# Bumps Options¶

Bumps has a number of options available to control the fits and the output. On the command line, each option is either –option if it is True/False or –option=value if the option takes a value. The fit control form is used by graphical users interfaces to set the optimizer and its controls and stopping conditions. The long form name of the the option will be used on the form. Not all controls will appear on the form, and will be set from the command line.

Need to describe the array of output files produced by optimizers, particularly dream. Some of them (convergence plot, model plot, par file, model file) are common to all. Others (mcmc points) are specific to one optimizer

## Bumps Command Line¶

Usage:

bumps [options] modelfile [modelargs]


The modelfile is a Python script (i.e., a series of Python commands) which sets up the data, the models, and the fittable parameters. The model arguments are available in the modelfile as sys.argv[1:]. Model arguments may not start with ‘-’. The options all start with ‘-’ and can appear in any order anywhere on the command line.

## Problem Setup¶

### --pars¶

Set initial parameter values from a previous fit. The par file is a list of lines with parameter name followed by parameter value on each line. The parameters must appear with the same name and in the same order as the fitted parameters in the model. Additional parameters are ignored. Missing parameters are filled using LHS. --preview will show the model parameters.

### --shake¶

Set random initial values for the parameters in the model. Note that shake happens after --simulate so that you can simulate a random model, shake it, then try to recover its initial values.

### --simulate¶

Simulate a dataset using the initial problem parameters. This is useful when setting up a model before an experiment to see what data it might produce, and for seeing how well the fitting program might recover the parameters of interest.

### --simrandom¶

Simulate a dataset using random initial parameters. Because --shake is applied after --simulate, we need a separate way to shake the parameters before simulating the model.

### --noise¶

Set the noise percentage on the simulated data. The default is 5 for 5% normally distributed uncertainty in the measured values. Use --noise=data to use the uncertainty on a dataset in the simulation.

### --seed¶

Set a specific seed to the random number generator. This happens before shaking and simulating so that fitting tests, and particularly failures, can be reliably reproduced. The numpy random number generator is used for all values, so any consistency guarantees between versions of bumps over time and across platforms depends on the consistency of the numpy generators. If no seed is specified then one will be generated and printed so that the fit can be rerun with the same random sequence.

## Stopping Conditions¶

### --steps¶

Steps is the number of iterations that the algorithm will perform. The meaning of iterations will differ from optimizer to optimizer. In the case of population based optimizers such as Differential Evolution, each step is an update to every member of the population. For local descent optimizers such as Nelder-Mead Simplex each step is an iteration of the algorithm. DREAM uses steps plus --burn for the total number of iterations.

### --samples¶

Samples sets the number of function evaluations. This is an alternative for setting the number of iterations of the algorithm, used when --steps is zero. Population optimizers perform --pop times the number of parameters in the fit for each step of the operation, so given the desired number of samples, you can control the number of steps. The number of samples is particularly convenient for DREAM (the only optimizer for which it is implemented at the moment), where 100,000 samples are needed to estimate the 1-sigma interval to 2 digits of accuracy (assuming an approximately gaussian distribution), and 1,000,000 samples are needed for the 95% confidence interval. Like --steps, the total evaluations does not include any --burn iterations.

### --ftol¶

f(x) tolerance uses differences in the function value to decide when the fit is complete. The different fitters will interpret this in different ways. The Newton descent algorithms (Quasi-Newton BFGS, Levenberg-Marquardt) will use this as the minimum improvement of the function value with each step. The population-based algorithms (Differential Evolution, Nelder-Mead Simplex) will use the maximum difference between highest and lowest value in the population. DREAM does not use this stopping condition.

### --xtol¶

x tolerance uses differences in the parameter value to decide when the fit is complete. The different fitters will interpret this in different ways. The Newton descent algorithms (Quasi-Newton BFGS, Levenberg-Marquardt) will use this as the minimum change in the parameter values with each step. The population-based algorithgms (Differential Evolution, Nelder-Mead Simplex) will use the maximum difference between highest and lowest parameter in the population. DREAM does not use this stopping condition.

### --time¶

Max time is the maximum running time of the optimizer. This forces the optimizer to stop even if tolerance or steps conditions are not met. It is particularly useful for batch jobs run in an environment where the queuing system stops the job unceremoniously when the time allocation is complete. Time is checked between iterations, so be sure to set it well below the queue allocation so that it does not stop in the middle of an iteration, and so that it has time to save its state.

### --alpha¶

Convergence is the test criterion to use when deciding if stopping conditions are met. This is for the variety of stopping tests built into the DREAM algorithm. Usual values are –alpha=0.01 or –alpha=0.05. Note that various stopping criteria depend on the the number samples and the chain length (where chain length x #pars x #pop = #samples), so there is no definitive value to use for alpha, but larger values will allow the fit to stop sooner.

