New import error in CellProfiler

Hi,
I successfully used CellProfiler-3.1.8 in a cluster environment.

Unfortunately the last attempts failed as shown on the screenshot attached.
It seems that it cannot allocate memory…
This error message is completely new, I never faced it before.
Moreover, running the same CellProfiler script with the same file and directories on my laptop work just fine. It is estimated to require 153hours to complete which explain my need of a working computing cluster…
thank you for your help

Do you get that same exact error when trying to run a headless command (ie cellprofiler -c -r -p some_pipeline.cpproj)? Can you try running the same exact command that you are most confident recently succeeded, to see if there’s been a change in your environment? Can you post a pip freeze of that environment (Text please, not a screenshot).

Beth,
thank you for your answer
When run in a headless command I did not get the same exact error (see attached file:

.
The most confident command is working! Nothing wrong with the environment.
made a mistake when requesting cores/vmem. Dont you think?
thank you for your help

Your stack trace is cut off; please also do post the text of these, not screen shots, as screen shots aren’t searchable if someone has the same issue in the future.

made a mistake when requesting cores/vmem. Dont you think?

Maybe? I don’t know. You can try to get a sense how many CPUs/how much memory one worker needs on your own machine, then work with your IT department to make sure you are allocating at least as many resources your job needs.

The most confident command is working!

What was the command that did work?

Sorry for the delay
did not save the text of the previous error message (only the screenshot)
Attached, a script to run CellProfiler in a headless command which work…UGER_CellProfiler.pdf (39.7 KB)
thank you for your help

So in the one that did work, once you use ish it puts you on a uger node (see below how it switches from login03; in the screenshot you posted above, you use a slightly different UGER command (transcribing, but approximately ish -l os=RedHat7 -pe smp 4 -binding linear:4 vmem=16G), but note that you never actually kick into UGER, you’re still (in both screenshots) on your login node.

Talk with your local IT , but I suspect that’s the issue, not anything to do with CellProfiler at all.

-bash:login03:~ 1000 $ use UGER
Prepending: UGER (ok)
-bash:login03:~ 1001 $ ish -l os=RedHat7 -l h_vmem=16G
-bash:uger-c001:~ 1000 $ use .python-2.7.9-sqlite3-rtrees