Avogadro 1.0.1+ 64bit Linux binary build with GUI installer is open for testing

Konstantin_Tokarev · May 18, 2010, 1:10pm

You can download it from http://linuxchemist.webatu.com/avogadro/1.0.1/
It’s actually build of 1.0.1 + some backports from trunks of Avogadro and OpenBabel.

It should work out-of-box on any Linux distribution without additional manipulations. If it doesn’t, please, report about it.

This build has some specific configuration settings in file avogadro.config, installed to the installation root. There you can choose GUI theme and control what libraries are used from system instead of packaged ones (to decrease memory usage and slightly improve performance)

The only requirements are 64 bit kernal and core 64bit libraries. On 32bit Debian with amd64 kernel you’ll need to use packaged OpenGL libraries (set GL=1 in avogadro.config)

–
Regards,
Konstantin

allison.vacanti · May 18, 2010, 1:45pm

Hi Konstantin,

On Tue, May 18, 2010 at 9:10 AM, Konstantin Tokarev annulen@yandex.ru wrote:

You can download it from http://linuxchemist.webatu.com/avogadro/1.0.1/
It’s actually build of 1.0.1 + some backports from trunks of Avogadro and OpenBabel.

It should work out-of-box on any Linux distribution without additional manipulations. If it doesn’t, please, report about it.

This build has some specific configuration settings in file avogadro.config, installed to the installation root. There you can choose GUI theme and control what libraries are used from system instead of packaged ones (to decrease memory usage and slightly improve performance)

The only requirements are 64 bit kernal and core 64bit libraries. On 32bit Debian with amd64 kernel you’ll need to use packaged OpenGL libraries (set GL=1 in avogadro.config)

Sounds like a great idea – I’m looking for a way to simplify the
installation of the dev versions of Avo and OB, and this sounds
perfect. Installing dev OB is quite a daunting task for some users of
XtalOpt, and this may be of great use to me. Will there be 32 bit
versions as well?

I’ll test it out in a VM later (hopefully today…) and let you know
if I run into any trouble.

Dave

Konstantin_Tokarev · May 18, 2010, 1:59pm

18.05.10, 17:45, “David Lonie” loniedavid@gmail.com:

Hi Konstantin,

On Tue, May 18, 2010 at 9:10 AM, Konstantin Tokarev wrote:

You can download it from http://linuxchemist.webatu.com/avogadro/1.0.1/
It’s actually build of 1.0.1 + some backports from trunks of Avogadro and OpenBabel.

It should work out-of-box on any Linux distribution without additional manipulations. If it doesn’t, please, report about it.

This build has some specific configuration settings in file avogadro.config, installed to the installation root. There you can choose GUI theme and control what libraries are used from system instead of packaged ones (to decrease memory usage and slightly improve performance)

The only requirements are 64 bit kernal and core 64bit libraries. On 32bit Debian with amd64 kernel you’ll need to use packaged OpenGL libraries (set GL=1 in avogadro.config)

Sounds like a great idea – I’m looking for a way to simplify the
installation of the dev versions of Avo and OB, and this sounds
perfect. Installing dev OB is quite a daunting task for some users of
XtalOpt, and this may be of great use to me.

This build is not trunk (but trunk could be build the same way)
And I’m not sure it’s possible to compile extension against installation of this build, better compile all in one process (installer contains development files as additional option though).

Will there be 32 bit
versions as well?

Yes. Unexpectedly, I had some problems with it, but they should be solved easily
I’ve tried to get at least one build working

I’ll test it out in a VM later (hopefully today…) and let you know
if I run into any trouble.

Thanks!

Regards,
Konstantin

Яндекс.Почта. Письма есть. Спама - нет. http://mail.yandex.ru/nospam/sign

allison.vacanti · May 18, 2010, 3:21pm

2010/5/18 Konstantin Tokarev annulen@yandex.ru:

This build is not trunk (but trunk could be build the same way)
And I’m not sure it’s possible to compile extension against installation of this build, better compile all in one process (installer contains development files as additional option though).

How difficult is it to generate such a package? I’d be interested in
creating some OB/Avo packages like this while waiting for OB 2.3 and
Avo 1.1.

It shouldn’t be a problem as far as the extension goes – I’ve started
distributing some avopkgs, which has gone well so far

Dave

Konstantin_Tokarev · May 18, 2010, 3:37pm

18.05.10, 19:21, “David Lonie” loniedavid@gmail.com:

2010/5/18 Konstantin Tokarev :

This build is not trunk (but trunk could be build the same way)
And I’m not sure it’s possible to compile extension against installation of this build, better compile all in one process (installer contains development files as additional option though).

How difficult is it to generate such a package? I’d be interested in
creating some OB/Avo packages like this while waiting for OB 2.3 and
Avo 1.1.

Not so difficult. Everything (scripts, some other stuff) is on http://github.com/annulen/avogadro-super
I use CentOS for building since it has old glibc which makes binaries more portable.

I use Intel compiler for more aggressive optimization of Qt, OpenBabel and Avogadro (interoperable with GCC, any GCC compiled plugin must work), and bunch of system libraries from CentOS (I’ll upload archives later).

I also tried to compile 1.1 with enabled Python, but it didn’t run properly (freezed when accessing Python terminal). Maybe there was error(s) in my builds of python, sip, and pyqt4 though

I use InstallJammer to create installers. It’s also able to generate packages for Windows, but my current project is strictly Linux-oriented. It can also generate installers for other Unix systems, but they’re not so divergent as Linux, and if one builds binary it should work for others without any headache

It shouldn’t be a problem as far as the extension goes – I’ve started
distributing some avopkgs, which has gone well so far

Nice to hear!

–
Regards,
Konstantin

Konstantin_Tokarev · May 18, 2010, 3:51pm

How difficult is it to generate such a package?

How do I (assume that avogadro-super is installed, and there are symlinks avogadro and openbabel in root directory pointing to right versions of them)

Run scripts/unix/build-… script (there are set proper keys for cmake, compilers, compiler flags,…)
I run build-intel-x86_64-sse2 -j8 (for 8-thread build)
At the end, it installs everything into build-intel-x86_64-sse2/install_prefix and upacks there archives with Qt and system libraries.
Create a symlink from build-intel-x86_64-sse2/install_prefix to prefix
Run installjammer, choose avogadro-1.0.1-64.mpi (for 32 bit build, 32-bit installer should be chosen instead of 64bit; for 1.1.x file group contents should be slightly revised), click “build package”
Profit!

–
Regards,
Konstantin

Konstantin_Tokarev · May 18, 2010, 4:58pm

18.05.10, 20:51, “David Lonie” loniedavid@gmail.com:

On Tue, May 18, 2010 at 9:10 AM, Konstantin Tokarev wrote:

You can download it from http://linuxchemist.webatu.com/avogadro/1.0.1/
It’s actually build of 1.0.1 + some backports from trunks of Avogadro and OpenBabel.

It should work out-of-box on any Linux distribution without additional manipulations. If it doesn’t, please, report about it.

It seems the library path isn’t set on a fresh install of 64 bit arch
linux (running ~/Avogadro/bin/avogadro complains about not being able
to find libopenbabel.so)

run avogadro.sh
Sorry for inconvenience
It should automatically run when desktop icon is clicked
If you still experience problems, play with avogadro.config. There’s also avogadro-check, it shows output of ldd in GUI

–
Regards,
Konstantin

allison.vacanti · May 18, 2010, 5:07pm

On Tue, May 18, 2010 at 12:58 PM, Konstantin Tokarev annulen@yandex.ru wrote:

It seems the library path isn’t set on a fresh install of 64 bit arch
linux (running ~/Avogadro/bin/avogadro complains about not being able
to find libopenbabel.so)

run avogadro.sh
Sorry for inconvenience
It should automatically run when desktop icon is clicked
If you still experience problems, play with avogadro.config. There’s also avogadro-check, it shows output of ldd in GUI

Still some problems:

[dl@ez05 Avogadro]$ ./avogadro.sh
Setting LD_LIBRARY_PATH=/home/dl/Avogadro/./lib:/home/dl/Avogadro/./lib/qt/lib:/home/dl/Avogadro/./lib/intel:/home/dl/Avogadro/./lib/X11:/home/dl/Avogadro/./lib/sys:/bin/lib:/bin/lib/qt/lib:/bin/lib/intel:
linux-vdso.so.1 => (0x00007fffbe7ff000)
libc.so.6 => /lib/libc.so.6 (0x00007f15ef1d5000)
libopenbabel.so.3 => /home/dl/Avogadro/./lib/libopenbabel.so.3
(0x00007f15eebd5000)
libQtOpenGL.so.4 =>
/home/dl/Avogadro/./lib/qt/lib/libQtOpenGL.so.4 (0x00007f15ee8bc000)
libGLU.so.1 => /usr/lib/libGLU.so.1 (0x00007f15ee64c000)
libGL.so.1 => /usr/lib/libGL.so.1 (0x00007f15ee3c8000)
libQtGui.so.4 => /home/dl/Avogadro/./lib/qt/lib/libQtGui.so.4
(0x00007f15ed126000)
libSM.so.6 => /home/dl/Avogadro/./lib/X11/libSM.so.6
(0x0000003471600000)
libICE.so.6 => /home/dl/Avogadro/./lib/X11/libICE.so.6
(0x000000346f600000)
libXrender.so.1 => /home/dl/Avogadro/./lib/X11/libXrender.so.1
(0x000000346d600000)
libfreetype.so.6 => /home/dl/Avogadro/./lib/libfreetype.so.6
(0x000000346a000000)
libfontconfig.so.1 =>
/home/dl/Avogadro/./lib/libfontconfig.so.1 (0x000000346a400000)
libXext.so.6 => /home/dl/Avogadro/./lib/X11/libXext.so.6
(0x0000003469800000)
libX11.so.6 => /home/dl/Avogadro/./lib/X11/libX11.so.6
(0x0000003468c00000)
libm.so.6 => /lib/libm.so.6 (0x00007f15ecea4000)
libQtNetwork.so.4 =>
/home/dl/Avogadro/./lib/qt/lib/libQtNetwork.so.4 (0x00007f15ecac3000)
libQtCore.so.4 =>
/home/dl/Avogadro/./lib/qt/lib/libQtCore.so.4 (0x00007f15ec486000)
libgthread-2.0.so.0 =>
/home/dl/Avogadro/./lib/sys/libgthread-2.0.so.0 (0x0000003470600000)
libglib-2.0.so.0 =>
/home/dl/Avogadro/./lib/sys/libglib-2.0.so.0 (0x0000003467400000)
libgobject-2.0.so.0 =>
/home/dl/Avogadro/./lib/sys/libgobject-2.0.so.0 (0x0000003468400000)
librt.so.1 => /lib/librt.so.1 (0x00007f15ec27e000)
libpthread.so.0 => /lib/libpthread.so.0 (0x00007f15ec062000)
libdl.so.2 => /home/dl/Avogadro/./lib/sys/libdl.so.2
(0x0000003466000000)
libavogadro.so.1 => /home/dl/Avogadro/./lib/libavogadro.so.1
(0x00007f15ebca4000)
libGLEW.so.1.5 => /home/dl/Avogadro/./lib/libGLEW.so.1.5
(0x00000036ee600000)
libstdc++.so.6 => /home/dl/Avogadro/./lib/sys/libstdc++.so.6
(0x0000003479a00000)
libgcc_s.so.1 => /home/dl/Avogadro/./lib/sys/libgcc_s.so.1
(0x0000003477200000)
/lib64/ld-linux-x86-64.so.2 (0x00007f15ef531000)
libxml2.so.2 => /home/dl/Avogadro/./lib/libxml2.so.2
(0x0000003470a00000)
libz.so.1 => /home/dl/Avogadro/./lib/libz.so.1 (0x0000003467000000)
libimf.so => /home/dl/Avogadro/./lib/intel/libimf.so
(0x00007f15eb912000)
libsvml.so => /home/dl/Avogadro/./lib/intel/libsvml.so
(0x00007f15eb6fc000)
libintlc.so.5 => /home/dl/Avogadro/./lib/intel/libintlc.so.5
(0x00007f15ef5e8000)
libXxf86vm.so.1 => /home/dl/Avogadro/./lib/X11/libXxf86vm.so.1
(0x0000003293e00000)
libXdamage.so.1 => /usr/lib/libXdamage.so.1 (0x00007f15eb4fa000)
libXfixes.so.3 => /usr/lib/libXfixes.so.3 (0x00007f15eb2f5000)
libX11-xcb.so.1 => /usr/lib/libX11-xcb.so.1 (0x00007f15eb0f4000)
libxcb-glx.so.0 => /usr/lib/libxcb-glx.so.0 (0x00007f15eaee0000)
libxcb.so.1 => /usr/lib/libxcb.so.1 (0x00007f15eacc5000)
libdrm.so.2 => /usr/lib/libdrm.so.2 (0x00007f15eaabb000)
libexpat.so.0 => /home/dl/Avogadro/./lib/sys/libexpat.so.0
(0x0000003469c00000)
libXau.so.6 => /home/dl/Avogadro/./lib/X11/libXau.so.6
(0x0000003468800000)
libXdmcp.so.6 => /home/dl/Avogadro/./lib/X11/libXdmcp.so.6
(0x0000003468000000)
Segmentation fault

[dl@ez05 Avogadro]$ ./avogadro-check
Setting LD_LIBRARY_PATH=/home/dl/Avogadro/./lib:/home/dl/Avogadro/./lib/qt/lib:/home/dl/Avogadro/./lib/intel:/home/dl/Avogadro/./lib/X11:/home/dl/Avogadro/./lib/sys:/bin/lib:/bin/lib/qt/lib:/bin/lib/intel:
zenity: symbol lookup error: /usr/lib/libgio-2.0.so.0: undefined
symbol: g_thread_gettime
symbol _dl_tls_get_addr_soft, version GLIBC_PRIVATE not defined in
file ld-linux-x86-64.so.2 with link time reference
(/home/dl/Avogadro/./lib/sys/libdl.so.2)

I tried running it through gdb, but alas, there are no debugging symbols.

