Problems on Ubuntu with MarvinSpace
User e63e59b5d1
12-12-2008 11:16:04
Hello
I must admit I'm very pleased to have found this program to use it on Linux because there was a great lack and need for it.
Unfortunately my enjoyment stopped when I tried to use MarvisSpace:
the visualization window turned grey and didn't show a molecule unless I clicked with the mouse into the window and kept on moving the molecule about... not too handy. Apart from this, exporting resulted in a neat image.
Hardware is an ATI mobility x700 with latest drivers
OpenGL: 2.1.8087 Release
Jogl version: 1.1.0-rc2
Thank you in advance
ChemAxon efa1591b5a
15-12-2008 08:56:03
Did you try the MarvinSpace application program or the Applet. If latter, which browser did you use?
Thanks,
Miklos
User e63e59b5d1
15-12-2008 09:35:38
I used the installed application. I'm afraid it may have to do with the open source drivers, but I have no idea as to how to solve it.
ChemAxon 909aee4527
15-12-2008 13:22:25
Dear Rick,
can you please check if MarvinSpace actually sees the appropriate hardware and OpenGL by using the Help>About dialog.
You may have copied the information from there, but it's better to be sure it is not a configuration issue.
Thanks,
Judit
User 25d107bd42
15-12-2008 20:37:52
Hi,
I am using Ubuntu 8.0.4 and there are no problems.
Can you start mspace from the command line to see the failure comments? Use:
$ cd ~/ChemAxon/MarvinBeans/bin/
$ ./mspace
and then post the failure comments here.
Regards, Hans-Ulrich
User e63e59b5d1
16-12-2008 08:52:48
| Code: |
Locking assertion failure. Backtrace:
#0 /usr/lib/libxcb-xlib.so.0 [0xb4b7d7c7]
#1 /usr/lib/libxcb-xlib.so.0(xcb_xlib_unlock+0x31) [0xb4b7d891]
#2 /usr/lib/libX11.so.6(_XReply+0x254) [0xb4bcc494]
#3 /home/*****/.chemaxon/lib/jogl_1.1.0-rc2/libjogl.so(XineramaQueryScreens+0xd1) [0xb45783f7]
#4 /home/*****/.chemaxon/lib/jogl_1.1.0-rc2/libjogl.so(XineramaEnabled+0x5f) [0xb45c7f37]
#5 /home/******/.chemaxon/lib/jogl_1.1.0-rc2/libjogl.so(Java_com_sun_opengl_impl_x11_GLX_XineramaEnabled__J+0x2a) [0xb457c145]
#6 [0xb553ae9d]
#7 [0xb5533edd]
#8 [0xb5533edd]
#9 [0xb5533e17]
#10 [0xb5533cb1]
#11 [0xb5533cb1]
#12 [0xb5533cb1]
#13 [0xb5533cb1]
#14 [0xb5533cb1]
#15 [0xb5531249]
#16 /usr/lib/jvm/java-6-openjdk/jre/lib/i386/client/libjvm.so [0xb77c5c27]
#17 /usr/lib/jvm/java-6-openjdk/jre/lib/i386/client/libjvm.so [0xb789eb89]
#18 /usr/lib/jvm/java-6-openjdk/jre/lib/i386/client/libjvm.so [0xb77c4eff]
#19 /usr/lib/jvm/java-6-openjdk/jre/lib/i386/client/libjvm.so [0xb78d2395]
Locking assertion failure. Backtrace:
#0 /usr/lib/libxcb-xlib.so.0 [0xb4b7d7c7]
#1 /usr/lib/libxcb-xlib.so.0(xcb_xlib_lock+0x2e) [0xb4b7d96e]
#2 /usr/lib/libX11.so.6 [0xb4bcb619]
#3 /usr/lib/libX11.so.6(XQueryExtension+0x26) [0xb4bb9196]
#4 /usr/lib/libX11.so.6(XInitExtension+0x41) [0xb4bad771]
#5 /usr/lib/libXext.so.6(XextAddDisplay+0x52) [0xb4c85692]
#6 /usr/lib/libGL.so.1 [0xb474958b]
#7 /usr/lib/libGL.so.1(glXChooseVisual+0x37) [0xb4745b97]
#8 /home/vonkrolok/.chemaxon/lib/jogl_1.1.0-rc2/libjogl.so(Java_com_sun_opengl_impl_x11_GLX_glXChooseVisual1__JILjava_lang_Object_2I+0x5e) [0xb457c87a]
#9 [0xb553ae9d]
#10 [0xb5533e17]
#11 [0xb5533e17]
#12 [0xb5533e17]
#13 [0xb5533cb1]
#14 [0xb5533cb1]
#15 [0xb5533cb1]
#16 [0xb5533cb1]
#17 [0xb5533cb1]
#18 [0xb5531249]
#19 /usr/lib/jvm/java-6-openjdk/jre/lib/i386/client/libjvm.so [0xb77c5c27]
|
This is the result after I entered the folder /root/ChemAxon/MarvinBeans/ and entered MarvinSpace (it appears as if we have different settings after all...). Edited out text is just my machine name.
