Github prolem

Development
1

Hi all.

I updated the GitHub version of avogadro this morning.
The program compiles O.K., but fails opening files
with “Reading molecule file failed”. The svn version 1873
works. Both versions compiled with openbabel v2.2.0
and a recent version of Eigen2 on an Intel Mac.

Should I move to a more recent openbabel version?

Louis

2

Hi Louis,

The program compiles O.K., but fails opening files
with “Reading molecule file failed”.

Can you be a little more precise? What file types have you tried? If
you run “babel -H” do you get back all the formats?

Should I move to a more recent openbabel version?

Certainly you can do that. I’ve been using the 2.2.x branch and
obviously there are a number of bug fixes. But it shouldn’t cause (or
fix) this issue.

Thanks for reporting it – I hope we can track it down ASAP.
-Geoff

3

Geoffrey Hutchison wrote:

Hi Louis,

The program compiles O.K., but fails opening files
with “Reading molecule file failed”.

Can you be a little more precise? What file types have you tried? If
you run “babel -H” do you get back all the formats?

This seems to have hit a few people over the last few weeks, but I
haven’t been able to reproduce it.

Should I move to a more recent openbabel version?

Certainly you can do that. I’ve been using the 2.2.x branch and
obviously there are a number of bug fixes. But it shouldn’t cause (or
fix) this issue.

Thanks for reporting it – I hope we can track it down ASAP.

I am using the released OpenBabel 2.2.0 provided by my distro. At work I
am using a checkout of the branch I think. Both seem to work on Linux at
least. Hopefully we can solve the issue.

Happy New Year too!

Thanks,

Marcus

4

Hi Louis,

I’m facing that problem as well.

Currently that bug is tracked here:
http://sourceforge.net/tracker/index.php?func=detail&aid=2468621&group_id=165310&atid=835077

If you think something is missing, you might add some further
details …

I use the latest OB 2.2 branch from svn.

Bye

Simon

5

Hi Geoff

I have tried reading xyz, cif and fchk. All of them failed, but work
with the svn version. Under Fedora 10, the git version works
with all the formats I tried. I also noted a difference in the orbitals
menu : the “Van der Walls” panel is not showing up on the Mac.

And yes, “babel -H” returns all formats.

Louis

Le 1 janv. 09 à 18:19, Geoffrey Hutchison a écrit :

Can you be a little more precise? What file types have you tried? If
you run “babel -H” do you get back all the formats?

-Geoff

6

Hi Geoff.

Following Carsten’s last message, I git-pulled again:
“Updating 4142afd…4e50ebe”.

Trying to compile avo against openbabel trunk version 2798
produces the same errors as those already reported by Simon,
but using openbabel2.2.0 is O.K… Moreover, all menu items
that were missing earlier this morning (unit cell, gamess, …)
are now present.

Cheers,

Louis

Le 2 janv. 09 à 08:48, Louis Ricard a écrit :

Hi Geoff

I have tried reading xyz, cif and fchk. All of them failed, but work
with the svn version. Under Fedora 10, the git version works
with all the formats I tried. I also noted a difference in the
orbitals
menu : the “Van der Walls” panel is not showing up on the Mac.

And yes, “babel -H” returns all formats.

Louis

Le 1 janv. 09 à 18:19, Geoffrey Hutchison a écrit :

Can you be a little more precise? What file types have you tried? If
you run “babel -H” do you get back all the formats?

-Geoff

Avogadro-devel mailing list
Avogadro-devel@lists.sourceforge.net
avogadro-devel List Signup and Options

7

Hi Louis,

Trying to compile avo against openbabel trunk version 2798

Well, I wouldn’t compile against OB trunk. I’m compiling against OB
branch 2.2.x.

But your comment leads me to a question. How are you compiling OB? Are
you using ./configure; make or Cmake? (I’ve continued to use autoconf
for OB 2.2.x)

What happens when you run “babel -H” from the command-line? Better
yet, if you choose “File > Import > Molecule File…” what do you see
in the formats combo box?

Thanks,
-Geoff

8

Hi Geoff

Trying to compile avo against openbabel trunk version 2798

Well, I wouldn’t compile against OB trunk. I’m compiling against OB
branch 2.2.x.

Well, you told me that some weeks ago and using OB 2.2.0
did solve the problem on my Intel Mac.

But your comment leads me to a question. How are you compiling OB? Are

you using ./configure; make or Cmake? (I’ve continued to use autoconf
for OB 2.2.x)

Recently, I have been using cmake for all versions, including OB 2.2.0
on the Mac as well as under Linux.

What happens when you run “babel -H” from the command-line? Better
yet, if you choose “File > Import > Molecule File…” what do you see
in the formats combo box?

“babel -H” displays all formats. Similarly, “File Import Molecule
File” displays
everything. When invoked with the default “Autodetect from extension” =
“Reading molecular file failed”. If selected say xyz, same error.

I am puzzled by the fact that the Linux version compiles and runs
correctly
when compiled against any OB trunk version (I tried 2798 and the current
one, forgot the version).

Louis

9

Louis Ricard wrote:

Hi Geoff

Trying to compile avo against openbabel trunk version 2798

Well, I wouldn’t compile against OB trunk. I’m compiling against OB
branch 2.2.x.

