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Code to produce analysis ntuples (pico) from the CMS NanoAOD.

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nano2pico

Utility package for converting CMS NanoAOD to analysis-ready ntuples called "pico". These have been used in the HH+MET and H to Zgamma analyses.

Installation, environment, and compilation

If you are not on one of the UCSB servers, prerequisites that must be installed include CERN ROOT and optionally Scons for building nano2pico. Assuming your ROOT environment is active, you can build nano2pico after cloning this repository by running scons if you have Scons installed, or by running compile.sh otherwise.

If you are using one of the UCSB servers that supports CMSSW (e.g. cms1,cms3,cms4,cms5...), you can use the following commands to install nano2pico and set up the environment:

# Setup git version for SL6.5
. /cvmfs/cms.cern.ch/cmsset_default.sh;cd /net/cms29/cms29r0/pico/CMSSW_10_2_11_patch1/src;eval `scramv1 runtime -sh`;cd -
# Clone git
git clone --recurse-submodules [email protected]:richstu/nano2pico.git
# If did not use recurse at clone, use following command: git submodule update --init --remote --recursive
# Setup environemnt
source set_env.sh

You can then compile via scons or compile.sh.

Productions

Variables stored in the pico can be seen in variables/pico. For an overview of the available branches, see the dedicated section at the bottom of this README.

To see the sizes and number of files in all available productions do:

  ./scripts/count_root_files.py -f /net/cms29/cms29r0/pico/NanoAODv5/

How does nano2pico work?

This package is used to do the Nano -> pico conversion in three steps in order to allow parallelizing the production at the sub-dataset level:

  1. All variables and event weights (except normalization) are calculated using src/process_nano.cxx. For Monte Carlo events, this step also keeps a tally of the weights for all events in the file being run over as input to the next step. For data events, only this step is needed.
  2. The sums of weights from step 1 are further aggregate to get the total per dataset. A correction is then calculated to ensure that the weights do not change the total expected number of events for the dataset. This is done in src/merge_corrections.cxx. The luminosity normalization weight w_lumi to be applied to get the yield in 1fb-1 is also calculated for each dataset in this step.
  3. The raw_pico files from step 1 are corrected by the per-dataset correction factors derived in step 2 and written to the unskimmed folder.

At this point, various skims can be made as defined in scripts/skim_file.py.

Note: The input path in which the input NanoAOD files are stored as well as the output path are analyzed to determine the behavior of nano2pico. To run with settings for the Higgs to Z gamma analysis, the 'out_dir' should contian "zgamma" in its name. To run on custom NanoAODv9 files, the input directory must contain "NanoAODv9UCSB" in its name.

Interactive test usage

Define some paths, e.g.:

export INDIR=/net/cms29/cms29r0/pico/NanoAODv5/nano/2016/TChiHH/
export INFILE=SMS-TChiHH_mChi-1000_mLSP-1_TuneCUETP8M1_13TeV-madgraphMLM-pythia8__RunIISummer16NanoAODv5__PUSummer16v3Fast_94X_mcRun2_asymptotic_v3-v1.root

Step 1. Make an output directory out/ with subdirectories wgt_sums and raw_pico. Produce raw pico ntuple from a nano input file:

./compile.sh && ./run/process_nano.exe --in_file $INFILE --in_dir $INDIR --out_dir out/ --nent 10000

‼️ Code functionality relies on the input NanoAOD filename! Specifically, INFILE is parsed for:

  • flag isData = infile.Contains("Run201") ? true : false;
  • flag isFastsim = infile.Contains("Fast") ? true : false;
  • flag isSignal = Contains(in_file, "TChiHH") || Contains(in_file, "T5qqqqZH") ? true : false;
  • variable year = infile.Contains("RunIISummer16") ? 2016 : (infile.Contains("RunIIFall17") ? 2017 : 2018)
  • output branch type is set based on the presence of dataset name substrings (see event_tools.cpp)
  • branches related on ISR also depend on the presence of dataset name substrings

Step 2. If you are using data, you are done! If you are using MC, for each dataset, add up the sums of weights obtained for each file in step 1 and calculate the corrections needed to normalize each individual weight as well as the total weight. Note that the order of options is fixed with the arguments after the first being the input files. This is to allow arbitrary number of input files. Note that again functionality depends on the naming, e.g. correction file name is used to decide what cross-section to use. Make subdirectory corrections in out.

./compile.sh && ./run/merge_corrections.exe out/corrections/corr_$INFILE out/wgt_sums/wgt_sums_$INFILE

Step 3. Make subdirectory unskimmed in out`. Using the pico file from step 1 and the corrections file from step 2 as input, we can renormalize the weight branches as follows:

./compile.sh && ./run/apply_corrections.exe --in_file raw_pico_$INFILE --in_dir out/raw_pico/ --corr_file corr_$INFILE

Batch system usage

nano2pico supports batch system usage to process many datasets in parallel. Currently, this system is only configured for use at UCSB, and must be modified if nano2pico is being run on another system.

While previous versions of nano2pico used the custom UCSB batch system, the current version now uses HTCondor. For this reason, jobs must be run on the cms11 server. To get permission to run jobs on HTCondor, please contact Jaebak.

Step 0. Setup environment

source set_env.sh

Step 1. Converting Nano to Pico:

First, generate a text file containing the datasets in DAS format (this is produced by copy_dataset) or the filenames to be processed, one per line. If you use filenames, you must add the argument --list_format filename when invoking scripts/write_process_nano_cmds.py.

