Empty MarvinSpace window in Linux 64bit

Hi,

regardless of the way I start MarvinSpace (from MarvinSketch or from the cmdline) and after I load a molecule into it (e.g. from the PDB), the molecule windows stays completely black, no molecule is displayed.

I am using Linux 64 bit (Arch Linux) on a laptop, with this Java version:

java version "1.7.0_09"
OpenJDK Runtime Environment (IcedTea7 2.3.4) (ArchLinux build 7.u9_2.3.4-1-x86_64)
OpenJDK 64-Bit Server VM (build 23.2-b09, mixed mode)

 

This is what I get when I start mspace from the cmdline:

[bin]$ sh mspace -v
JOGL specification version 2.0
JOGL implementation version 2.0-b58-20120620
JOGL implementation vendor JogAmp Community
libEGL warning: failed to create a pipe screen for i965
sun.java2d.noddraw: true
jogl.GLContext.noopt: true
sun.awt.noerasebackground: true
OpenGL2 Renderer = Mesa DRI Intel(R) Sandybridge Mobile
OpenGL2 Version = 3.1 Mesa 9.0.2
OpenGL2 Vendor = Intel Open Source Technology Center
Initialize draw, setting projection matrices:  >>>  invalid operation  <<<  
Initialize draw, setting projection matrices:  >>>  invalid operation  <<<  
Initialize draw, setting projection matrices:  >>>  invalid operation  <<<  
Initialize draw, setting projection matrices:  >>>  invalid operation  <<<  
Initialize draw, setting projection matrices:  >>>  invalid operation  <<<  
Initialize draw, setting projection matrices:  >>>  invalid operation  <<<

 

I should mention that other Java apps like Knime or Nixnote run fine and also MarvinSketch runs perfectly.

Any help is very much appreciated.

Many thanks in advance.

Axel

Dear Axel!

   I think OpenJDK can be the problem. Could you try to reinstall Marvin, but this time "Linux Installer with Java", to test it with the Oracle JRE?

Regards:
Balázs 

Hi Balázs,

thanks for your help.

Unfortunately, the Linux version with Java does not solve my problem.
In fact, in this version I am not able to run any Marvin apps, instead I just
get the following error:

[progs]$ cd marvin/bin/
[bin]$ sh mspace -v
Exception in thread
"main" java.lang.UnsatisfiedLinkError:
/home/xxxxx/.i4j_jres/1.6.0_33_x86/lib/i386/xawt/libmawt.so:
libXtst.so.6: cannot open shared object file: No such file or directory
        at java.lang.ClassLoader$NativeLibrary.load(Native Method)
        at java.lang.ClassLoader.loadLibrary0(Unknown Source)
        at java.lang.ClassLoader.loadLibrary(Unknown Source)
        at java.lang.Runtime.load0(Unknown Source)
        at java.lang.System.load(Unknown Source)
        at java.lang.ClassLoader$NativeLibrary.load(Native Method)
        at java.lang.ClassLoader.loadLibrary0(Unknown Source)
        at java.lang.ClassLoader.loadLibrary(Unknown Source)
        at java.lang.Runtime.loadLibrary0(Unknown Source)
        at java.lang.System.loadLibrary(Unknown Source)
        at sun.security.action.LoadLibraryAction.run(Unknown Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at sun.awt.NativeLibLoader.loadLibraries(Unknown Source)
        at sun.awt.DebugHelper.<clinit>(Unknown Source)
        at java.awt.Component.<clinit>(Unknown Source)
Could not find the main class: chemaxon.marvin.space.gui.MSpace.  Program will exit.

 

But this probably a separate issue.

Are there any further ideas on how to get the original version to
work, in which, as I mentioned, the other Marvin apps like Sketch and
also the 3d viewer just run fine!

Many thanks again.

Kind regards,

Axel

Hi Axel,

 

Which version of Marvin do you use?

In any case I suggest upgrading to the latest one.

Blank screen may appear on Linux machines when there's no 3D acceleration enabled/available:

Please make sure to install the latest graphic card drivers with 3D support (the built in drivers usually don't have

3D acceleration infrastructure).

 

Also, JRE 1.7 not officially supported yet.

Regards,

Andras

Hi Andras,

I am running marvinbeans 5.11.4 and 3d acceleration is enabled, similar programs like PyMOL, run fine ( I mean, I know that I do not have a great graphics card in my laptop, but nonetheless..).

Thanks for your help.

Kind regards,

Axel

Are you absolutely sure 3d - hardware - acceleration is enabled?

Let me clarify it:

You can still 3D with software rendering in other software, but post-8.03 Mesa  
software renderer libaries produces this blank screen effect with JOGL2/MarvinSpace.
So hardware acceleration is a must.

I can't decide software or hardware rendering is used based on the command line info you pasted.
But, the line 'libEGL warning: failed to create a pipe screen for i965'
suggest, the rendering might be fallen back to software.

Could you send the result of the 'glxinfo' command?
Enter this into a shell:
LIBGL_DEBUG=verbose glxinfo

I attached my result with software/hardware rendering.

Dear Andras,

I have attached the output of the glxinfo command.

It seems ok to me.

 

Could you enter the following in a shell:

EGL_LOG_LEVEL=debug

then run marvinspace in the shell.

Please attach the results.

Tnahks,

Andras

Dear Andras,

please find the result  attached.

Many thanks for your help.

Axel

Hi,

It seems libEGL has some problems initializing the screen on your machine.

You should eliminate this problem beforhend and see if it helps.

I
suggest, you should change the video-card driver from this open-source
to a proper one, for example the official (if there is). Maybe it will
help.

Otherwise, I'm afraid we cannot support your environment in this state.

 

I have last advice:

I attached the latest Jogl2 libraries you might try (replace appropriate files in the Marvin directory).

Maybe, they contain workaround for this case, but I'm not convinced it would help.

 

Regards,

Andras

Dear Andras,
thanks for your efforts, they are really appreciated.
What makes you think, that the open source driver is not a "proper one" ? This is the official driver supplied by Intel, certainly you are aware that Intel supplies the Linux community with open source drivers for their devices as opposed to, say, Nvidia.
Again, I thank you for your support, maybe the next driver update will fix it.
Kind regards,
Axel

Hi,

 

Well, my previous experiences suggested that open source drivers or the ones supplied with the distrib. not always the best choice.

Maybe upcoming jogl2 libraries will provide workaround for this situation.

Regards,

Andras