Installing Avogadro

General Discussion
1

Hi Jerry,

There’s a separate support list for Avogadro at avogadro-discuss (cc’ed on this message). On principal, I’d also suggest grabbing OB-2.2.3, since it has quite a few bug fixes.

There are two options for handling this.

  1. The current Avogadro releases use pkg-config to “fall back” when they can’t find packages. If you have it, just make sure /cluster/home/tanoury is included in the PKG_CONFIG_PATH, e.g.

export PKG_CONFIG_PATH=/opt/local/lib/pkgconfig:/usr/lib/pkgconfig:/usr/local/lib/pkgconfig:/cluster/home/tanoury/lib/pkgconfig

  1. Make sure to include -DOPENBABEL2_VERSION_MET=true as suggested in the wiki build instructions:

http://avogadro.openmolecules.net/wiki/Compiling_on_Linux_and_Mac_OS_X

Hope that helps,
-Geoff

Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoff.hutchison@gmail.com
web: http://hutchison.chem.pitt.edu/

From: Jerry_Tanoury@vrtx.com
Sent: Monday, August 16, 2010 8:22 AM
To: support@q-chem.com
Subject: Installing Avogadro

Hi,
I don’t know if you can help me with installing Avogadro on my Linux box, but it seems to be the preferred gui for running Q-Chem. The avogadro install script is having significant trouble finding openbabel. Here is what has happened:

[tanoury@tanourylnx:build]$ cmake -DCMAKE_INSTALL_PREFIX=/cluster/home/tanoury -DEIGEN_INCLUDE_DIR=/cluster/home/tanoury/eigen/Eigen -DCMAKE_INSTALL_DIR=/cluster/home/tanoury/lib -DOPENBABEL2_INCLUDE_DIR=/cluster/home/tanoury/include/openbabel-2.0 -DOPENBABEL2_LIBRARIES=/cluster/home/tanoury/lib/openbabel/2.2.2 …/
– The build type is Release
– Found lupdate: /cluster/home/tanoury/Trolltech/Qt-4.5.3/bin/lupdate
– Found lrelease: /cluster/home/tanoury/Trolltech/Qt-4.5.3/bin/lrelease
– Found lconvert: /cluster/home/tanoury/Trolltech/Qt-4.5.3/bin/lconvert
– Found ZLIB: /usr/include
– checking for module ‘openbabel-2.0>=2.2.2’
– package ‘openbabel-2.0>=2.2.2’ not found
CMake Error at cmake/modules/FindOpenBabel2.cmake:81 (message):
Could NOT find OpenBabel 2.2 or later
Call Stack (most recent call first):
CMakeLists.txt:131 (find_package)

– Configuring incomplete, errors occurred!

I have installed Qt-4.5.3, eigen and openbabel. Running “make check” with openbabel works.

Thanks,
Jerry

2

Hi Geoff,
I used option 2 and got it installed.

Thanks,
Jerry

From:
Geoffrey Hutchison geoff.hutchison@gmail.com
To:
Jerry_Tanoury@vrtx.com
Cc:
support@q-chem.com, avogadro-discuss@lists.sourceforge.net
Date:
08/16/2010 11:04 AM
Subject:
Re: Installing Avogadro

Hi Jerry,

There’s a separate support list for Avogadro at avogadro-discuss (cc’ed on
this message). On principal, I’d also suggest grabbing OB-2.2.3, since it
has quite a few bug fixes.

There are two options for handling this.

  1. The current Avogadro releases use pkg-config to “fall back” when they
    can’t find packages. If you have it, just make sure /cluster/home/tanoury
    is included in the PKG_CONFIG_PATH, e.g.

export
PKG_CONFIG_PATH=/opt/local/lib/pkgconfig:/usr/lib/pkgconfig:/usr/local/lib/pkgconfig:/cluster/home/tanoury/lib/pkgconfig

  1. Make sure to include -DOPENBABEL2_VERSION_MET=true as suggested in the
    wiki build instructions:

http://avogadro.openmolecules.net/wiki/Compiling_on_Linux_and_Mac_OS_X

Hope that helps,
-Geoff

Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoff.hutchison@gmail.com
web: http://hutchison.chem.pitt.edu/

From: Jerry_Tanoury@vrtx.com
Sent: Monday, August 16, 2010 8:22 AM
To: support@q-chem.com
Subject: Installing Avogadro

Hi,
I don’t know if you can help me with installing Avogadro on my Linux
box, but it seems to be the preferred gui for running Q-Chem. The
avogadro install script is having significant trouble finding openbabel.
Here is what has happened:

[tanoury@tanourylnx:build]$ cmake
-DCMAKE_INSTALL_PREFIX=/cluster/home/tanoury
-DEIGEN_INCLUDE_DIR=/cluster/home/tanoury/eigen/Eigen
-DCMAKE_INSTALL_DIR=/cluster/home/tanoury/lib
-DOPENBABEL2_INCLUDE_DIR=/cluster/home/tanoury/include/openbabel-2.0
-DOPENBABEL2_LIBRARIES=/cluster/home/tanoury/lib/openbabel/2.2.2 …/
– The build type is Release
– Found lupdate: /cluster/home/tanoury/Trolltech/Qt-4.5.3/bin/lupdate
– Found lrelease: /cluster/home/tanoury/Trolltech/Qt-4.5.3/bin/lrelease
– Found lconvert: /cluster/home/tanoury/Trolltech/Qt-4.5.3/bin/lconvert
– Found ZLIB: /usr/include
– checking for module ‘openbabel-2.0>=2.2.2’
– package ‘openbabel-2.0>=2.2.2’ not found
CMake Error at cmake/modules/FindOpenBabel2.cmake:81 (message):
Could NOT find OpenBabel 2.2 or later
Call Stack (most recent call first):
CMakeLists.txt:131 (find_package)

– Configuring incomplete, errors occurred!

I have installed Qt-4.5.3, eigen and openbabel. Running “make check”
with openbabel works.

Thanks,
Jerry