Mac OS X

I installed MarvinSpace today. Once I set the java classpath I was able to get MarvinSketch to load from the command line. MarvinSpace almost loads and then stops with part of the GUI showing and throws the exception included below. I am running 10.4.2 with the most recent java 1.4.2.





The applet and webstart sort of run with Safari 2.0.1. Sometimes the file loads and draws sometimes not. None of the menu selections worked though.





We are really excited about this product at Carnegie Mellon University. Two professors have a huge amount of chime and rasmol scripts that are quickly becoming obselete due to lack of support and ignoring the mac platform. We really need MarvinSpace!





Jim Burnette


Department of Biological Sciences.





effie:/Applications/Marvin/bin jim$ ./mspace


License key file not found: /Users/jim/.chemaxon/licenses.dat


apple.awt.EventQueueExceptionHandler Caught Throwable : java.lang.UnsatisfiedLinkError: createContext


java.lang.UnsatisfiedLinkError: createContext


at net.java.games.jogl.impl.macosx.CGL.createContext(Native Method)


at net.java.games.jogl.impl.macosx.MacOSXGLContext.create(MacOSXGLContext.java:138)


at net.java.games.jogl.impl.macosx.MacOSXGLContext.create(MacOSXGLContext.java:121)


at net.java.games.jogl.impl.macosx.MacOSXGLContext.makeCurrent(MacOSXGLContext.java:175)


at net.java.games.jogl.impl.macosx.MacOSXOnscreenGLContext.makeCurrent(MacOSXOnscreenGLContext.java:118)


at net.java.games.jogl.impl.GLContext.invokeGL(GLContext.java:248)


at net.java.games.jogl.GLCanvas.maybeDoSingleThreadedWorkaround(GLCanvas.java:236)


at net.java.games.jogl.GLCanvas.display(GLCanvas.java:77)


at net.java.games.jogl.GLCanvas.paint(GLCanvas.java:86)


at sun.awt.RepaintArea.paint(RepaintArea.java:194)


at apple.awt.ComponentModel.handleEvent(ComponentModel.java:290)


at java.awt.Component.dispatchEventImpl(Component.java:3744)


at java.awt.Component.dispatchEvent(Component.java:3543)


at java.awt.EventQueue.dispatchEvent(EventQueue.java:480)


at java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:234)


at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:184)


at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:178) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:170) at java.awt.EventDispatchThread.run(EventDispatchThread.java:100)


apple.awt.EventQueueExceptionHandler

Dear Jim,





the OpenGL native library is not found by MarvinSpace, probably it was not installed properly. (Please note, that the installation of MarvinSpace is quite premature in the available distribution. A new release is due within days and it will solve this problem.)





Did you download the most recent Marvin Beans package?





The mspace application should pop up an error dialog in case it fails to install the JOGL library (ie. it cannot copy library file to an appropriate folder). Did such dialog appear on your display when you launched mspace?





The Safari browser related problems (menus don't work, instability) will be inverstigated and fixed ASAP. Thank you for reporting these problems.





Mac will be supported by MarvinSpace, though at present I cannot tell when will scripting be available. Chime and RasMol scripts will be accepted by MarvinSpace.





Regards,


Miklos

Yet another idea that could helps us to figure out what went wrong on your Mac with MarvinSpace: try to run the application with the -v flag in the command line. That runs MarvinSpace in verbose mode when it should give detailed report about configuration problems.


Could you please try it and send us the message that appear o your terminal window?





Cheers


Miklos

the OpenGL native library is not found by MarvinSpace, probably it was not installed properly. (Please note, that the installation of MarvinSpace is quite premature in the available distribution. A new release is due within days and it will solve this problem.)





On request is that when a folder is picked that the installer put everything into a sub folder called Marvin or Marvin Beans.To me this is the expected behavior on the mac. On the first install I choose /Applications and then the installer put a bunch of files scattered throughout the applications folder. I uninstalled and re-installed after creating a specific sub-folder and choosing that one.








