Ansul
November 27, 2023, 3:08pm
1
Hi,
I am PyMC version: 5.10.0 and I use pip to install pymc.
Based on this link , it seems this warning is leading to poor performance and slowness. And I have not installed theano for my work. My python version is - Python 3.9.1
I know this is just a warning but wasn’t sure if this slows down performance.
Theano is no longer relevant for PyMC. The current backend is called Pytensor.
The warning is telling you that you haven’t installed a BLAS package for your specific hardware. This is a suite of highly specialized linear algebra routines that significantly speed up computation.
The installation instructions recommend using conda precisely for this reason. Conda is configured to help handle these sorts of non-python requirements, whereas pip is not.
I might add that even with conda/mamba installed environments things are currently not as smooth as we’d like them to be.here ) and if I understand correctly the issue of BLAS flags detection is not fully sorted out yet: BUG: Regression in C blas flags detection · Issue #508 · pymc-devs/pytensor · GitHub
1 Like
Ansul
November 30, 2023, 10:46am
4
Hi,
Output
Name
Version
_libgcc_mutex
0.1
_openmp_mutex
4.5
arviz
0.16.1
atk-1.0
2.38.0
binutils_impl_linux-64
2.4
binutils_linux-64
2.4
blas
2.12
blas-devel
3.9.0
brotli
1.1.0
brotli-bin
1.1.0
bzip2
1.0.8
c-ares
1.22.1
ca-certificates
2023.11.17
cached-property
1.5.2
cached_property
1.5.2
cachetools
5.3.2
cairo
1.18.0
certifi
2023.11.17
cloudpickle
3.0.0
cons
0.4.6
contourpy
1.2.0
cycler
0.12.1
etuples
0.3.9
expat
2.5.0
fastprogress
1.0.3
filelock
3.13.1
font-ttf-dejavu-sans-mono
2.37
font-ttf-inconsolata
3
font-ttf-source-code-pro
2.038
font-ttf-ubuntu
0.83
fontconfig
2.14.2
fonts-conda-ecosystem
1
fonts-conda-forge
1
fonttools
4.45.1
freetype
2.12.1
fribidi
1.0.10
gcc
12.3.0
gcc_impl_linux-64
12.3.0
gcc_linux-64
12.3.0
gdk-pixbuf
2.42.10
gettext
0.21.1
giflib
5.2.1
graphite2
1.3.13
graphviz
9.0.0
gtk2
2.24.33
gts
0.7.6
gxx
12.3.0
gxx_impl_linux-64
12.3.0
gxx_linux-64
12.3.0
h5netcdf
1.3.0
h5py
3.10.0
harfbuzz
8.3.0
hdf5
1.14.2
icu
73.2
kernel-headers_linux-64
2.6.32
keyutils
1.6.1
kiwisolver
1.4.5
krb5
1.21.2
lcms2
2.15
ld_impl_linux-64
2.4
lerc
4.0.0
libaec
1.1.2
libblas
3.9.0
libbrotlicommon
1.1.0
libbrotlidec
1.1.0
libbrotlienc
1.1.0
libcblas
3.9.0
libcurl
8.4.0
libdeflate
1.19
libedit
3.1.20191231
libev
4.33
libexpat
2.5.0
libffi
3.4.2
libgcc-devel_linux-64
12.3.0
libgcc-ng
13.2.0
libgd
2.3.3
libgfortran-ng
13.2.0
libgfortran5
13.2.0
libglib
2.78.1
libgomp
13.2.0
libhwloc
2.9.3
libiconv
1.17
libjpeg-turbo
3.0.0
liblapack
3.9.0
liblapacke
3.9.0
libnghttp2
1.58.0
libnsl
2.0.1
libopenblas
0.3.25
libpng
1.6.39
librsvg
2.56.3
libsanitizer
12.3.0
libsqlite
3.44.2
libssh2
1.11.0
libstdcxx-devel_linux-64
12.3.0
libstdcxx-ng
