When running pm.sample() on my MacBook Air M2, I get the error as in the screenshot (also WARNING at the beginning):
I installed pymc using mamba with an environment.yml file.
Running “mamba list” shows me this:
Anyone know how to fix this problem?
Welcome!
In general, it is advisable to install PyMC using the official procedure described here. That being said, @aloctavodia may have a different recommendation to get that specific set of packages installed on your machine.
The warning you are getting upon import of PyMC suggests that the relevant C toolchain is not being install correctly and should be fixed before trying to do much of anything.
Namely installing a more recent version of pymc/pymc-bart/PyTensor may automatically solve all the problems
Following the official procedure wth adding “-c nodefaults” and setting “pymc=3.10.0”, I created a fresh environment. However, I still get the pytensor.tensor.blas WARNING as well as CompileError.
mamba list now looks like this:
# Name Version Build Channel
accelerate 0.29.2 pyhd8ed1ab_0 conda-forge
arviz 0.18.0 pyhd8ed1ab_0 conda-forge
atk-1.0 2.38.0 hcb7b3dd_1 conda-forge
blas 2.122 openblas conda-forge
blas-devel 3.9.0 22_osxarm64_openblas conda-forge
brotli 1.1.0 hb547adb_1 conda-forge
brotli-bin 1.1.0 hb547adb_1 conda-forge
brotli-python 1.1.0 py311ha891d26_1 conda-forge
bzip2 1.0.8 h93a5062_5 conda-forge
c-ares 1.28.1 h93a5062_0 conda-forge
ca-certificates 2024.3.11 hca03da5_0
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cachetools 5.3.3 pyhd8ed1ab_0 conda-forge
cairo 1.18.0 hd1e100b_0 conda-forge
cctools_osx-arm64 986 h62378fb_0 conda-forge
certifi 2024.2.2 pyhd8ed1ab_0 conda-forge
charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge
clang 16.0.6 h30cc82d_6 conda-forge
clang-16 16.0.6 default_he012953_6 conda-forge
clang_impl_osx-arm64 16.0.6 hc421ffc_11 conda-forge
clang_osx-arm64 16.0.6 h54d7cd3_11 conda-forge
clangxx 16.0.6 default_h4cf2255_6 conda-forge
clangxx_impl_osx-arm64 16.0.6 hcd7bac0_11 conda-forge
clangxx_osx-arm64 16.0.6 h54d7cd3_11 conda-forge
cloudpickle 3.0.0 pyhd8ed1ab_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
compiler-rt 16.0.6 h3808999_2 conda-forge
compiler-rt_osx-arm64 16.0.6 h3808999_2 conda-forge
cons 0.4.6 pyhd8ed1ab_0 conda-forge
contourpy 1.2.1 py311hcc98501_0 conda-forge
cycler 0.12.1 pyhd8ed1ab_0 conda-forge
dm-tree 0.1.8 py311hea19e3d_4 conda-forge
etuples 0.3.9 pyhd8ed1ab_0 conda-forge
expat 2.6.2 hebf3989_0 conda-forge
fastprogress 1.0.3 pyhd8ed1ab_0 conda-forge
filelock 3.13.4 pyhd8ed1ab_0 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 h77eed37_1 conda-forge
fontconfig 2.14.2 h82840c6_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.51.0 py311h05b510d_0 conda-forge
freetype 2.12.1 hadb7bae_2 conda-forge
fribidi 1.0.10 h27ca646_0 conda-forge
fsspec 2024.3.1 pyhca7485f_0 conda-forge
gdk-pixbuf 2.42.10 hcea6d13_5 conda-forge
gettext 0.22.5 h8fbad5d_2 conda-forge
gettext-tools 0.22.5 h8fbad5d_2 conda-forge
giflib 5.2.2 h93a5062_0 conda-forge
gmp 6.3.0 hebf3989_1 conda-forge
gmpy2 2.1.2 py311h2ba9262_1 conda-forge
graphite2 1.3.13 hebf3989_1003 conda-forge
