Marvin Space not working in Ubuntu 12.04

I just installed the latest Marvin version on a Ubuntu 12.04 machine. Marvin Sketch seems to be working but Marevin space doesnt open. See error messages below. Any Ideas? Help is greatly appreciated.

ERROR:
Error opening MarvinSpace

STACK TRACE:
javax.media.opengl.GLException: Profile GL_DEFAULT is not available on null, but: []
    at javax.media.opengl.GLProfile.get(GLProfile.java:655)
    at javax.media.opengl.GLProfile.getDefault(GLProfile.java:478)
    at javax.media.opengl.GLProfile.getDefault(GLProfile.java:486)
    at chemaxon.marvin.space.GraphicScene.<init>(GraphicScene.java:164)
    at chemaxon.marvin.space.MSpaceEasy.<init>(MSpaceEasy.java:119)
    at chemaxon.marvin.space.MSpaceEasy.<init>(MSpaceEasy.java:98)
    at chemaxon.marvin.space.gui.MSpaceFrameViewer.getMSpaceFrame(MSpaceFrameViewer.java:68)
    at chemaxon.marvin.space.gui.MSpaceFrameViewer.getMSpaceViewer(MSpaceFrameViewer.java:59)
    at chemaxon.marvin.space.gui.MSpaceViewerBase.get(MSpaceViewerBase.java:117)
    at chemaxon.marvin.space.gui.MSpaceFrameViewer.get(MSpaceFrameViewer.java:51)
    at chemaxon.marvin.space.gui.MSpaceViewerBase.callback(MSpaceViewerBase.java:100)
    at chemaxon.marvin.common.swing.MolPanel.getMSpaceViewer(MolPanel.java:5906)
    at chemaxon.marvin.sketch.swing.SketchPanel.openMSpace(SketchPanel.java:3316)
    at chemaxon.marvin.sketch.swing.SketchPanel.doOpenMSpace(SketchPanel.java:2620)
    at chemaxon.marvin.sketch.swing.actions.OpenMarvinSpaceAction.actionPerformed(OpenMarvinSpaceAction.java:26)
    at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
    at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
    at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
    at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
    at javax.swing.AbstractButton.doClick(Unknown Source)
    at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
    at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source)
    at java.awt.Component.processMouseEvent(Unknown Source)
    at javax.swing.JComponent.processMouseEvent(Unknown Source)
    at java.awt.Component.processEvent(Unknown Source)
    at java.awt.Container.processEvent(Unknown Source)
    at java.awt.Component.dispatchEventImpl(Unknown Source)
    at java.awt.Container.dispatchEventImpl(Unknown Source)
    at java.awt.Component.dispatchEvent(Unknown Source)
    at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
    at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
    at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
    at java.awt.Container.dispatchEventImpl(Unknown Source)
    at java.awt.Window.dispatchEventImpl(Unknown Source)
    at java.awt.Component.dispatchEvent(Unknown Source)
    at java.awt.EventQueue.dispatchEvent(Unknown Source)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
    at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
    at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    at java.awt.EventDispatchThread.run(Unknown Source)

Hi,

Could you provide some details, what video-card/GPU do you using?

Did you install the offical (not the one in the Package Manager) video card drivers?

Could you please run MarvinSpace in a shell:

sh mspace -v

and send the information displayed?

 

Regards,

Andras

Hi,

it seems to me once more a problem of the Java version. Is it OpenJDK or Oracle Java ?

Please look in the topic Installation on 64-bit linux

To morrow we will actualize this procedure and test it once more.

But before: What is the answer giving the command line java -version  ?

Best regards, Hans-Ulrich

Output of java -version

java version "1.6.0_24"
OpenJDK Runtime Environment (IcedTea6 1.11.3) (6b24-1.11.3-1ubuntu0.10.04.1)
OpenJDK Server VM (build 20.0-b12, mixed mode)

output of sh mspace -v

sh: Can't open mspace

Ok, you don't need that.

You need to install official Sun/Oracle Java in order to get MarvinSpace working.

(You might need to remove OpenJDK and IcedTea packages beforehand.)

