Graphic problem with Olex2 and (X)Ubuntu

[celdrion]

Alright installing with yum did work on that way. Thanks a lot!
Olex2 is working now pretty fine, although it starts every time now with "Applying Olex2 Downloaded Updates".
And with the repo, I tried it again, but http://fedora.debroglie.net/RPMS/12/noarch/debroglie-release-12-1.fc12.debroglie.noarch.rpm
gives me 404 - Not found.

[johnewarren]

Olex2 is working now pretty fine, although it starts every time now with "Applying Olex2 Downloaded Updates".

Yeah, that is me, again, basically as Olex2 will pull downloads automatically but then requires unirun to install them. Unirun needs to be run before Olex2 on every startup. So rather nothing happening on startup whilst unirun is doing the updates I made the pop-up to appear.

I've altered the code in my test version to try and check if Olex2 has downloaded anything and only then for it to run unirun but it is a bit temperamental.

[johnewarren]

And with the repo, I tried it again, but http://fedora.debroglie.net/RPMS/12/noa ... noarch.rpm
gives me 404 - Not found.

Yeah try:
FEDORA 12

It is the .debroglie which is causing the problem -

Code: Select all

http://fedora.debroglie.net/RPMS/12/noarch/debroglie-release-12-1.fc12.debroglie.noarch.rpm

BAD

Code: Select all

http://fedora.debroglie.net/RPMS/12/noarch/debroglie-release-12-1.fc12.noarch.rpm

GOOD
Tiny typo sorry!

[celdrion]

OK, now I got the repo as well, although it still says it has no gpg key for it, but that's not really a problem now.

But I've seen a different problem now. When I open a cif-file or res-file with olex2 it makes mistakes with drawing the structure. Some of the bonds whcich should be in the background are drawn before other bonds which should be in the foreground. Is that a known problem? Should I open a new thread for it?

[oleg]

yeah, please use that OLEX2_GL_DEFAULT=True setting... This is common for ubuntu

[celdrion]

No, sorry probably my messages have been a bit confusing. I switched to Fedora and I have that problem there. But because of some other problems I had to upgrade already to Fedora 13 (which is the reason why it took me so long to answer). So I probably wait until there´s a repo for it and open a new thread then in case there are still any problems, so that it is not in the ubuntu thread anymore. Thank´s a lot so far.

[johnewarren]

have you tried running the Suse executables ?
http://olex2.opencryst.net/olex2-distro/1.1-beta/
just in case...

Sorry Oleg for this decay. I again back to Olex2 on Ubuntu 10.04. I checked Suse version and found interesting dependence. Why do i need library libglitz.so? I am asking you because i built Olex2 from source and i didn't need this library. Also, i couldn't find 64 bit version of Olex2 and i got error when i started it:
/home/pasha/olex/olex2: error while loading shared libraries: libglitz.so.1: wrong ELF class: ELFCLASS64

Ok. I compiled Last version of Olex2 from CVS trunk and branches/1.1 . I tried both. I changed compiled options to -O0 -g2 and also added --debug=yes to wx-config
Then i ran program via gdb using script provided by johnewarren on this forum. I got this.

Code: Select all

/home/pasha/.olex-config present
starting reading user config
completed reading users config
Olex2 directory         : /home/pasha/olex
Olex2 datadir           : /home/pasha/.olex
Olex2 cctbx directory   : /home/pasha/pasha/development/known/cctbx
Olex2 cctbx library     : /home/pasha/pasha/development/known/cctbx/cctbx_build/lib
Olex2 cctbx bin : /home/pasha/pasha/development/known/cctbx/cctbx_build/bin
Using defaults, Setting OLEX2_DIR: /home/pasha/olex
/home/pasha/olex olex2 home present
/home/pasha/olex/usettings.dat present
olex2.tag present this is a new install
GNU gdb (GDB) 7.1-ubuntu
Copyright (C) 2010 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-linux-gnu".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>...
Reading symbols from /home/pasha/olex/olex2...done.
(gdb) run
Starting program: /home/pasha/olex/olex2
[Thread debugging using libthread_db enabled]
[Debug] 04:42:12 PM: ../src/gtk/glcanvas.cpp(351): assert "m_vi" failed in Create(): required visual couldn't be found
[Debug] 04:42:16 PM: ../src/gtk/glcanvas.cpp(75): assert "vi" failed in wxGLContext(): invalid visual for OpenGl
[Debug] 04:42:17 PM: ../src/gtk/window.cpp(3286): assert "m_widget != __null" failed in SetFocus(): invalid window
[Debug] 04:42:18 PM: ../src/gtk/app.cpp(82): assert "wxAssertFailure" failed in Yield(): wxYield called recursively
[Debug] 04:42:19 PM: ../src/gtk/window.cpp(2714): assert "(m_widget != NULL)" failed in DoSetSize(): invalid window
[Debug] 04:42:20 PM: ../src/gtk/window.cpp(2715): assert "(m_parent != NULL)" failed in DoSetSize(): wxWindowGTK::SetSize requires parent.

[Debug] 04:42:21 PM: ../src/gtk/window.cpp(2981): assert "(m_widget != __null)" failed in DoGetPosition(): invalid window

