Guide to Compiling CPCluster


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Directions to compile CPCluster.m
These directions will guide you in compiling and running the CPCluster.m file for using CellProfiler on a cluster without MatLab licenses. The directions are guided for use with Linux computers, since almost all computing clusters are Linux or Macintosh based.

Step 1: Unzip CPCluster files into folder (this is probably done already! e.g. /home/username/CPCluster)

Step 2: In MatLab, go to File -> Set Path -> Add With Subfolders and choose the CPCluster folder you just created

Step 3: In MatLab, type “mcc -m CPCluster.m” This will create the CPCluster executable file. However, to work independently of MatLab, you must provide it with the MatLab library files

Step 4: In MatLab, type “buildmcr” and hit enter. This will take some time.

Step 5: The output of this command is the pathname to MCRInstaller.zip and it is usually something like: /usr/local/bin/MatLab/toolbox/compiler/deploy/glnx86/MCRInstaller.zip

Step 6: Unzip the contents of MCRInstaller (should be one folder, v73) into a foldercalled MCR. Then move this MCR folder into the same folder as the CPCluster executable (e.g. /home/username/CPCluster/MCR/)

To test that the compiled version is working, open the CPCluster folder and run CPCluster.command. The first time it is run, it should say it is unzipping a CTF file, and then it should fail because it cannot find the batch or cluster file.

If compiling CPCluster worked, you can move the entire folder to somewhere on your cluster where all nodes can see it.


CellProfiler on Linux