Java Mac OSX 10.6 Update 12 Problem with Matlabpool?

I recently installed an automatic update for Java (yesterday). And since doing so, I am getting the following error when I attempt to run computations in parallel using matlabpool:

"??? Error using ==> matlabpool at 125 Java exception occurred: java.lang.NullPointerException at java.util.logging.Logger.demandLogger(Logger.java:286) at java.util.logging.Logger.getLogger(Logger.java:321)

Error in ==> LR_SL at 50 matlabpool open 4;"

Before installing this update to Java, I have had no problems running matlabpool in the local configuration. It seems that this error is thrown in the subroutine iVerifyJava().

I am running Matlab 2010b. I have tried running the matlabpool command in 2010a, but to no avail.

Any help would be greatly appreciated.

Thanks!

[Kruthika Venkatathri]

Please follow the steps in this bug report: http://www.mathworks.com/support/bugreports/919688

It resolves the issue.

Answer 1

[Andreas Goser]

MathWorks Development created a patch for this. It will be published soon - together with a related issue. I will post the link to this bug report and patch as soon as it is available. If the workarounds don't work for you, or you have an urgent need for the patch, please contact Technical Support and refer to this thread and they will provide the patch.

[Andreas Goser]

This is the link to the bug report with the patch

http://www.mathworks.com/support/bugreports/919688

[Andi]

Hi, I unzipped the patch in the /Applications folder (where Matlab app resides, Mac OS 10.6.8), restarted Matlab. I am getting two types of error msgs after successively trying to open matlabpool:

>> matlabpool open (FIRST TIME)
??? Error using ==> matlabpool at 125
Java exception occurred:
java.lang.NullPointerException
  at java.util.logging.Logger.demandLogger(Logger.java:286)
  at java.util.logging.Logger.getLogger(Logger.java:321)

>> matlabpool open(SECOND TIME)
??? Error using ==> matlabpool at 125
The class distcomp.typechecker has no property or method named 'getDefaultValue'.

...Then when I run matlabpool close:

>> matlabpool close
??? Error using ==> matlabpool at 133
Undefined function or variable 'distcomp.interactiveclient'.

[Andreas Goser]

I just come off the phone with a user who successfully installed the patch for R2012b. Which release are you using? This user pointed out step 3 was important (exit MATLAB).

[Andi]

I am using R2011a. I cannot update to R2012 because of financial considerations. I did exit Matlab and I also tried it after restarting the computer. Is the patch designed around R2012 specifically or is it a general one? I am using Java 1.6.0_39. Is it be worth updating to 1.6.0_41? Many thanks in advance!

[Jorik]

Hi Andi, in your message you state you extracted the patch to /Applications. The patch was designed to be extracted in matlabroot.

1. Please first run the following in MATLAB:

>> matlabroot

This will give you the path into which you should extract the zip-file.

2. Open the Terminal application, that is part of Mac OS X and is installed in /Applications/Utilities

3. Once Terminal is open, please change to the directory given with matlabroot, for instance:

$ cd /Applications/MATLAB_R2011a.app

4. Make sure MATLAB is closed and then extract the downloaded patch with the unzip command, if the patch is in your Downloads folder, you could use the following command

$ unzip ~/Downloads/attachment_919688_10b_11a_2013-02-27.zip

If you receive any warning or error message, you may need to have administrative rights to unzip the files, if so, please use the sudo command:

$ sudo unzip ~/Downloads/attachment_919688_10b_11a_2013-02-27.zip

This will prompt for you own password.

[Jorik]

If you downloaded the .zip with Safari, it may have extracted it automatically. Please use a different browser, or disable the automatic extraction as explained on this page, such that you actually have the .zip-file instead of the extracted version in a directory.

[Andi]

Jorik, thanks. My mistake was that I was unzipping to /Applications and not to /Applications/MATLAB_R2011a.app... Everything works now! Many thanks to everybody and kudos to Matlab people for the prompt action!

[Boyu]

I am having the same issue with 2010a, do you provide fix for this version?