Program received signal SIGSEGV, Segmentation fault.
wxWindow::DoSetSize (this=0x18a7930, x=0, y=0, width=65, height=446, sizeFlags=3) at ../src/gtk/window.cpp:2763
2763    ../src/gtk/window.cpp: No such file or directory.
        in ../src/gtk/window.cpp
(gdb) backtrace
#0  wxWindow::DoSetSize (this=0x18a7930, x=0, y=0, width=65, height=446, sizeFlags=3) at ../src/gtk/window.cpp:2763
#1  0x0000000000faee65 in wxWindowBase::SetSize (this=0x18a7930, x=0, y=0, width=65, height=446, sizeFlags=3) at /usr/include/wx-2.8/wx/window.h:225
#2  0x0000000000f9dca1 in TMainForm::OnResize (this=0x1834370) at /home/pasha/pasha/development/known/olex2/trunk/olex/mainform.cpp:2915
#3  0x0000000001031eb2 in TMainForm::macShowWindow (this=0x1834370, Cmds=..., Options=..., E=...) at /home/pasha/pasha/development/known/olex2/trunk/olex/xpprocs.cpp:5890
#4  0x0000000000fc1a11 in esdl::TMacro<TMainForm>::Run (this=0x1a7f190, Params=..., Options=..., E=...) at /home/pasha/pasha/development/known/olex2/trunk/sdl/function.h:319
#5  0x0000000000a71128 in esdl::TEMacroLib::ProcessMacro (this=0x1834ab0, Cmd=..., Error=...) at /home/pasha/pasha/development/known/olex2/trunk/sdl/macrolib.cpp:221
#6  0x0000000000fb39ed in esdl::TEMacroLib::ProcessTopMacro<TMainForm> (this=0x1834ab0, Cmd=..., Error=..., base_instance=...,
    ErrorAnalyser=0xfa83bc <TMainForm::AnalyseError(esdl::TMacroError&)>) at /home/pasha/pasha/development/known/olex2/trunk/sdl/macrolib.h:179
#7  0x0000000000fb1f17 in TMainForm::ProcessMacro (this=0x1834370, cmd=..., location=...) at /home/pasha/pasha/development/known/olex2/trunk/olex/mainform.h:163
#8  0x0000000000f913b1 in TMainForm::StartupInit (this=0x1834370) at /home/pasha/pasha/development/known/olex2/trunk/olex/mainform.cpp:1392
#9  0x0000000000fa74b7 in TMainForm::OnInternalIdle (this=0x1834370) at /home/pasha/pasha/development/known/olex2/trunk/olex/mainform.cpp:3706
#10 0x00007ffff77defbd in wxAppBase::SendIdleEvents (this=0x17e3e80, win=0xffffffff, event=...) at ../src/common/appcmn.cpp:471
#11 0x00007ffff77df1c4 in wxAppBase::ProcessIdle (this=0x17e3e80) at ../src/common/appcmn.cpp:443
#12 0x00007ffff773585a in wxApp::Yield (this=0x17e3e80, onlyIfNeeded=<value optimized out>) at ../src/gtk/app.cpp:117
#13 0x0000000000fa7493 in TMainForm::OnInternalIdle (this=0x1834370) at /home/pasha/pasha/development/known/olex2/trunk/olex/mainform.cpp:3703
#14 0x00007ffff77defbd in wxAppBase::SendIdleEvents (this=0x17e3e80, win=0xffffffff, event=...) at ../src/common/appcmn.cpp:471
#15 0x00007ffff77df1c4 in wxAppBase::ProcessIdle (this=0x17e3e80) at ../src/common/appcmn.cpp:443
#16 0x00007ffff7735599 in wxapp_idle_callback () at ../src/gtk/app.cpp:206
#17 0x00007ffff2b8f8c2 in g_main_context_dispatch () from /lib/libglib-2.0.so.0
#18 0x00007ffff2b93748 in ?? () from /lib/libglib-2.0.so.0
#19 0x00007ffff2b93c55 in g_main_loop_run () from /lib/libglib-2.0.so.0
#20 0x00007ffff4a8fbb7 in gtk_main () from /usr/lib/libgtk-x11-2.0.so.0
#21 0x00007ffff774eb48 in wxEventLoop::Run (this=0x18af850) at ../src/gtk/evtloop.cpp:76
#22 0x00007ffff77deec8 in wxAppBase::MainLoop (this=0x17e3e80) at ../src/common/appcmn.cpp:312
#23 0x00007ffff6b0a3bc in wxEntry (argc=<value optimized out>, argv=<value optimized out>) at ../src/common/init.cpp:460
#24 0x0000000000ff6a60 in main (argc=1, argv=0x7fffffffe0b8) at /home/pasha/pasha/development/known/olex2/trunk/olex/xglapp.cpp:257
(gdb) kill
Kill the program being debugged? (y or n) y
(gdb) q
$

I don't understand were problem is. I checked simple test program for wxWidget+OpenGL, and it works fine. Also i have couple another software with wx+GL and they also work fine.

Any advice?

Thanks, for your help.

Best, Pavel.

[johnewarren]

I'm not Oleg but can you try:

Code: Select all

export OLEX2_GL_STEREO=FALSE

In the terminal before running Olex2? It is just a test. I have added it to my .olex2-config file if it works you may want to do the same.

[johnewarren]

I'm not Oleg but can you try:

Code: Select all

export OLEX2_GL_STEREO=FALSE

Hi, johnewarren. Thank you for your advice. I tried. And really, it looks like i can run Olex2. But i tried to open any *.ins file and my Olex2 crashed immediately. Below you can find output information. (I changed name of binary file from Olex2->Olex2.db for debug propose). I didn't use dbg software.

