unexplainable memory limit in ImageJ64

[Robert Dougherty]

Dear ImageJ people,

I'm getting <Out of memory> errors at 653 MB in ImageJ64, regardless  
of the amount of memory assigned in Options/Memory & Threads.  The  
patient is a MacBook Pro with 4 GB of memory running OS X 10.5.2.  
ImageJ version 1.4.1k, Java version 1.4.2_16.  It does not seem to  
matter how I get to 653 MB: the same thing happens with a complicated  
plugin or just opening the mri-stack sample and scaling it up.  The  
memory monitor shows only 35% used, or so. The problem is specific to  
ImageJ64.  The 32-bit version of ImageJ works fine.  I suspected a  
hardware problem because the memory expansion from 2 GB to 4 GB  
included breaking the little clips that retain the cards.  (The proper  
way to disengage the clips is to spread them horizontally, not pry  
them up...) However, an extended hardware test revealed no problems.  
Any ideas?  Another ImageJ64 puzzle is that Quicktime works on one  
MacBook pro, but not a seemingly identical other one when running  
ImageJ64.  It works on both machines with regular ImageJ.

Bob


Robert Dougherty, Ph.D.
President, OptiNav, Inc.
10900 NE 8th St, Suite 900
Bellevue, WA 98004
Tel. [phone]
FAX [phone]
www.optinav.com
[hidden email]

[Albert Cardona]

Bob,

Unless I am very confused, MacOSX supports 64-bit only for java 1.6.0,
and not all 1.6.0 packages --you have to download it from the
developer.apple.com. AFAIK the 1.4.2_16 won't work in 64-bit mode.


Albert

--
Albert Cardona
http://www.mcdb.ucla.edu/Research/Hartenstein/acardona

[Robert Dougherty]

Albert,

That's it. Thanks.  I'll try it soon.

Bob

On Sep 9, 2008, at 3:06 PM, Albert Cardona wrote:

> Bob,
>
> Unless I am very confused, MacOSX supports 64-bit only for java  
> 1.6.0, and not all 1.6.0 packages --you have to download it from  
> the developer.apple.com. AFAIK the 1.4.2_16 won't work in 64-bit mode.
>
>
> Albert
>
> --
> Albert Cardona
> http://www.mcdb.ucla.edu/Research/Hartenstein/acardona
>

[Wayne Rasband]

On Sep 9, 2008, at 5:46 PM, Robert Dougherty wrote:

> Dear ImageJ people,
>
> I'm getting <Out of memory> errors at 653 MB in ImageJ64,  
> regardless of the amount of memory assigned in Options/Memory &  
> Threads.  The patient is a MacBook Pro with 4 GB of memory running  
> OS X 10.5.2.  ImageJ version 1.4.1k, Java version 1.4.2_16.  It  
> does not seem to matter how I get to 653 MB: the same thing happens  
> with a complicated plugin or just opening the mri-stack sample and  
> scaling it up.  The memory monitor shows only 35% used, or so. The  
> problem is specific to ImageJ64.  The 32-bit version of ImageJ  
> works fine.  I suspected a hardware problem because the memory  
> expansion from 2 GB to 4 GB included breaking the little clips that  
> retain the cards.  (The proper way to disengage the clips is to  
> spread them horizontally, not pry them up...) However, an extended  
> hardware test revealed no problems.  Any ideas?

ImageJ64 requires Java 1.5 or later, Mac OS X 10.5 and a 64-bit Intel  
processor. Java 1.6, which is 64-bit only, is available via Software  
Update, although it is is not made the default version of Java.  To  
make it the default, switch to "Java SE 6 (64-bit)" in /Applications/
Utilities/Java/Java Preferences.

>   Another ImageJ64 puzzle is that Quicktime works on one MacBook  
> pro, but not a seemingly identical other one when running  
> ImageJ64.  It works on both machines with regular ImageJ.

QuickTime for Java is not 64-bit compatible. The machine it is  
working on is probably running 32-bit Java and the other one is  
probably running 64-bit Java. The title of the Edit>Options>Memory &  
Threads dialog box changes to "Memory (64-bit)" when ImageJ is  
running on a 64-bit version of Java.

-wayne

[sisan]

Wayne Rasband wrote

On Sep 9, 2008, at 5:46 PM, Robert Dougherty wrote:

> Dear ImageJ people,
>
> I'm getting <Out of memory> errors at 653 MB in ImageJ64,  
> regardless of the amount of memory assigned in Options/Memory &  
> Threads.  The patient is a MacBook Pro with 4 GB of memory running  
> OS X 10.5.2.  ImageJ version 1.4.1k, Java version 1.4.2_16.  It  
> does not seem to matter how I get to 653 MB: the same thing happens  
> with a complicated plugin or just opening the mri-stack sample and  
> scaling it up.  The memory monitor shows only 35% used, or so. The  
> problem is specific to ImageJ64.  The 32-bit version of ImageJ  
> works fine.  I suspected a hardware problem because the memory  
> expansion from 2 GB to 4 GB included breaking the little clips that  
> retain the cards.  (The proper way to disengage the clips is to  
> spread them horizontally, not pry them up...) However, an extended  
> hardware test revealed no problems.  Any ideas?

