Speedup sample and allow specifying compile_kwargs (several major changes related to step samplers)

[ricardoV94]

Major changes

1. internal uses of logp_dlogp_function now work with raveled inputs. External use will issue a warning unless ravel_inputs is specified explicitly. Eventually it will only be possible to use ravel_inputs=True.
2. Step samplers arguments besides vars must be passed by keyword
3. RaveledVars point_map_info is now a 4-n tuple, with size introduced.
4. assign_step_method does not call instantiate_steppers, but returns arguments needed for the latter.
5. Allow passing compile_kwargs to pm.sample which is then forwarded to the step samplers functions

Enhancement

This PR speedups NUTS (and other step samplers), by:

1. Avoiding many variable unravel and copies, by doing it inside PyTensor
2. Avoiding copies when setting shared variables (borrow=True)
3. Setting trust_input=True which can have a large overhead.
4. Disabling GC collection for the C-backend function (related to Consider disabling PyTensor GC in sampling functions #7539)
5. Using slots for faster attribute access in the Tree class (and smaller footprint)
6. Inlining some functions and being more lazy when possible

This PR speedups sample by:

1. Avoiding way too many pytensor function compilations (model.initial_point() and very silly trace.fn after slicing at the end. It's also silly to compile the same function for every trace. We should just copy it.
2. Avoid initializing NUTS step sampler just for most of the times then immediately discard it and using the one inside init_nuts. This will also reduce the path towards external samplers with nutpie/numpyro as it avoids the costly and useless compilation of the logp_dlogp_function
3. Using trust_input and avoiding deepcopies in the trace function by using pytensor.In(borrow=True) and pytensor.Out(borrow=True).

Further speedups should come for free from #7539, specially for the Numba backend.

Benchmark

In the example below, sampling time is now only 7x slower than nutpie (5s vs 0.7s), compared to 13.5x slower (9.45s vs 0.7s) before. This assuming the same number of logp evals, in fact nutpie tuning allows us to get out with half the evals! We can hopefully bring it over.

Full time until from pm.sample to getting a trace is roughly halved as well (7.5s vs 14.4s), although this gain is not proportional to the number of draws.

With compile_kwargs=(mode="NUMBA"), sampling time is only 3x slower (2.3s).

import time
import pymc as pm
import numpy as np
import nutpie
import pandas as pd

# Load the radon dataset
data = pd.read_csv(pm.get_data("radon.csv"))
data["log_radon"] = data["log_radon"].astype(np.float64)
county_idx, counties = pd.factorize(data.county)
coords = {"county": counties, "obs_id": np.arange(len(county_idx))}

# Create a simple hierarchical model for the radon dataset
with pm.Model(coords=coords, check_bounds=False) as model:
    intercept = pm.Normal("intercept", sigma=10)

    # County effects
    raw = pm.ZeroSumNormal("county_raw", dims="county")
    sd = pm.HalfNormal("county_sd")
    county_effect = pm.Deterministic("county_effect", raw * sd, dims="county")

    # Global floor effect
    floor_effect = pm.Normal("floor_effect", sigma=2)

    # County:floor interaction
    raw = pm.ZeroSumNormal("county_floor_raw", dims="county")
    sd = pm.HalfNormal("county_floor_sd")
    county_floor_effect = pm.Deterministic(
        "county_floor_effect", raw * sd, dims="county"
    )

    mu = (
        intercept
        + county_effect[county_idx]
        + floor_effect * data.floor.values
        + county_floor_effect[county_idx] * data.floor.values
    )

    sigma = pm.HalfNormal("sigma", sigma=1.5)
    pm.Normal(
        "log_radon", mu=mu, sigma=sigma, observed=data.log_radon.values, dims="obs_id"
    )

from pymc.model.transform.optimization import freeze_dims_and_data
model = freeze_dims_and_data(model)

compiled_model = nutpie.compile_pymc_model(model)

start = time.perf_counter()
# More draws to make up for the fact that nutpie tunes better
trace_pymc = nutpie.sample(compiled_model, chains=1, tune=500, draws=1500, progress_bar=False)
end = time.perf_counter()
print(end - start)

idata = pm.sample(
    model=model, 
    chains=1,
    tune=500, 
    draws=500, 
    progressbar=False, 
    compute_convergence_checks=False, 
    return_inferencedata=False,
    # compile_kwargs=dict(mode="NUMBA")
)
print(idata._report.t_sampling)

---

📚 Documentation preview 📚: https://pymc--7578.org.readthedocs.build/en/7578/

[ricardoV94]

10 minutes seem to be saved in pytest CI time compared to previous runs

[codecov]

Codecov Report

Attention: Patch coverage is 94.28571% with 14 lines in your changes missing coverage. Please review.

Project coverage is 92.84%. Comparing base (fe0e0d7) to head (bd232d2).
Report is 82 commits behind head on main.

Files with missing lines	Patch %	Lines
pymc/step_methods/hmc/quadpotential.py	0.00%	8 Missing ⚠️
pymc/sampling/mcmc.py	89.36%	5 Missing ⚠️
pymc/model/core.py	96.15%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #7578      +/-   ##
==========================================
- Coverage   92.84%   92.84%   -0.01%     
==========================================
  Files         106      106              
  Lines       17686    17719      +33     
==========================================
+ Hits        16421    16451      +30     
- Misses       1265     1268       +3     

Files with missing lines	Coverage Δ
pymc/backends/__init__.py	91.89% <100.00%> (+0.22%)	⬆️
pymc/backends/base.py	88.69% <100.00%> (+0.25%)	⬆️
pymc/backends/ndarray.py	80.00% <100.00%> (+0.90%)	⬆️
pymc/blocking.py	97.67% <100.00%> (+1.92%)	⬆️
pymc/pytensorf.py	90.97% <100.00%> (ø)
pymc/sampling/parallel.py	88.73% <100.00%> (-0.12%)	⬇️
pymc/step_methods/arraystep.py	96.10% <100.00%> (+1.43%)	⬆️
pymc/step_methods/hmc/base_hmc.py	91.91% <100.00%> (ø)
pymc/step_methods/hmc/integration.py	84.12% <100.00%> (+2.46%)	⬆️
pymc/step_methods/hmc/nuts.py	97.43% <100.00%> (+0.03%)	⬆️
... and 7 more

... and 1 file with indirect coverage changes

[jessegrabowski]

lgtm, left a few small comments