Re: relax 1.3.13/14 oddities -- April 10, 2012

On Tue, Apr 10, 2012 at 05:50:53PM +0200, Edward d'Auvergne wrote:

Hi,

I've now used the info and patch files for fink and rebuilt the
wxPython fink package.  Initially the MemoryError was still present on
my remote build system.  But this is now solved as I have managed to
convince the sys admin to increase amount of RAM available to the
remote virtual machine from ~850 Mb to ~960 Mb.

I do not see the problem you are seeing, it's unfortunately not
reproducible on my system.  I have a fully maximised relax window.  Do
you see the same if you run:

$ /sw/bin/python2.7 /sw/bin/relax --gui --debug

This should set the window size to the default of 1000x600 pixels.
Without the --debug flag, I use the wx.MAXIMIZE style for the main
window (as well as a call to wx.Frame.Maximize() for the problematic
MS Windows version), so this should be maximised twice on the Mac (the
native Mac widgets ignore both of these!).


Edward,
   Using...

/sw/bin/python2.7 /sw/bin/relax --gui --debug

does produce the smaller window which is the correct size for the
surrounding window frame. If I remove the --debug, I see to get the
same 1000x600 pixel of content drawn into a much larger window frame.
I've attached a screen capture of the window as a tiff file.


I do however see a little frameless window in the top left hand corner
with the relax Ulysses butterfly icon in it.  I'm guessing this is the
failure of the dock icon described below, though this needs testing.


Are you always running relax on Mac OS X remotely? What happens if you
log directly into the Mac where the fink relax package is installed and
execute...

/sw/bin/python2.7 /sw/bin/relax --gui


As for the test suite, once the GUI tests run I see the little
frameless window with the relax butterfly icon in it, and a new one
appears for each test!?  However this completes successfully and these
windows are all closed at the end.  All tests pass (apart from the
skipped scipy tests as scientific-python is installed by fink
instead), and the segfault you saw is not present on my 10.6.8 Mac
system.

There are a few strange behaviours with this wxPython version
(2.8.12.1) from fink.  The first is that the relax menu bar is not
integrated into the standard Mac toolbar at the top of the screen but
is a normal GTK+ menubar in addition to the Mac toolbar.  The second
is that the relax icon in the dock is not set on the fink version, it
should be the relax butterfly icon.  Lastly, the fink version is
running via X.


This should be expected as we are building relax against the X version of
wxgtk. I don't believe either fink or macports has a native Mac interface
gtk package (as far as I know everything goes through X11).


This is not the case if I use the Xcode python version.  From the
'/usr/bin/python2.6 relax -i' print out, I see:

wxPython             True            2.8.12.1
/usr/local/lib/wxPython-unicode-2.8.12.1/lib/python2.6/site-packages/wx-2.8-mac-unicode/wx

I think this wxPython was manually installed using the
wxPython2.8-osx-unicode-2.8.12.1-universal-py2.6.dmg file from
http://wxpython.org/download.php on top of the fink Python2.6 install
(I cannot remember exactly, as I have so many Python and wxPython
installs and reinstalls on this system).  From the fink version
'/sw/bin/python2.7 relax -i', I see:

wxPython             True            2.8.12.1
/sw/lib/python2.7/site-packages/wx-2.8-gtk2-unicode/wx

Using the first version, the menubar is integrated into the toolbar,
the relax icon is set for the dock icon, and X is not being used.
Though the maximize calls are ignored and the default 1000x600 is
being used for the main window, and the test suite adds the relax icon
to the dock when the GUI tests are run (this is currently
unavoidable).  So the wxPython from the official website is not using
wxGTK for the widget set but is using the native Mac widgets.  I will
now fully test out the GUI under wxGTK from the fink install, but
without being able to reproduce the main window problem or the
segfault, I unfortunately cannot do much about that until I work out
how to make this fail in my own hands.  I'll play around and try to
fix the wxGTK dock icon problem anyway.  Is there a reason why the
native Mac widgets are not being used with the fink version of
wxPython?

Cheers,

Edward


2012/4/6 Jack Howarth <howarth@xxxxxxxxxxxxxxxx>:

On Thu, Apr 05, 2012 at 03:22:47PM +0200, Edward d'Auvergne wrote:

Hi,

Ok, this is bad, the error is clearly here in fink:
http://fink.cvs.sourceforge.net/fink/dists/10.4/stable/main/finkinfo/languages/wxgtk2.8-py.info?view=markup.
 Specifically the lines:

-----
Package: wxgtk2.8-py%type_pkg[python]
Version: 2.8.9.1
-----

and:

-----
     wxgtk2.8 (>=2.8.10-24),
-----

This is wxPython 2.8.9.1 running with wxGTK 2.8.10-24 (or higher) -
that cannot work.  The versions need to match.  Maybe fixing this
wxPython/wxGTK problem within fink will eliminate the problems for the
fink install of relax (but unfortunately not the relax Application in
the DMG image file that others are seeing).

