I see some dead unresolved threads from 2019 and 2020 (unlike Osment). Wondering if there is an update.
I’ve got this message
WARNING (theano.tensor.blas): Using NumPy C-API based implementation for BLAS functions.
This appears common. Pymc3 works but apparently can be sped up.
What BLAS must I install? I am running Ubuntu 18.04, if that helps, Pymc3 was installed via conda, version 3.11.2, using the wiki on installation for linux machines. But no cigar.
See this link for a previous (and incomplete) discussion on BLAS
Theano Has a Blas
If you type conda search pymc3 --info, the following information appears:
pymc3 3.11.2 pyhd8ed1ab_0
-------------------------
file name : pymc3-3.11.2-pyhd8ed1ab_0.tar.bz2
name : pymc3
version : 3.11.2
build : pyhd8ed1ab_0
build number: 0
size : 616 KB
license : Apache-2.0
subdir : noarch
url : https://conda.anaconda.org/conda-forge/noarch/pymc3-3.11.2-pyhd8ed1ab_0.tar.bz2
md5 : 0c8fda4ca867ec8c8dc5ed63ee8efbeb
timestamp : 2021-03-15 13:09:55 UTC
dependencies:
- arviz >=0.11.0
- cachetools >=4.2.1
- dill
- fastprogress >=0.2.0
- mkl-service
- numpy >=1.15.0
- pandas >=0.24.0
- patsy >=0.5.1
- python >=3.7
- scipy >=1.2.0
- semver
- theano-pymc 1.1.2
- typing-extensions >=3.7.4
I assume that you have the most recent version for every package. Next, check the output for:
import numpy as np
np.show_config()
For me, the output is:
blas_info:
libraries = ['cblas', 'blas', 'cblas', 'blas']
library_dirs = ['/home/rosgori/anaconda3/lib']
include_dirs = ['/home/rosgori/anaconda3/include']
language = c
define_macros = [('HAVE_CBLAS', None)]
blas_opt_info:
define_macros = [('NO_ATLAS_INFO', 1), ('HAVE_CBLAS', None)]
libraries = ['cblas', 'blas', 'cblas', 'blas']
library_dirs = ['/home/rosgori/anaconda3/lib']
include_dirs = ['/home/rosgori/anaconda3/include']
language = c
lapack_info:
libraries = ['lapack', 'blas', 'lapack', 'blas']
library_dirs = ['/home/rosgori/anaconda3/lib']
language = f77
lapack_opt_info:
libraries = ['lapack', 'blas', 'lapack', 'blas', 'cblas', 'blas', 'cblas', 'blas']
library_dirs = ['/home/rosgori/anaconda3/lib']
language = c
define_macros = [('NO_ATLAS_INFO', 1), ('HAVE_CBLAS', None)]
include_dirs = ['/home/rosgori/anaconda3/include']
Supported SIMD extensions in this NumPy install:
baseline = SSE,SSE2,SSE3
found = SSSE3,SSE41,POPCNT,SSE42,AVX,F16C,FMA3,AVX2
not found = AVX512F,AVX512CD,AVX512_KNL,AVX512_KNM,AVX512_SKX,AVX512_CLX,AVX512_CNL,AVX512_ICL
From here, you have to install the library you want. I have in my environment
$ conda list mkl
# packages in environment at /home/rosgori/anaconda3:
#
# Name Version Build Channel
mkl 2020.4 h726a3e6_304 conda-forge
mkl-service 2.3.0 py38h1e0a361_2 conda-forge
$ conda list blas
# packages in environment at /home/rosgori/anaconda3:
#
# Name Version Build Channel
blas 2.110 openblas conda-forge
blas-devel 3.9.0 10_openblas conda-forge
libblas 3.9.0 10_openblas conda-forge
libcblas 3.9.0 10_openblas conda-forge
libopenblas 0.3.17 pthreads_h8fe5266_1 conda-forge
openblas 0.3.17 pthreads_h4748800_1 conda-forge
It really helps to be in the conda-forge channel.
@rosgori, What’s the OS in which you ran these commands? Struggling here to correctly install pymc3 in Windows 10, even by just referencing to conda-forge channel. Same warning reported by @pythonometrist showing up here.
