MLIR translation rule for primitive ‘celerite2_factor’ not found for platform cuda

[connorourke]

I'm having an issue running a numpyro model with celerite2:

Trying to run one of the examples on the celerite2 docs:

from jax import config

config.update("jax_enable_x64", True)

from jax import random
import jax.numpy as jnp

import numpyro
import numpyro.distributions as dist
from numpyro.infer import MCMC, NUTS

import celerite2.jax
from celerite2.jax import terms as jax_terms

import numpy as np

np.random.seed(42)

t = np.sort(
    np.append(
        np.random.uniform(0, 3.8, 57),
        np.random.uniform(5.5, 10, 68),
    )
)  # The input coordinates must be sorted
yerr = np.random.uniform(0.08, 0.22, len(t))
y = (
    0.2 * (t - 5)
    + np.sin(3 * t + 0.1 * (t - 5) ** 2)
    + yerr * np.random.randn(len(t))
)

true_t = np.linspace(0, 10, 500)
true_y = 0.2 * (true_t - 5) + np.sin(3 * true_t + 0.1 * (true_t - 5) ** 2)
prior_sigma = 2.0



def numpyro_model(t, yerr, y=None):
    mean = numpyro.sample("mean", dist.Normal(0.0, prior_sigma))
    log_jitter = numpyro.sample("log_jitter", dist.Normal(0.0, prior_sigma))

    log_sigma1 = numpyro.sample("log_sigma1", dist.Normal(0.0, prior_sigma))
    log_rho1 = numpyro.sample("log_rho1", dist.Normal(0.0, prior_sigma))
    log_tau = numpyro.sample("log_tau", dist.Normal(0.0, prior_sigma))
    term1 = jax_terms.SHOTerm(
        sigma=jnp.exp(log_sigma1), rho=jnp.exp(log_rho1), tau=jnp.exp(log_tau)
    )

    log_sigma2 = numpyro.sample("log_sigma2", dist.Normal(0.0, prior_sigma))
    log_rho2 = numpyro.sample("log_rho2", dist.Normal(0.0, prior_sigma))
    term2 = jax_terms.SHOTerm(
        sigma=jnp.exp(log_sigma2), rho=jnp.exp(log_rho2), Q=0.25
    )

    kernel = term1 + term2
    gp = celerite2.jax.GaussianProcess(kernel, mean=mean)
    gp.compute(t, diag=yerr**2 + jnp.exp(log_jitter), check_sorted=False)

    numpyro.sample("obs", gp.numpyro_dist(), obs=y)
    numpyro.deterministic("psd", kernel.get_psd(omega))


nuts_kernel = NUTS(numpyro_model, dense_mass=True)
mcmc = MCMC(
    nuts_kernel,
    num_warmup=1000,
    num_samples=1000,
    num_chains=2,
    progress_bar=False,
)
rng_key = random.PRNGKey(34923)
mcmc.run(rng_key, t, yerr, y=y)

Is throwing the following error when trying to run on the GPU:

