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 ---
 title: "Exercise 3: Filling out your benchmark"
 teaching: 20
 exercises: 10
 questions: How do we fill in each stage of the benchmark pipeline?
 objectives:
 - "Fill out the many steps of your benchmark"
 - "Collect templates for the benchmark stages"
 keypoints:
 - "Create `setup.config` to switch between using the simulation campaign and re-simulating events"
 - "Each stage of the benchmark pipeline is defined in `config.yml`"
 - "`config.yml` takes normal bash scripts as input"
 - "Copy resulting figures over to the `results` directory to turn them into artifacts"
 ---
 
 In this lesson we will be beefing up our benchmark by filling out several of the pipeline stages.
 
 ## Setting up
 
 Before filling out the stages for GitLab's CI and pipelines, we want to first create a file that contains some settings used by our benchmark.
 
 Create a new file: [`benchmarks/your_benchmark/setup.config`](https://github.com/eic/tutorial-developing-benchmarks/blob/gh-pages/files/setup.config) with the following contents
 ```bash
 #!/bin/bash
 source strict-mode.sh
 
 export ENV_MODE=eicweb
 
 USE_SIMULATION_CAMPAIGN=true
 
 N_EVENTS=100
 
 FILE_BASE=sim_output/rho_10x100_uChannel_Q2of0to10_hiDiv.hepmc3.tree
 INPUT_FILE=root://dtn-eic.jlab.org//work/eic2/EPIC/EVGEN/EXCLUSIVE/UCHANNEL_RHO/10x100/rho_10x100_uChannel_Q2of0to10_hiDiv.hepmc3.tree.root
 OUTPUT_FILE=${FILE_BASE}.detectorsim.root
 
 REC_FILE_BASE=${FILE_BASE}.detectorsim.edm4eic
 REC_FILE=${REC_FILE_BASE}.root
 ```
 The `export ENV_MODE=eicweb` lets our Snakefile know to use the paths for running on eicweb.
 
 Here we've defined a switch `USE_SIMULATION_CAMPAIGN` which will allow us to alternate between using output from the simulation campaign, and dynamically simulating new events.
 
 When not using the simulation campaign, the `N_EVENTS` variable defines how many events the benchmark should run.
 The rest of these variables define file names to be used in the benchmark.
 
 Also create a new file [`benchmarks/your_benchmark/simulate.sh`](https://github.com/eic/tutorial-developing-benchmarks/blob/gh-pages/files/simulate.sh) with the following contents:
 ```bash
 #!/bin/bash
 source strict-mode.sh
 source benchmarks/your_benchmark/setup.config $*
 
 if [ -f ${INPUT_FILE} ]; then
   echo "ERROR: Input simulation file does ${INPUT_FILE} not exist."
 else
   echo "GOOD: Input simulation file ${INPUT_FILE} exists!"
 fi
 
 # Simulate
 ddsim --runType batch \
       -v WARNING \
       --numberOfEvents ${N_EVENTS} \
       --part.minimalKineticEnergy 100*GeV  \
       --filter.tracker edep0 \
       --compactFile ${DETECTOR_PATH}/${DETECTOR_CONFIG}.xml \
       --inputFiles ${INPUT_FILE} \
       --outputFile  ${OUTPUT_FILE}
 if [[ "$?" -ne "0" ]] ; then
   echo "ERROR running ddsim"
   exit 1
 fi
 ```
 
 This script uses ddsim to simulate the detector response to your benchmark events.
 
 Create a script named [`benchmarks/your_benchmark/reconstruct.sh`](https://github.com/eic/tutorial-developing-benchmarks/blob/gh-pages/files/reconstruct.sh) to manage the reconstruction:
 ```bash
 #!/bin/bash
 source strict-mode.sh
 source benchmarks/your_benchmark/setup.config $*
 
 # Reconstruct
 if [ ${RECO} == "eicrecon" ] ; then
   eicrecon ${OUTPUT_FILE} -Ppodio:output_file=${REC_FILE}
   if [[ "$?" -ne "0" ]] ; then
     echo "ERROR running eicrecon"
     exit 1
   fi
 fi
 
 if [[ ${RECO} == "juggler" ]] ; then
   gaudirun.py options/reconstruction.py || [ $? -eq 4 ]
   if [ "$?" -ne "0" ] ; then
     echo "ERROR running juggler"
     exit 1
   fi
 fi
 
 if [ -f jana.dot ] ; then cp jana.dot ${REC_FILE_BASE}.dot ; fi
 
 #rootls -t ${REC_FILE_BASE}.tree.edm4eic.root
 rootls -t ${REC_FILE}
 ```
 
