From b76f32aa9c8138143fd94c8f2935b01d720e79b5 Mon Sep 17 00:00:00 2001
From: Dmitry Kalinkin <dmitry.kalinkin@gmail.com>
Date: Wed, 19 Jun 2024 15:18:54 -0400
Subject: [PATCH] benchmarks/dis: convert to Snakemake

---
 Snakefile                       |   1 +
 benchmarks/dis/README.md        |  12 ---
 benchmarks/dis/Snakefile        | 144 +++++++++++++++++++++++++++++
 benchmarks/dis/analysis-only.sh | 134 ---------------------------
 benchmarks/dis/config.yml       |   6 +-
 benchmarks/dis/dis.sh           | 157 --------------------------------
 benchmarks/dis/env.sh           |  58 ------------
 benchmarks/dis/gen.sh           |  98 --------------------
 benchmarks/dis/get.sh           |  80 ----------------
 9 files changed, 148 insertions(+), 542 deletions(-)
 delete mode 100644 benchmarks/dis/README.md
 create mode 100644 benchmarks/dis/Snakefile
 delete mode 100755 benchmarks/dis/analysis-only.sh
 delete mode 100755 benchmarks/dis/dis.sh
 delete mode 100644 benchmarks/dis/env.sh
 delete mode 100755 benchmarks/dis/gen.sh
 delete mode 100644 benchmarks/dis/get.sh

diff --git a/Snakefile b/Snakefile
index b01ad5e2..ac3778f6 100644
--- a/Snakefile
+++ b/Snakefile
@@ -31,3 +31,4 @@ ddsim \
 """
 
 include: "benchmarks/diffractive_vm/Snakefile"
+include: "benchmarks/dis/Snakefile"
diff --git a/benchmarks/dis/README.md b/benchmarks/dis/README.md
deleted file mode 100644
index 7a8890b6..00000000
--- a/benchmarks/dis/README.md
+++ /dev/null
@@ -1,12 +0,0 @@
-# DIS Benchmarks
-
-## Compiling Pythia example
-
-```
-g++ src/pythia_dis.cc -o pythia_dis  \
-   -I/home/whit/stow/hepmc3/include  \
-   -I../include -O2 -std=c++11 -pedantic -W -Wall -Wshadow -fPIC  \
-   -L../lib -Wl,-rpath,../lib -lpythia8 -ldl \
-   -L/home/whit/stow/hepmc3/lib -Wl,-rpath,/home/whit/stow/hepmc3/lib -lHepMC3
-```
-
diff --git a/benchmarks/dis/Snakefile b/benchmarks/dis/Snakefile
new file mode 100644
index 00000000..f4f8d1fe
--- /dev/null
+++ b/benchmarks/dis/Snakefile
@@ -0,0 +1,144 @@
+import os
+import shutil
+
+from snakemake.remote.S3 import RemoteProvider as S3RemoteProvider
+
+
+S3 = S3RemoteProvider(
+    endpoint_url="https://eics3.sdcc.bnl.gov:9000",
+    access_key_id=os.environ["S3_ACCESS_KEY"],
+    secret_access_key=os.environ["S3_SECRET_KEY"],
+)
+
+
+rule dis_compile:
+    input:
+        ROOT_BUILD_DIR_PREFIX + "benchmarks/dis/analysis/dis_electrons_cxx.so",
+        ROOT_BUILD_DIR_PREFIX + "benchmarks/dis/analysis/jets_cxx.so",
+
+
+rule dis_get:
+    input:
+        lambda wildcards: S3.remote(f"eictest/EPIC/EVGEN/DIS/NC/{wildcards.EBEAM}x{wildcards.PBEAM}/minQ2={wildcards.MINQ2}/pythia8NCDIS_{wildcards.EBEAM}x{wildcards.PBEAM}_minQ2={wildcards.MINQ2}_beamEffects_xAngle=-0.025_hiDiv_vtxfix_1.hepmc"),
+    output:
+        "input/dis/pythia8NCDIS_{EBEAM}x{PBEAM}_minQ2={MINQ2}_beamEffects_xAngle=-0.025_hiDiv_vtxfix_1.hepmc",
+    run:
+        shutil.move(input[0], output[0])
+
+
+rule dis_sim:
+    input:
+        hepmc="input/dis/pythia8NCDIS_{EBEAM}x{PBEAM}_minQ2={MINQ2}_beamEffects_xAngle=-0.025_hiDiv_vtxfix_1.hepmc",
+        warmup="warmup/{DETECTOR_CONFIG}.edm4hep.root",
+    output:
+        "sim/{DETECTOR_CONFIG}/pythia8NCDIS_{EBEAM}x{PBEAM}_minQ2={MINQ2}_beamEffects_xAngle=-0.025_hiDiv_1.edm4hep.root",
+    params:
