PyTensor Problem with PyMC-BART in Google Colab?

[thedarredondo]

Short Description

Hi all,

I'm trying to run the first BART model example from Bayesian Analysis with Python in Google Colab.

I'm getting some errors that I think are related to pytensor? I'm an absolute novice, so I have no idea.

When I run the following:

with pm.Model() as model_pen:
    σ = pm.HalfNormal("σ", 1)
    μ = pmb.BART("μ", X, Y, m=50)
    y = pm.Normal("y", mu=μ, sigma=σ, observed=Y)
    idata_pen = pm.sample()

I get a long series of errors. One in particular sorta repeats for while. See below.

---

/usr/local/lib/python3.10/site-packages/pytensor/tensor/random/op.py:84: FutureWarning: ndim_supp is deprecated. Provide signature instead. warnings.warn( /usr/local/lib/python3.10/site-packages/pytensor/tensor/random/op.py:94: FutureWarning: ndims_params is deprecated. Provide signature instead. warnings.warn( ERROR (pytensor.graph.rewriting.basic): Rewrite failure due to: constant_folding ERROR (pytensor.graph.rewriting.basic): node: Cast{float32}(1) ERROR (pytensor.graph.rewriting.basic): TRACEBACK: ERROR (pytensor.graph.rewriting.basic): Traceback (most recent call last): File "/usr/local/lib/python3.10/site-packages/pytensor/graph/rewriting/basic.py", line 1909, in process_node replacements = node_rewriter.transform(fgraph, node) File "/usr/local/lib/python3.10/site-packages/pytensor/graph/rewriting/basic.py", line 1081, in transform return self.fn(fgraph, node) File "/usr/local/lib/python3.10/site-packages/pytensor/tensor/rewriting/basic.py", line 1121, in constant_folding thunk = node.op.make_thunk(node, storage_map, compute_map, no_recycling=[]) File "/usr/local/lib/python3.10/site-packages/pytensor/link/c/op.py", line 119, in make_thunk return self.make_c_thunk(node, storage_map, compute_map, no_recycling) File "/usr/local/lib/python3.10/site-packages/pytensor/link/c/op.py", line 84, in make_c_thunk outputs = cl.make_thunk( File "/usr/local/lib/python3.10/site-packages/pytensor/link/c/basic.py", line 1182, in make_thunk cthunk, module, in_storage, out_storage, error_storage = self.compile( File "/usr/local/lib/python3.10/site-packages/pytensor/link/c/basic.py", line 1103, in compile thunk, module = self.cthunk_factory( File "/usr/local/lib/python3.10/site-packages/pytensor/link/c/basic.py", line 1627, in cthunk_factory module = cache.module_from_key(key=key, lnk=self) File "/usr/local/lib/python3.10/site-packages/pytensor/link/c/cmodule.py", line 1255, in module_from_key module = lnk.compile_cmodule(location) File "/usr/local/lib/python3.10/site-packages/pytensor/link/c/basic.py", line 1528, in compile_cmodule module = c_compiler.compile_str( File "/usr/local/lib/python3.10/site-packages/pytensor/link/c/cmodule.py", line 2654, in compile_str raise CompileError( pytensor.link.c.exceptions.CompileError: Compilation failed (return status=1): /usr/local/bin/g++ -shared -g -O3 -fno-math-errno -Wno-unused-label -Wno-unused-variable -Wno-write-strings -Wno-c++11-narrowing -fno-exceptions -fno-unwind-tables -fno-asynchronous-unwind-tables -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -m64 -fPIC -I/usr/local/lib/python3.10/dist-packages/numpy/core/include -I/usr/include/python3.10 -I/usr/local/lib/python3.10/site-packages/pytensor/link/c/c_code -L/usr/lib/x86_64-linux-gnu -L/usr/lib -fvisibility=hidden -o /root/.pytensor/compiledir_Linux-6.1.85+-x86_64-with-glibc2.35-x86_64-3.10.12-64/tmpa484ve2i/mbb1a558a69b3834cbd8bb5160f53dcb1edcf00af31190d19c71508ba0bcc380a.so /root/.pytensor/compiledir_Linux-6.1.85+-x86_64-with-glibc2.35-x86_64-3.10.12-64/tmpa484ve2i/mod.cpp -lpython3.10 In file included from /usr/include/python3.10/Python.h:8, from /root/.pytensor/compiledir_Linux-6.1.85+-x86_64-with-glibc2.35-x86_64-3.10.12-64/tmpa484ve2i/mod.cpp:1: /usr/include/python3.10/pyconfig.h:3:12: fatal error: x86_64-linux-gnu/python3.10/pyconfig.h: No such file or directory 3 | # include <x86_64-linux-gnu/python3.10/pyconfig.h> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated.