ImageJ64 requires Java 1.5 or later, Mac OS X 10.5 and a 64-bit Intel  
processor. Java 1.6, which is 64-bit only, is available via Software  
Update, although it is is not made the default version of Java.  To  
make it the default, switch to "Java SE 6 (64-bit)" in /Applications/
Utilities/Java/Java Preferences.

>   Another ImageJ64 puzzle is that Quicktime works on one MacBook  
> pro, but not a seemingly identical other one when running  
> ImageJ64.  It works on both machines with regular ImageJ.

QuickTime for Java is not 64-bit compatible. The machine it is  
working on is probably running 32-bit Java and the other one is  
probably running 64-bit Java. The title of the Edit>Options>Memory &  
Threads dialog box changes to "Memory (64-bit)" when ImageJ is  
running on a 64-bit version of Java.

-wayne

I get a similar <Out of Memory> error at around 640MB regardless of the Memory setting, like the original poster, except I'm running 64-bit Java--1.6.0_12.  In "About ImageJ..." the last line says 465MB of 3000MB (15%).  The title of the Edit>Options>Memory is "Memory (64-bit)".  I tried rebooting and updating to the latest ImageJ 1.42m to no avail.  I'm running 64-bit Vista w/ 4GB of RAM, no other programs open.

[sisan]

sisan wrote

I get a similar <Out of Memory> error at around 640MB regardless of the Memory setting, like the original poster, except I'm running 64-bit Java--1.6.0_12.  In "About ImageJ..." the last line says 465MB of 3000MB (15%).  The title of the Edit>Options>Memory is "Memory (64-bit)".  I tried rebooting and updating to the latest ImageJ 1.42m to no avail.  I'm running 64-bit Vista w/ 4GB of RAM, no other programs open.

OK, I solved my problem by running ImageJ as an Administrator, by right clicking on ImageJ.exe and then checking the box in the "Compatibility" panel.  Mind you, running as Administrator was suggested in the Install notes, but there it is implied that this is only necessary to use the "Memory & Threads..." option.  Indeed, I WAS initially prevented from using this option, but then I gave Users in the imagej directory (in "Program Files (x86)") full permissions and then I was able to generate the ImageJ.cfg file, and the max memory seemed to be updated.  However, as mentioned in the previous post, I would still run out of memory at around 640MB, followed by other oddities.  So I would recommend that the Run as Administrator box be checked as a matter of course if ImageJ is installed in the default folder.

[David Webster]

I don't know if this is the same thing, but Windows (XP, ME) limits an
application to a total (physical and virtual) memory allocation around 600
Mbytes. This has bitten me before with Matlab, so I assume it is the same
with imageJ.

David

On Fri, Apr 24, 2009 at 8:14 PM, sisan <[hidden email]> wrote:

> Wayne Rasband wrote:
> >
> > On Sep 9, 2008, at 5:46 PM, Robert Dougherty wrote:
> >
> >> Dear ImageJ people,
> >>
> >> I'm getting <Out of memory> errors at 653 MB in ImageJ64,
> >> regardless of the amount of memory assigned in Options/Memory &
> >> Threads.  The patient is a MacBook Pro with 4 GB of memory running
> >> OS X 10.5.2.  ImageJ version 1.4.1k, Java version 1.4.2_16.  It
> >> does not seem to matter how I get to 653 MB: the same thing happens
> >> with a complicated plugin or just opening the mri-stack sample and
> >> scaling it up.  The memory monitor shows only 35% used, or so. The
> >> problem is specific to ImageJ64.  The 32-bit version of ImageJ
> >> works fine.  I suspected a hardware problem because the memory
> >> expansion from 2 GB to 4 GB included breaking the little clips that
> >> retain the cards.  (The proper way to disengage the clips is to
> >> spread them horizontally, not pry them up...) However, an extended
> >> hardware test revealed no problems.  Any ideas?
> >
> > ImageJ64 requires Java 1.5 or later, Mac OS X 10.5 and a 64-bit Intel
> > processor. Java 1.6, which is 64-bit only, is available via Software
> > Update, although it is is not made the default version of Java.  To
> > make it the default, switch to "Java SE 6 (64-bit)" in /Applications/
> > Utilities/Java/Java Preferences.
> >
> >>   Another ImageJ64 puzzle is that Quicktime works on one MacBook
> >> pro, but not a seemingly identical other one when running
> >> ImageJ64.  It works on both machines with regular ImageJ.
> >
> > QuickTime for Java is not 64-bit compatible. The machine it is
> > working on is probably running 32-bit Java and the other one is
> > probably running 64-bit Java. The title of the Edit>Options>Memory &
> > Threads dialog box changes to "Memory (64-bit)" when ImageJ is
> > running on a 64-bit version of Java.
> >
> > -wayne
> >
> >
>
> I get a similar <Out of Memory> error at around 640MB regardless of the
> Memory setting, like the original poster, except I'm running 64-bit
> Java--1.6.0_12.  In "About ImageJ..." the last line says 465MB of 3000MB
> (15%).  The title of the Edit>Options>Memory is "Memory (64-bit)".  I tried
> rebooting and updating to the latest ImageJ 1.42m to no avail.  I'm running
> 64-bit Vista w/ 4GB of RAM, no other programs open.
> --
> View this message in context:
> http://n2.nabble.com/unexplainable-memory-limit-in-ImageJ64-tp1078657p2701372.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>

