I am trying to install PyMC on my Ubuntu 20.04 (64 bit). I tried using conda install -c conda-forge pymc, which ran without any errors, but when I try running import pymc to check my installation, it throws the following error :
ImportError: /lib/x86_64-linux-gnu/liblapack.so.3: undefined symbol: ATL_dgeset
I don’t know how to rectify this at this point. Any help would be great!
Can you show what the output of conda list is?
Actually, can you show the entire error message you are getting?
Here it is :
# Name Version Build Channel
_libgcc_mutex 0.1 main
_openmp_mutex 5.1 1_gnu
arviz 0.11.2 pyhd3eb1b0_0
binutils_impl_linux-64 2.33.1 he6710b0_7
binutils_linux-64 2.33.1 h9595d00_15
blas 1.0 mkl
bottleneck 1.3.4 py39hce1f21e_0
brotli 1.0.9 he6710b0_2
bzip2 1.0.8 h7b6447c_0
c-ares 1.18.1 h7f8727e_0
ca-certificates 2022.6.15 ha878542_0 conda-forge
cachetools 4.2.2 pyhd3eb1b0_0
certifi 2022.6.15 py39hf3d152e_0 conda-forge
cftime 1.5.1.1 py39hce1f21e_0
curl 7.82.0 h7f8727e_0
cycler 0.11.0 pyhd3eb1b0_0
cython 0.29.28 py39h295c915_0
dbus 1.13.18 hb2f20db_0
dill 0.3.4 pyhd3eb1b0_0
expat 2.4.4 h295c915_0
fastprogress 1.0.0 pyhb85f177_0
filelock 3.6.0 pyhd3eb1b0_0
fontconfig 2.13.1 h6c09931_0
fonttools 4.25.0 pyhd3eb1b0_0
freetype 2.11.0 h70c0345_0
gcc_impl_linux-64 7.3.0 habb00fd_1
gcc_linux-64 7.3.0 h553295d_15
giflib 5.2.1 h7b6447c_0
glib 2.69.1 h4ff587b_1
gst-plugins-base 1.14.0 h8213a91_2
gstreamer 1.14.0 h28cd5cc_2
gxx_impl_linux-64 7.3.0 hdf63c60_1
gxx_linux-64 7.3.0 h553295d_15
hdf4 4.2.13 h3ca952b_2
hdf5 1.10.6 hb1b8bf9_0
icu 58.2 he6710b0_3
intel-openmp 2021.4.0 h06a4308_3561
jpeg 9e h7f8727e_0
kiwisolver 1.4.2 py39h295c915_0
krb5 1.19.2 hac12032_0
lcms2 2.12 h3be6417_0
ld_impl_linux-64 2.33.1 h53a641e_7
libblas 3.9.0 12_linux64_mkl conda-forge
libcblas 3.9.0 12_linux64_mkl conda-forge
libcurl 7.82.0 h0b77cf5_0
libedit 3.1.20210910 h7f8727e_0
libev 4.33 h7f8727e_1
libffi 3.3 he6710b0_2
libgcc-ng 11.2.0 h1234567_1
libgfortran-ng 7.5.0 ha8ba4b0_17
libgfortran4 7.5.0 ha8ba4b0_17
libgomp 11.2.0 h1234567_1
libnetcdf 4.8.1 h42ceab0_1
libnghttp2 1.46.0 hce63b2e_0
libpng 1.6.37 hbc83047_0
libssh2 1.10.0 h8f2d780_0
libstdcxx-ng 11.2.0 h1234567_1
libtiff 4.2.0 h2818925_1
libuuid 1.0.3 h7f8727e_2
libwebp 1.2.2 h55f646e_0
libwebp-base 1.2.2 h7f8727e_0
libxcb 1.15 h7f8727e_0
libxml2 2.9.14 h74e7548_0
libzip 1.8.0 h5cef20c_0
lz4-c 1.9.3 h295c915_1
matplotlib 3.5.1 py39h06a4308_1
matplotlib-base 3.5.1 py39ha18d171_1
mkl 2021.4.0 h06a4308_640
mkl-service 2.4.0 py39h7f8727e_0
mkl_fft 1.3.1 py39hd3c417c_0
mkl_random 1.2.2 py39h51133e4_0
munkres 1.1.4 py_0
ncurses 6.3 h7f8727e_2
netcdf4 1.5.7 py39ha0f2276_1
numexpr 2.8.1 py39h807cd23_2
numpy 1.21.5 py39he7a7128_2
numpy-base 1.21.5 py39hf524024_2
openssl 1.1.1o h166bdaf_0 conda-forge
