JVM out of memory in Marvin space

hello!


I am using Marvin space to display PDB structure, I call Marvin in Java Applet, it works fine in the first 10 structures, but gradually becomes slow. At last, prompt an error:


Not enough memory to complete operation.


Either close unnecessary components,or restart the program and increase the memory available to the JVM.


MarvinSketch/Swing 4.1.8


JVM: Sun Microsystems Inc. Java 1.6.0_01


Browser: sun.plugin 1.1


OS: x86 Windows XP 5.1


Running environment: Trusted Applet


Memory: 95.3M maximum, 30.4M total, 10.1M free





After viewing 10 PDB structures,iexplore.exe process cost 157MB memory, I think there maybe memory leaks, how to fix this problem?


this error is throwed by JVM or Marvin? Thanks!





my Email: liuhai _at_ mail.ustc.edu.cn liuhai _at_ mail.sioc.ac.cn

Hello Liu,





thank you for the report, we also got the stack trace you've sent to mspacebugs _at_ chemaxon.com.





It seems there is a problem with the secondary structures. We will analyse the report and get back soon!





Kind regards,


Judit

Judit wrote:

Hello Liu, thank you for the report, we also got the stack trace you've sent to mspacebugs _at_ chemaxon.com. It seems there is a problem with the secondary structures. We will analyse the report and get back soon! Kind regards, Judit

Hello,Judit





Glad to hear there exists the same problem, so Marvin has some bugs when dealing with the secondary structures,or the PDB format is not correct? Thanks for your team efforts to solve the problem,May you succeed!

We couldn't reproduce the problem yet, but from the report you've sent it has to be a MarvinSpace problem.


If the PDB file you used is not confidential and you could send us, it would be a great help!

Judit wrote:

We couldn't reproduce the problem yet, but from the report you've sent it has to be a MarvinSpace problem. If the PDB file you used is not confidential and you could send us, it would be a great help!

I can normally display the PDBs in Jmol, Jmol don't use hardware to render. It seems Marvin Space uses openGL to get better rendering quality, it just cost too many memory and throw java exception.





I will send some PDB files to your email box, that maybe helpful.

Marvin space applet parameter:molecule,seems can't recognize


relative path and dynamic files from database.





relative path can't find structure files:


<param name="molecule" value="./pdb/10gs.pdb">





And files readed from database also can't work


<param name="molecule" value="./pdb/outputfile?pdbcode=10gs">





absolute path works like


<param name="molecule" value="D:/pdb/10gs.pdb">








when using Jmol,<param> can read dynamic files,so I hope Marvin can also support this parameter.





<applet name="Jmol" code="JmolApplet" archive="JmolApplet.jar"


width="800" height="800">


<param name="load" value="outputfile.asp?pdbcode=10gs&pdbtype=ligand">


<param name="progressbar" value="true">


<param name="bgcolor" value="#000000">


<param name="style" value="shaded">


<param name="label" value="number">


<param name="script" value="move 0 0 360 0 0 0 0 0 5">


<param name="script" value="animate next">


<param name="perspectiveDepth" value="true">


</applet>

hi,judit:





You can test the problem I mentioned above, refresh the html page in marvin\examples\applets\example-mspace8.html, note to observe the memory that web browser costs, grow from 10MB to 150MB soon. You only need about 10 times page refreshments to get the OutofMemory Exception.





BTW: I have a PentiumD dualcore 3Ghz CPU,1G DDR RAM and a quadro FX540 video card. Can I use Anti-aliasing in Applet? Thank You!

Hi Liu,


1. We will try to investigate this memory problem.





2. The anti-aliasing applet parameter is missing indeed, we will include it.





You can now try it if you have a menubar in the applet.


To enable, check Anti-alias in the Display menu. However by default MarvinSpace disables this instantly on a mouse event. This is because weaker graphics cards have problems with it.





But since you have a good card it is worth trying it this way:


open the Options panel from the Display menu, choose the Controls tab, and uncheck 'Disable antialias on mouse move'. Now enable antialias, and give it a try!





3. We have to consult this internally and we will get back with an answer soon.

Judit:





Thanks for your patient reply! Good luck! Hope for a robust Marvin!





btw: Marvin space can't display anything in these platforms


Ubuntu Linux 7.04


Firefox2.0


J2SE 6u1





Redhat Linux Advanced Server


Firefox 1.5


J2SE 6u1





Windows XP


IE 7.0


JRE 6u1





but Marvin Sketch works on all platforms and browsers. Programs concerned with OpenGL are really difficult to keep compatible.

Hi Liu,





thank you for the detailed report, though it's still not really clear what the problem could have been. Was it the "natives already loaded by another classloader"?


After your report we checked


Ubuntu Linux 7.04


Firefox2.0


J2SE 6u1





Windows XP


IE 7.0


JRE 6u1





and MarvinSpace run without problem.


Actually we have tested MarvinSpace with a large scale of configurations (different platforms, browsers, graphic cards, java versions), and found that MarvinSpace can run without errors.


Perhaps it's easier and more robust to use Java Web Start to prevent running applets with different classloaders by chance.





Kind regards,


Judit

Judit wrote:

Hi Liu, thank you for the detailed report, though it's still not really clear what the problem could have been. Was it the "natives already loaded by another classloader"? After your report we checked Ubuntu Linux 7.04 Firefox2.0 J2SE 6u1 Windows XP IE 7.0 JRE 6u1 and MarvinSpace run without problem. Actually we have tested MarvinSpace with a large scale of configurations (different platforms, browsers, graphic cards, java versions), and found that MarvinSpace can run without errors. Perhaps it's easier and more robust to use Java Web Start to prevent running applets with different classloaders by chance. Kind regards, Judit

sorry, I forgot to change the PDB structure file path, because marvin space's java codebase was not in the same directory. When tested in my own computer, it worked well so i didn't find the problem cause.