Thanks.

[Saurabh Bhatia]

Is there a fix for 2010a?

[Wynn]

Just repeating the previous requests for a 2010a fix. This is the most recent available version of 32-bit MATLAB for Mac, so I need to use this version.

Answer 2

[Danny]

It seems I have the same problem.

'matlabpool' command doesn't work anymore after I've installed Mac OS X Java update yesterday.

The environment is, Mac OS X 10.6.8, Java 1.6.0_39 (build 1.6.0_39-b04-442-10M4008), Matlab 2012a and 2012b.

But I guess I managed to fix the problem.

First, start up the Matlab.

Before executing your codes (probably containing 'matlabpool' command), just run the Cluster Profile Manager'. (In the menu, 'Parallel' >> 'Manage Cluster Profiles')

Then, close the Cluster Profile Manager. You don't have to do anything in it. Just open and close.

Now, try to run your codes.

This has fixed my problem though I have no idea why it works.

Good luck.

[Andi]

This doesn't work in R2011a. I am thinking of reverting back to Java 1.6.0_37 since I cannot afford to wait too much until a fix is found. Would it be safe to just install it or do I have to uninstall Java 1.6.0_39 first? Many thanks!

[Danny]

My tip works only if you do it right after starting up Matlab.

If you've already run your codes before trying to open and close the Cluster Profile Manager, then my tip doesn't work.

I recommend you to try it again as I said.

Anyhow, I'm not sure, but I don't think it's a good idea to revert the installed Java version back to the old one. Hmm..

[Jack]

This trick worked for me, too, running R2012a on 10.7.5 after applying yesterday's Java update to 1.6.0_41. It does appear essential to open the Cluster Profile Manager immediately upon startup, before executing any commands.

[Theda]

This trick used to work fine for me in the past, now every time I open "Parallel -> Manage Configurations", I get the following error:

_??? The class distcomp.typechecker has no property or method named 'getDefaultValue'.

Error in ==> distcomp.configsection.configsection at 50 obj.PropValue{i} = distcomp.typechecker.getDefaultValue(obj.Types{i});

Error in ==> distcomp.configuration.pConstructFromClassTypes at 39 obj.findResource = distcomp.configsection('findResource', props, types, isRW);

Error in ==> distcomp.configuration.pInitializeFromName at 21 obj.pConstructFromClassTypes(type);

Error in ==> distcomp.configuration.getJavaReference at 15 conf.pInitializeFromName(name);_

I use R2010a, so the bug report does not work for me. Does anyone else have found another way to go about this?

[Tiago]

Amazing, it actually works!!! Great. Type 'prefdir', go to that folder and delete file parallel.setting. Initiate MATLAB, go to 'parallel' and 'manage cluster profiles', then close it. Matlab will create a new parallel.setting file inside prefdir folder. Then you can use parallel computing. Worked for me!! Thanks!!! Environment: MacOS 10.9.1, JAVA 1.7.0_51-b13, MATLAB 2013a. Cheeeeeeers!!!

Answer 3

[Andreas Goser]

This issue was brought to the attention of MathWorks Technical Support earlier this week. This issue is reproducible and being investigated together with Development. In case you contact MathWorks Technical Support, you can refer to this thread and 'SR 1-LF8FNT'.

[Andreas Goser]

In addition, we tried to apply Danny's workaround and this one also works here.

[Andi]

On R2012 or R2011?

Answer 4

[Thomas]

What java version are you at.

Open terminal and type

java -version

I tested with

java version "1.6.0_37"
Java(TM) SE Runtime Environment (build 1.6.0_37-b06-434-11M3909)
Java HotSpot(TM) 64-Bit Server VM (build 20.12-b01-434, mixed mode)

on R 2010b sp1 --- R2012b (all releases in between)

on OSX 10.7.5 and on OSX 10.6.8 and the local matlabpool works fine on both.

[Thomas]

I guess updating to JAVA 1.6.0_39 causes matlabpool to break on Matlab R2011b and older. Maltabpool works fine on R 2012a. I would hold off upgrading if one is on 2011b or older till a solutions is found.