I am using Ubuntu 20.04, using conda (as you can see) and the main channel is conda-forge.
Wow you are fortunate - couldnt get Pymc3 to work on windows at all. Did you just follow the wiki?
Very helpful:
I went through your steps:
pymc3 3.8 py_0
--------------
file name : pymc3-3.8-py_0.conda
name : pymc3
version : 3.8
build : py_0
build number: 0
size : 694 KB
license : Apache-2.0
subdir : noarch
url : https://repo.anaconda.com/pkgs/main/noarch/pymc3-3.8-py_0.conda
md5 : 0e9fc9b6e0687e5bf40238586876ca31
timestamp : 2020-02-20 20:01:46 UTC
dependencies:
- arviz
- h5py >=2.7.0
- numpy >=1.13.0
- pandas >=0.18.0
- patsy >=0.4.0
- python >=3.5
- scipy >=0.18.1
- theano >=1.0.4
- tqdm >=4.8.4
Interestingly 3.11.2 doesnt show up (even though I was able to install it. Neither does theano-pymc.
It shows lots of versions before and including pymc 3.8
Then
2. np.show_config says
blas_mkl_info:
NOT AVAILABLE
blis_info:
NOT AVAILABLE
openblas_info:
libraries = ['openblas', 'openblas']
library_dirs = ['/usr/local/lib']
language = c
define_macros = [('HAVE_CBLAS', None)]
blas_opt_info:
libraries = ['openblas', 'openblas']
library_dirs = ['/usr/local/lib']
language = c
define_macros = [('HAVE_CBLAS', None)]
lapack_mkl_info:
NOT AVAILABLE
openblas_lapack_info:
libraries = ['openblas', 'openblas']
library_dirs = ['/usr/local/lib']
language = c
define_macros = [('HAVE_CBLAS', None)]
lapack_opt_info:
libraries = ['openblas', 'openblas']
library_dirs = ['/usr/local/lib']
language = c
define_macros = [('HAVE_CBLAS', None)]
So clearly I am missing some blas libraries
# Name Version Build Channel
mkl 2021.2.0 h06a4308_296
mkl-service 2.3.0 py38h27cfd23_1
mkl_fft 1.3.0 py38h42c9631_2
mkl_random 1.2.1 py38ha9443f7_2
So mkl is in play
4. And conda list blas says:
# packages in environment at /home/ubuntu/anaconda3:
#
# Name Version Build Channel
blas 1.0 mkl
missing blas libraries. Next step will be to try and fgure out f I can install some blas library.
For Windows, try creating a new fresh conda environment following the instructions on Installation Guide (Windows) · pymc-devs/pymc3 Wiki · GitHub.
I’ve had the same problem with blas in Windows, and this procedure worked for me. Hopefully, it can help you as well.
The crucial catch seems to be: install dependencies with conda and conda-forge, but install pymc3 using pip afterwards.
That’s an inception level twist . Many thanks - will check with pip at the end.
