Java Heap Memory, JVMHeapMB, CellProfiler won't start

I ran into a problem that I didn’t see a solution for on the forum. I then figured out how to fix it and just wanted to document it in the case that it hasn’t been covered yet. If I set my Java Memory preference too high (in this case 4000 on a mac with 8G of ram), then Cell profiler wouldn’t even open. I also didn’t get an error message. I suspected it was the change in memory preference that I made but I couldn’t open the software to change it. I tried closing all other apps, problem persisted. I tried restarting, issue persisted. Likewise, I couldn’t immediately find information on where the preference file was. Eventually located though (/Users//Library/Preferences/CellProfilerLocal.cfg), and lowered the “JVMHeapMB” property to a lower value (1000). Hope this helps anyone who runs into this.

Sorry for the random subject but I thought I would throw in as many keywords as I could for searching later :smile: Likewise totally correct my post here if you think there was something else that was going on but seems like this was clearly the issue.


Thanks for bringing this to our attention (and the community’s)!

There’s not much we can do on our end to prevent a user from exceeding such limits; there are always cases where trying to infer the limit from the computer can be misleading. So for the meantime, we’ll leave this post here as a reminder for others. Thanks again!

Thanks for posting this. I am having the same problem, and I increased the Java memory to 2000MB, and after that CellProfiler won’t open at all. I have tried looking for the configuration file you mentioned but I can’t find it (I am looking at ~/Library/Preferences). Any suggestions on how to get CellProfiler working again? I already tried deleting everything and reinstalling, to no avail…


Hi @andresm,

Would you mind posting your Console log for the CP crash event? It should write something, even if CP crashes immediately, and might help us.