bugGnome Chemistry Utils - Bugs: bug #36583, gcrystal hangs when opening a...

 
 

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bug #36583: gcrystal hangs when opening a crystal structure

Submitted by:  Julian Sikorski <belegdol>
Submitted on:  Sun 03 Jun 2012 10:27:12 AM UTC  
 
Category: NoneSeverity: 3 - Normal
Item Group: NoneStatus: Fixed
Privacy: PublicAssigned to: Jean Bréfort <jean_brefort>
Open/Closed: Closed

(Jump to the original submission Jump to the original submission)

Mon 11 Jun 2012 10:23:20 PM UTC, comment #15:

Yes, it is. Thank you.

Julian Sikorski <belegdol>
Project Member
Mon 11 Jun 2012 08:21:50 AM UTC, comment #14:

Should be fixed.

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Sun 10 Jun 2012 02:30:31 PM UTC, comment #13:

The fix is actually trivial, I should have seen it at first glance. I just fould some other minor issues in gcrystal so I'll commit the fix later. Btw, gcrystal will now open pdb files when they have a cell geometry data.

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Sun 10 Jun 2012 11:14:44 AM UTC, comment #12:

I can reproduce now using debian sid.
The message actually arises because the socket used to commincate with the openbabel server has not been destroyed. You can use "rm /tmp/babelsocket*" to get rid of it.

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Sun 03 Jun 2012 04:39:04 PM UTC, comment #11:

I don't understand this message. Might be an X server message, but not sure.

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Sun 03 Jun 2012 04:28:45 PM UTC, comment #10:

I added it before the first while and the only thing new is the following error message:

Julian Sikorski <belegdol>
Project Member
Sun 03 Jun 2012 04:13:02 PM UTC, comment #9:

add the following line before the loops:
printf("x=%g y=%g z=%g\n",x,y,z);

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Sun 03 Jun 2012 03:52:27 PM UTC, comment #8:

How do I do that?

Julian Sikorski <belegdol>
Project Member
Sun 03 Jun 2012 03:51:05 PM UTC, comment #7:

I really can't reproduce, things work for me, so I need your help. The only infinite loop case I can imagine there is an infinite coordinate. Can you check the x, y and z values around libs/gcr/document.cc:1134?

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Sun 03 Jun 2012 01:42:27 PM UTC, comment #6:

The space group database is an essential part of gcrystal, without it crashes are not surprising.

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Sun 03 Jun 2012 12:50:53 PM UTC, comment #5:

Moreover, when you try to go to Crystal → Lattice with the space groups database out of the way, the program will crash. This is probably caused by the file being missing, though:

Julian Sikorski <belegdol>
Project Member
Sun 03 Jun 2012 12:45:26 PM UTC, comment #4:

I am not sure if this helps, but I have renamed the said file and checked again. While the console is full of error messages, the file actually opens and is shown in the gcrystal window.

Julian Sikorski <belegdol>
Project Member
Sun 03 Jun 2012 12:40:38 PM UTC, comment #3:

Yes, this one. I have no other idea at the moment, I'll have a look at the code later.

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Sun 03 Jun 2012 12:32:04 PM UTC, comment #2:

$ rpm -ql gnome-chemistry-utils | grep space-groups
/usr/share/gchemutils/0.14/space-groups.xml

Is this the one you are asking for?

Julian Sikorski <belegdol>
Project Member
Sun 03 Jun 2012 12:28:39 PM UTC, comment #1:

I can't reproduce this one, did you install the space group database?

Jean Bréfort <jean_brefort>
Project AdministratorIn charge of this item.
Sun 03 Jun 2012 10:27:12 AM UTC, original submission:

Another bug I have discovered is that gcrystal would stop responding when trying to open any of the sample files (I have tried diamond.gcrystal). Running it via gdb and hitting Ctrl-C when it is frozen reveals the following:

Julian Sikorski <belegdol>
Project Member

 

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    Follow 3 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Sun 12 Aug 2012 10:09:18 AM UTCjean_brefortOpen/ClosedOpen=>Closed
    Mon 11 Jun 2012 08:21:50 AM UTCjean_brefortStatusNone=>Fixed
      Assigned toNone=>jean_brefort

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