13.2.0
libtiff
4.6.0
libuuid
2.38.1
libwebp
1.3.2
libwebp-base
1.3.2
libxcb
1.15
libxml2
2.11.6
libzlib
1.2.13
llvm-openmp
17.0.6
logical-unification
0.4.6
matplotlib-base
3.8.2
minikanren
1.0.3
mkl
2022.2.1
mkl-service
2.4.0
multipledispatch
0.6.0
munkres
1.1.4
ncurses
6.4
numpy
1.26.2
openblas
0.3.25
openjpeg
2.5.0
openssl
3.2.0
packaging
23.2
pandas
2.1.3
pango
1.50.14
pcre2
10.42
pillow
10.1.0
pip
23.3.1
pixman
0.42.2
pthread-stubs
0.4
pymc
5.10.0
pymc-base
5.10.0
pyparsing
3.1.1
pytensor
2.18.1
pytensor-base
2.18.1
python
3.11.6
python-dateutil
2.8.2
python-graphviz
0.20.1
python-tzdata
2023.3
python_abi
3.11
pytz
2023.3.post1
readline
8.2
scipy
1.11.4
setuptools
68.2.2
six
1.16.0
sysroot_linux-64
2.12
tbb
2021.10.0
tk
8.6.13
toolz
0.12.0
typing-extensions
4.8.0
typing_extensions
4.8.0
tzdata
2023c
wheel
0.42.0
xarray
2023.11.0
xarray-einstats
0.6.0
xorg-kbproto
1.0.7
xorg-libice
1.1.1
xorg-libsm
1.2.4
xorg-libx11
1.8.7
xorg-libxau
1.0.11
xorg-libxdmcp
1.1.3
xorg-libxext
1.3.4
xorg-libxrender
0.9.11
xorg-renderproto
0.11.1
xorg-xextproto
7.3.0
xorg-xproto
7.0.31
xz
5.2.6
zlib
1.2.13
zstd
1.5.5
Did you use the conda-forge channel specifically?
Can you show the output of conda list?
Ansul
November 30, 2023, 2:55pm
6
I have used conda-forge channel and the output of conda list is shared above
The output seems to be missing information. Mine includes build and channel info:
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_kmp_llvm conda-forge
absl-py 1.4.0 pyhd8ed1ab_0 conda-forge
alsa-lib 1.2.9 hd590300_0 conda-forge
arviz 0.16.1 pyhd8ed1ab_0 conda-forge
asttokens 2.2.1 pyhd8ed1ab_0 conda-forge
atk-1.0 2.38.0 hd4edc92_1 conda-forge
attr 2.5.1 h166bdaf_1 conda-forge
Ansul
November 30, 2023, 3:49pm
8
Sorry, I had removed the last two columns -
Output
Name
Version
Build
Channel
_libgcc_mutex
0.1
conda_forge
conda-forge
_openmp_mutex
4.5
2_kmp_llvm
conda-forge
arviz
0.16.1
pyhd8ed1ab_1
conda-forge
atk-1.0
2.38.0
hd4edc92_1
conda-forge
binutils_impl_linux-64
2.4
hf600244_0
conda-forge
binutils_linux-64
2.4
hbdbef99_2
conda-forge
blas
2.12
openblas
conda-forge
blas-devel
3.9.0
20_linux64_openblas
conda-forge
brotli
1.1.0
hd590300_1
conda-forge
brotli-bin
1.1.0
hd590300_1
conda-forge
bzip2
1.0.8
hd590300_5
conda-forge
c-ares
1.22.1
hd590300_0
conda-forge
ca-certificates
2023.11.17
hbcca054_0
conda-forge
cached-property
1.5.2
hd8ed1ab_1
conda-forge
cached_property
1.5.2
pyha770c72_1
conda-forge
cachetools
5.3.2
pyhd8ed1ab_0
conda-forge
cairo
1.18.0
h3faef2a_0
conda-forge
certifi
2023.11.17
pyhd8ed1ab_0
conda-forge
cloudpickle
3.0.0
pyhd8ed1ab_0
conda-forge
cons
0.4.6
pyhd8ed1ab_0
conda-forge
contourpy
1.2.0
py311h9547e67_0
conda-forge
cycler
0.12.1
pyhd8ed1ab_0
conda-forge
etuples
0.3.9
pyhd8ed1ab_0
conda-forge
expat
2.5.0
hcb278e6_1
