Build / Run problem

Hi guys.

I’ve just updated avogadro from svn(r1580), but I can’t run it. I tried the
previous versions also, but I’ve got the same.

I believe that is something related to my Qt installation, but I can’t say
what.

The building passed without problems, but when I run avogadro, happens the
following:

alfeto@amebamovel:~/workspace/avogadro/build$ avogadro
System has OpenGL support.
Locale: "en_US"
Loaded translations (if needed) about to test OpenGL capabilities.
OpenGL capabilities found:
Double Buffering.
Direct Rendering.
Antialiasing.

Searching for plugins in "/opt/avogadro/lib/avogadro/engines"
Searching for plugins in "/opt/avogadro/lib/avogadro/tools"
Searching for plugins in "/opt/avogadro/lib/avogadro/extensions"
Searching for plugins in “/opt/avogadro/lib/avogadro/colors”
“libelementcolor.so” failed to load. "The file
’/opt/avogadro/lib/avogadro/colors/libelementcolor.so’ is not a valid Qt
plugin."
avogadro: symbol lookup error:
/opt/avogadro/lib/avogadro/extensions/libpythonextension.so: undefined
symbol: _ZN8Avogadro17PythonInterpreterC1Ev

Any suggestion?


Leandro A. Boscariol

Hi Leandro,

I’ve just updated avogadro from svn(r1580), but I can’t run it. I
tried the previous versions also, but I’ve got the same.

Searching for plugins in "/opt/avogadro/lib/avogadro/engines"
Searching for plugins in “/opt/avogadro/lib/avogadro/tools”

Try removing everything in /opt/avogadro/lib/avogadro and then re-
installing. I suspect you may have old plugins lying around, and the
new code doesn’t load them correctly.

Hope that helps,
-Geoff

Hi Geoff.

I did what you told me.

But I can’t say if it helped, because now I’ve got another problem…

alfeto@amebamovel:~/workspace/avogadro/build$ make
Linking CXX shared library libavogadro.so
/usr/lib/python2.5/config/libpython2.5.a(posixmodule.o): In function
posix_forkpty': posixmodule.c:(.text+0x3a49): undefined reference toforkpty’
/usr/lib/python2.5/config/libpython2.5.a(posixmodule.o): In function
posix_openpty': posixmodule.c:(.text+0x3ad8): undefined reference toopenpty’
collect2: ld returned 1 exit status
make[2]: *** [libavogadro/src/libavogadro.so.0.8.2] Error 1
make[1]: *** [libavogadro/src/CMakeFiles/avogadro-lib.dir/all] Error 2
make: *** [all] Error 2

On Thu, Oct 9, 2008 at 19:00, Geoffrey Hutchison
geoff.hutchison@gmail.comwrote:

Hi Leandro,

I’ve just updated avogadro from svn(r1580), but I can’t run it. I tried

the previous versions also, but I’ve got the same.

Searching for plugins in "/opt/avogadro/lib/avogadro/engines"
Searching for plugins in “/opt/avogadro/lib/avogadro/tools”

Try removing everything in /opt/avogadro/lib/avogadro and then
re-installing. I suspect you may have old plugins lying around, and the new
code doesn’t load them correctly.

Hope that helps,
-Geoff


Leandro A. Boscariol

On Friday 10 October 2008 08:03:40 Leandro Boscariol wrote:

Hi Geoff.

I did what you told me.

But I can’t say if it helped, because now I’ve got another problem…

alfeto@amebamovel:~/workspace/avogadro/build$ make
Linking CXX shared library libavogadro.so
/usr/lib/python2.5/config/libpython2.5.a(posixmodule.o): In function
posix_forkpty': posixmodule.c:(.text+0x3a49): undefined reference toforkpty’
/usr/lib/python2.5/config/libpython2.5.a(posixmodule.o): In function
posix_openpty': posixmodule.c:(.text+0x3ad8): undefined reference toopenpty’
collect2: ld returned 1 exit status
make[2]: *** [libavogadro/src/libavogadro.so.0.8.2] Error 1
make[1]: *** [libavogadro/src/CMakeFiles/avogadro-lib.dir/all] Error 2
make: *** [all] Error 2

This looks like the old Python bug that several Linux distros still haven’t
patched and KitWare seems unwilling to patch… I have commented on several
upstream bugs, patched Gentoo’s version and generally tried to make noise.
They just offered me the opportunity to maintain the FindPythonLibs module
which I didn’t feel I necessarily had the time for!

You could add a -DPYTHON_LIBRARIES=/usr/lib/python2.5/libpythson2.5.so or
something to that effect. It is trying to using the static lib in the config
directory that virtually no distro uses and is not the way the default Python
build system installs it :confused:

Otherwise you could disable the Python support for now.

Hi Marcus!