## Optimizer Controls¶

### --fit¶

Fit Algorithm selects the optimizer. The available optimizers are:

 amoeba Nelder-Mead Simplex de Differential Evolution dream DREAM lm Levenberg-Marquardt newton Quasi-Newton BFGS pt Parallel Tempering ps Particle Swarm rl Random Lines

The default fit method is --fit=amoeba.

### --pop¶

Population determines the size of the population. For Differential Evolution and DREAM it is a scale factor, where the number of individuals, $$k$$, is equal to the number of fitted parameters times pop. For Nelder-Mead Simplex the number of individuals is one plus the number of fitted parameters, as determined by the size of the simplex.

### --init¶

Initializer is used by population-based algorithms (DREAM) to set the initial population. The options are as follows:

lhs (latin hypersquare), which chops the bounds within each dimension in $$k$$ equal sized chunks where $$k$$ is the size of the population and makes sure that each parameter has at least one value within each chunk across the population.

eps (epsilon ball), in which the entire initial population is chosen at random from within a tiny hypersphere centered about the initial point

cov (covariance matrix), in which the uncertainty is estimated using the covariance matrix at the initial point, and points are selected at random from the corresponding gaussian ellipsoid

rand (uniform random), in which the points are selected at random within the bounds of the parameters

Nelder-Mead Simplex uses --radius to initialize its simplex. Differential Evolution uses a random number from the prior distribution for the parameter, if any.

### --burn¶

Burn-in Steps is the number of iterations to required for the Markov chain to converge to the equilibrium distribution. If the fit ends early, the tail of the burn will be saved to the start of the steps. DREAM uses burn plus steps as the total number of iterations to run.

### --thin¶

Thinning is used by the Markov chain analysis to give samples time to wander to different points in parameter space. In an ideal chain, there would be no correlation between points in the chain other than that which is dictated by the equilibrium distribution. However, if the space has complicated boundaries and taking a step can easily lead to a highly improbable point, then the chain may be stuck at the same value for long periods of time. If this is observed, then thinning can be used to only keep every $$n^\text{th}$$ step, giving the saved chain a better opportunity for good mixing.

### --CR¶

Crossover ratio indicates the proportion of mixing which occurs with each iteration. This is a value in [0,1] giving the probability that each individual dimension will be selected for update in the next generation.

### --outliers¶

Outliers is used to identify chains that are stuck in high local minima during dream burn-in. Options are:

• iqr: Use the interquartile range to determine the width of the distribution then exclude all chains whose log likelihood is more that two standard deviations below the first quartile.
• grubbs: Use a t-test to determine whether the samples in each chain are significantly different from the mean.
• mahal: Use the mahalanobis distance to determine whether the lowest probability chain is close to the remaining chain in parameter space. Only this chain will be marked as an outlier if the test fails.
• none: Don’t do any outlier trimming.

The default is --outliers=none. Outlier removal occurs every $$2n$$ steps where $$n$$ is #samples/(#pars #pop), or when the convergence test indicates the chains are stable.

Note that outliers are marked at the end of the fit using IQR and not included in the statistics, though they are saved in the MCMC files. This is independent of the --outliers setting.

### --F¶

Scale is a factor applied to the difference vector before adding it to the parent in differential evolution.

### --radius¶

Simplex radius is the radius of the initial simplex in Nelder-Mead Simplex

### --nT¶

# Temperatures is the number of temperature chains to run using parallel tempering. Default is 25.

### --Tmin¶

Min temperature is the minimum temperature in the log-spaced series of temperatures to run using parallel tempering. Default is 0.1.

### --Tmax¶

Max temperature is the maximum temperature in the log-spaced series of temperatures to run using parallel tempering. Default is 10.

### --starts¶

Starts is the number of times to run the fit from random starting points.

### --keep_best¶

If Keep best is set, then the each subsequent restart for the multi-start fitter keeps the best value from the previous fit(s).

## Execution Controls¶

### --store¶

Directory in which to store the results of the fit. Fits produce multiple files and plots. Rather than cluttering up the current directory, all the outputs are written to the store directory along with a copy of the model file.

### --overwrite¶

If the store directory already exists then you need to include overwrite on the command line to reuse it. While inconvenient, this prevents accidental overwriting of fits that may have taken hours to generate.

### --checkpoint¶

Save fit state every --checkpoint=n hours. [dream only]

### --resume¶

Continue fit from a previous store directory. Use --resume or --resume=- to reuse the existing store directory.

### --parallel¶

Run fit using multiprocessing for parallelism. Use “–parallel=0” for all CPUs or “–parallel=n” for only “n” CPUs.

