Linux problems with Marvin

I just installed the linux version of JChem and Marvin on the supercomputer of my University (series of 2cpus-4cores Intel L5420 in 64-bits). The installation apparently went well thus I started MarvinSketch and I got the usual window that I see with a MS-Windows version.

However, the drop-down menus, though apparently showing correctly, do not activate the sub-menu options, or do it improperly sometimes. By using the shortcut Ctrl-O, I can open a .mrv file and check that all the clickable commands do work correctly. 

So my problem is to access all the other commands, by changing the options in the menu.

I launch the programs from my PC (which runs Windows XP), and I use a Xming server to display graphical contents.

Thus I found some comments about using

export AWT_TOOLKIT=MToolkit 

and it partially solved my problems (MarvinSketch and MarvinView run nearly OK, with a warning only [Warning: Cannot convert string "-b&h-lucidasans-medium-r-normal-sans-*-140-*-*-p-*-iso8859-1" to type FontStruct]) but MarvinSpace does not start.

With the default option (AWT_TOOLKIT=XToolkit), MarvinSpace opens but the working space is blank, and the menu is not visible. Thus, unusable.

With the option AWT_TOOLKIT=MToolkit, MarvinSpace bugs, with the following error message

 

 Warning: Cannot convert string "-b&h-lucidasans-medium-r-normal-sans-*-140-*-*-p-*-iso8859-1" to type FontStruct

#

# An unexpected error has been detected by Java Runtime Environment:

#

#  SIGSEGV (0xb) at pc=0x003cdc2d, pid=19499, tid=4159851408

#

# Java VM: Java HotSpot(TM) Server VM (11.3-b02 mixed mode linux-x86)

# Problematic frame:

# C  [libpthread.so.0+0x7c2d]  pthread_mutex_lock+0x1d

#

# An error report file with more information is saved as:

# /home/4157cip1/dehareng/ChemAxon/MarvinBeans/hs_err_pid19499.log

#

# If you would like to submit a bug report, please visit:

#   http://java.sun.com/webapps/bugreport/crash.jsp

# The crash happened outside the Java Virtual Machine in native code.

# See problematic frame for where to report the bug.

#

 

Can you help me?

Hi,

Which version of Marvin do you use?

Was there any earlier version of Marvin, where MarvinSpace worked in this same environment?

Is there a way to run a browser with this setup (through this xming remote desktop)?

If it is possible, could you try the following link in it

http://jogamp.org/deployment/jogamp-current/jogl-demos/applet-gears.html

?

Does the applet shows up on the page?

 

Regards.

Andras

Hello Andras,

 

Thank you for your quick reply.

 

"Which version of Marvin do you use?   

Was there any earlier version of Marvin, where MarvinSpace worked in this same environment?"

=> I downloaded two versions, one for windows and one for linux, each one being from jchem-5.10.3.

The windows version (my PC is an old XP one) works quite well.

 

"Is there a way to run a browser with this setup (through this xming remote desktop)?"

=>Firefox works OK, at least for the tests I did (since I do not use it from this supercomputer but directly from my PC), with just a warning:

(firefox:10095): Gtk-WARNING **: Unable to locate theme engine in module_path: "clearlooks",

 

"If it is possible, could you try the following link in it

http://jogamp.org/deployment/jogamp-current/jogl-demos/applet-gears.html

?

Does the applet shows up on the page?"

=> NO, and I cannot load any plugin (No suitable plugins were found).

Thus, what is missing?

 

++

Dominique

Hi Dominique,

We did a modification in 5.10.4(and 5.11) that fixed a similar issue in other environments, though.

I suggest you should try that version, when it's available and report back.


The "No suitable plugins were found" is not related to our case.
It means you cannot run Java Applets in your browser, because the suitable plugin is not installed.

It would just helped to determine, if the problem is on our side, or the graphical library we use.

Regards,
Andras

Thank you, I'll do that in time.