Dave

Konstantin_Tokarev · May 18, 2010, 5:12pm

Seems like some X11 libraries are taken from bundle, and others from system. Try to set X11=0 in avogadro.config

18.05.10, 21:07, “David Lonie” loniedavid@gmail.com:

On Tue, May 18, 2010 at 12:58 PM, Konstantin Tokarev wrote:

It seems the library path isn’t set on a fresh install of 64 bit arch
linux (running ~/Avogadro/bin/avogadro complains about not being able
to find libopenbabel.so)

run avogadro.sh
Sorry for inconvenience
It should automatically run when desktop icon is clicked
If you still experience problems, play with avogadro.config. There’s also avogadro-check, it shows output of ldd in GUI

Still some problems:

[dl@ez05 Avogadro]$ ./avogadro.sh
Setting LD_LIBRARY_PATH=/home/dl/Avogadro/./lib:/home/dl/Avogadro/./lib/qt/lib:/home/dl/Avogadro/./lib/intel:/home/dl/Avogadro/./lib/X11:/home/dl/Avogadro/./lib/sys:/bin/lib:/bin/lib/qt/lib:/bin/lib/intel:
linux-vdso.so.1 => (0x00007fffbe7ff000)
libc.so.6 => /lib/libc.so.6 (0x00007f15ef1d5000)
libopenbabel.so.3 => /home/dl/Avogadro/./lib/libopenbabel.so.3
(0x00007f15eebd5000)
libQtOpenGL.so.4 =>
/home/dl/Avogadro/./lib/qt/lib/libQtOpenGL.so.4 (0x00007f15ee8bc000)
libGLU.so.1 => /usr/lib/libGLU.so.1 (0x00007f15ee64c000)
libGL.so.1 => /usr/lib/libGL.so.1 (0x00007f15ee3c8000)
libQtGui.so.4 => /home/dl/Avogadro/./lib/qt/lib/libQtGui.so.4
(0x00007f15ed126000)
libSM.so.6 => /home/dl/Avogadro/./lib/X11/libSM.so.6
(0x0000003471600000)
libICE.so.6 => /home/dl/Avogadro/./lib/X11/libICE.so.6
(0x000000346f600000)
libXrender.so.1 => /home/dl/Avogadro/./lib/X11/libXrender.so.1
(0x000000346d600000)
libfreetype.so.6 => /home/dl/Avogadro/./lib/libfreetype.so.6
(0x000000346a000000)
libfontconfig.so.1 =>
/home/dl/Avogadro/./lib/libfontconfig.so.1 (0x000000346a400000)
libXext.so.6 => /home/dl/Avogadro/./lib/X11/libXext.so.6
(0x0000003469800000)
libX11.so.6 => /home/dl/Avogadro/./lib/X11/libX11.so.6
(0x0000003468c00000)
libm.so.6 => /lib/libm.so.6 (0x00007f15ecea4000)
libQtNetwork.so.4 =>
/home/dl/Avogadro/./lib/qt/lib/libQtNetwork.so.4 (0x00007f15ecac3000)
libQtCore.so.4 =>
/home/dl/Avogadro/./lib/qt/lib/libQtCore.so.4 (0x00007f15ec486000)
libgthread-2.0.so.0 =>
/home/dl/Avogadro/./lib/sys/libgthread-2.0.so.0 (0x0000003470600000)
libglib-2.0.so.0 =>
/home/dl/Avogadro/./lib/sys/libglib-2.0.so.0 (0x0000003467400000)
libgobject-2.0.so.0 =>
/home/dl/Avogadro/./lib/sys/libgobject-2.0.so.0 (0x0000003468400000)
librt.so.1 => /lib/librt.so.1 (0x00007f15ec27e000)
libpthread.so.0 => /lib/libpthread.so.0 (0x00007f15ec062000)
libdl.so.2 => /home/dl/Avogadro/./lib/sys/libdl.so.2
(0x0000003466000000)
libavogadro.so.1 => /home/dl/Avogadro/./lib/libavogadro.so.1
(0x00007f15ebca4000)
libGLEW.so.1.5 => /home/dl/Avogadro/./lib/libGLEW.so.1.5
(0x00000036ee600000)
libstdc++.so.6 => /home/dl/Avogadro/./lib/sys/libstdc++.so.6
(0x0000003479a00000)
libgcc_s.so.1 => /home/dl/Avogadro/./lib/sys/libgcc_s.so.1
(0x0000003477200000)
/lib64/ld-linux-x86-64.so.2 (0x00007f15ef531000)
libxml2.so.2 => /home/dl/Avogadro/./lib/libxml2.so.2
(0x0000003470a00000)
libz.so.1 => /home/dl/Avogadro/./lib/libz.so.1 (0x0000003467000000)
libimf.so => /home/dl/Avogadro/./lib/intel/libimf.so
(0x00007f15eb912000)
libsvml.so => /home/dl/Avogadro/./lib/intel/libsvml.so
(0x00007f15eb6fc000)
libintlc.so.5 => /home/dl/Avogadro/./lib/intel/libintlc.so.5
(0x00007f15ef5e8000)
libXxf86vm.so.1 => /home/dl/Avogadro/./lib/X11/libXxf86vm.so.1
(0x0000003293e00000)
libXdamage.so.1 => /usr/lib/libXdamage.so.1 (0x00007f15eb4fa000)
libXfixes.so.3 => /usr/lib/libXfixes.so.3 (0x00007f15eb2f5000)
libX11-xcb.so.1 => /usr/lib/libX11-xcb.so.1 (0x00007f15eb0f4000)
libxcb-glx.so.0 => /usr/lib/libxcb-glx.so.0 (0x00007f15eaee0000)
libxcb.so.1 => /usr/lib/libxcb.so.1 (0x00007f15eacc5000)
libdrm.so.2 => /usr/lib/libdrm.so.2 (0x00007f15eaabb000)
libexpat.so.0 => /home/dl/Avogadro/./lib/sys/libexpat.so.0
(0x0000003469c00000)
libXau.so.6 => /home/dl/Avogadro/./lib/X11/libXau.so.6
(0x0000003468800000)
libXdmcp.so.6 => /home/dl/Avogadro/./lib/X11/libXdmcp.so.6
(0x0000003468000000)
Segmentation fault

[dl@ez05 Avogadro]$ ./avogadro-check
Setting LD_LIBRARY_PATH=/home/dl/Avogadro/./lib:/home/dl/Avogadro/./lib/qt/lib:/home/dl/Avogadro/./lib/intel:/home/dl/Avogadro/./lib/X11:/home/dl/Avogadro/./lib/sys:/bin/lib:/bin/lib/qt/lib:/bin/lib/intel:
zenity: symbol lookup error: /usr/lib/libgio-2.0.so.0: undefined
symbol: g_thread_gettime
symbol _dl_tls_get_addr_soft, version GLIBC_PRIVATE not defined in
file ld-linux-x86-64.so.2 with link time reference
(/home/dl/Avogadro/./lib/sys/libdl.so.2)

I tried running it through gdb, but alas, there are no debugging symbols.

Dave

–
Regards,
Konstantin

Яндекс.Почта. Письма есть. Спама - нет. http://mail.yandex.ru/nospam/sign

allison.vacanti · May 18, 2010, 5:14pm

2010/5/18 Konstantin Tokarev annulen@yandex.ru:

Seems like some X11 libraries are taken from bundle, and others from system. Try to set X11=0 in avogadro.config

Same problem

18.05.10, 21:07, “David Lonie” loniedavid@gmail.com:

On Tue, May 18, 2010 at 12:58 PM, Konstantin Tokarev wrote:

It seems the library path isn’t set on a fresh install of 64 bit arch
linux (running ~/Avogadro/bin/avogadro complains about not being able
to find libopenbabel.so)

run avogadro.sh
Sorry for inconvenience
It should automatically run when desktop icon is clicked
If you still experience problems, play with avogadro.config. There’s also avogadro-check, it shows output of ldd in GUI

Still some problems:

[dl@ez05 Avogadro]$ ./avogadro.sh
Setting LD_LIBRARY_PATH=/home/dl/Avogadro/./lib:/home/dl/Avogadro/./lib/qt/lib:/home/dl/Avogadro/./lib/intel:/home/dl/Avogadro/./lib/X11:/home/dl/Avogadro/./lib/sys:/bin/lib:/bin/lib/qt/lib:/bin/lib/intel:
linux-vdso.so.1 => (0x00007fffbe7ff000)
libc.so.6 => /lib/libc.so.6 (0x00007f15ef1d5000)
libopenbabel.so.3 => /home/dl/Avogadro/./lib/libopenbabel.so.3
(0x00007f15eebd5000)
libQtOpenGL.so.4 =>
/home/dl/Avogadro/./lib/qt/lib/libQtOpenGL.so.4 (0x00007f15ee8bc000)
libGLU.so.1 => /usr/lib/libGLU.so.1 (0x00007f15ee64c000)
libGL.so.1 => /usr/lib/libGL.so.1 (0x00007f15ee3c8000)
libQtGui.so.4 => /home/dl/Avogadro/./lib/qt/lib/libQtGui.so.4
(0x00007f15ed126000)
libSM.so.6 => /home/dl/Avogadro/./lib/X11/libSM.so.6
(0x0000003471600000)
libICE.so.6 => /home/dl/Avogadro/./lib/X11/libICE.so.6
(0x000000346f600000)
libXrender.so.1 => /home/dl/Avogadro/./lib/X11/libXrender.so.1
(0x000000346d600000)
libfreetype.so.6 => /home/dl/Avogadro/./lib/libfreetype.so.6
(0x000000346a000000)
libfontconfig.so.1 =>
/home/dl/Avogadro/./lib/libfontconfig.so.1 (0x000000346a400000)
libXext.so.6 => /home/dl/Avogadro/./lib/X11/libXext.so.6
(0x0000003469800000)
libX11.so.6 => /home/dl/Avogadro/./lib/X11/libX11.so.6
(0x0000003468c00000)
libm.so.6 => /lib/libm.so.6 (0x00007f15ecea4000)
libQtNetwork.so.4 =>
/home/dl/Avogadro/./lib/qt/lib/libQtNetwork.so.4 (0x00007f15ecac3000)
libQtCore.so.4 =>
/home/dl/Avogadro/./lib/qt/lib/libQtCore.so.4 (0x00007f15ec486000)
libgthread-2.0.so.0 =>
/home/dl/Avogadro/./lib/sys/libgthread-2.0.so.0 (0x0000003470600000)
libglib-2.0.so.0 =>
/home/dl/Avogadro/./lib/sys/libglib-2.0.so.0 (0x0000003467400000)
libgobject-2.0.so.0 =>
/home/dl/Avogadro/./lib/sys/libgobject-2.0.so.0 (0x0000003468400000)
librt.so.1 => /lib/librt.so.1 (0x00007f15ec27e000)
libpthread.so.0 => /lib/libpthread.so.0 (0x00007f15ec062000)
libdl.so.2 => /home/dl/Avogadro/./lib/sys/libdl.so.2
(0x0000003466000000)
libavogadro.so.1 => /home/dl/Avogadro/./lib/libavogadro.so.1
(0x00007f15ebca4000)
libGLEW.so.1.5 => /home/dl/Avogadro/./lib/libGLEW.so.1.5
(0x00000036ee600000)
libstdc++.so.6 => /home/dl/Avogadro/./lib/sys/libstdc++.so.6
(0x0000003479a00000)
libgcc_s.so.1 => /home/dl/Avogadro/./lib/sys/libgcc_s.so.1
(0x0000003477200000)
/lib64/ld-linux-x86-64.so.2 (0x00007f15ef531000)
libxml2.so.2 => /home/dl/Avogadro/./lib/libxml2.so.2
(0x0000003470a00000)
libz.so.1 => /home/dl/Avogadro/./lib/libz.so.1 (0x0000003467000000)
libimf.so => /home/dl/Avogadro/./lib/intel/libimf.so
(0x00007f15eb912000)
libsvml.so => /home/dl/Avogadro/./lib/intel/libsvml.so
(0x00007f15eb6fc000)
libintlc.so.5 => /home/dl/Avogadro/./lib/intel/libintlc.so.5
(0x00007f15ef5e8000)
libXxf86vm.so.1 => /home/dl/Avogadro/./lib/X11/libXxf86vm.so.1
(0x0000003293e00000)
libXdamage.so.1 => /usr/lib/libXdamage.so.1 (0x00007f15eb4fa000)
libXfixes.so.3 => /usr/lib/libXfixes.so.3 (0x00007f15eb2f5000)
libX11-xcb.so.1 => /usr/lib/libX11-xcb.so.1 (0x00007f15eb0f4000)
libxcb-glx.so.0 => /usr/lib/libxcb-glx.so.0 (0x00007f15eaee0000)
libxcb.so.1 => /usr/lib/libxcb.so.1 (0x00007f15eacc5000)
libdrm.so.2 => /usr/lib/libdrm.so.2 (0x00007f15eaabb000)
libexpat.so.0 => /home/dl/Avogadro/./lib/sys/libexpat.so.0
(0x0000003469c00000)
libXau.so.6 => /home/dl/Avogadro/./lib/X11/libXau.so.6
(0x0000003468800000)
libXdmcp.so.6 => /home/dl/Avogadro/./lib/X11/libXdmcp.so.6
(0x0000003468000000)
Segmentation fault

[dl@ez05 Avogadro]$ ./avogadro-check
Setting LD_LIBRARY_PATH=/home/dl/Avogadro/./lib:/home/dl/Avogadro/./lib/qt/lib:/home/dl/Avogadro/./lib/intel:/home/dl/Avogadro/./lib/X11:/home/dl/Avogadro/./lib/sys:/bin/lib:/bin/lib/qt/lib:/bin/lib/intel:
zenity: symbol lookup error: /usr/lib/libgio-2.0.so.0: undefined
symbol: g_thread_gettime
symbol _dl_tls_get_addr_soft, version GLIBC_PRIVATE not defined in
file ld-linux-x86-64.so.2 with link time reference
(/home/dl/Avogadro/./lib/sys/libdl.so.2)

I tried running it through gdb, but alas, there are no debugging symbols.

