I have the following PyMC3 code in Python, which are originated from here. In the last line, I got the error RuntimeError: An attempt has been made to start a new process before the current process has finished its bootstrapping phase.
I believe this error is similar to the error in this post. But I don't really understand how to fix the code. I tried to put from distributed import Client or from dask.distributed import progress at the front of my code, but my code still failed. I would just simply get ModuleNotFoundError: No module named 'distributed' or ModuleNotFoundError: No module named 'dask' if I tried to apply those fixes.
How can I get my code work? Thanks.
import numpy as np
import pymc3 as pm3
from scipy.stats import norm
sigma = 3 # Note this is the std of our data
data = norm(10,sigma).rvs(100)
mu_prior = 8
sigma_prior = 1.5 # Note this is our prior on the std of mu
basic_model = pm3.Model()
with basic_model:
# Priors for unknown model parameters
mu = pm3.Normal('Mean of Data',mu_prior,sigma_prior)
# Likelihood (sampling distribution) of observations
data_in = pm3.Normal('Y_obs', mu=mu, sd=sigma, observed=data)
chain_length = 10000
with basic_model:
# obtain starting values via MAP
startvals = pm3.find_MAP(model=basic_model)
print(startvals)
# instantiate sampler
step = pm3.Metropolis()
# draw 5000 posterior samples
trace = pm3.sample(chain_length, step=step, start=startvals)
Updates 1
If I added cores=1 to pm3.sample() at the last line (i.e. suggested by merv in the comment), the error will disappear. And then if I tried to draw the trace plot by pm3.plot_trace(trace,figsize=(20,5)), I will get the warning Got error No model on context stack. trying to find log_likelihood in translation but I will also obtain the trace-plot which looks well. But I have no idea why cores=1 works while cores=2 doesn't.
Besides, if I checked the version:
print(sys.version)
print(pymc3.__version__)
print(theano.__version__)
print(arviz.__version__)
I got
3.9.7 (default, Sep 16 2021, 16:59:28) [MSC v.1916 64 bit (AMD64)]
3.11.4
1.1.2
0.11.4
The Python codes are run in conda environment and my conda version is 4.10.3, installed in my Windows 10 Education version 21H1 (OS build 19043.1348).
Updates 2
Below is what I got after entering my conda environment pymc_env and run conda env export:
channels:
- conda-forge
- http://conda.anaconda.org/gurobi
- defaults
dependencies:
- alabaster=0.7.12=pyhd3eb1b0_0
- appdirs=1.4.4=pyhd3eb1b0_0
- argh=0.26.2=py39haa95532_0
- arrow=0.13.1=py39haa95532_0
- astroid=2.6.6=py39haa95532_0
