.gitlab-ci.yml: introduce global SNAKEMAKE_FLAGS, don't re-run based on mtime (#92)

6e99ae8b · Dmitry Kalinkin · GitHub · 2a39b59c · 6e99ae8b · 6e99ae8b
Unverified Commit 6e99ae8b authored 5 months ago by Dmitry Kalinkin Committed by GitHub 5 months ago
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -5,6 +5,7 @@ variables:
  DETECTOR_CONFIG: epic_craterlake
  GITHUB_SHA: ''
  GITHUB_REPOSITORY: ''
+  SNAKEMAKE_FLAGS: '--cache --rerun-triggers code input params software-env'

 workflow:
  name: '$PIPELINE_NAME'

--- a/benchmarks/backgrounds/config.yml
+++ b/benchmarks/backgrounds/config.yml
@@ -5,7 +5,7 @@ sim:backgrounds:
    - mkdir -p $LOCAL_DATA_PATH/input
    - ln -s $LOCAL_DATA_PATH/input input
    - |
-      snakemake --cache --cores 2 \
+      snakemake $SNAKEMAKE_FLAGS --cores 2 \
        sim_output/$DETECTOR_CONFIG/backgrounds/EPIC/EVGEN/BACKGROUNDS/BEAMGAS/electron/GETaLM1.0.0-1.0/10GeV/GETaLM1.0.0-1.0_ElectronBeamGas_10GeV_foam_emin10keV_run001.edm4hep.root \
        sim_output/$DETECTOR_CONFIG/backgrounds/EPIC/EVGEN/DIS/NC/10x100/minQ2=1/pythia8NCDIS_10x100_minQ2=1_beamEffects_xAngle=-0.025_hiDiv_1.edm4hep.root \
        sim_output/$DETECTOR_CONFIG/backgrounds/EPIC/EVGEN/BACKGROUNDS/BEAMGAS/proton/pythia8.306-1.0/100GeV/pythia8.306-1.0_ProtonBeamGas_100GeV_run001.edm4hep.root
@@ -19,7 +19,7 @@ bench:backgrounds_emcal_backwards:
    - ln -s $LOCAL_DATA_PATH/input input
    - export PYTHONUSERBASE=$LOCAL_DATA_PATH/deps
    - pip install -r benchmarks/backgrounds/requirements.txt
-    - snakemake --cores 8 backgrounds_ecal_backwards
+    - snakemake $SNAKEMAKE_FLAGS --cores 8 backgrounds_ecal_backwards

 collect_results:backgrounds:
  extends: .det_benchmark
@@ -29,5 +29,5 @@ collect_results:backgrounds:
  script:
    - ls -lrht
    - mv results{,_save}/ # move results directory out of the way to preserve it
-    - snakemake --cores 1 --delete-all-output backgrounds_ecal_backwards
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 --delete-all-output backgrounds_ecal_backwards
    - mv results{_save,}/
--- a/benchmarks/backwards_ecal/config.yml
+++ b/benchmarks/backwards_ecal/config.yml
@@ -16,7 +16,7 @@ sim:backwards_ecal:
        ]
  script:
    - |
-      snakemake --cache --cores 5 sim_output/backwards_ecal/${DETECTOR_CONFIG}/${PARTICLE}/${MOMENTUM}/130to177deg/flag
+      snakemake $SNAKEMAKE_FLAGS --cores 5 sim_output/backwards_ecal/${DETECTOR_CONFIG}/${PARTICLE}/${MOMENTUM}/130to177deg/flag

 bench:backwards_ecal:
  extends: .det_benchmark
@@ -26,7 +26,7 @@ bench:backwards_ecal:
  script:
    - export PYTHONUSERBASE=$LOCAL_DATA_PATH/deps
    - pip install -r benchmarks/backwards_ecal/requirements.txt
-    - snakemake --cores 1 backwards_ecal
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 backwards_ecal

