Need more info on "embedded Open Babel"

I’m working on distribution independent package of Avogadro for Linux. I’ve almost succeeded (most hard is to get OpenBabel load plugins properly, since it uses dlopen(). How simple things will be if LD_LIBRARY_PATH was enough…)

But I have some problems: 1)building requires a lot of manual work on copying files 2)Avogadro can’t initialize force fields, the same issue occured when I try to manually run ‘make test’ for OB

Maybe Avogadro+OB superpackage can help me? (But I still don’t know if it differs from Avogadro and OB separate building)
What is meant under “embedded Open Babel” (e.g., http://github.com/ghutchis/avogadro/commit/fff721bbc7f36976980c657f6f6d1f4dd5b0d051)?


Regards,
Konstantin

Maybe Avogadro+OB superpackage can help me? (But I still don’t know if it differs from Avogadro and OB separate building)
What is meant under “embedded Open Babel” (e.g., http://github.com/ghutchis/avogadro/commit/fff721bbc7f36976980c657f6f6d1f4dd5b0d051)?

The “superpackage” is how Avogadro is built on Mac and Windows. Both Avogadro and OB are built together and linked. Marcus should be able to provide a bit more detail, but the idea is to put everything in a directory tree together with relative paths for linking.

Hope that helps,
-Geoff

On Sun, Mar 21, 2010 at 12:39 PM, Konstantin Tokarev annulen@yandex.ru wrote:

I’m working on distribution independent package of Avogadro for Linux. I’ve almost succeeded (most hard is to get OpenBabel load plugins properly, since it uses dlopen(). How simple things will be if LD_LIBRARY_PATH was enough…)

But I have some problems: 1)building requires a lot of manual work on copying files 2)Avogadro can’t initialize force fields, the same issue occured when I try to manually run ‘make test’ for OB

The force fields failing is probably due to not finding the parameter
files. This can be fixed by defining BABEL_DATADIR IIRC.

Maybe Avogadro+OB superpackage can help me? (But I still don’t know if it differs from Avogadro and OB separate building)
What is meant under “embedded Open Babel” (e.g., http://github.com/ghutchis/avogadro/commit/fff721bbc7f36976980c657f6f6d1f4dd5b0d051)?


Regards,
Konstantin


Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev


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

The force fields failing is probably due to not finding the parameter
files. This can be fixed by defining BABEL_DATADIR IIRC.

I’ve tried, seems not to work (maybe absolute path is needed?)
However, atomic radii are loaded


Regards,
Konstantin

23.03.10, 18:54, “Tim Vandermeersch” tim.vandermeersch@gmail.com:

On Sun, Mar 21, 2010 at 12:39 PM, Konstantin Tokarev wrote:

I’m working on distribution independent package of Avogadro for Linux. I’ve almost succeeded (most hard is to get OpenBabel load plugins properly, since it uses dlopen(). How simple things will be if LD_LIBRARY_PATH was enough…)

But I have some problems: 1)building requires a lot of manual work on copying files 2)Avogadro can’t initialize force fields, the same issue occured when I try to manually run ‘make test’ for OB
The force fields failing is probably due to not finding the parameter
files. This can be fixed by defining BABEL_DATADIR IIRC.

Do you mean it must be defined when compiling Avogadro? is relative path acceptable?

Maybe Avogadro+OB superpackage can help me? (But I still don’t know if it differs from Avogadro and OB separate building)
What is meant under “embedded Open Babel” (e.g., http://github.com/ghutchis/avogadro/commit/fff721bbc7f36976980c657f6f6d1f4dd5b0d051)?


Regards,
Konstantin


Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev


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


Regards,
Konstantin

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

23.03.10, 11:18, “Geoffrey Hutchison” geoff.hutchison@gmail.com:

Maybe Avogadro+OB superpackage can help me? (But I still don’t know if it differs from Avogadro and OB separate building)
What is meant under “embedded Open Babel” (e.g., http://github.com/ghutchis/avogadro/commit/fff721bbc7f36976980c657f6f6d1f4dd5b0d051)?
The “superpackage” is how Avogadro is built on Mac and Windows. Both Avogadro and OB are built together and linked. Marcus should be able to provide a bit more detail, but the idea is to put everything in a directory tree together with relative paths for linking.

How to build superpackage? I’ve create build drectory and ran cmake, but it fails with error “Could NOT find OpenBabel 2.2 or later”


Regards,
Konstantin

files. This can be fixed by defining BABEL_DATADIR IIRC.
I’ve tried, seems not to work (maybe absolute path is needed?)
However, atomic radii are loaded

Some minimal amount of data is embedded into the libopenbabel binary itself. But if you aren’t able to access force fields, it’s quite clear that BABEL_DATADIR isn’t set correctly.

-Geoff

23.03.10, 18:54, “Tim Vandermeersch” tim.vandermeersch@gmail.com:

On Sun, Mar 21, 2010 at 12:39 PM, Konstantin Tokarev wrote:

I’m working on distribution independent package of Avogadro for Linux. I’ve almost succeeded (most hard is to get OpenBabel load plugins properly, since it uses dlopen(). How simple things will be if LD_LIBRARY_PATH was enough…)

But I have some problems: 1)building requires a lot of manual work on copying files 2)Avogadro can’t initialize force fields, the same issue occured when I try to manually run ‘make test’ for OB

The force fields failing is probably due to not finding the parameter
files. This can be fixed by defining BABEL_DATADIR IIRC.

Unfortunately, it doesn’t help. I’ve tryed relative nd absolute pathes, run avogadro with that variable or export it before. Nothing works


Regards,
Konstantin

Hi,

On Sat, Mar 27, 2010 at 6:05 PM, Konstantin Tokarev annulen@yandex.ru wrote:

23.03.10, 18:54, “Tim Vandermeersch” tim.vandermeersch@gmail.com:

On Sun, Mar 21, 2010 at 12:39 PM, Konstantin Tokarev wrote:

I’m working on distribution independent package of Avogadro for Linux. I’ve almost succeeded (most hard is to get OpenBabel load plugins properly, since it uses dlopen(). How simple things will be if LD_LIBRARY_PATH was enough…)

But I have some problems: 1)building requires a lot of manual work on copying files 2)Avogadro can’t initialize force fields, the same issue occured when I try to manually run ‘make test’ for OB

The force fields failing is probably due to not finding the parameter
files. This can be fixed by defining BABEL_DATADIR IIRC.

Unfortunately, it doesn’t help. I’ve tryed relative nd absolute pathes, run avogadro with that variable or export it before. Nothing works

The force fields use OpenDatafile (in tokenst.[h/cpp]). The
documentation in the cpp file describes how the function works. There
code checks both a env. var. BABEL_DATADIR and a compile time constant
also named BABEL_DATADIR (this is the one in the cpp file, the other
is in the header file as default to OpenDatafile’s 3th argument.

To get OpenDatafile to work with your build, adding some std::cout
statements to debug could always help.

In case the code looks for the file in the wrong place, you could
always modify the compile time path:

CMakeLists.txt (toplevel)

set(BABEL_DATADIR “${CMAKE_INSTALL_PREFIX}/share/openbabel”)

The variable is eventually set by generating babelconfig.h from
src/config.h.cmake

Tim


Regards,
Konstantin