So now numpy shows :
blas_info:
libraries = ['cblas', 'blas', 'cblas', 'blas']
library_dirs = ['/root/anaconda3/envs/bayes/lib']
include_dirs = ['/root/anaconda3/envs/bayes/include']
language = c
define_macros = [('HAVE_CBLAS', None)]
blas_opt_info:
define_macros = [('NO_ATLAS_INFO', 1), ('HAVE_CBLAS', None)]
libraries = ['cblas', 'blas', 'cblas', 'blas']
library_dirs = ['/root/anaconda3/envs/bayes/lib']
include_dirs = ['/root/anaconda3/envs/bayes/include']
language = c
lapack_info:
libraries = ['lapack', 'blas', 'lapack', 'blas']
library_dirs = ['/root/anaconda3/envs/bayes/lib']
language = f77
lapack_opt_info:
libraries = ['lapack', 'blas', 'lapack', 'blas', 'cblas', 'blas', 'cblas', 'blas']
library_dirs = ['/root/anaconda3/envs/bayes/lib']
language = c
define_macros = [('NO_ATLAS_INFO', 1), ('HAVE_CBLAS', None)]
include_dirs = ['/root/anaconda3/envs/bayes/include']
Supported SIMD extensions in this NumPy install:
baseline = SSE,SSE2,SSE3
found = SSSE3,SSE41,POPCNT,SSE42,AVX,F16C,FMA3,AVX2,AVX512F,AVX512CD,AVX512_SKX,AVX512_CLX
not found = AVX512_KNL,AVX512_KNM,AVX512_CNL,AVX512_ICL
So looks good
# Name Version Build Channel
mkl 2021.3.0 h06a4308_520
mkl-devel 2021.3.0 h66538d2_520
mkl-include 2021.3.0 h06a4308_520
mkl-service 2.4.0 py38h497a2fe_0 conda-forge
Could be that I need mkl also on conda-forge
# Name Version Build Channel
blas 1.0 mkl
blas-devel 3.9.0 10_mkl conda-forge
libblas 3.9.0 10_mkl conda-forge
libcblas 3.9.0 10_mkl conda-forge
libopenblas 0.3.13 h4367d64_0
openblas 0.3.3 h9ac9557_1001 conda-forge
But the infor search results in this
pymc3 3.6 py37_0
----------------
file name : pymc3-3.6-py37_0.conda
name : pymc3
version : 3.6
build : py37_0
build number: 0
size : 983 KB
license : Apache-2.0
subdir : linux-64
url : https://repo.anaconda.com/pkgs/main/linux-64/pymc3-3.6-py37_0.conda
md5 : d10609e94d0532ab4f69c87ac822cb55
timestamp : 2018-12-28 17:03:42 UTC
dependencies:
- h5py >=2.7.0
- joblib <0.13.0
- matplotlib >=1.5.0
- numpy >=1.13.0
- pandas >=0.18.0
- patsy >=0.4.0
- python >=3.7,<3.8.0a0
- scipy >=0.12.0
- six >=1.10.0
- theano >=1.0.0
- tqdm >=4.8.4
pymc3 3.7 py_0
--------------
file name : pymc3-3.7-py_0.conda
name : pymc3
version : 3.7
build : py_0
build number: 0
size : 652 KB
license : Apache-2.0
subdir : noarch
url : https://repo.anaconda.com/pkgs/main/noarch/pymc3-3.7-py_0.conda
md5 : 776f4475d2402db993650f64300a6e81
timestamp : 2019-09-24 21:19:22 UTC
dependencies:
- h5py >=2.7.0
- numpy >=1.13.0
- pandas >=0.18.0
- patsy >=0.4.0
- python >=3.5
- scipy >=0.18.1
- theano >=1.0.4
- tqdm >=4.8.4
pymc3 3.8 py_0
--------------
file name : pymc3-3.8-py_0.conda
name : pymc3
version : 3.8
build : py_0
build number: 0
size : 694 KB
license : Apache-2.0
subdir : noarch
url : https://repo.anaconda.com/pkgs/main/noarch/pymc3-3.8-py_0.conda
md5 : 0e9fc9b6e0687e5bf40238586876ca31
timestamp : 2020-02-20 20:01:46 UTC
dependencies:
- arviz
- h5py >=2.7.0
- numpy >=1.13.0
- pandas >=0.18.0
- patsy >=0.4.0
- python >=3.5
- scipy >=0.18.1
- theano >=1.0.4
- tqdm >=4.8.4
In the notebook though
print(f"Running on PyMC3 v{pm.__version__}")
Running on PyMC3 v3.11.2
Any clues would be welcome.
May I add, on ubuntu 18.04, the default conda-forge pymc3 is 3.9. I have to specify the version 3.11.2 in order to get it
Wait a minute, did you install conda in the root directory?