 collect_results:backwards_ecal:
  extends: .det_benchmark
@@ -36,5 +36,5 @@ collect_results:backwards_ecal:
  script:
    - ls -lrht
    - mv results{,_save}/ # move results directory out of the way to preserve it
-    - snakemake --cores 1 --delete-all-output backwards_ecal
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 --delete-all-output backwards_ecal
    - mv results{_save,}/
--- a/benchmarks/barrel_ecal/config.yml
+++ b/benchmarks/barrel_ecal/config.yml
@@ -2,13 +2,13 @@ sim:emcal_barrel_pions:
  extends: .det_benchmark
  stage: simulate
  script:
-    - snakemake --cores 1 $DETECTOR_CONFIG/sim_output/sim_emcal_barrel_{piplus,piminus}_energies5.0_5.0.edm4hep.root
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 $DETECTOR_CONFIG/sim_output/sim_emcal_barrel_{piplus,piminus}_energies5.0_5.0.edm4hep.root

 sim:emcal_barrel_pi0:
  extends: .det_benchmark
  stage: simulate
  script:
-    - snakemake --cores 1 $DETECTOR_CONFIG/sim_output/sim_emcal_barrel_pi0_energies5.0_5.0.edm4hep.root
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 $DETECTOR_CONFIG/sim_output/sim_emcal_barrel_pi0_energies5.0_5.0.edm4hep.root

 sim:emcal_barrel_electrons:
  extends: .det_benchmark
@@ -16,20 +16,20 @@ sim:emcal_barrel_electrons:
  script:
    - if [[ "$RUN_EXTENDED_BENCHMARK" == "true" ]] ; then snakemake --cores $DETECTOR_CONFIG/results/energy_scan/emcal_barrel_electron_fsam_scan.png; fi
    - export JUGGLER_N_EVENTS=400
-    - snakemake --cores 1 $DETECTOR_CONFIG/sim_output/sim_emcal_barrel_electron_energies5.0_5.0.edm4hep.root
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 $DETECTOR_CONFIG/sim_output/sim_emcal_barrel_electron_energies5.0_5.0.edm4hep.root

 sim:emcal_barrel_photons:
  extends: .det_benchmark
  stage: simulate
  script:
    - if [[ "$RUN_EXTENDED_BENCHMARK" == "true" ]] ; then snakemake --cores $DETECTOR_CONFIG/results/energy_scan/emcal_barrel_proton_fsam_scan.png; fi
-    - snakemake --cores 1 $DETECTOR_CONFIG/sim_output/sim_emcal_barrel_photon_energies5.0_5.0.edm4hep.root
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 $DETECTOR_CONFIG/sim_output/sim_emcal_barrel_photon_energies5.0_5.0.edm4hep.root

 sim:emcal_barrel_pion_rejection:
  extends: .det_benchmark
  stage: simulate
  script:
-    - snakemake --cores 1 $DETECTOR_CONFIG/sim_output/sim_emcal_barrel_{piminus,electron}_energies1.0_18.0.edm4hep.root
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 $DETECTOR_CONFIG/sim_output/sim_emcal_barrel_{piminus,electron}_energies1.0_18.0.edm4hep.root

 calib:emcal_barrel_electrons:
  extends: .det_benchmark
@@ -39,7 +39,7 @@ calib:emcal_barrel_electrons:
  script:
    - ls -lhtR sim_output/
    - rootls -t sim_output/sim_emcal_barrel_electron_energies5.0_5.0.edm4hep.root
-    - snakemake --cores 1 $DETECTOR_CONFIG/results/emcal_barrel_electron_calibration.json
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 $DETECTOR_CONFIG/results/emcal_barrel_electron_calibration.json
    - mv sim_output/sim_emcal_barrel_electron.edm4hep.root results/.
    - echo "JSON file(s) from analysis:" ; cat results/*.json