### --mpi¶

Run fit using MPI for parallelism. Use command “mpirun -n cpus …” to run bumps for MPI. This will usually be the last line of a queue submission script. Be sure to include --time=... to limit the fit to run within the queue allocation time.

### --batch¶

Run fit in batch mode. Progress updates are sent to STORE/MODEL.mon, and can be monitored using tail -f (unix, mac). When the fit is complete, the plot png files are created as usual, but the interactive plots are not shown. This allows you to set up a sequence of runs in a shell script where the first run completes before the next run starts. Batch is also useful for cluster computing where the cluster nodes do not have access to the outside network and can’t display an interactive window. Batch is automatic when running with --mpi.

### --stepmon¶

Create a log file tracking each point examined during the fit. This does not provide any real utility except for generating plots of the population over time, which can be useful for understanding the different fitting methods.

## Output Controls¶

### --err¶

Show uncertainties at the end of the fit using the square root of the diagonals of the covariance matrix. See --cov.

### --cov¶

Compute the covariance matrix for the model at the minimum. With gaussian uncertainties on the data, bumps is minimizing the sum of squares, so the Jacobian matrix is used for the covariance, formed from the numerical derivative of each residual with respect to each parameter. If the likelihood function is not a simple sum of squared residuals, then the Hessian matrix is used for the covariance, formed from the numerical derivative of the likelihood with respect to pairs of parameters.

### --entropy¶

Calculate entropy is a flag which indicates whether entropy should be computed for the final fit. Entropy an estimate of the number of bits of information available from the fit. Use “–entropy=method” to specify the entropy calcualation method. This can be one of:

• gmm: fit sample to a gaussian mixture model (GMM) with $$5 \sqrt{d}$$ components where $$d$$ is the number fitted parameters and estimate entropy by sampling from the GMM.
• llf: estimates likelihood scale factor from ratio of density estimate to model likelihood, then computes Monte Carlo entropy from sample; this does not work for marginal likelihood estimates. DOI:10.1109/CCA.2010.5611198
• mvn: fit sample to a multi-variate Gaussian and return the entropy of the best fit gaussian; uses bootstrap to estimate uncertainty. This method is only valid if the sample distribution is approximately Gaussian.
• wnn: estimate entropy from weighted nearest-neighbor distances in sample. Note: use with caution. The results from this implementation are not consistent with other methods. DOI:10.1214/18-AOS1688

### --plot¶

For problems that have different view options for plotting, select the default option to display. For example, when fitting a power law to a dataset, you may want to choose log or linear as the output plot type.

### --trim¶

Burn-in trim finds the “burn point” after which the DREAM Markov chains appear to have converged and ignores all points before it when plotting or computing covariance and entropy. The trimmed points are still written to the MCMC output files so they will be available when the fit is resumed. Use --trim=true to set trimming.

### --noshow¶

No show suppresses the plot window after the fit. This is done automatically when --batch is selected.

## Bumps Controls¶

### --preview¶

If the command contains preview then display model but do not perform a fitting operation. Use this to see the initial model before running a fit. It will also show the fit range.

### --chisq¶

If the command contains chisq then show $$\chi^2$$ and exit. Use this to check that the model does not have any syntax errors.

### --resynth¶

Run a resynth uncertainty analysis on the model. After finding a good minimum, you can rerun bumps with:

bumps –store=T1 –pars=T1/model.par –fit=amoeba –resynth=20 model.py

This will generate 20 data simulated datasets using the initial data values as the mean and the data uncertainty as the standard deviation. Each of these datasets will be fit with the specified optimizer, and the resulting parameters saved in T1/model.rsy. On completion, the parameter values can be loaded into python and averaged or histogrammed.

### --time_model¶

Run the model --steps times and find the average run time per step. If --parallel is used, then the models will be run in parallel.

### --profile¶

Run the model --steps times using the python profiler. This can be useful for identifying slow parts of your model definition, or alternatively, finding out that the model runtime is smaller than the Bumps overhead. Use a larger value of steps for better statistics.

## Special Options¶

### --edit¶

If the command contains edit then start the Bumps user interface so that you can interact with the model, adjusting fitted parameters with a slider and seeing how they impact the result.

### --help, -h, -?¶

Use -?, -h or --help to show a brief description of each command line option.

### -i, -m, -c, -p¶

The bumps program can be used as a python interpreter with numpy, scipy, matplotlib and bumps packages available. This is useful if you do not have python set up on your system, and you are using a bundled executable like Bumps or Refl1D on windows. Even if you have python, you may want to run the bumps post-analysis scripts through the bumps command which already has the appropriate path set up to bumps on your system.

The options are:

• -i: run an interactive interpreter.
• -m package.module: run a module as main. This is similar to python -m package.module with the python interpreter.
• -c expression: run a python command and quit.
• -p script.py`: run a python script.