 

Regards,

Andras

Hi,

sorry, replacing OpenJDK by Oracle Java does not help. Evaluating the problem we found the following:

c1113@nb-lehre ~ $ cd ChemAxon/MarvinBeans/bin
c1113@nb-lehre ~/ChemAxon/MarvinBeans/bin $

c1113@nb-lehre ~/ChemAxon/MarvinBeans/bin $ ls
cxcalc  cxtrain  evaluate  java.ini  license  molconvert  msketch  mspace  mview  setup  structurecheck

c1113@nb-lehre ~/ChemAxon/MarvinBeans/bin $ cat /etc/lsb-release
DISTRIB_ID=LinuxMint
DISTRIB_RELEASE=13
DISTRIB_CODENAME=maya
DISTRIB_DESCRIPTION="Linux Mint 13 Maya"

c1113@nb-lehre ~/ChemAxon/MarvinBeans/bin $ java -version
java version "1.6.0_31"
Java(TM) SE Runtime Environment (build 1.6.0_31-b04)
Java HotSpot(TM) 64-Bit Server VM (build 20.6-b01, mixed mode)

c1113@nb-lehre ~/ChemAxon/MarvinBeans/bin $ ./mspace
Info: XInitThreads() called for concurrent Thread support
javax.media.opengl.GLException: X11GLXDrawableFactory - Could not initialize shared resources for :0.0
    at jogamp.opengl.x11.glx.X11GLXDrawableFactory$SharedResourceImplementation.createSharedResource(X11GLXDrawableFactory.java:267)
    at jogamp.opengl.SharedResourceRunner.run(SharedResourceRunner.java:261)
    at java.lang.Thread.run(Thread.java:662)
Caused by: java.lang.NullPointerException
    at jogamp.opengl.GLContextImpl.makeCurrent(GLContextImpl.java:419)
    at jogamp.opengl.x11.glx.X11GLXDrawableFactory$SharedResourceImplementation.createSharedResource(X11GLXDrawableFactory.java:246)
    ... 2 more

You see, the reason is not the Java version.

MarvinSpace does not run on Linux Mint 13 = Ubunbu 12.04. On Linux Mint 10 there were no problems.

May be it's a problem of Java and the new opengl version installed on Ubuntu 12.04.

How to solve this ugly problem ?

Best regards, Hans-Ulrich

Ok, I try o create a test environment.

Meanwhile could you paste here the output of lspci and glxinfo?

A.

I'm not Linux savvy enough to contribute to the diagnosis. If there is anything I can contribute let me know, otherwise I'll stand in awe and watch what you guys are pulling off.

I managed to reproduce the problem with Mint Maya.

I'm on it.

Hi,

here the output of glxinfo > glxinfo.txt

I'm trying to evaluate the problem on other distributions.

Regards, Hans-Ulrich

I managed to get MarvinSpace working by replacing jogl libraries with the latest ones (jogl2-rc9)

MarvinSpace now starts OK, but no molecule is visible.

Investigating further.

Hi Andras,

now I tested it on Fedora 17 and Java 7.0_05 and I got the same result:

javax.media.opengl.GLExeption: X11GLXDrawableFactory - Could not initialize ...

I couldn't install the Java 6 version, but MarvinSketch and MarvinView work without problems.

Is it a problem concerning the handling of X11 windows ?

Best regards

Well, since updating jogl fixed this kind of issue, I suppose it is an X vs. jogl2-rc5 incompatibility.

I attached the files you might need to be able to test the latest (rc9) jogl2 implementation.

Hi Andras,

I have copied these jar-files into the lib folder and tested once more. Now we have a new error message:

ERROR:
Error opening MarvinSpace

STACK TRACE:
java.lang.NoClassDefFoundError: javax/media/opengl/GLEventListener
    at java.lang.ClassLoader.defineClass1(Native Method)

... more

Best regards, Hans-Ulrich

PS: One addition: This machine uses java version "1.7.0_05"
Java(TM) SE Runtime Environment (build 1.7.0_05-b06)
Java HotSpot(TM) 64-Bit Server VM (build 23.1-b03, mixed mode)

Should I test on Java 1.6 ?

Uhm, sorry, I managed to attach some wrong jars. I attach the good ones.

Hi Andras,

now it works, see screenshot :-)

But only starting the program directly.

Calling mspace from MarvinSketch "View - MarvinSpace" opens a gray window and all is blocked.

The only way to stop both programs is using ps ax and kill 9 ...

Best regards, Hans-Ulrich

Finally, some good news.

I will add the latest jogl packages into the next Marvin release.

However, I could not reproduce the issue

Could you attach the output of the shell and/or java console in this case.

