Installation issues


VNL/ATK very slow to start on Windows

Some users have experienced that ATK or VNL can be very slow (several minutes) to start up on Windows, when you are not Administrator on the machine. It is not actually necessary to be administrator to run ATK, but if you are not, the license system may try very hard to write a lock file to the C:\Windows\Temp directory, to which it then does not have permissions.

The solution is to remove the directory C:\Windows\Temp\x-formation (as Administrator, of course), and then run ATK or VNL as the regular user. The directory will then be recreated with more suitable priviledges.

Note: VNL can sometimes be a bit slow to start after an upgrade, or if you have large projects with many files, or when using a demo license for the first time. The case where the above solution is relevant is only where startup takes really long time, like 3-5 minutes or more.

libgomp.so.1: cannot open shared object file: No such file or directory

If the error message

ImportError: libgomp.so.1: cannot open shared object file: No such file or directory.

appears when you try to launch VNL, fix it by running

apt-get install libgomp1

This error typically appears on Ubuntu version 14.04 and later, where this library is not installed by default, as it was in earlier versions.

libjpeg.so.62: cannot open shared object file: No such file or directory

If the error message

ImportError: libjpeg.so.62: cannot open shared object file: No such file or directory

appears when you try to launch VNL, fix it by running

sudo apt-get install libjpeg62

This error typically appears on Ubuntu version 12.04 and later, where this library is not installed by default, as it was in earlier versions.

"Side-by-side" configuration error

When running ATK on Windows 2008 Server edition (possibly also Windows 2010 Server), some users have experiened problems with the "side-by-side configuration". The error message reads:

The application has failed to start because its side-by-side configuration is incorrect.

To resolve this, download and install the relevant package in the list below:

Some links to additional information:

 

Segmentation fault when running (Linux)

If you get a segmentation fault while trying to run atkpython or vnl after installation, a solution might be to add the line

export LD_PRELOAD="libGLU.so libstdc++.so.6"

or perhaps just

export LD_PRELOAD="libstdc++.so.6"

to your .bashrc file (in your home directory). We have seen this helps on Debian, Redhat 6.5 (and 6.2), and a few other platforms.

Command not found (Linux)

If you get the error message "Command not found" when trying to run "vnl" or "atkpython" from a terminal window after installing ATK, then first of all try to close the terminal window and open a new one; this is needed for changes to the PATH and license environment variables to take effect.

If the problem persists, there are primarily two possibilities:

  1. ATK was installed by a different user, e.g. root. In this case you must set up the PATH manually to include the atkpython/bin and vnl/bin directories in the ATK installation directory.
  2. If you are using tcsh (or any other shell than bash), you must also manually define the PATH (and license environment variables) in .tcshrc (or similar for your particular shell). Type "echo $SHELL" to find out which shell you are using.

In both cases you need to restart the terminal for the changes to take effect. Check that the relevant ATK directories are in your PATH by typing "echo $PATH".

Cannot start VNL from the desktop icon, after installing

Linux

Solution: Log out and back in.

Why? During installation, the license configuration is written to the file .profile in your home directory. The Desktop only reads this file on login, however. If you prefer not to log out, for the moment, you can still launch VNL by opening a (new) terminal window and type "vnl".

 

Windows (should only appear in ATK 2014)

Solution: Right-click the desktop icon and choose Properties. Check the "Start in" folder - it should be the same folder as where vnl.exe resides, i.e. the "bin" directory in the installation folder. If not, VNL will not start.

Why? Kind of a bug in ATK 2014.x, some Qt libraries are in the "bin" folder. We will move them to the native Qt location for the 2014.2 bug fix release, and then you can set the Start in folder to anything you want.

 

libpng12.so.0: cannot open shared object file

On some Linux distributions, like OpenSUSE, the default version of the libpng library is different from what ATK needs.

If you get the error message

ImportError: libpng12.so.0: cannot open shared object file: No such file or directory

when launching VNL, you need to install libpng12.so (most likely you have libpng14.so, in /usr/lib).

To install the older library version, launch the package manager Yast2 (as root/admin) and search for "libpng". In the list of matches, pick and install the "libpng12-0" package.