Regards,

Edward


Edward,
  Try the attached packaging in /sw/fink/10.6/local/main/finkinfo. It 
updates
wxgtk2.8 to 2.8.12 (the latest 2.8) and wxgtk2.8-py to 2.8.12.1. I've also
required wxgtk2.8-py >= 2.8.12.1 for relax-py-1.3.14-1. I still see the 
window
viewport being drawn to small initially but I don't get the warnings from 
wxgtk
any more.
       Jack





On 5 April 2012 15:09, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:

Hi Jack,

I am having extreme difficulty in finding what is wrong here.  I
cannot avoid the memory error message!  I can chase it to a wx Timer
element in something called the relax controller, but that's it.  This
really looks like a broken wxPython install in fink.  The starting
message that we both see:

/sw/lib/python2.7/site-packages/wx-2.8-gtk2-unicode/wx/_core.py:14448:
UserWarning: wxPython/wxWidgets release number mismatch
 warnings.warn("wxPython/wxWidgets release number mismatch")

might be indicating the failure point.  wxPython and wxWidgets should
both really be at the same version.  I would guess that the
http://pdb.finkproject.org/pdb/package.php/wxgtk2.8-py27 fink package
(the 2.8.9.1-6 version) is broken.  I am completely stuck and cannot
move further with this problem.  How do we get in contact with the
maintainer of this package?

Sorry,

Edward




On 3 April 2012 13:43, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:

Hi,

I think I'll have to do some more testing for this!  Due to my very
limited access to the Mac I am testing this on, progress will be slow.
 I will probably need some time to debug relax using the old Mac gtk+
version of the wx widgets, and will definitely release a new version
(1.3.15) prior to that.  So maybe it's safe to send out the newer
relax versions to fink, as the prompt/scripting UI modes function
perfectly anyway?

Cheers,

Edward




On 2 April 2012 23:04, Jack Howarth <howarth@xxxxxxxxxxxxxxxx> wrote:

On Mon, Apr 02, 2012 at 10:18:15PM +0200, Edward d'Auvergne wrote:

Hi Jack,

I've finally placed the relax-py.info and relax-py.patch files into
/sw/fink/10.4/local/main/finkinfo and installed the 1.3.14 relax
version via fink (with 'fink install relax-py27').  I have to be
careful as I have three different relax installs (the fink one, an 
svn
copy, and the DMG file version) as well as three different Python
installs (2 from fink and a manual install with Mac framework).  
When
I test the GUI with the fink version, my message is:

$ /sw/bin/python2.7 /sw/bin/relax --gui
/sw/lib/python2.7/site-packages/wx-2.8-gtk2-unicode/wx/_core.py:14448:
UserWarning: wxPython/wxWidgets release number mismatch
  warnings.warn("wxPython/wxWidgets release number mismatch")

***MEMORY-ERROR***: python2.7[878]: GSlice: assertion failed:
aligned_memory == (gpointer) addr
Abort trap
$

This is using the 2.8 version of wxPython which fink automatically
installs and which appears to be fatal!  How do I install wxPython 
2.9
into the /sw directory without damaging the fink setup?  For my
testing and included in the DMG file, I has used wxPython 2.9.2.4.

Cheers,

Edward


Edward,
   I did a build against Xcode 4.2 on x86_64 fink for darwin10 and
it didn't crash. I have...

ii  wxgtk2.8                     2.8.10-30                    
Cross-platform GUI API - unix/gtk version
ii  wxgtk2.8-py27                2.8.9.1-6                    Python 
bindings for the wxGTK library
ii  wxgtk2.8-shlibs              2.8.10-30                    Shared 
libraries for wxgtk2.8-shlibs

Did you do a 'fink selfupdate-cvs' and 'fink update-all' to make 
sure you
are getting the lastest packaging?
                 Jack
ps I get...

 relax --gui
/sw/lib/python2.7/site-packages/wx-2.8-gtk2-unicode/wx/_core.py:14448:
 UserWarning: wxPython/wxWidgets release number mismatch
 warnings.warn("wxPython/wxWidgets release number mismatch")


Thank you for citing:


relaxGUI
========

Bieri, M., d'Auvergne, E. J. and Gooley, P. R. (2011). relaxGUI: a 
new software for fast and simple
NMR relaxation data analysis and calculation of ps-ns and micro-s 
motion of proteins J. Biomol. NMR,
(http://dx.doi.org/10.1007/s10858-011-9509-1).



relax
=====

d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR 
dynamic models I. Minimisation
algorithms and their performance within the model-free and Brownian 
rotational diffusion spaces. J.
Biomol. NMR, 40(2), 107-119 
(http://dx.doi.org/10.1007/s10858-007-9214-2).

d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR 
dynamic models II. A new methodology
for the dual optimisation of the model-free parameters and the 
Brownian rotational diffusion tensor.
J. Biomol. NMR, 40(2), 121-133 
(http://dx.doi.org/10.1007/s10858-007-9213-3).



