Posted by
Fred Damen on
Dec 25, 2020; 10:46pm
URL: http://imagej.273.s1.nabble.com/OutOfMemoryError-tp5024312p5024316.html
Greetings,
Shorter version of the solution to your issue is to pass -x5120 to the
imagej bash script for 5G of memory.
Longer version...
I use Fedora package installation of ImageJ and do not seem to have the
ImageJ.cfg file that Wayne has mentioned, and my imagej bash script does
not reference ImageJ.cfg, so I do not think there is any connection
between these two possible ways of setting this memory option. I do not
know how Edit>Options>Memory & Threads is supposed to work and have not
tried to use it on Linux so I can not comment further...
The code snippet that you provided below is not perfect, i.e., it defines
default_mem to 4000 and in the subsequent code compares against the value
4000 and not to the value of the default_mem variable. So changing the
value of of the default_mem variable is mute without correcting the
subsequent code to use $default_mem instead of 4000. Although this is the
answer to your inquire, you can ignore this paragraph if you use the
initial suggested solution, as it renders this code irrelevant during
command line parameter evaluation.
It is interesting that this script uses the amount of free swap as the
free_mem instead of the actual RAM...
Enjoy,
Fred
On Fri, December 25, 2020 3:08 pm, Wayne Rasband wrote:
>> On Dec 25, 2020, at 6:46 AM, Thomas Fischer <
[hidden email]>
>> wrote:
>>
>> Hi altogether,
>>
>> my laptop runs under linux debian 10 and has 8 GB RAM. Edit ⺠Options
>> âº
>> Memory & Threads does not allow me to increase the value above 2666MB.
>
> Try the Linux version of ImageJ available at
>
https://imagej.nih.gov/ij/download.html. The Edit>Options>Memory & Threads
> command updates the third line of the ImageJ.cfg file. For example, it
> changes this line to "-Xmx4000m -cp ij.jar ij.ImageJâ when you set the
> value to 4000 in the Memory & Threads dialog.
>
> -wayne
>
>> relevant lines in /usr/bin/imagej (a not so simple wrapper script used
>> to
>> run ImageJ) are
>>
>> declare -i mem
>> declare -i default_mem=4000
>> declare -i min_mem=16
>> declare -i max_mem
>> declare -i free_mem
>>
>> and further down
>>
>> elif [[ `uname` == 'Linux' ]] ; then
>> if [[ `uname -m` == 'x86_64' ]] ; then
>> java_path="${ij_path}/jre64/bin/java"
>> max_mem=`free | awk 'NR == 2 {fmem=int($2 / 1024); if (fmem <
>> 4000)
>> {print fmem} else {print 4000}}'`
>> free_mem=`free | awk 'NR == 3 {fmem=int($4 / 1024); if (fmem <
>> 4000) {print fmem} else {print 4000}}'`
>> mem=${free_mem}/3*2
>> if (( $mem > $default_mem || $mem < $min_mem )) ; then
>> mem=$default_mem ; fi
>> else
>>
>> typing free:
>> total used free shared buff/cache
>> available
>> Mem: 8064332 1579956 2659136 183288 3825240
>> 5998348
>> Swap: 8282108 0 8282108
>>
>> changing declare -i default_mem=4000 to declare -i default_mem=8000 has
>> no
>> effect on the lines further down
>>
>> where is the superior position where the change to 8000 makes a
>> difference
>> in the file imagej?
>>
>> thank you, Thomas
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
--
ImageJ mailing list:
http://imagej.nih.gov/ij/list.html