conda-forge
fastprogress
1.0.3
pyhd8ed1ab_0
conda-forge
filelock
3.13.1
pyhd8ed1ab_0
conda-forge
font-ttf-dejavu-sans-mono
2.37
hab24e00_0
conda-forge
font-ttf-inconsolata
3
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
h14ed4e7_0
conda-forge
fonts-conda-ecosystem
1
0
conda-forge
fonts-conda-forge
1
0
conda-forge
fonttools
4.45.1
py311h459d7ec_0
conda-forge
freetype
2.12.1
h267a509_2
conda-forge
fribidi
1.0.10
h36c2ea0_0
conda-forge
gcc
12.3.0
h8d2909c_2
conda-forge
gcc_impl_linux-64
12.3.0
he2b93b0_3
conda-forge
gcc_linux-64
12.3.0
h76fc315_2
conda-forge
gdk-pixbuf
2.42.10
h829c605_4
conda-forge
gettext
0.21.1
h27087fc_0
conda-forge
giflib
5.2.1
h0b41bf4_3
conda-forge
graphite2
1.3.13
h58526e2_1001
conda-forge
graphviz
9.0.0
h78e8752_1
conda-forge
gtk2
2.24.33
h90689f9_2
conda-forge
gts
0.7.6
h977cf35_4
conda-forge
gxx
12.3.0
h8d2909c_2
conda-forge
gxx_impl_linux-64
12.3.0
he2b93b0_3
conda-forge
gxx_linux-64
12.3.0
h8a814eb_2
conda-forge
h5netcdf
1.3.0
pyhd8ed1ab_0
conda-forge
h5py
3.10.0
nompi_py311h3839ddf_100
conda-forge
harfbuzz
8.3.0
h3d44ed6_0
conda-forge
hdf5
1.14.2
nompi_h4f84152_100
conda-forge
icu
73.2
h59595ed_0
conda-forge
kernel-headers_linux-64
2.6.32
he073ed8_16
conda-forge
keyutils
1.6.1
h166bdaf_0
conda-forge
kiwisolver
1.4.5
py311h9547e67_1
conda-forge
krb5
1.21.2
h659d440_0
conda-forge
lcms2
2.15
hb7c19ff_3
conda-forge
ld_impl_linux-64
2.4
h41732ed_0
conda-forge
lerc
4.0.0
h27087fc_0
conda-forge
libaec
1.1.2
h59595ed_1
conda-forge
libblas
3.9.0
20_linux64_openblas
conda-forge
libbrotlicommon
1.1.0
hd590300_1
conda-forge
libbrotlidec
1.1.0
hd590300_1
conda-forge
libbrotlienc
1.1.0
hd590300_1
conda-forge
libcblas
3.9.0
20_linux64_openblas
conda-forge
libcurl
8.4.0
hca28451_0
conda-forge
libdeflate
1.19
hd590300_0
conda-forge
libedit
3.1.20191231
he28a2e2_2
conda-forge
libev
4.33
h516909a_1
conda-forge
libexpat
2.5.0
hcb278e6_1
conda-forge
libffi
3.4.2
h7f98852_5
conda-forge
libgcc-devel_linux-64
12.3.0
h8bca6fd_103
conda-forge
libgcc-ng
13.2.0
h807b86a_3
conda-forge
libgd
2.3.3
h119a65a_9
conda-forge
libgfortran-ng
13.2.0
h69a702a_3
conda-forge
libgfortran5
13.2.0
ha4646dd_3
conda-forge
libglib
2.78.1
h783c2da_1
conda-forge
libgomp
13.2.0
h807b86a_3
conda-forge
libhwloc
2.9.3
default_h554bfaf_1009
conda-forge
libiconv
1.17
h166bdaf_0
conda-forge
libjpeg-turbo
3.0.0
hd590300_1
conda-forge
liblapack
3.9.0
20_linux64_openblas
conda-forge
liblapacke
3.9.0
20_linux64_openblas
conda-forge
libnghttp2
1.58.0
h47da74e_0
conda-forge
libnsl
2.0.1
hd590300_0
conda-forge
libopenblas
0.3.25
pthreads_h413a1c8_0
conda-forge
libpng
1.6.39
h753d276_0
conda-forge
librsvg
2.56.3
h98fae49_0
conda-forge
libsanitizer
12.3.0
h0f45ef3_3
conda-forge
libsqlite
3.44.2
h2797004_0
conda-forge
libssh2
1.11.0
h0841786_0
conda-forge
libstdcxx-devel_linux-64