User 25d107bd42
16-12-2008 09:12:27
Hi Rick,
I have three comments/questions:
1) Why is .chemaxon in the root directory ? This is not a normal directory.
Perhaps the problems come from this situation.
2) Why in .chemaxon (with point in the begining)? There should only be the settings and the license file.
On our machines we have the Marvin-software in a normal user directory, f.e.
/home/user/ChemAxon/
We put the installscript in this directory, start it and all installs fine.
And other users can use these programs with a link in /usr/local/bin.
3) Did you start using "MarvinSpace" or "mspace" ?
Here the answer is important for me, as I was discussing already what's the difference.
Regards, Hans-Ulrich
User e63e59b5d1
16-12-2008 09:41:18
As I executed the script from the Desktop, it installed directly there, I didn't change any default installation setting. As for the starting I started MarvinSpace and not mspace. As for the dot... can't help you there.
And yes Judit, I copied the info from exactly the panel you mentioned.
User 25d107bd42
16-12-2008 09:47:09
Hi Rick,
1) what's the name of the Desktop user?
2) Try to start mspace !
Regards, Hans-Ulrich
User e63e59b5d1
16-12-2008 10:12:26
It's me, that's the name edited out.
This is the result loading ./mspace... pretty much nothing changed.
| Code: |
****@ยงยงยงยง19:/root/ChemAxon/MarvinBeans/bin$ ./mspace
Locking assertion failure. Backtrace:
#0 /usr/lib/libxcb-xlib.so.0 [0xb4d0f7c7]
#1 /usr/lib/libxcb-xlib.so.0(xcb_xlib_unlock+0x31) [0xb4d0f891]
#2 /usr/lib/libX11.so.6(_XReply+0x254) [0xb4aa3494]
#3 /home/****/.chemaxon/lib/jogl_1.1.0-rc2/libjogl.so(XineramaQueryScreens+0xd1) [0xb44783f7]
#4 /home/****/.chemaxon/lib/jogl_1.1.0-rc2/libjogl.so(XineramaEnabled+0x5f) [0xb44c7f37]
#5 /home/****/.chemaxon/lib/jogl_1.1.0-rc2/libjogl.so(Java_com_sun_opengl_impl_x11_GLX_XineramaEnabled__J+0x2a) [0xb447c145]
#6 [0xb5495e9d]
#7 [0xb548eedd]
#8 [0xb548eedd]
#9 [0xb548ee17]
#10 [0xb548ecb1]
#11 [0xb548ecb1]
#12 [0xb548ecb1]
#13 [0xb548ecb1]
#14 [0xb548ecb1]
#15 [0xb548c249]
#16 /usr/lib/jvm/java-6-openjdk/jre/lib/i386/client/libjvm.so [0xb7720c27]
#17 /usr/lib/jvm/java-6-openjdk/jre/lib/i386/client/libjvm.so [0xb77f9b89]
#18 /usr/lib/jvm/java-6-openjdk/jre/lib/i386/client/libjvm.so [0xb771feff]
#19 /usr/lib/jvm/java-6-openjdk/jre/lib/i386/client/libjvm.so [0xb77297fa]
Locking assertion failure. Backtrace:
#0 /usr/lib/libxcb-xlib.so.0 [0xb4d0f7c7]
#1 /usr/lib/libxcb-xlib.so.0(xcb_xlib_lock+0x2e) [0xb4d0f96e]
#2 /usr/lib/libX11.so.6 [0xb4aa2619]
#3 /usr/lib/libX11.so.6(XQueryExtension+0x26) [0xb4a90196]
#4 /usr/lib/libX11.so.6(XInitExtension+0x41) [0xb4a84771]
#5 /usr/lib/libXext.so.6(XextAddDisplay+0x52) [0xb4d30692]
#6 /usr/lib/libGL.so.1 [0xb463c58b]
#7 /usr/lib/libGL.so.1(glXChooseVisual+0x37) [0xb4638b97]
#8 /home/vonkrolok/.chemaxon/lib/jogl_1.1.0-rc2/libjogl.so(Java_com_sun_opengl_impl_x11_GLX_glXChooseVisual1__JILjava_lang_Object_2I+0x5e) [0xb447c87a]
#9 [0xb5495e9d]
#10 [0xb548ee17]
#11 [0xb548ee17]
#12 [0xb548ee17]
#13 [0xb548ecb1]
#14 [0xb548ecb1]
#15 [0xb548ecb1]
#16 [0xb548ecb1]
#17 [0xb548ecb1]
#18 [0xb548c249]
#19 /usr/lib/jvm/java-6-openjdk/jre/lib/i386/client/libjvm.so [0xb7720c27] |
User 25d107bd42
16-12-2008 10:28:11
Hi Rick,
in the first line I read:
/root/ChemAxon/MarvinBeans/bin$ ./mspace
Are you really working as root ? Try it as normal user.