Traceback (most recent call last):
  File "/computefs/scratch/username/mypackage/notebooks/temp/test.py", line 16, in <module>
    import matplotlib.pyplot as plt
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/matplotlib/__init__.py", line 264, in <module>
    _check_versions()
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/matplotlib/__init__.py", line 258, in _check_versions
    module = importlib.import_module(modname)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/computefs/ixsoftware/python/3.12.6/install/lib/python3.12/importlib/__init__.py", line 90, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ModuleNotFoundError: No module named 'dateutil'
(.venv_cuda) [username@node10 temp]$ python test.py 
Traceback (most recent call last):
  File "/computefs/scratch/username/mypackage/notebooks/temp/test.py", line 16, in <module>
    import matplotlib.pyplot as plt
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/matplotlib/__init__.py", line 264, in <module>
    _check_versions()
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/matplotlib/__init__.py", line 258, in _check_versions
    module = importlib.import_module(modname)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/computefs/ixsoftware/python/3.12.6/install/lib/python3.12/importlib/__init__.py", line 90, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ModuleNotFoundError: No module named 'dateutil'
(.venv_cuda) [username@node10 temp]$ 
(.venv_cuda) [username@node10 temp]$ python test.py 
/computefs/scratch/username/mypackage/notebooks/temp/test.py:64: UserWarning: There are not enough devices to run parallel chains: expected 2 but got 1. Chains will be drawn sequentially. If you are running MCMC in CPU, consider using `numpyro.set_host_device_count(2)` at the beginning of your program. You can double-check how many devices are available in your system using `jax.local_device_count()`.
  mcmc = MCMC(
Traceback (most recent call last):
  File "/computefs/scratch/username/mypackage/notebooks/temp/test.py", line 72, in <module>
    mcmc.run(rng_key, t, yerr, y=y)
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/numpyro/infer/mcmc.py", line 706, in run
    states, last_state = _laxmap(partial_map_fn, map_args)
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/numpyro/infer/mcmc.py", line 177, in _laxmap
    ys.append(f(x))
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/numpyro/infer/mcmc.py", line 465, in _single_chain_mcmc
    new_init_state = self.sampler.init(
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/numpyro/infer/hmc.py", line 749, in init
    init_params = self._init_state(
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/numpyro/infer/hmc.py", line 693, in _init_state
    ) = initialize_model(
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/numpyro/infer/util.py", line 688, in initialize_model
    ) = _get_model_transforms(substituted_model, model_args, model_kwargs)
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/numpyro/infer/util.py", line 482, in _get_model_transforms
    model_trace = trace(model).get_trace(*model_args, **model_kwargs)
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/numpyro/handlers.py", line 191, in get_trace
    self(*args, **kwargs)
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/numpyro/primitives.py", line 121, in __call__
    return self.fn(*args, **kwargs)
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/numpyro/primitives.py", line 121, in __call__
    return self.fn(*args, **kwargs)
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/numpyro/primitives.py", line 121, in __call__
    return self.fn(*args, **kwargs)
  File "/computefs/scratch/username/mypackage/notebooks/temp/test.py", line 57, in numpyro_model
    gp.compute(t, diag=yerr**2 + jnp.exp(log_jitter), check_sorted=False)
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/celerite2/core.py", line 317, in compute
    self._do_compute(quiet)
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/celerite2/jax/celerite2.py", line 34, in _do_compute
    self._d, self._W = ops.factor(
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/celerite2/jax/ops.py", line 39, in factor
    d, W, S = factor_p.bind(t, c, a, U, V)
jax._src.source_info_util.JaxStackTraceBeforeTransformation: NotImplementedError: MLIR translation rule for primitive 'celerite2_factor' not found for platform cuda

The preceding stack trace is the source of the JAX operation that, once transformed by JAX, triggered the following exception.