 Create a file called [`benchmarks/your_benchmark/analyze.sh`](https://github.com/eic/tutorial-developing-benchmarks/blob/gh-pages/files/analyze.sh) which will run the analysis and plotting scripts:
 ```bash
 #!/bin/bash
 source strict-mode.sh
 source benchmarks/your_benchmark/setup.config $*
 
 OUTPUT_PLOTS_DIR=sim_output/nocampaign
 mkdir -p ${OUTPUT_PLOTS_DIR}
 # Analyze
 command time -v \
 root -l -b -q "benchmarks/your_benchmark/analysis/uchannelrho.cxx(\"${REC_FILE}\",\"${OUTPUT_PLOTS_DIR}/plots.root\")"
 if [[ "$?" -ne "0" ]] ; then
   echo "ERROR analysis failed"
   exit 1
 fi
 
 if [ ! -d "${OUTPUT_PLOTS_DIR}/plots_figures" ]; then
     mkdir "${OUTPUT_PLOTS_DIR}/plots_figures"
     echo "${OUTPUT_PLOTS_DIR}/plots_figures directory created successfully."
 else
     echo "${OUTPUT_PLOTS_DIR}/plots_figures directory already exists."
 fi
 root -l -b -q "benchmarks/your_benchmark/macros/plot_rho_physics_benchmark.C(\"${OUTPUT_PLOTS_DIR}/plots.root\")"
 cat benchmark_output/*.json
 ```
 
 Let's copy over our analysis script, our plotting macro & header, and our Snakefile:
 ```bash
 mkdir benchmarks/your_benchmark/analysis
 mkdir benchmarks/your_benchmark/macros
 
 cp ../starting_script/Snakefile benchmarks/your_benchmark/
 cp ../starting_script/analysis/uchannelrho.cxx benchmarks/your_benchmark/analysis/
 cp ../starting_script/macros/RiceStyle.h benchmarks/your_benchmark/macros/
 cp ../starting_script/macros/plot_rho_physics_benchmark.C benchmarks/your_benchmark/macros/
 ```
 
 
 
 Your benchmark directory should now look like this: 
 ![Add a title]({{ page.root }}/fig/your_bench_dir_new.png) 
 
 In order to use your Snakefile, let GitLab know it's there. Open the main `Snakefile`, NOT this one `benchmarks/your_benchmark/Snakefile`, but the one at the same level as the `benchmarks` directory.
 
 Go to the very end of the file and include a path to your own Snakefile:
 ```python
 include: "benchmarks/diffractive_vm/Snakefile"
 include: "benchmarks/dis/Snakefile"
 include: "benchmarks/demp/Snakefile"
 include: "benchmarks/your_benchmark/Snakefile"
 ```
 
 Once that's all setup, we can move on to actually adding these to our pipeline!
 
 ## The "simulate" pipeline stage
 We now fill out the `simulate` stage in GitLab's pipelines. Currently the instructions for this rule should be contained in `benchmarks/your_benchmark/config.yml` as: 
 ```yaml
 your_benchmark:simulate:
   extends: .phy_benchmark
   stage: simulate
   script:
     - echo "I will simulate detector response here!"
 ```
 
 In order to make sure the previous stages finish before this one starts, add a new line below `stage:simulate`: `needs: ["common:setup"]`.
 
 This step can take a long time if you simulate too many events. So let's add an upper limit on the allowed run time of 10 hours:
 In a new line below `needs: ["common:setup"]`, add this: `timeout: 10 hour`.
 
 Now in the `script` section of the rule, add two new lines to source the `setup.config` file:
 ```yaml
     - config_file=benchmarks/your_benchmark/setup.config
     - source $config_file
 ```
 
 Add instructions that if using the simulation campaign you can skip detector simulations. Otherwise simulate
 ```yaml
     - if [ "$USE_SIMULATION_CAMPAIGN" = true ] ; then
     -     echo "Using simulation campaign so skipping this step!"
     - else
     -     echo "Grabbing raw events from S3 and running Geant4"
     -     bash benchmarks/your_benchmark/simulate.sh
     -     echo "Geant4 simulations done! Starting eicrecon now!"
     -     bash benchmarks/your_benchmark/reconstruct.sh
     - fi
     - echo "Finished simulating detector response"
 ```
 
 Finally, add an instruction to retry the simulation if it fails:
 ```yaml
   retry:
     max: 2
     when:
       - runner_system_failure
 ```
 The final `simulate` rule should look like this:
 ```yaml
 your_benchmark:simulate:
   extends: .phy_benchmark
   stage: simulate
   needs: ["common:setup"]
   timeout: 10 hour
   script:
     - echo "I will simulate detector response here!"
     - config_file=benchmarks/your_benchmark/setup.config
     - source $config_file
     - if [ "$USE_SIMULATION_CAMPAIGN" = true ] ; then
     -     echo "Using simulation campaign!"
     - else
     -     echo "Grabbing raw events from S3 and running Geant4"
     -     bash benchmarks/your_benchmark/simulate.sh
     -     echo "Geant4 simulations done! Starting eicrecon now!"
     -     bash benchmarks/your_benchmark/reconstruct.sh
     - fi
     - echo "Finished simulating detector response"
   retry:
     max: 2
     when:
       - runner_system_failure
 ```
 
 ## The "results" pipeline stage
 
 The `results` stage in `config.yml` is right now just this:
 ```yaml
 your_benchmark:results:
   extends: .phy_benchmark
   stage: collect
   script:
     - echo "I will collect results here!"
 ```
 
