Merge pull request #15 from emanueledimarco/vbfac-dev

A lot of changes in the AC fits using now all the STXS categories

Background/config_test.py

@@ -3,16 +3,16 @@
 backgroundScriptCfg = {
 
     # Setup
-    'inputWSDir':'cards/cards_current/data_Run2', # location of 'allData.root' file
+    'inputWSDir':'cards/data_run2', # location of 'allData.root' file
     'cats':'auto', # auto: automatically inferred from input ws
     'catOffset':0, # add offset to category numbers (useful for categories from different allData.root files)  
-    'ext':'2022-11-21', # extension to add to output directory
+    'ext':'2023-02-13', # extension to add to output directory
     'year':'combined', # Use combined when merging all years in category (for plots)
     'xvar': 'CMS_hgg_mass', # not yet used, should be passed to the C++ macros
     'plotdir': 'plots',
 
     # Job submission options
-    'batch':'condor', # [condor,SGE,IC,local]
-    'queue':'espresso' # for condor e.g. espresso
+    'batch':'Rome', # [condor,SGE,IC,Rome,local]
+    'queue':'cmsan' # for condor e.g. espresso
 
 }

Background/runBackgroundScripts.sh

@@ -92,7 +92,7 @@ done
 
 OUTDIR="outdir_${EXT}"
 if [[ $PLOTDIR == "" ]]; then
-    PLOTDIR=OUTDIR
+    PLOTDIR=$OUTDIR
 fi
 
 echo "[INFO] outdir is $OUTDIR, plotdir is $PLOTDIR INTLUMI $INTLUMI" 
@@ -168,7 +168,11 @@ OPT=" --isData 1"
 fi
 
 mkdir -p "${PLOTDIR}/bkgfTest${DATAEXT}"
-cp "/afs/cern.ch/user/g/gpetrucc/php/index.php" "${PLOTDIR}/bkgfTest${DATAEXT}"
+if test -f "/afs/cern.ch/user/g/gpetrucc/php/index.php"; then
+    cp "/afs/cern.ch/user/g/gpetrucc/php/index.php" "${PLOTDIR}/bkgfTest${DATAEXT}"
+elif test -f "/cmshome/dimarcoe/php/index.php"; then
+    cp "/cmshome/dimarcoe/php/index.php" "${PLOTDIR}/bkgfTest${DATAEXT}"
+fi
 echo " ./bin/fTest -i $FILE --saveMultiPdf $OUTDIR/CMS-HGG_multipdf_$EXT_$CATS.root  -D $OUTDIR/bkgfTest$DATAEXT -f $CATS $OPT --year $YEAR --catOffset $CATOFFSET"
 ./bin/fTest -i $FILE --saveMultiPdf $OUTDIR/CMS-HGG_multipdf_$EXT_$CATS.root  -D $OUTDIR/bkgfTest$DATAEXT -P $PLOTDIR/bkgfTest$DATAEXT -f $CATS $OPT --year $YEAR --catOffset $CATOFFSET
 

Background/run_sequence.sh

@@ -1,2 +1,2 @@
-python scripts/mergeMultiYearsData.py -i cards/cards_current -o cards/cards_current/data_Run2/allData.root
+#python scripts/mergeMultiYearsData.py -i cards/cards_current -o cards/cards_current/data_Run2/allData.root
 python RunBackgroundScripts.py --inputConfig config_test.py --mode fTestParallel

Background/tools/submissionTools.py

@@ -73,7 +73,7 @@ def writeSubFiles(_opts):
     _fsub.close()
 
   # SGE...
-  if (_opts['batch'] == "IC")|(_opts['batch'] == "SGE")|(_opts['batch'] == "local" ):
+  if (_opts['batch'] == "IC")|(_opts['batch'] == "SGE")|(_opts['batch'] == "Rome")|(_opts['batch'] == "local" ):
     _executable = "sub_%s_%s"%(_opts['mode'],_opts['ext'])
 
     # Write details depending on mode
@@ -102,8 +102,9 @@ def submitFiles(_opts):
     print "  --> Finished submitting files"
 