Even on R2012a I have to run the validation of the local configuration before I can use matlabpool every time I start MATLAB.

[Andi]

Thomas, do you know if it's safe to install Java 1.6.0_37 after I've installed 0_39? Do I have to uninstall 0_39?

Answer 5

[Jason]

Hi all, Glad to see there's a common audience for this. The 'trick' of validating upon startup seems to work, but this is unnecessarily cumbersome. It is a downgrade, rather than an upgrade.

Mathworks people, do you have an automated work-around for this? Perhaps a way to run the validation upon startup? Even still, this is time-consuming for launching Matlab so a proper fix for this Java incompatibility would be best. Please update on when this will be happening.

[Andreas Goser]

Development is working on this. I will keep you updated.

Answer 6

[Hiroki]

I am also getting the same error on OSX 10.6.8. Java for Mac OSX 10.6 Update 12 came with:

 java version "1.6.0_39"
 Java(TM) SE Runtime Environment (build 1.6.0_39-b04-442-10M4008)
 Java HotSpot(TM) 64-Bit Server VM (build 20.14-b01-442, mixed mode)

Answer 7

[Thomas]

I have the latest version of Java and had no luck until uninstalling R2011B and updating to R2012B. At this point, I had to run a validation before the system ran correctly. FYI

Answer 8

[Reynaldo]

The trick Danny proposed works for me too. I am using 1.6.0_41. Please notify us as soon as a fix is found!

Answer 9

[Jason]

Thanks, all, for responding on this. But is there any way to have the parallel work without having to run validation manually upon startup??

[Jason Ross]

See Andreas' response above -- a patch is in the works, or you can contact Technical Support directly.

Answer 10

[Jon]

I just did everything as explained above, updated toolbox cache in the preferences and tried matlabpool and got:

Error using matlabpool (line 134) Undefined function 'distcomp.fileserializer' for input arguments of type 'distcomp.filestorage'.

I cannot find this file anywhere. Any ideas?

Best Jon

[Akitada]

I am having the same problem...

[Jason Ross]

There is a patch available now. See

http://www.mathworks.com/support/bugreports/919688

[Akitada]

That perfectly worked for me. Thanks!

Answer 11

[Ferenc]

Hello,

I am getting these errors with Matlab 2013a on OS X 10.8.2.

>> matlabpool
Error using matlabpool (line 134)
Java exception occurred:
java.lang.NullPointerException
  at java.util.logging.Logger.demandLogger(Logger.java:286)
  at java.util.logging.Logger.getLogger(Logger.java:321)

>> matlabpool
Starting matlabpool using the 'local' profile ... Warning: an error occurred while parsing class distcomp.fileserializer:
Attempt to reference field of non-structure array.

> In distcomp.filestorage.filestorage at 49
  In CJSCluster>CJSCluster.CJSCluster at 487
  In Local.Local>Local.Local at 302
  In parcluster at 51
  In ProfileConfigHelper>ProfileConfigHelper.buildScheduler at 76
  In MatlabpoolHelper>MatlabpoolHelper.parseMatlabpoolInputs at 290
  In MatlabpoolHelper>MatlabpoolHelper.parseInputsAndCheckOutputsForFunction at 100
  In matlabpool at 130 

Error using matlabpool (line 134)
Undefined function 'distcomp.fileserializer' for input arguments of type
'distcomp.filestorage'.

>> matlabpool
Starting matlabpool using the 'local' profile ... 
Error using matlabpool (line 134)
Undefined function 'distcomp.fileserializer' for input arguments of type
'distcomp.filestorage'.

Can anyone help?

Thanks, Ferenc

[Jason Ross]

http://www.mathworks.com/support/bugreports/919688

Answer 12

[Koji]

Hi,

I am trying to work on Distributed Computing Toolbox 3.2 (R2007b) installed on OSX 10.8.3, and I think I am having a similar JVM problem:

-------------

>> matlabpool

??? Undefined function or variable 'distcomp.interactiveclient'.

