Questions about Avogadro

Development
1

Hey guys, long time mailing the list.

So the other day I built Avogadro from scratch, starting off by downloading the latest Eigen and OpenBabel from code repositories. I built both successfully but had problems building Avogadro I originally chalked it up to being Eigen3 instead of Eigen2.

But then when I went back to Eigen2 and used the latest development version of OpenBabel, I still had problems building.

So then I went back to the latest releases for OpenBabel and Eigen2 and everything built nicely…. BUT…

I notice there were a lot of crashes on my end. I don’t know offhand what they relate to, but I have to guess it’s the development version of Avogadro that is having the problems. Because I downloaded the latest Avo release and things actually ran pretty smooth.

In the end my major questions are:

  1. is anyone working on migrating things to Eigen2?

  2. How does the 1.0 branch relate to the master branch?

  3. Who is the guy that put together the Mac build stuff. It is very nice – and maybe part of cmake ? – but it’s pretty cool. Though, I’d like to know more about how I should do development from a Mac. Should I be opening Avogadro.app that is in my build directory or should I be running the executable that is in Avogadro.app/Contents/MacOS?

  4. Am I missing a lot of documentation somewhere. The only thing I could find were my older docs about building the development version and some docs about building on Mac OSX which seemed to leave a bit to the imagination.

Thanks.

Also, is anyone planning to put up a Google Summer of Code for this project? I am wanting to put something together with a Chemistry prof here but I’m not sure what Google looks for. Is adding features that are relevant to education a big enough pull?

Hope all is well elsewhere.

–
Donald Curtis
d@milkbox.net
8231

Coe College
Department of Computer Science

2

On Sun, Feb 19, 2012 at 3:44 PM, Donald Ephraim Curtis
dcurtis@milkbox.net wrote:

Hey guys, long time mailing the list.

So the other day I built Avogadro from scratch, starting off by downloading the latest Eigen and OpenBabel from code repositories. I built both successfully but had problems building Avogadro I originally chalked it up to being Eigen3 instead of Eigen2.

Still using Eigen2.

But then when I went back to Eigen2 and used the latest development version of OpenBabel, I still had problems building.

So then I went back to the latest releases for OpenBabel and Eigen2 and everything built nicely…. BUT…

I am not tracking OB head, but any Eigen2 release should work just
fine. Geoff would know better on OB.

I notice there were a lot of crashes on my end. I don’t know offhand what they relate to, but I have to guess it’s the development version of Avogadro that is having the problems. Because I downloaded the latest Avo release and things actually ran pretty smooth.

In the end my major questions are:

  1. is anyone working on migrating things to Eigen2?

We are already on Eigen2.

  1. How does the 1.0 branch relate to the master branch?

1.0 forked when we released 1.0, it contains bug fixes and backports.
Master is what will be 1.1, if you look back in the mailing list a few
threads we are working on stabilizing master for a 1.1 release.

  1. Who is the guy that put together the Mac build stuff. It is very nice – and maybe part of cmake ? – but it’s pretty cool. Though, I’d like to know more about how I should do development from a Mac. Should I be opening Avogadro.app that is in my build directory or should I be running the executable that is in Avogadro.app/Contents/MacOS?

I did a lot of the build bundle stuff, when I did it the code only
worked on Macs. It has actually been generalized since, and will work
on Windows, Mac and Linux. Geoff does the Mac packaging (or at least
has done all of the previous Mac packages). I did some work getting
Mac builds to work out of the build tree, so you should be able to run
the app in the build tree. Opening Avogadro.app, or directly executing
the exe inside should both work.

If you have trouble you can always try a make install to see if it is
a build tree issue. I do some development on the Mac and don’t see
lots of crashes, I haven’t tried with Lion yet, but that should work.

  1. Am I missing a lot of documentation somewhere. The only thing I could find were my older docs about building the development version and some docs about building on Mac OSX which seemed to leave a bit to the imagination.

There are docs on the wiki we wrote, and they should be up to date.

http://avogadro.openmolecules.net/wiki/Building:Development_Version

Thanks.

