Coming back to PyMC3 after a break caused by too much teaching
I’m totally inept when it comes to keeping everything sorted, so I’m starting with a fresh Anaconda install. Following the MacOS instructions on the wiki, I installed with conda install -c conda-forge mkl pymc3. Although that seems to give me pymc3-3.9.3 and theano-1.0.5, not Theano-PyMC. Is that supposed to happen?
In a vein attempt to get something done, I tried to progress with that, but when importing pymc3, I’m met with my nemesis – Theano compilation errors.
Running conda install -c conda-forge mkl pymc3 seems to be the recommended install method , and it seems to be not working as advertised, so just letting you know. Any ideas?
Do you have an old version of Theano installed? PyMC is now using the forked Theano-pymc, and having both installed can lead to issues. That’s the only thing I know about the new version…
Is this Intel hardware or Apple M1? Also, are your Xcode command line tools up to date?
twiecki
January 18, 2021, 10:41pm
4
I tried this on my OSX and I get the right version:
>>conda create -n pymc3conda
Collecting package metadata (current_repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 4.8.5
latest version: 4.9.2
Please update conda by running
$ conda update -n base conda
## Package Plan ##
environment location: /Users/twiecki/miniconda3/envs/pymc3conda
Proceed ([y]/n)? y
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate pymc3conda
#
# To deactivate an active environment, use
#
# $ conda deactivate
(base) --(23:36:25)--(Thomass-MacBook-Pro-3)--(~/projects/pymc )--(master)
>>conda activate pymc3conda
(pymc3conda) --(23:36:30)--(Thomass-MacBook-Pro-3)--(~/projects/pymc )--(master)
>>conda install -c conda-forge mkl pymc3
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 4.8.5
latest version: 4.9.2
Please update conda by running
$ conda update -n base conda
## Package Plan ##
environment location: /Users/twiecki/miniconda3/envs/pymc3conda
added / updated specs:
- mkl
- pymc3
The following packages will be downloaded:
package | build
---------------------------|-----------------
absl-py-0.11.0 | py38h50d1736_0 169 KB conda-forge
arviz-0.11.0 | pyhd8ed1ab_0 1.4 MB conda-forge
bzip2-1.0.8 | hc929b4f_4 155 KB conda-forge
c-ares-1.17.1 | hc929b4f_0 95 KB conda-forge
cctools_osx-64-949.0.1 | h2f0f38f_19 1.8 MB conda-forge
certifi-2020.12.5 | py38h50d1736_1 143 KB conda-forge
cftime-1.3.1 | py38hc7193ba_0 264 KB conda-forge
curl-7.71.1 | hcb81553_8 131 KB conda-forge
dill-0.3.3 | pyhd8ed1ab_0 60 KB conda-forge
freetype-2.10.4 | h4cff582_1 890 KB conda-forge
hdf4-4.2.13 | h71d84a9_1004 850 KB conda-forge
hdf5-1.10.6 |nompi_hc5d9132_1114 3.1 MB conda-forge
