ImageJ

out of memory ? plenty of RAM

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Heinrich Bürgers

out of memory ? plenty of RAM

Hi,
I am using debian, actual ImageJ, java 1.4.2 on a 2-way ia64.

my memory according to "free" (nothing special running):
total used free shared buffers cached
Mem: 9350656 1790016 7560640 0 83040 1421616
-/+ buffers/cache: 285360 9065296
Swap: 2060512 0 2060512

my "run" file looks like:
/usr/j2sdk1.4.2/jre/bin/java -Xmx8192m -cp ij.jar ij.ImageJ

I want to process a composite (486400x19200 8bit grey) image with median
filter 5x5

I get following message:

>>>>>>>>>>>>>>>>>>>>>>>>>>>
<Out of memory>
<All available memory (6459MB) has been>
...
>>>>>>>>>>>>>>>>>>>>>>>>>>>

according to vmstat there's nearly 2.9 GB total RAM left!
where's the restriction?

thanks for your help in advance!
Heinrich

Sergio Caballero

Re: out of memory ? plenty of RAM

From the Menu Bar open Edit->Options->Memory... and enter a new memory
allocation for ImageJ (currently supports up to 1 GB, i.e. 1024 MB,
regardless of how much additional RAM is on the machine).

HTH, Sergio

Sergio Caballero, Jr., MS
Pharmacology & Therapeutics
University of Florida
1600 SW Archer Road Rm R5-283 (shipping)
PO Box 100267 (mailing)
Gainesville, FL 32610-0267
O: 352-392-7958
F: 352-392-9696
M: 352-246-1429

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Heinrich Bürgers
Sent: Monday, April 10, 2006 7:35 AM
To: [hidden email]
Subject: out of memory ? plenty of RAM

Hi,
I am using debian, actual ImageJ, java 1.4.2 on a 2-way ia64.

my memory according to "free" (nothing special running):
total used free shared buffers cached
Mem: 9350656 1790016 7560640 0 83040 1421616
-/+ buffers/cache: 285360 9065296
Swap: 2060512 0 2060512

my "run" file looks like:
/usr/j2sdk1.4.2/jre/bin/java -Xmx8192m -cp ij.jar ij.ImageJ

I want to process a composite (486400x19200 8bit grey) image with median
filter 5x5

I get following message:

>>>>>>>>>>>>>>>>>>>>>>>>>>>
<Out of memory>
<All available memory (6459MB) has been>
...
>>>>>>>>>>>>>>>>>>>>>>>>>>>

according to vmstat there's nearly 2.9 GB total RAM left!
where's the restriction?

thanks for your help in advance!
Heinrich

Heinrich Bürgers

Re: out of memory ? plenty of RAM

Hi Sergio,
I already enabled more than 8GB and that's what optons-> memory is
telling me.
This particularly function breaks down not using all the memory
available to IMAGEJ. Other things (deconvolution/fourier-transformations
etc.) work well and really use the 8 gibabyte RAM fully.

Sergio Caballero wrote:

>>From the Menu Bar open Edit->Options->Memory... and enter a new memory
> allocation for ImageJ (currently supports up to 1 GB, i.e. 1024 MB,
> regardless of how much additional RAM is on the machine).
>
> HTH, Sergio
>
> Sergio Caballero, Jr., MS
> Pharmacology & Therapeutics
> University of Florida
> 1600 SW Archer Road Rm R5-283 (shipping)
> PO Box 100267 (mailing)
> Gainesville, FL 32610-0267
> O: 352-392-7958
> F: 352-392-9696
> M: 352-246-1429
>
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Heinrich Bürgers
> Sent: Monday, April 10, 2006 7:35 AM
> To: [hidden email]
> Subject: out of memory ? plenty of RAM
>
> Hi,
> I am using debian, actual ImageJ, java 1.4.2 on a 2-way ia64.
>
> my memory according to "free" (nothing special running):
> total used free shared buffers cached
> Mem: 9350656 1790016 7560640 0 83040 1421616
> -/+ buffers/cache: 285360 9065296
> Swap: 2060512 0 2060512
>
> my "run" file looks like:
> /usr/j2sdk1.4.2/jre/bin/java -Xmx8192m -cp ij.jar ij.ImageJ
>
> I want to process a composite (486400x19200 8bit grey) image with median
> filter 5x5
>
> I get following message:
>
>
> <Out of memory>
> <All available memory (6459MB) has been>
> ...
>
>
> according to vmstat there's nearly 2.9 GB total RAM left!
> where's the restriction?
>
> thanks for your help in advance!
> Heinrich
>

--
Heinrich Bürgers Diplom-Biologe univ.
Im Neuenheimer Feld 326
Institut für Physiologie & Pathophysiologie
AG Prof. Dr. Kuschinsky
69120 Heidelberg
Fon +49 (0)6221 54-5385
Lab +49 (0)6221 54-4046
Fax +49 (0)6221 54-4561
[hidden email]

Gabriel Landini

Re: out of memory ? plenty of RAM

In reply to this post by Sergio Caballero

On Monday 10 April 2006 13:48, Sergio Caballero wrote:
> >From the Menu Bar open Edit->Options->Memory... and enter a new memory
>
> allocation for ImageJ (currently supports up to 1 GB, i.e. 1024 MB,
> regardless of how much additional RAM is on the machine).

I can allocate up to -Xmx1800m under suse linux 10.0 but not more.
At startup the Helpt>About ImageJ... window shows:
2007K used out of 1786MB (<1%)

G.

Heinrich Bürgers

Re: out of memory ? plenty of RAM

I am using 64-bit architecture!!!!
read this: (right now java uses 3.5 GB (res) and can take up to 9.5 GB
(virt.)

heini@pc:~$top
top - 15:46:54 up 3 days, 18:28, 3 users, load average: 1.05, 1.01, 1.00
Tasks: 49 total, 1 running, 48 sleeping, 0 stopped, 0 zombie
Cpu(s): 51.9% us, 0.3% sy, 0.0% ni, 47.7% id, 0.0% wa, 0.0% hi, 0.1% si
Mem: 9350656k total, 5644976k used, 3705680k free, 140352k buffers
Swap: 2060512k total, 0k used, 2060512k free, 1517040k cached

PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND

13868 heini 16 0 9424m 3.5g 31m S 100 39.8 69:32.66 java

...

Gabriel Landini wrote:

> On Monday 10 April 2006 13:48, Sergio Caballero wrote:
>
>>>From the Menu Bar open Edit->Options->Memory... and enter a new memory
>>
>>allocation for ImageJ (currently supports up to 1 GB, i.e. 1024 MB,
>>regardless of how much additional RAM is on the machine).
>
>
> I can allocate up to -Xmx1800m under suse linux 10.0 but not more.
> At startup the Helpt>About ImageJ... window shows:
> 2007K used out of 1786MB (<1%)
>
> G.
>