Re: relax GUI -- August 08, 2012

Hi ,

Here is how wx-python was installed.

./configure --prefix=/programs/x86_64-linux/wxpython/2.8.12.1 --enable-unicode --with-gtk --with-gnomeprint --with-opengl --with-libjpeg=builtin --with-libpng=builtin --with-libtiff=builtin --with-zlib=builtin --enable-optimize --enable-debug_flag --enable-rpath=/programs/x86_64-linux/wxpython/2.8.12.1/lib
make && make install
cd contrib
make && make install
cd ../wxPython
export PATH=programs/system/x86_64-linux/wxpython/2.8.12.1/bin:$PATH
python setup.py install

Output of relax --info

relax --info

relax 2.1.0

Molecular dynamics by NMR data analysis

This is free software which you are welcome to modify and redistribute under the conditions of the

GNU General Public License (GPL). This program, including all modules, is licensed under the GPL

and comes with absolutely no warranty. For details type 'GPL' within the relax prompt.

Assistance in using the relax prompt and scripting interface can be accessed by typing 'help' within

the prompt.

Processor fabric: Uni-processor.

Hardware information:

Machine: x86_64

Processor: x86_64

Endianness: little

Total RAM size: 2011 Mb

Total swap size: 509 Mb

Operating system information:

System: Linux

Release: 2.6.18-194.17.1.el5

Version: #1 SMP Wed Sep 29 12:50:31 EDT 2010

GNU/Linux version: CentOS 5.8 Final

Distribution: redhat 5.8 Final

Full platform string: Linux-2.6.18-194.17.1.el5-x86_64-with-redhat-5.8-Final

Python information:

Architecture: 64bit ELF

Python version: 2.7.2

Python branch:

Python build: default, Oct 27 2011 16:10:58

Python compiler: GCC 4.1.2 20080704 (Red Hat 4.1.2-51)

Libc version: glibc 2.2.5

Python implementation: CPython

Python revision:

Python executable: /programs/x86_64-linux/python/2.7.2/bin/python

Python flags: sys.flags(debug=0, py3k_warning=0, division_warning=0, division_new=0, inspect=0, interactive=0, optimize=0, dont_write_bytecode=0, no_user_site=0, no_site=0, ignore_environment=0, tabcheck=0, verbose=0, unicode=0, bytes_warning=0)

Python float info: sys.float_info(max=1.7976931348623157e+308, max_exp=1024, max_10_exp=308, min=2.2250738585072014e-308, min_exp=-1021, min_10_exp=-307, dig=15, mant_dig=53, epsilon=2.220446049250313e-16, radix=2, rounds=1)

Python module path: ['/programs/x86_64-linux/relax/2.1.0', '/programs/x86_64-linux/python/2.7.2/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg', '/programs/x86_64-linux/python/2.7.2/lib/python2.7/site-packages/pip-1.0.2-py2.7.egg', '/programs/x86_64-linux/python/2.7.2/lib/python2.7/site-packages/matplotlib-1.1.0-py2.7-linux-x86_64.egg', '/programs/x86_64-linux/python/2.7.2/lib/python2.7/site-packages/yolk-0.4.1-py2.7.egg', '/programs/x86_64-linux/python/2.7.2/lib/python2.7/site-packages/MySQL_python-1.2.3-py2.7-linux-x86_64.egg', '/programs/x86_64-linux/python/2.7.2/lib/python2.7/site-packages/VTK-5.6.1-py2.7.egg', '/programs/x86_64-linux/python/2.7.2/lib/python2.7/site-packages/MDAnalysis-0.7.5.1-py2.7-linux-x86_64.egg', '/programs/x86_64-linux/python/2.7.2/lib/python2.7/site-packages/GridDataFormats-0.2.2-py2.7.egg', '/programs/x86_64-linux/python/2.7.2/lib/python2.7/site-packages/networkx-1.6-py2.7.egg', '/programs/x86_64-linux/python/2.7.2/lib/python2.7/site-packages/MDAnalysisTests-0.7.5.1-py2.7.egg', '/programs/x86_64-linux/ccp4/6.2.0/ccp4-6.2.0/share/python', '/programs/x86_64-linux/ccpnmr/2.2.1/ccpnmr2.2/python', '/programs/x86_64-linux/csrosetta/20120626/python', '/programs/x86_64-linux/eman/1.9/lib', '/programs/x86_64-linux/eman2/20120806/lib', '/programs/x86_64-linux/eman2/20120806/bin', '/programs/x86_64-linux/haddock/2.1', '/programs/x86_64-linux/python/2.7.2/lib/python27.zip', '/programs/x86_64-linux/python/2.7.2/lib/python2.7', '/programs/x86_64-linux/python/2.7.2/lib/python2.7/plat-linux2', '/programs/x86_64-linux/python/2.7.2/lib/python2.7/lib-tk', '/programs/x86_64-linux/python/2.7.2/lib/python2.7/lib-old', '/programs/x86_64-linux/python/2.7.2/lib/python2.7/lib-dynload', '/programs/x86_64-linux/python/2.7.2/lib/python2.7/site-packages', '/programs/x86_64-linux/python/2.7.2/lib/python2.7/site-packages/PIL', '/programs/x86_64-linux/python/2.7.2/lib/python2.7/site-packages', '/programs/x86_64-linux/python/2.7.2/lib/python2.7/site-packages/wx-2.8-gtk2-unicode', '/programs/x86_64-linux/relax/2.1.0/extern/scientific_python/linux2']

