Build problems

I’m new to Avogadro, and never will become a veteran at the rate I’m
going! I download version 1.0.1 (also 1.0, with identical results),
built the executable using the simple method described in INSTALL –
with no indication of errors or problems. I’m running Ubuntu 9.10 - 64
bit on an AMD quad core cpu and Nvidea GTX275 graphics (ought to be
pretty standard.)

The programs starts find, in the gui window. But the simplest of
operations fail: e.g when I try to open an existing cml file, I am
unable to, because the file exploration window that comes up doesn’t
allow to descend into the subdirectories of my home directory.
(Curiously, clicking the “recent files” entry brings up the canned
example file okay – but then other operations go wrong.)

Clearly the python modules are not interacting properly with my
operating system, though no explicit error messages are returned to help
trouble-shoot. Generally, my system seems functional: e.g. the whole
VMD/NAMD suite works well, as do other python-based applications.

Any hints what’s wrong? Surely other people use Avogadro on
Ubuntu-9.10-amd64 without problem.

Thanks,

Bob Wohlhueter

On May 6, 2010, at 11:24 AM, Robert Wohlhueter wrote:

unable to, because the file exploration window that comes up doesn’t
allow to descend into the subdirectories of my home directory.

What version of Qt are you using? This doesn’t sound like an Avogadro problem.

Clearly the python modules are not interacting properly with my
operating system, though no explicit error messages are returned to help
trouble-shoot.

Can you give us some more details here?

Also, have you tried the pre-packaged Avogadro packages?
http://avogadro.openmolecules.net/wiki/Distribution_Packages#Ubuntu
https://launchpad.net/~debichem/+archive/ppa

I’d like to know if it’s a Qt problem, a problem with your compiled Avogadro, etc.

The Python issues are separate. Let’s follow those in a different message thread.

Sorry you’re having trouble,
-Geoff

Bob,

As I mentioned in my previous message, have you tried the pre-compiled Avogadro binaries for Ubuntu? Do you have similar problems (e.g., choosing a file) with other Qt or KDE programs?

I’m afraid I can’t personally help you much, since I don’t use Ubuntu. But perhaps others on the list can help?

-Geoff

On May 7, 2010, at 8:00 AM, Robert Wohlhueter wrote:

Geoff,

Like you I suspect the problem is not in the Avogadro code itself, but in the underlying “support” on my Linux machine. My problem is that I have only the vaguest notion of what support Avogadro needs.

As for Qt, what I have is straight off the Synaptic Package Manager (I’m running Ubuntu 9.10-6bit on an AMD cpu). “Qt” - as one sees in Synaptic - has a thousand components; predominantly I’m seeing version 4.5.3 (for packages libqt4-qt3-support, libqt4-scripttools, qt4-qtconfig, qt4-designer, qt4-devtool, libqt4-designer, qt4-make, libqt4-opengl-dev, libqt4-opengl, libqt4-core4, libqt-gui4) from Ubuntu.

Does that provide any clues to you?

Thanks for the help,

Bob W.

Like you I suspect the problem is not in the Avogadro code itself,
but in the underlying “support” on my Linux machine. My problem is
that I have only the vaguest notion of what support Avogadro needs.

As for Qt, what I have is straight off the Synaptic Package Manager
(I’m running Ubuntu 9.10-6bit on an AMD cpu). “Qt” - as one sees
in Synaptic - has a thousand components; predominantly I’m seeing
version 4.5.3 (for packages libqt4-qt3-support, libqt4-scripttools,
qt4-qtconfig, qt4-designer, qt4-devtool, libqt4-designer, qt4-make,
libqt4-opengl-dev, libqt4-opengl, libqt4-core4, libqt-gui4) from
Ubuntu.

Does that provide any clues to you?

Thanks for the help,

Bob W.

One universal way of checking dependencies on almost any Unix-like
system: ldd command. Type man ldd to find more information.

Basic usage: ldd -r /usr/local/bin/avogadro
(replace path to avogadro with path on your system. Command “which
avogadro” will help you if you’re in doubt

It’ll type all libraries Avogadro needs. If something is missing,
you’ll see “not found” message(s)

If you’ve installed Avogadro from package (.deb), it can’t install
without all required dependencies (dpkg will fail). If maintainer
missed some dependencies, feel free to throw thunder into him :slight_smile:


Regards,
Konstantin

Hi Robert,

If the Ubuntu package has the same problem, I’d suggest filing an Ubuntu / Kubuntu bug report for this. I’m not sure the cause, but we use the normal Qt open file methods so it seems to be a non-Avogadro bug. That said, I want to see if we can help you fix it.

Are there any newer Qt packages for Ubuntu? Maybe Qt-4.6.x?

Don’t worry about the “errors” from the command-line these are warnings. They come up for many users without any problems.

Thanks,
-Geoff

On May 7, 2010, at 7:49 PM, Robert Wohlhueter wrote:

Geoff,

Okay, I have apt-get’ed the distribution from ppa.lauchpad.net, indeed the one specifically for Ubuntu “Karmic” 9.10 on AMD64 architecture. Exactly the same problem. (The “open file” window does not display, and therefore one cannot select, e.g. cml files to open. Curiously, the “recently opened” window shows the canned example trifluoroethanol cml, which does open, and can be manipulated in the main window.)

Other KDE applications run and their “open file” windows behave properly. Qt-designer and Qt-creator also behave properly (I guess they are “Qt programs”; I’m not sure how to recognize other Qt apps.)

Konstantin Tokarev had suggested I try checking dependencies with ldd: all seem to be satisfied (I attach the output from ldd, in case you want to look.)

When I start Avogadro from the command line (as opposed to the Ubuntu “main menu”), I get a error report:

bobw@winter-linux: ~…build/bin (29%)> ./avogadro
./avogadro
QStackedLayout::setCurrentWidget: Widget 0x27c1b00 not contained in stack
libpng warning: Ignoring attempt to set cHRM RGB triangle with zero area

Does that provide you a lead?

Thanks,

Bob W.

Hi, Robert
if your Ubuntu installation is 64-bit, you can try binary from this
place (experimental!):


Regards,
Konstantin