packaging 21.3 pyhd3eb1b0_0
pandas 1.4.2 py39h295c915_0
patsy 0.5.2 py39h06a4308_1
pcre 8.45 h295c915_0
pillow 9.0.1 py39h22f2fdc_0
pip 21.2.4 py39h06a4308_0
pymc 2.3.8 py39hc807aa8_2 conda-forge
pymc3 3.11.4 py39hb070fc8_0
pyparsing 3.0.4 pyhd3eb1b0_0
pyqt 5.9.2 py39h2531618_6
pystan 2.19.1.1 py39ha9443f7_0
python 3.9.12 h12debd9_1
python-dateutil 2.8.2 pyhd3eb1b0_0
python_abi 3.9 2_cp39 conda-forge
pytz 2022.1 py39h06a4308_0
qt 5.9.7 h5867ecd_1
readline 8.1.2 h7f8727e_1
scipy 1.7.3 py39hc147768_0
semver 2.13.0 pyhd3eb1b0_0
setuptools 61.2.0 py39h06a4308_0
sip 4.19.13 py39h295c915_0
six 1.16.0 pyhd3eb1b0_1
sqlite 3.38.5 hc218d9a_0
statsmodels 0.13.2 py39h7f8727e_0
theano-pymc 1.1.2 py39h51133e4_0
tk 8.6.12 h1ccaba5_0
tornado 6.1 py39h27cfd23_0
typing-extensions 4.1.1 hd3eb1b0_0
typing_extensions 4.1.1 pyh06a4308_0
tzdata 2022a hda174b7_0
wheel 0.37.1 pyhd3eb1b0_0
xarray 0.20.1 pyhd3eb1b0_1
xz 5.2.5 h7f8727e_1
zlib 1.2.12 h7f8727e_2
zstd 1.5.2 ha4553b6_0
And here is my entire error message :
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/PATH/TO/anaconda3/envs/bayes/lib/python3.9/site-packages/pymc/__init__.py", line 29, in <module>
from .InstantiationDecorators import *
File "/PATH/TO/anaconda3/envs/bayes/lib/python3.9/site-packages/pymc/InstantiationDecorators.py", line 28, in <module>
from .utils import get_signature
File "/PATH/TO/anaconda3/envs/bayes/lib/python3.9/site-packages/pymc/utils.py", line 14, in <module>
from . import flib
ImportError: /lib/x86_64-linux-gnu/liblapack.so.3: undefined symbol: ATL_dgeset
Hi, it seems that you have installed an old version of pymc (2.3.8 and 3.11.4). You can create a conda environment with the latest PyMC v4 using conda install -c conda-forge "pymc>=4.0.0" or using these follow commands to create a new fresh environment with mamba:
conda create --name pymc4 -c conda-forge python=3.9
conda activate pymc4
conda install -c conda-forge mamba
mamba install -c conda-forge "pymc>=4.0.0"
I tried installing using mini-forge and with the usual steps. That did not work. I found these instructions and I eventually got pymc 5.1.2 installed. These instructions should really be placed in the section on installation.
There have been discussions about including mamba installation instructions in addition to the conda installation (or even replacing the conda recommendation with mamba). But I think there has been a sense that having a single “official” installation saves many more headaches than trying to accommodate the many combinations of package manager (conda, mamba, pip, pyenv, homebrew, chocolatey, etc.) and platform (Windows, Mac M1, Mac M2, Linux, etc.). But if you think that the installation instructions should change, I would encourage you to open an issue.