And install it in a normal user directory.
Regards, Hans-Ulrich
User e63e59b5d1
16-12-2008 11:36:23
I definitely think that working as root is pretty irrelevant to the rendering and, no, I ain't working as root, just simply the prog is in the root folder, in order to work as root I would need to punch in the root password which doesn't actually happen.
User 25d107bd42
16-12-2008 12:14:47
Hi Rick, to your sentence:
"I definitely think that working as root is pretty irrelevant to the rendering"
I cannot agree. The paths for root are different as for normal users.
Regards, Hans-Ulrich
ChemAxon 7c2d26e5cf
16-12-2008 14:18:23
| Quote: |
| Why in .chemaxon (with point in the begining)? There should only be the settings and the license file. |
Under Linux, Marvin Beans installer offers $HOME/ChemAxon/MarvinBeans as target directory for installation, of course you can select another directory but it is the default value.
Marvin applications and applets automatically generates $HOME/.chemaxon directory to store settings and cache some resources. For example MarvinSpace extracts native libraries (like libjogl.so) into this directory and load the extracted version into the classpath after that.
Loading natives from the above directory is the normal behaviour of MarvinSpace.
User e63e59b5d1
16-12-2008 14:19:01
ChemAxon efa1591b5a
16-12-2008 14:26:45
Hi Rick,
thank you for the detailed backlog. It appears to me that the problem you encountered is an openjdk problem. Have your tried sun java?
The jogl manual says:
| Quote: |
| The Sun JDK "compatibility" RPMs (java-1.5.0-sun-compat, java-1.6.0-sun-compat) provided by jpackage.org are incompatible with JOGL. These RPMs symlink an internal JDK directory to /usr/lib, which overrides how both NVidia and ATI currently provide their drivers to some Linux distributions, which is through an override in /etc/ld.so.conf (actually, in /etc/ld.so.conf.d). The implicit presence of /usr/lib on LD_LIBRARY_PATH forces the /usr/lib/libGL.so.1 version of OpenGL to be used, which is typically Mesa and which will provide only software rendering. |
If you search the ubuntu forum you find that many users experienced similar failures.
Hope this helps.