Code: Select all

$ olex
/home/pasha/.olex-config present
starting reading user config
completed reading users config
Olex2 directory         : /home/pasha/olex
Olex2 datadir           : /home/pasha/.olex
Olex2 cctbx directory   : /home/pasha/pasha/development/known/cctbx
Olex2 cctbx library     : /home/pasha/pasha/development/known/cctbx/cctbx_build/lib
Olex2 cctbx bin : /home/pasha/pasha/development/known/cctbx/cctbx_build/bin
Using defaults, Setting OLEX2_DIR: /home/pasha/olex
/home/pasha/olex olex2 home present
/home/pasha/olex/usettings.dat present
olex2.tag present this is a new install
[Debug] 11:43:55 PM: ../src/gtk/app.cpp(82): assert "wxAssertFailure" failed in Yield(): wxYield called recursively
[Debug] 23:44:03: wxColour::Set - couldn't set to colour string 'FFBBBB'
[Debug] 23:44:03: wxColour::Set - couldn't set to colour string 'FFBBBB'
[Debug] 23:44:03: wxColour::Set - couldn't set to colour string 'bbffbb'
[Debug] 23:44:03: wxColour::Set - couldn't set to colour string 'FFBBBB'
[Debug] 23:44:03: wxColour::Set - couldn't set to colour string 'bbffbb'
[Debug] 23:44:03: ../src/gtk/app.cpp(82): assert "wxAssertFailure" failed in Yield(): wxYield called recursively
*** glibc detected *** /home/pasha/olex/olex2.db: double free or corruption (fasttop): 0x00000000043caeb0 ***
======= Backtrace: =========
/lib/libc.so.6(+0x775b6)[0x7f0186c535b6]
/lib/libc.so.6(cfree+0x73)[0x7f0186c59e53]
/home/pasha/olex/olex2.db(_ZN4esdl10TArrayListIdE8SetCountEm+0x8f)[0x81450b]
/home/pasha/olex/olex2.db(_ZN4esdl10TArrayListIdE5ClearEv+0x1d)[0x80ce53]
/home/pasha/olex/olex2.db(_ZN4xlib15RefinementModel5ClearEj+0x280)[0xae0ada]
/home/pasha/olex/olex2.db(_ZN4xlib6TXFile12LoadFromFileERKN4esdl9TTSStringINS1_8TWStringEwEE+0x2c1)[0xef85b3]
/home/pasha/olex/olex2.db(_ZN5gxlib6TGXApp9LoadXFileERKN4esdl9TTSStringINS1_8TWStringEwEE+0x3c)[0x99fa72]
/home/pasha/olex/olex2.db(_ZN9TMainForm7macReapERN4esdl12TStrPObjListINS0_9TTSStringINS0_8TWStringEwEEPNS0_8IEObjectEEERKNS0_10TParamListERNS0_11TMacroErrorE+0x18b1)[0x1024635]
/home/pasha/olex/olex2.db(_ZN4esdl6TMacroI9TMainFormE3RunERNS_12TStrPObjListINS_9TTSStringINS_8TWStringEwEEPNS_8IEObjectEEERKNS_10TParamListERNS_11TMacroErrorE+0x395)[0xfc1a11]
/home/pasha/olex/olex2.db(_ZN4esdl10TEMacroLib12ProcessMacroERKNS_9TTSStringINS_8TWStringEwEERNS_11TMacroErrorE+0x94a)[0xa71128]
/home/pasha/olex/olex2.db(_ZN4esdl10TEMacroLib12ProcessMacroERKNS_9TTSStringINS_8TWStringEwEERNS_11TMacroErrorE+0xb4d)[0xa7132b]
/home/pasha/olex/olex2.db(_ZN4esdl10TEMacroLib15ProcessTopMacroI9TMainFormEEvRKNS_9TTSStringINS_8TWStringEwEERNS_11TMacroErrorERT_MSA_FvS9_E+0x3d)[0xfb39ed]                                   
/home/pasha/olex/olex2.db(_ZN9TMainForm12ProcessMacroERKN4esdl9TTSStringINS0_8TWStringEwEES5_+0x97)[0xfb1f17]                                                                                   
/home/pasha/olex/olex2.db(_ZN9TMainForm12ProcessEventER7wxEvent+0x1ba)[0xfa887c]                                                                                                               
/usr/lib/libwx_gtk2ud_core-2.8.so.0(+0x25d10a)[0x7f0188c2310a]                                                                                                                                 
/usr/lib/libgobject-2.0.so.0(g_closure_invoke+0x15e)[0x7f01848ad5de]
/usr/lib/libgobject-2.0.so.0(+0x21598)[0x7f01848c1598]
/usr/lib/libgobject-2.0.so.0(g_signal_emit_valist+0x7f6)[0x7f01848c2a76]
/usr/lib/libgobject-2.0.so.0(g_signal_emit+0x83)[0x7f01848c3033]
/usr/lib/libgtk-x11-2.0.so.0(gtk_widget_activate+0x6e)[0x7f0186010a2e]
/usr/lib/libgtk-x11-2.0.so.0(gtk_menu_shell_activate_item+0xfd)[0x7f0185f0456d]
/usr/lib/libgtk-x11-2.0.so.0(+0x151c9b)[0x7f0185f05c9b]
/usr/lib/libgtk-x11-2.0.so.0(+0x142178)[0x7f0185ef6178]
/usr/lib/libgobject-2.0.so.0(g_closure_invoke+0x15e)[0x7f01848ad5de]
/usr/lib/libgobject-2.0.so.0(+0x211dd)[0x7f01848c11dd]
/usr/lib/libgobject-2.0.so.0(g_signal_emit_valist+0x639)[0x7f01848c28b9]
/usr/lib/libgobject-2.0.so.0(g_signal_emit+0x83)[0x7f01848c3033]
/usr/lib/libgtk-x11-2.0.so.0(+0x2590bf)[0x7f018600d0bf]
/usr/lib/libgtk-x11-2.0.so.0(gtk_propagate_event+0xc3)[0x7f0185eee643]
/usr/lib/libgtk-x11-2.0.so.0(gtk_main_do_event+0x2eb)[0x7f0185eef71b]
/usr/lib/libgdk-x11-2.0.so.0(+0x5c86c)[0x7f0185b6386c]
/lib/libglib-2.0.so.0(g_main_context_dispatch+0x1f2)[0x7f0183fef8c2]
/lib/libglib-2.0.so.0(+0x42748)[0x7f0183ff3748]
/lib/libglib-2.0.so.0(g_main_loop_run+0x195)[0x7f0183ff3c55]
/usr/lib/libgtk-x11-2.0.so.0(gtk_main+0xa7)[0x7f0185eefbb7]
/usr/lib/libwx_gtk2ud_core-2.8.so.0(_ZN11wxEventLoop3RunEv+0x48)[0x7f0188baeb48]
/usr/lib/libwx_gtk2ud_core-2.8.so.0(_ZN9wxAppBase8MainLoopEv+0x48)[0x7f0188c3eec8]