Next, generate a python file that prints the commands to be run in the batch (input for the queue system):

./scripts/write_process_nano_cmds.py --in_dir /mnt/hadoop/pico/NanoAODv5/nano/2016/mc/ \
                                      --production higgsino_angeles \
                                      --dataset_list datasets/higgsino_2016_mc_dataset_list.txt

or for signal, just specify the appropriate input folder and omit the --dataset_list argument to run on all files in the input folder.

To run on data, use --list_format filename in order to interpret the lines in the file passes to --dataset_list as a list of filenames with wildcards. For an example file, see txt/datasets/higgsino_data_infile_list.txt. For example:

./scripts/write_process_nano_cmds.py --in_dir /net/cms29/cms29r0/pico/NanoAODv5/nano/2016/data/ \
                                     --production higgsino_humboldt \
                                     --dataset_list txt/datasets/higgsino_data_infile_list.txt \
                                     --list_format filename

This produces the commands in cmds.py. You can perform a last check by running one of the commands interactively. Next, submit the jobs to the batch system. Note the -c option which allows to attach a script that compares the input and output number of entries when each job is done. Note the check can be performed later if one needs to detach the session. Alternatively, this command can be started in screen:

auto_submit_jobs.py process_nano_cmds.json -c scripts/check_process_nano_job.py

For data use the scripts/check_data_process_nano_job.py like below

auto_submit_jobs.py process_nano_cmds.json -c scripts/check_data_process_nano_job.py

If the above script is interrupted, one can check whether the jobs were successful later on by passing the json produced by auto_submit_job.py to check_jobs.py:

check_jobs.py auto_higgsino_angeles.json -c scripts/check_process_nano_job.py

This command will result in checked_auto_higgsino_angeles.json, which can then be used to resubmit failed jobs if any:

select_resubmit_jobs.py checked_auto_higgsino_angeles.json -c scripts/check_process_nano_job.py 
auto_submit_jobs.py resubmit_checked_auto_higgsino_angeles.json -c scripts/check_process_nano_job.py

One can also resume the auto_submit_job.py like below

auto_submit_jobs.py auto_higgsino_angeles.json -c scripts/check_process_nano_job.py -o auto_higgsino_angeles.json

If processing Monte Carlo, then proceed to steps 2 and 3 (MC). If processing data, proceed directly to step 4.

Step 2 (MC). Merge sums of weights

For example:

./scripts/merge_corrections.py --wgt_dir /net/cms29/cms29r0/pico/NanoAODv5/higgsino_angeles/2016/mc/wgt_sums/ \
                               --corr_dir /net/cms29/cms29r0/pico/NanoAODv5/higgsino_angeles/2016/mc/corrections/

Step 3 (MC). Submit the weight correction jobs

To generate the commands use:

./scripts/write_apply_corrections_cmds.py --in_dir /net/cms29/cms29r0/pico/NanoAODv5/higgsino_angeles/2016/mc/raw_pico/

Follow similar process as in Step 1 to submit the commands as batch jobs.

Step 4. Making skims

It's recommended to start with a relatively inclusive skim which would then serve as the starting point for tighter skims to minimize total time spent on skimming. For example:

./scripts/write_skim_cmds.py --in_dir /net/cms29/cms29r0/pico/NanoAODv5/higgsino_angeles/2016/TChiHH/skim_higloose/ \
                             --skim_name higtight \
                             --tag apples
auto_submit_jobs.py skim_hightight_cmds_apples.json -c scripts/check_skim.py

The skim names are defined in scripts/skim_file.py. If defining a new skim, please commit the definition!! This eliminates confusion of what is in various folders on disk later on.

The argument --tag is optional. It is used to differentiate the JSON files created by the queue system in case of running multiple skims of the same type. It will not affect the folder structure.

Use --overwrite to run over all files even if output already exists. Otherwise, restarting the process of batch submission will skip files that have already been processed. Note that if you just re-issue the auto_submit_jobs.py with the original json file WILL overwrite. To omit files with existing output re-start from this step.

Note that this step works also on slims produced by Step 5.

Step 5. Making slims

Finally, one can remove branches that are not commonly used and merge all files pertaining to one dataset into a single file to further reduce size and speed up making plots. For example:

./scripts/write_slim_and_merge_cmds.py --in_dir /net/cms29/cms29r0/pico/NanoAODv5/higgsino_angeles/2016/mc/skim_met150/ \
                                       --slim_name higmc

Here the slim name must correspond to a txt file in the slim_rules folder, so in this example txt/slim_rules/higmc.txt. The file contains the list of branches to be dropped/kept.

Similarly to above, one can optionally use --overwrite or --tag.

Step 6. Prior to DNN training: Prepare tree with DNN inputs (deprecated)

For the higgsino analysis, one can prepare a tree with all the necessary DNN inputs for either training or inference using the executable make_higfeats.exe, and in the batch system, e.g.:

./scripts/write_generic_cmds.py ./scripts/write_generic_cmds.py \
           -i /net/cms29/cms29r0/pico/NanoAODv5/higgsino_eldorado/2017/mc/merged_higmc_higloose/ \
           -o /net/cms29/cms29r0/pico/NanoAODv5/higgsino_eldorado/2017/mc/higfeats_higloose/ \
           -e ./run/make_higfeats.exe -t mc2017

As usual, the tag is optional and only relevant for the filename of the resulting cmd file.

Step 7. After DNN evaluation: Merge pico with DNN output (deprecated)

After training the DNN and evaluating its output for all samples of interest using the diboson_ml package, one can update the corresponding pico trees to add a new branch containing the DNN output. This relies on having the events in the same order, so one has to update the pico ntuples used as input to higfeats! Given it is rather quick, it's done interactively.