+        N_EVENTS=100
+    shell:
+        """
+ddsim \
+  --runType batch \
+  --part.minimalKineticEnergy 1000*GeV  \
+  --filter.tracker edep0 \
+  -v WARNING \
+  --numberOfEvents {params.N_EVENTS} \
+  --compactFile $DETECTOR_PATH/{wildcards.DETECTOR_CONFIG}.xml \
+  --inputFiles {input.hepmc} \
+  --outputFile {output}
+"""
+
+
+rule dis_reco_eicrecon:
+    input:
+        "sim/{DETECTOR_CONFIG}/{file}.edm4hep.root",
+    output:
+        "reco/{DETECTOR_CONFIG}/{file}.edm4eic.root",
+    shell:
+        """
+DETECTOR_CONFIG={wildcards.DETECTOR_CONFIG} eicrecon {input} -Ppodio:output_file={output}
+"""
+
+
+rule dis_generate_config:
+    input:
+        data="reco/{DETECTOR_CONFIG}/pythia8NCDIS_{EBEAM}x{PBEAM}_minQ2={MINQ2}_beamEffects_xAngle=-0.025_hiDiv_1.edm4eic.root",
+    output:
+        config="results/{DETECTOR_CONFIG}/dis/{EBEAM}on{PBEAM}/minQ2={MINQ2}/config.json",
+    shell: """
+cat > {output.config} <<EOF
+{{
+  "rec_file": "{input.data}",
+  "detector": "{wildcards.DETECTOR_CONFIG}",
+  "output_prefix": "$(dirname "{output.config}")/dis_{wildcards.EBEAM}x{wildcards.PBEAM}_minQ2={wildcards.MINQ2}",
+  "results_path": "$(dirname "{output.config}")",
+  "ebeam": {wildcards.EBEAM},
+  "pbeam": {wildcards.PBEAM},
+  "minq2": {wildcards.MINQ2},
+  "plot_tag": "dis_{wildcards.EBEAM}x{wildcards.PBEAM}_minQ2={wildcards.MINQ2}",
+  "test_tag": "dis_{wildcards.EBEAM}x{wildcards.PBEAM}_minQ2={wildcards.MINQ2}"
+}}
+EOF
+"""
+
+
+rule dis_analysis_electrons:
+    input:
+        script="benchmarks/dis/analysis/dis_electrons.cxx",
+        script_compiled=ROOT_BUILD_DIR_PREFIX + "benchmarks/dis/analysis/dis_electrons_cxx.so",
+        data="reco/{DETECTOR_CONFIG}/pythia8NCDIS_{EBEAM}x{PBEAM}_minQ2={MINQ2}_beamEffects_xAngle=-0.025_hiDiv_1.edm4eic.root",
+        config="results/{DETECTOR_CONFIG}/dis/{EBEAM}on{PBEAM}/minQ2={MINQ2}/config.json",
+    output:
+        expand("results/{{DETECTOR_CONFIG}}/dis/{{EBEAM}}on{{PBEAM}}/minQ2={{MINQ2}}/{FILENAME}", FILENAME=[
+          "dis_{EBEAM}x{PBEAM}_minQ2={MINQ2}_logQ2_panels.png",
+          "dis_{EBEAM}x{PBEAM}_minQ2={MINQ2}_logQ2_overlays.png",
+          "dis_{EBEAM}x{PBEAM}_minQ2={MINQ2}_Q2_res_panels.png",
+          "dis_{EBEAM}x{PBEAM}_minQ2={MINQ2}_Q2_res_overlays.png",
+          "dis_{EBEAM}x{PBEAM}_minQ2={MINQ2}_x_panels.png",
+          "dis_{EBEAM}x{PBEAM}_minQ2={MINQ2}_x_overlays.png",
+          "dis_{EBEAM}x{PBEAM}_minQ2={MINQ2}_x_res_panels.png",
+          "dis_{EBEAM}x{PBEAM}_minQ2={MINQ2}_x_res_overlays.png",
+          "dis_{EBEAM}x{PBEAM}_minQ2={MINQ2}dis_electrons.json"
+        ]),
+    shell: """
+root -l -b -q '{input.script}+("{input.config}")'
+"""
+
+
+rule dis_analysis_jets:
+    input:
+        script="benchmarks/dis/analysis/jets.cxx",
+        script_compiled=ROOT_BUILD_DIR_PREFIX + "benchmarks/dis/analysis/jets_cxx.so",
+        data="reco/{DETECTOR_CONFIG}/pythia8NCDIS_{EBEAM}x{PBEAM}_minQ2={MINQ2}_beamEffects_xAngle=-0.025_hiDiv_1.edm4eic.root",
+        config="results/{DETECTOR_CONFIG}/dis/{EBEAM}on{PBEAM}/minQ2={MINQ2}/config.json",
+    output:
+        results_path=directory("results/{DETECTOR_CONFIG}/dis/{EBEAM}on{PBEAM}/minQ2={MINQ2}/jets"),
+    shell: """
+mkdir {output.results_path}
+root -l -b -q '{input.script}+("{input.config}")'