(You still testing with Java 1.7 x64, right?)

 

Hi Andras,

yes, I' m testing with Java 1.7.x64, Mint 13.

There is a curiuos difference:

Starting MarvinSketch with ...MarvinBeans/bin/msketch and calling MSpace using View etc. MarvinSpace works !

But starting MarvinSketch with ...MarvinBeans/MarvinSketch (= desktop-icon-starter) the grey "dead" window is produced (no error message) and the program must be killed.

I changed the icon starter to "...MarvinBeans/bin/msketch" (without "bin sh") and now MarvinSpace works with both start procedures.

Super !

We will produce a package and distribute it in our student pools.

Or, is it possible you produce a beta version, as I got one some months ago from Efi ?

Best regards, Hans-Ulrich

BTW: Do you see the double bond in the glycerinaldehyde above ?

5.10.2 Will be released on 07.27 I will try to push these packages into it.

Is it OK for you?

As for the double(triple) bonds:

There is an option (Display/Options...)/Visualizers/Front Facing Bonds in MarvinSpace:

If it is checked, the double and triple bonds are always "facing" to the viewpoint.

Is that what you think of?

Hi Andras,

yes: "5.10.2 will be released on 07.27" is OK ! It's super !

And the bug starting with the icon-starter ? .../MarvinBeans/MarvinSketch

And obviously Marvin now works using Java 1.7, too ?

Best regards, Hans-Ulrich

And now to the BTW:

Concerning the invisible double bonds I referred to my very old topic:

MSpace bugs: triple bonds, sp carbon, phenylgroups

 

The icon-starter issue: I transferred it to the packaging/release team for investigation.

Java 1.7.: As far as I know, it can work, but not yet supported.

But, that may not be the 'offical' standpoint.

Double bonds: Yeah, I know about the topic. If you refer to the 'make-it-default' request: well, I'm not against it, but I have to discuss it with Miklos.

Hi Hans-Urlich,

We still cannot reproduce the issue.

Could you send us the following files:

$HOME/ChemAxon/MarvinBeans/.install4j/inst_jre.cfg

$HOME/ChemAxon/MarvinBeans/bin/java.ini

$HOME/ChemAxon/MarvinBeans/error.log

?

 

Thanks,

Andras

Hi Andras,

before sending the files you mentioned I want to show you another result of my evaluations, see attached screenshots (produced with a real camera   ) and it seems to me, this corresponds to your suspicions:

After starting MarvinSketch using .../Marvinbeans/bin/msketch it uses Java 1.6

After starting MarvinSketch using .../Marvinbeans/MarvinSketch it uses Java 1.7

( Sorry, the image shows starting MarvinSpace, but the results are corresponding to each other.)

Installed on this machine is:

c1113@nb-lehre ~ $ java -version
java version "1.7.0_05"
Java(TM) SE Runtime Environment (build 1.7.0_05-b06)
Java HotSpot(TM) 64-Bit Server VM (build 23.1-b03, mixed mode)

I think version 1.6 comes from installing Marvin_with_jre, isn't it ?

My conclusion is: The seven new jar files are OK and usable with msketch - Java 1.6

So my suggestion is: Please produce a beta version with the new seven *.jar files and let me download it in a version ..._with_jre.

I cannot downgrade the java version because of other programs.

Best regards, Hans-Ulrich

Hi Hans-Ulrich,

The referred installer bundled with Java (32bit) 1.6.0_18. So, the msketch script can not use the bundled Java, if it prints 1.6.0_31.

The msketch script retrieves Java path from java.ini. If it does not exist, use the system default one.

The MarvinSketch launcher gets Java path from .install4j/inst_jre.cfg.

Both file are generated by the installer. Theoretically, they should include the same value.

After that, I am really wonder what is your settings. Can you send us those files that Andras mentioned in the previous post? It would help us a lot to understand this strange behaviour of the installer.

The installation log file ($HOME/ChemAxon/Marvinbeans/.install4j/installation.log) can be also useful.

If you do not want to share these info with the forum community, drop an email to us.

Hi Tamas,

it's my test machine and the install story is (as I remember) the following.

1) According to the missing desktop icons, I installed first Marvin 5.5.0.1 corresponding to the topic

Missing Linux Desktop Marvin Starter Icons.

( BTW: You know this topic and your answer was in the next release the desktop icons will be included. I found it and tested it, but on some machines it still has problems. We will discuss this, when I have more information...)