   # SGE
-  elif _opts['batch'] in ['IC','SGE']:
+  elif _opts['batch'] in ['IC','SGE','Rome']:
     _executable = "sub_%s_%s"%(_opts['mode'],_opts['ext'])
+    _subcmd = 'bsub' if _opts['batch']=='Rome' else 'qsub'
 
     # Extract job opts
     jobOptsStr = _opts['jobOpts']
@@ -113,7 +114,7 @@ def submitFiles(_opts):
       for cidx in range(_opts['nCats']):
         c = _opts['cats'].split(",")[cidx]
         _subfile = "%s/%s_%s"%(_jobdir,_executable,c)
-        cmdLine = "qsub -q hep.q %s -o %s.log -e %s.err %s.sh"%(jobOptsStr,_subfile,_subfile,_subfile)
+        cmdLine = "%s -q %s %s -o %s.log -e %s.err %s.sh"%(_subcmd,_opts['queue'],jobOptsStr,_subfile,_subfile,_subfile)
         run(cmdLine)
     print "  --> Finished submitting files"
 

Combine/CollectFits.py

@@ -40,7 +40,13 @@ def run(cmd):
   if _fit.split(":")[2] == "all": _fitpois = pois
   else: _fitpois = _fit.split(":")[2].split(",")
   _name = "%s_%s"%(_fit.split(":")[0],_fit.split(":")[1])
-  if opt.doObserved: _name += "_obs"
+  if opt.doObserved: 
+    _name += "_obs"
+    mainlabel = "Observed"
+  else:
+    mainlabel = "Expected"
+  # add this to distinguish different fits with same POI
+  _name += "_"+opt.ext
 
   if( _fit.split(":")[0] == "bestfit" ):
     for poi in _fitpois:
@@ -56,9 +62,20 @@ def run(cmd):
 
   elif( _fit.split(":")[0] == "profile1D")|( _fit.split(":")[0] == "scan1D" ):
     for poi in _fitpois:
+      if poi in ["r_ggH","r_VBF","r_top","r_VH"]:
+        translate_json = "pois_mu.json" 
+      elif poi=='CMS_zz4l_fai1':
+        if 'ALT_0M' in opt.ext: translate_json = "pois_fa3.json"
+        if 'ALT_0PH' in opt.ext: translate_json = "pois_fa2.json"
+        if 'ALT_L1' in opt.ext: translate_json = "pois_flambda1.json"
+        if 'ALT_L1Zg' in opt.ext: translate_json = "pois_flambda1zgamma.json"
+      else:
+        print "Warning: unknown poi. Use r as default"
+        translate_json = "pois_mu.json"
       haddcmd = "cd runFits%s_%s; hadd -f %s_%s.root higgsCombine_%s_%s.POINTS.*.*.root; cd .."%(opt.ext,opt.mode,_name,poi,_name,poi)
       run(haddcmd)
-      plotcmd = "cd runFits%s_%s; plot1DScan.py %s_%s.root --y-cut 20 --y-max 20 -o Plots/%s_%s%s --POI %s; cd .."%(opt.ext,opt.mode,_name,poi,_name,poi,opt.ext,poi)
+      plotcmd = "cd runFits%s_%s; plot1DScan.py %s_%s.root --y-cut 30 --y-max 30 -o Plots/%s_%s%s --POI %s --main-label %s --translate %s/src/flashggFinalFit/Plots/%s; cd .."%(opt.ext,opt.mode,_name,poi,_name,poi,opt.ext,poi,mainlabel,os.environ['CMSSW_BASE'],translate_json)
+      print "plotcmd = ",plotcmd
       run(plotcmd)
 
   elif( _fit.split(":")[0] == "scan2D")|( _fit.split(":")[0] == "profile2D" ):