blas_info:
libraries = ['cblas', 'blas', 'cblas', 'blas']
library_dirs = ['/root/anaconda3/envs/bayes/lib']
include_dirs = ['/root/anaconda3/envs/bayes/include']
language = c
define_macros = [('HAVE_CBLAS', None)]
blas_opt_info:
define_macros = [('NO_ATLAS_INFO', 1), ('HAVE_CBLAS', None)]
libraries = ['cblas', 'blas', 'cblas', 'blas']
library_dirs = ['/root/anaconda3/envs/bayes/lib']
include_dirs = ['/root/anaconda3/envs/bayes/include']
language = c
lapack_info:
libraries = ['lapack', 'blas', 'lapack', 'blas']
library_dirs = ['/root/anaconda3/envs/bayes/lib']
language = f77
lapack_opt_info:
libraries = ['lapack', 'blas', 'lapack', 'blas', 'cblas', 'blas', 'cblas', 'blas']
library_dirs = ['/root/anaconda3/envs/bayes/lib']
language = c
define_macros = [('NO_ATLAS_INFO', 1), ('HAVE_CBLAS', None)]
include_dirs = ['/root/anaconda3/envs/bayes/include']
Supported SIMD extensions in this NumPy install:
baseline = SSE,SSE2,SSE3
found = SSSE3,SSE41,POPCNT,SSE42,AVX,F16C,FMA3,AVX2,AVX512F,AVX512CD,AVX512_SKX,AVX512_CLX
Don’t do that, it is better to install in home/$USER. Try to upgrade blas. Try to use python 3.8 or 3.9. Also, to check the requirements of pymc3:
$ conda list pymc3
# packages in environment at /home/rosgori/anaconda3:
#
# Name Version Build Channel
pymc3 3.11.2 py38h83c9d95_3 conda-forge
Pay attention to build.
$ conda search pymc3 --info | grep -A 20 -i py38h83c9d95_3
pymc3 3.11.2 py38h83c9d95_3
---------------------------
file name : pymc3-3.11.2-py38h83c9d95_3.tar.bz2
name : pymc3
version : 3.11.2
build : py38h83c9d95_3
build number: 3
size : 1.1 MB
license : Apache-2.0
subdir : linux-64
url : https://conda.anaconda.org/conda-forge/linux-64/pymc3-3.11.2-py38h83c9d95_3.tar.bz2
md5 : 3d3d2895184b4e077ac19e2e7dd5dfc9
timestamp : 2021-06-21 11:58:03 UTC
dependencies:
- arviz >=0.11.0
- cachetools >=4.2.1
- cxx-compiler
- dill
- fastprogress >=0.2.0
- mkl-service
- numpy >=1.15.0
- pandas >=0.24.0
- patsy >=0.5.1
- python >=3.8,<3.9.0a0
- python_abi 3.8.* *_cp38
- scipy >=1.2.0
- semver
- theano-pymc 1.1.2
- typing-extensions >=3.7.4
Of course, the version you use may vary.
Thanks for the quick response -
Yes conda is in the root, and I am trying to use the bayes env to install pymc3. In my case I am the root owner and sole user of the vultr server.
Python is already 3.8, and while conda-forge did install 3.11.2 (after updating to ubuntu 20.04), it still shows pymc3 3.8 in the conda search pymc3 --info. Let me reinstall conda and see what happens in one of my environments
Not sure whats going on.
Update - resintalled anaconda from scratch. This time blas was already loaded (so very good), but it kept wanting to isntall v 3.8 of pymc3 by default. I wonder if there is something wrong now with conda forge channel for pymc3.
Alright - Some cigar
After upgrading ubuntu to 20.04, reinstalling anaconda, and then installing each package of blas, mkl, from conda-forge, and then installing numpy, pandas and scikity learn, and then using conda forge for pymc3==3.11.2 (the other channels have older versions and so does conda-forge.And catching an error that said
WARNING (theano.configdefaults): g++ not detected !
And then installing g++,
I finally have no error message around blas or theano. WHen I feel saner, I will document the steps here, so other newbies can feel a little less overwhelmed.
For any new reader who’s having this same problem:
WARNING (theano.tensor.blas): Using NumPy C-API based implementation for BLAS functions.
this is what fixed it for me: when you look at conda list mkl and you see a 2021.-- (vesion of mkl) try downgrading it to 2020.4 version by using the comand conda intall mkl=2020.4 I Hope this helps, it took me 2 days trying to figure out what was going on. Perhaps someone can try using a few versions of mkl and see if it is trully related to that. Happy pymc3 learning.