For now, copy the input folder just in case...

cp -r /net/cms29/cms29r0/pico/NanoAODv5/higgsino_eldorado/2016/mc/merged_higmc_higloose/ \
      /net/cms29/cms29r0/pico/NanoAODv5/higgsino_eldorado/2016/mc/mergednn_higmc_higloose/ 
./scripts/run_update_pico.py \
     --pico_dir /net/cms29/cms29r0/pico/NanoAODv5/higgsino_eldorado/2016/mc/mergednn_higmc_higloose/ \
     --dnnout_dir /net/cms29/cms29r0/pico/NanoAODv5/higgsino_eldorado/2016/mc/dnnout_higloose/

Calculating b-tagging efficiencies (deprecated)

Use parameterize_efficiency.cxx, giving the directory with all the MC files and the year as arguments. Below is an example run for 2016 MC.

./compile.sh && ./run/parameterize_efficiency.exe -i /mnt/hadoop/jbkim/2019_09_30/2016/mc/ -y 2016

Description of pico branches

This section describes the event content (branches) of pico n-tuples.

📘 Documentation of the Nano variables used as input throughout the code can be found here.

Global

Filled by various files including event_tools, jetmet_producer, and process_nano:

  • run, lumiblock, event - as expected
  • type - integer encoding the physics process, see src/event_tools.cpp.
  • stitch, stitch_* - include stitch in order to run on an inclusive sample together with an overlapping slice in a different dataset, e.g. stitch = false for events with GenMET > 150 in the inclusive TTJets sample, in order to remove them when using the inclusive sample together with the deidicated genMET-150 samples, see here. The full stitch variable is determined by the stich_* pieces.
  • is_overlap, use_event - overlap removal similar to stitch, but as implemented for the H to Z gamma analysis. Mostly deals with overlap between inclusive samples (ex. Z to ll) and those with photons generated at matrix level. use_event will be true for events in one overlapping sample, but not the other
  • npv, npv_good - number of (good) reconstructed PVs
  • rho - pileup energy density calculated from all PF candidates without foreground removal
  • ht, ht5 - sum of pt of jets not associated with a lepton, including jets with |eta|<2.4 (|eta|<5)
  • mht, mht_phi - negative vector sums of jets not associated with a lepton
  • met, met_phi, met_calo - PF/calorimeter missing transverse momentum, as expected
  • mt - transverse mass, only calculated for nlep==1

Jets

Filled in jetmet_producer:

  • nbl, nbm, nbt - number of loose, medium and tight tagged jets according to DeepCSV tagger

  • nbdfl, nbdfm, nbdft - number of loose, medium and tight tagged jets according to DeepFlavour tagger

  • njet - number of jets that pass the pt and eta cuts and do not overlap with a signal lepton

  • jet_* - basic jet related variables and also:

    • jet_h1d, jet_h2d - booleans indicating whether this jet is one of the two jets in Higgs 1 or Higgs 2 of the 0th pair of Higgs candidates stored in hig_cand_*
    • jet_fjet_idx - index of any fat jets within 0.8

  • nfjet - number of AK8 jets that pass the pt and eta cuts

  • fjet_* - basic fat jet related variables and also:

    • fjet_deep_md_hbb_btv - Mass-decorrelated Deep Double B, H->bb vs QCD discriminator, endorsed by BTV
    • fjet_deep_md_hbb_jme - Mass-decorrelated DeepAk8, H->bb vs QCD discriminator, endorsed by JME

  • nsubfjet - number of AK8 jet subjets

  • subfjet_* - AK8 jet subjet variables

Leptons

  • nlep = nel + nmu
  • nvlep = nvel + nvmu
  • lep_* - signal leptons (electron and muon) variables

Calculated in mu_producer:

  • nmu - number of muons satisfying all signal muon requirements for resolved Higgsino analysis
  • nvmu - number of muons satisfying all veto muon requirements for resolved Higgsino analysis
  • mu_* - variables of interest for all muons satisfying the veto id, eta and pt requirements, but no isolation requirements

Calculated in el_producer:

  • nel - number of electrons satisfying all signal electron requirements for resolved Higgsino analysis
  • nvel - number of electrons satisfying all veto electron requirements for resolved Higgsino analysis
  • el_* - variables of interest for all electrons satisfying the veto id, eta and pt requirements, but no isolation

Photons

Calculated in photon_producer:

  • nphoton - number of signal photons

  • photon_* - photon variables

  • nfsrphoton - number of FSR photons

  • fsrphoton_* - FSR photon variables

Tracks

Calculated in tk_producer:

  • ntk - number of tracks passing criteria for resolved Higgsino analysis
  • tk_* - track variables

Higgsino (HH->4b+MET) candidates

Using the 4-jet with highest DeepCSV, calculate the higgsino variables for the three possible pairings. The 0th index stores the pairing with smalled Delta m

  • hig_cand_dm - Mass difference between the two Higgs candidates
  • hig_cand_am - Average mass between the two Higgs candidates
  • hig_cand_drmax - Max opening angle between the two b jets out of the two Higgs candidates.

Same variables using the 4-jet with highest DeepFlavour discriminant value are stored in:

  • hig_df_cand_*

  • low_dphi_* - require dPhi(jet, MET) be less than 0.5 for jets 1,2 and less than 0.3 for jets 3,4

Higgs to Z gamma-related variables

Calculated in dilep_producer and zgamma_producer.