Combine/PlotScans.py

@@ -74,10 +74,10 @@ def run(cmd):
       if poi in ["r_ggH","r_VBF","r_top","r_VH"]:
         translate_json = "pois_mu.json" 
       elif poi=='CMS_zz4l_fai1':
-        if 'ALT0M' in opt.ext: translate_json = "pois_fa3.json"
-        if 'ALT0PH' in opt.ext: translate_json = "pois_fa2.json"
-        if 'ALT0L1' in opt.ext: translate_json = "pois_flambda1.json"
-        if 'ALT0L1Zg' in opt.ext: translate_json = "pois_flambda1zgamma.json"
+        if 'ALT_0M' in opt.ext: translate_json = "pois_fa3.json"
+        if 'ALT_0PH' in opt.ext: translate_json = "pois_fa2.json"
+        if 'ALT_L1' in opt.ext: translate_json = "pois_flambda1.json"
+        if 'ALT_L1Zg' in opt.ext: translate_json = "pois_flambda1zgamma.json"
       else:
         print "Warning: unknown poi. Use r as default"
         translate_json = "pois_mu.json"

Combine/RunFits.py

@@ -19,7 +19,7 @@ def get_options():
   parser.add_option('--doObserved', dest='doObserved', action="store_true", default=False, help="Fit to data")
   parser.add_option('--snapshotWSFile', dest='snapshotWSFile', default='', help="Full path to snapshot WS file (use when running observed statonly as nuisances are froze at postfit values)")
   parser.add_option('--commonOpts', dest='commonOpts', default="--cminDefaultMinimizerStrategy 0 --X-rtd MINIMIZER_freezeDisassociatedParams --X-rtd MINIMIZER_multiMin_hideConstants --X-rtd MINIMIZER_multiMin_maskConstraints --X-rtd MINIMIZER_multiMin_maskChannels=2", help="Common combine options for running fits")
-  parser.add_option('--batch', dest='batch', default='condor', help='Batch: [crab,condor/SGE/IC]')
+  parser.add_option('--batch', dest='batch', default='condor', help='Batch: [crab,condor/SGE/IC/lxbatch]')
   parser.add_option('--queue', dest='queue', default='espresso', help='Queue e.g. for condor=workday, for IC=hep.q')
   parser.add_option('--subOpts', dest='subOpts', default="", help="Submission options")
   parser.add_option('--doCustomCrab', dest='doCustomCrab', default=False, action="store_true", help="Load crab options from custom_crab.py file")
@@ -65,11 +65,11 @@ def getPdfIndicesFromJson(pdfjson):
   if opt.subOpts != "": sub_opts += "\n%s"%opt.subOpts
   sub_opts += "\'"
   job_opts = "--job-mode condor %s"%sub_opts
-elif( opt.batch == 'SGE' )|( opt.batch == 'IC' ):
+elif( opt.batch == 'SGE' )|( opt.batch == 'IC' )|( opt.batch == 'lxbatch' ):
   sub_opts = "--sub-opts=\'-q %s"%opt.queue
   if opt.subOpts != "": sub_opts += " %s"%opt.subOpts
   sub_opts += "\'"
-  job_opts = "--job-mode SGE %s"%sub_opts
+  job_opts = "--job-mode %s %s"%(opt.batch,sub_opts)
 elif opt.batch == "local":
   print "--> Will print the commands to run combine without combineTool interactively\n\n"
 else:

Combine/RunText2Workspace.py

@@ -37,7 +37,7 @@ def run(cmd):
 fsub.write("#!/bin/bash\n\n")
 fsub.write("cd %s\n\n"%os.environ['PWD'])
 fsub.write("eval `scramv1 runtime -sh`\n\n")
-fsub.write("text2workspace.py Datacard_%s.txt -o Datacard_%s.root %s %s"%(opt.ext,opt.ext,opt.common_opts,models[opt.mode]))
+fsub.write("text2workspace.py Datacard_%s.txt -o Datacard_%s.root %s %s\n"%(opt.ext,opt.ext,opt.common_opts,models[opt.mode]))
 fsub.close()
 