/usr/lib/libwx_baseud-2.8.so.0(_Z7wxEntryRiPPw+0x4c)[0x7f0187f6a3bc]
/home/pasha/olex/olex2.db(main+0x22)[0xff6a60]
/lib/libc.so.6(__libc_start_main+0xfd)[0x7f0186bfac4d]
/home/pasha/olex/olex2.db[0x7c3519]
======= Memory map: ========
00400000-0134c000 r-xp 00000000 08:08 3932255                            /home/pasha/olex/olex2.db
0154b000-0154c000 r--p 00f4b000 08:08 3932255                            /home/pasha/olex/olex2.db
0154c000-01676000 rw-p 00f4c000 08:08 3932255                            /home/pasha/olex/olex2.db
01676000-01704000 rw-p 00000000 00:00 0
0232b000-04a93000 rw-p 00000000 00:00 0                                  [heap]
7f0158a4d000-7f0158a4e000 ---p 00000000 00:00 0
7f0158a4e000-7f015924e000 rw-p 00000000 00:00 0
7f015924e000-7f015924f000 ---p 00000000 00:00 0
7f015924f000-7f0159a4f000 rw-p 00000000 00:00 0
7f0159a4f000-7f015e37f000 r--p 00000000 08:05 1507                       /usr/share/icons/hicolor/icon-theme.cache
7f015e37f000-7f0162caf000 r--p 00000000 08:05 1507                       /usr/share/icons/hicolor/icon-theme.cache
7f0162caf000-7f016701b000 r--p 00000000 08:05 1545                       /usr/share/icons/oxygen/icon-theme.cache
7f016701b000-7f016b387000 r--p 00000000 08:05 1545                       /usr/share/icons/oxygen/icon-theme.cache
7f016b387000-7f016b39b000 r-xp 00000000 08:05 16646                      /usr/lib/gio/modules/libgioremote-volume-monitor.so
7f016b39b000-7f016b59a000 ---p 00014000 08:05 16646                      /usr/lib/gio/modules/libgioremote-volume-monitor.so
7f016b59a000-7f016b59b000 r--p 00013000 08:05 16646                      /usr/lib/gio/modules/libgioremote-volume-monitor.so
7f016b59b000-7f016b59c000 rw-p 00014000 08:05 16646                      /usr/lib/gio/modules/libgioremote-volume-monitor.so
7f016b59c000-7f016b5a7000 r-xp 00000000 08:05 7688                       /lib/libudev.so.0.6.1
7f016b5a7000-7f016b7a6000 ---p 0000b000 08:05 7688                       /lib/libudev.so.0.6.1
7f016b7a6000-7f016b7a7000 r--p 0000a000 08:05 7688                       /lib/libudev.so.0.6.1
7f016b7a7000-7f016b7a8000 rw-p 0000b000 08:05 7688                       /lib/libudev.so.0.6.1
7f016b7a8000-7f016b7e5000 r-xp 00000000 08:05 14891                      /lib/libdbus-1.so.3.4.0
7f016b7e5000-7f016b9e5000 ---p 0003d000 08:05 14891                      /lib/libdbus-1.so.3.4.0
7f016b9e5000-7f016b9e6000 r--p 0003d000 08:05 14891                      /lib/libdbus-1.so.3.4.0
7f016b9e6000-7f016b9e7000 rw-p 0003e000 08:05 14891                      /lib/libdbus-1.so.3.4.0
7f016b9e7000-7f016b9ff000 r-xp 00000000 08:05 7288                       /usr/lib/libgvfscommon.so.0.0.0
7f016b9ff000-7f016bbfe000 ---p 00018000 08:05 7288                       /usr/lib/libgvfscommon.so.0.0.0
7f016bbfe000-7f016bbff000 r--p 00017000 08:05 7288                       /usr/lib/libgvfscommon.so.0.0.0
7f016bbff000-7f016bc00000 rw-p 00018000 08:05 7288                       /usr/lib/libgvfscommon.so.0.0.0
7f016bc00000-7f016c000000 rw-s 153308000 00:05 3880                      /dev/dri/card0
7f016c000000-7f016c115000 rw-p 00000000 00:00 0
7f016c115000-7f0170000000 ---p 00000000 00:00 0
7f0170074000-7f017008f000 r--s 00000000 08:05 11931                      /usr/share/mime/mime.cache
7f017008f000-7f01700b8000 r-xp 00000000 08:05 16650                      /usr/lib/gio/modules/libgvfsdbus.so
7f01700b8000-7f01702b8000 ---p 00029000 08:05 16650                      /usr/lib/gio/modules/libgvfsdbus.so
7f01702b8000-7f01702b9000 r--p 00029000 08:05 16650                      /usr/lib/gio/modules/libgvfsdbus.so
7f01702b9000-7f01702ba000 rw-p 0002a000 08:05 16650                      /usr/lib/gio/modules/libgvfsdbus.so
7f01702ba000-7f0172964000 rw-p 00000000 00:00 0
7f0172964000-7f0172969000 r-xp 00000000 08:05 5970                       /lib/libnss_dns-2.11.1.so
7f0172969000-7f0172b68000 ---p 00005000 08:05 5970                       /lib/libnss_dns-2.11.1.so
7f0172b68000-7f0172b69000 r--p 00004000 08:05 5970                       /lib/libnss_dns-2.11.1.so
7f0172b69000-7f0172b6a000 rw-p 00005000 08:05 5970                       /lib/libnss_dns-2.11.1.so
7f0172b6a000-7f0172b6c000 r-xp 00000000 08:05 52238                      /lib/libnss_mdns4_minimal.so.2
7f0172b6c000-7f0172d6b000 ---p 00002000 08:05 52238                      /lib/libnss_mdns4_minimal.so.2
7f0172d6b000-7f0172d6c000 r--p 00001000 08:05 52238                      /lib/libnss_mdns4_minimal.so.2
7f0172d6c000-7f0172d6d000 rw-p 00002000 08:05 52238                      /lib/libnss_mdns4_minimal.so.2
7f0172d78000-7f0172d93000 r--s 00000000 08:05 11931                      /usr/share/mime/mime.cache/home/pasha/bin/olex: line 154: 19923 Aborted     $HOME/olex/olex2.db
$ 