Python packages and modules (most are optional):

Name Installed Version Path

minfx True Unknown /programs/x86_64-linux/relax/2.1.0/minfx

bmrblib True Unknown /programs/x86_64-linux/relax/2.1.0/bmrblib

numpy True 1.6.1 /programs/x86_64-linux/python/2.7.2/lib/python2.7/site-packages/numpy

scipy True 0.10.0 /programs/x86_64-linux/python/2.7.2/lib/python2.7/site-packages/scipy

wxPython True 2.8.12.1 (gtk2-unicode) /programs/x86_64-linux/python/2.7.2/lib/python2.7/site-packages/wx-2.8-gtk2-unicode/wx

mpi4py False

epydoc False

optparse True 1.5.3 /programs/x86_64-linux/python/2.7.2/lib/python2.7/optparse.pyc

readline True /programs/x86_64-linux/python/2.7.2/lib/python2.7/lib-dynload/readline.so

profile True /programs/x86_64-linux/python/2.7.2/lib/python2.7/profile.pyc

bz2 True /programs/x86_64-linux/python/2.7.2/lib/python2.7/lib-dynload/bz2.so

gzip True /programs/x86_64-linux/python/2.7.2/lib/python2.7/gzip.pyc

os.devnull True /programs/x86_64-linux/python/2.7.2/lib/python2.7/os.pyc

xml True 0.8.4 (internal) /programs/x86_64-linux/python/2.7.2/lib/python2.7/xml/__init__.pyc

xml.dom.minidom True /programs/x86_64-linux/python/2.7.2/lib/python2.7/xml/dom/minidom.pyc

relax information:

Version: 2.1.0

Processor fabric: Uni-processor.

relax C modules:

Module Compiled File type Path

maths_fns.relax_fit True ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped /programs/x86_64-linux/relax/2.1.0/maths_fns/relax_fit.so

Will get the wx_python o/p by tomorrow

venkat

On Wed, Aug 8, 2012 at 5:09 PM, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:

Hi Venkat,

I have seen the log file attached to your bug report
(https://gna.org/bugs/?19987). There seems to be two separate issues
here. The first is the two failures in the system tests. As you can
probably see, this is for Art Palmer's Modelfree4 program. From the
lower precision of the chi-squared values from your installed version,
I would assume that you have a version much older than the current
(though still very old) 4.20 version which includes a number of
patches I sent to Art to fix bugs and to compile with GCC
(http://biochemistry.hs.columbia.edu/labs/palmer/software/modelfree.html).
You can ignore these two failures.

The second problem is in the GUI tests. I think these messages
clearly identify the problem. The important error message is the very
first:

Traceback (most recent call last):
File "/programs/x86_64-linux/relax/2.1.0/test_suite/gui_tests/base_classes.py",
line 198, in setUp
self.app.gui = Main(parent=None, id=-1, title="")
File "/programs/x86_64-linux/relax/2.1.0/gui/relax_gui.py", line
162, in __init__
self.add_start_screen()
File "/programs/x86_64-linux/relax/2.1.0/gui/relax_gui.py", line
259, in add_start_screen
image = wx.StaticBitmap(self, -1,
bitmap_setup(paths.IMAGE_PATH+'ulysses_shadowless_400x168.png'))
File "/programs/x86_64-linux/relax/2.1.0/gui/misc.py", line 133, in
bitmap_setup
bitmap.SetMaskColour(None)
File "/programs/x86_64-linux/python/2.7.2/lib/python2.7/site-packages/wx-2.8-gtk2-unicode/wx/_gdi.py",
line 632, in SetMaskColour
return _gdi_.Bitmap_SetMaskColour(*args, **kwargs)
PyAssertionError: C++ assertion "Ok()" failed at
./src/gtk/colour.cpp(146) in Blue(): invalid colour

The second is just an error caused by the failure of the first test -
nothing to worry about. You can then see that these two error
messages are alternatively repeated for all the GUI tests. The key is
the failure of the setting of the mask
(http://en.wikipedia.org/wiki/Mask_%28computing%29#Image_masks) for
the bitmap image. This clearly indicates that your wxPython install
is broken (for your sys admin - I'm guessing because of the linking to
the GTK+ libraries). You might be able to test this with the wxPython
demos for this wxPython version. Try the following and see if you
observe error messages:

$ /programs/x86_64-linux/python/2.7.2/bin/python run.py GenericButtons.py
$ /programs/x86_64-linux/python/2.7.2/bin/python run.py StaticBitmap.py
$ /programs/x86_64-linux/python/2.7.2/bin/python run.py ComboCtrl.py

These should all run fine. Note you need to be in the wx_demo
directory containing the run.py and other files. Could you copy and
paste the output of these tests. Also, I just noticed that your
information from:

$ relax --info

was accidentally not sent to the mailing lists. Could you copy and
paste that output as well for reference. Remember to click on
'reply-to-all' rather than just 'reply' when responding. Other
information that would be useful is how is this wxPython installed?
Is it installed from the package management system, is it downloaded
binaries, or is it self compiled? Is it also installed locally or on
an NFS share, for example?

Cheers,

Edward

P.S. To summarize, here is a check list of needed information:

1. wx_demo tests output.
2. relax --info output.
3. wxPython install info.

On 8 August 2012 13:07, venkataraman <venkat@xxxxxxxxxxxxxxxxxxx> wrote:
> I had sent the error report as a text file for the o/p of
> relax --test-suite on x86_64-linux on centOS5.
>
>
>
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