I’ve tried as you said:

-DPYTHON_LIBRARIES=/usr/lib/libpython2.5.so

but still doesn’t worked.

Then I’ve tried:

-DENABLE_PYTHON=OFF

And now I could build, and even run avogadro!

But, when I click inside the view, trying to use any tool, avogadro crashes.

Here is the output:

alfeto@amebamovel:~/workspace/avogadro/build$
/opt/avogadro/bin/avogadro

System has OpenGL
support.

Locale:
“en_US”

Loaded translations (if needed) about to test OpenGL
capabilities.

OpenGL capabilities
found:

    Double

Buffering.

    Direct Rendering.
    Antialiasing.

Searching for plugins in "/opt/avogadro/lib/avogadro/engines"
Searching for plugins in "/opt/avogadro/lib/avogadro/tools"
Searching for plugins in "/opt/avogadro/lib/avogadro/extensions"
Searching for plugins in "/opt/avogadro/lib/avogadro/colors"
Found Extension: “Animation” - "Animation Plugin"
Found Extension: “ForceField” - "ForceField Plugin"
Found Extension: “GAMESS” - "GAMESS Input Deck Generator"
Found Extension: “Gaussian Input Deck” - "Gaussian input deck generator"
Found Extension: “H2Methyl” - "H2Methyl Plugin"
Found Extension: “Hydrogens” - "Hydrogens Plugin"
Found Extension: “Lin Morph” - "Lin Morph Extension."
Found Extension: “Orbitals” - "Orbital cube generator"
Found Extension: “Properties” - "Properties Plugin"
Found Extension: “Selections” - "Selection Plugin"
Found Extension: “SuperCell” - "Super Cell Builder"
Found Extension: “UnitCell” - "Unit Cell Parameters Plugin"
SetMolecule Called!
GLWidget initialisation…
GLWidget initialised…
createObjects()
Loading File
SetMolecule Called!
/opt/avogadro/bin/avogadro: symbol lookup error:
/opt/avogadro/lib/avogadro/tools/libnavigatetool.so: undefined symbol:
_ZNK8Avogadro6Camera8distanceERKN5Eigen6MatrixIdLi3ELi1ELi0ELi3ELi1EEE

What can it be now?

Cheers,
Leandro.

On Fri, Oct 10, 2008 at 11:33, Marcus D. Hanwell marcus@cryos.org wrote:

On Friday 10 October 2008 08:03:40 Leandro Boscariol wrote:

Hi Geoff.

I did what you told me.

But I can’t say if it helped, because now I’ve got another problem…

alfeto@amebamovel:~/workspace/avogadro/build$ make
Linking CXX shared library libavogadro.so
/usr/lib/python2.5/config/libpython2.5.a(posixmodule.o): In function
posix_forkpty': posixmodule.c:(.text+0x3a49): undefined reference toforkpty’
/usr/lib/python2.5/config/libpython2.5.a(posixmodule.o): In function
posix_openpty': posixmodule.c:(.text+0x3ad8): undefined reference toopenpty’
collect2: ld returned 1 exit status
make[2]: *** [libavogadro/src/libavogadro.so.0.8.2] Error 1
make[1]: *** [libavogadro/src/CMakeFiles/avogadro-lib.dir/all] Error 2
make: *** [all] Error 2

This looks like the old Python bug that several Linux distros still haven’t
patched and KitWare seems unwilling to patch… I have commented on several
upstream bugs, patched Gentoo’s version and generally tried to make noise.
They just offered me the opportunity to maintain the FindPythonLibs module
which I didn’t feel I necessarily had the time for!

You could add a -DPYTHON_LIBRARIES=/usr/lib/python2.5/libpythson2.5.so or
something to that effect. It is trying to using the static lib in the
config
directory that virtually no distro uses and is not the way the default
Python
build system installs it :confused:

Otherwise you could disable the Python support for now.


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Leandro A. Boscariol

Leandro,

it seems that you have stale tools installed around.
Can you try to empty /opt/avogadro/lib/avogadro/tools/
and while you’re at it erase other avogadro libraries, such as the
extensions etc, and libavogadro itself.

Cheers,
Benoit

Quoting Leandro Boscariol leandroboscariol@gmail.com:

Hi Marcus!

I’ve tried as you said:

-DPYTHON_LIBRARIES=/usr/lib/libpython2.5.so

but still doesn’t worked.

Then I’ve tried:

-DENABLE_PYTHON=OFF

And now I could build, and even run avogadro!

But, when I click inside the view, trying to use any tool, avogadro crashes.

Here is the output:

alfeto@amebamovel:~/workspace/avogadro/build$
/opt/avogadro/bin/avogadro

System has OpenGL
support.

Locale:
“en_US”

Loaded translations (if needed) about to test OpenGL
capabilities.