Dave

–
Regards,
Konstantin

Яндекс.Почта. Письма есть. Спама - нет. http://mail.yandex.ru/nospam/sign

Konstantin_Tokarev · May 18, 2010, 5:15pm

18.05.10, 21:07, “David Lonie” loniedavid@gmail.com:

On Tue, May 18, 2010 at 12:58 PM, Konstantin Tokarev wrote:

It seems the library path isn’t set on a fresh install of 64 bit arch
linux (running ~/Avogadro/bin/avogadro complains about not being able
to find libopenbabel.so)

run avogadro.sh
Sorry for inconvenience
It should automatically run when desktop icon is clicked
If you still experience problems, play with avogadro.config. There’s also avogadro-check, it shows output of ldd in GUI

Still some problems:

[dl@ez05 Avogadro]$ ./avogadro.sh
Setting LD_LIBRARY_PATH=/home/dl/Avogadro/./lib:/home/dl/Avogadro/./lib/qt/lib:/home/dl/Avogadro/./lib/intel:/home/dl/Avogadro/./lib/X11:/home/dl/Avogadro/./lib/sys:/bin/lib:/bin/lib/qt/lib:/bin/lib/intel:
linux-vdso.so.1 => (0x00007fffbe7ff000)
libc.so.6 => /lib/libc.so.6 (0x00007f15ef1d5000)
libopenbabel.so.3 => /home/dl/Avogadro/./lib/libopenbabel.so.3
(0x00007f15eebd5000)
libQtOpenGL.so.4 =>
/home/dl/Avogadro/./lib/qt/lib/libQtOpenGL.so.4 (0x00007f15ee8bc000)
libGLU.so.1 => /usr/lib/libGLU.so.1 (0x00007f15ee64c000)
libGL.so.1 => /usr/lib/libGL.so.1 (0x00007f15ee3c8000)
libQtGui.so.4 => /home/dl/Avogadro/./lib/qt/lib/libQtGui.so.4
(0x00007f15ed126000)
libSM.so.6 => /home/dl/Avogadro/./lib/X11/libSM.so.6
(0x0000003471600000)
libICE.so.6 => /home/dl/Avogadro/./lib/X11/libICE.so.6
(0x000000346f600000)
libXrender.so.1 => /home/dl/Avogadro/./lib/X11/libXrender.so.1
(0x000000346d600000)
libfreetype.so.6 => /home/dl/Avogadro/./lib/libfreetype.so.6
(0x000000346a000000)
libfontconfig.so.1 =>
/home/dl/Avogadro/./lib/libfontconfig.so.1 (0x000000346a400000)
libXext.so.6 => /home/dl/Avogadro/./lib/X11/libXext.so.6
(0x0000003469800000)
libX11.so.6 => /home/dl/Avogadro/./lib/X11/libX11.so.6
(0x0000003468c00000)
libm.so.6 => /lib/libm.so.6 (0x00007f15ecea4000)
libQtNetwork.so.4 =>
/home/dl/Avogadro/./lib/qt/lib/libQtNetwork.so.4 (0x00007f15ecac3000)
libQtCore.so.4 =>
/home/dl/Avogadro/./lib/qt/lib/libQtCore.so.4 (0x00007f15ec486000)
libgthread-2.0.so.0 =>
/home/dl/Avogadro/./lib/sys/libgthread-2.0.so.0 (0x0000003470600000)
libglib-2.0.so.0 =>
/home/dl/Avogadro/./lib/sys/libglib-2.0.so.0 (0x0000003467400000)
libgobject-2.0.so.0 =>
/home/dl/Avogadro/./lib/sys/libgobject-2.0.so.0 (0x0000003468400000)
librt.so.1 => /lib/librt.so.1 (0x00007f15ec27e000)
libpthread.so.0 => /lib/libpthread.so.0 (0x00007f15ec062000)
libdl.so.2 => /home/dl/Avogadro/./lib/sys/libdl.so.2
(0x0000003466000000)
libavogadro.so.1 => /home/dl/Avogadro/./lib/libavogadro.so.1
(0x00007f15ebca4000)
libGLEW.so.1.5 => /home/dl/Avogadro/./lib/libGLEW.so.1.5
(0x00000036ee600000)
libstdc++.so.6 => /home/dl/Avogadro/./lib/sys/libstdc++.so.6
(0x0000003479a00000)
libgcc_s.so.1 => /home/dl/Avogadro/./lib/sys/libgcc_s.so.1
(0x0000003477200000)
/lib64/ld-linux-x86-64.so.2 (0x00007f15ef531000)
libxml2.so.2 => /home/dl/Avogadro/./lib/libxml2.so.2
(0x0000003470a00000)
libz.so.1 => /home/dl/Avogadro/./lib/libz.so.1 (0x0000003467000000)
libimf.so => /home/dl/Avogadro/./lib/intel/libimf.so
(0x00007f15eb912000)
libsvml.so => /home/dl/Avogadro/./lib/intel/libsvml.so
(0x00007f15eb6fc000)
libintlc.so.5 => /home/dl/Avogadro/./lib/intel/libintlc.so.5
(0x00007f15ef5e8000)
libXxf86vm.so.1 => /home/dl/Avogadro/./lib/X11/libXxf86vm.so.1
(0x0000003293e00000)
libXdamage.so.1 => /usr/lib/libXdamage.so.1 (0x00007f15eb4fa000)
libXfixes.so.3 => /usr/lib/libXfixes.so.3 (0x00007f15eb2f5000)
libX11-xcb.so.1 => /usr/lib/libX11-xcb.so.1 (0x00007f15eb0f4000)
libxcb-glx.so.0 => /usr/lib/libxcb-glx.so.0 (0x00007f15eaee0000)
libxcb.so.1 => /usr/lib/libxcb.so.1 (0x00007f15eacc5000)
libdrm.so.2 => /usr/lib/libdrm.so.2 (0x00007f15eaabb000)
libexpat.so.0 => /home/dl/Avogadro/./lib/sys/libexpat.so.0
(0x0000003469c00000)
libXau.so.6 => /home/dl/Avogadro/./lib/X11/libXau.so.6
(0x0000003468800000)
libXdmcp.so.6 => /home/dl/Avogadro/./lib/X11/libXdmcp.so.6
(0x0000003468000000)
Segmentation fault

[dl@ez05 Avogadro]$ ./avogadro-check
Setting LD_LIBRARY_PATH=/home/dl/Avogadro/./lib:/home/dl/Avogadro/./lib/qt/lib:/home/dl/Avogadro/./lib/intel:/home/dl/Avogadro/./lib/X11:/home/dl/Avogadro/./lib/sys:/bin/lib:/bin/lib/qt/lib:/bin/lib/intel:
zenity: symbol lookup error: /usr/lib/libgio-2.0.so.0: undefined
symbol: g_thread_gettime
symbol _dl_tls_get_addr_soft, version GLIBC_PRIVATE not defined in
file ld-linux-x86-64.so.2 with link time reference
(/home/dl/Avogadro/./lib/sys/libdl.so.2)

Oh. Probably, your zenity is confused by LD_LIBRARY_PATH set for Avogadro

–
Regards,
Konstantin

Konstantin_Tokarev · May 18, 2010, 5:17pm

Try to set everything (gl,X11,sys) to 1
If doesn’t help, everything to 0 (will fail probably)

18.05.10, 21:14, “David Lonie” loniedavid@gmail.com:

2010/5/18 Konstantin Tokarev :

Seems like some X11 libraries are taken from bundle, and others from system. Try to set X11=0 in avogadro.config

Same problem

18.05.10, 21:07, “David Lonie” :

On Tue, May 18, 2010 at 12:58 PM, Konstantin Tokarev wrote:

It seems the library path isn’t set on a fresh install of 64 bit arch
linux (running ~/Avogadro/bin/avogadro complains about not being able
to find libopenbabel.so)

run avogadro.sh
Sorry for inconvenience
It should automatically run when desktop icon is clicked
If you still experience problems, play with avogadro.config. There’s also avogadro-check, it shows output of ldd in GUI

Still some problems:

[dl@ez05 Avogadro]$ ./avogadro.sh
Setting LD_LIBRARY_PATH=/home/dl/Avogadro/./lib:/home/dl/Avogadro/./lib/qt/lib:/home/dl/Avogadro/./lib/intel:/home/dl/Avogadro/./lib/X11:/home/dl/Avogadro/./lib/sys:/bin/lib:/bin/lib/qt/lib:/bin/lib/intel:
linux-vdso.so.1 => (0x00007fffbe7ff000)
libc.so.6 => /lib/libc.so.6 (0x00007f15ef1d5000)
libopenbabel.so.3 => /home/dl/Avogadro/./lib/libopenbabel.so.3
(0x00007f15eebd5000)
libQtOpenGL.so.4 =>
/home/dl/Avogadro/./lib/qt/lib/libQtOpenGL.so.4 (0x00007f15ee8bc000)
libGLU.so.1 => /usr/lib/libGLU.so.1 (0x00007f15ee64c000)
libGL.so.1 => /usr/lib/libGL.so.1 (0x00007f15ee3c8000)
libQtGui.so.4 => /home/dl/Avogadro/./lib/qt/lib/libQtGui.so.4
(0x00007f15ed126000)
libSM.so.6 => /home/dl/Avogadro/./lib/X11/libSM.so.6
(0x0000003471600000)
libICE.so.6 => /home/dl/Avogadro/./lib/X11/libICE.so.6
(0x000000346f600000)
libXrender.so.1 => /home/dl/Avogadro/./lib/X11/libXrender.so.1
(0x000000346d600000)
libfreetype.so.6 => /home/dl/Avogadro/./lib/libfreetype.so.6
(0x000000346a000000)
libfontconfig.so.1 =>
/home/dl/Avogadro/./lib/libfontconfig.so.1 (0x000000346a400000)
libXext.so.6 => /home/dl/Avogadro/./lib/X11/libXext.so.6
(0x0000003469800000)
libX11.so.6 => /home/dl/Avogadro/./lib/X11/libX11.so.6
(0x0000003468c00000)
libm.so.6 => /lib/libm.so.6 (0x00007f15ecea4000)
libQtNetwork.so.4 =>
/home/dl/Avogadro/./lib/qt/lib/libQtNetwork.so.4 (0x00007f15ecac3000)
libQtCore.so.4 =>
/home/dl/Avogadro/./lib/qt/lib/libQtCore.so.4 (0x00007f15ec486000)
libgthread-2.0.so.0 =>
/home/dl/Avogadro/./lib/sys/libgthread-2.0.so.0 (0x0000003470600000)
libglib-2.0.so.0 =>
/home/dl/Avogadro/./lib/sys/libglib-2.0.so.0 (0x0000003467400000)
libgobject-2.0.so.0 =>
/home/dl/Avogadro/./lib/sys/libgobject-2.0.so.0 (0x0000003468400000)
librt.so.1 => /lib/librt.so.1 (0x00007f15ec27e000)
libpthread.so.0 => /lib/libpthread.so.0 (0x00007f15ec062000)
libdl.so.2 => /home/dl/Avogadro/./lib/sys/libdl.so.2
(0x0000003466000000)
libavogadro.so.1 => /home/dl/Avogadro/./lib/libavogadro.so.1
(0x00007f15ebca4000)
libGLEW.so.1.5 => /home/dl/Avogadro/./lib/libGLEW.so.1.5
(0x00000036ee600000)
libstdc++.so.6 => /home/dl/Avogadro/./lib/sys/libstdc++.so.6
(0x0000003479a00000)
libgcc_s.so.1 => /home/dl/Avogadro/./lib/sys/libgcc_s.so.1
(0x0000003477200000)
/lib64/ld-linux-x86-64.so.2 (0x00007f15ef531000)
libxml2.so.2 => /home/dl/Avogadro/./lib/libxml2.so.2
(0x0000003470a00000)
libz.so.1 => /home/dl/Avogadro/./lib/libz.so.1 (0x0000003467000000)
libimf.so => /home/dl/Avogadro/./lib/intel/libimf.so
(0x00007f15eb912000)
libsvml.so => /home/dl/Avogadro/./lib/intel/libsvml.so
(0x00007f15eb6fc000)
libintlc.so.5 => /home/dl/Avogadro/./lib/intel/libintlc.so.5
(0x00007f15ef5e8000)
libXxf86vm.so.1 => /home/dl/Avogadro/./lib/X11/libXxf86vm.so.1
(0x0000003293e00000)
libXdamage.so.1 => /usr/lib/libXdamage.so.1 (0x00007f15eb4fa000)
libXfixes.so.3 => /usr/lib/libXfixes.so.3 (0x00007f15eb2f5000)
libX11-xcb.so.1 => /usr/lib/libX11-xcb.so.1 (0x00007f15eb0f4000)
libxcb-glx.so.0 => /usr/lib/libxcb-glx.so.0 (0x00007f15eaee0000)
libxcb.so.1 => /usr/lib/libxcb.so.1 (0x00007f15eacc5000)
libdrm.so.2 => /usr/lib/libdrm.so.2 (0x00007f15eaabb000)
libexpat.so.0 => /home/dl/Avogadro/./lib/sys/libexpat.so.0
(0x0000003469c00000)
libXau.so.6 => /home/dl/Avogadro/./lib/X11/libXau.so.6
(0x0000003468800000)
libXdmcp.so.6 => /home/dl/Avogadro/./lib/X11/libXdmcp.so.6
(0x0000003468000000)
Segmentation fault

[dl@ez05 Avogadro]$ ./avogadro-check
Setting LD_LIBRARY_PATH=/home/dl/Avogadro/./lib:/home/dl/Avogadro/./lib/qt/lib:/home/dl/Avogadro/./lib/intel:/home/dl/Avogadro/./lib/X11:/home/dl/Avogadro/./lib/sys:/bin/lib:/bin/lib/qt/lib:/bin/lib/intel:
zenity: symbol lookup error: /usr/lib/libgio-2.0.so.0: undefined
symbol: g_thread_gettime
symbol _dl_tls_get_addr_soft, version GLIBC_PRIVATE not defined in
file ld-linux-x86-64.so.2 with link time reference
(/home/dl/Avogadro/./lib/sys/libdl.so.2)

I tried running it through gdb, but alas, there are no debugging symbols.

