Re: relax GUI -- August 09, 2012

Hi,

I'm a bit confused, the RDP server is a MS Windows only product
(http://en.wikipedia.org/wiki/Remote_Desktop_Protocol).  Did you
install 1.3.16 on Windows or Linux?  I'm almost 100% sure that the
problem is, however, the wxPython installation.  Please try to compile
the 2.9 version and test that instead.  As the internal tests of the
wxPython demos fail, then there will be no way to ever make the
wxPython execute the relax GUI.  These tests must, without question,
pass otherwise there is no point even trying the relax GUI as the GUI
will never work.  If you can compile the latest 2.9 version and run
the same tests using the demos for that exact 2.9 version, then the
relax GUI should instantly be visible via SSH, VNC, RDP, telnet, etc.
I would recommend VNC or RDP though as this is much faster for modern
apps.

Regards,

Edward


On 9 August 2012 19:38, Venkat V <venkat@xxxxxxxxxxxxxxxxxxx> wrote:

Hi Edward,


To make sure wx_python has issues I tried the following:

I tried the earlier version of relax 1.3.16 via ssh and that seg faults.
But relax version 1.3.16 works when use RDP and try it with the same
wx_python.


venkat


On Thu, Aug 9, 2012 at 9:03 PM, Edward d'Auvergne <edward@xxxxxxxxxxxxx>
wrote:


Hi,

Those are very strange errors!  It might be an indication that the
wxPython compilation failed.  Does the version.py file that came with
the wxPython demos match the wxPython version you have installed?  I
would suggest trying the 2.9 wxPython versions, or having a close look
at the compilation messages.  In any case, your wxPython installation
does not appear to be in a healthy state.

Regards,

Edward



On 9 August 2012 17:15, Venkat V <venkat@xxxxxxxxxxxxxxxxxxx> wrote:

Hi Edward,

Here is the o/p of the wx tests.

$ which python
/programs/x86_64-linux/python/2.7.2/bin/python
sbtest@vm-11 [centos-5-x86_64] ~/test/relax/wxtest/demo
 $ python run.py Ge
GenericButtons.py  GenericDirCtrl.py  GetMouseState.py
sbtest@vm-11 [centos-5-x86_64] ~/test/relax/wxtest/demo
 $ python run.py Gene
GenericButtons.py  GenericDirCtrl.py
sbtest@vm-11 [centos-5-x86_64] ~/test/relax/wxtest/demo
 $ python run.py GenericButtons.py
Python 2.7.2 (default, Oct 27 2011, 16:10:58)
[GCC 4.1.2 20080704 (Red Hat 4.1.2-51)]
wx.version: 2.8.12.1 (gtk2-unicode)
pid: 32382
Traceback (most recent call last):
  File "run.py", line 162, in <module>
    main(sys.argv)
  File "run.py", line 156, in main
    app = RunDemoApp(name, module, useShell)
  File "run.py", line 50, in __init__
    wx.App.__init__(self, redirect=False)
  File

"/programs/x86_64-linux/python/2.7.2/lib/python2.7/site-packages/wx-2.8-gtk2-unicode/wx/_core.py",
line 7981, in __init__
    self._BootstrapApp()
  File

"/programs/x86_64-linux/python/2.7.2/lib/python2.7/site-packages/wx-2.8-gtk2-unicode/wx/_core.py",
line 7555, in _BootstrapApp
    return _core_.PyApp__BootstrapApp(*args, **kwargs)
  File "run.py", line 57, in OnInit
    self.InitInspection()  # for the InspectionMixin base class
AttributeError: 'RunDemoApp' object has no attribute 'InitInspection'
sbtest@vm-11 [centos-5-x86_64] ~/test/relax/wxtest/demo
 $ python run.py StaticBitmap.py
Python 2.7.2 (default, Oct 27 2011, 16:10:58)
[GCC 4.1.2 20080704 (Red Hat 4.1.2-51)]
wx.version: 2.8.12.1 (gtk2-unicode)
pid: 32429
Traceback (most recent call last):
  File "run.py", line 162, in <module>
    main(sys.argv)
  File "run.py", line 156, in main
    app = RunDemoApp(name, module, useShell)
  File "run.py", line 50, in __init__
    wx.App.__init__(self, redirect=False)
  File

"/programs/x86_64-linux/python/2.7.2/lib/python2.7/site-packages/wx-2.8-gtk2-unicode/wx/_core.py",
line 7981, in __init__
    self._BootstrapApp()
  File

"/programs/x86_64-linux/python/2.7.2/lib/python2.7/site-packages/wx-2.8-gtk2-unicode/wx/_core.py",
line 7555, in _BootstrapApp
    return _core_.PyApp__BootstrapApp(*args, **kwargs)
  File "run.py", line 57, in OnInit
    self.InitInspection()  # for the InspectionMixin base class
AttributeError: 'RunDemoApp' object has no attribute 'InitInspection'
sbtest@vm-11 [centos-5-x86_64] ~/test/relax/wxtest/demo
 $ python run.py ComboCtrl.py
Python 2.7.2 (default, Oct 27 2011, 16:10:58)
[GCC 4.1.2 20080704 (Red Hat 4.1.2-51)]
wx.version: 2.8.12.1 (gtk2-unicode)
pid: 32476
Traceback (most recent call last):
  File "run.py", line 162, in <module>
    main(sys.argv)
  File "run.py", line 156, in main
    app = RunDemoApp(name, module, useShell)
  File "run.py", line 50, in __init__
    wx.App.__init__(self, redirect=False)
  File

"/programs/x86_64-linux/python/2.7.2/lib/python2.7/site-packages/wx-2.8-gtk2-unicode/wx/_core.py",
line 7981, in __init__
    self._BootstrapApp()
  File

"/programs/x86_64-linux/python/2.7.2/lib/python2.7/site-packages/wx-2.8-gtk2-unicode/wx/_core.py",
line 7555, in _BootstrapApp
    return _core_.PyApp__BootstrapApp(*args, **kwargs)
  File "run.py", line 57, in OnInit
    self.InitInspection()  # for the InspectionMixin base class
AttributeError: 'RunDemoApp' object has no attribute 'InitInspection'
sbtest@vm-11 [centos-5-x86_64] ~/test/relax/wxtest/demo


sincerely,

Venkat

On Thu, Aug 9, 2012 at 1:40 AM, Edward d'Auvergne <edward@xxxxxxxxxxxxx>
wrote:


Hi,

Do you have the wx demos?  You can download them from

http://downloads.sourceforge.net/wxpython/wxPython-demo-2.8.12.1.tar.bz2
and run these directly.  The results of the following tests are
important:

$ /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

As you have compiled this version of wxPython and it seems to be
broken, I would recommend downloading the latest 2.9.4.0 version and
trying that.  I have extensively tested with 2.9.3.1 and everything
works very nicely, and the Mac OS X distribution dmg file has this
version built in.  Note that the 2.9 versions are much simpler to
compile and install.  The 2.8 version I have tested is 2.8.11.0,
therefore I would suggest that wxPython has introduced a bug between
2.8.11.0 and 2.8.12.1.

Regards,

Edward


P. S.  If the 2.9 versions work, the report from the wxPython 2.8
demos would still be very useful for any other relax users who
encounter the same problem.



On 8 August 2012 21:11, Venkat V <venkat@xxxxxxxxxxxxxxxxxxx> wrote:

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

                             Copyright (C) 2001-2006 Edward
d'Auvergne
                         Copyright (C) 2006-2012 the relax
development
team

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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