@@ -49,7 +49,7 @@ bench:emcal_barrel_pions:
  needs:
    - ["sim:emcal_barrel_pions"]
  script:
-    - snakemake --cores 1 $DETECTOR_CONFIG/results/emcal_barrel_pions_Ethr.png
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 $DETECTOR_CONFIG/results/emcal_barrel_pions_Ethr.png

 bench:emcal_barrel_electrons_scan:
  extends: .det_benchmark
@@ -66,7 +66,7 @@ bench:emcal_barrel_pi0:
    - ["sim:emcal_barrel_pi0", "calib:emcal_barrel_electrons"]
  script:
    - echo "JSON file(s) from analysis:" ; cat results/*.json
-    - snakemake --cores 1 epic_craterlake/results/Barrel_emcal_pi0.json
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 epic_craterlake/results/Barrel_emcal_pi0.json

 bench:emcal_barrel_photons:
  extends: .det_benchmark
@@ -76,7 +76,7 @@ bench:emcal_barrel_photons:
  script:
    - ls -lhtR sim_output/
    - rootls -t sim_output/sim_emcal_barrel_photon_energies5.0_5.0.edm4hep.root
-    - snakemake --cores 1 $DETECTOR_CONFIG/results/emcal_barrel_photon_calibration.json
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 $DETECTOR_CONFIG/results/emcal_barrel_photon_calibration.json
    - mv sim_output/sim_emcal_barrel_photon.edm4hep.root results/.
    - if [[ "$RUN_EXTENDED_BENCHMARK" == "true" ]] ; then snakemake --cores $DETECTOR_CONFIG/results/energy_scan/emcal_barrel_proton_fsam_scan.png; fi

@@ -89,7 +89,7 @@ bench:emcal_barrel_pion_rejection:
    - ls -lhtR sim_output/
    - rootls -t $DETECTOR_CONFIG/sim_output/sim_emcal_barrel_piminus_energies1.0_18.0.edm4hep.root
    - rootls -t $DETECTOR_CONFIG/sim_output/sim_emcal_barrel_electron_energies1.0_18.0.edm4hep.root
-    - snakemake --cores 1 $DETECTOR_CONFIG/results/Barrel_emcal_pion_rej.json
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 $DETECTOR_CONFIG/results/Barrel_emcal_pion_rej.json

 collect_results:barrel_ecal:
  extends: .det_benchmark

--- a/benchmarks/ecal_gaps/config.yml
+++ b/benchmarks/ecal_gaps/config.yml
@@ -4,7 +4,7 @@ sim:ecal_gaps:
  script:
    - mkdir -p $LOCAL_DATA_PATH/input
    - ln -s $LOCAL_DATA_PATH/input input
-    - snakemake --cache --cores 10 ecal_gaps --omit-from ecal_gaps
+    - snakemake $SNAKEMAKE_FLAGS --cache --cores 10 ecal_gaps --omit-from ecal_gaps

 bench:ecal_gaps:
  extends: .det_benchmark
@@ -15,7 +15,7 @@ bench:ecal_gaps:
    - ln -s $LOCAL_DATA_PATH/input input
    - export PYTHONUSERBASE=$LOCAL_DATA_PATH/deps
    - pip install -r benchmarks/ecal_gaps/requirements.txt
-    - snakemake --cores 8 ecal_gaps
+    - snakemake $SNAKEMAKE_FLAGS --cores 8 ecal_gaps

 collect_results:ecal_gaps:
  extends: .det_benchmark
@@ -25,5 +25,5 @@ collect_results:ecal_gaps:
  script:
    - ls -lrht
    - mv results{,_save}/ # move results directory out of the way to preserve it
-    - snakemake --cores 1 --delete-all-output ecal_gaps
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 --delete-all-output ecal_gaps
    - mv results{_save,}/
--- a/benchmarks/femc_electron/config.yml
+++ b/benchmarks/femc_electron/config.yml
@@ -13,7 +13,7 @@ sim:femc_electron:
      - P: 80
  timeout: 1 hours
  script:
-    - snakemake --cores 1 sim_output/femc_electron/epic_craterlake_rec_e-_${P}GeV.edm4eic.root
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 sim_output/femc_electron/epic_craterlake_rec_e-_${P}GeV.edm4eic.root
  retry:
    max: 2
    when:
@@ -24,7 +24,7 @@ bench:femc_electron:
  stage: benchmarks
  needs: ["sim:femc_electron"]
  script:
-    - snakemake --cores 1 results/epic_craterlake/femc_electron
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 results/epic_craterlake/femc_electron