Regards,
Miklos
ChemAxon efa1591b5a
16-12-2008 15:10:31
User e63e59b5d1
16-12-2008 15:15:27
I have Sun Java 6 Runtime and OpenJDK... I ran update-alternatives --config java to switch between the two possibilities, and this is the resulting log after running ./mspace from within the folder it's installed:
| Code: |
Locking assertion failure. Backtrace:
#0 /usr/lib/libxcb-xlib.so.0 [0xb557d7c7]
#1 /usr/lib/libxcb-xlib.so.0(xcb_xlib_unlock+0x31) [0xb557d891]
#2 /usr/lib/libX11.so.6(_XReply+0x254) [0xb55d4494]
#3 /home/***/.chemaxon/lib/jogl_1.1.0-rc2/libjogl.so(XineramaQueryScreens+0xd1) [0xb50043f7]
#4 /home/***/.chemaxon/lib/jogl_1.1.0-rc2/libjogl.so(XineramaEnabled+0x5f) [0xb5053f37]
#5 /home/***/.chemaxon/lib/jogl_1.1.0-rc2/libjogl.so(Java_com_sun_opengl_impl_x11_GLX_XineramaEnabled__J+0x2a) [0xb5008145]
#6 [0xb5ccdf1d]
#7 [0xb5cc6da1]
#8 [0xb5cc6da1]
#9 [0xb5cc6e67]
#10 [0xb5cc6fcd]
#11 [0xb5cc6fcd]
#12 [0xb5cc6fcd]
#13 [0xb5cc6fcd]
#14 [0xb5cc6fcd]
#15 [0xb5cc42cc]
#16 /usr/lib/jvm/java-6-sun-1.6.0.10/jre/lib/i386/client/libjvm.so [0x621b03d]
#17 /usr/lib/jvm/java-6-sun-1.6.0.10/jre/lib/i386/client/libjvm.so [0x630f778]
#18 /usr/lib/jvm/java-6-sun-1.6.0.10/jre/lib/i386/client/libjvm.so [0x621aed0]
#19 /usr/lib/jvm/java-6-sun-1.6.0.10/jre/lib/i386/client/libjvm.so [0x6244686]
Locking assertion failure. Backtrace:
#0 /usr/lib/libxcb-xlib.so.0 [0xb557d7c7]
#1 /usr/lib/libxcb-xlib.so.0(xcb_xlib_lock+0x2e) [0xb557d96e]
#2 /usr/lib/libX11.so.6 [0xb55d3619]
#3 /usr/lib/libX11.so.6(XQueryExtension+0x26) [0xb55c1196]
#4 /usr/lib/libX11.so.6(XInitExtension+0x41) [0xb55b5771]
#5 /usr/lib/libXext.so.6(XextAddDisplay+0x52) [0xb568d692]
#6 /usr/lib/libGL.so.1 [0xb50b658b]
#7 /usr/lib/libGL.so.1(glXChooseVisual+0x37) [0xb50b2b97]
#8 /home/vonkrolok/.chemaxon/lib/jogl_1.1.0-rc2/libjogl.so(Java_com_sun_opengl_impl_x11_GLX_glXChooseVisual1__JILjava_lang_Object_2I+0x5e) [0xb500887a]
#9 [0xb5ccdf1d]
#10 [0xb5cc6e67]
#11 [0xb5cc6e67]
#12 [0xb5cc6e67]
#13 [0xb5cc6fcd]
#14 [0xb5cc6fcd]
#15 [0xb5cc6fcd]
#16 [0xb5cc6fcd]
#17 [0xb5cc6fcd]
#18 [0xb5cc42cc]
#19 /usr/lib/jvm/java-6-sun-1.6.0.10/jre/lib/i386/client/libjvm.so [0x621b03d]
|
| mvargyas wrote: |
Hi Rick,
thank you for the detailed backlog. It appears to me that the problem you encountered is an openjdk problem. Have your tried sun java?
The jogl manual says: | Quote: | | The Sun JDK "compatibility" RPMs (java-1.5.0-sun-compat, java-1.6.0-sun-compat) provided by jpackage.org are incompatible with JOGL. These RPMs symlink an internal JDK directory to /usr/lib, which overrides how both NVidia and ATI currently provide their drivers to some Linux distributions, which is through an override in /etc/ld.so.conf (actually, in /etc/ld.so.conf.d). The implicit presence of /usr/lib on LD_LIBRARY_PATH forces the /usr/lib/libGL.so.1 version of OpenGL to be used, which is typically Mesa and which will provide only software rendering. |
If you search the ubuntu forum you find that many users experienced similar failures.
Hope this helps.
Regards,
Miklos |
User e63e59b5d1
16-12-2008 15:45:08
Just a last minute note:
tried to install Sun JDK from the repos and the result is pretty much the same.
User 25d107bd42
16-12-2008 15:57:05
Hi Rick,
I must insist on my suggestion.
Why do you not try to install it in a normal home directory.
Do you think as user you have all the necessary write permissions in the directory you use?
Each new version of Marvin is installed on my machine using the install script,
There are now 16 ChemAxonXX directories, where XX is the number of the version.