  • dijet_* - variables for pairs of two highest pT signal jets
  • zg_cutBitMap - stores whether events pass a particular version of the H to Z gamma baseline selection
  • nllphoton - number of Higgs to Z gamma candidates
  • llphoton_* - Higgs candidate variables

Higgsino (HH->bbgammagamma+MET) candidates

  • nphotonphoton - number of diphoton Higgs candidates
  • photonphoton_* - diphoton Higgs candidate variables
  • nbb - number of b bbar Higgs candidates using deepCSV
  • bb_* - b bbar Higgs candidate variables
  • nbb_df - number of b bbar Higgs candidates using deep flavor
  • bb_df_* - b bbar Higgs candidate variables
  • nbbphotonphoton - number of bb gammagamma Higgs candidate pairs using deepCSV
  • bbphotonphoton_* - bb gammagamma Higgs candidate pair variables
  • nbbphotonphoton_df - number of bb gammagamma Higgs candidate pairs using deep flavor
  • bbphotonphoton_df_* - bb gammagamma Higgs candidate pair variables

Quality

  • pass_* - recommended MET filters
  • pass_jets - set to false if any of the jets fails loose ID
  • pass - logical AND of recommended and optional filters (currently not including RA2b for UL)

Truth

  • mc_* - information for a set of the generator particles in the hard process
  • ntrumu,ntruel,ntrutauh,ntrutaul - # of true leptons of particular type, where tauh is hadronically decaying taus and taul is leptonically decaying taus
  • ntrulep = ntrumu + ntruel + ntrutaul
  • isr_tru_* - MC truth, hadronic recoil, used for ISR reweighting used by the SUS PAG for weak production
  • mprod, mlsp - higgsino and lsp mass, with lsp mass always equal to one for the higgsino model
  • npu_tru, npu_tru_mean - true number of pileup vertices
  • mt_tru - transverse mass at truth level, only calculated for ntrulep==1
  • met_tru, met_tru_phi - true missing transverse momentum
  • ht_isr_me - scalar sum of parton pT at matrix element level
  • ngenjet - number of truth jets
  • genjet_* - truth jet variables

ISR

  • nisr - number of ISR jets according to matching to truth, used for ISR reweighting used by the SUS PAG for strong production

  • jetsys_* - hadronic recoil, i.e. vector sum of all jets, used in V+jets ISR studies

  • jetsys_nob_* - hadronic recoil, i.e. vector sum of all jets that are not b-tagged, used in 2L tt+jets ISR studies

Weights

Previously calculated in many dedicated files, but for UL, now calculated in event_weighter and trigger_weighter and then re-normalized in subsequent production steps:

  • weight - product of some of the individual weights below
  • w_lumi - weight to be applied to get the expected yield in 1 fb-1.
  • w_lep - weights to correct lepton ID efficiency, product of w_el and w_mu
  • w_el - weights to correct electron ID efficiency
  • w_mu - weights to correct muon ID efficiency
  • w_fs_lep - weights to correct FastSim lepton ID efficiency
  • w_photon - weights to correct photon ID and electron veto efficiency currently not correct
  • w_photon_id - weights to correct photon ID efficiency currently not correct
  • w_photon_csev - weights to correct photon electron-veto efficiency
  • w_btag - weight to correct medium WP only of deepCSV b-jet ID efficiency
  • w_btag_df - weight to correct medium WP only of deepFlavor b-jet ID efficiency
  • w_bhig - weight to correct all WPs of deepCSV b-jet ID efficiency
  • w_bhig_df - weight to correct all WPs of deepFlavor b-jet ID efficiency. This should be used as the primary b-tag weight
  • w_isr - 1., except for TTJets 2016 and signal, SUSY ISR reweighting
  • w_pu - weight to correct pileup distribution
  • w_prefire - weight to correct for inefficiency caused by run 2 trigger prefiring
  • w_trig - weight to correct for trigger efficiency

Trigger

The final trigger menus from each year from a post on the Trigger HN: 2016, 2017, 2018. Trigger menus for run 3: 2022?, 2023.

Calcalated in event_tools.

  • trig_single_el, trig_double_el, trig_single_mu, trig_double_mu - flag indicating events passed the lowest unprescaled single/double electron/muon trigger for the particular data taking era considered
  • HLT_* - trigger decisions

Systematic uncertainties

  • sys_* - systematic variations of weights up=0, down=1

  • sys_bchig, sys_udsghig, sys_fs_bchig, sys_fs_udsghig - variations in (FastSim) b-tagging weights, split by heavy flavor (b/c) and light flavor (u/d/s/g) jets

  • sys_murf - variations in renormalization and factorization scales, see nano documentation for indexing

  • sys_ps - variations in parton shower, see nano documentation for indexing

  • sys_jet_* - systematic variations in jet pt/mass

  • sys_photon_* - systematic variations in photon pt

  • sys_el_* - systematic variations in electron pt

For the following uncertainties the indices correspond to 0=JER up, 1=JER down, 2=JES up, 3=JES down.

  • sys_njet - njet as jet systematics are varied
  • sys_nb* - nb* as jet systematics are varied
  • sys_hig_cand_* - hig_cand_* as jet systematics are varied
  • sys_low_dphi_met - low_dphi_met as jet systematics are varied
  • sys_ht - ht as jet systematics are varied

For the following uncertainties the indices correspond to 0=JER up, 1=JER down, 2=JES up, 3=JES down, 4=unclustered energy up, 5=unclustered energy down, 6=lepton/photon up, 7=lepton/photon down

  • sys_met - met as jet systematics are varied
  • sys_met_phi - met_phi as jet systematics are varied

Spliting Higgsino signal

Step 0. Setup environment

source set_env.sh

Step . Correct FastSim JEC on NanoAODs / Add variations on FullSIM signal

./scripts/write_fastsim_jmeCorrection_cmds.py --inputNanoAodFolder /net/cms25/cms25r0/pico/NanoAODv7/nano/2016/SMS-TChiHH_2D_unsplit
                                              --outputNanoAodFolder /net/cms24/cms24r0/pico/NanoAODv7/nano/2016/SMS-TChiHH_2D_unsplit_fastSimJmeCorrection
                                              --commandFilename apply_fastsim_jmeCorrection_2016.py

