[phenixbb] phenix GUI freezing during refinement and file naming issues

Nathaniel Echols NEchols at lbl.gov
Tue Dec 22 11:19:34 PST 2009

On Dec 22, 2009, at 9:35 AM, Christina Bourne wrote:
> I have a similar problem on Ubuntu 8.04 (nVidia card with X-server 11.0).  I only run as a local copy.  I can switch desktops and applications mostly, but if the computer goes to screen saver then it definitely freezes the gui.  It does happen on other occasions, but as near as I can tell seems random.

Does this only freeze the GUI when it's running a process, or is it happening any time the screensaver goes on?  I tried 1.5-2 on a similar system (Ubuntu 8.10, nvidia-glx-96) and the phenix.refine GUI was still working after exiting the screensaver, but I wasn't running anything at the time.  (Although the laptop I bought for grad school is showing its age - there are probably a few more things I can do to make the GUI more responsive.)

One other thought: as many of you have discovered, when an error occurs, a window pops up with a message containing the Python traceback.  As long as one of these windows is open, the rest of the GUI will be inaccessible.  If you're switching around desktops while this happens, it is easy to miss the error, and this has confused me several times while testing.  This doesn't explain the screensaver problem, of course.

> Is there a way to restore a properly completed job to the gui (or alternatively, maybe it hasn't completed properly, but it does create a pdb and mtz and other files)?

Yes, assuming the GUI is still running and the issue is entirely with the display or underlying libraries, it will save all of the result data (i.e. validation info, statistics, and assorted internal data) for re-use later.  In the main GUI, click on "Job history", select a job, and click "Restore results".  This should resurrect the window with both the configuration and result tabs more or less as you left them.  Alternately, use the "restore last result" toolbar button.

If the GUI is truly frozen, it won't save its result data, but phenix.refine is running in a separate process, so if it completes it will write out the PDB and MTZ files to the output directory anyway.  You can get most of the same result information in the GUI relatively quickly by running the comprehensive validation.

Nathaniel Echols
Lawrence Berkeley Lab
NEchols at lbl.gov

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