Failure to load the latest MarvinSketch and web applet

Upon opening the latest MarvinSketch 5.3.8, I got this error.

java.lang.IllegalArgumentException: Malformed \uxxxx encoding.
    at java.util.Properties.loadConvert(Unknown Source)
    at java.util.Properties.load0(Unknown Source)
    at java.util.Properties.load(Unknown Source)
    at chemaxon.marvin.common.UserSettings.tryToLoad(Unknown Source)
    at chemaxon.marvin.common.UserSettings.tryToLoad(Unknown Source)
    at chemaxon.marvin.Sketch.main(Unknown Source)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
    at java.lang.reflect.Method.invoke(Unknown Source)
    at com.exe4j.runtime.LauncherEngine.launch(Unknown Source)
    at com.exe4j.runtime.WinLauncher.main(Unknown Source)

And when I try to load the web applet, first the security window pops out. I know this error should be fixed in 5.3.3, but I do not know how to fix that on the web page. Then after I click no to the warning windows, the whole applet window just either freezes at loading or just turns grey and not repsonding to me at all.

Trust me, I reinstalled all the browers(firefox, safari, IE), Java platform and marvinsketch I have but none of them fixes the web applet problem.

Please help me.

Can you show your applet page or the relevant part of the html document where you embed applet code?

I guess the problem may be with the embedded code.

How do you use applet (via web server or load it from the local machine)?

In second case, I can imagine that you can get malformedurl exception.

Please also describe your software environment (operating system, java and browser version). It can also help a lot in debugging of the issue for us.

I went to the Marvin 5.3.8 demo page at your site.  After Marvin loaded, I clicked the house cyclopentane and then clicked on the canvas.  Three times in a row, I got the beach ball of death and had to force-quit Safari.  This happened even after I cleared my Java and browser caches before trying again.

Needless to say, I don't think I will be upgrading to Marvin 5.3.8.  I sincerely hope that Marvin 5.4 is significantly improved.

An example of the web applet failure can be the mechanism calculator page, which is http://aceorganic.pearsoncmg.com/epoch-plugin/public/mechmarvin.jsp

But generally, marvinsketch does not work on any pages I opened up, including ace organic, ace organic browser check up, or the demo webpages.

I use the web applet via web servers, and my operating system is win 7 home premier. Java is the latest one standard version 6 update 21, 1.6.0_21- b07, all browsers updated to the latest one, and I mainly use firefox 3.6.8.

I uninstalled my anti-virus softwares and turned off firewalls, cleaned all caches and temporary files, reinstalled all browsers and java, but still could not get the thing to work. Gray screen on every web marvinsketch applet window. The weird thing is that I can neither use Marvinsketch web applet nor the application on my computer, while they can both work well on other computers.

bobgr wrote:

I went to the Marvin 5.3.8 demo page at your site.  After Marvin loaded, I clicked the house cyclopentane and then clicked on the canvas.  Three times in a row, I got the beach ball of death and had to force-quit Safari.  This happened even after I cleared my Java and browser caches before trying again. Needless to say, I don't think I will be upgrading to Marvin 5.3.8.  I sincerely hope that Marvin 5.4 is significantly improved.

Dear Bob,

We have checked all our examples and trhe demo page on all 3 Macs we have, and we can not reproduce this bug, I can draw everything without clearing caches, and after clearing them. Is this happening on all machines You use? Is there any information, or error message on the Java console? On which Mac version did You try that example? IS only the demo page buggy, or the oher MarvinSketch examples also?

Best Regards,

Peter

This example works for me under Windows 7 with latest JRE (1.6.0_21). When the warning message displays that Java attempts download untrusted resources, say NO. In this case, applet loads properly. If you choose Yes, downloading of certain resources will be blocked. So Marvin applet initalization will fail in this case. It is a Java specific issue that is introduced by Java 1.6.0_19 (loading policy is more strict than earlier). Newer Marvin versions (5.3.4 and above) includes workaround for this problem. If you use older Marvin version, downgrade Java version or switch off untrusted content checking in Java Control Panel. An example of the web applet failure can be the mechanism calculator page, which is http://aceorganic.pearsoncmg.com/epoch-plugin/public/mechmarvin.jsp

I clicked NO for the warning about it gives me the gray box.