2) Then I installed Marvin 5.10.0 (with or without jre ? I don't remember).

3) And at last I installed Marvin 5.10.1. This definitely without jre.

While installing a new Marvin version, I don't kill the elder version. I only rename the folder MarvinBeans for example to MarvinBeans-5-5-0-1 in the folder ChemAxon.

Should I install Marvin 5.10.1 once more ?

I will send the installation log file to Alex.

Best regards, Hans-Ulrich

Hi Tamas,

please send me an email to my personal address. So we can correspond directly.

Best regards, Hans-Ulrich

Hi All,

The release 5.10.2 will consist the latest jogl libaries that fixes this issue on these Linux dists.

Regards,

Andras

Dear Hans-Ulrich,

Thanks for the install log, I have received it via the support address.

Your install log proves that the 5.10.1 installer launched with Java 1.6.0_31.

That's why the installer wrote this Java version into the bin/java.ini file into the target directory of the installation.

Java Path=/usr/lib/jvm/jdk1.6.0_31/jre/

That's why msketch always run with 1.6.

It seems that your MarvinSketch launcher always uses the system default Java. Its lookup mechanism prefer the default Java. In this case, it is a Java 1.7 version.

Would you like forcing  Java 1.6 to MarvinSketch launcher (without overwriting system settings)?

Dear Tamas,

yes, of course, we need to have an installer ...

... like forcing  Java 1.6 to MarvinSketch launcher (without overwriting system settings)

And we need to install Marvin first ..._with_jre, yes ?

Thank you and best regards, Hans-Ulrich

To resolve this issue, there are two workarounds:

 

#1. Install Marvin Beans 5.10.1 again with the bundled Java version. It includes a Oracle JRE 1.6.0_18.

In this case, both the script and the launcher uses this Java 1.6.0_18 (ignore the system settings).

 

#2. Create the .install4j/pref_jre.cfg file in the directory of Marvin Beans 5.10.1 and write the path of the preferred Java.

/usr/lib/jvm/jdk1.6.0_31/jre/

Actually, the installer with bundled Java creates it automatically. The desktop launchers check this file each startup to lookup "bundled" java version. If the file does not exist, it uses the system Java.

Of course, the second solution is a bit smelly but it is effective. :)
But, take care that uninstaller does not remove the manually created pref_jre.cfg file. It deleted only those file that are created during the installation process.

Hi Tamas,

we will try the first method, it seems to me, it's not a workaround but can be used by all users having this Java problem. Isn't it ?

Should I wait for Marvin 5.10.2 ?

It should come this evening

Best regards, Hans-Ulrich

Hi Tamas,

being interested in "workarounds" I couldn't wait and I tried to use the second method you mentioned.

To say it in two words: It works !

Now all three Marvin launchers use Java 1.6.0_31 instead of Java 1.7 !

And the original problem of this topic is also solved, too.

Calling MarvinSpace from MarvinSketch works on Mint 13 as usual, and it should do the same on Ubuntu 12.04.

Problems fixed. Thank you.

Best regards, Hans-Ulrich

Dear Hans-Ulrich,

Thanks for the feedback.

I am glad that the problem has been solved. :-)

I think we should update bundled Java in the Marvin Beans installer.

I don't think that Marvin 5.10.2 come out this evening. My colleague has found a critical bug during its testing.

Best Regards,

Tamas

Hi Tamas,

having now Marvin 5.10.2 the problems are not soved at all.

Installing with the jre produces the program call "bin/unpack200"

c1113@nb-lehre ~/ChemAxon $ ./marvinbeans-5.10.2-linux_with_jre.sh
Unpacking JRE ...
Preparing JRE ...
./marvinbeans-5.10.2-linux_with_jre.sh: 203: ./marvinbeans-5.10.2-linux_with_jre.sh: bin/unpack200: not found
Error unpacking jar files. The architecture or bitness (32/64)
of the bundled JVM might not match your machine.