 # Change permission for file
@@ -58,6 +58,6 @@ def run(cmd):
 # Submit
 if opt.batch == "condor": subcmd = "condor_submit ./t2w_jobs/t2w_%s.sub"%(opt.ext)
 elif opt.batch == 'local': subcmd = "bash ./t2w_jobs/t2w_%s.sh"%(opt.ext)
-else: subcmd = "qsub -q hep.q -l h_rt=6:0:0 -l h_vmem=24G ./t2w_jobs/t2w_%s.sh"%(opt.ext)
+else: subcmd = "bsub -q cmsan -o ./t2w_jobs/t2w_%s.log -e ./t2w_jobs/t2w_%s.err ./t2w_jobs/t2w_%s.sh"%(opt.ext,opt.ext,opt.ext)
 if opt.dryRun: print "[DRY RUN] %s"%subcmd
 else: run(subcmd)

Combine/inputs.json

@@ -1,38 +1,32 @@
 {
     "xsec":{
-        "pois":"r_VBF",
+        "pois":"r_ggH,r_VBF,r_VH,r_top",
         "fits":"profile1D:syst:all+bestfit:syst:all",
-        "points":"20:1+:",
-        "fit_opts":"--setParameters r_ggH=1,r_top=1,r_VH=1 --setParameterRanges r_VBF=0,3:r_ggH=0.99,1.01:r_top=0.99,1.01:r_VH=0.99,1.01 --saveSpecifiedNuis all --saveInactivePOI 1 --freezeParameters MH,r_ggH,r_top,r_VH  --autoBoundsPOIs 'r_VBF' --autoMaxPOIs 'r_VBF' --fastScan+--setParameters r_ggH=1,r_top=1,r_VH=1 --setParameterRanges r_VBF=0,3:r_ggH=0.99,1.01:r_top=0.99,1.01:r_VH=0.99,1.01 --saveSpecifiedNuis all --saveInactivePOI 1 --freezeParameters MH,r_ggH,r_top,r_VH --saveWorkspace"
+        "points":"41:1+:",
+        "fit_opts":"--setParameters r_ggH=1,r_top=1,r_VH=1,r_VBF=1 --setParameterRanges r_ggH=0.0,2.0:r_VBF=0.0,2.0:r_VH=0.0,3.0:r_top=0.0,4.0 --X-rtd FITTER_NEW_CROSSING_ALGO --X-rtd FITTER_BOUND --saveSpecifiedNuis all --saveInactivePOI 1 --fastScan+--setParameters r_ggH=1,r_top=1,r_VH=1,r_VBF=1 --setParameterRanges r_ggH=0.0,2.0:r_VBF=0.0,2.0:r_VH=0.0,3.0:r_top=0.0,4.0 --robustFit=1 --setRobustFitAlgo=Minuit2,Migrad --X-rtd FITTER_NEW_CROSSING_ALGO --setRobustFitTolerance=0.1 --X-rtd FITTER_NEVER_GIVE_UP --X-rtd FITTER_BOUND --cminFallbackAlgo \"Minuit2,0:1.\" --saveSpecifiedNuis all --saveInactivePOI 1 --saveWorkspace"
     },
-    "cp":{
-        "pois":"x",
-        "fits":"profile1D:syst:all",
-        "points":"20:1",
-        "fit_opts":"--saveSpecifiedNuis all --saveInactivePOI 1 --cminApproxPreFitTolerance=10 --freezeParameters MH --fastScan --setParameters r=1 --setParameterRanges x=0,0.5"
-    },
-    "ALT0M":{
+    "ALT_0M":{
         "pois":"CMS_zz4l_fai1",
         "fits":"profile1D:syst:all",
-        "points":"200:1",
-        "fit_opts":"--saveSpecifiedNuis all --saveInactivePOI 1 --cminApproxPreFitTolerance=10  --setParameterRanges CMS_zz4l_fai1=-0.003,0.003 --freezeParameters MH,fa3_ggH,muf --fastScan --setParameters muV=1,muf=1,fa3_ggH=1 --autoMaxPOIs 'CMS_zz4l_fai1' --autoBoundsPOIs 'CMS_zz4l_fai1' "
+        "points":"41:1",