graphviz 9.0.0 h3face73_1 conda-forge
gtk2 2.24.33 h7895bb2_4 conda-forge
gts 0.7.6 he42f4ea_4 conda-forge
h5netcdf 1.3.0 pyhd8ed1ab_0 conda-forge
h5py 3.11.0 nompi_py311hd00467f_100 conda-forge
harfbuzz 8.3.0 h8f0ba13_0 conda-forge
hdf5 1.14.3 nompi_h5bb55e9_100 conda-forge
huggingface_hub 0.22.2 pyhd8ed1ab_0 conda-forge
icu 73.2 hc8870d7_0 conda-forge
idna 3.6 pyhd8ed1ab_0 conda-forge
iniconfig 1.1.1 pyhd3eb1b0_0
jinja2 3.1.3 pyhd8ed1ab_0 conda-forge
kiwisolver 1.4.5 py311he4fd1f5_1 conda-forge
krb5 1.21.2 h92f50d5_0 conda-forge
lcms2 2.16 ha0e7c42_0 conda-forge
ld64_osx-arm64 711 ha4bd21c_0 conda-forge
lerc 4.0.0 h9a09cb3_0 conda-forge
libabseil 20240116.1 cxx17_hebf3989_2 conda-forge
libaec 1.1.3 hebf3989_0 conda-forge
libasprintf 0.22.5 h8fbad5d_2 conda-forge
libasprintf-devel 0.22.5 h8fbad5d_2 conda-forge
libblas 3.9.0 22_osxarm64_openblas conda-forge
libbrotlicommon 1.1.0 hb547adb_1 conda-forge
libbrotlidec 1.1.0 hb547adb_1 conda-forge
libbrotlienc 1.1.0 hb547adb_1 conda-forge
libcblas 3.9.0 22_osxarm64_openblas conda-forge
libclang-cpp16 16.0.6 default_he012953_6 conda-forge
libcurl 8.7.1 h2d989ff_0 conda-forge
libcxx 16.0.6 h4653b0c_0 conda-forge
libdeflate 1.20 h93a5062_0 conda-forge
libedit 3.1.20191231 hc8eb9b7_2 conda-forge
libev 4.33 h93a5062_2 conda-forge
libexpat 2.6.2 hebf3989_0 conda-forge
libffi 3.4.2 h3422bc3_5 conda-forge
libgd 2.3.3 hfdf3952_9 conda-forge
libgettextpo 0.22.5 h8fbad5d_2 conda-forge
libgettextpo-devel 0.22.5 h8fbad5d_2 conda-forge
libgfortran 5.0.0 13_2_0_hd922786_3 conda-forge
libgfortran5 13.2.0 hf226fd6_3 conda-forge
libglib 2.80.0 hfc324ee_4 conda-forge
libiconv 1.17 h0d3ecfb_2 conda-forge
libintl 0.22.5 h8fbad5d_2 conda-forge
libintl-devel 0.22.5 h8fbad5d_2 conda-forge
libjpeg-turbo 3.0.0 hb547adb_1 conda-forge
liblapack 3.9.0 22_osxarm64_openblas conda-forge
liblapacke 3.9.0 22_osxarm64_openblas conda-forge
libllvm16 16.0.6 haab561b_3 conda-forge
libnghttp2 1.58.0 ha4dd798_1 conda-forge
libopenblas 0.3.27 openmp_h6c19121_0 conda-forge
libpng 1.6.43 h091b4b1_0 conda-forge
libprotobuf 3.21.12 ha614eb4_2 conda-forge
librsvg 2.58.0 hb3d354b_0 conda-forge
libsqlite 3.45.2 h091b4b1_0 conda-forge
libssh2 1.11.0 h7a5bd25_0 conda-forge
libtiff 4.6.0 h07db509_3 conda-forge
libuv 1.48.0 h93a5062_0 conda-forge
libwebp 1.3.2 hf30222e_1 conda-forge
libwebp-base 1.3.2 h93a5062_1 conda-forge
libxcb 1.15 hf346824_0 conda-forge
libxml2 2.12.6 h0d0cfa8_1 conda-forge
libzlib 1.2.13 h53f4e23_5 conda-forge
llvm-openmp 18.1.3 hcd81f8e_0 conda-forge
llvm-tools 16.0.6 haab561b_3 conda-forge
llvmlite 0.42.0 pypi_0 pypi
logical-unification 0.4.6 pyhd8ed1ab_0 conda-forge
markupsafe 2.1.5 py311h05b510d_0 conda-forge
matplotlib-base 3.8.4 py311hb58f1d1_0 conda-forge
minikanren 1.0.3 pyhd8ed1ab_0 conda-forge
mpc 1.3.1 h91ba8db_0 conda-forge
mpfr 4.2.1 h41d338b_1 conda-forge
mpmath 1.3.0 pyhd8ed1ab_0 conda-forge
multipledispatch 0.6.0 py_0 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
ncurses 6.4.20240210 h078ce10_0 conda-forge
networkx 3.3 pyhd8ed1ab_1 conda-forge
nomkl 1.0 h5ca1d4c_0 conda-forge
numba 0.59.1 pypi_0 pypi
numpy 1.24.4 pypi_0 pypi