Well, you told me that some weeks ago and using OB 2.2.0
did solve the problem on my Intel Mac.

But your comment leads me to a question. How are you compiling OB? Are

you using ./configure; make or Cmake? (I’ve continued to use autoconf
for OB 2.2.x)

Recently, I have been using cmake for all versions, including OB 2.2.0
on the Mac as well as under Linux.

CMake should work on the Mac and Linux - any development work I have
done on the Mac has used CMake to compile OpenBabel. That said CMake has
received less testing and I haven’t really been using any Macs in the
last few months for any period of time…

10

Marcus.

Presently installed OB 2.2.99. Compiled using cmake 2.6.0
I tried a few common file format conversion from the command
line and they all behave correctly. ???

Louis

Le 2 janv. 09 à 16:33, Marcus D. Hanwell a écrit :

Louis Ricard wrote:

Hi Geoff

Trying to compile avo against openbabel trunk version 2798

Well, I wouldn’t compile against OB trunk. I’m compiling against OB
branch 2.2.x.

Well, you told me that some weeks ago and using OB 2.2.0
did solve the problem on my Intel Mac.

But your comment leads me to a question. How are you compiling OB?
Are

you using ./configure; make or Cmake? (I’ve continued to use
autoconf
for OB 2.2.x)

Recently, I have been using cmake for all versions, including OB
2.2.0
on the Mac as well as under Linux.

CMake should work on the Mac and Linux - any development work I have
done on the Mac has used CMake to compile OpenBabel. That said CMake
has
received less testing and I haven’t really been using any Macs in the
last few months for any period of time…

Avogadro-devel mailing list
Avogadro-devel@lists.sourceforge.net
avogadro-devel List Signup and Options

11

Louis Ricard wrote:

Marcus.

Presently installed OB 2.2.99. Compiled using cmake 2.6.0
I tried a few common file format conversion from the command
line and they all behave correctly. ???

Louis

Hi Louis,

I can test further when I am in work on Monday and have access to the
Intel iMac. I don’t have any Mac equipment at home. At home I am just
using OpenBabel 2.2.0 release on 64 bit Linux. You can now download the
latest CMake and use that on the Mac, but it shouldn’t be hurting you
using an older one.

As far as I was aware switching to the OpenBabel 2.2 branch was fixing
this issue when people hit it. I think it would be worth trying the
autotools (./configure, make) approach if CMake is still not working.
Geoff is the real OpenBabel expert on here. As far as I knew if babel
knew its file formats then we should be able to use them too.

Thanks,

Marcus

12

Hi Louis,

Well, you told me that some weeks ago and using OB 2.2.0
did solve the problem on my Intel Mac.

OK, so let me see if I can summarize. OB-2.2.0 works, but not trunk or
branch? And in all cases, you’ve been compiling OB by cmake?

“babel -H” displays all formats. Similarly, “File Import Molecule
File” displays
everything. When invoked with the default “Autodetect from
extension” =
“Reading molecular file failed”. If selected say xyz, same error.

That’s strange. If you use babel on the command-line, I assume you can
convert files fine? It’s just reading files in Avogadro?

I am puzzled by the fact that the Linux version compiles and runs
correctly
when compiled against any OB trunk version (I tried 2798 and the
current
one, forgot the version).

Well, linking libraries is very different on Mac and Linux. (It’s one
of the few differences.) So it’s strange, but not impossible to
believe. Since I can’t reproduce the bug, I’m trying to narrow down
the source of the problem.

Thanks very much,
-Geoff

13

Hi Geoff.

Well, you told me that some weeks ago and using OB 2.2.0
did solve the problem on my Intel Mac.

OK, so let me see if I can summarize. OB-2.2.0 works, but not trunk or
branch? And in all cases, you’ve been compiling OB by cmake?
Absolutely correct.
Actually, I tried only the trunk versions.
Here is a command line session:

"macbook-de-louis-ricard:gautest ricard$ babel --version
No output file or format spec!
Open Babel 2.2.99 – Jan 2 2009 – 10:36:41
Usage: babel [-i] [-o]
Try -H option for more information.
macbook-de-louis-ricard:gautest ricard$ babel cysteine.xyz cysteine.pdb
1 molecule converted
17 audit log messages
macbook-de-louis-ricard:gautest ricard$ cd …/ah075/
macbook-de-louis-ricard:ah075 ricard$ babel ah075.res ah075.xyz
1 molecule converted
17 audit log messages
macbook-de-louis-ricard:ah075 ricard$ babel ah075.cif ah075.pdb
WARNING: did not understand :
1 molecule converted
19 audit log messages 1 debugging messages
macbook-de-louis-ricard:ah075 ricard$ "

Woks fine, but for the warning with cif file. The pdb is correct.

That’s strange. If you use babel on the command-line, I assume you can
convert files fine? It’s just reading files in Avogadro?

Exactly.

I now have two versions : OB2.2.0 and trunk 2798.
When I recompile, I delete all files in the openbabel and avogadro
library
tree and reinstall OB before recompiling Avo.
Strange that you are unable to reproduce this.
You probably have seen this from Simon?
http://sourceforge.net/tracker/index.php?func=detail&aid=2468621&group_id=165310&atid=835077

Louis