Note: The two library versions libpng12 and libpng14 do not conflict and can safely be installed side-by-side.

libGLU.so.1: cannot open shared object file

The error message

ImportError: libGLU.so.1: cannot open shared object file: No such file or directory

may appear on Linux systems when you try to launch VNL for the first time.

To solve it, install the related OpenGL utility library:

  • on Ubuntu: apt-get install libglu1-mesa
  • on openSuSe: install libGLU1
  • on Fedora: install mesa-libGLU

libGL.so: cannot open shared object file

The error message

OSError: libGL.so: cannot open shared object file: No such file or directory

may appear on Linux systems when you try to launch VNL for the first time.

To solve it, create (as administrator) a new link in /usr/lib:

sudo ln -s /usr/lib/libGL.so.1.2 /usr/lib/libGL.so

If you have a 64-bit Linux, use /usr/lib64 instead.

However, first check that you actually have "libGL.so.1.2" in /usr/lib or /usr/lib64; it might be called "libGL.so.1" or something else instead, or located in another directory, depending on the video drivers. You can use

locate libGL

to find the correct file to link to.

On some systems we have seen that the same link needs to be created for libGLU.so as well. Note that in this case, the error message may still complain about libGL.so!

Cannot restore segment prot after reloc: Permission denied

When launching ATK for the first time, you may experience the following kind of error message:

QT ('Not available', '/home/user/atk/atkpython/lib/python2.6/site-packages/qtext.so: cannot restore segment prot after reloc: Permission denied')

The cause of this error are the new kernel security extensions from the Security-Enhanced Linux (SELinux) project, which are enabled in some newer Linux distributions, to allow finer-grained control over system security and shared library loading.

The solution is to register the relevant libraries in the security module to allow them to be relocated in memory. For each library for which the error appears, do

chcon -t texrel_shlib_t lib.so

where lib.so is the offending file.

Send To button stops working on Ubuntu

On Ubuntu 12.04 and later, you may experience that the "Send To" button in VNL 12.8.0 only works once - after that it stops responding to clicks. To fix this, follow these steps:

  1. From the command line, run: qtconfig.
    • This program may not be installed, in which case it will give some suggestions, like qt3-config and qt4-config.
    • If so, install at4-config (ATK uses Qt 4.8) using the command
      sudo apt-get install qt4-config
    • Now qtconfig should start
  2. Under GUI style, select "Cleanlooks"
  3. Save the setup File>Save
  4. Exit qtconfig.
  5. Start VNL again

Hopefully the problem is now resolved. We are working on a more proper solution for upcoming versions of VNL, however this is really a bug in Qt, so there's only so much we can do.

 

VNL problems on Ubuntu

VNL has problems on Ubuntu, like fails to start up, or freezes immediately after startup, or is unable to show the 3D graphics windows properly.

Solution:

  1. Disable "compiz" and use the Ubuntu Classic window manager without effects (detailed instructions).
  2. Run "qtconfig" and select GUI Style = "Cleanlooks" (or something else - just not "GTK+")

You may need to apply both - or only one - of these fixes, depending on your setup.

Notes

There are many reported problems on the incompatibility between compiz and Qt apps, so this is not something we can fix in VNL. See for example:

  • http://stackoverflow.com/questions/14128259/compiz-and-opengl-window
  • https://bugs.launchpad.net/ubuntu/+source/compiz/+bug/204238

GLIBC_2.4 not found

ATK 11.2 and higher is expected to run almost any newer Linux distribution, whether they use GLIBC 2.3 or 2.4. For ATK 10.8, there are however separate versions for GLIBC 2.3 and 2.4, so make sure to pick the relevant version for your platform.

Firewall issues

The LM-X license server by default communicates on TCP port 6200. This port must be opened on any firewalls separating the client and the license server. You can also open UDP port 6200 in order for the server to automatically broadcast its presence on the network.

Here are some links with information about how to open ports in firewalls for different platforms.

Windows
http://windows.microsoft.com/en-us/windows/open-port-windows-firewall

Linux
http://www.wikihow.com/Open-Ports-in-Linux-Server-Firewall
http://www.cyberciti.biz/faq/linux-iptables-firewall-open-port-80/
(the instructions are for different ports, you should of course open TCP and possibly UDP ports 6200, both inbound and outbound).