---

There's lots of other stuff, but here' the final error message:

---

ImportError: Version check of the existing lazylinker compiled file. Looking for version 0.212, but found None. Extra debug information: force_compile=False, _need_reload=True

During handling of the above exception, another exception occurred:

CompileError Traceback (most recent call last) /usr/local/lib/python3.10/site-packages/pytensor/link/c/cmodule.py in compile_str(module_name, src_code, location, include_dirs, lib_dirs, libs, preargs, py_module, hide_symbols) 2652 # difficult to read. 2653 # compile_stderr = compile_stderr.replace("\n", ". ") -> 2654 raise CompileError( 2655 f"Compilation failed (return status={status}):\n{' '.join(cmd)}\n{compile_stderr}" 2656 )

CompileError: Compilation failed (return status=1): /usr/local/bin/g++ -shared -g -Wno-c++11-narrowing -fno-exceptions -fno-unwind-tables -fno-asynchronous-unwind-tables -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -m64 -fPIC -I/usr/local/lib/python3.10/dist-packages/numpy/core/include -I/usr/include/python3.10 -I/usr/local/lib/python3.10/site-packages/pytensor/link/c/c_code -L/usr/lib/x86_64-linux-gnu -L/usr/lib -fvisibility=hidden -o /root/.pytensor/compiledir_Linux-6.1.85+-x86_64-with-glibc2.35-x86_64-3.10.12-64/lazylinker_ext/lazylinker_ext.so /root/.pytensor/compiledir_Linux-6.1.85+-x86_64-with-glibc2.35-x86_64-3.10.12-64/lazylinker_ext/mod.cpp -lpython3.10 In file included from /usr/include/python3.10/Python.h:8, from /usr/local/lib/python3.10/site-packages/pytensor/link/c/c_code/pytensor_mod_helper.h:4, from /root/.pytensor/compiledir_Linux-6.1.85+-x86_64-with-glibc2.35-x86_64-3.10.12-64/lazylinker_ext/mod.cpp:1: /usr/include/python3.10/pyconfig.h:3:12: fatal error: x86_64-linux-gnu/python3.10/pyconfig.h: No such file or directory 3 | # include <x86_64-linux-gnu/python3.10/pyconfig.h> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated.

---

Sorry for including so much text, but these errors are all way above my understanding, and I don't know what's relevant. Maybe the problem is colab? As in, I might not have the appropriate version of some library?

Anyway, all of my code is below.

All my code

#downloads conda
!pip install -q condacolab
import condacolab
condacolab.install()

#makes sure I have pymc v5
!conda install -c conda-forge "pymc>=5"

#bleeding edge pymc_bart
!pip install git+https://github.com/pymc-devs/pymc-bart.git

import arviz as az
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import pymc as pm
import pymc_bart as pmb

#data
penguins = pd.read_csv("https://raw.githubusercontent.com/thedarredondo/data-science-fundamentals/main/Data/penguins.csv").dropna()
Y = penguins["body_mass"]
pen = penguins
pen['sex'] = pen['sex'].replace(['male', 'female'],[0, 1])
pen['species'] = pen['species'].replace(['Adelie', 'Chinstrap', 'Gentoo'],[0, 1, 2])
X = pen[["flipper_length", "bill_depth", "bill_length"]]

#the textbook example
with pm.Model() as model_pen:
    σ = pm.HalfNormal("σ", 1)
    μ = pmb.BART("μ", X, Y, m=50)
    y = pm.Normal("y", mu=μ, sigma=σ, observed=Y)
    idata_pen = pm.sample()