--------------------

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/computefs/scratch/username/mypackage/notebooks/temp/test.py", line 72, in <module>
    mcmc.run(rng_key, t, yerr, y=y)
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/numpyro/infer/mcmc.py", line 706, in run
    states, last_state = _laxmap(partial_map_fn, map_args)
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/numpyro/infer/mcmc.py", line 177, in _laxmap
    ys.append(f(x))
              ^^^^
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/numpyro/infer/mcmc.py", line 465, in _single_chain_mcmc
    new_init_state = self.sampler.init(
                     ^^^^^^^^^^^^^^^^^^
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/numpyro/infer/hmc.py", line 749, in init
    init_params = self._init_state(
                  ^^^^^^^^^^^^^^^^^
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/numpyro/infer/hmc.py", line 693, in _init_state
    ) = initialize_model(
        ^^^^^^^^^^^^^^^^^
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/numpyro/infer/util.py", line 688, in initialize_model
    ) = _get_model_transforms(substituted_model, model_args, model_kwargs)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/numpyro/infer/util.py", line 482, in _get_model_transforms
    model_trace = trace(model).get_trace(*model_args, **model_kwargs)
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/numpyro/handlers.py", line 191, in get_trace
    self(*args, **kwargs)
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/numpyro/primitives.py", line 121, in __call__
    return self.fn(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/numpyro/primitives.py", line 121, in __call__
    return self.fn(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/numpyro/primitives.py", line 121, in __call__
    return self.fn(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/computefs/scratch/username/mypackage/notebooks/temp/test.py", line 57, in numpyro_model
    gp.compute(t, diag=yerr**2 + jnp.exp(log_jitter), check_sorted=False)
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/celerite2/core.py", line 317, in compute
    self._do_compute(quiet)
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/celerite2/jax/celerite2.py", line 34, in _do_compute
    self._d, self._W = ops.factor(
                       ^^^^^^^^^^^
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/celerite2/jax/ops.py", line 39, in factor
    d, W, S = factor_p.bind(t, c, a, U, V)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/jax/_src/core.py", line 438, in bind
    return self.bind_with_trace(find_top_trace(args), args, params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/jax/_src/core.py", line 442, in bind_with_trace
    out = trace.process_primitive(self, map(trace.full_raise, args), params)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/jax/_src/core.py", line 948, in process_primitive
    return primitive.impl(*tracers, **params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/jax/_src/dispatch.py", line 90, in apply_primitive
    outs = fun(*args)
           ^^^^^^^^^^
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/jax/_src/traceback_util.py", line 180, in reraise_with_filtered_traceback
    return fun(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/jax/_src/pjit.py", line 356, in cache_miss
    outs, out_flat, out_tree, args_flat, jaxpr, attrs_tracked = _python_pjit_helper(
                                                                ^^^^^^^^^^^^^^^^^^^^
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/jax/_src/pjit.py", line 189, in _python_pjit_helper
    out_flat = pjit_p.bind(*args_flat, **p.params)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/jax/_src/core.py", line 2781, in bind
    return self.bind_with_trace(top_trace, args, params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/jax/_src/core.py", line 442, in bind_with_trace
    out = trace.process_primitive(self, map(trace.full_raise, args), params)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/jax/_src/core.py", line 948, in process_primitive
    return primitive.impl(*tracers, **params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/jax/_src/pjit.py", line 1764, in _pjit_call_impl
    return xc._xla.pjit(
           ^^^^^^^^^^^^^
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/jax/_src/pjit.py", line 1739, in call_impl_cache_miss
    out_flat, compiled = _pjit_call_impl_python(
                         ^^^^^^^^^^^^^^^^^^^^^^^
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/jax/_src/pjit.py", line 1661, in _pjit_call_impl_python
    compiled = _resolve_and_lower(
               ^^^^^^^^^^^^^^^^^^^
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/jax/_src/pjit.py", line 1628, in _resolve_and_lower
    lowered = _pjit_lower(
              ^^^^^^^^^^^^
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/jax/_src/pjit.py", line 1780, in _pjit_lower
    return _pjit_lower_cached(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/jax/_src/pjit.py", line 1801, in _pjit_lower_cached
    return pxla.lower_sharding_computation(
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/jax/_src/profiler.py", line 333, in wrapper
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/jax/_src/interpreters/pxla.py", line 2232, in lower_sharding_computation
    nreps, tuple_args, shape_poly_state) = _cached_lowering_to_hlo(
                                           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/jax/_src/interpreters/pxla.py", line 1952, in _cached_lowering_to_hlo
    lowering_result = mlir.lower_jaxpr_to_module(
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/jax/_src/interpreters/mlir.py", line 1152, in lower_jaxpr_to_module
    lower_jaxpr_to_fun(
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/jax/_src/interpreters/mlir.py", line 1610, in lower_jaxpr_to_fun
    out_vals, tokens_out = jaxpr_subcomp(
                           ^^^^^^^^^^^^^^
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/jax/_src/interpreters/mlir.py", line 1825, in jaxpr_subcomp
    ans = lower_per_platform(rule_ctx, str(eqn.primitive),
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/computefs/scratch/username/mypackage/notebooks/temp/.venv_cuda/lib/python3.12/site-packages/jax/_src/interpreters/mlir.py", line 1914, in lower_per_platform
    raise NotImplementedError(
NotImplementedError: MLIR translation rule for primitive 'celerite2_factor' not found for platform cuda

is this something that hasnt been properly implemented in celerite2?

Any suggestions on how to get the example to run properly on the GPU?

Thanks

[hawkinsp]

I have to tag @dfm for that :-)