12.3.0
h8bca6fd_103
conda-forge
libstdcxx-ng
13.2.0
h7e041cc_3
conda-forge
libtiff
4.6.0
ha9c0a0a_2
conda-forge
libuuid
2.38.1
h0b41bf4_0
conda-forge
libwebp
1.3.2
h658648e_1
conda-forge
libwebp-base
1.3.2
hd590300_0
conda-forge
libxcb
1.15
h0b41bf4_0
conda-forge
libxml2
2.11.6
h232c23b_0
conda-forge
libzlib
1.2.13
hd590300_5
conda-forge
llvm-openmp
17.0.6
h4dfa4b3_0
conda-forge
logical-unification
0.4.6
pyhd8ed1ab_0
conda-forge
matplotlib-base
3.8.2
py311h54ef318_0
conda-forge
minikanren
1.0.3
pyhd8ed1ab_0
conda-forge
mkl
2022.2.1
h84fe81f_16997
conda-forge
mkl-service
2.4.0
py311hb711fc7_0
conda-forge
multipledispatch
0.6.0
py_0
conda-forge
munkres
1.1.4
pyh9f0ad1d_0
conda-forge
ncurses
6.4
h59595ed_2
conda-forge
numpy
1.26.2
py311h64a7726_0
conda-forge
openblas
0.3.25
pthreads_h7a3da1a_0
conda-forge
openjpeg
2.5.0
h488ebb8_3
conda-forge
openssl
3.2.0
hd590300_1
conda-forge
packaging
23.2
pyhd8ed1ab_0
conda-forge
pandas
2.1.3
py311h320fe9a_0
conda-forge
pango
1.50.14
ha41ecd1_2
conda-forge
pcre2
10.42
hcad00b1_0
conda-forge
pillow
10.1.0
py311ha6c5da5_0
conda-forge
pip
23.3.1
pyhd8ed1ab_0
conda-forge
pixman
0.42.2
h59595ed_0
conda-forge
pthread-stubs
0.4
h36c2ea0_1001
conda-forge
pymc
5.10.0
hd8ed1ab_0
conda-forge
pymc-base
5.10.0
pyhd8ed1ab_0
conda-forge
pyparsing
3.1.1
pyhd8ed1ab_0
conda-forge
pytensor
2.18.1
py311hb755f60_0
conda-forge
pytensor-base
2.18.1
py311h320fe9a_0
conda-forge
python
3.11.6
hab00c5b_0_cpython
conda-forge
python-dateutil
2.8.2
pyhd8ed1ab_0
conda-forge
python-graphviz
0.20.1
pyh22cad53_0
conda-forge
python-tzdata
2023.3
pyhd8ed1ab_0
conda-forge
python_abi
3.11
4_cp311
conda-forge
pytz
2023.3.post1
pyhd8ed1ab_0
conda-forge
readline
8.2
h8228510_1
conda-forge
scipy
1.11.4
py311h64a7726_0
conda-forge
setuptools
68.2.2
pyhd8ed1ab_0
conda-forge
six
1.16.0
pyh6c4a22f_0
conda-forge
sysroot_linux-64
2.12
he073ed8_16
conda-forge
tbb
2021.10.0
h00ab1b0_2
conda-forge
tk
8.6.13
noxft_h4845f30_101
conda-forge
toolz
0.12.0
pyhd8ed1ab_0
conda-forge
typing-extensions
4.8.0
hd8ed1ab_0
conda-forge
typing_extensions
4.8.0
pyha770c72_0
conda-forge
tzdata
2023c
h71feb2d_0
conda-forge
wheel
0.42.0
pyhd8ed1ab_0
conda-forge
xarray
2023.11.0
pyhd8ed1ab_0
conda-forge
xarray-einstats
0.6.0
pyhd8ed1ab_0
conda-forge
xorg-kbproto
1.0.7
h7f98852_1002
conda-forge
xorg-libice
1.1.1
hd590300_0
conda-forge
xorg-libsm
1.2.4
h7391055_0
conda-forge
xorg-libx11
1.8.7
h8ee46fc_0
conda-forge
xorg-libxau
1.0.11
hd590300_0
conda-forge
xorg-libxdmcp
1.1.3
h7f98852_0
conda-forge
xorg-libxext
1.3.4
h0b41bf4_2
conda-forge
xorg-libxrender
0.9.11
hd590300_0
conda-forge
xorg-renderproto
0.11.1
h7f98852_1002
conda-forge
xorg-xextproto
7.3.0
h0b41bf4_1003
conda-forge
xorg-xproto
7.0.31
h7f98852_1007
conda-forge
xz
5.2.6
h166bdaf_0
conda-forge
zlib
1.2.13
