relax (molecular dynamics analysis)

Hi, I am planning in a few weeks time on merging the frame_order_cleanup branch back into the relax trunk. Despite the name, this branch is a huge change containing many, many commits and it completes the frame order theory implementation in relax ... [More] - which in trunk is very rudimentary, incomplete and unusable - and brings it up to publication quality. The merger of the new theory will correspond to a publication. As this change is so big and brings in a completely new analysis category into relax, I am thinking of incrementing the major version number and releasing this as relax 4.0. Regards, Edward [Less]

For reference, I've created another test which uses many more GUI elements and which causes a segmentation fault on Mac systems after less than 300 iterations: $ ./relax devel_scripts/memory_management/GUI_uf_align_tensor_init.py This script works ... [More] flawlessly on Linux and Windows systems. Regards, Edward On 17 March 2015 at 11:54, Edward d'Auvergne <edward-kqII41Zox2pDPfheJLI6IQ< at >public.gmane.org> wrote: [Less]

Hi, Here is a good example of where the Mac GUI limits can be tested: $ ./relax devel_scripts/memory_management/GUI_uf_time.py This repetitively calls the time user function 10000 times. This uses the muppy module from the powerful Pympler ... [More] package (https://pythonhosted.org/Pympler/). Looking at the 'muppy_log' file produced, it can be seen that no extra memory is being leaked. I.e. all the GUI objects are released. The memory between iteration 100 and the last iteration is the same (except for some extra Python objects after iteration 1700 when the first invisible problems probably occur). The way the time user function is called is that the user function window is created and then destroyed each time. No wxPython objects are present in memory after the user function is destroyed. This is different to the GUI behaviour where the window is created and then closed by being hidden, and a second call simply reopens the original window. However this test demonstrates the Mac GUI object failure point ex [Less]

Hi, Would anyone know of any tools in Mac OS X which can be used to track GUI object usage? In MS Windows, the task manager can be set up to display "USER Objects" and "GUI Objects". I have used this for debugging to allow the GUI tests to pass ... [More] again on that system and not run into the 10,000 object limits. But in Mac and Linux systems, I have no idea what can be used for a GUI debugging tool! If I could see these and have an idea about their usage, I might be able to track down possible GUI object leaks and maybe get the tests to run again. It might be possible to save memory in other areas, or to even force Macs to release the GUI objects. But we are currently completely blind as to what is happening with wxPython, GUI objects, and the Mac way of handling these. Cheers, Edward On 15 March 2015 at 14:11, Edward d'Auvergne <edward-kqII41Zox2pDPfheJLI6IQ< at >public.gmane.org> wrote: [Less]

Hi, The error I see is: """ $ ./relax --gui-tests ============= = GUI tests = ============= .........................................Sun Mar 15 13:53:41 Mac.local Python[248] <Error>: kCGErrorFailure: _CGSBindWindowBacking: cannot map ... [More] backing data shmem Sun Mar 15 13:53:41 Mac.local Python[248] <Error>: kCGErrorFailure: Set a breakpoint < at > CGErrorBreakpoint() to catch errors as they are logged. Sun Mar 15 13:53:41 Mac.local Python[248] <Error>: kCGErrorFailure: _CGSLockWindow: Unable to lock window Sun Mar 15 13:53:41 Mac.local Python[248] <Error>: kCGErrorFailure: _CGSBindWindowBacking: cannot map backing data shmem Sun Mar 15 13:53:41 Mac.local Python[248] <Error>: kCGErrorFailure: _CGSLockWindow: Unable to lock window Sun Mar 15 13:53:41 Mac.local Python[248] <Error>: kCGErrorFailure: _CGSBindWindowBacking: cannot map backing data shmem Sun Mar 15 13:53:41 Mac.local Python[248] <Error>: kCGErrorFailure: _CGSLockWindow: Unable to lock window """ This is repeated many, many times until I see: """ Pyt [Less]

Hi Jack, Maybe you might be able to help solve this problem. It is rather difficult and I think the easiest solution is to blacklist GUI tests from running on Mac OS X. However despite the segfaults, I find the tests useful to make sure all is ... [More] well in the GUI on a Mac. The problem is either a bug in wxPython, well really wxWidgets, or a design flaw in Mac OS X. From what I've read, it sounds more like a Mac design flaw. This was previously a problem on MS Windows, but I have solved it for that OS in relax 3.3.6 (http://wiki.nmr-relax.com/Relax_3.3.6). All operating systems have a hard limit for the number of GUI objects that can be created (windows, panels, buttons, etc.). In MS Windows, this is called "User Objects" and there the limit is 10,000, and "GDI Object" which has the same limit. In Mac systems, I'm not sure what the equivalent are called. In Linux, the limits are so high that we'll never encountered the problem. In relax these limits are reached due to the design of the GUI, specificall [Less]

Follow-up Comment #1, bug #23389 (project relax): This failure also appears in 3.3.6 with 'relax --test-suite'. Oddly it doesn't occur with 'relax --gui-tests'. _______________________________________________________ Reply to this item at: ... [More] <http://gna.org/bugs/?23389> _______________________________________________ Message sent via/by Gna! http://gna.org/ [Less]

URL: <http://gna.org/bugs/?23389> Summary: GUI tests segfaults in 3.3.7 Project: relax Submitted by: jhowarth Submitted on: Sat 14 Mar 2015 07:25:26 PM UTC Category: ... [More] GUI Specific analysis category: None Priority: 5 - Normal Severity: 3 - Normal Status: None Assigned to: None Originator Name: Originator Email: Open/Closed: Open Release: 3.3.7 Discussion Lock: Any Operating System: Mac OS X _______________________________________________________ Details: The 3.3.7 release exhibits gui test suite failures of the form... 2015-03-14 15:00:17.780 python2.7[97122:1548460] -[QNSApplication transformToForegroundApplication]: unrecognized selector sent to instance 0x7fa9899c0360 2015-03-14 15:00:17.989 python2.7[97122:1548460] An uncaught exception was raised 2015-03-14 15:00:17.989 python2.7[97122:1548460] [Less]

Update of sr #3219 (project relax): Operating System: Microsoft Windows => All systems _______________________________________________________ Reply to this item at: <http://gna.org/support/?3219> _______________________________________________ Message sent via/by Gna! http://gna.org/

Update of sr #3219 (project relax): Status: None => Done Open/Closed: Open => Closed Summary: Help for inputting CPMG ... [More] dispersion data from heigh list => Help for inputting CPMG dispersion data from height list. _______________________________________________________ Follow-up Comment #6: The following pseudo-script will read the data out of the attached Sam.csv file: """ # Create the data pipe. pipe.create(pipe_name='test', pipe_type='relax_disp') # Load the sequence. sequence.read('Sam.csv', dir='.', res_num_col=1, sep=',') # Name the spins so they can be matched to the assignments, and the isotope for field strength scaling. spin.name(name='N') spin.isotope(isotope='15N') # Load the peak intensities. spectrum.read_intensities('Sam.csv', dir='.', spectrum_id='test', int_method='height', int_col=2, res_num_col=1, sep=',') """ This is just a demonstration. If using the GUI, j [Less]