Mac OS X
http://www.macinstruct.com/node/165

 

No module named ipy_user_conf

If you enter ATK in interactive mode (i.e., if you just  type "atkpython" on the command line), you may be greeted with a rather lengthy message, asking you to "upgrade":

ImportError        Traceback (most recent call last)
/opt/QuantumWise/atk-10.8/atkpython/lib/site-packages/IPython/ipmaker.pyc in force_import(modname, force_reload)
     61         reload(sys.modules[modname])
     62     else:
---> 63         __import__(modname)
     64
     65

ImportError: No module named ipy_user_conf
WARNING: /home/username/ipy_user_conf.py does not exist, please run %upgrade!
WARNING: Loading of ipy_user_conf failed.

As the message suggests, enter the command (while you are still in ATK)

%upgrade

to resolve the issue.

The reason is that an existing configuration from a previous version of IPython (either an older ATK or another Python) exists for the user account. Upgrading in this way will not interfere with those older versions.

Segmentation fault (VNL closes down when clicking an icon)

The symptoms of this error - which only should appear on Linux for ATK 10.8 - is that VNL launches fine, and you can open the Editor and Analyzer, but any attempt to open an instrument with a 3D viewport (like, the Builder, Viewer, Database, etc) results in VNL shutting down immediately.

If you are running from the command line, you will probably see a "Segmentation fault" error message.

The problem is caused by the video driver, specifically the OpenGL drivers, which doesn't support proper 3D manipulations. Most likely you are using Mesa drivers, which can be verified by running "glxinfo | grep -i mesa".

The solution is to upgrade to a newer version of ATK (11.2 or later), or upgrade your drivers to the vendor-specific ones from NVIDIA, ATI, etc, as relevant for your graphics card. The latter is always a good idea even for newer ATK versions, since it will enhance the 3D graphics performance significantly.

ImportError: DLL load failed: The specified procedure could not be found.

When using version 2014 on Windows, you may have problems running ATK/VNL or starting calculations in the Job Manager inside VNL, and it shows the following error:

Traceback (most recent call last):
  File "", line 1, in
  File ".\zipdir\NL\__init__.py", line 5, in
  File ".\zipdir\NLEngine.py", line 36, in
  File ".\zipdir\NLEngine.py", line 18, in swig_import_helper
ImportError: DLL load failed: The specified procedure could not be found.
This is caused by having multiple versions of ATK installed at the same time. That's in principle possible, but exactly in the 2014 version (not 13.8, and not 2015 or later), ATK resolves the DLL location by the PATH environment variable, which means that the 2014.x "bin" directory must come first in the path, before any other ATK bin directory.
Since the directory is added last to the path upon installation, the issue typically only occurs if you have 13.8 or an older 2014.x version installed. The easiest solution is therefore to uninstall all older versions, or at least remove them from your PATH, then all should work fine. If you want to keep 13.8 (you really should not keep 2014.2 if you install 2014.3), you must ensure the 2014 version "bin" directory comes before the 13.8 bin directory in the PATH. If you have access to 2015 or later, you might as well uninstall both 13.8 and 2014 and just use the newer version!

For instructions on editing the PATH on Windows, see e.g. http://www.computerhope.com/issues/ch000549.htm.

 

Could not find or load the Qt platform plugin "xcb"

If the error message

This application failed to start because it could not find or load the Qt platform plugin "xcb".
 
Reinstalling the application may fix this problem.

Aborted (core dumped) 
 
appears when you try to launch VNL, fix it by running
 
apt-get install libx11-xcb1
 
This error typically appears on (K)Ubuntu version 10.10 or older.

Interactive mode prints black on black in Windows 8 and 10 (ATK 2015)

If you run "atkpython" in interactive mode, and if you are using ATK version 2014 and 2015, you may experience that the text color is set to black, so you can't see anything. It does not help to change the text color, or background color.

Apparently Microsoft has made some small changes to the console API in Windows 8 and 10, and these changes are only included in pyreadline 2.1, to which we have upgrade for ATK 2016. But as a workaround in ATK 2014 and 2015, you will need to download this patched version of console.py and place it in

C:\Program Files (x86)\QuantumWise\VNL-ATK-2015.1\lib\site-packages\pyreadline\console