./scripts/write_fastsim_jmeCorrection_cmds.py --inputNanoAodFolder /net/cms25/cms25r0/pico/NanoAODv7/nano/2017/SMS-TChiHH_2D_unsplit
                                              --outputNanoAodFolder /net/cms24/cms24r0/pico/NanoAODv7/nano/2017/SMS-TChiHH_2D_unsplit_fastSimJmeCorrection
                                              --commandFilename apply_fastsim_jmeCorrection_2017.py

./scripts/write_fastsim_jmeCorrection_cmds.py --inputNanoAodFolder /net/cms25/cms25r0/pico/NanoAODv7/nano/2018/SMS-TChiHH_2D_unsplit
                                              --outputNanoAodFolder /net/cms24/cms24r0/pico/NanoAODv7/nano/2018/SMS-TChiHH_2D_unsplit_fastSimJmeCorrection
                                              --commandFilename apply_fastsim_jmeCorrection_2018.py
./scripts/write_fastsim_jmeCorrection_cmds.py --inputNanoAodFolder /net/cms24/cms24r0/pico/NanoAODv7/nano/2016/SMS-T5qqqqZH_unsplit
                                              --outputNanoAodFolder /net/cms24/cms24r0/pico/NanoAODv7/nano/2016/SMS-T5qqqqZH_unsplit_fastSimJmeCorrection
                                              --commandFilename gluino_apply_fastsim_jmeCorrection_2016.py

./scripts/write_fastsim_jmeCorrection_cmds.py --inputNanoAodFolder /net/cms24/cms24r0/pico/NanoAODv7/nano/2017/SMS-T5qqqqZH_unsplit
                                              --outputNanoAodFolder /net/cms24/cms24r0/pico/NanoAODv7/nano/2017/SMS-T5qqqqZH_unsplit_fastSimJmeCorrection
                                              --commandFilename gluino_apply_fastsim_jmeCorrection_2017.py

./scripts/write_fastsim_jmeCorrection_cmds.py --inputNanoAodFolder /net/cms24/cms24r0/pico/NanoAODv7/nano/2018/SMS-T5qqqqZH_unsplit
                                              --outputNanoAodFolder /net/cms24/cms24r0/pico/NanoAODv7/nano/2018/SMS-T5qqqqZH_unsplit_fastSimJmeCorrection
                                              --commandFilename gluino_apply_fastsim_jmeCorrection_2018.py
auto_submit_jobs.py apply_fastsim_jmeCorrection_2016.json -c scripts/check_jmeCorrection.py
auto_submit_jobs.py apply_fastsim_jmeCorrection_2017.json -c scripts/check_jmeCorrection.py
auto_submit_jobs.py apply_fastsim_jmeCorrection_2018.json -c scripts/check_jmeCorrection.py

For FullSIM,

./scripts/write_fullsim_jmeCorrection_cmds.py --inputNanoAodFolder /net/cms24/cms24r0/pico/NanoAODv7/nano/2016/SMS-T5qqqqZH_FullSim
                                              --outputNanoAodFolder /net/cms24/cms24r0/pico/NanoAODv7/nano/2016/SMS-T5qqqqZH_FullSimJmeVariations
                                              --commandFilename gluino_apply_fullsim_jmeCorrection_2016.py
./scripts/write_fullsim_jmeCorrection_cmds.py --inputNanoAodFolder /net/cms24/cms24r0/pico/NanoAODv7/nano/2017/SMS-T5qqqqZH_FullSim
                                              --outputNanoAodFolder /net/cms24/cms24r0/pico/NanoAODv7/nano/2017/SMS-T5qqqqZH_FullSimJmeVariations
                                              --commandFilename gluino_apply_fullsim_jmeCorrection_2017.py
./scripts/write_fullsim_jmeCorrection_cmds.py --inputNanoAodFolder /net/cms24/cms24r0/pico/NanoAODv7/nano/2018/SMS-T5qqqqZH_FullSim
                                              --outputNanoAodFolder /net/cms24/cms24r0/pico/NanoAODv7/nano/2018/SMS-T5qqqqZH_FullSimJmeVariations
                                              --commandFilename gluino_apply_fullsim_jmeCorrection_2018.py
auto_submit_jobs.py apply_fullsim_jmecorrection_2016.json -c scripts/check_jmeCorrection.py
auto_submit_jobs.py apply_fullsim_jmecorrection_2017.json -c scripts/check_jmeCorrection.py
auto_submit_jobs.py apply_fullsim_jmecorrection_2018.json -c scripts/check_jmeCorrection.py

Step 1. Split scan

Generate a python file that prints the commands to be run in the batch (input for the queue system):