Output information below was obtained using gdb program.
$ olex
/home/pasha/.olex-config present
starting reading user config
completed reading users config
Olex2 directory         : /home/pasha/olex
Olex2 datadir           : /home/pasha/.olex
Olex2 cctbx directory   : /home/pasha/pasha/development/known/cctbx
Olex2 cctbx library     : /home/pasha/pasha/development/known/cctbx/cctbx_build/lib
Olex2 cctbx bin : /home/pasha/pasha/development/known/cctbx/cctbx_build/bin
Using defaults, Setting OLEX2_DIR: /home/pasha/olex
/home/pasha/olex olex2 home present
/home/pasha/olex/usettings.dat present
olex2.tag present this is a new install
GNU gdb (GDB) 7.1-ubuntu
Copyright (C) 2010 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-linux-gnu".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>...
Reading symbols from /home/pasha/olex/olex2...done.
(gdb) run
Starting program: /home/pasha/olex/olex2
[Thread debugging using libthread_db enabled]
[Debug] 11:57:06 PM: ../src/gtk/app.cpp(82): assert "wxAssertFailure" failed in Yield(): wxYield called recursively
[Debug] 23:57:17: wxColour::Set - couldn't set to colour string 'FFBBBB'
[Debug] 23:57:17: wxColour::Set - couldn't set to colour string 'FFBBBB'
[Debug] 23:57:17: wxColour::Set - couldn't set to colour string 'bbffbb'
[Debug] 23:57:17: wxColour::Set - couldn't set to colour string 'FFBBBB'
[Debug] 23:57:17: wxColour::Set - couldn't set to colour string 'bbffbb'
[New Thread 0x7fffe2132710 (LWP 20531)]
[Debug] 23:57:18: ../src/gtk/app.cpp(82): assert "wxAssertFailure" failed in Yield(): wxYield called recursively
[Thread 0x7fffe2132710 (LWP 20531) exited]
[New Thread 0x7fffcc67c710 (LWP 20539)]
[New Thread 0x7fffcbe7b710 (LWP 20540)]
[Thread 0x7fffcc67c710 (LWP 20539) exited]
[New Thread 0x7fffcc67c710 (LWP 20544)]
[Thread 0x7fffcbe7b710 (LWP 20540) exited]
[New Thread 0x7fffcbe7b710 (LWP 20545)]
[Thread 0x7fffcc67c710 (LWP 20544) exited]
[New Thread 0x7fffcc67c710 (LWP 20546)]
[Thread 0x7fffcc67c710 (LWP 20546) exited]
*** glibc detected *** /home/pasha/olex/olex2: double free or corruption (fasttop): 0x000000000379fe50 ***
======= Backtrace: =========
/lib/libc.so.6(+0x775b6)[0x7ffff57f35b6]
/lib/libc.so.6(cfree+0x73)[0x7ffff57f9e53]
/home/pasha/olex/olex2(_ZN4esdl10TArrayListIdE8SetCountEm+0x8f)[0x81450b]
/home/pasha/olex/olex2(_ZN4esdl10TArrayListIdE5ClearEv+0x1d)[0x80ce53]
/home/pasha/olex/olex2(_ZN4xlib15RefinementModel5ClearEj+0x280)[0xae0ada]
/home/pasha/olex/olex2(_ZN4xlib6TXFile12LoadFromFileERKN4esdl9TTSStringINS1_8TWStringEwEE+0x2c1)[0xef85b3]
/home/pasha/olex/olex2(_ZN5gxlib6TGXApp9LoadXFileERKN4esdl9TTSStringINS1_8TWStringEwEE+0x3c)[0x99fa72]
/home/pasha/olex/olex2(_ZN9TMainForm7macReapERN4esdl12TStrPObjListINS0_9TTSStringINS0_8TWStringEwEEPNS0_8IEObjectEEERKNS0_10TParamListERNS0_11TMacroErrorE+0x18b1)[0x1024635]
/home/pasha/olex/olex2(_ZN4esdl6TMacroI9TMainFormE3RunERNS_12TStrPObjListINS_9TTSStringINS_8TWStringEwEEPNS_8IEObjectEEERKNS_10TParamListERNS_11TMacroErrorE+0x395)[0xfc1a11]
/home/pasha/olex/olex2(_ZN4esdl10TEMacroLib12ProcessMacroERKNS_9TTSStringINS_8TWStringEwEERNS_11TMacroErrorE+0x94a)[0xa71128]
/home/pasha/olex/olex2(_ZN4esdl10TEMacroLib12ProcessMacroERKNS_9TTSStringINS_8TWStringEwEERNS_11TMacroErrorE+0xb4d)[0xa7132b]
/home/pasha/olex/olex2(_ZN4esdl10TEMacroLib15ProcessTopMacroI9TMainFormEEvRKNS_9TTSStringINS_8TWStringEwEERNS_11TMacroErrorERT_MSA_FvS9_E+0x3d)[0xfb39ed]
/home/pasha/olex/olex2(_ZN9TMainForm12ProcessMacroERKN4esdl9TTSStringINS0_8TWStringEwEES5_+0x97)[0xfb1f17]
/home/pasha/olex/olex2(_ZN9TMainForm12ProcessEventER7wxEvent+0x1ba)[0xfa887c]
/usr/lib/libwx_gtk2ud_core-2.8.so.0(+0x25d10a)[0x7ffff77c310a]
/usr/lib/libgobject-2.0.so.0(g_closure_invoke+0x15e)[0x7ffff344d5de]
/usr/lib/libgobject-2.0.so.0(+0x21598)[0x7ffff3461598]
/usr/lib/libgobject-2.0.so.0(g_signal_emit_valist+0x7f6)[0x7ffff3462a76]
/usr/lib/libgobject-2.0.so.0(g_signal_emit+0x83)[0x7ffff3463033]
/usr/lib/libgtk-x11-2.0.so.0(gtk_widget_activate+0x6e)[0x7ffff4bb0a2e]
/usr/lib/libgtk-x11-2.0.so.0(gtk_menu_shell_activate_item+0xfd)[0x7ffff4aa456d]
/usr/lib/libgtk-x11-2.0.so.0(+0x151c9b)[0x7ffff4aa5c9b]
/usr/lib/libgtk-x11-2.0.so.0(+0x142178)[0x7ffff4a96178]
/usr/lib/libgobject-2.0.so.0(g_closure_invoke+0x15e)[0x7ffff344d5de]
/usr/lib/libgobject-2.0.so.0(+0x211dd)[0x7ffff34611dd]
/usr/lib/libgobject-2.0.so.0(g_signal_emit_valist+0x639)[0x7ffff34628b9]
/usr/lib/libgobject-2.0.so.0(g_signal_emit+0x83)[0x7ffff3463033]
/usr/lib/libgtk-x11-2.0.so.0(+0x2590bf)[0x7ffff4bad0bf]
/usr/lib/libgtk-x11-2.0.so.0(gtk_propagate_event+0xc3)[0x7ffff4a8e643]
/usr/lib/libgtk-x11-2.0.so.0(gtk_main_do_event+0x2eb)[0x7ffff4a8f71b]
/usr/lib/libgdk-x11-2.0.so.0(+0x5c86c)[0x7ffff470386c]
/lib/libglib-2.0.so.0(g_main_context_dispatch+0x1f2)[0x7ffff2b8f8c2]
/lib/libglib-2.0.so.0(+0x42748)[0x7ffff2b93748]
/lib/libglib-2.0.so.0(g_main_loop_run+0x195)[0x7ffff2b93c55]
/usr/lib/libgtk-x11-2.0.so.0(gtk_main+0xa7)[0x7ffff4a8fbb7]
/usr/lib/libwx_gtk2ud_core-2.8.so.0(_ZN11wxEventLoop3RunEv+0x48)[0x7ffff774eb48]
/usr/lib/libwx_gtk2ud_core-2.8.so.0(_ZN9wxAppBase8MainLoopEv+0x48)[0x7ffff77deec8]
/usr/lib/libwx_baseud-2.8.so.0(_Z7wxEntryRiPPw+0x4c)[0x7ffff6b0a3bc]
/home/pasha/olex/olex2(main+0x22)[0xff6a60]
/lib/libc.so.6(__libc_start_main+0xfd)[0x7ffff579ac4d]
/home/pasha/olex/olex2[0x7c3519]
======= Memory map: ========
00400000-0134c000 r-xp 00000000 08:08 3932255                            /home/pasha/olex/olex2
