment.
OK, excellent, thanks for letting us know.
I'll merge in PR #370 straight away now, so the fix will be part of the
next EasyBuild release.
regards,
Kenneth
Concerning the "'self' not defined", I guess I did a sloppy installation which
messed things up.
Best regards and have a nice weekend!
Olaf
-----Ursprüngliche Nachricht-----
Von: [email protected] [mailto:[email protected]]
Im Auftrag von Kenneth Hoste
Gesendet: Samstag, 22. März 2014 15:09
An: [email protected]
Betreff: Re: [easybuild] Python and readline
Hi Olaf,
Trying the lastest develop version of easybuild-easyblocks will not
resolve the readline problem. Pull request #370 isn't merged into
develop yet.
If you just copy the easyblock as it is in PR #370, it should work
though, and you shouldn't get the error you're mentioning.
Please try this:
- download the updated Python easyblock from
https://raw.githubusercontent.com/boegel/easybuild-easyblocks/python_readline/easybuild/easyblocks/p/python.py
(from the PR: click "View" and then "Raw" to get there).
- Use the file python.py to overwrite the python.py file in your current
EasyBuild installation (it should be in a subdirectory named
'easybuild/easyblocks/p/' somewhere).
I'm not sure why you're running into the "name 'self' is not defined"
error, it looks weird...
Can you provide more details on what you did exactly?
regards,
Kenneth
On 22/03/14 12:52, Olaf Walter wrote:
I tried the newest easybuild-easyblocks-develop, and Python compiles now. The
resulting executable has no readline capabilities, though.
Olaf
-----Original Message-----
From: [email protected]
[mailto:[email protected]] On Behalf Of Olaf Walter
Sent: Saturday, March 22, 2014 12:23 PM
To: [email protected]
Subject: RE: AW: [easybuild] Python and readline
Hi Kenneth,
I downloaded and installed the easybuild at the pull request 370, but then I
get:
== temporary log file in case of crash /tmp/easybuild-eY4r_c/easybuild-0FU0Lc.log
== resolving dependencies ...
== processing EasyBuild easyconfig
/gpfs01/home/bioadmn/eb20140322py/eb/Python-2.7.6-goolf-1.4.12-no-OFED.eb
== ERROR: Failed to get application instance for Python (easyblock: None):
EasyBuild crashed with an error (at
easybuild/1.11.1_p370_bin/lib/python2.6/site-packages/easybuild/framework/easyblock.py:1990
in get_class): Failed to obtain class for None easyblock (not available?):
name 'self' is not defined
I attached the log file. Did I get the wrong files from git?
Olaf
-----Original Message-----
From: [email protected]
[mailto:[email protected]] On Behalf Of Kenneth Hoste
Sent: Wednesday, March 19, 2014 6:14 PM
To: [email protected]
Subject: Re: AW: AW: [easybuild] Python and readline
Hi Olaf,
On 14/03/14 14:36, Olaf Walter wrote:
Thanks! I'll check this out next week and let you know.
Did you get the chance to try the fixed easyblock available in
https://github.com/hpcugent/easybuild-easyblocks/pull/370 ?
We're holding off merging that PR until the fix is confirmed.
regards,
Kenneth
Have a nice weekend,
Olaf
-----Ursprüngliche Nachricht-----
Von: [email protected] [mailto:[email protected]]
Im Auftrag von Kenneth Hoste
Gesendet: Donnerstag, 13. März 2014 22:36
An: [email protected]
Betreff: Re: AW: [easybuild] Python and readline
OK, I have this figured out now, and have a fix that resolves the
problem implemented in the Python easyblock.
See https://github.com/hpcugent/easybuild-easyblocks/pull/370 .
It boils down to having to specify both -lreadline and -lncurses, and
point Python to their respective non-standard locations.
I also extend the list of sanity check commands for Python to include
"import readline", such that this doesn't pass by unnoticed again.
I've rebuilt all existing Python easyconfigs with this adjusted
easyblock, works like a charm for all of them (so all builds now
properly have readline support).
As soon as the PR is reviewed, I'll merge it in. Feel free to also test
it on your end and report back.
regards,
Kenneth
On 13/03/14 14:56, Kenneth Hoste wrote:
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