+        "fit_opts":"--saveSpecifiedNuis all --saveInactivePOI 1 --setParameterRanges muV=0.0,4.0:muf=0.0,10.0:fa3_ggH=0.,1.:CMS_zz4l_fai1=-0.003,0.003 --fastScan --setParameters muV=1.,CMS_zz4l_fai1=0.,muf=1.,fa3_ggH=0. --robustFit=1 --setRobustFitAlgo=Minuit2,Migrad --X-rtd FITTER_NEW_CROSSING_ALGO --setRobustFitTolerance=0.1 --X-rtd FITTER_NEVER_GIVE_UP --X-rtd FITTER_BOUND --cminFallbackAlgo \"Minuit2,0:1.\" "
     },
-    "ALT0PH":{
+    "ALT_0PH":{
         "pois":"CMS_zz4l_fai1",
         "fits":"profile1D:syst:all",
-        "points":"200:1",
-        "fit_opts":"--saveSpecifiedNuis all --saveInactivePOI 1 --cminApproxPreFitTolerance=10  --setParameterRanges CMS_zz4l_fai1=-0.003,0.003 --freezeParameters MH,fa3_ggH,muf --fastScan --setParameters muV=1,muf=1,fa3_ggH=1 --autoMaxPOIs 'CMS_zz4l_fai1' --autoBoundsPOIs 'CMS_zz4l_fai1' "
+        "points":"41:1",
+        "fit_opts":"--saveSpecifiedNuis all --saveInactivePOI 1 --setParameterRanges muV=0.0,4.0:muf=0.0,10.0:CMS_zz4l_fai1=-0.01,0.01   --fastScan --setParameters muV=1.,CMS_zz4l_fai1=0.,muf=1. --robustFit=1 --setRobustFitAlgo=Minuit2,Migrad --X-rtd FITTER_NEW_CROSSING_ALGO --setRobustFitTolerance=0.1 --X-rtd FITTER_NEVER_GIVE_UP --X-rtd FITTER_BOUND --cminFallbackAlgo \"Minuit2,0:1.\" "
     },
-    "ALT0L1":{
+    "ALT_L1":{
         "pois":"CMS_zz4l_fai1",
         "fits":"profile1D:syst:all",
-        "points":"200:1",
-        "fit_opts":"--saveSpecifiedNuis all --saveInactivePOI 1 --cminApproxPreFitTolerance=10  --setParameterRanges CMS_zz4l_fai1=-0.003,0.003 --freezeParameters MH,fa3_ggH,muf --fastScan --setParameters muV=1,muf=1,fa3_ggH=1 --autoMaxPOIs 'CMS_zz4l_fai1' --autoBoundsPOIs 'CMS_zz4l_fai1' "
+        "points":"41:1",
+        "fit_opts":"--saveSpecifiedNuis all --saveInactivePOI 1 --setParameterRanges muV=0.0,4.0:muf=0.0,10.0:CMS_zz4l_fai1=-0.001,0.001   --fastScan --setParameters muV=1.,CMS_zz4l_fai1=0.,muf=1. --robustFit=1 --setRobustFitAlgo=Minuit2,Migrad --X-rtd FITTER_NEW_CROSSING_ALGO --setRobustFitTolerance=0.1 --X-rtd FITTER_NEVER_GIVE_UP --X-rtd FITTER_BOUND --cminFallbackAlgo \"Minuit2,0:1.\" "
     },
-    "ALT0L1Zg":{
+    "ALT_L1Zg":{
         "pois":"CMS_zz4l_fai1",
         "fits":"profile1D:syst:all",
-        "points":"200:1",
-        "fit_opts":"--saveSpecifiedNuis all --saveInactivePOI 1 --cminApproxPreFitTolerance=10  --setParameterRanges CMS_zz4l_fai1=-0.003,0.003 --freezeParameters MH,fa3_ggH,muf --fastScan --setParameters muV=1,muf=1,fa3_ggH=1 --autoMaxPOIs 'CMS_zz4l_fai1' --autoBoundsPOIs 'CMS_zz4l_fai1' "
+        "points":"41:1",
+        "fit_opts":"--saveSpecifiedNuis all --saveInactivePOI 1 --setParameterRanges muV=0.0,4.0:muf=0.0,10.0:CMS_zz4l_fai1=-0.01,0.01   --fastScan --setParameters muV=1.,CMS_zz4l_fai1=0.,muf=1. --robustFit=1 --setRobustFitAlgo=Minuit2,Migrad --X-rtd FITTER_NEW_CROSSING_ALGO --setRobustFitTolerance=0.1 --X-rtd FITTER_NEVER_GIVE_UP --X-rtd FITTER_BOUND --cminFallbackAlgo \"Minuit2,0:1.\" "
     }
 }