0154b000-0154c000 r--p 00f4b000 08:08 3932255                            /home/pasha/olex/olex2
0154c000-01676000 rw-p 00f4c000 08:08 3932255                            /home/pasha/olex/olex2
01676000-03e3f000 rw-p 00000000 00:00 0                                  [heap]
7fffbc000000-7fffbc021000 rw-p 00000000 00:00 0
7fffbc021000-7fffc0000000 ---p 00000000 00:00 0
7fffc4000000-7fffc4021000 rw-p 00000000 00:00 0
7fffc4021000-7fffc8000000 ---p 00000000 00:00 0
7fffcb67b000-7fffcb67c000 ---p 00000000 00:00 0
7fffcb67c000-7fffcbe7c000 rw-p 00000000 00:00 0
7fffcbe7c000-7fffcbe7d000 ---p 00000000 00:00 0
7fffcbe7d000-7fffcc67d000 rw-p 00000000 00:00 0
7fffcc67d000-7fffd0fad000 r--p 00000000 08:05 1507                       /usr/share/icons/hicolor/icon-theme.cache
7fffd0fad000-7fffd58dd000 r--p 00000000 08:05 1507                       /usr/share/icons/hicolor/icon-theme.cache
7fffd58dd000-7fffd9c49000 r--p 00000000 08:05 1545                       /usr/share/icons/oxygen/icon-theme.cache
7fffd9c49000-7fffddfb5000 r--p 00000000 08:05 1545                       /usr/share/icons/oxygen/icon-theme.cache
7fffddfb5000-7fffddfc9000 r-xp 00000000 08:05 16646                      /usr/lib/gio/modules/libgioremote-volume-monitor.so
7fffddfc9000-7fffde1c8000 ---p 00014000 08:05 16646                      /usr/lib/gio/modules/libgioremote-volume-monitor.so
7fffde1c8000-7fffde1c9000 r--p 00013000 08:05 16646                      /usr/lib/gio/modules/libgioremote-volume-monitor.so
7fffde1c9000-7fffde1ca000 rw-p 00014000 08:05 16646                      /usr/lib/gio/modules/libgioremote-volume-monitor.so
7fffde1ca000-7fffde1d5000 r-xp 00000000 08:05 7688                       /lib/libudev.so.0.6.1
7fffde1d5000-7fffde3d4000 ---p 0000b000 08:05 7688                       /lib/libudev.so.0.6.1
7fffde3d4000-7fffde3d5000 r--p 0000a000 08:05 7688                       /lib/libudev.so.0.6.1
7fffde3d5000-7fffde3d6000 rw-p 0000b000 08:05 7688                       /lib/libudev.so.0.6.1
7fffde3d6000-7fffde413000 r-xp 00000000 08:05 14891                      /lib/libdbus-1.so.3.4.0
7fffde413000-7fffde613000 ---p 0003d000 08:05 14891                      /lib/libdbus-1.so.3.4.0
7fffde613000-7fffde614000 r--p 0003d000 08:05 14891                      /lib/libdbus-1.so.3.4.0
7fffde614000-7fffde615000 rw-p 0003e000 08:05 14891                      /lib/libdbus-1.so.3.4.0
7fffde615000-7fffde62d000 r-xp 00000000 08:05 7288                       /usr/lib/libgvfscommon.so.0.0.0
7fffde62d000-7fffde82c000 ---p 00018000 08:05 7288                       /usr/lib/libgvfscommon.so.0.0.0
7fffde82c000-7fffde82d000 r--p 00017000 08:05 7288                       /usr/lib/libgvfscommon.so.0.0.0
7fffde82d000-7fffde82e000 rw-p 00018000 08:05 7288                       /usr/lib/libgvfscommon.so.0.0.0
7fffde82e000-7fffde857000 r-xp 00000000 08:05 16650                      /usr/lib/gio/modules/libgvfsdbus.so
7fffde857000-7fffdea57000 ---p 00029000 08:05 16650                      /usr/lib/gio/modules/libgvfsdbus.so
7fffdea57000-7fffdea58000 r--p 00029000 08:05 16650                      /usr/lib/gio/modules/libgvfsdbus.so
7fffdea58000-7fffdea59000 rw-p 0002a000 08:05 16650                      /usr/lib/gio/modules/libgvfsdbus.so
7fffdea59000-7fffdee59000 rw-s 155d44000 00:05 3880                      /dev/dri/card0
7fffdee59000-7fffe1503000 rw-p 00000000 00:00 0
7fffe1503000-7fffe1508000 r-xp 00000000 08:05 5970                       /lib/libnss_dns-2.11.1.so
7fffe1508000-7fffe1707000 ---p 00005000 08:05 5970                       /lib/libnss_dns-2.11.1.so
7fffe1707000-7fffe1708000 r--p 00004000 08:05 5970                       /lib/libnss_dns-2.11.1.so
7fffe1708000-7fffe1709000 rw-p 00005000 08:05 5970                       /lib/libnss_dns-2.11.1.so
7fffe1709000-7fffe170b000 r-xp 00000000 08:05 52238                      /lib/libnss_mdns4_minimal.so.2
7fffe170b000-7fffe190a000 ---p 00002000 08:05 52238                      /lib/libnss_mdns4_minimal.so.2
7fffe190a000-7fffe190b000 r--p 00001000 08:05 52238                      /lib/libnss_mdns4_minimal.so.2
7fffe190b000-7fffe190c000 rw-p 00002000 08:05 52238                      /lib/libnss_mdns4_minimal.so.2
7fffe1932000-7fffe1933000 ---p 00000000 00:00 0
7fffe1933000-7fffe2133000 rw-p 00000000 00:00 0
7fffe2133000-7fffe2166000 r--p 00000000 08:05 132228                     /usr/share/fonts/truetype/msttcorefonts/Arial_Italic.ttf
7fffe2166000-7fffe21ac000 r--p 00000000 08:05 132229                     /usr/share/fonts/truetype/msttcorefonts/Arial_Bold.ttf
7fffe21ac000-7fffe21bc000 r--p 00000000 08:08 3932406                    /home/pasha/olex/etc/gui/fonts/Vera.ttf
7fffe21d6000-7fffe221a000 r--p 00000000 08:05 132232                     /usr/share/fonts/truetype/msttcorefonts/Arial.ttf
7fffe221a000-7fffe2222000 rw-s 1559dc000 00:05 3880                      /dev/dri/card0
7fffe2222000-7fffe222a000 rw-s 1559d4000 00:05 3880                      /dev/dri/card0
7fffe222a000-7fffe2232000 rw-s 15587a000 00:05 3880                      /dev/dri/card0
7fffe2232000-7fffe223a000 rw-s 155872000 00:05 3880                      /dev/dri/card0
7fffe223a000-7fffe2242000 rw-s 15586a000 00:05 3880                      /dev/dri/card0
7fffe2242000-7fffe229a000 rw-p 00000000 00:00 0
7fffe229a000-7fffe229e000 r-xp 00000000 08:05 7573                       /usr/lib/python2.6/dist-packages/PIL/_imagingft.so