hd590300_5
conda-forge
zstd
1.5.5
hfc55251_0
conda-forge
Is this a fresh env, or did you conda install into the same one you had previously pip installed into?
Ansul
November 30, 2023, 4:57pm
10
I created a new env and installed pymc -
AFalk
December 3, 2023, 9:45pm
11
Having similar issues on my end when performing a fresh conda install using the recommended install command.
Conda install command:conda create -c conda-forge -n pymc_env "pymc>=5"
When attempting the following imports in a jupyter notebook, I get the following error:
import arviz as az
import numpy as np
import pandas as pd
import math
import pymc as pm
import pytensor
import pytensor.tensor as pt
import scipy.stats as stats
import matplotlib.pyplot as plt
---------------------------------------------------------------------------
NoSectionError Traceback (most recent call last)
File ~/miniconda3/envs/pymc_env/lib/python3.11/site-packages/pytensor/configparser.py:201, in PyTensorConfigParser.fetch_val_for_key(self, key, delete_key)
200 try:
--> 201 return self._pytensor_cfg.get(section, option)
202 except InterpolationError:
File ~/miniconda3/envs/pymc_env/lib/python3.11/configparser.py:797, in RawConfigParser.get(self, section, option, raw, vars, fallback)
796 try:
--> 797 d = self._unify_values(section, vars)
798 except NoSectionError:
File ~/miniconda3/envs/pymc_env/lib/python3.11/configparser.py:1168, in RawConfigParser._unify_values(self, section, vars)
1167 if section != self.default_section:
-> 1168 raise NoSectionError(section) from None
1169 # Update with the entry specific variables
NoSectionError: No section: 'blas'
During handling of the above exception, another exception occurred:
KeyError Traceback (most recent call last)
File ~/miniconda3/envs/pymc_env/lib/python3.11/site-packages/pytensor/configparser.py:317, in ConfigParam.__get__(self, cls, type_, delete_key)
316 try:
--> 317 val_str = cls.fetch_val_for_key(self.name, delete_key=delete_key)
...
-> 2720 blas_info = np.__config__.get_info("blas_opt")
2722 # If we are in a EPD installation, mkl is available
2723 if "EPD" in sys.version:
AttributeError: module 'numpy.__config__' has no attribute 'get_info'
That suggests you have installed an old version of PyMC and numpy>2.6. Can you confirm which version of PyMC got installed?
AFalk
December 4, 2023, 3:13pm
13
Interesting, is this just a result of conda trying to find compatible versions?
From the conda environment:
pymc 5.6.1 py311hea593b9_0
numpy 1.26.2 py311h6d074dd_0
AFalk
December 4, 2023, 3:57pm
15
Ah gotcha, adding nodefaults worked for me, thank you!
If I am not using Conda but Pycharm and getting the same warning, do I:
Set warning level
Install a particular package
Thanks
You can still use conda as the interpreter/package manager in a pycharm project