Did you download the most recent Marvin Beans package?








Yes. Downloaded yesterday from the standard download link. No MarvinSpace icon appeared after download.





The mspace application should pop up an error dialog in case it fails to install the JOGL library (ie. it cannot copy library file to an appropriate folder). Did such dialog appear on your display when you launched mspace?





No. In fact it kept throwing null pointer exceptions as the partial window came in and of focus.





I found these two files at the root level of my hard drive. Do they really need to be at root?


libjogl_cg.jnilib


libjogl.jnilib





I also found libraries at /Applications/Marvin/bin





MarvinSketch opens just fine from the command line.





Can MarvinSketch scripts be generated on the pc and then used on the mac? That is just fine right now.





I tried MarvinSpace as a webstart and it had some of the problems I reported yesterday. When I double clicked the app that web start created the program seems to be fine. The menu options work (at least the couple I tried) and it loaded 1hkg.pdb. It could not load 1ereAB-1.pdb.





With 1hkg.pdb I can change the protein wire frame to ball and stic. It takes a while and the screen doesn't re-fresh until I click on the molecule. I tried doing secondary structure but it is bogged down in the computation. This is on a 1.67 MHz G4 powerbook with 512 mb memory.





Yet another idea that could helps us to figure out what went wrong on your Mac with MarvinSpace: try to run the application with the -v flag in the command line. That runs MarvinSpace in verbose mode when it should give detailed report about configuration problems.


Could you please try it and send us the message that appear o your terminal window?





I also looked in the system and console logs but found no java errors.





Hope all of this helps. Let me know if you need more information or want me to try something out.





Jim








effie:/Applications/Marvin/bin jim$ ./mspace -v


sun.java2d.noddraw: true


Java home directory: /System/Library/Frameworks/JavaVM.framework/Versions/1.4.2/Home


java.library.path = .:/Library/Java/Extensions:/System/Library/Java/Extensions:/usr/lib/java


libjogl.jnilib found at ./libjogl.jnilib


License key file not found: /Users/jim/.chemaxon/licenses.dat


JOGL version 1.1.0


Using single-threaded workaround of dispatching display() on event thread


apple.awt.EventQueueExceptionHandler Caught Throwable : java.lang.UnsatisfiedLinkError: createContext


java.lang.UnsatisfiedLinkError: createContext


at net.java.games.jogl.impl.macosx.CGL.createContext(Native Method)


at net.java.games.jogl.impl.macosx.MacOSXGLContext.create(MacOSXGLContext.java:138)


at net.java.games.jogl.impl.macosx.MacOSXGLContext.create(MacOSXGLContext.java:121)


at net.java.games.jogl.impl.macosx.MacOSXGLContext.makeCurrent(MacOSXGLContext.java:175)


at net.java.games.jogl.impl.macosx.MacOSXOnscreenGLContext.makeCurrent(MacOSXOnscreenGLContext.java:118)


at net.java.games.jogl.impl.GLContext.invokeGL(GLContext.java:248)


at net.java.games.jogl.GLCanvas.maybeDoSingleThreadedWorkaround(GLCanvas.java:236)


at net.java.games.jogl.GLCanvas.display(GLCanvas.java:77)


at net.java.games.jogl.GLCanvas.paint(GLCanvas.java:86)


at sun.awt.RepaintArea.paint(RepaintArea.java:194)

Dear Jim,





thank you for the details, it helped a lot. It seems that unfortunately we put incorrect version of jogl into the release.


Please delete the libjogl.jnilib from your root directory and place the attached libjogl.jnilib file into one of the following directories:


root , /Library/Java/Extensions, /System/Library/Java/Extensions, /usr/lib/java.


In the new version of MSpace the installation of jogl is fully rewritten. It will place libjogl.jnilib into your .chemaxon/lib directory. It will be released in the next days.


The other file, libjogl_cg.jnilib is unnecessary, please delete it from your root dir.


Please let us know how you succeed.