 collect_results:femc_electron:
  extends: .det_benchmark
@@ -33,5 +33,5 @@ collect_results:femc_electron:
  script:
    - ls -al
    - mv results{,_save}/ # move results directory out of the way to preserve it
-    - snakemake --cores 1 --delete-all-output results/epic_craterlake/femc_electron
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 --delete-all-output results/epic_craterlake/femc_electron
    - mv results{_save,}/
--- a/benchmarks/femc_photon/config.yml
+++ b/benchmarks/femc_photon/config.yml
@@ -13,7 +13,7 @@ sim:femc_photon:
      - P: 80
  timeout: 1 hours
  script:
-    - snakemake --cores 1 sim_output/femc_photon/epic_craterlake_rec_photon_${P}GeV.edm4eic.root
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 sim_output/femc_photon/epic_craterlake_rec_photon_${P}GeV.edm4eic.root
  retry:
    max: 2
    when:
@@ -24,7 +24,7 @@ bench:femc_photon:
  stage: benchmarks
  needs: ["sim:femc_photon"]
  script:
-    - snakemake --cores 1 results/epic_craterlake/femc_photon
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 results/epic_craterlake/femc_photon

 collect_results:femc_photon:
  extends: .det_benchmark
@@ -33,5 +33,5 @@ collect_results:femc_photon:
  script:
    - ls -al
    - mv results{,_save}/ # move results directory out of the way to preserve it
-    - snakemake --cores 1 --delete-all-output results/epic_craterlake/femc_photon
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 --delete-all-output results/epic_craterlake/femc_photon
    - mv results{_save,}/
--- a/benchmarks/femc_pi0/config.yml
+++ b/benchmarks/femc_pi0/config.yml
@@ -12,7 +12,7 @@ sim:femc_pi0:
      - P: 70
      - P: 80
  script:
-    - snakemake --cores 1 sim_output/femc_pi0/epic_craterlake_rec_pi0_${P}GeV.edm4eic.root
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 sim_output/femc_pi0/epic_craterlake_rec_pi0_${P}GeV.edm4eic.root
  retry:
    max: 2
    when:
@@ -23,7 +23,7 @@ bench:femc_pi0:
  stage: benchmarks
  needs: ["sim:femc_pi0"]
  script:
-    - snakemake --cores 1 results/epic_craterlake/femc_pi0
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 results/epic_craterlake/femc_pi0

 collect_results:femc_pi0:
  extends: .det_benchmark
@@ -32,5 +32,5 @@ collect_results:femc_pi0:
  script:
    - ls -al
    - mv results{,_save}/ # move results directory out of the way to preserve it
-    - snakemake --cores 1 --delete-all-output results/epic_craterlake/femc_pi0
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 --delete-all-output results/epic_craterlake/femc_pi0
    - mv results{_save,}/
--- a/benchmarks/insert_muon/config.yml
+++ b/benchmarks/insert_muon/config.yml
@@ -5,7 +5,7 @@ sim:insert_muon:
    matrix:
      - P: 50
  script:
-    - snakemake --cores 5 sim_output/insert_muon/epic_craterlake_sim_mu-_${P}GeV_{0,1,2,3,4}.edm4hep.root
+    - snakemake $SNAKEMAKE_FLAGS --cores 5 sim_output/insert_muon/epic_craterlake_sim_mu-_${P}GeV_{0,1,2,3,4}.edm4hep.root
  retry:
    max: 2
    when:
@@ -16,7 +16,7 @@ bench:insert_muon:
  stage: benchmarks
  needs: ["sim:insert_muon"]
  script:
-    - snakemake --cores 1 results/epic_craterlake/insert_muon
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 results/epic_craterlake/insert_muon