To call bin/unpack200 is of course not possible. Using UNIX since 1980 I cannot understand the meaning of this command, the syntax is simply wrong. There are nine "unpack200" on my test machine:

c1113@nb-lehre / $ sudo find . -name "unpack200"
[sudo] password for c1113:
./etc/alternatives/unpack200
./usr/lib/jvm/jdk1.7.0_05/jre/bin/unpack200
./usr/lib/jvm/jdk1.7.0_05/bin/unpack200
./usr/lib/jvm/java-6-openjdk-amd64/jre/bin/unpack200
./usr/lib/jvm/java-6-openjdk-amd64/bin/unpack200
./usr/lib/jvm/jdk1.6.0_31/jre/bin/unpack200
./usr/lib/jvm/jdk1.6.0_31/bin/unpack200
./usr/bin/unpack200
./var/lib/dpkg/alternatives/unpack200

So I must once more use your workaround #2, you have shown four posts above.

I will report in the following post a workaround "recipe".

Best regards, Hans-Ulrich.

BTW: There was once more no email information about the new version.

Here the workaround recipe I am using:

1) You may look which Java verison(s) you have installed, by using the command

...$ ls -l /usr/lib/jvm/

If there is no answer having "1.6.0_xx" then you must install Java 1.6.

On my machine the version is "xx"="31" and you must replace "xx" by the number of your version.

Download and install a Java 1.6 version from

http://www.oracle.com/technetwork/java/javase/downloads/index.html

2) Download Marvin without jre and install it to ../MarvinBeans

(And here a hint: Installing a new Marvin version I first rename the old folder, for example to "MarvinBeans-5-10-1". So if the new version doesn't work, you can use the old one simply by renaming the new and then the old to "MarvinBeans".)

3) Edit a file called "inst_jre.cfg" and put the following line in it:

/usr/lib/jvm/jdk1.6.0_xx/jre/

xx means your version number.

4) Copy this file to the folder ../MarvinBeans/.install4j/  (There is a little point in front of install4j ! )

Now calling MarvinSketch / View / Space should use Java 1.6 and all is OK.

You can test it immediately using  in Marvin /Help/About MarvinSketch / View / Space.

Here you should find the line: "Java: Sun Microsystems Inc. Java 1.6.0_xx"

Please let me know, if there are any mistakes in this " workaround recipe".

Best regards, Hans-Ulrich

Just one note about your workaround:

inst_jre.cfg stores the Java path that installer used during the installation process. This information is important only for the uninstaller. The uninstaller needs this info to launch itself with the same Java that installer used.

To override Java path for Marvin desktop launchers, you have to create/edit .install4j/pref_jre.cfg in the Marvin Beans directory as I described it earlier in this topic.

I share one more trick how you can force Java version for the installer:

Set INSTALL4J_JAVA_HOME_OVERRIDE system environment variable on your machine to the desired Java that you would like to use with Marvin.

export INSTALL4j_JAVA_HOME_OVERRIDE=/opt/java/jdk6_64/jre

Then install Marvin without Java.

sh marvinbeans-5.10.2-linux.sh

The installer will run with the above Java.

Thus the value of this Java path will be registered in bin/java.ini. It means scripts from the MarvinBeans/bin folder will always use this Java. Desktop launchers check the value of the above variable at startup. If it exists, they prefer this one. Else they use the default Java lookup mechanism.

After following this topic for quite some time, I'll step in now.

I have some problems with the whole topic per se, so I'll start where I feel that all this is beginning (at least for me):

Windows:

We had a course where we used Marvin (Sketch, Space and View) with students. They had their own laptops, we installed the normal Marvin without jre, and on some of them Java 7 (Oracle) was installed. Problems: Saving didn't work everytime and lots of calculations hung up.

Solved by: installing Marvin with jre, because it comes with a java that is supportet by Marvin and doesn't mess with the original system installed on the laptop. No need for the user to do anything else than install Marvin with jre the way they install Marvin without jre.

Linux:

Same problems as above with the saving and the calculations.

In addition to that, it is not possible, to install the Marvin with jre, because of this unpack200 (or something else).

Solutions, offered by this topic:

Install an Oracle Java and edit pathways to make Marvin use the desired Java 6.

My problem with all this:

I want to use my original system, no matter the java provided, and install a working Marvin without any knowledge of pathways or deeper knowledge of the system - it's always far easier to make something not work anymore on computers than to make something work.

And I especially do not want having to change the whole system settings for every program to use the java-version which Marvin supports. This is described in the post above mine.

This topic offers various workarounds, but these are no good to the course-participants which we want to introduce to Marvin: They are chemists, students, and not programmers.

I can use this workaround just fine, but it neither suits our need when doing courses with Marvin nor is it good for anyone else that works with Linux and a different java than the Oracle one.