On 26 March 2012 19:54, Jack Howarth <howarth@xxxxxxxxxxxxxxxx> 
wrote:

On Mon, Mar 26, 2012 at 07:16:31PM +0200, Edward d'Auvergne wrote:

Hi Jack,

Thank you for updating this!  From memory, I did see a similar 
problem
when I was using the fink versions of all the software required.
Though I also had many problems with dependency clashes with 
Python,
wxPython, numpy, and scipy (note this is different to Scientific
Python which is no longer a dependency, see
http://pdb.finkproject.org/pdb/package.php/scipy-py27) - I had 
to use
the sources and these different relax dependencies had their own
dependencies which were not compatible with each other.  The 
problem,
I think, was the dependance on different gcc versions, so each 
was
taking a day or longer to build as fink kept rebuilding the full 
tool
chain.  Anyway, that's not completely related to this problem and
might already be resolved in fink.

The problem looks more like a wxPython issue.  Would you be able 
to
tell me the fink repository software and versions you used for 
this so
I can try to replicate the problem?  Do you use the binary
distribution archive for the dependencies or have fink compile 
from
the source archives?  I am using XCode 3.2.2, but I don't think 
using
4.2 will change this problem.  If you had the exact sequence of 
fink
commnds to set the relax dependencies up, that would be 
appreciated as
I could then be sure that I have close to the same setup as you. 
 Then
I could debug and find the exact xwgtk problem, and come up with 
a
special work around.

Cheers!

Edward


Edward,
   Try the attached packaging placed in 
/sw/fink/10.4/local/main/finkinfo. I don't
know how old your fink installation is. If it is rather old, you 
might want to consider
a clean bootstrap following the instructions on 
http://www.finkproject.org/download/srcdist.php.
You will want to move aside your current fink installation from 
/sw to /sw.old beforehand.
Also make sure you do 'fink selfupdate-cvs' and 'fink update-all' 
to keep your
trees and installation current. You should be able to just use 
'fink install relax-py27'
to install relax 1.3.14. I would also consider upgrading your 
Xcode to 3.2.6 which
is the last release of the 3.2.x series. Oh, on darwin10, I used 
the gcc46 compilers
for the build, when prompted, if that makes any difference.
                    Jack
ps I also have built relax 1.3.14 under fink but had to use the 
2.9.3 release of
wxPython because that is the only wxPython they have for python 
2.7 in macports.
Have you tested relax against the wxPython 2.9.3 release on linux 
or any other target?





On 26 March 2012 18:14, Jack Howarth <howarth@xxxxxxxxxxxxxxxx> 
wrote:

Edward,
  I am in the process of updating the relax-py and relax 
packages in fink and
macports to the latest release. However I am seeing some 
oddities with the new
gui interface. In both cases, relax 1.3.13 and 1.3.14 exhibits 
a bug when
executed as 'relax --gui'. The gui interface window opens much 
larger than the
displayed contents. Only if I refresh the window does the 
contents properly
expand out to the actual size of the window (by clicking on 
the green zoom
button in the window frame twice). If I move aside the window, 
I also see a small
square with a butterfly icon left on the screen. This square 
can't be closed or
moved. Running 'relax --test-suite' is even more problematic 
as it seems to
be trapped in an endless loop of display the squares with the 
butterfly icon
and segfaults on exiting...

% relax --test-suite
/sw/lib/python2.7/site-packages/wx-2.8-gtk2-unicode/wx/_core.py:14448:
 UserWarning: wxPython/wxWidgets release number mismatch
 warnings.warn("wxPython/wxWidgets release number mismatch")
Echoing of user function calls has been enabled.




#############################
# System / functional tests #
#############################


.........................................................................................................................................................................................................................................
----------------------------------------------------------------------
Ran 233 tests in 291.075s

OK




##############
# Unit tests #
##############


................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
----------------------------------------------------------------------
Ran 1232 tests in 11.183s

OK




#############
# GUI tests #
#############



(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type
.
(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type
.
(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type

(python2.7:9037): Gtk-WARNING **: Unable to find default local 
directory monitor type
..
----------------------------------------------------------------------
Ran 4 tests in 70.926s

OK




###################################
# Summary of the relax test suite #
###################################


# Optional packages/modules
###########################

No tests skipped due to missing modules.

# Synopsis
##########

System/functional tests 
......................................... [ OK ]
Unit tests 
...................................................... [ OK ]
GUI tests 
....................................................... [ OK ]
Synopsis 
........................................................ [ OK ]



Segmentation fault

It is odd that the GUI tests pass but that relax segfaults in 
the process.
                Jack
ps This is on x86_64 fink under darwin10 using Xcode 4.2.

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Re: relax 1.3.13/14 oddities

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