FilterByObjectMeasurement fails in Cluster

cellprofiler

#1

when running a batch job on CPCluster (compiled) I received the following error message. The same script was working fine on my personal computer.

I presume that this error message refers to the image loaded initially by the LoadImg module, but adjusting SpeedUpCellProfiler settings made no difference.

Batch Error: FilterByObjectMeasurement Error using ==> CPretrieveimage
Image processing was canceled in the FilterByObjectMeasurement module because the input image could not be found. It was supposed to be named 2 but an image with that name does not exist. Perhaps there is a typo in the name.
a??? Error using ==> CPretrieveimage
Image processing was canceled in the FilterByObjectMeasurement module because the input image could not be found. It was supposed to be named 2 but an image with that name does not exist. Perhaps there is a typo in the name.

srun: error: n22: task0: Exited with exit code 255


#2

Hi Aidan,

The LoadImages module should always load a new image in each cycle, so that if you have SpeedUpCellProfiler as one of the last modules (after everything except ExportXXX and CreateBatchFiles), there should be no problem. However, if you are using LoadSingleImage, the image is only loaded on the first cycle and you must make sure this image is saved in following cycles. What does your pipeline look like?

Mike


#3

This error message refers to problem between LoadImages and FilterByObjectMeasurement within a single cycle. I’ve looked at various alterations of a) SpeedUpCellProfiler and b) naming images and neither seems to resolve this issue. The first time FilterByObjectMeasurement is called in the compiled version of CP, it crashes.

local computer: works
cp on cluster: works
cpcluster: fails.

Batch Error: FilterByObjectMeasurement Error using ==> CPretrieveimage
Image processing was canceled in the FilterByObjectMeasurement module because the input image could not be found. It was supposed to be named 2 but an image with that name does not exist. Perhaps there is a typo in the name.
a??? Error using ==> CPretrieveimage
Image processing was canceled in the FilterByObjectMeasurement module because the input image could not be found. It was supposed to be named 2 but an image with that name does not exist. Perhaps there is a typo in the name.


#4

This was a version conflict and has been resolved.

Mike