The newest directory is named ChemAxon5104pre1
I'm using the standard installation Ubuntu 8.0.4 without any problems.
java version "1.6.0_07"
Java(TM) SE Runtime Environment (build 1.6.0_07-b06)
Java HotSpot(TM) Client VM (build 10.0-b23, mixed mode, sharing)
For installation look in my topic
http://www.chemaxon.com/forum/viewpost18966.html#18966
Look at post Wed Jul 09, 2008 8:04 am
Regards, Hans-Ulrich
ChemAxon efa1591b5a
16-12-2008 16:07:56
Hi Hans-Ulrich,
thanks for your help and useful tips. I reckon the major difference between your configuration and Rick's is the particular graphics hardware you use. His got an ATI card and the hardware acceleration in his 3D driver and his java runtime (including jogl) cannot work properly together.
This is what I suspect form the message. The message comes from 'somewhere deep', under the X11 application layer. I am convinced it's got nothing to do with file system level permissions etc.
Regards,
Miklos
User e63e59b5d1
16-12-2008 16:13:36
I agree with mvargyas, especially considering that I didn't change, and I shall stress this one out again, I didn't change any install setting, the installation was just left with the default and for the nature of this thing I shall assume that the default installation settings should be all right, otherwise people at ChemAxon would have changed them long ago.
User 25d107bd42
16-12-2008 16:33:04
Hi,
and what's about Jmol or SHMO. Do these programs run?
Regards, Hans-Ulrich
ChemAxon efa1591b5a
16-12-2008 16:34:13
Hi Rick,
thanks for your attempts to trace this problem, it's rather puzzling. Try to search ubuntu and jogl forums - and so do I.
Regards,
Miklos
ChemAxon efa1591b5a
16-12-2008 16:36:00
Those do not rely on OpenGL and have no HW acceleration capabilities.
Miklos
User e63e59b5d1
17-12-2008 10:55:55
I'll do my best, but I'm no tech specialist
| mvargyas wrote: |
Hi Rick,
thanks for your attempts to trace this problem, it's rather puzzling. Try to search ubuntu and jogl forums - and so do I.
Regards,
Miklos |
ChemAxon efa1591b5a
05-01-2009 11:34:03
Hi,
do other JOGL applications run? I mean sg like JOGL demos...
Have you installed the proper graphics driver? Can you send/copy your xorg.conf file?
Thanks
Miklos
User e63e59b5d1
05-01-2009 14:21:38
Following: my xorg.conf
| Code: |
# xorg.conf (X.Org X Window System server configuration file)
#
# This file was generated by dexconf, the Debian X Configuration tool, using
# values from the debconf database.
#
# Edit this file with caution, and see the xorg.conf manual page.
# (Type "man xorg.conf" at the shell prompt.)
#
# This file is automatically updated on xserver-xorg package upgrades *only*
# if it has not been modified since the last upgrade of the xserver-xorg
# package.
#
# If you have edited this file but would like it to be automatically updated
# again, run the following command:
# sudo dpkg-reconfigure -phigh xserver-xorg
# commented out by update-manager, HAL is now used
#Section "InputDevice"
# Identifier "Generic Keyboard"
# Driver "kbd"
# Option "XkbRules" "xorg"
# Option "XkbModel" "pc105"
# Option "XkbLayout" "gb"
#EndSection
# commented out by update-manager, HAL is now used
#Section "InputDevice"
# Identifier "Configured Mouse"
# Driver "mouse"
# Option "CorePointer"
#EndSection
# commented out by update-manager, HAL is now used
#Section "InputDevice"
# Identifier "Synaptics Touchpad"
# Driver "synaptics"
# Option "SendCoreEvents" "true"
# Option "Device" "/dev/psaux"
# Option "Protocol" "auto-dev"
# Option "HorizEdgeScroll" "0"
#EndSection
Section "Device"
Identifier "Configured Video Device"
Driver "fglrx"
EndSection
Section "Monitor"
Identifier "Configured Monitor"
EndSection
Section "Screen"
Identifier "Default Screen"
Monitor "Configured Monitor"
Device "Configured Video Device"
Defaultdepth 24
EndSection
Section "ServerLayout"
Identifier "Default Layout"
screen "Default Screen"
# commented out by update-manager, HAL is now used
# Inputdevice "Synaptics Touchpad"
EndSection
Section "Module"
Load "glx"
EndSection |
ChemAxon efa1591b5a
05-01-2009 15:05:13
That looks good.
So what does fglrxinfo say? Does it recognise your card properly.
And does fglrxgears (or fglrx-gears) work well?
Miklos