Also, is anyone planning to put up a Google Summer of Code for this project? I am wanting to put something together with a Chemistry prof here but I’m not sure what Google looks for. Is adding features that are relevant to education a big enough pull?

We talked about this, but haven’t done anything yet. We do need to get
moving, I would like to establish how we want to apply.

Marcus

3

On Tue, Feb 21, 2012 at 10:41 AM, Marcus D. Hanwell
mhanwell@gmail.com wrote:

On Sun, Feb 19, 2012 at 3:44 PM, Donald Ephraim Curtis
dcurtis@milkbox.net wrote:

  1. Am I missing a lot of documentation somewhere. The only thing I could find were my older docs about building the development version and some docs about building on Mac OSX which seemed to leave a bit to the imagination.

There are docs on the wiki we wrote, and they should be up to date.

Sorry, I sent you the wrong link, and the one I meant is below,

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

I will add a note to the other page to say those instructions are out of date.

Marcus

4

Sorry, I meant Eigen3, not Eigen2.

On Feb 21, 2012, at 09:41, Marcus D. Hanwell wrote:

On Sun, Feb 19, 2012 at 3:44 PM, Donald Ephraim Curtis
dcurtis@milkbox.net wrote:

Hey guys, long time mailing the list.

So the other day I built Avogadro from scratch, starting off by downloading the latest Eigen and OpenBabel from code repositories. I built both successfully but had problems building Avogadro I originally chalked it up to being Eigen3 instead of Eigen2.

Still using Eigen2.

But then when I went back to Eigen2 and used the latest development version of OpenBabel, I still had problems building.

So then I went back to the latest releases for OpenBabel and Eigen2 and everything built nicely…. BUT…

I am not tracking OB head, but any Eigen2 release should work just
fine. Geoff would know better on OB.

I notice there were a lot of crashes on my end. I don’t know offhand what they relate to, but I have to guess it’s the development version of Avogadro that is having the problems. Because I downloaded the latest Avo release and things actually ran pretty smooth.

In the end my major questions are:

  1. is anyone working on migrating things to Eigen2?

We are already on Eigen2.

  1. How does the 1.0 branch relate to the master branch?

1.0 forked when we released 1.0, it contains bug fixes and backports.
Master is what will be 1.1, if you look back in the mailing list a few
threads we are working on stabilizing master for a 1.1 release.

  1. Who is the guy that put together the Mac build stuff. It is very nice – and maybe part of cmake ? – but it’s pretty cool. Though, I’d like to know more about how I should do development from a Mac. Should I be opening Avogadro.app that is in my build directory or should I be running the executable that is in Avogadro.app/Contents/MacOS?

I did a lot of the build bundle stuff, when I did it the code only
worked on Macs. It has actually been generalized since, and will work
on Windows, Mac and Linux. Geoff does the Mac packaging (or at least
has done all of the previous Mac packages). I did some work getting
Mac builds to work out of the build tree, so you should be able to run
the app in the build tree. Opening Avogadro.app, or directly executing
the exe inside should both work.

If you have trouble you can always try a make install to see if it is
a build tree issue. I do some development on the Mac and don’t see
lots of crashes, I haven’t tried with Lion yet, but that should work.

  1. Am I missing a lot of documentation somewhere. The only thing I could find were my older docs about building the development version and some docs about building on Mac OSX which seemed to leave a bit to the imagination.

There are docs on the wiki we wrote, and they should be up to date.

http://avogadro.openmolecules.net/wiki/Building:Development_Version

Thanks.

Also, is anyone planning to put up a Google Summer of Code for this project? I am wanting to put something together with a Chemistry prof here but I’m not sure what Google looks for. Is adding features that are relevant to education a big enough pull?

We talked about this, but haven’t done anything yet. We do need to get
moving, I would like to establish how we want to apply.

Marcus

5

Sorry, I meant Eigen3, not Eigen2.

IIRC, Open Babel trunk should compile with Eigen 3, but I don’t think we’ve done anything towards Avogadro.

BTW, it might be good to at least detect Eigen3 and use a staged support mode for Avogadro:
http://eigen.tuxfamily.org/dox/Eigen2SupportModes.html

This way, people don’t have to instal Eigen2 if they already have v3.

-Geoff