+"""
+
+
+rule dis_analysis_kinematics_correlations:
+    input:
+        data="reco/{DETECTOR_CONFIG}/pythia8NCDIS_{EBEAM}x{PBEAM}_minQ2={MINQ2}_beamEffects_xAngle=-0.025_hiDiv_1.edm4eic.root",
+    output:
+        results_path=directory("results/{DETECTOR_CONFIG}/dis/{EBEAM}on{PBEAM}/minQ2={MINQ2}/kinematics_correlations"),
+    params:
+        N_EVENTS=100
+    shell: """
+mkdir {output.results_path}
+python benchmarks/dis/analysis/kinematics_correlations.py --rec_file "{input.data}" --config dis_{wildcards.EBEAM}x{wildcards.PBEAM}_minQ2={wildcards.MINQ2}_{wildcards.DETECTOR_CONFIG} --results_path {output.results_path} --nevents {params.N_EVENTS}
+"""
+
+
+rule dis_analysis_truth_reconstruction:
+    input:
+        data="reco/{DETECTOR_CONFIG}/pythia8NCDIS_{EBEAM}x{PBEAM}_minQ2={MINQ2}_beamEffects_xAngle=-0.025_hiDiv_1.edm4eic.root",
+    output:
+        results_path=directory("results/{DETECTOR_CONFIG}/dis/{EBEAM}on{PBEAM}/minQ2={MINQ2}/truth_reconstruction"),
+    params:
+        N_EVENTS=100
+    shell: """
+mkdir {output.results_path}
+python benchmarks/dis/analysis/truth_reconstruction.py --rec_file "{input.data}" --config dis_{wildcards.EBEAM}x{wildcards.PBEAM}_minQ2={wildcards.MINQ2}_{wildcards.DETECTOR_CONFIG} --results_path $(dirname {output.results_path}) --nevents {params.N_EVENTS}
+"""
diff --git a/benchmarks/dis/analysis-only.sh b/benchmarks/dis/analysis-only.sh
deleted file mode 100755
index d3685aaf..00000000
--- a/benchmarks/dis/analysis-only.sh
+++ /dev/null
@@ -1,134 +0,0 @@
-#!/bin/bash
-source strict-mode.sh
-
-## =============================================================================
-## Run the DIS benchmarks in 5 steps:
-## 1. Parse the command line and setup environment
-## 2. Detector simulation through ddsim
-## 3. Digitization and reconstruction through Juggler
-## 4. Root-based Physics analyses
-## 5. Finalize
-## =============================================================================
-
-## make sure we launch this script from the project root directory
-PROJECT_ROOT="$( cd "$(dirname "$0")" >/dev/null 2>&1 ; pwd -P )"/../..
-pushd ${PROJECT_ROOT}
-
-echo "Running the DIS benchmarks"
-
-## =============================================================================
-## Step 1: Setup the environment variables
-##
-## First parse the command line flags.
-## This sets the following environment variables:
-## - CONFIG:   The specific generator configuration
-## - EBEAM:    The electron beam energy
-## - PBEAM:    The ion beam energy
-source parse_cmd.sh $@
-
-## To run the reconstruction, we need the following global variables:
-## - DETECTOR:       the detector package we want to use for this benchmark
-## - DETECTOR_PATH:          full path to the detector definitions
-##
-
-## We also need the following benchmark-specific variables:
-##
-## - BENCHMARK_TAG: Unique identified for this benchmark process.
-## - BEAM_TAG:      Identifier for the chosen beam configuration
-## - INPUT_PATH:    Path for generator-level input to the benchmarks
-## - TMP_PATH:      Path for temporary data (not exported as artifacts)
-## - RESULTS_PATH:  Path for benchmark output figures and files
-##
-## You can read dvmp/env.sh for more in-depth explanations of the variables.