After writing this wall of text, I'd like to know:

Are you working on locating the problem and making Marvin once more the best choice for Linux users when it comes to chemistry? I think it could be worth the time to check this pathway of unpack200 .

Right now, it looks like I have to install an Oracle-java beforehand to install a Marvin, which definitely defeats the purpose of this version with bundled java.

Hi, I must repeat some sentences from above:

Installing with the jre produces the program call "bin/unpack200"

c1113@nb-lehre ~/ChemAxon $ ./marvinbeans-5.10.2-linux_with_jre.sh
Unpacking JRE ...
Preparing JRE ...
./marvinbeans-5.10.2-linux_with_jre.sh: 203: ./marvinbeans-5.10.2-linux_with_jre.sh: bin/unpack200: not found
Error unpacking jar files. The architecture or bitness (32/64)
of the bundled JVM might not match your machine.

Of course "bin/unpack200" cannot be found. The syntax is wrong.

Analysing several machines having different Linux systems I found:

All these versions have the program unpack200 in the folder /usr/bin/

(/usr/bin/ is a very basic program folder having many many basic programs.)

So, once more the question: Which program produces the wrong program call ?

The correct call should be /usr/bin/unpack200

Regards, Hans-Ulrich

I admit that Marvin Beans installer with bundled Java does not work in certain Linux configuration.

We use Install4j to generate the Marvin Beans installer script.

The generated script attempts to run the unpack200 tool from the directory of the bundled JRE.

This issue has been discussed in the following topic: Problem installing Marvin with JRE

We are investigating the issue to find a workaround.

 

Investigating the issue, we assume that providing Java 6 64bit to the Marvin installer for Linux platform solves the problem.

Since 5.11, we deploy Marvin / JChem installers with 64bit bundled Java for Linux platform too.

In marvinbeans-<VERSION>-linux_with_jre.sh and in jchem-<VERSION>-linux_with_jre.sh, the 32bit bundled JRE will be also updated (to 1.6.0_33).

Hi Tamas,

so we will eagerly await for Marvin 5.11

And one further result of may evaluations:

When the program unpack200 is called in the sub-directory bin, there is not yet this sub-directory bin,

please see attached screenshot.

Perhaps this will help you to fix the installation bug.

Best regards, Hans-Ulrich

I just downloaded the latest Marvin Version (Linux Installer WITHOUT java). Made sure that a java-1.6.0 version was already installed and started the installer.

It used the java-1.6.0-openjdk-i386 version, which on my system was set as default-java (this information I got from the output of the terminal command ls -l usr/lib/jvm)

The result is promising, MarvinSpace opens as expected.

In conclusion, however, I agree with jube, that a normal user shouldn't be bothered with this background work. On the other hand: there is no free lunch ;-)

Dear Hans-Ulrich,

Please see the last two posts in this forum topic:

http://forums.visual-paradigm.com/posts/list/2501.html

It explains when and why this unpack200 issue occurs.

It also gives a workaround (install missing package).

This post also confirm my assumption that the 32bit Java causes the problem.

Dear Tamas,

thank you for the information. It seems to be a problem at least two years old.

I'm very interested to be informed how you solved these problems. Please let me know.

Best regards, Hans-Ulrich

 

I guess the answer is very simple: 64bit Java for 64bit platform! :)

Let's see ...

 

I am having a similar difficulty. I have tried installing the latest versions of everything, but just cannot find the combination that will make it work. MarvinSketch and MarvinView work fine, but MarvinSpace will not launch.

When attempting to launch MarvinSpace I get the following error:
ERROR:
Error opening MarvinSpace