Combine/models.py

@@ -1,7 +1,7 @@
 models = {
     "mu_inclusive":"",
 
-    "xsec":"-P HiggsAnalysis.CombinedLimit.PhysicsModel:multiSignalModel \
+    "mu":"-P HiggsAnalysis.CombinedLimit.PhysicsModel:multiSignalModel \
     --PO \"map=.*/ggH.*hgg:r_ggH[1,0,3]\" \
     --PO \"map=.*/qqH.*hgg:r_VBF[1,0,3]\" \
     --PO \"map=.*/ttH.*hgg:r_top[1,-1,2]\" \
@@ -11,26 +11,28 @@
     "cp":"-P HiggsAnalysis.CombinedLimit.HiggsJPC:twoHypothesisHiggs \
     --PO=muFloating", 
 
-    "ALT0M":"-P HiggsAnalysis.CombinedLimit.HiggsSingleAnomalousCoupling:FA3_Interference_JHU_ggHSyst_rw_MengsMuV_HeshyXsec_ggHInt_ggHphase \
-    --PO altSignal=ALT0M",
+    "ALT_0M":"-P HiggsAnalysis.CombinedLimit.FA3_Interference_JHU_ggHSyst_rw_MengsMuV_HeshyXsec_ggHInt_ggHphase:FA3_Interference_JHU_ggHSyst_rw_MengsMuV_HeshyXsec_ggHInt_ggHphase \
+    --PO altSignal=ALT_0M",
 
-    "ALT0PH":"-P HiggsAnalysis.CombinedLimit.HiggsSingleAnomalousCoupling:FA3_Interference_JHU_ggHSyst_rw_MengsMuV_HeshyXsec_ggHInt_ggHphase \
-    --PO altSignal=ALT0PH",
+    "ALT_0PH":"-P HiggsAnalysis.CombinedLimit.FA2_Interference_JHU_rw_MengsMuV:FA2_Interference_JHU_rw_MengsMuV \
+    --PO altSignal=ALT_0PH",
 
-    "ALT0L1":"-P HiggsAnalysis.CombinedLimit.HiggsSingleAnomalousCoupling:FA3_Interference_JHU_ggHSyst_rw_MengsMuV_HeshyXsec_ggHInt_ggHphase \
-    --PO \"altSignal=ALT0L1\"",
+    "ALT_L1":"-P HiggsAnalysis.CombinedLimit.FL1_Interference_JHU_rw_MengsMuV:FL1_Interference_JHU_rw_MengsMuV \
+    --PO \"altSignal=ALT_L1\"",
 
-    "ALT0L1Zg":"-P HiggsAnalysis.CombinedLimit.HiggsSingleAnomalousCoupling:FA3_Interference_JHU_ggHSyst_rw_MengsMuV_HeshyXsec_ggHInt_ggHphase \
-    --PO altSignal=ALT0L1Zg",
+    "ALT_L1Zg":"-P HiggsAnalysis.CombinedLimit.FL1Zg_Interference_JHU_rw_MengsMuV:FL1Zg_Interference_JHU_rw_MengsMuV \
+    --PO altSignal=ALT_L1Zg",
 
