The basic condor setup for a job processing a simple cell image using KNIME

batchimage.condor

##################################################################
##
## Run a parameter sweep with threshold and filter using condor
##	Filename: batchimage.condor
##
##################################################################


universe	= vanilla
getenv		= True		# KNIME needs local environment


my_prefix	= FilterTest

#
# Seek max floating point performance
#
Rank		= Kflops

#
# Filter and Threshold Settings
#
thresh_count= 30
filter_count = 1
job_count	= $(thresh_count) * $(filter_count)
threshold_start	= 50
threshold_end	= 200

#
# MATLAB does all the math there,
# Condor just does string substitution
#
cur_threshold	= ( $(threshold_start) + ($(threshold_end) - $(threshold_start))*$(Process)/$(thresh_count) )
cur_filter = 1

#
# The name of the csv file to write and the image file to read
#
current_path=$(readlink -e .)

output_file		= $(current_path)$(my_prefix).t.$(Process).csv

image_file=$(readlink -e input_image.jpg)


#
# For KNIME and other SEPP packages, the executable must be a script wrapper.
#
executable	= filterandthreshold.sh
arguments	= "-workflow.variable=inputimage,$(image_file),String -workflow.variable=threshold,$(cur_threshold),double -workflow.variable=outputcsv,$output_file),String"


#
# To redirect stdout and/or stderr to /dev/null, comment these out.
#
log		= $(my_prefix).log
output		= $(my_prefix).$(Process).out
error		= $(my_prefix).$(Process).err

#
# Lastly, tell condor how many jobs to queue up.
#
queue $(job_count)

CellWorkflow.zip

filterandthreshold.sh

#!/bin/sh
#
#	Filename: filterandthreshold.sh

#
# We use a shell wrapper for two reasons:
#
#   1)	By using "$*" we ensure that the matlab command string is
#	passed as a single argument even if it contains spaces.
#
#   2)	Condor changes argv[0], which causes problems for SEPP.  Hence,
#	whenever we run a program from /usr/sepp/bin/* we must use a
#	shell script wrapper.
#
exec /usr/sepp/bin/knime -nosplash -application org.knime.product.KNIME_BATCH_APPLICATION -workflowFile=CellWorkflow.zip "$*"

input_image.jpg