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Merged
KSkwarczynski merged 4 commits into from
Nov 11, 2026
+5 −5
Merged

standardise the order of config argument first #313

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412543b
standardise the order of config argument first
alexanderrichards Nov 4, 2026
4e11525
update mach3 diag instruction in readme for new order
Charlotte-Knight Nov 10, 2026
7e8916a
Update CLI validation commands for new subcommand names
alexanderrichards Nov 11, 2026
9a925d0
Update MCMC diagnostic command in README
alexanderrichards Nov 11, 2026
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8 changes: 4 additions & 4 deletions CIValidations/MaCh3CLI
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Expand Up @@ -47,12 +47,12 @@ run_fitter_validations() {
${MaCh3Tutorial_ROOT}/CIValidations/FitterValidations
${MaCh3_ROOT}/bin/ProcessMCMC ${MaCh3Tutorial_ROOT}/bin/TutorialDiagConfig.yaml MCMC_Test.root
# Chain diagnostic
${MaCh3_ROOT}/bin/DiagMCMC MCMC_Test.root ${MaCh3Tutorial_ROOT}/bin/TutorialDiagConfig.yaml
${MaCh3_ROOT}/bin/DiagMCMC ${MaCh3Tutorial_ROOT}/bin/TutorialDiagConfig.yaml MCMC_Test.root
${MaCh3_ROOT}/bin/RHat 2 MCMC_Test.root MCMC_Test.root MCMC_Test.root MCMC_Test.root
${MaCh3_ROOT}/bin/RHat_HighMem 10 MCMC_Test.root MCMC_Test.root MCMC_Test.root MCMC_Test.root
${MaCh3_ROOT}/bin/PlotMCMCDiag MCMC_Test_MCMC_Diag.root "test_plot_1" MCMC_Test_MCMC_Diag.root "test_plot_2"
${MaCh3_ROOT}/bin/CombineMaCh3Chains -o MergedChain.root MCMC_Test.root MCMC_Test.root MCMC_Test.root MCMC_Test.root
${MaCh3_ROOT}/bin/GetPenaltyTerm MCMC_Test.root ${MaCh3Tutorial_ROOT}/bin/TutorialDiagConfig.yaml
${MaCh3_ROOT}/bin/GetPenaltyTerm ${MaCh3Tutorial_ROOT}/bin/TutorialDiagConfig.yaml MCMC_Test.root
# Fancy plotting
${MaCh3_ROOT}/bin/MatrixPlotter ${MaCh3Tutorial_ROOT}/bin/TutorialDiagConfig.yaml MCMC_Test_drawCorr.root
${MaCh3_ROOT}/bin/GetPostfitParamPlots MCMC_Test_drawCorr.root
Expand Down Expand Up @@ -157,8 +157,8 @@ run_multicanoical_validations() {
run_CLI_validations() {
mach3 tutorial TutorialConfigs/FitterConfig.yaml --MCMCSteps 10000
mach3 process ${MaCh3Tutorial_ROOT}/bin/TutorialDiagConfig.yaml Test.root --corr --MakeCredibleIntervals
mach3 diag Test.root ${MaCh3Tutorial_ROOT}/bin/TutorialDiagConfig.yaml
mach3 penterm Test.root ${MaCh3Tutorial_ROOT}/bin/TutorialDiagConfig.yaml
mach3 diagnostics mcmc ${MaCh3Tutorial_ROOT}/bin/TutorialDiagConfig.yaml Test.root
mach3 penaltyterm ${MaCh3Tutorial_ROOT}/bin/TutorialDiagConfig.yaml Test.root
}


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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -658,7 +658,7 @@ The latter class deals with actual event reweighting and general heavy lifting.
## MCMC Diagnostic
A crucial part of MCMC is diagnosing whether a chain has converged or not. You can produce chain diagnostics by running:
```bash
mach3 diag Test.root bin/TutorialDiagConfig.yaml
mach3 diagnostics mcmc bin/TutorialDiagConfig.yaml Test.root
```
This will produce a plethora of diagnostic information. One of most important of these are the autocorrelations for each of the parameters. Autocorrelation indicates how correlated MCMC steps are when they are n-steps apart in the chain.
Generally speaking, we want the autocorrelation to drop to 0 fast and stay around there (like in the plot below). You can read about other diagnostics [here](https://mach3-software.github.io/MaCh3/MCMCconvergance.html), but it is sufficient for now to focus on autocorrelation.
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