Dave

–
Regards,
Konstantin

Яндекс.Почта. Письма есть. Спама - нет. http://mail.yandex.ru/nospam/sign

–
Regards,
Konstantin

Яндекс.Почта. Письма есть. Спама - нет. http://mail.yandex.ru/nospam/sign

allison.vacanti · May 18, 2010, 5:24pm

2010/5/18 Konstantin Tokarev annulen@yandex.ru:

Try to set everything (gl,X11,sys) to 1
If doesn’t help, everything to 0 (will fail probably)

No luck

18.05.10, 21:14, “David Lonie” loniedavid@gmail.com:

2010/5/18 Konstantin Tokarev :

Seems like some X11 libraries are taken from bundle, and others from system. Try to set X11=0 in avogadro.config

Same problem

18.05.10, 21:07, “David Lonie” :

On Tue, May 18, 2010 at 12:58 PM, Konstantin Tokarev wrote:

It seems the library path isn’t set on a fresh install of 64 bit arch
linux (running ~/Avogadro/bin/avogadro complains about not being able
to find libopenbabel.so)

run avogadro.sh
Sorry for inconvenience
It should automatically run when desktop icon is clicked
If you still experience problems, play with avogadro.config. There’s also avogadro-check, it shows output of ldd in GUI

Still some problems:

[dl@ez05 Avogadro]$ ./avogadro.sh
Setting LD_LIBRARY_PATH=/home/dl/Avogadro/./lib:/home/dl/Avogadro/./lib/qt/lib:/home/dl/Avogadro/./lib/intel:/home/dl/Avogadro/./lib/X11:/home/dl/Avogadro/./lib/sys:/bin/lib:/bin/lib/qt/lib:/bin/lib/intel:
linux-vdso.so.1 => (0x00007fffbe7ff000)
libc.so.6 => /lib/libc.so.6 (0x00007f15ef1d5000)
libopenbabel.so.3 => /home/dl/Avogadro/./lib/libopenbabel.so.3
(0x00007f15eebd5000)
libQtOpenGL.so.4 =>
/home/dl/Avogadro/./lib/qt/lib/libQtOpenGL.so.4 (0x00007f15ee8bc000)
libGLU.so.1 => /usr/lib/libGLU.so.1 (0x00007f15ee64c000)
libGL.so.1 => /usr/lib/libGL.so.1 (0x00007f15ee3c8000)
libQtGui.so.4 => /home/dl/Avogadro/./lib/qt/lib/libQtGui.so.4
(0x00007f15ed126000)
libSM.so.6 => /home/dl/Avogadro/./lib/X11/libSM.so.6
(0x0000003471600000)
libICE.so.6 => /home/dl/Avogadro/./lib/X11/libICE.so.6
(0x000000346f600000)
libXrender.so.1 => /home/dl/Avogadro/./lib/X11/libXrender.so.1
(0x000000346d600000)
libfreetype.so.6 => /home/dl/Avogadro/./lib/libfreetype.so.6
(0x000000346a000000)
libfontconfig.so.1 =>
/home/dl/Avogadro/./lib/libfontconfig.so.1 (0x000000346a400000)
libXext.so.6 => /home/dl/Avogadro/./lib/X11/libXext.so.6
(0x0000003469800000)
libX11.so.6 => /home/dl/Avogadro/./lib/X11/libX11.so.6
(0x0000003468c00000)
libm.so.6 => /lib/libm.so.6 (0x00007f15ecea4000)
libQtNetwork.so.4 =>
/home/dl/Avogadro/./lib/qt/lib/libQtNetwork.so.4 (0x00007f15ecac3000)
libQtCore.so.4 =>
/home/dl/Avogadro/./lib/qt/lib/libQtCore.so.4 (0x00007f15ec486000)
libgthread-2.0.so.0 =>
/home/dl/Avogadro/./lib/sys/libgthread-2.0.so.0 (0x0000003470600000)
libglib-2.0.so.0 =>
/home/dl/Avogadro/./lib/sys/libglib-2.0.so.0 (0x0000003467400000)
libgobject-2.0.so.0 =>
/home/dl/Avogadro/./lib/sys/libgobject-2.0.so.0 (0x0000003468400000)
librt.so.1 => /lib/librt.so.1 (0x00007f15ec27e000)
libpthread.so.0 => /lib/libpthread.so.0 (0x00007f15ec062000)
libdl.so.2 => /home/dl/Avogadro/./lib/sys/libdl.so.2
(0x0000003466000000)
libavogadro.so.1 => /home/dl/Avogadro/./lib/libavogadro.so.1
(0x00007f15ebca4000)
libGLEW.so.1.5 => /home/dl/Avogadro/./lib/libGLEW.so.1.5
(0x00000036ee600000)
libstdc++.so.6 => /home/dl/Avogadro/./lib/sys/libstdc++.so.6
(0x0000003479a00000)
libgcc_s.so.1 => /home/dl/Avogadro/./lib/sys/libgcc_s.so.1
(0x0000003477200000)
/lib64/ld-linux-x86-64.so.2 (0x00007f15ef531000)
libxml2.so.2 => /home/dl/Avogadro/./lib/libxml2.so.2
(0x0000003470a00000)
libz.so.1 => /home/dl/Avogadro/./lib/libz.so.1 (0x0000003467000000)
libimf.so => /home/dl/Avogadro/./lib/intel/libimf.so
(0x00007f15eb912000)
libsvml.so => /home/dl/Avogadro/./lib/intel/libsvml.so
(0x00007f15eb6fc000)
libintlc.so.5 => /home/dl/Avogadro/./lib/intel/libintlc.so.5
(0x00007f15ef5e8000)
libXxf86vm.so.1 => /home/dl/Avogadro/./lib/X11/libXxf86vm.so.1
(0x0000003293e00000)
libXdamage.so.1 => /usr/lib/libXdamage.so.1 (0x00007f15eb4fa000)
libXfixes.so.3 => /usr/lib/libXfixes.so.3 (0x00007f15eb2f5000)
libX11-xcb.so.1 => /usr/lib/libX11-xcb.so.1 (0x00007f15eb0f4000)
libxcb-glx.so.0 => /usr/lib/libxcb-glx.so.0 (0x00007f15eaee0000)
libxcb.so.1 => /usr/lib/libxcb.so.1 (0x00007f15eacc5000)
libdrm.so.2 => /usr/lib/libdrm.so.2 (0x00007f15eaabb000)
libexpat.so.0 => /home/dl/Avogadro/./lib/sys/libexpat.so.0
(0x0000003469c00000)
libXau.so.6 => /home/dl/Avogadro/./lib/X11/libXau.so.6
(0x0000003468800000)
libXdmcp.so.6 => /home/dl/Avogadro/./lib/X11/libXdmcp.so.6
(0x0000003468000000)
Segmentation fault

[dl@ez05 Avogadro]$ ./avogadro-check
Setting LD_LIBRARY_PATH=/home/dl/Avogadro/./lib:/home/dl/Avogadro/./lib/qt/lib:/home/dl/Avogadro/./lib/intel:/home/dl/Avogadro/./lib/X11:/home/dl/Avogadro/./lib/sys:/bin/lib:/bin/lib/qt/lib:/bin/lib/intel:
zenity: symbol lookup error: /usr/lib/libgio-2.0.so.0: undefined
symbol: g_thread_gettime
symbol _dl_tls_get_addr_soft, version GLIBC_PRIVATE not defined in
file ld-linux-x86-64.so.2 with link time reference
(/home/dl/Avogadro/./lib/sys/libdl.so.2)

I tried running it through gdb, but alas, there are no debugging symbols.

Dave

–
Regards,
Konstantin

Яндекс.Почта. Письма есть. Спама - нет. http://mail.yandex.ru/nospam/sign

–
Regards,
Konstantin

Яндекс.Почта. Письма есть. Спама - нет. http://mail.yandex.ru/nospam/sign

Konstantin_Tokarev · May 18, 2010, 5:34pm

Try to put attached libraries to X11 dir of Avogadro installation and set everything to 1.
Send ldd output again if doesn’t work

–
Regards,
Konstantin

allison.vacanti · May 18, 2010, 5:45pm

On Tue, May 18, 2010 at 1:34 PM, Konstantin Tokarev annulen@yandex.ru wrote:

Try to put attached libraries to X11 dir of Avogadro installation and set everything to 1.
Send ldd output again if doesn’t work

Still getting a segfault:

[dl@ez05 Avogadro] ./avogadro.sh Setting LD_LIBRARY_PATH=/home/dl/Avogadro/./lib:/home/dl/Avogadro/./lib/qt/lib:/home/dl/Avogadro/./lib/intel:/home/dl/Avogadro/./lib/gl:/home/dl/Avogadro/./lib/X11:/home/dl/Avogadro/./lib/sys: linux-vdso.so.1 => (0x00007fff9d3ff000) libc.so.6 => /lib/libc.so.6 (0x00007f2fcc247000) libopenbabel.so.3 => /home/dl/Avogadro/./lib/libopenbabel.so.3 (0x00007f2fcbc47000) libQtOpenGL.so.4 => /home/dl/Avogadro/./lib/qt/lib/libQtOpenGL.so.4 (0x00007f2fcb92e000) libGLU.so.1 => /home/dl/Avogadro/./lib/gl/libGLU.so.1 (0x0000003059c00000) libGL.so.1 => /home/dl/Avogadro/./lib/gl/libGL.so.1 (0x0000003059800000) libQtGui.so.4 => /home/dl/Avogadro/./lib/qt/lib/libQtGui.so.4 (0x00007f2fca68c000) libSM.so.6 => /home/dl/Avogadro/./lib/X11/libSM.so.6 (0x0000003471600000) libICE.so.6 => /home/dl/Avogadro/./lib/X11/libICE.so.6 (0x000000346f600000) libXrender.so.1 => /home/dl/Avogadro/./lib/X11/libXrender.so.1 (0x000000346d600000) libfreetype.so.6 => /home/dl/Avogadro/./lib/libfreetype.so.6 (0x000000346a000000) libfontconfig.so.1 => /home/dl/Avogadro/./lib/libfontconfig.so.1 (0x000000346a400000) libXext.so.6 => /home/dl/Avogadro/./lib/X11/libXext.so.6 (0x0000003469800000) libX11.so.6 => /home/dl/Avogadro/./lib/X11/libX11.so.6 (0x0000003468c00000) libm.so.6 => /lib/libm.so.6 (0x00007f2fca40a000) libQtNetwork.so.4 => /home/dl/Avogadro/./lib/qt/lib/libQtNetwork.so.4 (0x00007f2fca029000) libQtCore.so.4 => /home/dl/Avogadro/./lib/qt/lib/libQtCore.so.4 (0x00007f2fc99ec000) libgthread-2.0.so.0 => /home/dl/Avogadro/./lib/sys/libgthread-2.0.so.0 (0x0000003470600000) libglib-2.0.so.0 => /home/dl/Avogadro/./lib/sys/libglib-2.0.so.0 (0x0000003467400000) libgobject-2.0.so.0 => /home/dl/Avogadro/./lib/sys/libgobject-2.0.so.0 (0x0000003468400000) librt.so.1 => /lib/librt.so.1 (0x00007f2fc97e4000) libpthread.so.0 => /lib/libpthread.so.0 (0x00007f2fc95c8000) libdl.so.2 => /home/dl/Avogadro/./lib/sys/libdl.so.2 (0x0000003466000000) libavogadro.so.1 => /home/dl/Avogadro/./lib/libavogadro.so.1 (0x00007f2fc920a000) libGLEW.so.1.5 => /home/dl/Avogadro/./lib/libGLEW.so.1.5 (0x00000036ee600000) libstdc++.so.6 => /home/dl/Avogadro/./lib/sys/libstdc++.so.6 (0x0000003479a00000) libgcc_s.so.1 => /home/dl/Avogadro/./lib/sys/libgcc_s.so.1 (0x0000003477200000) /lib64/ld-linux-x86-64.so.2 (0x00007f2fcc5a3000) libxml2.so.2 => /home/dl/Avogadro/./lib/libxml2.so.2 (0x0000003470a00000) libz.so.1 => /home/dl/Avogadro/./lib/libz.so.1 (0x0000003467000000) libimf.so => /home/dl/Avogadro/./lib/intel/libimf.so (0x00007f2fc8e78000) libsvml.so => /home/dl/Avogadro/./lib/intel/libsvml.so (0x00007f2fc8c62000) libintlc.so.5 => /home/dl/Avogadro/./lib/intel/libintlc.so.5 (0x00007f2fcc65a000) libXxf86vm.so.1 => /home/dl/Avogadro/./lib/X11/libXxf86vm.so.1 (0x0000003293e00000) libdrm.so.2 => /home/dl/Avogadro/./lib/gl/libdrm.so.2 (0x0000003467c00000) libexpat.so.0 => /home/dl/Avogadro/./lib/sys/libexpat.so.0 (0x0000003469c00000) libXau.so.6 => /home/dl/Avogadro/./lib/X11/libXau.so.6 (0x0000003468800000) libXdmcp.so.6 => /home/dl/Avogadro/./lib/X11/libXdmcp.so.6 (0x0000003468000000) Segmentation fault [dl@ez05 Avogadro] ls lib/X11/
libdrm.so libICE.so.6.3.0 libX11.so.6 libXdamage.so
libXdmcp.so.6.0.0 libXfixes.so.3 libXxf86vm.so
libdrm.so.2 libSM.so libX11.so.6.2.0 libXdamage.so.1
libXext.so libXfixes.so.3.1.0 libXxf86vm.so.1
libdrm.so.2.0.0 libSM.so.6 libXau.so libXdamage.so.1.0.0
libXext.so.6 libXrender.so libXxf86vm.so.1.0.0
libICE.so libSM.so.6.0.0 libXau.so.6 libXdmcp.so
libXext.so.6.4.0 libXrender.so.1
libICE.so.6 libX11.so libXau.so.6.0.0 libXdmcp.so.6
libXfixes.so libXrender.so.1.3.0