Besides, how do you explain this error in marvin 5.3.8

 

java.lang.IllegalArgumentException: Malformed \uxxxx encoding.
    at java.util.Properties.loadConvert(Unknown Source)
    at java.util.Properties.load0(Unknown Source)
    at java.util.Properties.load(Unknown Source)
    at chemaxon.marvin.common.UserSettings.tryToLoad(Unknown Source)
    at chemaxon.marvin.common.UserSettings.tryToLoad(Unknown Source)
    at chemaxon.marvin.Sketch.main(Unknown Source)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
    at java.lang.reflect.Method.invoke(Unknown Source)
    at com.exe4j.runtime.LauncherEngine.launch(Unknown Source)
    at com.exe4j.runtime.WinLauncher.main(Unknown Source)

And this is the web applet error shown in the java console

 

JMSketch initalization has failed in Awt-EventQueue thread:
java.lang.IllegalArgumentException: Malformed \uxxxx encoding.
    at java.util.Properties.loadConvert(Unknown Source)
    at java.util.Properties.load0(Unknown Source)
    at java.util.Properties.load(Unknown Source)
    at chemaxon.marvin.common.UserSettings.tryToLoad(Unknown Source)
    at chemaxon.marvin.common.swing.MolPanel.<init>(Unknown Source)
    at chemaxon.marvin.sketch.swing.SketchPanel.<init>(Unknown Source)
    at JMSketch.a(Unknown Source)
    at JMSketch.init(Unknown Source)
    at JMSketchLaunch.changeSlapshToApplet(Unknown Source)
    at AppletLaunch$2.run(Unknown Source)
    at java.awt.event.InvocationEvent.dispatch(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,

i have an assupmtion about the cause of the problem. It can be your marvin.properties file itself.

Can you send me the file either via e-mail, or via this topic, and in paralel delete the file contents and test your site against the empty file?

The file is located under the user home directory in chemaxon or .chemaxon folder depending on your operating system.

Regards,
Istvan

Thanks a lot Istvan! Problem solved!

I'm glad to hear, thank you for the report.

Istvan

pvadasz wrote:

bobgr wrote: I went to the Marvin 5.3.8 demo page at your site.  After Marvin loaded, I clicked the house cyclopentane and then clicked on the canvas.  Three times in a row, I got the beach ball of death and had to force-quit Safari.  This happened even after I cleared my Java and browser caches before trying again. Needless to say, I don't think I will be upgrading to Marvin 5.3.8.  I sincerely hope that Marvin 5.4 is significantly improved. Dear Bob, We have checked all our examples and trhe demo page on all 3 Macs we have, and we can not reproduce this bug, I can draw everything without clearing caches, and after clearing them. Is this happening on all machines You use? Is there any information, or error message on the Java console? On which Mac version did You try that example? IS only the demo page buggy, or the oher MarvinSketch examples also? Best Regards, Peter

The Marvin example pages exhibit similar behavior as the demo page, though not as severe.  It seems to me that the initial applet load and the loading of individual modules is what is causing the problem.  If I try a new action, like Insert -> Templates -> Generics -> benzene, and my browser doesn't hang while the module is loading, after that the action can usually be done without any delay at all.  But it's unacceptable to wait 45 seconds to draw my first bond, and when I see the beach ball of death, it usually means I have to force-quit my browser.  

I'm running MacOS 10.5.8, Java 1.5.0_24, Safari 5.0.2 on a desktop iMac.  I don't recall whether I tried it on either of my Macs at home.  

Dear Bob,

We have a machine with the same configuration. I have tried again drawing bonds, inserting templates from the menu, and from the toolbar and after the first tests again with empty cache in the demo page, and in most of the examples. Drawing and inserting generic tamplates works without a delay, opening the menus may require a small module loading (the icons for the menus the first time, if the cache is empty).

It's really strange that it takes so much time to draw Your first bond on Mac or that Safari freezes... I have one more idea: We are loading rarely used modules in the background after the applet is loading, and maybe that slows the applet - we have been using this backgound loading for a long time, and it is working good since then, but the applet does nothing else before You draw the first bond. We have an applet example where it is switched off, maybe that would work for You:

https://www.chemaxon.com/devel/marvin/examples/applets/sketch/preload.html

When there is a big delay, or a crash in Safari, is there any messages on the java console?