STACK TRACE:
javax.media.opengl.GLException: Profile GL_DEFAULT is not available on X11GraphicsDevice[type X11, connection :0.0, unitID 0, handle 0x0], but: []
at javax.media.opengl.GLProfile.get(GLProfile.java:779)
at javax.media.opengl.GLProfile.getDefault(GLProfile.java:563)
at javax.media.opengl.GLProfile.getDefault(GLProfile.java:574)
at chemaxon.marvin.space.GraphicScene.<init>(GraphicScene.java:217)
at chemaxon.marvin.space.MSpaceEasy.<init>(MSpaceEasy.java:119)
at chemaxon.marvin.space.MSpaceEasy.<init>(MSpaceEasy.java:98)
at chemaxon.marvin.space.gui.MSpaceFrameViewer.getMSpaceFrame(MSpaceFrameViewer.java:68)
at chemaxon.marvin.space.gui.MSpaceFrameViewer.getMSpaceViewer(MSpaceFrameViewer.java:59)
at chemaxon.marvin.space.gui.MSpaceViewerBase.get(MSpaceViewerBase.java:117)
at chemaxon.marvin.space.gui.MSpaceFrameViewer.get(MSpaceFrameViewer.java:51)
at chemaxon.marvin.space.gui.MSpaceViewerBase.callback(MSpaceViewerBase.java:100)
at chemaxon.marvin.common.swing.MolPanel.getMSpaceViewer(MolPanel.java:5962)
at chemaxon.marvin.sketch.swing.SketchPanel.openMSpace(SketchPanel.java:3342)
at chemaxon.marvin.sketch.swing.SketchPanel.doOpenMSpace(SketchPanel.java:2646)
at chemaxon.marvin.sketch.swing.actions.OpenMarvinSpaceAction.actionPerformed(OpenMarvinSpaceAction.java:26)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2018)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2341)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
at javax.swing.AbstractButton.doClick(AbstractButton.java:376)
at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833)
at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:877)
at java.awt.Component.processMouseEvent(Component.java:6505)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3321)
at java.awt.Component.processEvent(Component.java:6270)
at java.awt.Container.processEvent(Container.java:2229)
at java.awt.Component.dispatchEventImpl(Component.java:4861)
at java.awt.Container.dispatchEventImpl(Container.java:2287)
at java.awt.Component.dispatchEvent(Component.java:4687)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4832)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4492)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4422)
at java.awt.Container.dispatchEventImpl(Container.java:2273)
at java.awt.Window.dispatchEventImpl(Window.java:2719)
at java.awt.Component.dispatchEvent(Component.java:4687)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:723)
at java.awt.EventQueue.access$200(EventQueue.java:103)
at java.awt.EventQueue$3.run(EventQueue.java:682)
at java.awt.EventQueue$3.run(EventQueue.java:680)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:87)
at java.awt.EventQueue$4.run(EventQueue.java:696)
at java.awt.EventQueue$4.run(EventQueue.java:694)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:693)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:244)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:163)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:151)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:147)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:139)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:97)

When I look to see what version of Java I have installed (in the terminal: java -version), I get:
java version "1.7.0_07"
Java(TM) SE Runtime Environment (build 1.7.0_07-b10)
Java HotSpot(TM) 64-Bit Server VM (build 23.3-b01, mixed mode)

From the About window in MarvinSketch:
I am using: MarvinSketch 5.11.1,
My OS (Ubuntu 12.04 64-bit): amd64 Linux 3.2.0-31-generic
It is using: Oracle Corporation Java 1.7.0_07

Hi,

 

Java 7 is not officially supported by Marvin.

I see you tried to launch MarvinSpace from MarvinSketch.

Did you try running MarvinSpace separately?

Could you paste the contents of the terminal after running 'glxgears -info' ?

Regards,

Andras

akovacs wrote:

Hi,   Java 7 is not officially supported by Marvin. I see you tried to launch MarvinSpace from MarvinSketch. Did you try running MarvinSpace separately? Could you paste the contents of the terminal after running 'glxgears -info' ? Regards, Andras

Perhaps Java 7 is not helping, but I was originally having this problem using Java 1.6 and only upgraded in an attempt to see if it would work with that instead.  I can try and switch back.

If I try to run MarvinSpace using the Desktop icon I have, I do not see any error message, nothing happens at all (I guess the error is being surpressed and it just crashes quietly);  That is why I was opening it from MarvinSketch.

When I run "glxgears -info" in my termial (doing nothing else beforehand), the output I get is:
X Error of failed request: BadRequest (invalid request code or no such operation)
Major opcode of failed request: 136 (GLX)
Minor opcode of failed request: 19 (X_GLXQueryServerString)
Serial number of failed request: 12
Current serial number in output stream: 12

 

 

Hi,

The output of glxgears tells me, that your machine doesn't have the graphical capabilities to run MarvinSpace.

(OpenGL is not supported by your OS.)

 

You should fix this issue beforehand.

(I am not quite of a Linux expert, but if your Linux install does not have OpenGL support out-of-the-box you will have a hard time to hack it in. Unfortunately, I cannot help you in this.)

 

Regards,

Andras