Konstantin_Tokarev · May 18, 2010, 5:54pm

Does gdb output something (e.g., hint what library causes problem)?
You may also try to remove (or rename) your Avogadro.conf in ~/.config/SourceForge

18.05.10, 21:45, “David Lonie” loniedavid@gmail.com:

On Tue, May 18, 2010 at 1:34 PM, Konstantin Tokarev wrote:

Try to put attached libraries to X11 dir of Avogadro installation and set everything to 1.
Send ldd output again if doesn’t work

Still getting a segfault:

[dl@ez05 Avogadro] ./avogadro.sh Setting LD_LIBRARY_PATH=/home/dl/Avogadro/./lib:/home/dl/Avogadro/./lib/qt/lib:/home/dl/Avogadro/./lib/intel:/home/dl/Avogadro/./lib/gl:/home/dl/Avogadro/./lib/X11:/home/dl/Avogadro/./lib/sys: linux-vdso.so.1 => (0x00007fff9d3ff000) libc.so.6 => /lib/libc.so.6 (0x00007f2fcc247000) libopenbabel.so.3 => /home/dl/Avogadro/./lib/libopenbabel.so.3 (0x00007f2fcbc47000) libQtOpenGL.so.4 => /home/dl/Avogadro/./lib/qt/lib/libQtOpenGL.so.4 (0x00007f2fcb92e000) libGLU.so.1 => /home/dl/Avogadro/./lib/gl/libGLU.so.1 (0x0000003059c00000) libGL.so.1 => /home/dl/Avogadro/./lib/gl/libGL.so.1 (0x0000003059800000) libQtGui.so.4 => /home/dl/Avogadro/./lib/qt/lib/libQtGui.so.4 (0x00007f2fca68c000) libSM.so.6 => /home/dl/Avogadro/./lib/X11/libSM.so.6 (0x0000003471600000) libICE.so.6 => /home/dl/Avogadro/./lib/X11/libICE.so.6 (0x000000346f600000) libXrender.so.1 => /home/dl/Avogadro/./lib/X11/libXrender.so.1 (0x000000346d600000) libfreetype.so.6 => /home/dl/Avogadro/./lib/libfreetype.so.6 (0x000000346a000000) libfontconfig.so.1 => /home/dl/Avogadro/./lib/libfontconfig.so.1 (0x000000346a400000) libXext.so.6 => /home/dl/Avogadro/./lib/X11/libXext.so.6 (0x0000003469800000) libX11.so.6 => /home/dl/Avogadro/./lib/X11/libX11.so.6 (0x0000003468c00000) libm.so.6 => /lib/libm.so.6 (0x00007f2fca40a000) libQtNetwork.so.4 => /home/dl/Avogadro/./lib/qt/lib/libQtNetwork.so.4 (0x00007f2fca029000) libQtCore.so.4 => /home/dl/Avogadro/./lib/qt/lib/libQtCore.so.4 (0x00007f2fc99ec000) libgthread-2.0.so.0 => /home/dl/Avogadro/./lib/sys/libgthread-2.0.so.0 (0x0000003470600000) libglib-2.0.so.0 => /home/dl/Avogadro/./lib/sys/libglib-2.0.so.0 (0x0000003467400000) libgobject-2.0.so.0 => /home/dl/Avogadro/./lib/sys/libgobject-2.0.so.0 (0x0000003468400000) librt.so.1 => /lib/librt.so.1 (0x00007f2fc97e4000) libpthread.so.0 => /lib/libpthread.so.0 (0x00007f2fc95c8000) libdl.so.2 => /home/dl/Avogadro/./lib/sys/libdl.so.2 (0x0000003466000000) libavogadro.so.1 => /home/dl/Avogadro/./lib/libavogadro.so.1 (0x00007f2fc920a000) libGLEW.so.1.5 => /home/dl/Avogadro/./lib/libGLEW.so.1.5 (0x00000036ee600000) libstdc++.so.6 => /home/dl/Avogadro/./lib/sys/libstdc++.so.6 (0x0000003479a00000) libgcc_s.so.1 => /home/dl/Avogadro/./lib/sys/libgcc_s.so.1 (0x0000003477200000) /lib64/ld-linux-x86-64.so.2 (0x00007f2fcc5a3000) libxml2.so.2 => /home/dl/Avogadro/./lib/libxml2.so.2 (0x0000003470a00000) libz.so.1 => /home/dl/Avogadro/./lib/libz.so.1 (0x0000003467000000) libimf.so => /home/dl/Avogadro/./lib/intel/libimf.so (0x00007f2fc8e78000) libsvml.so => /home/dl/Avogadro/./lib/intel/libsvml.so (0x00007f2fc8c62000) libintlc.so.5 => /home/dl/Avogadro/./lib/intel/libintlc.so.5 (0x00007f2fcc65a000) libXxf86vm.so.1 => /home/dl/Avogadro/./lib/X11/libXxf86vm.so.1 (0x0000003293e00000) libdrm.so.2 => /home/dl/Avogadro/./lib/gl/libdrm.so.2 (0x0000003467c00000) libexpat.so.0 => /home/dl/Avogadro/./lib/sys/libexpat.so.0 (0x0000003469c00000) libXau.so.6 => /home/dl/Avogadro/./lib/X11/libXau.so.6 (0x0000003468800000) libXdmcp.so.6 => /home/dl/Avogadro/./lib/X11/libXdmcp.so.6 (0x0000003468000000) Segmentation fault [dl@ez05 Avogadro] ls lib/X11/
libdrm.so libICE.so.6.3.0 libX11.so.6 libXdamage.so
libXdmcp.so.6.0.0 libXfixes.so.3 libXxf86vm.so
libdrm.so.2 libSM.so libX11.so.6.2.0 libXdamage.so.1
libXext.so libXfixes.so.3.1.0 libXxf86vm.so.1
libdrm.so.2.0.0 libSM.so.6 libXau.so libXdamage.so.1.0.0
libXext.so.6 libXrender.so libXxf86vm.so.1.0.0
libICE.so libSM.so.6.0.0 libXau.so.6 libXdmcp.so
libXext.so.6.4.0 libXrender.so.1
libICE.so.6 libX11.so libXau.so.6.0.0 libXdmcp.so.6
libXfixes.so libXrender.so.1.3.0

–
Regards,
Konstantin

Яндекс.Почта. Письма есть. Спама - нет. http://mail.yandex.ru/nospam/sign

allison.vacanti · May 18, 2010, 5:57pm

2010/5/18 Konstantin Tokarev annulen@yandex.ru:

Does gdb output something (e.g., hint what library causes problem)?

No luck – (I’m running gdb by modifying avogadro.sh):

[dl@ez05 Avogadro]$ ./avogadro.sh
Setting LD_LIBRARY_PATH=/home/dl/Avogadro/./lib:/home/dl/Avogadro/./lib/qt/lib:/home/dl/Avogadro/./lib/intel:/home/dl/Avogadro/./lib/gl:/home/dl/Avogadro/./lib/X11:/home/dl/Avogadro/./lib/sys:
linux-vdso.so.1 => (0x00007fffd53aa000)
libc.so.6 => /lib/libc.so.6 (0x00007f8476fe1000)
libopenbabel.so.3 => /home/dl/Avogadro/./lib/libopenbabel.so.3
(0x00007f84769e1000)
libQtOpenGL.so.4 =>
/home/dl/Avogadro/./lib/qt/lib/libQtOpenGL.so.4 (0x00007f84766c8000)
libGLU.so.1 => /home/dl/Avogadro/./lib/gl/libGLU.so.1
(0x0000003059c00000)
libGL.so.1 => /home/dl/Avogadro/./lib/gl/libGL.so.1 (0x0000003059800000)
libQtGui.so.4 => /home/dl/Avogadro/./lib/qt/lib/libQtGui.so.4
(0x00007f8475426000)
libSM.so.6 => /home/dl/Avogadro/./lib/X11/libSM.so.6
(0x0000003471600000)
libICE.so.6 => /home/dl/Avogadro/./lib/X11/libICE.so.6
(0x000000346f600000)
libXrender.so.1 => /home/dl/Avogadro/./lib/X11/libXrender.so.1
(0x000000346d600000)
libfreetype.so.6 => /home/dl/Avogadro/./lib/libfreetype.so.6
(0x000000346a000000)
libfontconfig.so.1 =>
/home/dl/Avogadro/./lib/libfontconfig.so.1 (0x000000346a400000)
libXext.so.6 => /home/dl/Avogadro/./lib/X11/libXext.so.6
(0x0000003469800000)
libX11.so.6 => /home/dl/Avogadro/./lib/X11/libX11.so.6
(0x0000003468c00000)
libm.so.6 => /lib/libm.so.6 (0x00007f84751a4000)
libQtNetwork.so.4 =>
/home/dl/Avogadro/./lib/qt/lib/libQtNetwork.so.4 (0x00007f8474dc3000)
libQtCore.so.4 =>
/home/dl/Avogadro/./lib/qt/lib/libQtCore.so.4 (0x00007f8474786000)
libgthread-2.0.so.0 =>
/home/dl/Avogadro/./lib/sys/libgthread-2.0.so.0 (0x0000003470600000)
libglib-2.0.so.0 =>
/home/dl/Avogadro/./lib/sys/libglib-2.0.so.0 (0x0000003467400000)
libgobject-2.0.so.0 =>
/home/dl/Avogadro/./lib/sys/libgobject-2.0.so.0 (0x0000003468400000)
librt.so.1 => /lib/librt.so.1 (0x00007f847457e000)
libpthread.so.0 => /lib/libpthread.so.0 (0x00007f8474362000)
libdl.so.2 => /home/dl/Avogadro/./lib/sys/libdl.so.2
(0x0000003466000000)
libavogadro.so.1 => /home/dl/Avogadro/./lib/libavogadro.so.1
(0x00007f8473fa4000)
libGLEW.so.1.5 => /home/dl/Avogadro/./lib/libGLEW.so.1.5
(0x00000036ee600000)
libstdc++.so.6 => /home/dl/Avogadro/./lib/sys/libstdc++.so.6
(0x0000003479a00000)
libgcc_s.so.1 => /home/dl/Avogadro/./lib/sys/libgcc_s.so.1
(0x0000003477200000)
/lib64/ld-linux-x86-64.so.2 (0x00007f847733d000)
libxml2.so.2 => /home/dl/Avogadro/./lib/libxml2.so.2
(0x0000003470a00000)
libz.so.1 => /home/dl/Avogadro/./lib/libz.so.1 (0x0000003467000000)
libimf.so => /home/dl/Avogadro/./lib/intel/libimf.so
(0x00007f8473c12000)
libsvml.so => /home/dl/Avogadro/./lib/intel/libsvml.so
(0x00007f84739fc000)
libintlc.so.5 => /home/dl/Avogadro/./lib/intel/libintlc.so.5
(0x00007f84773f4000)
libXxf86vm.so.1 => /home/dl/Avogadro/./lib/X11/libXxf86vm.so.1
(0x0000003293e00000)
libdrm.so.2 => /home/dl/Avogadro/./lib/gl/libdrm.so.2
(0x0000003467c00000)
libexpat.so.0 => /home/dl/Avogadro/./lib/sys/libexpat.so.0
(0x0000003469c00000)
libXau.so.6 => /home/dl/Avogadro/./lib/X11/libXau.so.6
(0x0000003468800000)
libXdmcp.so.6 => /home/dl/Avogadro/./lib/X11/libXdmcp.so.6
(0x0000003468000000)
GNU gdb (GDB) 7.1
Copyright © 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-unknown-linux-gnu”.
For bug reporting instructions, please see:
http://www.gnu.org/software/gdb/bugs/…
Reading symbols from /home/dl/Avogadro/bin/avogadro…(no debugging
symbols found)…done.
(gdb) run
Starting program: /home/dl/Avogadro/bin/avogadro
Segmentation fault

You may also try to remove (or rename) your Avogadro.conf in ~/.config/SourceForge

This is a fresh distro with no other avo’s on it, so this file doesn’t
exist yet.