-source benchmarks/dis/env.sh
-
-## Get a unique file names based on the configuration options
-GEN_FILE=${INPUT_PATH}/gen-${CONFIG}_${JUGGLER_N_EVENTS}.hepmc
-
-SIM_FILE=${TMP_PATH}/sim-${CONFIG}.edm4hep.root
-SIM_LOG=${TMP_PATH}/sim-${CONFIG}.log
-
-
-REC_FILE=${TMP_PATH}/rec-${CONFIG}.root
-REC_LOG=${TMP_PATH}/sim-${CONFIG}.log
-
-PLOT_TAG=${CONFIG}
-
-## =============================================================================
-## Step 2: Run the simulation
-echo "Running Geant4 simulation"
-#ddsim --runType batch \
-#      --part.minimalKineticEnergy 1000*GeV  \
-#      --filter.tracker edep0 \
-#      -v WARNING \
-#      --numberOfEvents ${JUGGLER_N_EVENTS} \
-#      --compactFile ${DETECTOR_PATH}/${DETECTOR_CONFIG}.xml \
-#      --inputFiles ${GEN_FILE} \
-#      --outputFile ${SIM_FILE}
-#if [ "$?" -ne "0" ] ; then
-#  echo "ERROR running ddsim"
-#  exit 1
-#fi
-
-## =============================================================================
-## Step 3: Run digitization & reconstruction
-#echo "Running the digitization and reconstruction"
-## FIXME Need to figure out how to pass file name to juggler from the commandline
-## the tracker_reconstruction.py options file uses the following environment
-## variables:
-## - JUGGLER_SIM_FILE:    input detector simulation
-## - JUGGLER_REC_FILE:    output reconstructed data
-## - JUGGLER_N_EVENTS:    number of events to process (part of global environment)
-## - DETECTOR:    detector package (part of global environment)
-#export JUGGLER_SIM_FILE=${SIM_FILE}
-#export JUGGLER_REC_FILE=${REC_FILE}
-#gaudirun.py options/tracker_reconstruction.py 
-## on-error, first retry running juggler again as there is still a random
-## crash we need to address FIXME
-#if [ "$?" -ne "0" ] ; then
-#  echo "Juggler crashed, retrying..."
-#  gaudirun.py options/tracker_reconstruction.py \
-#    2>&1 > ${REC_LOG}
-#  if [ "$?" -ne "0" ] ; then
-#    echo "ERROR running juggler, both attempts failed"
-#    exit 1
-#  fi
-#fi
-
-## =============================================================================
-## Step 4: Analysis
-## write a temporary configuration file for the analysis script
-echo "Running analysis"
-CONFIG="${TMP_PATH}/${PLOT_TAG}.json"
-cat << EOF > ${CONFIG}
-{
-  "rec_file": "${REC_FILE}",
-  "detector": "${DETECTOR}",
-  "output_prefix": "${RESULTS_PATH}/${PLOT_TAG}",
-  "test_tag": "${BEAM_TAG}"
-}
-EOF
-#cat ${CONFIG}
-root -b -q "benchmarks/dis/analysis/dis_electrons.cxx+(\"${CONFIG}\")"
-#root -b -q "benchmarks/dis/analysis/dis_electrons.cxx(\"${CONFIG}\")"
-if [[ "$?" -ne "0" ]] ; then
-  echo "ERROR running rec_dis_electron script"
-  exit 1
-fi
-
-## =============================================================================
-## Step 5: finalize
-#echo "Finalizing DIS benchmark"
-
-## Move over reconsturction artifacts as long as we don't have
-## too many events
-#if [ "${JUGGLER_N_EVENTS}" -lt "500" ] ; then 
-#  cp ${REC_FILE} ${RESULTS_PATH}
-#fi
-
-## Always move over log files to the results path
-#cp ${REC_LOG} ${RESULTS_PATH}
-
-## =============================================================================
-## All done!