 collect_results:insert_muon:
  extends: .det_benchmark
@@ -25,5 +25,5 @@ collect_results:insert_muon:
  script:
    - ls -al
    - mv results{,_save}/ # move results directory out of the way to preserve it
-    - snakemake --cores 1 --delete-all-output results/epic_craterlake/insert_muon
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 --delete-all-output results/epic_craterlake/insert_muon
    - mv results{_save,}/
--- a/benchmarks/insert_neutron/config.yml
+++ b/benchmarks/insert_neutron/config.yml
@@ -11,7 +11,7 @@ sim:insert_neutron:
      - P: 70
      - P: 80
  script:
-    - snakemake --cores 5 sim_output/insert_neutron/epic_craterlake_rec_neutron_${P}GeV_{0,1,2,3,4}.edm4eic.root
+    - snakemake $SNAKEMAKE_FLAGS --cores 5 sim_output/insert_neutron/epic_craterlake_rec_neutron_${P}GeV_{0,1,2,3,4}.edm4eic.root
  retry:
    max: 2
    when:
@@ -22,7 +22,7 @@ bench:insert_neutron:
  stage: benchmarks
  needs: ["sim:insert_neutron"]
  script:
-    - snakemake --cores 1 results/epic_craterlake/insert_neutron
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 results/epic_craterlake/insert_neutron

 collect_results:insert_neutron:
  extends: .det_benchmark
@@ -31,5 +31,5 @@ collect_results:insert_neutron:
  script:
    - ls -al
    - mv results{,_save}/ # move results directory out of the way to preserve it
-    - snakemake --cores 1 --delete-all-output results/epic_craterlake/insert_neutron
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 --delete-all-output results/epic_craterlake/insert_neutron
    - mv results{_save,}/
--- a/benchmarks/lfhcal/config.yml
+++ b/benchmarks/lfhcal/config.yml
@@ -16,7 +16,7 @@ bench:lfhcal:
  needs:
    - ["sim:lfhcal"]
  script:
-    - snakemake --cores 3 lfhcal_local
+    - snakemake $SNAKEMAKE_FLAGS --cores 3 lfhcal_local

 collect_results:lfhcal:
  extends: .det_benchmark
@@ -26,7 +26,7 @@ collect_results:lfhcal:
  script:
    - ls -lrht
    - mv results{,_save}/ # move results directory out of the way to preserve it
-    - snakemake --cores 1 --delete-all-output lfhcal_local
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 --delete-all-output lfhcal_local
    - mv results{_save,}/

 bench:lfhcal_campaigns:
@@ -34,7 +34,7 @@ bench:lfhcal_campaigns:
  stage: benchmarks
  #when: manual
  script:
-    - snakemake --cores 1 lfhcal_campaigns
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 lfhcal_campaigns

 collect_results:lfhcal_campaigns:
  extends: .det_benchmark
@@ -44,5 +44,5 @@ collect_results:lfhcal_campaigns:
  script:
    - ls -lrht
    - mv results{,_save}/ # move results directory out of the way to preserve it
-    - snakemake --cores 1 --delete-all-output lfhcal_campaigns
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 --delete-all-output lfhcal_campaigns
    - mv results{_save,}/
--- a/benchmarks/material_scan/config.yml
+++ b/benchmarks/material_scan/config.yml
@@ -2,7 +2,7 @@ bench:material_scan:
  extends: .det_benchmark
  stage: benchmarks
  script:
-    - snakemake --cores 1 epic_craterlake/results/material_scan_details.pdf
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 epic_craterlake/results/material_scan_details.pdf

 collect_results:material_scan:
  extends: .det_benchmark

--- a/benchmarks/tracking_performances/config.yml
+++ b/benchmarks/tracking_performances/config.yml
@@ -18,7 +18,7 @@ bench:tracking_performance:
  needs:
    - ["sim:tracking_performance"]
  script:
-    - snakemake --cores 3 tracking_performance_local
+    - snakemake $SNAKEMAKE_FLAGS --cores 3 tracking_performance_local