./scripts/write_split_signal_mass_points_cmds.py --two_dim
                                                 --in_dir /net/cms29/cms29r0/pico/NanoAODv5/nano/2016/SMS-TChiHH_2D_unsplit 
                                                 --target_dir /net/cms29/cms29r0/pico/NanoAODv5/nano/2016/SMS-TChiHH_2D 
                                                 --dataset_filenames SMS-TChiHH_*_TuneCUETP8M1_13TeV-madgraphMLM-pythia8__RunIISummer16NanoAODv5__PUSummer16v3Fast_Nano1June2019_102X_mcRun2_asymptotic_v7-v1_*.root
                                                 --out_cmd_filename cmds_split.py
./scripts/write_split_signal_mass_points_cmds.py --in_dir /net/cms24/cms24r0/pico/NanoAODv7/nano/2016/SMS-TChiHH_2D_unsplit_fastSimJmeCorrection 
                                                 --target_dir /net/cms24/cms24r0/pico/NanoAODv7/nano/2016/SMS-TChiHH_2D_fastSimJmeCorrection 
                                                 --dataset_filenames SMS-TChiHH_HToBB_HToBB_TuneCUETP8M1_13TeV-madgraphMLM-pythia8__RunIISummer16NanoAODv7__PUSummer16v3Fast_Nano02Apr2020_102X_mcRun2_asymptotic_v8-v1*.root
                                                 --out_cmd_filename cmds_split_2016_1D.py
./scripts/write_split_signal_mass_points_cmds.py --two_dim --in_dir /net/cms24/cms24r0/pico/NanoAODv7/nano/2016/SMS-TChiHH_2D_unsplit_fastSimJmeCorrection 
                                                 --target_dir /net/cms24/cms24r0/pico/NanoAODv7/nano/2016/SMS-TChiHH_2D_fastSimJmeCorrection 
                                                 --dataset_filenames SMS-TChiHH_HToBB_HToBB_2D_TuneCUETP8M1_13TeV-madgraphMLM-pythia8__RunIISummer16NanoAODv7__PUSummer16v3Fast_Nano02Apr2020_102X_mcRun2_asymptotic_v8-v1*.root
                                                 --out_cmd_filename cmds_split_2016_2D.py
./scripts/write_split_signal_mass_points_cmds.py --in_dir /net/cms24/cms24r0/pico/NanoAODv7/nano/2017/SMS-TChiHH_2D_unsplit_fastSimJmeCorrection 
                                                 --target_dir /net/cms24/cms24r0/pico/NanoAODv7/nano/2017/SMS-TChiHH_2D_fastSimJmeCorrection 
                                                 --dataset_filenames SMS-TChiHH_HToBB_HToBB_TuneCP2_13TeV-madgraphMLM-pythia8__RunIIFall17NanoAODv7__PUFall17Fast_Nano02Apr2020_102X_mc2017_realistic_v8-v1*.root
                                                 --out_cmd_filename cmds_split_2017_1D.py
./scripts/write_split_signal_mass_points_cmds.py --two_dim --in_dir /net/cms24/cms24r0/pico/NanoAODv7/nano/2017/SMS-TChiHH_2D_unsplit_fastSimJmeCorrection 
                                                 --target_dir /net/cms24/cms24r0/pico/NanoAODv7/nano/2017/SMS-TChiHH_2D_fastSimJmeCorrection 
                                                 --dataset_filenames SMS-TChiHH_HToBB_HToBB_2D_TuneCP2_13TeV-madgraphMLM-pythia8__RunIIFall17NanoAODv7__PUFall17Fast_Nano02Apr2020_102X_mc2017_realistic_v8-v1*.root
                                                 --out_cmd_filename cmds_split_2017_2D.py
./scripts/write_split_signal_mass_points_cmds.py --in_dir /net/cms24/cms24r0/pico/NanoAODv7/nano/2018/SMS-TChiHH_2D_unsplit_fastSimJmeCorrection 
                                                 --target_dir /net/cms24/cms24r0/pico/NanoAODv7/nano/2018/SMS-TChiHH_2D_fastSimJmeCorrection 
                                                 --dataset_filenames SMS-TChiHH_HToBB_HToBB_TuneCP2_13TeV-madgraphMLM-pythia8__RunIIAutumn18NanoAODv7__PUFall18Fast_Nano02Apr2020_102X_upgrade2018_realistic_v21-v1*.root
                                                 --out_cmd_filename cmds_split_2018_1D.py
./scripts/write_split_signal_mass_points_cmds.py --two_dim --in_dir /net/cms24/cms24r0/pico/NanoAODv7/nano/2018/SMS-TChiHH_2D_unsplit_fastSimJmeCorrection 
                                                 --target_dir /net/cms24/cms24r0/pico/NanoAODv7/nano/2018/SMS-TChiHH_2D_fastSimJmeCorrection 
                                                 --dataset_filenames SMS-TChiHH_HToBB_HToBB_2D_TuneCP2_13TeV-madgraphMLM-pythia8__RunIIAutumn18NanoAODv7__PUFall18Fast_Nano02Apr2020_102X_upgrade2018_realistic_v21-v1*.root
                                                 --out_cmd_filename cmds_split_2018_2D.py

convert_cl_to_jobs_info.py cmds_split.py cmds_split.py.json
auto_submit_jobs.py cmds_split.py.json -c jobscript_check.py -n cms1

model in the below commands are use for globbing files in the input directory.

./scripts/write_split_gluino_mass_points_cmds.py --in_dir /net/cms24/cms24r0/pico/NanoAODv7/nano/2016/SMS-T5qqqqZH_unsplit_fastSimJmeCorrection 
                                                 --out_cmd_filename split_gluino_2016.py 
                                                 --target_dir /net/cms24/cms24r0/pico/NanoAODv7/nano/2016/SMS-T5qqqqZH_fastSimJmeCorrection 
                                                 --model "SMS-T5qqqqZH_HToBB-mGluino"
./scripts/write_split_gluino_mass_points_cmds.py --in_dir /net/cms24/cms24r0/pico/NanoAODv7/nano/2016/SMS-T5qqqqZH_unsplit_fastSimJmeCorrection 
                                                 --out_cmd_filename split_gluino_mN2_2016.py 
                                                 --target_dir /net/cms24/cms24r0/pico/NanoAODv7/nano/2016/SMS-T5qqqqZH_fastSimJmeCorrection 
                                                 --model "SMS-T5qqqqZH_HToBB-mN2"

convert_cl_to_jobs_info.py split_gluino_2016.py split_gluino_2016.json
auto_submit_jobs.py split_gluino_2016.json -c jobscript_check.py -n cms1
convert_cl_to_jobs_info.py split_gluino_mN2_2016.py split_gluino_mN2_2016.json
auto_submit_jobs.py split_gluino_mN2_2016.json -c jobscript_check.py -n cms1