openblas 0.3.27 openmp_h55c453e_0 conda-forge
openjpeg 2.5.2 h9f1df11_0 conda-forge
openssl 3.2.1 h0d3ecfb_1 conda-forge
packaging 24.0 pyhd8ed1ab_0 conda-forge
pandas 2.2.2 py311hfbe21a1_0 conda-forge
pango 1.52.2 hb067d4f_0 conda-forge
pcre2 10.43 h26f9a81_0 conda-forge
pillow 10.3.0 py311h0b5d0a1_0 conda-forge
pip 24.0 pyhd8ed1ab_0 conda-forge
pixman 0.43.4 hebf3989_0 conda-forge
pluggy 1.0.0 py311hca03da5_1
preliz 0.5.0 pypi_0 pypi
psutil 5.9.8 py311h05b510d_0 conda-forge
pthread-stubs 0.4 h27ca646_1001 conda-forge
pymc 5.10.0 hd8ed1ab_0 conda-forge
pymc-bart 0.5.11 pypi_0 pypi
pymc-base 5.10.0 pyhd8ed1ab_0 conda-forge
pyparsing 3.1.2 pyhd8ed1ab_0 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
pytensor 2.18.6 py311hbc2cede_0 conda-forge
pytensor-base 2.18.6 py311hfbe21a1_0 conda-forge
pytest 7.4.0 py311hca03da5_0
python 3.11.6 h47c9636_0_cpython conda-forge
python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge
python-graphviz 0.20.3 pyh717bed2_0 conda-forge
python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge
python_abi 3.11 4_cp311 conda-forge
pytorch 2.0.0 cpu_generic_py311ha38e979_1 conda-forge
pytz 2024.1 pyhd8ed1ab_0 conda-forge
pyyaml 6.0.1 py311heffc1b2_1 conda-forge
readline 8.2 h92ec313_1 conda-forge
requests 2.31.0 pyhd8ed1ab_0 conda-forge
safetensors 0.4.2 py311h94f323b_0 conda-forge
scipy 1.12.0 pypi_0 pypi
setuptools 69.2.0 pyhd8ed1ab_0 conda-forge
sigtool 0.1.3 h44b9a77_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sleef 3.5.1 h156473d_2 conda-forge
sympy 1.12 pypyh9d50eac_103 conda-forge
tapi 1100.0.11 he4954df_0 conda-forge
tk 8.6.13 h5083fa2_1 conda-forge
toolz 0.12.1 pyhd8ed1ab_0 conda-forge
tqdm 4.66.2 pyhd8ed1ab_0 conda-forge
typing-extensions 4.11.0 hd8ed1ab_0 conda-forge
typing_extensions 4.11.0 pyha770c72_0 conda-forge
tzdata 2024a h0c530f3_0 conda-forge
urllib3 2.2.1 pyhd8ed1ab_0 conda-forge
wheel 0.43.0 pyhd8ed1ab_1 conda-forge
xarray 2024.3.0 pyhd8ed1ab_0 conda-forge
xarray-einstats 0.7.0 pyhd8ed1ab_0 conda-forge
xorg-libxau 1.0.11 hb547adb_0 conda-forge
xorg-libxdmcp 1.1.3 h27ca646_0 conda-forge
xz 5.2.6 h57fd34a_0 conda-forge
yaml 0.2.5 h3422bc3_2 conda-forge
zlib 1.2.13 h53f4e23_5 conda-forge
zstd 1.5.5 h4f39d0f_0 conda-forge
I appreciate any suggestions
Just to rule out silly stuff, are you sure the notebook is running on the installed environment? Or alternatively you get the same error running pymc from a terminal?
I didn’t change anything but now everything (from terminal, pycharm, jupyter) works! I still get the WARNING regrading BLAS functions when I run with pycharm but not when I use terminal. Is it not a problem?
Anyway, thank you so much!
[Update] Running with terminal always works, but running with IDE as well as Jupyter is unstable, i.e. sometimes works but sometimes doesn’t. Can you think of a potential reason for this latency and differene between terminal and inconsistent runs with IDE?
My guess is you’re not accessing the correct environment from jupyter/pycharm. Check out if sys.executable is the same
PyMC-BART can be installed with conda, preliz not yet (I just opened an issue).