-echo "DIS benchmarks complete"
diff --git a/benchmarks/dis/config.yml b/benchmarks/dis/config.yml
index 48ef68c9..8c61b46f 100644
--- a/benchmarks/dis/config.yml
+++ b/benchmarks/dis/config.yml
@@ -2,7 +2,7 @@ dis:compile:
   stage: compile
   extends: .compile_benchmark
   script:
-    - compile_analyses.py dis
+    - snakemake --cores 1 dis_compile
 
 dis:generate:
   stage: generate
@@ -21,7 +21,7 @@ dis:generate:
         MINQ2: [1, 10, 100, 1000]
   timeout: 1 hours
   script:
-    - bash benchmarks/dis/get.sh --config dis_${EBEAM}x${PBEAM}_minQ2=${MINQ2} --ebeam ${EBEAM} --pbeam ${PBEAM} --minq2 ${MINQ2}
+    - snakemake --cores 1 input/dis/pythia8NCDIS_${EBEAM}x${PBEAM}_minQ2=${MINQ2}_beamEffects_xAngle=-0.025_hiDiv_vtxfix_1.hepmc
 
 dis:simulate:
   stage: simulate
@@ -40,7 +40,7 @@ dis:simulate:
         MINQ2: [1, 10, 100, 1000]
   timeout: 2 hours
   script:
-    - bash benchmarks/dis/dis.sh --config dis_${EBEAM}x${PBEAM}_minQ2=${MINQ2} --ebeam ${EBEAM} --pbeam ${PBEAM} --minq2 ${MINQ2}
+    - snakemake --cores 1 results/epic_craterlake/dis/${EBEAM}on${PBEAM}/minQ2=${MINQ2}/dis_${EBEAM}x${PBEAM}_minQ2=${MINQ2}dis_electrons.json results/epic_craterlake/dis/${EBEAM}on${PBEAM}/minQ2=${MINQ2}/kinematics_correlations results/epic_craterlake/dis/${EBEAM}on${PBEAM}/minQ2=${MINQ2}/truth_reconstruction
   retry:
     max: 2
     when:
diff --git a/benchmarks/dis/dis.sh b/benchmarks/dis/dis.sh
deleted file mode 100755
index f1a551d9..00000000
--- a/benchmarks/dis/dis.sh
+++ /dev/null
@@ -1,157 +0,0 @@
-#!/bin/bash
-source strict-mode.sh
-
-## =============================================================================
-## Run the DIS benchmarks in 5 steps:
-## 1. Parse the command line and setup environment
-## 2. Detector simulation through ddsim
-## 3. Digitization and reconstruction through Juggler
-## 4. Root-based Physics analyses
-## 5. Finalize
-## =============================================================================
-
-## make sure we launch this script from the project root directory
-PROJECT_ROOT="$( cd "$(dirname "$0")" >/dev/null 2>&1 ; pwd -P )"/../..
-pushd ${PROJECT_ROOT}
-
-echo "Running the DIS benchmarks"
-
-## =============================================================================
-## Step 1: Setup the environment variables
-##
-## First parse the command line flags.
-## This sets the following environment variables:
-## - CONFIG:   The specific generator configuration
-## - EBEAM:    The electron beam energy
-## - PBEAM:    The ion beam energy
-export REQUIRE_MINQ2=true
-source ${LOCAL_PREFIX}/bin/parse_cmd.sh $@
-
-## To run the reconstruction, we need the following global variables:
-## - DETECTOR:       the detector package we want to use for this benchmark
-## - DETECTOR_PATH:          full path to the detector definitions
-##
-## defined in common_bench repo
-## You can ready bin/env.sh for more in-depth explanations of the variables
-## and how they can be controlled.
-
-## We also need the following benchmark-specific variables:
-##
-## - BENCHMARK_TAG: Unique identified for this benchmark process.
-## - BEAM_TAG:      Identifier for the chosen beam configuration
-## - INPUT_PATH:    Path for generator-level input to the benchmarks
-## - TMP_PATH:      Path for temporary data (not exported as artifacts)
-## - RESULTS_PATH:  Path for benchmark output figures and files
-##
-## You can read dvmp/env.sh for more in-depth explanations of the variables.
-source benchmarks/dis/env.sh
-
-## Get a unique file names based on the configuration options
-GEN_FILE=${INPUT_PATH}/gen-${CONFIG}_${JUGGLER_N_EVENTS}.hepmc
-
-SIM_FILE=${TMP_PATH}/sim-${CONFIG}.edm4hep.root
-SIM_LOG=${TMP_PATH}/sim-${CONFIG}.log
-
-# JUGGLER_REC_FILE_BASE= ${TMP_PATH}/rec-${CONFIG}
-REC_FILE=${TMP_PATH}/rec-${CONFIG}.root
-REC_LOG=${TMP_PATH}/sim-${CONFIG}.log
-
-PLOT_TAG=${CONFIG}
-
-## =============================================================================
-## Step 2: Run the simulation
-echo "Running Geant4 simulation"
-if [ ! -f ${SIM_FILE} ] ; then
-ddsim --runType batch \
-      --part.minimalKineticEnergy 1000*GeV  \