Best Regards,

Peter

The example where you turn off background loading also takes a while to load, giving me the beach ball, but once it loads, it does indeed perform much better.  There is no longer a delay in using templates or drawing bonds and atoms.  There was a slight delay when I right-clicked to bring up an atom menu, but nothing terrible.

Incidentally, the page to which you pointed me is showing MarvinSketch 5.3.7beta1, not 5.3.8.  

My Mac at home displays the same behavior on the Marvin 5.3.8 demo page that my Mac at work does.  My Mac at home is running MacOS 10.5.8, Safari 5.0.2, Java 1.5.0_24.  

I just noticed that when I get the beach ball on your Marvin demo page, the status bar at the bottom of the Safari window says, "Modeule is loading..."  I have attached the stack report from after I force-quit Safari after it hangs.

bobgr wrote:

The example where you turn off background loading also takes a while to load, giving me the beach ball, but once it loads, it does indeed perform much better.  There is no longer a delay in using templates or drawing bonds and atoms.  There was a slight delay when I right-clicked to bring up an atom menu, but nothing terrible. Incidentally, the page to which you pointed me is showing MarvinSketch 5.3.7beta1, not 5.3.8.   My Mac at home displays the same behavior on the Marvin 5.3.8 demo page that my Mac at work does.  My Mac at home is running MacOS 10.5.8, Safari 5.0.2, Java 1.5.0_24.   I just noticed that when I get the beach ball on your Marvin demo page, the status bar at the bottom of the Safari window says, "Modeule is loading..."  I have attached the stack report from after I force-quit Safari after it hangs.

Dear Bob,

Sorry, the right link is:

 https://www.chemaxon.com/marvin/examples/applets/sketch/preload.html

I do not know how did I get into the devel directory...

Thank You for the tests, I will show these to the developer working on the modules, and the background loading.

Best Regards,

Peter

Hi Bob,

We know about a Safari freezing issue. It occurs when you would like to detach a dialog from the sketch applet.

If the "Module is loading" dialog appears before the desired dialog, Safari may freezes. We are still investigating this issue. Our assumption is that there is a conflict among drawing threads ("Module is loading" vs. other dialog).

This problem appears only in Safari.

Can you confirm that you met with the same problem on the Marvin demo page? Can you give a scenario how to reproduce the same issue that you have reported? What had you done before "Module is loading" text appeared?

Tamas wrote:

Can you confirm that you met with the same problem on the Marvin demo page? Can you give a scenario how to reproduce the same issue that you have reported? What had you done before "Module is loading" text appeared?

Yes, the problem occurs on the Marvin demo page.

For example:

1. Click Insert, wait a second.


2. Click Template Library, wait 10-15 seconds.


3. Click Generic, wait a few seconds.


4. Click on Cyclopentane, wait a second, and close.


5. Click on the canvas, wait a few seconds, move the cursor, see the beach ball appear.

I see "Module is loading..." after pretty much every action.

Hi,

I have followed your scenario.

After placing the template to the canvas and moving the mouse, I got the beachball as you had described.

But after a couple of seconds I got back the control and I could draw again. The "Module is loading" dialog did not displayed to me.

I have tested it on OS X 10.5.8 with Safari 5.0 and Java 1.5.0_24.

I continue to have problems with MarvinSketch at this page on MacOS 10.5.8, Safari 5.0.

This time I opened the Java console before going to your page.  I noticed that after MarvinSketch appeared, the Java console continued to scroll by for what seemed like 5 minutes with output like this:

]

security: Comparing certificate against Root CA certificate:

[

[

  Version: V3

  Subject: CN=GlobalSign, O=GlobalSign, OU=GlobalSign Root CA - R2

  Signature Algorithm: SHA1withRSA, OID = 1.2.840.113549.1.1.5



  Key:  Sun RSA public key, 2048 bits

  modulus: 21057703584475184807565557524537816321491861642060041763647257260224980509300477196924243590718942686590709107534863816871998744486217397041943036790668349398596465655712023148303173173625617456109014852791089527884590320201838663822684972532489783525944263241117811947512306928924706019699374824809368116805968844700689553244922646662031817428598871924656385681991340984751484716908148967287908171187321560857250025694833777855463632395686856225456740364321799926634676042609958611723658984406384068047734580405304178873193147583468071249577706812402337331306461396767845742998827081874578148453783909473879293336463

  public exponent: 65537

  Validity: [From: Fri Dec 15 03:00:00 EST 2006,

               To: Wed Dec 15 03:00:00 EST 2021]

  Issuer: CN=GlobalSign, O=GlobalSign, OU=GlobalSign Root CA - R2

  SerialNumber: [    04000000 00010f86 26e60d]



Certificate Extensions: 5

[1]: ObjectId: 2.5.29.14 Criticality=false

SubjectKeyIdentifier [

KeyIdentifier [

0000: 9B E2 07 57 67 1C 1E C0   6A 06 DE 59 B4 9A 2D DF  ...Wg...j..Y..-.