OpenGL capabilities
found:

    Double

Buffering.

    Direct Rendering.
    Antialiasing.

Searching for plugins in "/opt/avogadro/lib/avogadro/engines"
Searching for plugins in "/opt/avogadro/lib/avogadro/tools"
Searching for plugins in "/opt/avogadro/lib/avogadro/extensions"
Searching for plugins in "/opt/avogadro/lib/avogadro/colors"
Found Extension: “Animation” - "Animation Plugin"
Found Extension: “ForceField” - "ForceField Plugin"
Found Extension: “GAMESS” - "GAMESS Input Deck Generator"
Found Extension: “Gaussian Input Deck” - "Gaussian input deck generator"
Found Extension: “H2Methyl” - "H2Methyl Plugin"
Found Extension: “Hydrogens” - "Hydrogens Plugin"
Found Extension: “Lin Morph” - "Lin Morph Extension."
Found Extension: “Orbitals” - "Orbital cube generator"
Found Extension: “Properties” - "Properties Plugin"
Found Extension: “Selections” - "Selection Plugin"
Found Extension: “SuperCell” - "Super Cell Builder"
Found Extension: “UnitCell” - "Unit Cell Parameters Plugin"
SetMolecule Called!
GLWidget initialisation…
GLWidget initialised…
createObjects()
Loading File
SetMolecule Called!
/opt/avogadro/bin/avogadro: symbol lookup error:
/opt/avogadro/lib/avogadro/tools/libnavigatetool.so: undefined symbol:
_ZNK8Avogadro6Camera8distanceERKN5Eigen6MatrixIdLi3ELi1ELi0ELi3ELi1EEE

What can it be now?

Cheers,
Leandro.

On Fri, Oct 10, 2008 at 11:33, Marcus D. Hanwell marcus@cryos.org wrote:

On Friday 10 October 2008 08:03:40 Leandro Boscariol wrote:

Hi Geoff.

I did what you told me.

But I can’t say if it helped, because now I’ve got another problem…

alfeto@amebamovel:~/workspace/avogadro/build$ make
Linking CXX shared library libavogadro.so
/usr/lib/python2.5/config/libpython2.5.a(posixmodule.o): In function
posix_forkpty': posixmodule.c:(.text+0x3a49): undefined reference toforkpty’
/usr/lib/python2.5/config/libpython2.5.a(posixmodule.o): In function
posix_openpty': posixmodule.c:(.text+0x3ad8): undefined reference toopenpty’
collect2: ld returned 1 exit status
make[2]: *** [libavogadro/src/libavogadro.so.0.8.2] Error 1
make[1]: *** [libavogadro/src/CMakeFiles/avogadro-lib.dir/all] Error 2
make: *** [all] Error 2

This looks like the old Python bug that several Linux distros still haven’t
patched and KitWare seems unwilling to patch… I have commented on several
upstream bugs, patched Gentoo’s version and generally tried to make noise.
They just offered me the opportunity to maintain the FindPythonLibs module
which I didn’t feel I necessarily had the time for!

You could add a -DPYTHON_LIBRARIES=/usr/lib/python2.5/libpythson2.5.so or
something to that effect. It is trying to using the static lib in the
config
directory that virtually no distro uses and is not the way the default
Python
build system installs it :confused:

Otherwise you could disable the Python support for now.


This SF.Net email is sponsored by the Moblin Your Move Developer’s
challenge
Build the coolest Linux based applications with Moblin SDK & win great
prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/


Avogadro-devel mailing list
Avogadro-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-devel


Leandro A. Boscariol


This message was sent using IMP, the Internet Messaging Program.

Hi Jacob.

You told me the same thing that Geoff did before, and I did it again.
Removed everything, and installed again.

But I’ve found an old and forgotten link named libavogadro.so, pointing to
somewhere unknown.

Removed it, and now it works!

Thanks for your help guys!

Cheers,
Leandro.

On Fri, Oct 10, 2008 at 15:05, jacob@math.jussieu.fr wrote:

Leandro,

it seems that you have stale tools installed around.
Can you try to empty /opt/avogadro/lib/avogadro/tools/
and while you’re at it erase other avogadro libraries, such as the
extensions etc, and libavogadro itself.

Cheers,
Benoit

Quoting Leandro Boscariol leandroboscariol@gmail.com:

Hi Marcus!

I’ve tried as you said:

-DPYTHON_LIBRARIES=/usr/lib/libpython2.5.so

but still doesn’t worked.

Then I’ve tried:

-DENABLE_PYTHON=OFF

And now I could build, and even run avogadro!

But, when I click inside the view, trying to use any tool, avogadro
crashes.

Here is the output:

alfeto@amebamovel:~/workspace/avogadro/build$
/opt/avogadro/bin/avogadro

System has OpenGL
support.