[Joachim Wesner]

Hi David,

>I don't know if this is the same thing, but Windows (XP, ME) limits an
>application to a total (physical and virtual) memory allocation around 600
>Mbytes. This has bitten me before with Matlab, so I assume it is the same
>with imageJ.

Where did you get this info from? Microsoft claims different (even on
Windows 2000)

http://msdn.microsoft.com/en-us/library/aa366778.aspx

"User-mode virtual address space for each 32-bit process

      2 GB: Up to 3 GB with IMAGE_FILE_LARGE_ADDRESS_AWARE and 4GT"

Never heard about this before!

Joachim

____________________________________________

Leica Microsystems CMS GmbH | GmbH mit Sitz in Wetzlar | Amtsgericht
Wetzlar  HRB 2432
Geschäftsführer:  Dr. Stefan Traeger | Dr. Wolf-Otto Reuter | Dr. David Roy
Martyr | Colin Davis


______________________________________________________________________
This email has been scanned by the MessageLabs Email Security System.
For more information please visit http://www.messagelabs.com/email 
______________________________________________________________________

[dscho]

Hi,

On Tue, 28 Apr 2009, Joachim Wesner wrote:

> >I don't know if this is the same thing, but Windows (XP, ME) limits an
> >application to a total (physical and virtual) memory allocation around
> >600 Mbytes. This has bitten me before with Matlab, so I assume it is
> >the same with imageJ.
>
> Where did you get this info from? Microsoft claims different (even on
> Windows 2000)
>
> http://msdn.microsoft.com/en-us/library/aa366778.aspx
>
> "User-mode virtual address space for each 32-bit process
>
>       2 GB: Up to 3 GB with IMAGE_FILE_LARGE_ADDRESS_AWARE and 4GT"

Umm.  Did the subject not state that the issue is about 64-bit?

Ciao,
Dscho

[David Webster]

Joachim
Got it by direct experiment. For instance by using "zeros" to allocate
memory in MatLab. This has been the same for Windows ME, NT, W2K, and XP. I
suppose it coud be a MatLab problem as I've never tried it with say a C++
program, but MathWorks says not.


David

On Tue, Apr 28, 2009 at 12:25 PM, Joachim Wesner <
[hidden email]> wrote:

> Hi David,
>
> >I don't know if this is the same thing, but Windows (XP, ME) limits an
> >application to a total (physical and virtual) memory allocation around 600
> >Mbytes. This has bitten me before with Matlab, so I assume it is the same
> >with imageJ.
>
> Where did you get this info from? Microsoft claims different (even on
> Windows 2000)
>
> http://msdn.microsoft.com/en-us/library/aa366778.aspx
>
> "User-mode virtual address space for each 32-bit process
>
>      2 GB: Up to 3 GB with IMAGE_FILE_LARGE_ADDRESS_AWARE and 4GT"
>
> Never heard about this before!
>
> Joachim
>
> ____________________________________________
>
> Leica Microsystems CMS GmbH | GmbH mit Sitz in Wetzlar | Amtsgericht
> Wetzlar  HRB 2432
> Geschäftsführer:  Dr. Stefan Traeger | Dr. Wolf-Otto Reuter | Dr. David Roy
> Martyr | Colin Davis
>
>
> ______________________________________________________________________
> This email has been scanned by the MessageLabs Email Security System.
> For more information please visit http://www.messagelabs.com/email
> ______________________________________________________________________
>

[Joachim Wesner]

Hi Dscho,

originally, maybe, yes, but as I understood the later poster wanted to make
the point that there is a limit also in Win32 ,
as there is no ME 64 bit and also the very same site I cited talks about 64
Bit windows and also indicates NO
hint about a strange 640 MB limit especially in Win64!

