Error whilst running CPCluster directly

cellprofiler

#1

I’m trying to get CPCluster running on the SBS pipeline and images from cellprofiler.org/examples.htm. My pipeline is the same as the one in the example apart from adding CreateBatchFiles at the end. Whilst trying to get the code running I’m testing the CPCluster executable whilst logged onto a node and I’m seeing this error:

[holwani1@compute-0-6 ~]$ /usr/prog/imageanalysis/CompiledCPCluster/CPCluster /users/holwani1/cellprofiler/cluster-new/Batch_data.mat 1 10 /users/holwani1/cellprofiler/cluster-new/ Batch_ yes 1 Analyzing set 1. Pipeline: module 1 - LoadImages module 2 - LoadSingleImage module 3 - LoadText module 4 - CorrectIllumination_Apply module 5 - CorrectIllumination_Apply module 6 - IdentifyPrimAutomatic module 7 - IdentifyPrimAutomatic module 8 - IdentifySecondary module 9 - IdentifySecondary module 10 - IdentifyTertiarySubregion module 11 - IdentifyTertiarySubregion module 12 - MeasureCorrelation module 13 - MeasureObjectIntensity module 14 - MeasureObjectIntensity module 15 - MeasureObjectAreaShape module 16 - MeasureTexture module 17 - MeasureTexture module 18 - CalculateRatios module 19 - CalculateRatios module 20 - ClassifyObjects module 21 - ClassifyObjects module 22 - ClassifyObjects module 23 - CalculateStatistics module 24 - ExportToExcel module 25 - CreateBatchFiles /bin/bash: 1: command not found executing module 1 - LoadImages Batch Error: LoadImages: Error using ==> CPimread at 119 Image processing was canceled in the LoadImages module because an error occurred when trying to load the first set of images. Please check the settings. A common problem is that there are non-image files in the directory you are trying to analyze. Matlab says the problem is: Error using ==> CPimread at 119 Image processing was canceled because the module could not load the image "/users/holwani1/cellprofiler/ExampleSBSImages/Channel1-01-A-01.tif" in directory "/users/holwani1". The error message was "Error using ==> rtifc Invalid TIFF image index specified." (file: /usr/prog/imageanalysis/CompiledCPCluster/CPCluster_mcr/CPsubfunctions/CPimread.m function: CPimread line: 119)

Does anyone know what the problem is? I’ve tried deleting all non-tif files from the directory.

Thanks

Nick


#2

Hi Nick,

First,

indicates that your PATH might not be set correctly. What does

return?

Second, we find the scripts BatchRunner.py and CPCluster.py help to circumvent these sorts of setup issues. Have you tried running BatchRunner.py rather than the CPCluster executable directly?

David


#3

Hi. Thanks for the response.

[quote=“David Logan”]Hi Nick,

First,

indicates that your PATH might not be set correctly. What does

return?[/quote]

[holwani1@compute-0-5 cluster]$ echo $PATH
/opt/gridengine/bin/lx26-amd64:/usr/kerberos/bin:/opt/gridengine/bin/lx26-amd64:/usr/java/latest/bin:/usr/local/bin:/bin:/usr/bin:/opt/ganglia/bin:/opt/ganglia/sbin:/opt/rocks/bin:/opt/rocks/sbin:/users/holwani1/bin
[holwani1@compute-0-5 cluster]$ echo $LD_LIBRARY_PATH
/usr/prog/matlab/MATLAB_Compiler_Runtime/v78/runtime/glnxa64/:/usr/prog/matlab/MATLAB_Compiler_Runtime/v78/runtime/glnxa64/l:/opt/gridengine/lib/lx26-amd64:/opt/gridengine/lib/lx26-amd64

[quote]Second, we find the scripts BatchRunner.py and CPCluster.py help to circumvent these sorts of setup issues. Have you tried running BatchRunner.py rather than the CPCluster executable directly?

David[/quote]

I wasn’t getting any output when I was running the script which is why I wanted to run it straight from the command line. We use SGE so the scripts will need some tweaking before we’re able to run them.


#4

Hi David / anyone else reading.

Did you have any more thoughts on this?