- async_generator=1.10=pyhd3eb1b0_0
- atomicwrites=1.4.0=py_0
- attrs=21.2.0=pyhd3eb1b0_0
- autopep8=1.5.7=pyhd3eb1b0_0
- babel=2.9.1=pyhd3eb1b0_0
- backcall=0.2.0=pyhd3eb1b0_0
- bcrypt=3.2.0=py39h196d8e1_0
- binaryornot=0.4.4=pyhd3eb1b0_1
- black=19.10b0=py_0
- bleach=4.0.0=pyhd3eb1b0_0
- brotlipy=0.7.0=py39h2bbff1b_1003
- ca-certificates=2021.10.26=haa95532_2
- certifi=2021.10.8=py39haa95532_0
- cffi=1.14.6=py39h2bbff1b_0
- chardet=4.0.0=py39haa95532_1003
- charset-normalizer=2.0.4=pyhd3eb1b0_0
- click=8.0.3=pyhd3eb1b0_0
- cloudpickle=2.0.0=pyhd3eb1b0_0
- colorama=0.4.4=pyhd3eb1b0_0
- cookiecutter=1.7.2=pyhd3eb1b0_0
- cryptography=35.0.0=py39h71e12ea_0
- debugpy=1.4.1=py39hd77b12b_0
- decorator=5.1.0=pyhd3eb1b0_0
- defusedxml=0.7.1=pyhd3eb1b0_0
- diff-match-patch=20200713=pyhd3eb1b0_0
- docutils=0.17.1=py39haa95532_1
- entrypoints=0.3=py39haa95532_0
- expat=2.4.1=h39d44d4_0
- flake8=3.9.2=pyhd3eb1b0_0
- font-ttf-dejavu-sans-mono=2.37=hab24e00_0
- font-ttf-inconsolata=3.000=h77eed37_0
- font-ttf-source-code-pro=2.038=h77eed37_0
- font-ttf-ubuntu=0.83=hab24e00_0
- fontconfig=2.13.1=h1989441_1005
- fonts-conda-ecosystem=1=0
- fonts-conda-forge=1=0
- freetype=2.10.4=h546665d_1
- fribidi=1.0.10=h8d14728_0
- getopt-win32=0.1=h8ffe710_0
- gettext=0.19.8.1=ha2e2712_1008
- graphite2=1.3.13=1000
- graphviz=2.38=hfd603c8_2
- gts=0.7.6=h7c369d9_2
- icu=58.2=ha925a31_3
- idna=3.2=pyhd3eb1b0_0
- imagesize=1.2.0=pyhd3eb1b0_0
- importlib-metadata=4.8.1=py39haa95532_0
- importlib_metadata=4.8.1=hd3eb1b0_0
- inflection=0.5.1=py39haa95532_0
- intel-openmp=2021.4.0=h57928b3_3556
- intervaltree=3.1.0=pyhd3eb1b0_0
- ipykernel=6.4.1=py39haa95532_1
- ipython=7.29.0=py39hd4e2768_0
- ipython_genutils=0.2.0=pyhd3eb1b0_1
- isort=5.9.3=pyhd3eb1b0_0
- jbig=2.1=h8d14728_2003
- jedi=0.18.0=py39haa95532_1
- jinja2=2.11.3=pyhd3eb1b0_0
- jinja2-time=0.2.0=pyhd3eb1b0_2
- jpeg=9d=h8ffe710_0
- jsonschema=3.2.0=pyhd3eb1b0_2
- jupyter_client=6.1.12=pyhd3eb1b0_0
- jupyter_core=4.8.1=py39haa95532_0
- jupyterlab_pygments=0.1.2=py_0
- keyring=23.1.0=py39haa95532_0
- lazy-object-proxy=1.6.0=py39h2bbff1b_0
- lerc=3.0=h0e60522_0
- libblas=3.9.0=12_win64_mkl
- libcblas=3.9.0=12_win64_mkl
- libdeflate=1.8=h8ffe710_0
- libffi=3.4.2=h0e60522_4
- libglib=2.70.0=h3be07f2_1
- libiconv=1.16=he774522_0
- liblapack=3.9.0=12_win64_mkl
- libpng=1.6.37=h1d00b33_2
- libpython=2.1=py39hcbf5309_1
- libspatialindex=1.9.3=h6c2663c_0
- libtiff=4.3.0=hd413186_2
- libwebp=1.2.1=h57928b3_0
- libwebp-base=1.2.1=h8ffe710_0
- libxcb=1.13=hcd874cb_1003