Joachim



                                                                           
             Johannes                                                      
             Schindelin                                                    
             <Johannes.Schinde                                          An
             [hidden email]>                Joachim Wesner                    
                                        <joachim.wesner@LEICA-MICROSYSTEMS
             29.04.2009 00:14           .COM>                              
                                                                     Kopie
                                        [hidden email]                
                                                                     Thema
                                        Re: Antwort: Re: unexplainable    
                                        memory limit in ImageJ64          
                                                                           
                                                                           
                                                                           
                                                                           
                                                                           
                                                                           




Hi,

On Tue, 28 Apr 2009, Joachim Wesner wrote:

> >I don't know if this is the same thing, but Windows (XP, ME) limits an
> >application to a total (physical and virtual) memory allocation around
> >600 Mbytes. This has bitten me before with Matlab, so I assume it is
> >the same with imageJ.
>
> Where did you get this info from? Microsoft claims different (even on
> Windows 2000)
>
> http://msdn.microsoft.com/en-us/library/aa366778.aspx
>
> "User-mode virtual address space for each 32-bit process
>
>       2 GB: Up to 3 GB with IMAGE_FILE_LARGE_ADDRESS_AWARE and 4GT"

Umm.  Did the subject not state that the issue is about 64-bit?

Ciao,
Dscho




______________________________________________________________________
This email has been scanned by the MessageLabs Email Security System.
For more information please visit http://www.messagelabs.com/email 
______________________________________________________________________

[Joachim Wesner]

Hi Dan,

sorry, but this must be a problem of your setup (and that Matlab cannot use
more than 2GB even if the system is set for 3GB user space) !?
What does "memory" say on your system?

On a somewhat loaded 32-bit system (some applications open) I get with
Matlab 2008b

Maximum possible array:            1279 MB (1.341e+009 bytes) *
Memory available for all arrays:   1600 MB (1.677e+009 bytes) **
Memory used by MATLAB:              220 MB (2.308e+008 bytes)
Physical Memory (RAM):             3326 MB (3.487e+009 bytes)

and as you suggested I just allocated three arrays of about 1200MB total
and there are now 63 MB left!

On 64 Bit that limit should not occur any more

http://www.mathworks.de/support/tech-notes/1100/1106.html

Mit freundlichen Grüßen / Best regards

Joachim
____________________________________________

Leica Microsystems CMS GmbH | GmbH mit Sitz in Wetzlar | Amtsgericht
Wetzlar  HRB 2432
Geschäftsführer:  Dr. Stefan Traeger | Dr. Wolf-Otto Reuter | Dr. David Roy
Martyr | Colin Davis


                                                                           
             David Webster                                                
             <dwwebster00@GMAI                                            
             L.COM>                                                     An
             Gesendet von:              [hidden email]                
             ImageJ Interest                                         Kopie
             Group                                                        
             <[hidden email].                                       Thema
             GOV>                       Re: unexplainable memory limit in  
                                        ImageJ64                          
                                                                           
             29.04.2009 01:33                                              
                                                                           
                                                                           
              Bitte antworten                                              
                    an                                                    
              ImageJ Interest                                              
                   Group                                                  
             <[hidden email].                                            
                   GOV>                                                    
                                                                           
                                                                           




Joachim
Got it by direct experiment. For instance by using "zeros" to allocate
memory in MatLab. This has been the same for Windows ME, NT, W2K, and XP. I
suppose it coud be a MatLab problem as I've never tried it with say a C++
program, but MathWorks says not.


David

On Tue, Apr 28, 2009 at 12:25 PM, Joachim Wesner <
[hidden email]> wrote:

> Hi David,
>
> >I don't know if this is the same thing, but Windows (XP, ME) limits an
> >application to a total (physical and virtual) memory allocation around
600
> >Mbytes. This has bitten me before with Matlab, so I assume it is the
same

> >with imageJ.
>
> Where did you get this info from? Microsoft claims different (even on
> Windows 2000)
>
> http://msdn.microsoft.com/en-us/library/aa366778.aspx
>
> "User-mode virtual address space for each 32-bit process
>
>      2 GB: Up to 3 GB with IMAGE_FILE_LARGE_ADDRESS_AWARE and 4GT"
>
> Never heard about this before!
>
> Joachim
>
> ____________________________________________
>
> Leica Microsystems CMS GmbH | GmbH mit Sitz in Wetzlar | Amtsgericht
> Wetzlar  HRB 2432
> Geschäftsführer:  Dr. Stefan Traeger | Dr. Wolf-Otto Reuter | Dr. David

Roy
> Martyr | Colin Davis
>
>
> ______________________________________________________________________
> This email has been scanned by the MessageLabs Email Security System.
> For more information please visit http://www.messagelabs.com/email
> ______________________________________________________________________
>



______________________________________________________________________
This email has been scanned by the MessageLabs Email Security System.
For more information please visit http://www.messagelabs.com/email 
______________________________________________________________________