0010: DC 19 86 2E                                        ....

]

]



[2]: ObjectId: 2.5.29.35 Criticality=false

AuthorityKeyIdentifier [

KeyIdentifier [

0000: 9B E2 07 57 67 1C 1E C0   6A 06 DE 59 B4 9A 2D DF  ...Wg...j..Y..-.

0010: DC 19 86 2E                                        ....

]



]



[3]: ObjectId: 2.5.29.31 Criticality=false

CRLDistributionPoints [

  [DistributionPoint:

     [URIName: http://crl.globalsign.net/root-r2.crl]

]]



[4]: ObjectId: 2.5.29.15 Criticality=true

KeyUsage [

  Key_CertSign

  Crl_Sign

]



[5]: ObjectId: 2.5.29.19 Criticality=true

BasicConstraints:[

CA:true

PathLen:2147483647

]



]

  Algorithm: [SHA1withRSA]

  Signature:

0000: 99 81 53 87 1C 68 97 86   91 EC E0 4A B8 44 0B AB  ..S..h.....J.D..

0010: 81 AC 27 4F D6 C1 B8 1C   43 78 B3 0C 9A FC EA 2C  ..'O....Cx.....,

0020: 3C 6E 61 1B 4D 4B 29 F5   9F 05 1D 26 C1 B8 E9 83  <na.MK)....&....

0030: 00 62 45 B6 A9 08 93 B9   A9 33 4B 18 9A C2 F8 87  .bE......3K.....

0040: 88 4E DB DD 71 34 1A C1   54 DA 46 3F E0 D3 2A AB  .N..q4..T.F?..*.

0050: 6D 54 22 F5 3A 62 CD 20   6F BA 29 89 D7 DD 91 EE  mT".:b. o.).....

0060: D3 5C A2 3E A1 5B 41 F5   DF E5 64 43 2D E9 D5 39  .\.>.[A...dC-..9

0070: AB D2 A2 DF B7 8B D0 C0   80 19 1C 45 C0 2D 8C E8  ...........E.-..

0080: F8 2D A4 74 56 49 C5 05   B5 4F 15 DE 6E 44 78 39  .-.tVI...O..nDx9

0090: 87 A8 7E BB F3 79 18 91   BB F4 6F 9D C1 F0 8C 35  .....y....o....5

00A0: 8C 5D 01 FB C3 6D B9 EF   44 6D 79 46 31 7E 0A FE  .]...m..DmyF1...

00B0: A9 82 C1 FF EF AB 6E 20   C4 50 C9 5F 9D 4D 9B 17  ......n .P._.M..

00C0: 8C 0C E5 01 C9 A0 41 6A   73 53 FA A5 50 B4 6E 25  ......AjsS..P.n%

00D0: 0F FB 4C 18 F4 FD 52 D9   8E 69 B1 E8 11 0F DE 88  ..L...R..i......

00E0: D8 FB 1D 49 F7 AA DE 95   CF 20 78 C2 60 12 DB 25  ...I..... x.`..%

00F0: 40 8C 6A FC 7E 42 38 40   64 12 F7 9E 81 E1 93 2E  @.j..B8@d.......

I wonder whether these background processes have something to do with the problems I'm seeing.  If I waited for the Console output to subside, Marvin's performance was acceptable.

In Java preferences, I have checked J2SE 5.0 32-bit, then Java SE 6 64-bit, then J2SE 5.0 64-bit in that order.  Perhaps the version of Java makes a difference for performance?  I know it does for MacOS 10.6.

As MarvinSketch started, a background thread has been launched to load-in rested modules (that are not in the memory yet).

It is useful to fast up the starting time of new modules.

You can switch this feature off/on by the bgloadEnabled parameter (in default, it is active).