7fffe229e000-7fffe249d000 ---p 00004000 08:05 7573                       /usr/lib/python2.6/dist-packages/PIL/_imagingft.so
7fffe249d000-7fffe249e000 r--p 00003000 08:05 7573                       /usr/lib/python2.6/dist-packages/PIL/_imagingft.so
7fffe249e000-7fffe249f000 rw-p 00004000 08:05 7573                       /usr/lib/python2.6/dist-packages/PIL/_imagingft.so
7fffe249f000-7fffe24dc000 r-xp 00000000 08:05 7572                       /usr/lib/python2.6/dist-packages/PIL/_imaging.so
Program received signal SIGABRT, Aborted.
0x00007ffff57afa75 in *__GI_raise (sig=<value optimized out>) at ../nptl/sysdeps/unix/sysv/linux/raise.c:64
64      ../nptl/sysdeps/unix/sysv/linux/raise.c: No such file or directory.
        in ../nptl/sysdeps/unix/sysv/linux/raise.c
(gdb) backtrace
#0  0x00007ffff57afa75 in *__GI_raise (sig=<value optimized out>) at ../nptl/sysdeps/unix/sysv/linux/raise.c:64
#1  0x00007ffff57b35c0 in *__GI_abort () at abort.c:92
#2  0x00007ffff57e94fb in __libc_message (do_abort=<value optimized out>, fmt=<value optimized out>) at ../sysdeps/unix/sysv/linux/libc_fatal.c:189
#3  0x00007ffff57f35b6 in malloc_printerr (action=3, str=0x7ffff58c6c50 "double free or corruption (fasttop)", ptr=<value optimized out>) at malloc.c:6264
#4  0x00007ffff57f9e53 in *__GI___libc_free (mem=<value optimized out>) at malloc.c:3738
#5  0x000000000081450b in esdl::TArrayList<double>::SetCount (this=0x1cd6c38, v=0) at /home/pasha/pasha/development/known/olex2/trunk/sdl/talist.h:274
#6  0x000000000080ce53 in esdl::TArrayList<double>::Clear (this=0x1cd6c38) at /home/pasha/pasha/development/known/olex2/trunk/sdl/talist.h:55
#7  0x0000000000ae0ada in xlib::RefinementModel::Clear (this=0x1cd5c38, clear_mask=4294967295) at /home/pasha/pasha/development/known/olex2/trunk/xlib/refmodel.cpp:86
#8  0x0000000000ef85b3 in xlib::TXFile::LoadFromFile (this=0x1cd59d0, FN=...) at /home/pasha/pasha/development/known/olex2/trunk/xlib/xfiles.cpp:156
#9  0x000000000099fa72 in gxlib::TGXApp::LoadXFile (this=0x1c1a400, fn=...) at /home/pasha/pasha/development/known/olex2/trunk/gxlib/gxapp.cpp:3117
#10 0x0000000001024635 in TMainForm::macReap (this=0x1834370, Cmds=..., Options=..., Error=...) at /home/pasha/pasha/development/known/olex2/trunk/olex/xpprocs.cpp:4535
#11 0x0000000000fc1a11 in esdl::TMacro<TMainForm>::Run (this=0x1d15460, Params=..., Options=..., E=...) at /home/pasha/pasha/development/known/olex2/trunk/sdl/function.h:319
#12 0x0000000000a71128 in esdl::TEMacroLib::ProcessMacro (this=0x1834ab0, Cmd=..., Error=...) at /home/pasha/pasha/development/known/olex2/trunk/sdl/macrolib.cpp:221
#13 0x0000000000a7132b in esdl::TEMacroLib::ProcessMacro (this=0x1834ab0, Cmd=..., Error=...) at /home/pasha/pasha/development/known/olex2/trunk/sdl/macrolib.cpp:243
#14 0x0000000000fb39ed in esdl::TEMacroLib::ProcessTopMacro<TMainForm> (this=0x1834ab0, Cmd=..., Error=..., base_instance=...,
    ErrorAnalyser=0xfa83bc <TMainForm::AnalyseError(esdl::TMacroError&)>) at /home/pasha/pasha/development/known/olex2/trunk/sdl/macrolib.h:179
#15 0x0000000000fb1f17 in TMainForm::ProcessMacro (this=0x1834370, cmd=..., location=...) at /home/pasha/pasha/development/known/olex2/trunk/olex/mainform.h:163
#16 0x0000000000fa887c in TMainForm::ProcessEvent (this=0x1834370, evt=...) at /home/pasha/pasha/development/known/olex2/trunk/olex/mainform.cpp:3874
#17 0x00007ffff77c310a in gtk_menu_clicked_callback (widget=<value optimized out>, menu=0x18be3e0) at ../src/gtk/menu.cpp:653
#18 0x00007ffff344d5de in g_closure_invoke () from /usr/lib/libgobject-2.0.so.0
#19 0x00007ffff3461598 in ?? () from /usr/lib/libgobject-2.0.so.0
#20 0x00007ffff3462a76 in g_signal_emit_valist () from /usr/lib/libgobject-2.0.so.0
#21 0x00007ffff3463033 in g_signal_emit () from /usr/lib/libgobject-2.0.so.0
#22 0x00007ffff4bb0a2e in gtk_widget_activate () from /usr/lib/libgtk-x11-2.0.so.0
#23 0x00007ffff4aa456d in gtk_menu_shell_activate_item () from /usr/lib/libgtk-x11-2.0.so.0
#24 0x00007ffff4aa5c9b in ?? () from /usr/lib/libgtk-x11-2.0.so.0
#25 0x00007ffff4a96178 in ?? () from /usr/lib/libgtk-x11-2.0.so.0
#26 0x00007ffff344d5de in g_closure_invoke () from /usr/lib/libgobject-2.0.so.0
#27 0x00007ffff34611dd in ?? () from /usr/lib/libgobject-2.0.so.0
#28 0x00007ffff34628b9 in g_signal_emit_valist () from /usr/lib/libgobject-2.0.so.0
#29 0x00007ffff3463033 in g_signal_emit () from /usr/lib/libgobject-2.0.so.0
#30 0x00007ffff4bad0bf in ?? () from /usr/lib/libgtk-x11-2.0.so.0
#31 0x00007ffff4a8e643 in gtk_propagate_event () from /usr/lib/libgtk-x11-2.0.so.0
#32 0x00007ffff4a8f71b in gtk_main_do_event () from /usr/lib/libgtk-x11-2.0.so.0
#33 0x00007ffff470386c in ?? () from /usr/lib/libgdk-x11-2.0.so.0
#34 0x00007ffff2b8f8c2 in g_main_context_dispatch () from /lib/libglib-2.0.so.0
#35 0x00007ffff2b93748 in ?? () from /lib/libglib-2.0.so.0
#36 0x00007ffff2b93c55 in g_main_loop_run () from /lib/libglib-2.0.so.0
#37 0x00007ffff4a8fbb7 in gtk_main () from /usr/lib/libgtk-x11-2.0.so.0
#38 0x00007ffff774eb48 in wxEventLoop::Run (this=0x18af770) at ../src/gtk/evtloop.cpp:76
#39 0x00007ffff77deec8 in wxAppBase::MainLoop (this=0x17e3e80) at ../src/common/appcmn.cpp:312
#40 0x00007ffff6b0a3bc in wxEntry (argc=<value optimized out>, argv=<value optimized out>) at ../src/common/init.cpp:460
#41 0x0000000000ff6a60 in main (argc=1, argv=0x7fffffffe098) at /home/pasha/pasha/development/known/olex2/trunk/olex/xglapp.cpp:257
(gdb)

