Not able to increase the size of the Java heap memory

[pau (Pau Carrillo-Barberà)]

Hi there folks,

I am trying to process a dataset of large images (156 MB) in CellProfiler 3.1.8. The message ‘Error while processing NamesAndTypes: Java heap space’ pops-up when I run the test mode. I found this topic and tried to follow @mbray 's instructions. However, when I type CellProfiler.exe --jvm-heap-size=4g this message appears:

Indeed if I type CellProfiler --help I do not find such option. I am not able to figure out how to fix it (sorry, my knowledge in this kind of things is quite limited ). I would really appreciate any help. Thank you!

Pau

[Research_Associate (MicroscopyRA)]

That was a very old thread, and in a lower post someone says that the memory should be adjustable within CellProfiler. They might have removed the command line option in a later version?

Java heap space error

Do you get this upon loading your images and/or during metadata extraction? You likely have a large image set? If so, this looks to be the same issue: viewtopic.php?f=16&t=4061 The basic suggestion there is to use LoadData instead of the Input modules. Side note: There is now a setting in Preferences (CellProfiler Menu -> Preferences -> Maximum memory for Java) to set the Java JVM heap size, rather than needing to use command-line. Cheers, David

[pau (Pau Carrillo-Barberà)]

Solved. Thank you very much for your help. I guess the command line may have been removed, as you say. My pipeline is working now after increasing the maximum memory for Java. I have not used the LoadData module (maybe I will need it if I increase the datset size).

Best,

Pau