Short summary of the problem:
An error occurs when trying to build HTML or PDF examples, either with make or manually with Quarto.
- List item
code_to_run_your_model(if_applicable):
bob@dana:~/stan-getting-started$ make
quarto render quarto/stan-getting-started.qmd --to html --no-execute-daemon
Starting python3 kernel...Done
Executing 'stan-getting-started.quarto_ipynb'
Cell 1/52: ''...Done
Cell 2/52: ''...
An error occurred while executing the following cell:
------------------
N = 100
theta = 0.3
data = {'N': N, 'theta': theta}
model = csp.CmdStanModel(stan_file = '../stan/binomial-rng.stan')
sample = model.sample(data = data, seed = 123, chains = 1,
iter_sampling = 10, iter_warmup = 0,
show_progress = False, show_console = False)
------------------
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
Cell In[2], line 5
3 data = {'N': N, 'theta': theta}
4 model = csp.CmdStanModel(stan_file = '../stan/binomial-rng.stan')
----> 5 sample = model.sample(data = data, seed = 123, chains = 1,
6 iter_sampling = 10, iter_warmup = 0,
7 show_progress = False, show_console = False)
File ~/.local/lib/python3.13/site-packages/cmdstanpy/model.py:1039, in CmdStanModel.sample(self, data, chains, parallel_chains, threads_per_chain, seed, chain_ids, inits, iter_warmup, iter_sampling, save_warmup, thin, max_treedepth, metric, step_size, adapt_engaged, adapt_delta, adapt_init_phase, adapt_metric_window, adapt_step_size, fixed_param, output_dir, sig_figs, save_latent_dynamics, save_profile, show_progress, show_console, refresh, time_fmt, timeout, force_one_process_per_chain)
1036 else:
1037 cmdstan_inits = _inits
-> 1039 args = CmdStanArgs(
1040 self._name,
1041 self._exe_file,
1042 chain_ids=chain_ids,
1043 data=_data,
1044 seed=seed,
1045 inits=cmdstan_inits,
1046 output_dir=output_dir,
1047 sig_figs=sig_figs,
1048 save_latent_dynamics=save_latent_dynamics,
1049 save_profile=save_profile,
1050 method_args=sampler_args,
1051 refresh=refresh,
1052 )
1054 if show_console:
1055 show_progress = False
File ~/.local/lib/python3.13/site-packages/cmdstanpy/cmdstan_args.py:797, in CmdStanArgs.__init__(self, model_name, model_exe, chain_ids, method_args, data, seed, inits, output_dir, sig_figs, save_latent_dynamics, save_profile, refresh)
793 else:
794 raise ValueError(
795 'Unsupported method args type: {}'.format(type(method_args))
796 )
--> 797 self.method_args.validate(len(chain_ids) if chain_ids else None)
798 self.validate()
File ~/.local/lib/python3.13/site-packages/cmdstanpy/cmdstan_args.py:143, in SamplerArgs.validate(self, chains)
138 raise ValueError(
139 'Value for iter_warmup must be a non-negative integer,'
140 ' found {}.'.format(self.iter_warmup)
141 )
142 if self.iter_warmup == 0 and self.adapt_engaged:
--> 143 raise ValueError(
144 'Must specify iter_warmup > 0 when adapt_engaged=True.'
145 )
146 if self.iter_sampling is not None:
147 if self.iter_sampling < 0 or not isinstance(
148 self.iter_sampling, (int, np.integer)
149 ):
ValueError: Must specify iter_warmup > 0 when adapt_engaged=True.
make: *** [makefile:2: quarto/stan-getting-started.html] Error 1
If possible, add also code to simulate data or attach a (subset of) the dataset you work with.
Please provide this additional information in addition to your question:
- Operating System: Fedora 41
- CmdStan Version: cmdstan-2.35.0
- Compiler/Toolkit: gcc 14.2.1
Looking forward to your topic!