def writeSingleTile(options):
"""Writes a single tile according to the options"""
# Determine the name of the tile we need to write
tileName = generateTileName(options.pixelStartX, options.pixelStartY, options.pixelStopX, options.pixelStopY)
tilePath = os.path.join(options.workDir, tileName)
# Just call the command for a single tile!
cmd = ['mapproject', '--t_pixelwin', str(options.pixelStartX), str(options.pixelStartY), str(options.pixelStopX), str(options.pixelStopY),
options.demPath, options.imagePath, tilePath]
cmd = cmd + options.extraArgs # Append other options
IrgSystemFunctions.executeCommand(cmd, options.suppressOutput)
if options.convertTiles: # Make uint8 version of the tile for debugging
tilePathU8 = os.path.splitext(tilePath)[0] + 'U8.tif'
cmd = ['gdal_translate', '-ot', 'byte', '-scale', tilePath, tilePathU8]
IrgSystemFunctions.executeCommand(cmd, options.suppressOutput)
return 0
def handleArguments(args):
"""Split up arguments into required and optional lists which will be passed to subprocess"""
requiredList = []
optionsList = []
# Loop through all entries.
iterable = iter(range(0, len(args)))
for i in iterable:
a = args[i]
if (i < len(args)-1): # Don't load the next value when we are at the end!
n = args[i+1]
else:
n = '-' # This will just cause us to get out of the loop
if IrgSystemFunctions.isCmdOption(a): # This is the start of an option.
optionsList.append(a) # Record this entry.
if IrgSystemFunctions.isCmdOption(n): # The next entry is the start of another option so this one has no values.
continue
optionsList.append(n) # Otherwise record the next entry as a value.
iterable.next() # Skip the next entry in the loop.
if (a == '--t_projwin') or (a == '--t_pixelwin'): # These arguments have four values, not just one.
optionsList.append(args[i+2]) # Add the additional three arguments and skip them in the loop.
optionsList.append(args[i+3])
optionsList.append(args[i+4])
iterable.next()
iterable.next()
iterable.next()
else: # This is one of the three positional arguments
requiredList.append(a)
# Return the two lists
return (requiredList, optionsList)
def main(argsIn):
try:
usage = "usage: pbs_parallel_stereo.py (same inputs as parallel_stereo plus new options)"
parser = IrgSystemFunctions.PassThroughOptionParser(
usage=usage) # Use parser that ignores unknown options
parser.add_option(
"--num-correlation-nodes",
dest="numCorrelationNodes",
type='int',
default=1,
help="Number of nodes to use for the two correlation steps")
parser.add_option(
"--num-triangulation-nodes",
dest="numTriangulationNodes",
type='int',
default=1,
help="Number of nodes to use for the triangulation steps")
parser.add_option(
'--node-type',
dest='nodeType',
default='wes',
help='Type of processing node to request (wes, san, or ivy)')
parser.add_option('--group-id',
dest='groupId',
default='',
help='GID to charge the hours to [REQUIRED]')
# This call handles all the specific options for this code.
(options, args) = parser.parse_args(argsIn)
# 'args' contains everything for parallel_stereo
# Check the required positional arguments.
if not options.groupId:
parser.error("Must input a group ID to charge to!")
# Any additional arguments need to be forwarded to the mapproject function
options.extraArgs = args
except optparse.OptionError, msg:
raise Usage(msg)
':model=' + options.nodeType +
' -W depend=afterok:$subjob2 -- ' +
scriptCalls[2] + ')')
# Triangulation stage
pbsStrings.append(corePbsString + ' -N pbs_stereo4 -l walltime="' +
stepHours[3] + '"' + ' -e ' + errLogPaths[3] + ' -o ' +
stdLogPaths[3] + ' -l select=' +
str(options.numTriangulationNodes) + ':ncpus=' +
str(cpusPerNode) + ':model=' + options.nodeType +
' -W depend=afterok:$subjob3 -- ' + scriptCalls[3])
# Set up the command line for parallel_stereo
commandList = ['parallel_stereo', '--nodes-list', '$PBS_NODEFILE']
commandList = commandList + options.extraArgs # Append other options
commandString = IrgSystemFunctions.argListToString(commandList)
phases = [
' --entry-point 0 --stop-point 1', # Init
' --entry-point 1 --stop-point 3', # Correlation
' --entry-point 3 --stop-point 4', # Filtering
' --entry-point 4 --stop-point 6'
] # Triangulation
# Generate a set of four script files
for i in range(4):
print 'Writing script file ' + scriptCalls[i]
scriptFile = open(scriptCalls[i], 'w')
scriptFile.write('#!/bin/bash\n\n')
thisCommandString = commandString + phases[i]
scriptFile.write(thisCommandString)
argumentFile.close()
# Indicate to GNU Parallel that there are multiple tab-seperated variables in the text file we just wrote
parallelArgs = ['--colsep', "\\t"]
# TODO: Move this to the lower level functions
# If using multiple computers, need to make sure the same program paths are available
if options.nodesListPath:
parallelArgs = parallelArgs + ['--env', 'PATH', '--env', 'PYTHONPATH', '--env', 'ISISROOT', '--env', 'ISIS3DATA']
# Get the number of available nodes and CPUs per node
numNodes = IrgPbsFunctions.getNumNodesInList(options.nodesListPath)
# We assume all machines have the same number of CPUs (cores)
cpusPerNode = IrgSystemFunctions.get_num_cpus()
# We don't actually know the best number here!
threadsPerCpu = 2
# Set the optimal number of processes if the user did not specify
if not options.numProcesses:
options.numProcesses = numNodes * cpusPerNode * threadsPerCpu
# Note: mapproject can run with multiple threads on non-ISIS data but we don't use that
# functionality here since we call mapproject with one tile at a time.
# No need for more processes than their are tiles!
if options.numProcesses > numTiles:
options.numProcesses = numTiles
# Filtering stage
pbsStrings.append('subjob3=$( ' + corePbsString + ' -N pbs_stereo3 -l walltime="'+stepHours[2]+'"'
+ ' -e '+ errLogPaths[2] +' -o '+ stdLogPaths[2]
+ ' -l select='+str(1)+':ncpus='+str(cpusPerNode)+':model='+options.nodeType
+ ' -W depend=afterok:$subjob2 -- '+ scriptCalls[2] +')')
# Triangulation stage
pbsStrings.append(corePbsString + ' -N pbs_stereo4 -l walltime="'+stepHours[3]+'"'
+ ' -e '+ errLogPaths[3] +' -o '+ stdLogPaths[3]
+ ' -l select='+str(options.numTriangulationNodes)+':ncpus='+str(cpusPerNode)+':model='+options.nodeType
+ ' -W depend=afterok:$subjob3 -- '+ scriptCalls[3])
# Set up the command line for parallel_stereo
commandList = ['parallel_stereo', '--nodes-list', '$PBS_NODEFILE']
commandList = commandList + options.extraArgs # Append other options
commandString = IrgSystemFunctions.argListToString(commandList)
phases = [' --entry-point 0 --stop-point 1', # Init
' --entry-point 1 --stop-point 3', # Correlation
' --entry-point 3 --stop-point 4', # Filtering
' --entry-point 4 --stop-point 6'] # Triangulation
# Generate a set of four script files
for i in range(4):
print 'Writing script file ' + scriptCalls[i]
scriptFile = open(scriptCalls[i], 'w')
scriptFile.write('#!/bin/bash\n\n')
thisCommandString = commandString + phases[i]
scriptFile.write(thisCommandString)
scriptFile.close()