./scripts/write_split_gluino_mass_points_cmds.py --in_dir /net/cms24/cms24r0/pico/NanoAODv7/nano/2017/SMS-T5qqqqZH_unsplit_fastSimJmeCorrection 
                                                 --out_cmd_filename split_gluino_2017.py 
                                                 --target_dir /net/cms24/cms24r0/pico/NanoAODv7/nano/2017/SMS-T5qqqqZH_fastSimJmeCorrection 
                                                 --model "SMS-T5qqqqZH_HToBB-mGluino"
./scripts/write_split_gluino_mass_points_cmds.py --in_dir /net/cms24/cms24r0/pico/NanoAODv7/nano/2017/SMS-T5qqqqZH_unsplit_fastSimJmeCorrection 
                                                 --out_cmd_filename split_gluino_mN2_2017.py 
                                                 --target_dir /net/cms24/cms24r0/pico/NanoAODv7/nano/2017/SMS-T5qqqqZH_fastSimJmeCorrection 
                                                 --model "SMS-T5qqqqZH_HToBB-mN2"

./scripts/write_split_gluino_mass_points_cmds.py --in_dir /net/cms24/cms24r0/pico/NanoAODv7/nano/2018/SMS-T5qqqqZH_unsplit_fastSimJmeCorrection 
                                                 --out_cmd_filename split_gluino_2018.py 
                                                 --target_dir /net/cms24/cms24r0/pico/NanoAODv7/nano/2018/SMS-T5qqqqZH_fastSimJmeCorrection 
                                                 --model "SMS-T5qqqqZH_HToBB-mGluino"
./scripts/write_split_gluino_mass_points_cmds.py --in_dir /net/cms24/cms24r0/pico/NanoAODv7/nano/2018/SMS-T5qqqqZH_unsplit_fastSimJmeCorrection 
                                                 --out_cmd_filename split_gluino_mN2_2018.py 
                                                 --target_dir /net/cms24/cms24r0/pico/NanoAODv7/nano/2018/SMS-T5qqqqZH_fastSimJmeCorrection 
                                                 --model "SMS-T5qqqqZH_HToBB-mN2"
./scripts/write_split_signal_mass_points_cmds.py --in_dir /net/cms25/cms25r5/pico/NanoAODv7/nano/2016/SMS-TChiHH_2D_unsplit 
                                                 --target_dir /net/cms25/cms25r5/pico/NanoAODv7/nano/2016/SMS-TChiHH_2D 
                                                 --dataset_filenames SMS-TChiHH_HToBB_HToBB_TuneCUETP8M1_13TeV-madgraphMLM-pythia8__RunIISummer16NanoAODv7__PUSummer16v3Fast_Nano02Apr2020_102X_mcRun2_asymptotic_v8-v1*.root
                                                 --out_cmd_filename cmds_split_2016_1D.py
./scripts/write_split_signal_mass_points_cmds.py --two_dim --in_dir /net/cms25/cms25r5/pico/NanoAODv7/nano/2016/SMS-TChiHH_2D_unsplit 
                                                 --target_dir /net/cms25/cms25r5/pico/NanoAODv7/nano/2016/SMS-TChiHH_2D 
                                                 --dataset_filenames SMS-TChiHH_HToBB_HToBB_2D_TuneCUETP8M1_13TeV-madgraphMLM-pythia8__RunIISummer16NanoAODv7__PUSummer16v3Fast_Nano02Apr2020_102X_mcRun2_asymptotic_v8-v1*.root
                                                 --out_cmd_filename cmds_split_2016_2D.py
./scripts/write_split_signal_mass_points_cmds.py --in_dir /net/cms25/cms25r5/pico/NanoAODv7/nano/2017/SMS-TChiHH_2D_unsplit 
                                                 --target_dir /net/cms25/cms25r5/pico/NanoAODv7/nano/2017/SMS-TChiHH_2D 
                                                 --dataset_filenames SMS-TChiHH_HToBB_HToBB_TuneCP2_13TeV-madgraphMLM-pythia8__RunIIFall17NanoAODv7__PUFall17Fast_Nano02Apr2020_102X_mc2017_realistic_v8-v1*.root
                                                 --out_cmd_filename cmds_split_2017_1D.py
./scripts/write_split_signal_mass_points_cmds.py --two_dim --in_dir /net/cms25/cms25r5/pico/NanoAODv7/nano/2017/SMS-TChiHH_2D_unsplit 
                                                 --target_dir /net/cms25/cms25r5/pico/NanoAODv7/nano/2017/SMS-TChiHH_2D 
                                                 --dataset_filenames SMS-TChiHH_HToBB_HToBB_2D_TuneCP2_13TeV-madgraphMLM-pythia8__RunIIFall17NanoAODv7__PUFall17Fast_Nano02Apr2020_102X_mc2017_realistic_v8-v1*.root
                                                 --out_cmd_filename cmds_split_2017_2D.py
./scripts/write_split_signal_mass_points_cmds.py --in_dir /net/cms25/cms25r5/pico/NanoAODv7/nano/2018/SMS-TChiHH_2D_unsplit 
                                                 --target_dir /net/cms25/cms25r5/pico/NanoAODv7/nano/2018/SMS-TChiHH_2D 
                                                 --dataset_filenames SMS-TChiHH_HToBB_HToBB_TuneCP2_13TeV-madgraphMLM-pythia8__RunIIAutumn18NanoAODv7__PUFall18Fast_Nano02Apr2020_102X_upgrade2018_realistic_v21-v1*.root
                                                 --out_cmd_filename cmds_split_2018_1D.py
./scripts/write_split_signal_mass_points_cmds.py --two_dim --in_dir /net/cms25/cms25r5/pico/NanoAODv7/nano/2018/SMS-TChiHH_2D_unsplit 
                                                 --target_dir /net/cms25/cms25r5/pico/NanoAODv7/nano/2018/SMS-TChiHH_2D 
                                                 --dataset_filenames SMS-TChiHH_HToBB_HToBB_2D_TuneCP2_13TeV-madgraphMLM-pythia8__RunIIAutumn18NanoAODv7__PUFall18Fast_Nano02Apr2020_102X_upgrade2018_realistic_v21-v1*.root
                                                 --out_cmd_filename cmds_split_2018_2D.py