Locale:
“en_US”

Loaded translations (if needed) about to test OpenGL
capabilities.

OpenGL capabilities
found:

    Double

Buffering.

    Direct Rendering.
    Antialiasing.

Searching for plugins in "/opt/avogadro/lib/avogadro/engines"
Searching for plugins in "/opt/avogadro/lib/avogadro/tools"
Searching for plugins in "/opt/avogadro/lib/avogadro/extensions"
Searching for plugins in "/opt/avogadro/lib/avogadro/colors"
Found Extension: “Animation” - "Animation Plugin"
Found Extension: “ForceField” - "ForceField Plugin"
Found Extension: “GAMESS” - "GAMESS Input Deck Generator"
Found Extension: “Gaussian Input Deck” - "Gaussian input deck
generator"
Found Extension: “H2Methyl” - "H2Methyl Plugin"
Found Extension: “Hydrogens” - "Hydrogens Plugin"
Found Extension: “Lin Morph” - "Lin Morph Extension."
Found Extension: “Orbitals” - "Orbital cube generator"
Found Extension: “Properties” - "Properties Plugin"
Found Extension: “Selections” - "Selection Plugin"
Found Extension: “SuperCell” - "Super Cell Builder"
Found Extension: “UnitCell” - "Unit Cell Parameters Plugin"
SetMolecule Called!
GLWidget initialisation…
GLWidget initialised…
createObjects()
Loading File
SetMolecule Called!
/opt/avogadro/bin/avogadro: symbol lookup error:
/opt/avogadro/lib/avogadro/tools/libnavigatetool.so: undefined symbol:
_ZNK8Avogadro6Camera8distanceERKN5Eigen6MatrixIdLi3ELi1ELi0ELi3ELi1EEE

What can it be now?

Cheers,
Leandro.

On Fri, Oct 10, 2008 at 11:33, Marcus D. Hanwell marcus@cryos.org
wrote:

On Friday 10 October 2008 08:03:40 Leandro Boscariol wrote:

Hi Geoff.

I did what you told me.

But I can’t say if it helped, because now I’ve got another problem…

alfeto@amebamovel:~/workspace/avogadro/build$ make
Linking CXX shared library libavogadro.so
/usr/lib/python2.5/config/libpython2.5.a(posixmodule.o): In function
posix_forkpty': posixmodule.c:(.text+0x3a49): undefined reference toforkpty’
/usr/lib/python2.5/config/libpython2.5.a(posixmodule.o): In function
posix_openpty': posixmodule.c:(.text+0x3ad8): undefined reference toopenpty’
collect2: ld returned 1 exit status
make[2]: *** [libavogadro/src/libavogadro.so.0.8.2] Error 1
make[1]: *** [libavogadro/src/CMakeFiles/avogadro-lib.dir/all] Error 2
make: *** [all] Error 2

This looks like the old Python bug that several Linux distros still
haven’t

patched and KitWare seems unwilling to patch… I have commented on
several

upstream bugs, patched Gentoo’s version and generally tried to make
noise.

They just offered me the opportunity to maintain the FindPythonLibs
module

which I didn’t feel I necessarily had the time for!

You could add a -DPYTHON_LIBRARIES=/usr/lib/python2.5/libpythson2.5.soor
something to that effect. It is trying to using the static lib in the
config
directory that virtually no distro uses and is not the way the default
Python
build system installs it :confused:

Otherwise you could disable the Python support for now.


This SF.Net email is sponsored by the Moblin Your Move Developer’s
challenge
Build the coolest Linux based applications with Moblin SDK & win great
prizes
Grand prize is a trip for two to an Open Source event anywhere in the
world

http://moblin-contest.org/redirect.php?banner_id=100&url=/


Avogadro-devel mailing list
Avogadro-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-devel


Leandro A. Boscariol


This message was sent using IMP, the Internet Messaging Program.


This SF.Net email is sponsored by the Moblin Your Move Developer’s
challenge
Build the coolest Linux based applications with Moblin SDK & win great
prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/


Avogadro-devel mailing list
Avogadro-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-devel


Leandro A. Boscariol

On Friday 10 October 2008 15:25:16 Leandro Boscariol wrote:

Hi Jacob.

You told me the same thing that Geoff did before, and I did it again.
Removed everything, and installed again.

But I’ve found an old and forgotten link named libavogadro.so, pointing to
somewhere unknown.

Removed it, and now it works!

Thanks for your help guys!

Those stray links can be tough to track down. I remember when I was working on
some fixes for Avogadro, couldn’t understand why the fixes to the function
were not working until I realised I had a libavogadro in /usr/lib64 that was
taking priority over the one in /usr/local/lib64…

Glad you got it working again.