 collect_results:tracking_performance:
  extends: .det_benchmark
@@ -27,14 +27,14 @@ collect_results:tracking_performance:
    - "bench:tracking_performance"
  script:
    - ls -lrht
-    - snakemake --cores 1 --delete-all-output tracking_performance_local
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 --delete-all-output tracking_performance_local

 bench:tracking_performance_campaigns:
  extends: .det_benchmark
  stage: benchmarks
  #when: manual
  script:
-    - snakemake --cores 1 tracking_performance_campaigns
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 tracking_performance_campaigns

 collect_results:tracking_performance_campaigns:
  extends: .det_benchmark
@@ -44,5 +44,5 @@ collect_results:tracking_performance_campaigns:
  script:
    - ls -lrht
    - mv results{,_save}/ # move results directory out of the way to preserve it
-    - snakemake --cores 1 --delete-all-output tracking_performance_campaigns
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 --delete-all-output tracking_performance_campaigns
    - mv results{_save,}/
--- a/benchmarks/tracking_performances_dis/config.yml
+++ b/benchmarks/tracking_performances_dis/config.yml
@@ -2,7 +2,7 @@ sim:tracking_performances_dis:
  extends: .det_benchmark
  stage: simulate
  script:
-    - snakemake --cache --cores 5 results/tracking_performances_dis/epic_craterlake_tracking_only/pythia8NCDIS_18x275_minQ2=1_combined_5/hists.root 
+    - snakemake $SNAKEMAKE_FLAGS --cores 5 results/tracking_performances_dis/epic_craterlake_tracking_only/pythia8NCDIS_18x275_minQ2=1_combined_5/hists.root
  retry:
    max: 2
    when:
@@ -14,7 +14,7 @@ bench:tracking_performances_dis:
  needs:
    - ["sim:tracking_performances_dis"]
  script:
-    - snakemake --cores 1 trk_dis_run_locally_trk_only
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 trk_dis_run_locally_trk_only
    # avoid uploading intermediate results
    - find results/tracking_performances_dis/ -mindepth 2 -maxdepth 2 -type d ! -name "*combined*" | xargs rm -rfv

@@ -26,7 +26,7 @@ collect_results:tracking_performances_dis:
  script:
    - ls -lrht
    - mv results{,_save}/ # move results directory out of the way to preserve it
-    - snakemake --cores 1 --delete-all-output trk_dis_run_locally_trk_only
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 --delete-all-output trk_dis_run_locally_trk_only
    - mv results{_save,}/
    # convert to png
    - |

--- a/benchmarks/zdc_lambda/config.yml
+++ b/benchmarks/zdc_lambda/config.yml
@@ -12,7 +12,7 @@ sim:zdc_lambda:
      - P: 250
      - P: 275
  script:
-    - snakemake --cores 5 sim_output/zdc_lambda/epic_zdc_sipm_on_tile_only_rec_lambda_dec_${P}GeV_{0,1,2,3,4}.edm4eic.root
+    - snakemake $SNAKEMAKE_FLAGS --cores 5 sim_output/zdc_lambda/epic_zdc_sipm_on_tile_only_rec_lambda_dec_${P}GeV_{0,1,2,3,4}.edm4eic.root
  retry:
    max: 2
    when:
@@ -23,7 +23,7 @@ bench:zdc_lambda:
  stage: benchmarks
  needs: ["sim:zdc_lambda"]
  script:
-    - snakemake --cores 1 results/epic_zdc_sipm_on_tile_only/zdc_lambda
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 results/epic_zdc_sipm_on_tile_only/zdc_lambda