Dave

18.05.10, 21:45, “David Lonie” loniedavid@gmail.com:

On Tue, May 18, 2010 at 1:34 PM, Konstantin Tokarev wrote:

Try to put attached libraries to X11 dir of Avogadro installation and set everything to 1.
Send ldd output again if doesn’t work

Still getting a segfault:

[dl@ez05 Avogadro] ./avogadro.sh Setting LD_LIBRARY_PATH=/home/dl/Avogadro/./lib:/home/dl/Avogadro/./lib/qt/lib:/home/dl/Avogadro/./lib/intel:/home/dl/Avogadro/./lib/gl:/home/dl/Avogadro/./lib/X11:/home/dl/Avogadro/./lib/sys: linux-vdso.so.1 => (0x00007fff9d3ff000) libc.so.6 => /lib/libc.so.6 (0x00007f2fcc247000) libopenbabel.so.3 => /home/dl/Avogadro/./lib/libopenbabel.so.3 (0x00007f2fcbc47000) libQtOpenGL.so.4 => /home/dl/Avogadro/./lib/qt/lib/libQtOpenGL.so.4 (0x00007f2fcb92e000) libGLU.so.1 => /home/dl/Avogadro/./lib/gl/libGLU.so.1 (0x0000003059c00000) libGL.so.1 => /home/dl/Avogadro/./lib/gl/libGL.so.1 (0x0000003059800000) libQtGui.so.4 => /home/dl/Avogadro/./lib/qt/lib/libQtGui.so.4 (0x00007f2fca68c000) libSM.so.6 => /home/dl/Avogadro/./lib/X11/libSM.so.6 (0x0000003471600000) libICE.so.6 => /home/dl/Avogadro/./lib/X11/libICE.so.6 (0x000000346f600000) libXrender.so.1 => /home/dl/Avogadro/./lib/X11/libXrender.so.1 (0x000000346d600000) libfreetype.so.6 => /home/dl/Avogadro/./lib/libfreetype.so.6 (0x000000346a000000) libfontconfig.so.1 => /home/dl/Avogadro/./lib/libfontconfig.so.1 (0x000000346a400000) libXext.so.6 => /home/dl/Avogadro/./lib/X11/libXext.so.6 (0x0000003469800000) libX11.so.6 => /home/dl/Avogadro/./lib/X11/libX11.so.6 (0x0000003468c00000) libm.so.6 => /lib/libm.so.6 (0x00007f2fca40a000) libQtNetwork.so.4 => /home/dl/Avogadro/./lib/qt/lib/libQtNetwork.so.4 (0x00007f2fca029000) libQtCore.so.4 => /home/dl/Avogadro/./lib/qt/lib/libQtCore.so.4 (0x00007f2fc99ec000) libgthread-2.0.so.0 => /home/dl/Avogadro/./lib/sys/libgthread-2.0.so.0 (0x0000003470600000) libglib-2.0.so.0 => /home/dl/Avogadro/./lib/sys/libglib-2.0.so.0 (0x0000003467400000) libgobject-2.0.so.0 => /home/dl/Avogadro/./lib/sys/libgobject-2.0.so.0 (0x0000003468400000) librt.so.1 => /lib/librt.so.1 (0x00007f2fc97e4000) libpthread.so.0 => /lib/libpthread.so.0 (0x00007f2fc95c8000) libdl.so.2 => /home/dl/Avogadro/./lib/sys/libdl.so.2 (0x0000003466000000) libavogadro.so.1 => /home/dl/Avogadro/./lib/libavogadro.so.1 (0x00007f2fc920a000) libGLEW.so.1.5 => /home/dl/Avogadro/./lib/libGLEW.so.1.5 (0x00000036ee600000) libstdc++.so.6 => /home/dl/Avogadro/./lib/sys/libstdc++.so.6 (0x0000003479a00000) libgcc_s.so.1 => /home/dl/Avogadro/./lib/sys/libgcc_s.so.1 (0x0000003477200000) /lib64/ld-linux-x86-64.so.2 (0x00007f2fcc5a3000) libxml2.so.2 => /home/dl/Avogadro/./lib/libxml2.so.2 (0x0000003470a00000) libz.so.1 => /home/dl/Avogadro/./lib/libz.so.1 (0x0000003467000000) libimf.so => /home/dl/Avogadro/./lib/intel/libimf.so (0x00007f2fc8e78000) libsvml.so => /home/dl/Avogadro/./lib/intel/libsvml.so (0x00007f2fc8c62000) libintlc.so.5 => /home/dl/Avogadro/./lib/intel/libintlc.so.5 (0x00007f2fcc65a000) libXxf86vm.so.1 => /home/dl/Avogadro/./lib/X11/libXxf86vm.so.1 (0x0000003293e00000) libdrm.so.2 => /home/dl/Avogadro/./lib/gl/libdrm.so.2 (0x0000003467c00000) libexpat.so.0 => /home/dl/Avogadro/./lib/sys/libexpat.so.0 (0x0000003469c00000) libXau.so.6 => /home/dl/Avogadro/./lib/X11/libXau.so.6 (0x0000003468800000) libXdmcp.so.6 => /home/dl/Avogadro/./lib/X11/libXdmcp.so.6 (0x0000003468000000) Segmentation fault [dl@ez05 Avogadro] ls lib/X11/
libdrm.so libICE.so.6.3.0 libX11.so.6 libXdamage.so
libXdmcp.so.6.0.0 libXfixes.so.3 libXxf86vm.so
libdrm.so.2 libSM.so libX11.so.6.2.0 libXdamage.so.1
libXext.so libXfixes.so.3.1.0 libXxf86vm.so.1
libdrm.so.2.0.0 libSM.so.6 libXau.so libXdamage.so.1.0.0
libXext.so.6 libXrender.so libXxf86vm.so.1.0.0
libICE.so libSM.so.6.0.0 libXau.so.6 libXdmcp.so
libXext.so.6.4.0 libXrender.so.1
libICE.so.6 libX11.so libXau.so.6.0.0 libXdmcp.so.6
libXfixes.so libXrender.so.1.3.0

–
Regards,
Konstantin

Яндекс.Почта. Письма есть. Спама - нет. http://mail.yandex.ru/nospam/sign

Konstantin_Tokarev · May 18, 2010, 6:06pm

Weird. This binary works perfectly on CentOS, Debian and Fedora 9…
I’ll try to investigate this problem. Maybe debug build can help

18.05.10, 21:57, “David Lonie” loniedavid@gmail.com:

2010/5/18 Konstantin Tokarev :

Does gdb output something (e.g., hint what library causes problem)?

No luck – (I’m running gdb by modifying avogadro.sh):

[dl@ez05 Avogadro]$ ./avogadro.sh
Setting LD_LIBRARY_PATH=/home/dl/Avogadro/./lib:/home/dl/Avogadro/./lib/qt/lib:/home/dl/Avogadro/./lib/intel:/home/dl/Avogadro/./lib/gl:/home/dl/Avogadro/./lib/X11:/home/dl/Avogadro/./lib/sys:
linux-vdso.so.1 => (0x00007fffd53aa000)
libc.so.6 => /lib/libc.so.6 (0x00007f8476fe1000)
libopenbabel.so.3 => /home/dl/Avogadro/./lib/libopenbabel.so.3
(0x00007f84769e1000)
libQtOpenGL.so.4 =>
/home/dl/Avogadro/./lib/qt/lib/libQtOpenGL.so.4 (0x00007f84766c8000)
libGLU.so.1 => /home/dl/Avogadro/./lib/gl/libGLU.so.1
(0x0000003059c00000)
libGL.so.1 => /home/dl/Avogadro/./lib/gl/libGL.so.1 (0x0000003059800000)
libQtGui.so.4 => /home/dl/Avogadro/./lib/qt/lib/libQtGui.so.4
(0x00007f8475426000)
libSM.so.6 => /home/dl/Avogadro/./lib/X11/libSM.so.6
(0x0000003471600000)
libICE.so.6 => /home/dl/Avogadro/./lib/X11/libICE.so.6
(0x000000346f600000)
libXrender.so.1 => /home/dl/Avogadro/./lib/X11/libXrender.so.1
(0x000000346d600000)
libfreetype.so.6 => /home/dl/Avogadro/./lib/libfreetype.so.6
(0x000000346a000000)
libfontconfig.so.1 =>
/home/dl/Avogadro/./lib/libfontconfig.so.1 (0x000000346a400000)
libXext.so.6 => /home/dl/Avogadro/./lib/X11/libXext.so.6
(0x0000003469800000)
libX11.so.6 => /home/dl/Avogadro/./lib/X11/libX11.so.6
(0x0000003468c00000)
libm.so.6 => /lib/libm.so.6 (0x00007f84751a4000)
libQtNetwork.so.4 =>
/home/dl/Avogadro/./lib/qt/lib/libQtNetwork.so.4 (0x00007f8474dc3000)
libQtCore.so.4 =>
/home/dl/Avogadro/./lib/qt/lib/libQtCore.so.4 (0x00007f8474786000)
libgthread-2.0.so.0 =>
/home/dl/Avogadro/./lib/sys/libgthread-2.0.so.0 (0x0000003470600000)
libglib-2.0.so.0 =>
/home/dl/Avogadro/./lib/sys/libglib-2.0.so.0 (0x0000003467400000)
libgobject-2.0.so.0 =>
/home/dl/Avogadro/./lib/sys/libgobject-2.0.so.0 (0x0000003468400000)
librt.so.1 => /lib/librt.so.1 (0x00007f847457e000)
libpthread.so.0 => /lib/libpthread.so.0 (0x00007f8474362000)
libdl.so.2 => /home/dl/Avogadro/./lib/sys/libdl.so.2
(0x0000003466000000)
libavogadro.so.1 => /home/dl/Avogadro/./lib/libavogadro.so.1
(0x00007f8473fa4000)
libGLEW.so.1.5 => /home/dl/Avogadro/./lib/libGLEW.so.1.5
(0x00000036ee600000)
libstdc++.so.6 => /home/dl/Avogadro/./lib/sys/libstdc++.so.6
(0x0000003479a00000)
libgcc_s.so.1 => /home/dl/Avogadro/./lib/sys/libgcc_s.so.1
(0x0000003477200000)
/lib64/ld-linux-x86-64.so.2 (0x00007f847733d000)
libxml2.so.2 => /home/dl/Avogadro/./lib/libxml2.so.2
(0x0000003470a00000)
libz.so.1 => /home/dl/Avogadro/./lib/libz.so.1 (0x0000003467000000)
libimf.so => /home/dl/Avogadro/./lib/intel/libimf.so
(0x00007f8473c12000)
libsvml.so => /home/dl/Avogadro/./lib/intel/libsvml.so
(0x00007f84739fc000)
libintlc.so.5 => /home/dl/Avogadro/./lib/intel/libintlc.so.5
(0x00007f84773f4000)
libXxf86vm.so.1 => /home/dl/Avogadro/./lib/X11/libXxf86vm.so.1
(0x0000003293e00000)
libdrm.so.2 => /home/dl/Avogadro/./lib/gl/libdrm.so.2
(0x0000003467c00000)
libexpat.so.0 => /home/dl/Avogadro/./lib/sys/libexpat.so.0
(0x0000003469c00000)
libXau.so.6 => /home/dl/Avogadro/./lib/X11/libXau.so.6
(0x0000003468800000)
libXdmcp.so.6 => /home/dl/Avogadro/./lib/X11/libXdmcp.so.6
(0x0000003468000000)
GNU gdb (GDB) 7.1
Copyright © 2010 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later
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-unknown-linux-gnu”.
For bug reporting instructions, please see:
…
Reading symbols from /home/dl/Avogadro/bin/avogadro…(no debugging
symbols found)…done.
(gdb) run
Starting program: /home/dl/Avogadro/bin/avogadro
Segmentation fault

You may also try to remove (or rename) your Avogadro.conf in ~/.config/SourceForge

This is a fresh distro with no other avo’s on it, so this file doesn’t
exist yet.

Dave

18.05.10, 21:45, “David Lonie” :

On Tue, May 18, 2010 at 1:34 PM, Konstantin Tokarev wrote:

Try to put attached libraries to X11 dir of Avogadro installation and set everything to 1.
Send ldd output again if doesn’t work

Still getting a segfault:

[dl@ez05 Avogadro] ./avogadro.sh Setting LD_LIBRARY_PATH=/home/dl/Avogadro/./lib:/home/dl/Avogadro/./lib/qt/lib:/home/dl/Avogadro/./lib/intel:/home/dl/Avogadro/./lib/gl:/home/dl/Avogadro/./lib/X11:/home/dl/Avogadro/./lib/sys: linux-vdso.so.1 => (0x00007fff9d3ff000) libc.so.6 => /lib/libc.so.6 (0x00007f2fcc247000) libopenbabel.so.3 => /home/dl/Avogadro/./lib/libopenbabel.so.3 (0x00007f2fcbc47000) libQtOpenGL.so.4 => /home/dl/Avogadro/./lib/qt/lib/libQtOpenGL.so.4 (0x00007f2fcb92e000) libGLU.so.1 => /home/dl/Avogadro/./lib/gl/libGLU.so.1 (0x0000003059c00000) libGL.so.1 => /home/dl/Avogadro/./lib/gl/libGL.so.1 (0x0000003059800000) libQtGui.so.4 => /home/dl/Avogadro/./lib/qt/lib/libQtGui.so.4 (0x00007f2fca68c000) libSM.so.6 => /home/dl/Avogadro/./lib/X11/libSM.so.6 (0x0000003471600000) libICE.so.6 => /home/dl/Avogadro/./lib/X11/libICE.so.6 (0x000000346f600000) libXrender.so.1 => /home/dl/Avogadro/./lib/X11/libXrender.so.1 (0x000000346d600000) libfreetype.so.6 => /home/dl/Avogadro/./lib/libfreetype.so.6 (0x000000346a000000) libfontconfig.so.1 => /home/dl/Avogadro/./lib/libfontconfig.so.1 (0x000000346a400000) libXext.so.6 => /home/dl/Avogadro/./lib/X11/libXext.so.6 (0x0000003469800000) libX11.so.6 => /home/dl/Avogadro/./lib/X11/libX11.so.6 (0x0000003468c00000) libm.so.6 => /lib/libm.so.6 (0x00007f2fca40a000) libQtNetwork.so.4 => /home/dl/Avogadro/./lib/qt/lib/libQtNetwork.so.4 (0x00007f2fca029000) libQtCore.so.4 => /home/dl/Avogadro/./lib/qt/lib/libQtCore.so.4 (0x00007f2fc99ec000) libgthread-2.0.so.0 => /home/dl/Avogadro/./lib/sys/libgthread-2.0.so.0 (0x0000003470600000) libglib-2.0.so.0 => /home/dl/Avogadro/./lib/sys/libglib-2.0.so.0 (0x0000003467400000) libgobject-2.0.so.0 => /home/dl/Avogadro/./lib/sys/libgobject-2.0.so.0 (0x0000003468400000) librt.so.1 => /lib/librt.so.1 (0x00007f2fc97e4000) libpthread.so.0 => /lib/libpthread.so.0 (0x00007f2fc95c8000) libdl.so.2 => /home/dl/Avogadro/./lib/sys/libdl.so.2 (0x0000003466000000) libavogadro.so.1 => /home/dl/Avogadro/./lib/libavogadro.so.1 (0x00007f2fc920a000) libGLEW.so.1.5 => /home/dl/Avogadro/./lib/libGLEW.so.1.5 (0x00000036ee600000) libstdc++.so.6 => /home/dl/Avogadro/./lib/sys/libstdc++.so.6 (0x0000003479a00000) libgcc_s.so.1 => /home/dl/Avogadro/./lib/sys/libgcc_s.so.1 (0x0000003477200000) /lib64/ld-linux-x86-64.so.2 (0x00007f2fcc5a3000) libxml2.so.2 => /home/dl/Avogadro/./lib/libxml2.so.2 (0x0000003470a00000) libz.so.1 => /home/dl/Avogadro/./lib/libz.so.1 (0x0000003467000000) libimf.so => /home/dl/Avogadro/./lib/intel/libimf.so (0x00007f2fc8e78000) libsvml.so => /home/dl/Avogadro/./lib/intel/libsvml.so (0x00007f2fc8c62000) libintlc.so.5 => /home/dl/Avogadro/./lib/intel/libintlc.so.5 (0x00007f2fcc65a000) libXxf86vm.so.1 => /home/dl/Avogadro/./lib/X11/libXxf86vm.so.1 (0x0000003293e00000) libdrm.so.2 => /home/dl/Avogadro/./lib/gl/libdrm.so.2 (0x0000003467c00000) libexpat.so.0 => /home/dl/Avogadro/./lib/sys/libexpat.so.0 (0x0000003469c00000) libXau.so.6 => /home/dl/Avogadro/./lib/X11/libXau.so.6 (0x0000003468800000) libXdmcp.so.6 => /home/dl/Avogadro/./lib/X11/libXdmcp.so.6 (0x0000003468000000) Segmentation fault [dl@ez05 Avogadro] ls lib/X11/
libdrm.so libICE.so.6.3.0 libX11.so.6 libXdamage.so
libXdmcp.so.6.0.0 libXfixes.so.3 libXxf86vm.so
libdrm.so.2 libSM.so libX11.so.6.2.0 libXdamage.so.1
libXext.so libXfixes.so.3.1.0 libXxf86vm.so.1
libdrm.so.2.0.0 libSM.so.6 libXau.so libXdamage.so.1.0.0
libXext.so.6 libXrender.so libXxf86vm.so.1.0.0
libICE.so libSM.so.6.0.0 libXau.so.6 libXdmcp.so
libXext.so.6.4.0 libXrender.so.1
libICE.so.6 libX11.so libXau.so.6.0.0 libXdmcp.so.6
libXfixes.so libXrender.so.1.3.0

–
Regards,
Konstantin

Яндекс.Почта. Письма есть. Спама - нет. http://mail.yandex.ru/nospam/sign

–
Regards,
Konstantin

Здесь спама нет http://mail.yandex.ru/nospam/sign

allison.vacanti · May 18, 2010, 6:12pm

2010/5/18 Konstantin Tokarev annulen@yandex.ru:

Weird. This binary works perfectly on CentOS, Debian and Fedora 9…
I’ll try to investigate this problem. Maybe debug build can help

Sure – send me a debug build and I’ll see if I can track down the
problem on Arch.

Dave

18.05.10, 21:57, “David Lonie” loniedavid@gmail.com:

2010/5/18 Konstantin Tokarev :

Does gdb output something (e.g., hint what library causes problem)?

No luck – (I’m running gdb by modifying avogadro.sh):

[dl@ez05 Avogadro]$ ./avogadro.sh
Setting LD_LIBRARY_PATH=/home/dl/Avogadro/./lib:/home/dl/Avogadro/./lib/qt/lib:/home/dl/Avogadro/./lib/intel:/home/dl/Avogadro/./lib/gl:/home/dl/Avogadro/./lib/X11:/home/dl/Avogadro/./lib/sys:
linux-vdso.so.1 => (0x00007fffd53aa000)
libc.so.6 => /lib/libc.so.6 (0x00007f8476fe1000)
libopenbabel.so.3 => /home/dl/Avogadro/./lib/libopenbabel.so.3
(0x00007f84769e1000)
libQtOpenGL.so.4 =>
/home/dl/Avogadro/./lib/qt/lib/libQtOpenGL.so.4 (0x00007f84766c8000)
libGLU.so.1 => /home/dl/Avogadro/./lib/gl/libGLU.so.1
(0x0000003059c00000)
libGL.so.1 => /home/dl/Avogadro/./lib/gl/libGL.so.1 (0x0000003059800000)
libQtGui.so.4 => /home/dl/Avogadro/./lib/qt/lib/libQtGui.so.4
(0x00007f8475426000)
libSM.so.6 => /home/dl/Avogadro/./lib/X11/libSM.so.6
(0x0000003471600000)
libICE.so.6 => /home/dl/Avogadro/./lib/X11/libICE.so.6
(0x000000346f600000)
libXrender.so.1 => /home/dl/Avogadro/./lib/X11/libXrender.so.1
(0x000000346d600000)
libfreetype.so.6 => /home/dl/Avogadro/./lib/libfreetype.so.6
(0x000000346a000000)
libfontconfig.so.1 =>
/home/dl/Avogadro/./lib/libfontconfig.so.1 (0x000000346a400000)
libXext.so.6 => /home/dl/Avogadro/./lib/X11/libXext.so.6
(0x0000003469800000)
libX11.so.6 => /home/dl/Avogadro/./lib/X11/libX11.so.6
(0x0000003468c00000)
libm.so.6 => /lib/libm.so.6 (0x00007f84751a4000)
libQtNetwork.so.4 =>
/home/dl/Avogadro/./lib/qt/lib/libQtNetwork.so.4 (0x00007f8474dc3000)
libQtCore.so.4 =>
/home/dl/Avogadro/./lib/qt/lib/libQtCore.so.4 (0x00007f8474786000)
libgthread-2.0.so.0 =>
/home/dl/Avogadro/./lib/sys/libgthread-2.0.so.0 (0x0000003470600000)
libglib-2.0.so.0 =>
/home/dl/Avogadro/./lib/sys/libglib-2.0.so.0 (0x0000003467400000)
libgobject-2.0.so.0 =>
/home/dl/Avogadro/./lib/sys/libgobject-2.0.so.0 (0x0000003468400000)
librt.so.1 => /lib/librt.so.1 (0x00007f847457e000)
libpthread.so.0 => /lib/libpthread.so.0 (0x00007f8474362000)
libdl.so.2 => /home/dl/Avogadro/./lib/sys/libdl.so.2
(0x0000003466000000)
libavogadro.so.1 => /home/dl/Avogadro/./lib/libavogadro.so.1
(0x00007f8473fa4000)
libGLEW.so.1.5 => /home/dl/Avogadro/./lib/libGLEW.so.1.5
(0x00000036ee600000)
libstdc++.so.6 => /home/dl/Avogadro/./lib/sys/libstdc++.so.6
(0x0000003479a00000)
libgcc_s.so.1 => /home/dl/Avogadro/./lib/sys/libgcc_s.so.1
(0x0000003477200000)
/lib64/ld-linux-x86-64.so.2 (0x00007f847733d000)
libxml2.so.2 => /home/dl/Avogadro/./lib/libxml2.so.2
(0x0000003470a00000)
libz.so.1 => /home/dl/Avogadro/./lib/libz.so.1 (0x0000003467000000)
libimf.so => /home/dl/Avogadro/./lib/intel/libimf.so
(0x00007f8473c12000)
libsvml.so => /home/dl/Avogadro/./lib/intel/libsvml.so
(0x00007f84739fc000)
libintlc.so.5 => /home/dl/Avogadro/./lib/intel/libintlc.so.5
(0x00007f84773f4000)
libXxf86vm.so.1 => /home/dl/Avogadro/./lib/X11/libXxf86vm.so.1
(0x0000003293e00000)
libdrm.so.2 => /home/dl/Avogadro/./lib/gl/libdrm.so.2
(0x0000003467c00000)
libexpat.so.0 => /home/dl/Avogadro/./lib/sys/libexpat.so.0
(0x0000003469c00000)
libXau.so.6 => /home/dl/Avogadro/./lib/X11/libXau.so.6
(0x0000003468800000)
libXdmcp.so.6 => /home/dl/Avogadro/./lib/X11/libXdmcp.so.6
(0x0000003468000000)
GNU gdb (GDB) 7.1
Copyright © 2010 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later
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-unknown-linux-gnu”.
For bug reporting instructions, please see:
…
Reading symbols from /home/dl/Avogadro/bin/avogadro…(no debugging
symbols found)…done.
(gdb) run
Starting program: /home/dl/Avogadro/bin/avogadro
Segmentation fault

You may also try to remove (or rename) your Avogadro.conf in ~/.config/SourceForge

This is a fresh distro with no other avo’s on it, so this file doesn’t
exist yet.

Dave

18.05.10, 21:45, “David Lonie” :

On Tue, May 18, 2010 at 1:34 PM, Konstantin Tokarev wrote:

Try to put attached libraries to X11 dir of Avogadro installation and set everything to 1.
Send ldd output again if doesn’t work

Still getting a segfault:

[dl@ez05 Avogadro] ./avogadro.sh Setting LD_LIBRARY_PATH=/home/dl/Avogadro/./lib:/home/dl/Avogadro/./lib/qt/lib:/home/dl/Avogadro/./lib/intel:/home/dl/Avogadro/./lib/gl:/home/dl/Avogadro/./lib/X11:/home/dl/Avogadro/./lib/sys: linux-vdso.so.1 => (0x00007fff9d3ff000) libc.so.6 => /lib/libc.so.6 (0x00007f2fcc247000) libopenbabel.so.3 => /home/dl/Avogadro/./lib/libopenbabel.so.3 (0x00007f2fcbc47000) libQtOpenGL.so.4 => /home/dl/Avogadro/./lib/qt/lib/libQtOpenGL.so.4 (0x00007f2fcb92e000) libGLU.so.1 => /home/dl/Avogadro/./lib/gl/libGLU.so.1 (0x0000003059c00000) libGL.so.1 => /home/dl/Avogadro/./lib/gl/libGL.so.1 (0x0000003059800000) libQtGui.so.4 => /home/dl/Avogadro/./lib/qt/lib/libQtGui.so.4 (0x00007f2fca68c000) libSM.so.6 => /home/dl/Avogadro/./lib/X11/libSM.so.6 (0x0000003471600000) libICE.so.6 => /home/dl/Avogadro/./lib/X11/libICE.so.6 (0x000000346f600000) libXrender.so.1 => /home/dl/Avogadro/./lib/X11/libXrender.so.1 (0x000000346d600000) libfreetype.so.6 => /home/dl/Avogadro/./lib/libfreetype.so.6 (0x000000346a000000) libfontconfig.so.1 => /home/dl/Avogadro/./lib/libfontconfig.so.1 (0x000000346a400000) libXext.so.6 => /home/dl/Avogadro/./lib/X11/libXext.so.6 (0x0000003469800000) libX11.so.6 => /home/dl/Avogadro/./lib/X11/libX11.so.6 (0x0000003468c00000) libm.so.6 => /lib/libm.so.6 (0x00007f2fca40a000) libQtNetwork.so.4 => /home/dl/Avogadro/./lib/qt/lib/libQtNetwork.so.4 (0x00007f2fca029000) libQtCore.so.4 => /home/dl/Avogadro/./lib/qt/lib/libQtCore.so.4 (0x00007f2fc99ec000) libgthread-2.0.so.0 => /home/dl/Avogadro/./lib/sys/libgthread-2.0.so.0 (0x0000003470600000) libglib-2.0.so.0 => /home/dl/Avogadro/./lib/sys/libglib-2.0.so.0 (0x0000003467400000) libgobject-2.0.so.0 => /home/dl/Avogadro/./lib/sys/libgobject-2.0.so.0 (0x0000003468400000) librt.so.1 => /lib/librt.so.1 (0x00007f2fc97e4000) libpthread.so.0 => /lib/libpthread.so.0 (0x00007f2fc95c8000) libdl.so.2 => /home/dl/Avogadro/./lib/sys/libdl.so.2 (0x0000003466000000) libavogadro.so.1 => /home/dl/Avogadro/./lib/libavogadro.so.1 (0x00007f2fc920a000) libGLEW.so.1.5 => /home/dl/Avogadro/./lib/libGLEW.so.1.5 (0x00000036ee600000) libstdc++.so.6 => /home/dl/Avogadro/./lib/sys/libstdc++.so.6 (0x0000003479a00000) libgcc_s.so.1 => /home/dl/Avogadro/./lib/sys/libgcc_s.so.1 (0x0000003477200000) /lib64/ld-linux-x86-64.so.2 (0x00007f2fcc5a3000) libxml2.so.2 => /home/dl/Avogadro/./lib/libxml2.so.2 (0x0000003470a00000) libz.so.1 => /home/dl/Avogadro/./lib/libz.so.1 (0x0000003467000000) libimf.so => /home/dl/Avogadro/./lib/intel/libimf.so (0x00007f2fc8e78000) libsvml.so => /home/dl/Avogadro/./lib/intel/libsvml.so (0x00007f2fc8c62000) libintlc.so.5 => /home/dl/Avogadro/./lib/intel/libintlc.so.5 (0x00007f2fcc65a000) libXxf86vm.so.1 => /home/dl/Avogadro/./lib/X11/libXxf86vm.so.1 (0x0000003293e00000) libdrm.so.2 => /home/dl/Avogadro/./lib/gl/libdrm.so.2 (0x0000003467c00000) libexpat.so.0 => /home/dl/Avogadro/./lib/sys/libexpat.so.0 (0x0000003469c00000) libXau.so.6 => /home/dl/Avogadro/./lib/X11/libXau.so.6 (0x0000003468800000) libXdmcp.so.6 => /home/dl/Avogadro/./lib/X11/libXdmcp.so.6 (0x0000003468000000) Segmentation fault [dl@ez05 Avogadro] ls lib/X11/
libdrm.so libICE.so.6.3.0 libX11.so.6 libXdamage.so
libXdmcp.so.6.0.0 libXfixes.so.3 libXxf86vm.so
libdrm.so.2 libSM.so libX11.so.6.2.0 libXdamage.so.1
libXext.so libXfixes.so.3.1.0 libXxf86vm.so.1
libdrm.so.2.0.0 libSM.so.6 libXau.so libXdamage.so.1.0.0
libXext.so.6 libXrender.so libXxf86vm.so.1.0.0
libICE.so libSM.so.6.0.0 libXau.so.6 libXdmcp.so
libXext.so.6.4.0 libXrender.so.1
libICE.so.6 libX11.so libXau.so.6.0.0 libXdmcp.so.6
libXfixes.so libXrender.so.1.3.0

–
Regards,
Konstantin

Яндекс.Почта. Письма есть. Спама - нет. http://mail.yandex.ru/nospam/sign

–
Regards,
Konstantin

Здесь спама нет http://mail.yandex.ru/nospam/sign

Konstantin_Tokarev · May 18, 2010, 6:15pm

18.05.10, 22:12, “David Lonie” loniedavid@gmail.com:

2010/5/18 Konstantin Tokarev :

Weird. This binary works perfectly on CentOS, Debian and Fedora 9…
I’ll try to investigate this problem. Maybe debug build can help

Sure – send me a debug build and I’ll see if I can track down the
problem on Arch.

