number of zobov threads and subdivisions now part of dataset definition

pipeline/datasets/multidark.py

@@ -48,9 +48,16 @@ numSubvolumes = 1
 # prefix to give all outputs
 prefix = "md_"
 
-# list of desired subsamples
+# list of desired subsamples - these are in unts of h Mpc^-3!
+#subSamples = [ 1.0 ]
 subSamples = ((0.1, 0.05, 0.01, 0.002, 0.001, 0.0004, 0.0002))
 
+# adjust these two parameters given the memory contraints on your system:
+#   numZobovDivisions: how many sub-volumes per dimension will zobov process
+#   numZobovThreads: how many sub-volumes to process at once?   
+numZobovDivisions = 4
+numZobovThreads = 2
+
 # simulation information
 numPart = 1024*1024*1024
 lbox = 1000 # Mpc/h

pipeline/generateCatalog.py

@@ -88,7 +88,8 @@ for sample in dataSampleList:
     sys.stdout.flush()
 
     launchZobov(sample, ZOBOV_PATH, zobovDir=zobovDir, logDir=logDir, 
-                continueRun=continueRun)
+                continueRun=continueRun, numZobovDivisions=numZobovDivisions,
+                 numZobovThreads=numZobovThreads)
 
   # -------------------------------------------------------------------------
   if (startCatalogStage <= 3) and (endCatalogStage >= 3) and not sample.isCombo:

pipeline/prepareCatalogs.py

@@ -115,10 +115,15 @@ workDir = "{voidOutputDir}/{setName}/"
 inputDataDir = "{inputDataDir}"
 figDir = "{figDir}/{setName}/"
 logDir = "{logDir}/{setName}/"
+
+numZobovDivisions = {numZobovDivisions}
+numZobovThreads = {numZobovThreads}
                """
   scriptFile.write(dataInfo.format(setName=setName, figDir=figDir,
                                    logDir=logDir, voidOutputDir=voidOutputDir,
-                                   inputDataDir=catalogDir))
+                                   inputDataDir=catalogDir, 
+                                   numZobovDivisions=numZobovDivisions,
+                                   numZobovThreads=numZobovThreads))
 
   sampleInfo = """
 newSample = Sample(dataFile = "{dataFile}",
@@ -139,7 +144,6 @@ newSample = Sample(dataFile = "{dataFile}",
                    usePecVel = {usePecVel},
                    numSubvolumes = {numSubvolumes},
                    mySubvolume = "{mySubvolume}",
-                   numSubDivisions = 4,
                    useLightCone = {useLightCone},
                    subsample = {subsample})
 dataSampleList.append(newSample)