 collect_results:zdc_lambda:
  extends: .det_benchmark
@@ -32,5 +32,5 @@ collect_results:zdc_lambda:
  script:
    - ls -al
    - mv results{,_save}/ # move results directory out of the way to preserve it
-    - snakemake --cores 1 --delete-all-output results/epic_zdc_sipm_on_tile_only/zdc_lambda
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 --delete-all-output results/epic_zdc_sipm_on_tile_only/zdc_lambda
    - mv results{_save,}/
--- a/benchmarks/zdc_lyso/config.yml
+++ b/benchmarks/zdc_lyso/config.yml
@@ -2,7 +2,7 @@ sim:zdc_lyso:
  extends: .det_benchmark
  stage: simulate
  script:
-    - snakemake --cache --cores 1 zdc_lyso_local
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 zdc_lyso_local
  retry:
    max: 2
    when:
@@ -16,5 +16,5 @@ collect_results:zdc_lyso:
  script:
    - ls -lrht
    - mv results{,_save}/ # move results directory out of the way to preserve it
-    - snakemake --cores 1 --delete-all-output zdc_lyso_local
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 --delete-all-output zdc_lyso_local
    - mv results{_save,}/
--- a/benchmarks/zdc_photon/config.yml
+++ b/benchmarks/zdc_photon/config.yml
@@ -12,7 +12,7 @@ sim:zdc_photon:
      - P: 200
      - P: 275
  script:
-    - snakemake --cores 5 sim_output/zdc_photon/epic_zdc_sipm_on_tile_only_rec_zdc_photon_${P}GeV_{0,1,2,3,4}.edm4eic.root
+    - snakemake $SNAKEMAKE_FLAGS --cores 5 sim_output/zdc_photon/epic_zdc_sipm_on_tile_only_rec_zdc_photon_${P}GeV_{0,1,2,3,4}.edm4eic.root
  retry:
    max: 2
    when:

--- a/benchmarks/zdc_pi0/config.yml
+++ b/benchmarks/zdc_pi0/config.yml
@@ -9,7 +9,7 @@ sim:zdc_pi0:
      - P: 130
      - P: 160
  script:
-    - snakemake --cores 5 sim_output/zdc_pi0/epic_zdc_sipm_on_tile_only_rec_zdc_pi0_${P}GeV_{0,1,2,3,4}.edm4eic.root
+    - snakemake $SNAKEMAKE_FLAGS --cores 5 sim_output/zdc_pi0/epic_zdc_sipm_on_tile_only_rec_zdc_pi0_${P}GeV_{0,1,2,3,4}.edm4eic.root
  retry:
    max: 2
    when:

--- a/benchmarks/zdc_sigma/config.yml
+++ b/benchmarks/zdc_sigma/config.yml
@@ -12,7 +12,7 @@ sim:zdc_sigma:
      - P: 250
      - P: 275
  script:
-    - snakemake --cores 5 sim_output/zdc_sigma/epic_zdc_sipm_on_tile_only_rec_sigma_dec_${P}GeV_{0,1,2,3,4}.edm4eic.root
+    - snakemake $SNAKEMAKE_FLAGS --cores 5 sim_output/zdc_sigma/epic_zdc_sipm_on_tile_only_rec_sigma_dec_${P}GeV_{0,1,2,3,4}.edm4eic.root
  retry:
    max: 2
    when:
@@ -23,7 +23,7 @@ bench:zdc_sigma:
  stage: benchmarks
  needs: ["sim:zdc_sigma"]
  script:
-    - snakemake --cores 1 results/epic_zdc_sipm_on_tile_only/zdc_sigma
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 results/epic_zdc_sipm_on_tile_only/zdc_sigma

 collect_results:zdc_sigma:
  extends: .det_benchmark
@@ -32,5 +32,5 @@ collect_results:zdc_sigma:
  script:
    - ls -al
    - mv results{,_save}/ # move results directory out of the way to preserve it
-    - snakemake --cores 1 --delete-all-output results/epic_zdc_sipm_on_tile_only/zdc_sigma
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 --delete-all-output results/epic_zdc_sipm_on_tile_only/zdc_sigma
    - mv results{_save,}/