-      --filter.tracker edep0 \
-      -v WARNING \
-      --numberOfEvents ${JUGGLER_N_EVENTS} \
-      --compactFile ${DETECTOR_PATH}/${DETECTOR_CONFIG}.xml \
-      --inputFiles ${GEN_FILE} \
-      --outputFile ${SIM_FILE}
-if [ "$?" -ne "0" ] ; then
-  echo "ERROR running ddsim"
-  exit 1
-fi
-fi
-
-## =============================================================================
-## Step 3: Run digitization & reconstruction
-echo "Running the digitization and reconstruction"
-if [ ${RECO} == "eicrecon" ] ; then
-  /usr/bin/time -v eicrecon ${SIM_FILE} -Ppodio:output_file=${REC_FILE}
-  if [ "$?" -ne "0" ] ; then
-    echo "ERROR running eicrecon"
-    exit 1
-  fi
-fi
-
-if [[ ${RECO} == "juggler" ]] ; then
-  export JUGGLER_SIM_FILE=${SIM_FILE}
-  export JUGGLER_REC_FILE=${REC_FILE}
-  gaudirun.py options/reconstruction.py || [ $? -eq 4 ]
-  if [ "$?" -ne "0" ] ; then
-    echo "ERROR running juggler"
-    exit 1
-  fi
-fi
-
-
-## =============================================================================
-## Step 4: Analysis
-## write a temporary configuration file for the analysis script
-echo "Running analysis"
-CONFIG="${TMP_PATH}/${PLOT_TAG}.json"
-cat << EOF > ${CONFIG}
-{
-  "rec_file": "${REC_FILE}",
-  "detector": "${DETECTOR}",
-  "output_prefix": "${RESULTS_PATH}/${PLOT_TAG}",
-  "results_path": "${RESULTS_PATH}",
-  "plot_tag": "${PLOT_TAG}",
-  "ebeam": ${EBEAM},
-  "pbeam": ${PBEAM},
-  "minq2": ${MINQ2},
-  "test_tag": "${BEAM_TAG}"
-}
-EOF
-
-root -b -q "benchmarks/dis/analysis/dis_electrons.cxx+g(\"${CONFIG}\")"
-if [[ "$?" -ne "0" ]] ; then
-  echo "ERROR running dis_electron script"
-  exit 1
-fi
-
-python benchmarks/dis/analysis/kinematics_correlations.py --rec_file ${REC_FILE} --config ${PLOT_TAG}_${DETECTOR_CONFIG} --results_path ${RESULTS_PATH} --nevents ${JUGGLER_N_EVENTS}
-if [[ "$?" -ne "0" ]] ; then
-  echo "ERROR running kinematics_correlations script"
-  exit 1
-fi
-
-python benchmarks/dis/analysis/truth_reconstruction.py --rec_file ${REC_FILE} --config ${PLOT_TAG}_${DETECTOR_CONFIG} --results_path ${RESULTS_PATH} --nevents ${JUGGLER_N_EVENTS}
-if [[ "$?" -ne "0" ]] ; then
-  echo "ERROR running truth_reconstruction script"
-  exit 1
-fi
-
-root -b -q "benchmarks/dis/analysis/jets.cxx+g(\"${CONFIG}\")"
-if [[ "$?" -ne "0" ]] ; then
-  echo "ERROR running dis_electron script"
-  exit 1
-fi
-
-
-## =============================================================================
-## Step 5: finalize
-echo "Finalizing DIS benchmark"
-
-## Move over reconsturction artifacts as long as we don't have
-## too many events
-if [ "${JUGGLER_N_EVENTS}" -lt "500" ] ; then 
-  cp ${REC_FILE} ${RESULTS_PATH}
-fi
-
-## =============================================================================
-## All done!
-echo "DIS benchmarks complete"
diff --git a/benchmarks/dis/env.sh b/benchmarks/dis/env.sh
deleted file mode 100644
index 50f6bb04..00000000
--- a/benchmarks/dis/env.sh
+++ /dev/null
@@ -1,58 +0,0 @@
-#!/bin/bash
-source strict-mode.sh
-
-## =============================================================================
-## Local configuration variables for this particular benchmark 
-## It defines the following additional variables: 
-##
-##  - BENCHMARK_TAG:          Tag to identify this particular benchmark
-##  - BEAM_TAG                Tag to identify the beam configuration
-##  - INPUT_PATH:             Path for generator-level input to the benchmarks
-##  - TMP_PATH:               Path for temporary data (not exported as artifacts)
-##  - RESULTS_PATH:           Path for benchmark output figures and files
-##
-## This script assumes that EBEAM and PBEAM are set as part of the
-## calling script (usually as command line argument).
-##
-## =============================================================================
-
-## Tag for the local benchmark. Should be the same as the directory name for
-## this particular benchmark set (for clarity). 
-## This tag is used for the output artifacts directory (results/${JUGGLER_TAG}) 
-## and a tag in some of the output files.
