Undefined variable "cluster" in CPCluster, batch m

cellprofiler

#1

I get the following message (Batch_data_mat.txt) when I ran CPCluster in batch mode. Although it generated an error message, all files appearred to be properly processed from the batch run. I get the warnings but not the error when I ran CPCluster from command line.
Do you have any susggestions of what I can do with the error message and the last 2 warnings?

Steven.

/share/data/Steven/Batch_data.mat /share/data/Steven/Batch_data.mat
??? Undefined variable “cluster” or class “cluster.StartImage”.

Warning: Unable to open display , MATLAB is starting without a display.
You will not be able to display graphics on the screen.
Warning:
MATLAB is starting without a display, using internal event queue.
You will not be able to display graphics on the screen.

Warning: No window system found. Java option ‘MWT’ ignored
Warning: Could not find appropriate function on path loading function handle /home/spoon/apps/MATLAB_CellProfiler/CellProfiler.m>LoadPipeline_Callback

In CPCluster at 6
Warning: Could not find appropriate function on path loading function handle /home/spoon/apps/MATLAB_CellProfiler/CellProfiler.m>LoadPipeline_Callback
In CPCluster at 7
Error in ==> CPCluster at 9

MATLAB:undefinedVarOrClass


Batch processing on a Single machine
#2

Hi Steven,

Looking at this error, I can only think of one possible problem. The batchrun.sh script attempts to run all .mat files in the directory with the exception of the Batch_data.mat file (or Prefixdata.mat, the prefix is by default Batch_). If you did not send the correct batch file prefix name to the batchrun.sh script, it would try to run the batch file as your error shows.

Let me know if this helps!

Mike