- libxml2=2.9.12=hf5bbc77_1
- libzlib=1.2.11=h8ffe710_1013
- llvmlite=0.37.0=py39ha0cd8c8_0
- lz4-c=1.9.3=h8ffe710_1
- m2w64-binutils=2.25.1=5
- m2w64-bzip2=1.0.6=6
- m2w64-crt-git=5.0.0.4636.2595836=2
- m2w64-gcc=5.3.0=6
- m2w64-gcc-ada=5.3.0=6
- m2w64-gcc-fortran=5.3.0=6
- m2w64-gcc-libgfortran=5.3.0=6
- m2w64-gcc-libs=5.3.0=7
- m2w64-gcc-libs-core=5.3.0=7
- m2w64-gcc-objc=5.3.0=6
- m2w64-gmp=6.1.0=2
- m2w64-headers-git=5.0.0.4636.c0ad18a=2
- m2w64-isl=0.16.1=2
- m2w64-libiconv=1.14=6
- m2w64-libmangle-git=5.0.0.4509.2e5a9a2=2
- m2w64-libwinpthread-git=5.0.0.4634.697f757=2
- m2w64-make=4.1.2351.a80a8b8=2
- m2w64-mpc=1.0.3=3
- m2w64-mpfr=3.1.4=4
- m2w64-pkg-config=0.29.1=2
- m2w64-toolchain=5.3.0=7
- m2w64-tools-git=5.0.0.4592.90b8472=2
- m2w64-windows-default-manifest=6.4=3
- m2w64-winpthreads-git=5.0.0.4634.697f757=2
- m2w64-zlib=1.2.8=10
- markupsafe=1.1.1=py39h2bbff1b_0
- matplotlib-inline=0.1.2=pyhd3eb1b0_2
- mccabe=0.6.1=py39haa95532_1
- mistune=0.8.4=py39h2bbff1b_1000
- mkl=2021.4.0=h0e2418a_729
- mkl-service=2.4.0=py39hb82d6ee_0
- msys2-conda-epoch=20160418=1
- mypy_extensions=0.4.3=py39haa95532_0
- nbclient=0.5.3=pyhd3eb1b0_0
- nbconvert=6.1.0=py39haa95532_0
- nbformat=5.1.3=pyhd3eb1b0_0
- nest-asyncio=1.5.1=pyhd3eb1b0_0
- numba=0.54.1=py39hb8cd55e_0
- numpy=1.20.3=py39h6635163_1
- numpydoc=1.1.0=pyhd3eb1b0_1
- openssl=1.1.1l=h2bbff1b_0
- pandocfilters=1.4.3=py39haa95532_1
- paramiko=2.7.2=py_0
- parso=0.8.2=pyhd3eb1b0_0
- pathspec=0.7.0=py_0
- pcre=8.45=h0e60522_0
- pexpect=4.8.0=pyhd3eb1b0_3
- pickleshare=0.7.5=pyhd3eb1b0_1003
- pip=21.3.1=pyhd8ed1ab_0
- pixman=0.40.0=h8ffe710_0
- pluggy=1.0.0=py39haa95532_0
- poyo=0.5.0=pyhd3eb1b0_0
- prompt-toolkit=3.0.20=pyhd3eb1b0_0
- psutil=5.8.0=py39h2bbff1b_1
- pthread-stubs=0.4=hcd874cb_1001
- ptyprocess=0.7.0=pyhd3eb1b0_2
- pycodestyle=2.7.0=pyhd3eb1b0_0
- pycparser=2.20=py_2
- pydocstyle=6.1.1=pyhd3eb1b0_0
- pyflakes=2.3.1=pyhd3eb1b0_0
- pygments=2.10.0=pyhd3eb1b0_0
- pylint=2.9.6=py39haa95532_1
- pyls-spyder=0.4.0=pyhd3eb1b0_0
- pynacl=1.4.0=py39hbd8134f_1
- pyopenssl=21.0.0=pyhd3eb1b0_1
- pyqt=5.9.2=py39hd77b12b_6
- pyrsistent=0.18.0=py39h196d8e1_0
- pysocks=1.7.1=py39haa95532_0
- python=3.9.7=h6244533_1
- python-dateutil=2.8.2=pyhd3eb1b0_0
- python-graphviz=0.16=pyhd3eb1b0_1
- python-lsp-black=1.0.0=pyhd3eb1b0_0
- python-lsp-jsonrpc=1.0.0=pyhd3eb1b0_0
- python-lsp-server=1.2.4=pyhd3eb1b0_0
- python-slugify=5.0.2=pyhd3eb1b0_0
- python_abi=3.9=2_cp39
- pywin32=228=py39hbaba5e8_1
- pywin32-ctypes=0.2.0=py39haa95532_1000
- pyyaml=6.0=py39h2bbff1b_1