Not today - that PC is doing heavy MP4 calculation
Maybe tomorrow

Dave

18.05.10, 21:57, “David Lonie” :

2010/5/18 Konstantin Tokarev :

Does gdb output something (e.g., hint what library causes problem)?

No luck – (I’m running gdb by modifying avogadro.sh):

[dl@ez05 Avogadro]$ ./avogadro.sh
Setting LD_LIBRARY_PATH=/home/dl/Avogadro/./lib:/home/dl/Avogadro/./lib/qt/lib:/home/dl/Avogadro/./lib/intel:/home/dl/Avogadro/./lib/gl:/home/dl/Avogadro/./lib/X11:/home/dl/Avogadro/./lib/sys:
linux-vdso.so.1 => (0x00007fffd53aa000)
libc.so.6 => /lib/libc.so.6 (0x00007f8476fe1000)
libopenbabel.so.3 => /home/dl/Avogadro/./lib/libopenbabel.so.3
(0x00007f84769e1000)
libQtOpenGL.so.4 =>
/home/dl/Avogadro/./lib/qt/lib/libQtOpenGL.so.4 (0x00007f84766c8000)
libGLU.so.1 => /home/dl/Avogadro/./lib/gl/libGLU.so.1
(0x0000003059c00000)
libGL.so.1 => /home/dl/Avogadro/./lib/gl/libGL.so.1 (0x0000003059800000)
libQtGui.so.4 => /home/dl/Avogadro/./lib/qt/lib/libQtGui.so.4
(0x00007f8475426000)
libSM.so.6 => /home/dl/Avogadro/./lib/X11/libSM.so.6
(0x0000003471600000)
libICE.so.6 => /home/dl/Avogadro/./lib/X11/libICE.so.6
(0x000000346f600000)
libXrender.so.1 => /home/dl/Avogadro/./lib/X11/libXrender.so.1
(0x000000346d600000)
libfreetype.so.6 => /home/dl/Avogadro/./lib/libfreetype.so.6
(0x000000346a000000)
libfontconfig.so.1 =>
/home/dl/Avogadro/./lib/libfontconfig.so.1 (0x000000346a400000)
libXext.so.6 => /home/dl/Avogadro/./lib/X11/libXext.so.6
(0x0000003469800000)
libX11.so.6 => /home/dl/Avogadro/./lib/X11/libX11.so.6
(0x0000003468c00000)
libm.so.6 => /lib/libm.so.6 (0x00007f84751a4000)
libQtNetwork.so.4 =>
/home/dl/Avogadro/./lib/qt/lib/libQtNetwork.so.4 (0x00007f8474dc3000)
libQtCore.so.4 =>
/home/dl/Avogadro/./lib/qt/lib/libQtCore.so.4 (0x00007f8474786000)
libgthread-2.0.so.0 =>
/home/dl/Avogadro/./lib/sys/libgthread-2.0.so.0 (0x0000003470600000)
libglib-2.0.so.0 =>
/home/dl/Avogadro/./lib/sys/libglib-2.0.so.0 (0x0000003467400000)
libgobject-2.0.so.0 =>
/home/dl/Avogadro/./lib/sys/libgobject-2.0.so.0 (0x0000003468400000)
librt.so.1 => /lib/librt.so.1 (0x00007f847457e000)
libpthread.so.0 => /lib/libpthread.so.0 (0x00007f8474362000)
libdl.so.2 => /home/dl/Avogadro/./lib/sys/libdl.so.2
(0x0000003466000000)
libavogadro.so.1 => /home/dl/Avogadro/./lib/libavogadro.so.1
(0x00007f8473fa4000)
libGLEW.so.1.5 => /home/dl/Avogadro/./lib/libGLEW.so.1.5
(0x00000036ee600000)
libstdc++.so.6 => /home/dl/Avogadro/./lib/sys/libstdc++.so.6
(0x0000003479a00000)
libgcc_s.so.1 => /home/dl/Avogadro/./lib/sys/libgcc_s.so.1
(0x0000003477200000)
/lib64/ld-linux-x86-64.so.2 (0x00007f847733d000)
libxml2.so.2 => /home/dl/Avogadro/./lib/libxml2.so.2
(0x0000003470a00000)
libz.so.1 => /home/dl/Avogadro/./lib/libz.so.1 (0x0000003467000000)
libimf.so => /home/dl/Avogadro/./lib/intel/libimf.so
(0x00007f8473c12000)
libsvml.so => /home/dl/Avogadro/./lib/intel/libsvml.so
(0x00007f84739fc000)
libintlc.so.5 => /home/dl/Avogadro/./lib/intel/libintlc.so.5
(0x00007f84773f4000)
libXxf86vm.so.1 => /home/dl/Avogadro/./lib/X11/libXxf86vm.so.1
(0x0000003293e00000)
libdrm.so.2 => /home/dl/Avogadro/./lib/gl/libdrm.so.2
(0x0000003467c00000)
libexpat.so.0 => /home/dl/Avogadro/./lib/sys/libexpat.so.0
(0x0000003469c00000)
libXau.so.6 => /home/dl/Avogadro/./lib/X11/libXau.so.6
(0x0000003468800000)
libXdmcp.so.6 => /home/dl/Avogadro/./lib/X11/libXdmcp.so.6
(0x0000003468000000)
GNU gdb (GDB) 7.1
Copyright © 2010 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later
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-unknown-linux-gnu”.
For bug reporting instructions, please see:
…
Reading symbols from /home/dl/Avogadro/bin/avogadro…(no debugging
symbols found)…done.
(gdb) run
Starting program: /home/dl/Avogadro/bin/avogadro
Segmentation fault

You may also try to remove (or rename) your Avogadro.conf in ~/.config/SourceForge

This is a fresh distro with no other avo’s on it, so this file doesn’t
exist yet.

Dave

18.05.10, 21:45, “David Lonie” :

On Tue, May 18, 2010 at 1:34 PM, Konstantin Tokarev wrote:

Try to put attached libraries to X11 dir of Avogadro installation and set everything to 1.
Send ldd output again if doesn’t work

Still getting a segfault:

[dl@ez05 Avogadro] ./avogadro.sh Setting LD_LIBRARY_PATH=/home/dl/Avogadro/./lib:/home/dl/Avogadro/./lib/qt/lib:/home/dl/Avogadro/./lib/intel:/home/dl/Avogadro/./lib/gl:/home/dl/Avogadro/./lib/X11:/home/dl/Avogadro/./lib/sys: linux-vdso.so.1 => (0x00007fff9d3ff000) libc.so.6 => /lib/libc.so.6 (0x00007f2fcc247000) libopenbabel.so.3 => /home/dl/Avogadro/./lib/libopenbabel.so.3 (0x00007f2fcbc47000) libQtOpenGL.so.4 => /home/dl/Avogadro/./lib/qt/lib/libQtOpenGL.so.4 (0x00007f2fcb92e000) libGLU.so.1 => /home/dl/Avogadro/./lib/gl/libGLU.so.1 (0x0000003059c00000) libGL.so.1 => /home/dl/Avogadro/./lib/gl/libGL.so.1 (0x0000003059800000) libQtGui.so.4 => /home/dl/Avogadro/./lib/qt/lib/libQtGui.so.4 (0x00007f2fca68c000) libSM.so.6 => /home/dl/Avogadro/./lib/X11/libSM.so.6 (0x0000003471600000) libICE.so.6 => /home/dl/Avogadro/./lib/X11/libICE.so.6 (0x000000346f600000) libXrender.so.1 => /home/dl/Avogadro/./lib/X11/libXrender.so.1 (0x000000346d600000) libfreetype.so.6 => /home/dl/Avogadro/./lib/libfreetype.so.6 (0x000000346a000000) libfontconfig.so.1 => /home/dl/Avogadro/./lib/libfontconfig.so.1 (0x000000346a400000) libXext.so.6 => /home/dl/Avogadro/./lib/X11/libXext.so.6 (0x0000003469800000) libX11.so.6 => /home/dl/Avogadro/./lib/X11/libX11.so.6 (0x0000003468c00000) libm.so.6 => /lib/libm.so.6 (0x00007f2fca40a000) libQtNetwork.so.4 => /home/dl/Avogadro/./lib/qt/lib/libQtNetwork.so.4 (0x00007f2fca029000) libQtCore.so.4 => /home/dl/Avogadro/./lib/qt/lib/libQtCore.so.4 (0x00007f2fc99ec000) libgthread-2.0.so.0 => /home/dl/Avogadro/./lib/sys/libgthread-2.0.so.0 (0x0000003470600000) libglib-2.0.so.0 => /home/dl/Avogadro/./lib/sys/libglib-2.0.so.0 (0x0000003467400000) libgobject-2.0.so.0 => /home/dl/Avogadro/./lib/sys/libgobject-2.0.so.0 (0x0000003468400000) librt.so.1 => /lib/librt.so.1 (0x00007f2fc97e4000) libpthread.so.0 => /lib/libpthread.so.0 (0x00007f2fc95c8000) libdl.so.2 => /home/dl/Avogadro/./lib/sys/libdl.so.2 (0x0000003466000000) libavogadro.so.1 => /home/dl/Avogadro/./lib/libavogadro.so.1 (0x00007f2fc920a000) libGLEW.so.1.5 => /home/dl/Avogadro/./lib/libGLEW.so.1.5 (0x00000036ee600000) libstdc++.so.6 => /home/dl/Avogadro/./lib/sys/libstdc++.so.6 (0x0000003479a00000) libgcc_s.so.1 => /home/dl/Avogadro/./lib/sys/libgcc_s.so.1 (0x0000003477200000) /lib64/ld-linux-x86-64.so.2 (0x00007f2fcc5a3000) libxml2.so.2 => /home/dl/Avogadro/./lib/libxml2.so.2 (0x0000003470a00000) libz.so.1 => /home/dl/Avogadro/./lib/libz.so.1 (0x0000003467000000) libimf.so => /home/dl/Avogadro/./lib/intel/libimf.so (0x00007f2fc8e78000) libsvml.so => /home/dl/Avogadro/./lib/intel/libsvml.so (0x00007f2fc8c62000) libintlc.so.5 => /home/dl/Avogadro/./lib/intel/libintlc.so.5 (0x00007f2fcc65a000) libXxf86vm.so.1 => /home/dl/Avogadro/./lib/X11/libXxf86vm.so.1 (0x0000003293e00000) libdrm.so.2 => /home/dl/Avogadro/./lib/gl/libdrm.so.2 (0x0000003467c00000) libexpat.so.0 => /home/dl/Avogadro/./lib/sys/libexpat.so.0 (0x0000003469c00000) libXau.so.6 => /home/dl/Avogadro/./lib/X11/libXau.so.6 (0x0000003468800000) libXdmcp.so.6 => /home/dl/Avogadro/./lib/X11/libXdmcp.so.6 (0x0000003468000000) Segmentation fault [dl@ez05 Avogadro] ls lib/X11/
libdrm.so libICE.so.6.3.0 libX11.so.6 libXdamage.so
libXdmcp.so.6.0.0 libXfixes.so.3 libXxf86vm.so
libdrm.so.2 libSM.so libX11.so.6.2.0 libXdamage.so.1
libXext.so libXfixes.so.3.1.0 libXxf86vm.so.1
libdrm.so.2.0.0 libSM.so.6 libXau.so libXdamage.so.1.0.0
libXext.so.6 libXrender.so libXxf86vm.so.1.0.0
libICE.so libSM.so.6.0.0 libXau.so.6 libXdmcp.so
libXext.so.6.4.0 libXrender.so.1
libICE.so.6 libX11.so libXau.so.6.0.0 libXdmcp.so.6
libXfixes.so libXrender.so.1.3.0

–
Regards,
Konstantin

Яндекс.Почта. Письма есть. Спама - нет. http://mail.yandex.ru/nospam/sign

–
Regards,
Konstantin

Здесь спама нет http://mail.yandex.ru/nospam/sign

–
Regards,
Konstantin

Яндекс.Почта. Письма есть. Спама - нет. http://mail.yandex.ru/nospam/sign