Latest Fiji update on OSX - problem with memory setting

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#1

Hi,

Tonight there was a big update in Fiji including OSX specific parts (from a glance at the update panel, btw is there a post somewhere describing this?). Once done, my Fiji install was set to ~4.5 GB memory so the first big task I did caused an out of memory error. I set it back to 14 GB (I have 16 GB total on this computer) but the setting is not retained, and when I restart Fiji it is back to 4.5 GB.

Luckily I had a backup version of my install from a week or so ago so I could revert to this. Does anyone else see this problem too?


#2

So after playing update and switch with the previous version, I can confirm that the new ImageJ-osx version in Fiji.app/Contents/MacOS/ is responsible for this. If I make a full update to the latest Fiji version (Java8 update site) and replace the new ImageJ-osx with the previous one, memory setting is retained again. With the new one, it is reset to ~4.8 GB at each launch, no matter what I set in the options.


#3

To pursue my monolog; the Info.plist in Fiji.app/Contents correctly lists the memory setting (14000m in my case) but with the new ImageJ-osx version, it’s not taken into account and invariably starts with a memory setting between 4.7. and 4.9 GB.


#4

hi, @christlet

I just updated and suddenly couldn’t open my files. I have tried to change the memory settings but I face the same problems you did. I do not know the first thing about computers, so needles to say I didn’t understand your comment above about how to fix it. I would be very grateful if you could explain it to me as if I were 5 years old…
2016 mb pro tb, 16gb ram, OSX High Sierra.
/Christian


#5

Hi christlet, I am having the same problem with Fiji and memory allocation from your experience what is the best solution to solve it.
Thank you so much


#6

Hi christlet, thank you for the hints.
Based your description, this is what we do to fix it:

  1. cp /Applications/Fiji.app/Contents/MacOS/ImageJ-macosx /Applications/Fiji.app/Contents/MacOS/ImageJ-macosx.new
  2. cp /Applications/Fiji.app/Contents/MacOS/ImageJ-macosx.old /Applications/Fiji.app/Contents/MacOS/ImageJ-macosx

Restart Fiji.


#7

This is what I did, hope there will be an official fix for ImageJ-macosx soon


#8

I will try to investigate + reproduce + fix tomorrow.


#9

Thanks Curtis! Let me know if you need any more info


#10

Back to the lab and I have the same problem on the mac there (also under High Sierra, but not APFS as it is a Fusion Drive).

Laptop under High Sierra (APFS) 16 GB RAM: memory stuck at 4.7 GB.
iMac under High Sierra (HFS+), 24 GB RAM: memory stuck at 12.3 GB.

Not sure it depends on the RAM installed or on the initial amount of memory specified at first launch of the new ImageJ-macosx.

@ctrueden did you get a chance to investigate?


#11

I have the exact same problem. Has there been a fix yet?
Would somebody care to describe a work around in “ImageJ/Fiji-newbie language”?

Looking forward for your help.

Kind regards,
Peter


#12

I don’t think so.

If I understood @christlet and @larry1 correctly, this should work:

  • Browse to your ./Fiji.app/Contents/MacOS (by right-clicking on your Fiji.app icon and selecting Show Package Contents)
  • Rename ImageJ-macosx to ImageJ-macosx.new
  • Rename ImageJ-macosx.old to ImageJ-macosx
  • Run Fiji by double-clicking on your Fiji.app icon

or, from the terminal, as described by @larry1:


#13

THANK you so much, it worked!


#14

Same issue here on MacOS High Sierra, i7 2.93GHz, 12GB RAM > actual ram in Fiji/ImageJ 1.51t stuck at 4325MB.


#15

I am not sure why this bug happens, but I believe I have fixed it:

The old launcher did not have the problem, whereas the new launcher did with both Java 8 and Java 9. (I tested only on High Sierra—but the old launcher still worked on High Sierra.)

I will upload the fix to the Java-8 update site after Travis deploys the new build.
Edit: The fix has been uploaded!