- pyzmq=22.2.1=py39hd77b12b_1
- qdarkstyle=3.0.2=pyhd3eb1b0_0
- qstylizer=0.1.10=pyhd3eb1b0_0
- qt=5.9.7=vc14h73c81de_0
- qtawesome=1.0.2=pyhd3eb1b0_0
- qtconsole=5.1.1=pyhd3eb1b0_0
- qtpy=1.10.0=pyhd3eb1b0_0
- regex=2021.8.3=py39h2bbff1b_0
- requests=2.26.0=pyhd3eb1b0_0
- rope=0.19.0=pyhd3eb1b0_0
- rtree=0.9.7=py39h2eaa2aa_1
- scipy=1.7.1=py39hc0c34ad_0
- setuptools=58.5.3=py39hcbf5309_0
- sip=4.19.13=py39hd77b12b_0
- six=1.16.0=pyh6c4a22f_0
- snowballstemmer=2.1.0=pyhd3eb1b0_0
- sortedcontainers=2.4.0=pyhd3eb1b0_0
- sphinx=4.2.0=pyhd3eb1b0_0
- sphinxcontrib-applehelp=1.0.2=pyhd3eb1b0_0
- sphinxcontrib-devhelp=1.0.2=pyhd3eb1b0_0
- sphinxcontrib-htmlhelp=2.0.0=pyhd3eb1b0_0
- sphinxcontrib-jsmath=1.0.1=pyhd3eb1b0_0
- sphinxcontrib-qthelp=1.0.3=pyhd3eb1b0_0
- sphinxcontrib-serializinghtml=1.1.5=pyhd3eb1b0_0
- spyder=5.1.5=py39haa95532_0
- spyder-kernels=2.1.3=py39haa95532_0
- sqlite=3.36.0=h8ffe710_2
- tbb=2021.4.0=h2d74725_1
- testpath=0.5.0=pyhd3eb1b0_0
- text-unidecode=1.3=pyhd3eb1b0_0
- textdistance=4.2.1=pyhd3eb1b0_0
- three-merge=0.1.1=pyhd3eb1b0_0
- tinycss=0.4=pyhd3eb1b0_1002
- toml=0.10.2=pyhd3eb1b0_0
- tornado=6.1=py39h2bbff1b_0
- traitlets=5.1.0=pyhd3eb1b0_0
- typed-ast=1.4.3=py39h2bbff1b_1
- typing_extensions=3.10.0.2=pyh06a4308_0
- tzdata=2021e=he74cb21_0
- ucrt=10.0.20348.0=h57928b3_0
- ujson=4.0.2=py39hd77b12b_0
- unidecode=1.2.0=pyhd3eb1b0_0
- urllib3=1.26.7=pyhd3eb1b0_0
- vc=14.2=hb210afc_5
- vs2015_runtime=14.29.30037=h902a5da_5
- watchdog=2.1.3=py39haa95532_0
- wcwidth=0.2.5=pyhd3eb1b0_0
- webencodings=0.5.1=py39haa95532_1
- wheel=0.37.0=pyhd8ed1ab_1
- whichcraft=0.6.1=pyhd3eb1b0_0
- win_inet_pton=1.1.0=py39haa95532_0
- wrapt=1.12.1=py39h196d8e1_1
- xorg-kbproto=1.0.7=hcd874cb_1002
- xorg-libice=1.0.10=hcd874cb_0
- xorg-libsm=1.2.3=hcd874cb_1000
- xorg-libx11=1.7.2=hcd874cb_0
- xorg-libxau=1.0.9=hcd874cb_0
- xorg-libxdmcp=1.1.3=hcd874cb_0
- xorg-libxext=1.3.4=hcd874cb_1
- xorg-libxpm=3.5.13=hcd874cb_0
- xorg-libxt=1.2.1=hcd874cb_2
- xorg-xextproto=7.3.0=hcd874cb_1002
- xorg-xproto=7.0.31=hcd874cb_1007
- xz=5.2.5=h62dcd97_1
- yaml=0.2.5=he774522_0
- yapf=0.31.0=pyhd3eb1b0_0
- zipp=3.6.0=pyhd3eb1b0_0
- zlib=1.2.11=h8ffe710_1013
- zstd=1.5.0=h6255e5f_0
- pip:
- arviz==0.11.4
- cachetools==4.2.4
- cftime==1.5.1.1
- cycler==0.11.0
- dill==0.3.4
- fastprogress==1.0.0
- filelock==3.3.2
- kiwisolver==1.3.2
- matplotlib==3.4.3
- netcdf4==1.5.7
- packaging==21.2
- pandas==1.3.4
- patsy==0.5.2
- pillow==8.4.0
- pymc3==3.11.4
- pyparsing==2.4.7
- pytz==2021.3
- semver==2.13.0
- theano-pymc==1.1.2
- xarray==0.20.1