Error in ==> matlabpool at 82

client = distcomp.getInteractiveObject();

>>

-------

I know a bug report is here:

http://www.mathworks.com/support/bugreports/919688

but a patch for R2007b looks remaining undeveloped.

Can anyone help me?

Best wishes,

Koji

[Thomas Ibbotson]

Hi Koji,

I'm afraid there's no patch available for R2007b. Your only options are to either upgrade your version of MATLAB or downgrade your version of the JVM.

Tom

[Koji]

Hi Tom,

Thank you for your suggestions. Do you have a recommendation for a version of JVM? My OSX currently has 1.6.0_45.

Thanks again,

Koji

Answer 13

[Joost]

Matlab 2013a generates a series of java errors when attempting to open the editor. This is what I get:

java.lang.NullPointerException at sun.reflect.UnsafeFieldAccessorImpl.ensureObj(UnsafeFieldAccessorImpl.java:36) at sun.reflect.UnsafeObjectFieldAccessorImpl.get(UnsafeObjectFieldAccessorImpl.java:18) at java.lang.reflect.Field.get(Field.java:358) at apple.awt.CAccessibility.getAccessibleRoleFor(CAccessibility.java:200) at apple.awt.CAccessibility$11.call(CAccessibility.java:215) at apple.awt.CAccessibility$11.call(CAccessibility.java:212) at apple.awt.CToolkit$CallableWrapper.run(CToolkit.java:1125) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:199) at apple.awt.CToolkit$CPeerEvent.dispatch(CToolkit.java:1215) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:708) at java.awt.EventQueue.access$400(EventQueue.java:82) at java.awt.EventQueue$2.run(EventQueue.java:669) at java.awt.EventQueue$2.run(EventQueue.java:667) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) at java.awt.EventQueue.dispatchEvent(EventQueue.java:678) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188) at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)

As a result, I can no longer use Matlab. I have removed matlab entirely and reinstalled it without effect. I have applied the fix mentioned above, no positive result.

Hopefully someone can help because I am dead in the water right now.

I am using java 7 update 21, OSX 10.8.3

Answer 14

[GradStudent]

Don't use http://www.mathworks.com/support/bugreports/919688 for R2013a!!

Just open the cluster manager, allow it to (automatically) create a local cluster, and then run the verification tests. More info here: http://www.mathworks.com/help/distcomp/clusters-and-cluster-profiles.html

I applied the patch, and Matlab wouldn't open (Mac OS 10.8.5, java version "1.6.0_65" - java 7, update 51). Only deleting matlab and reinstalling it fixed the problem (I had no indication what the problem was).

[David]

I have R2013a, OSX 10.7.5, and cluster manager wouldn't validate. I received several errors. I followed the bug report fix you linked and resolved my problem. But I see you have a newer version of OSX. So…

[Oi]

Same problem here

Answer 15

[Brian]

Can't use matlabpool too on Mac OS 10.9.2, R2013a student version, with :

java version "1.6.0_65"
Java(TM) SE Runtime Environment (build 1.6.0_65-b14-462-11M4609)
Java HotSpot(TM) 64-Bit Server VM (build 20.65-b04-462, mixed mode)

The trick proposed By Blake worked once but now i'm getting several errors when I try to use matlabpool or even when I just open the cluster manager. I also tried the patch but it didn't fix the problem.

Since I updated java I have many problems. For instance, I can't open matlab through the spotlight, I have to use the sudo sh command in the terminal!

Should I try to reinstall an older version of java ?

[Radwa]

I have R2012a and MAC 10.6.8 I upgrade java to update 17 , and matlab didn't open should I downgrade it?

Answer 16

[jacob lalaounis]

Hi all,

I used this http://www.mathworks.com/support/bugreports/919688 and now Matlab does not work, i am using Matlab 2012.a on Mac OSX 10.9.5

If you have find a solution, it would be great to share, thank you in advance, Jacob