-    "mu":"-P HiggsAnalysis.CombinedLimit.PhysicsModel:multiSignalModel \
+    "xsec":"-P HiggsAnalysis.CombinedLimit.PhysicsModel:multiSignalModel \
     --PO \"map=.*/ggH.*:r_ggH[1,0,2]\" \
     --PO \"map=.*/bbH.*:r_ggH[1,0,2]\" \
     --PO \"map=.*/qqH.*:r_VBF[1,0,3]\" \
-    --PO \"map=.*/WH_had.*:r_VH[1,0,3]\" \
+    --PO \"map=.*/WPLUSH2HQQ.*:r_VH[1,0,3]\" \
+    --PO \"map=.*/WMINUSH2HQQ.*:r_VH[1,0,3]\" \
     --PO \"map=.*/ZH_had.*:r_VH[1,0,3]\" \
     --PO \"map=.*/ggZH_had.*:r_VH[1,0,3]\" \
-    --PO \"map=.*/WH_lep.*:r_VH[1,0,3]\" \
+    --PO \"map=.*/WPLUSH_lep.*:r_VH[1,0,3]\" \
+    --PO \"map=.*/WMINUSH_lep.*:r_VH[1,0,3]\" \
     --PO \"map=.*/ZH_lep.*:r_VH[1,0,3]\" \
     --PO \"map=.*/ggZH_ll.*:r_VH[1,0,3]\" \
     --PO \"map=.*/ggZH_nunu.*:r_VH[1,0,3]\" \

Combine/run_sequence.sh

@@ -2,14 +2,15 @@ outdate=`date +%F`
 
 STEP=0
 usage(){
-    echo "Script to run yields and datacard making. Yields need to be done before running datacards"
+    echo "Script to run fits and plots of fit output. dryRun option is for the fitting only, that can be run in batch."
     echo "options:"
 
     echo "-h|--help) "
     echo "-s|--step) "
+    echo "-d|--dryRun) "
 }
 # options may be followed by one colon to indicate they have a required argument
-if ! options=$(getopt -u -o s:h -l help,step: -- "$@")
+if ! options=$(getopt -u -o s:hd -l help,step:,dryRun -- "$@")
 then
 # something went wrong, getopt will put out an error message for us
 exit 1
@@ -20,31 +21,44 @@ do
 case $1 in
 -h|--help) usage; exit 0;;
 -s|--step) STEP=$2; shift ;;
+-d|--dryRun) DR=$2; shift ;;
 (--) shift; break;;
 (-*) usage; echo "$0: error - unrecognized option $1" 1>&2; usage >> /dev/stderr; exit 1;;
 (*) break;;
 esac
 shift
 done
 
-fits=("xsec" "ALT0L1" "ALT0L1Zg" "ALT0PH" "ALT0M")
+DROPT=""
+if [[ $DR ]]; then
+    DROPT=" --dryRun "
+fi
+
+fits=("xsec" "ALT_L1" "ALT_L1Zg" "ALT_0PH" "ALT_0M")
 
 if [[ $STEP == "t2w" ]]; then
     for fit in ${fits[*]}
     do
-        python RunText2Workspace.py --ext $fit --mode $fit --batch local
+        python RunText2Workspace.py --ext $fit --mode $fit --batch Rome
     done
 elif [[ $STEP == "fit" ]]; then
     for obs in " " " --doObserved "
     do
         for fit in ${fits[*]}
         do
-            python RunFits.py --inputJson inputs.json --ext $fit --mode $fit --batch local $obs
+            python RunFits.py --inputJson inputs.json --ext $fit --mode $fit --batch lxbatch --queue cmsan ${DROPT} $obs
         done
     done
+elif [[ $STEP == "collect" ]]; then
+    for obs in " " " --doObserved "
+    do
+	for fit in ${fits[*]}
+	do
+	    python CollectFits.py --inputJson inputs.json --ext $fit --mode $fit $obs
+	done
+    done
 elif [[ $STEP == "plot" ]]; then
-    #for obs in " " " --doObserved "
-    for obs in " "
+    for obs in " " " --doObserved "
     do
         for fit in ${fits[*]}
         do