-export BENCHMARK_TAG="dis"
-echo "Setting up the local environment for the ${BENCHMARK_TAG^^} benchmarks"
-
-## Extra beam tag to identify the desired beam configuration
-export BEAM_TAG="${EBEAM}on${PBEAM}"
-
-if [[ ! -d "input" ]] ; then
-  echo " making local link to input "
-  mkdir_local_data_link  input
-fi
-## Data path for input data (generator-level hepmc file)
-INPUT_PATH="input/${BENCHMARK_TAG}/${BEAM_TAG}/minQ2=${MINQ2}"
-mkdir_local_data_link input
-#export INPUT_PATH=`realpath ${INPUT_PATH}`
-mkdir -p "${INPUT_PATH}"
-echo "INPUT_PATH:             ${INPUT_PATH}"
-
-
-## Data path for temporary data (not exported as artifacts)
-TMP_PATH=${LOCAL_DATA_PATH}/tmp/${BEAM_TAG}
-mkdir -p ${TMP_PATH}
-#export TMP_PATH=`realpath ${TMP_PATH}`
-echo "TMP_PATH:               ${TMP_PATH}"
-
-## Data path for benchmark output (plots and reconstructed files
-## if not too big).
-RESULTS_PATH="results/${BENCHMARK_TAG}/${BEAM_TAG}/minQ2=${MINQ2}"
-mkdir -p ${RESULTS_PATH}
-mkdir -p "${RESULTS_PATH}/truth_reconstruction"
-mkdir -p "${RESULTS_PATH}/jets"
-export RESULTS_PATH=`realpath ${RESULTS_PATH}`
-echo "RESULTS_PATH:           ${RESULTS_PATH}"
-
-## =============================================================================
-## That's all!
-echo "Local environment setup complete."
diff --git a/benchmarks/dis/gen.sh b/benchmarks/dis/gen.sh
deleted file mode 100755
index 4b27b95d..00000000
--- a/benchmarks/dis/gen.sh
+++ /dev/null
@@ -1,98 +0,0 @@
-#!/bin/bash
-source strict-mode.sh
-
-## =============================================================================
-## Standin for a proper pythia generation process, similar to how we
-## generate events for DVMP
-## Runs in 5 steps:
-##   1. Parse the command line and setup the environment
-##   2. Check if we can load the requested file from the cache
-##   3. Build generator exe 
-##   4. Run the actual generator
-##   5. Finalize
-## =============================================================================
-## =============================================================================
-
-## make sure we launch this script from the project root directory
-PROJECT_ROOT="$( cd "$(dirname "$0")" >/dev/null 2>&1 ; pwd -P )"/../..
-pushd ${PROJECT_ROOT}
-
-## =============================================================================
-## Step 1: Setup the environment variables
-## First parse the command line flags.
-## This sets the following environment variables:
-## - CONFIG:   The specific generator configuration --> not currenlty used FIXME
-## - EBEAM:    The electron beam energy --> not currently used FIXME
-## - PBEAM:    The ion beam energy --> not currently used FIXME
-source parse_cmd.sh $@
-
-## To run the generator, we need the following global variables:
-##
-## - LOCAL_PREFIX:      Place to cache local packages and data
-## - JUGGLER_N_EVENTS:  Number of events to process
-## - JUGGLER_RNG_SEED:  Random seed for event generation.
-##
-## defined in common_bench repo
-## You can ready bin/env.sh for more in-depth explanations of the variables
-## and how they can be controlled.
-
-
-## We also need the following benchmark-specific variables:
-##
-## - BENCHMARK_TAG: Unique identified for this benchmark process.
-## - INPUT_PATH:    Path for generator-level input to the benchmarks
-## - TMP_PATH:      Path for temporary data (not exported as artifacts)
-##
-## You can read dvmp/env.sh for more in-depth explanations of the variables.
-source benchmarks/dis/env.sh
-
-## Get a unique file name prefix based on the configuration options
-GEN_TAG=gen-${CONFIG}_${JUGGLER_N_EVENTS} ## Generic file prefix
-
-## =============================================================================
-## Step 2: Check if we really need to run, or can use the cache.
-if [ -f "${INPUT_PATH}/${GEN_TAG}.hepmc" ]; then
-  echo "Found cached generator output for $GEN_TAG, no need to rerun"
-  exit 0
-fi
-
-echo "Generator output for $GEN_TAG not found in cache, need to run generator"
-
-## =============================================================================
-## Step 3: Build generator exe 
-##         TODO: need to configurability to the generator exe 
-
-echo "Compiling   benchmarks/dis/generator/pythia_dis.cxx ..."