 

++

Dominique

Hi, it's me again,

I donwloaded the new version 5.11.2 but there is no change with MarvinSpace: the errors are exactly the same as before.

Dominique

Hi Dominique,

András is on Holiday. He will deal with your request when hes back on 24 October.

Please accept our apologies this problem might caused.

 

Regards

Miklos

Hi Dominique,

in the mean time I may have some idea that you can check, and see whether they are causing the issues or not.

Java takes the font configuration from a properties file located in the java_install_dir/lib/fontconfig.properties, if you do not have the file, that is not a problem, there is a precompiled one also in that folder, and the source of the precompiled one. If you copy the fontconfig.properties.src to fontconfig.properties, then the raw property file will take place of the precompiled one. After you created the file, you can try to delete those lines java have problems with.

Unfortunatelly in your case, I am not sure which java is running, the one from the server of the one from the client, as far as I know, the XForwarding option will work in a way where the program runs on the server, and only the graphical resources are used from the client, this tellls me, you should play with the fontconfig on the server.

An other thing you might try is to switch to an other look and feel supported by java (they may have requirements suitable in the environment), not the default on the environment, because that may also cause problems. To do so, you should use the -Dswing.defaultlaf=LOOKANDFEELCLASS as a command line parameter, you can define them directly in the msketch script, or as  an environment variable called JAVAOPTS. You can try different L&Fs for example
Motif: com.sun.java.swing.plaf.motif.MotifLookAndFeel
GTK: com.sun.java.swing.plaf.gtk.GTKLookAndFeel
Windows: com.sun.java.swing.plaf.windows.WindowsLookAndFeel

I hope some of theese ideas can help.

Regards,
Istvan

Hi,

 

Istvan: thanks for the ideas. I think the warning and the error are about two different things.

Segmentation faults mostly due to native calls  (jogl).)

I did some research about this topic (XMing + JOGL), and it seems problems can be expected.

 

Dominique: I will try to create a similar test environment, and try to determine it is really a JOGL problem, or we can fix/make a workaround for it in MarvinSpace.

Regards,

Andras

Hello Istvan and Andras,

I think that only the graphical part takes place on my PC, and the rest runs on the linux server.

I checked that the java version running is jre1.6.0_13 and that there exists a /usr/java/jre1.6.0_13/lib/fontconfig.properties.src file on that server.

Do you want the complete error logfile?

Dominique

That might help, thank you.

 

Andras

Here it is

Hi Dominique,

I managed to set up a Linux + XMing + Win7 x64 environment.
I did not experience any problem, MarvinSpace works(, although very slow (as expected)).
Here are the details:

MarvinBeans 5.11.3 installer without JRE
Ubuntu 12.04 LTS running on VMWare Player 5.0
Java 1.6.0_33 x86
XMing 6.9.0.31
Win7 x64 with all the latest updates
I manually installed an OpenSSH server on the Ubuntu.
After that, I started (my already installed PuTTY):
- Enabled X11 forwarding: Connection/SSH/X11 - 'Enable X11 forwarding'
- Created a session for Ubuntu SSH access.
- logged in and started mspace (for me, it was: sh ~/ChemAxon/MarvinBeans/bin/mspace)
- MarvinSpace started as expected, and I was able to load and display a molecule.

I tried the same with a Windows XP SP2, and it works there too.

If you are using the same version of XMing I can only think the difference is on the Linux side in software versions, or hardware configuration.
I attached screenshohts of MarvinSpace's 'about' boxes.
Maybe, the Admins of the Linux server can use this information somehow to fix the issue.

Regards,
Andras

Thank you very much for everything you've done. Now I know that it should run and it runs with Ubuntu.

I am going to investigate about the linux versions.

Again thank you

Friendly regards

Dominique

Hi,

It is not strictly an Ubuntu thing.

I think the latest Linux/Java/Xorg updates should also do the trick.

It just shows that the problem is not on the MarvinBeans/MarvinSpace side.

It most likely due to the environment configuration/software versions.

 

Regards,

A