convert_cl_to_jobs_info.py cmds_split.py cmds_split.py.json
auto_submit_jobs.py cmds_split.py.json -c jobscript_check.py

or 
[cms25] ./scripts/run_commands.py cmds_split_2018_2D.py 
Should check log file for error, segmentation..

Dataset name needs to be writen out like above. This produces the commands in cmds_split.py. You can perform a last check by running one of the commands interactively. Next, submit the jobs to the batch system. Note the -c option which allows to attach a script that compares the input and output number of entries when each job is done. Note the check can be performed later if one needs to detach the session. Alternatively, this command can be started in screen:

convert_cl_to_jobs_info.py cmds_split.py cmds_split.py.json
auto_submit_jobs.py cmds_split.py.json -c scripts/check_skim.py

This command will result in checked_auto_cmds_split.py.json, which can then be used to resubmit failed jobs if any:

select_resubmit_jobs.py checked_auto_cmds_split.py.json -c scripts/check_skim.py
auto_submit_jobs.py resubmit_checked_auto_cmds_split.py.json -c scripts/check_skim.py
./scripts/write_split_gluino_mass_points_cmds.py --in_dir /net/cms24/cms24r0/pico/NanoAODv7/nano/2016/SMS-T5qqqqZH_FullSim_unsplit 
                                                 --out_cmd_filename split_fullsim_gluino_2016.py 
                                                 --target_dir /net/cms24/cms24r0/pico/NanoAODv7/nano/2016/SMS-T5qqqqZH_FullSim 
                                                 --model "SMS-T5qqqqZH-mGluino"

Getting Higgsino cross-section

Step 1. Download cross-section files

scp -r lxplus:/afs/cern.ch/user/a/amete/public/EWKGauginoCrossSections_13TeV cross_section

Step 2. Fix bug in script

Set masses, xsecs, xsecUncs to 0 when initializing.

cd cross_section
sed -i 's/std::vector<double>\* masses;/std::vector<double>\* masses=0;/' get_gaugino.C
sed -i 's/std::vector<double>\* xsecs;/std::vector<double>\* xsecs=0;/' get_gaugino.C
sed -i 's/std::vector<double>\* xsecUncs;/std::vector<double>\* xsecUncs=0;/' get_gaugino.C

Getting Gluino cross-section

wget https://raw.githubusercontent.com/fuenfundachtzig/xsec/master/json/pp13_gluino_NNLO%2BNNLL.json scripts/get_gluino_cross_sections.py

Step 3. Run script for all mass points.

Use model "CN" (mixing) or "N1N2" (no mixing).

cd cross_section
../scripts/get_higgsino_cross_sections.py -i /net/cms29/cms29r0/pico/NanoAODv5/nano/2016/SMS-TChiHH_2D --model "N1N2"

Tagging code with git

Confirm tags: git tag

Add a lightweight tag: git tag <tagname>

Pushing tag: git push origin <tagname>

Deleting tag: git tag -d <tagname> and git push origin --delete <tagname>

Checking out tag: git checkout <tagname>

Update submodule

In case didn't checkout submodule: git submodule init and git submodule update

Update all submodules: git submodule update --recursive --remote --merge and then commit.

Validation

Validation is done by running ./script/produce_unit_test* on nano2pico code versions and then using ./script/validate_unit_test* to compare between results.

Below are examples

# Compares picos file between old code and new code. Also compares production time.
[In old code folder] ./scripts/produce_unit_test_htozgamma_NanoAODv9.py --output_folder unit_test_htozgamma_nanoaodv9 --output_log unit_test_htozgamma_nanoaodv9.log
[In new code folder] ./scripts/produce_unit_test_htozgamma_NanoAODv9.py --output_folder unit_test_htozgamma_nanoaodv9 --output_log unit_test_htozgamma_nanoaodv9.log
./scripts/validate_unit_test_picos.py --output_log_filename validate_unit_test_htozgamma_nanoaodv9.log --unit_test_log_filename unit_test_htozgamma_nanoaodv9.log --golden_base_folder OLD_CODE/unit_test_htozgamma_nanoaodv9 --validate_base_folder NEW_CODE/unit_test_htozgamma_nanoaodv9

# Compares cross section between old code and new code.
[In old code folder] ./scripts/produce_unit_test_cross_sections.py --output_log unit_test_cross_section.log
[In new code folder] ./scripts/produce_unit_test_cross_sections.py --output_log unit_test_cross_section.log
./scripts/validate_unit_test_cross_section.py --output_filename validate_unit_test_cross_section.log --golden_cross_section_log OLD_CODE/unit_test_cross_section.log --validate_cross_section_log NEW_CODE/unit_test_cross_section.log

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Code to produce analysis ntuples (pico) from the CMS NanoAOD.

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