-g++ benchmarks/dis/generator/pythia_dis.cxx -o ${TMP_PATH}/pythia_dis  \
-   -I/usr/local/include  -I${LOCAL_PREFIX}/include \
-   -O2 -std=c++11 -pedantic -W -Wall -Wshadow -fPIC  \
-   $(pythia8-config --cxxflags --ldflags) \
-   $(HepMC3-config --cxxflags --ldflags)
-if [[ "$?" -ne "0" ]] ; then
-  echo "ERROR compiling pythia"
-  exit 1
-fi
-echo "done"
-
-## =============================================================================
-## Step 4: Run the event generator
-echo "Running the generator"
-${TMP_PATH}/pythia_dis ${TMP_PATH}/${GEN_TAG}.hepmc
-if [[ "$?" -ne "0" ]] ; then
-  echo "ERROR running pythia"
-  exit 1
-fi
-
-
-## =============================================================================
-## Step 5: Finally, move relevant output into the artifacts directory and clean up
-## =============================================================================
-echo "Moving generator output into ${INPUT_PATH}"
-mv ${TMP_PATH}/${GEN_TAG}.hepmc ${INPUT_PATH}/${GEN_TAG}.hepmc
-## this step only matters for local execution
-echo "Cleaning up"
-## does nothing
-
-## =============================================================================
-## All done!
-echo "$BENCHMARK_TAG event generation complete"
diff --git a/benchmarks/dis/get.sh b/benchmarks/dis/get.sh
deleted file mode 100644
index a8718f9b..00000000
--- a/benchmarks/dis/get.sh
+++ /dev/null
@@ -1,80 +0,0 @@
-#!/bin/bash
-source strict-mode.sh
-
-## =============================================================================
-## Standin for a proper pythia generation process, similar to how we
-## generate events for DVMP
-## Runs in 5 steps:
-##   1. Parse the command line and setup the environment
-##   2. Check if we can download the file
-##   3. Finalize
-## =============================================================================
-## =============================================================================
-
-## make sure we launch this script from the project root directory
-PROJECT_ROOT="$( cd "$(dirname "$0")" >/dev/null 2>&1 ; pwd -P )"/../..
-pushd ${PROJECT_ROOT}
-
-## =============================================================================
-## Step 1: Setup the environment variables
-## First parse the command line flags.
-## This sets the following environment variables:
-## - CONFIG:   The specific generator configuration --> not currenlty used FIXME
-## - EBEAM:    The electron beam energy --> not currently used FIXME
-## - PBEAM:    The ion beam energy --> not currently used FIXME
-export REQUIRE_MINQ2=true
-source parse_cmd.sh $@
-
-## To run the generator, we need the following global variables:
-##
-## - LOCAL_PREFIX:      Place to cache local packages and data
-## - JUGGLER_N_EVENTS:  Number of events to process
-## - JUGGLER_RNG_SEED:  Random seed for event generation.
-##
-## defined in common_bench repo
-## You can ready bin/env.sh for more in-depth explanations of the variables
-## and how they can be controlled.
-
-
-## We also need the following benchmark-specific variables:
-##
-## - BENCHMARK_TAG: Unique identified for this benchmark process.
-## - INPUT_PATH:    Path for generator-level input to the benchmarks
-## - TMP_PATH:      Path for temporary data (not exported as artifacts)
-##
-## You can read dvmp/env.sh for more in-depth explanations of the variables.
-source benchmarks/dis/env.sh
-
-## Get a unique file name prefix based on the configuration options
-GEN_TAG=gen-${CONFIG}_${JUGGLER_N_EVENTS} ## Generic file prefix
-
-## =============================================================================
-## Step 2: Check if we can find the file
-if [ -f "${INPUT_PATH}/${GEN_TAG}.hepmc" ]; then
-  echo "Found cached generator output for $GEN_TAG, no need to rerun"
-  exit 0
-fi
-
-## =============================================================================
-## Step 3: Copy the file (about 180 lines per event in DIS NC files)
-nlines=$((190*${JUGGLER_N_EVENTS}))
-DATA_URL=S3/eictest/ATHENA/EVGEN/DIS/NC/${EBEAM}x${PBEAM}/minQ2=${MINQ2}/pythia8NCDIS_${EBEAM}x${PBEAM}_minQ2=${MINQ2}_beamEffects_xAngle=-0.025_hiDiv_vtxfix_1.hepmc
-mc config host add S3 https://eics3.sdcc.bnl.gov:9000 ${S3_ACCESS_KEY} ${S3_SECRET_KEY}
-mc head -n ${nlines} ${DATA_URL} | sanitize_hepmc3 > ${TMP_PATH}/${GEN_TAG}.hepmc
-if [[ "$?" -ne "0" ]] ; then
-  echo "ERROR downloading file"
-  exit 1
-fi
-
-## =============================================================================
-## Step 4: Finally, move relevant output into the artifacts directory and clean up
-## =============================================================================
-echo "Moving generator output to ${INPUT_PATH}/${GEN_TAG}.hepmc"
-mv ${TMP_PATH}/${GEN_TAG}.hepmc ${INPUT_PATH}/${GEN_TAG}.hepmc
-## this step only matters for local execution
-echo "Cleaning up"
-## does nothing
-
-## =============================================================================
-## All done!
-echo "$BENCHMARK_TAG event generation complete"
-- 
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