 Specify that we need to finish the simulate stage first:
 ```yaml
   needs:
     - ["your_benchmark:simulate"]
 ```
 
 Now make two directories to contain output from the benchmark analysis and source `setup.config` again:
 ```yaml
     - mkdir -p results/your_benchmark
     - mkdir -p benchmark_output
     - config_file=benchmarks/your_benchmark/setup.config
     - source $config_file
 ```
 
 If using the simulation campaign, we can request the rho mass benchmark with snakemake. Once snakemake has finished creating the benchmark figures, we copy them over to `results/your_benchmark/` in order to make them into artifacts:
 ```yaml
     - if [ "$USE_SIMULATION_CAMPAIGN" = true ] ; then
     -     echo "Using simulation campaign!"
     -     snakemake --cores 2 ../../sim_output/campaign_24.07.0_combined_45files.eicrecon.tree.edm4eic.plots_figures/benchmark_rho_mass.pdf
     -     cp ../../sim_output/campaign_24.07.0_combined_45files.eicrecon.tree.edm4eic.plots_figures/*.pdf results/your_benchmark/
 ```
 
 If not using the simulation campaign, we can just run the `analyze.sh` script and copy the results into `results/your_benchmark/` in order to make them into artifacts:
 ```yaml
     - else
     -     echo "Not using simulation campaign!"
     -     bash benchmarks/your_benchmark/analyze.sh
     -     cp sim_output/nocampaign/plots_figures/*.pdf results/your_benchmark/
     - fi
     - echo "Finished copying!"
 ```
 
 Your final `config.yml` should look like:
 ```yaml
 your_benchmark:compile:
   extends: .phy_benchmark 
   stage: compile
   script:
     - echo "You can compile your code here!"
 
 your_benchmark:simulate:
   extends: .phy_benchmark
   stage: simulate
   needs: ["common:setup"]
   timeout: 10 hour
   script:
     - echo "Simulating everything here!"
     - config_file=benchmarks/your_benchmark/setup.config
     - source $config_file
     - if [ "$USE_SIMULATION_CAMPAIGN" = true ] ; then
     -     echo "Using simulation campaign!"
     - else
     -     echo "Grabbing raw events from S3 and running Geant4"
     -     bash benchmarks/your_benchmark/simulate.sh
     -     echo "Geant4 simulations done! Starting eicrecon now!"
     -     bash benchmarks/your_benchmark/reconstruct.sh
     - fi
     - echo "Finished simulating detector response"
   retry:
     max: 2
     when:
       - runner_system_failure
 
 your_benchmark:results:
   extends: .phy_benchmark
   stage: collect
   script:
     - echo "I will collect results here!"
   needs:
     - ["your_benchmark:simulate"]
   script:
     - mkdir -p results/your_benchmark
     - mkdir -p benchmark_output
     - config_file=benchmarks/your_benchmark/setup.config
     - source $config_file
     - if [ "$USE_SIMULATION_CAMPAIGN" = true ] ; then
     -     echo "Using simulation campaign!"
     -     snakemake --cores 2 ../../sim_output/campaign_24.07.0_combined_45files.eicrecon.tree.edm4eic.plots_figures/benchmark_rho_mass.pdf
     -     cp ../../sim_output/campaign_24.07.0_combined_45files.eicrecon.tree.edm4eic.plots_figures/*.pdf results/your_benchmark/
     - else
     -     echo "Not using simulation campaign!"
     -     bash benchmarks/your_benchmark/analyze.sh
     -     cp sim_output/nocampaign/plots_figures/*.pdf results/your_benchmark/
     - fi
     - echo "Finished copying!"
 ```
 
 ## Testing Real Pipelines
 
 We've set up our benchmark to do some real analysis! As a first test, let's make sure we're still running only over the simulation campaign. The `USE_SIMULATION_CAMPAIGN` in `setup.config` should be set to true.
 
 Now let's add our changes and push them to GitHub!
 
 ```bash
 git status
 ```
 This command should show something like this:
 ![Add a title]({{ page.root }}/fig/gitstatus_example.png) 
 
 Now add all our changes:
 ```bash
 git add Snakefile
 git add benchmarks/your_benchmark/config.yml
 git add benchmarks/your_benchmark/Snakefile
 git add benchmarks/your_benchmark/analysis/uchannelrho.cxx 
 git add benchmarks/your_benchmark/analyze.sh
 git add benchmarks/your_benchmark/macros/plot_rho_physics_benchmark.C 
 git add benchmarks/your_benchmark/macros/RiceStyle.h 
 git add benchmarks/your_benchmark/reconstruct.sh
 git add benchmarks/your_benchmark/setup.config
 git add benchmarks/your_benchmark/simulate.sh
 
 git commit -m "I'm beefing up my benchmark!"
 git push origin pr/your_benchmark_<mylastname>
 ```
 
 Now monitor the pipeline you created:
 - [physics benchmark pipelines](https://eicweb.phy.anl.gov/EIC/benchmarks/physics_benchmarks/-/pipelines)
 - [detector benchmark pipleines](https://eicweb.phy.anl.gov/EIC/benchmarks/detector_benchmarks/-/pipelines)
 

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