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I'm working with a memory intensive plugin for imageJ on Linux which I run repeatedly though a macro. The plugin performs multiview deconvolutions.

I have increased the maximum memory available to 180 Gb (Out of 188GB available) and run the garbage collector multiple times after the completion of each step. This results in the memory usage never exceeding 100 Gb, as displayed by the system monitor and imageJ memory monitor.

However I still receive "Out of Memory" errors after around 10 hours of run time. Where is this memory limit coming from?

Ed Muir
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  • Maybe you should ask this on the [ImageJ forum](http://forum.imagej.net/) and also provide more details (which plugin etc.). – Jan Eglinger Feb 02 '17 at 15:37
  • Cross-referencing for the benefit of others: there is an [active ImageJ forum thread](http://forum.imagej.net/t/out-of-memory-error-below-memory-limit/4186/10) following this issue now. – ctrueden Mar 15 '17 at 16:34

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As discussed on ImageJ forum, the issue is actually that there is insufficient memory. The error message was simply misleading. The multiview deconvolution plugin can be extremely memory-hungry depending on what you are doing. Hopefully we can determine more details of why the plugin runs out of memory, but for the purposes of this SO post, I think the culprit has been discovered.

ctrueden
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  • Is that the case? The RAM limit is not being reached, so I am still confused at where the memory limit is coming from. Perhaps I am just confused in general. Thanks for the response, will continue the discussion on the imagej forum. – Ed Muir Mar 17 '17 at 17:29
  • You may be right. But there also can be other reasons for running out of memory, such as [memory fragmentation](https://blogs.oracle.com/jrockit/entry/repost_tips_and_tricks_for_dealing_with_a_fragmented_java_heap). Regardless, someone needs to profile the code using JVisualVM or similar tool, to get more insight into what's going on. – ctrueden Mar 20 '17 at 19:21