I hope this information will be useful.

Best, Pavel.

[Pavlo]

Before i ran Olex2 from gdb usin start command. If you need i can recompile Olex2 with -O0 -g3 + `wx-config --debug=yes` and run it with start command and line by line check execution of Olex2.

Best, Pavel.

[oleg]

OK, this makes sense - I did make a typo in TArrayList<> SetCount, so it was unstable around that source line,
what source is used for the compiling the executable? I think that trunk should be fine now.
I will update the release branch ASAP,

o

[Pavlo]

OK, this makes sense - I did make a typo in TArrayList<> SetCount, so it was unstable around that source line,
what source is used for the compiling the executable?

Yes, you right, i used trunk repository. Just let me know when new trunk will be ready. If you need put special compilation flags or define specific variables i can do this.

Thanks, Pavel.

[oleg]

It should be fine now, sorry...
That was the classical copy/paste:

Code: Select all

  template <class List> inline TArrayList& operator = (const List& list)  {
    return Assign(list);
  }

   template <class List> inline TArrayList& operator = (const TArrayList& list)  {
    return Assign(list);
  }


which forces gcc to use bit copying, when assigning one object to the other, whereas CL would use the template version...

[Pavlo]

Hi, Oleg.

Thanks, i checked fixed version and it seems i can start Olex2 and it works. I have some problem with rotation of the model. It is too slow. May be it is a problem with my OpenGL. i use Mesa DRI Mobile Intel® GM45 Express Chipset GEM 20091221 2009Q4 video (OpenGL). If you have any advice how can i reduce effect of frozen picture i will be very thankful.

Best, Pavel.

[oleg]

Unless you have a huge model, most graphics cards should be able to do the job. Just make sure that you have the hardware acceleration turned on. I have X3100 chipset on my Mac, which is older and supposedly slower than yours (http://en.wikipedia.org/wiki/Intel_GMA) but it still does a decent job even with complicated structure models (look below). There is however could be a problem with rasters rendering, i.e. text, you could test it by changing the number of lines of text in console

Code: Select all

lines n

(if n is -1, all lines are shown). You can use

Code: Select all

echo fps()

command to get some numbers for rendering speed. Also try adjusting the quality of the display (right click on background, Draw Quality of the context menu). But the driver software is the most probable cause.
__
For info, with no text on screen on my Mac, fps for 1024 atoms and 1088 bonds in medium draw quality:
7.2
which is not much but still is fine for a research work.