jax-0.2.8 | pyhd8ed1ab_0 453 KB conda-forge
jaxlib-0.1.59 | py38h50d1736_0 37.5 MB conda-forge
jpeg-9d | hbcb3906_0 250 KB conda-forge
kiwisolver-1.3.1 | py38hd9c93a9_1 57 KB conda-forge
krb5-1.17.2 | h60d9502_0 1.2 MB conda-forge
lcms2-2.11 | h11f7e16_1 387 KB conda-forge
ld64_osx-64-530 | hea264c1_17 1.3 MB conda-forge
libblas-3.9.0 | 7_openblas 11 KB conda-forge
libcblas-3.9.0 | 7_openblas 11 KB conda-forge
libcxx-11.0.0 | h4c3b8ed_1 1.0 MB conda-forge
libedit-3.1.20191231 | h0678c8f_2 103 KB conda-forge
libffi-3.3 | h046ec9c_2 45 KB conda-forge
libgfortran-5.0.0 |9_3_0_h6c81a4c_16 19 KB conda-forge
libgfortran5-9.3.0 | h6c81a4c_16 1.7 MB conda-forge
liblapack-3.9.0 | 7_openblas 11 KB conda-forge
libllvm11-11.0.1 | h223d4b2_0 22.4 MB conda-forge
libnetcdf-4.7.4 |nompi_h9d8a93f_107 1.2 MB conda-forge
libopenblas-0.3.12 |openmp_h54245bb_1 8.8 MB conda-forge
libpng-1.6.37 | h7cec526_2 313 KB conda-forge
libtiff-4.2.0 | h355d032_0 639 KB conda-forge
libwebp-base-1.1.0 | hbcb3906_3 757 KB conda-forge
llvm-openmp-11.0.1 | h7c73e74_0 268 KB conda-forge
lz4-c-1.9.3 | h046ec9c_0 155 KB conda-forge
mako-1.1.4 | pyh44b312d_0 58 KB conda-forge
markupsafe-1.1.1 | py38h5406a74_3 25 KB conda-forge
matplotlib-base-3.3.3 | py38hdcc317e_0 6.7 MB conda-forge
mkl-2020.4 | h08c4f10_301 145.2 MB conda-forge
ncurses-6.2 | h2e338ed_4 881 KB conda-forge
netcdf4-1.5.5.1 |nompi_py38h0bc7383_100 441 KB conda-forge
numpy-1.19.5 | py38h6ced74f_1 5.1 MB conda-forge
olefile-0.46 | pyh9f0ad1d_1 32 KB conda-forge
packaging-20.8 | pyhd3deb0d_0 34 KB conda-forge
pandas-1.2.0 | py38he9f00de_1 10.6 MB conda-forge
pillow-8.1.0 | py38hc1d52f7_1 646 KB conda-forge
pip-20.3.3 | pyhd8ed1ab_0 1.1 MB conda-forge
pygpu-0.7.6 |py38hc7193ba_1002 604 KB conda-forge
pymc3-3.10.0 | pyhd8ed1ab_0 1.4 MB conda-forge
python-3.8.6 |h624753d_4_cpython 12.4 MB conda-forge
python-flatbuffers-1.11 | py_0 18 KB conda-forge
pytz-2020.5 | pyhd8ed1ab_0 244 KB conda-forge
scipy-1.6.0 | py38h95ea19e_0 18.5 MB conda-forge
setuptools-49.6.0 | py38h50d1736_3 931 KB conda-forge
sqlite-3.34.0 | h17101e1_0 1.7 MB conda-forge
tapi-1100.0.11 | h9ce4665_0 196 KB conda-forge
theano-pymc-1.0.11 | py38hf416894_0 3.6 MB conda-forge
tk-8.6.10 | h0419947_1 3.3 MB conda-forge
tornado-6.1 | py38h5406a74_1 643 KB conda-forge
typing-extensions-3.7.4.3 | 0 8 KB conda-forge
typing_extensions-3.7.4.3 | py_0 25 KB conda-forge
wheel-0.36.2 | pyhd3deb0d_0 31 KB conda-forge
xarray-0.16.2 | pyhd8ed1ab_0 546 KB conda-forge
zstd-1.4.8 | hf387650_1 870 KB conda-forge
------------------------------------------------------------
Total: 303.1 MB
The following NEW packages will be INSTALLED:
absl-py conda-forge/osx-64::absl-py-0.11.0-py38h50d1736_0
arviz conda-forge/noarch::arviz-0.11.0-pyhd8ed1ab_0
bzip2 conda-forge/osx-64::bzip2-1.0.8-hc929b4f_4
c-ares conda-forge/osx-64::c-ares-1.17.1-hc929b4f_0
ca-certificates conda-forge/osx-64::ca-certificates-2020.12.5-h033912b_0
cctools_osx-64 conda-forge/osx-64::cctools_osx-64-949.0.1-h2f0f38f_19
certifi conda-forge/osx-64::certifi-2020.12.5-py38h50d1736_1
cftime conda-forge/osx-64::cftime-1.3.1-py38hc7193ba_0
clang conda-forge/osx-64::clang-10.0.1-default_hf57f61e_1
clang_osx-64 conda-forge/osx-64::clang_osx-64-10.0.1-h05bbb7f_10
clangxx conda-forge/osx-64::clangxx-10.0.1-default_hf57f61e_1
clangxx_osx-64 conda-forge/osx-64::clangxx_osx-64-10.0.1-h05bbb7f_10
compiler-rt conda-forge/osx-64::compiler-rt-10.0.1-he6db49b_0
compiler-rt_osx-64 conda-forge/noarch::compiler-rt_osx-64-10.0.1-h033240e_0
curl conda-forge/osx-64::curl-7.71.1-hcb81553_8
cycler conda-forge/noarch::cycler-0.10.0-py_2
dill conda-forge/noarch::dill-0.3.3-pyhd8ed1ab_0
fastprogress conda-forge/noarch::fastprogress-1.0.0-py_0
freetype conda-forge/osx-64::freetype-2.10.4-h4cff582_1
hdf4 conda-forge/osx-64::hdf4-4.2.13-h71d84a9_1004
hdf5 conda-forge/osx-64::hdf5-1.10.6-nompi_hc5d9132_1114
jax conda-forge/noarch::jax-0.2.8-pyhd8ed1ab_0
jaxlib conda-forge/osx-64::jaxlib-0.1.59-py38h50d1736_0
jpeg conda-forge/osx-64::jpeg-9d-hbcb3906_0
kiwisolver conda-forge/osx-64::kiwisolver-1.3.1-py38hd9c93a9_1
krb5 conda-forge/osx-64::krb5-1.17.2-h60d9502_0
lcms2 conda-forge/osx-64::lcms2-2.11-h11f7e16_1
ld64_osx-64 conda-forge/osx-64::ld64_osx-64-530-hea264c1_17
ldid conda-forge/osx-64::ldid-2.1.2-h7660a38_2
libblas conda-forge/osx-64::libblas-3.9.0-7_openblas
libcblas conda-forge/osx-64::libcblas-3.9.0-7_openblas
libclang-cpp10 conda-forge/osx-64::libclang-cpp10-10.0.1-default_hf57f61e_1
libcurl conda-forge/osx-64::libcurl-7.71.1-h9bf37e3_8
libcxx conda-forge/osx-64::libcxx-11.0.0-h4c3b8ed_1
libedit conda-forge/osx-64::libedit-3.1.20191231-h0678c8f_2
libev conda-forge/osx-64::libev-4.33-haf1e3a3_1
libffi conda-forge/osx-64::libffi-3.3-h046ec9c_2
libgfortran conda-forge/osx-64::libgfortran-5.0.0-9_3_0_h6c81a4c_16
libgfortran5 conda-forge/osx-64::libgfortran5-9.3.0-h6c81a4c_16
libgpuarray conda-forge/osx-64::libgpuarray-0.7.6-h1de35cc_1003
liblapack conda-forge/osx-64::liblapack-3.9.0-7_openblas
libllvm10 conda-forge/osx-64::libllvm10-10.0.1-h009f743_3
libllvm11 conda-forge/osx-64::libllvm11-11.0.1-h223d4b2_0
libnetcdf conda-forge/osx-64::libnetcdf-4.7.4-nompi_h9d8a93f_107
libnghttp2 conda-forge/osx-64::libnghttp2-1.41.0-h7580e61_2
libopenblas conda-forge/osx-64::libopenblas-0.3.12-openmp_h54245bb_1
libpng conda-forge/osx-64::libpng-1.6.37-h7cec526_2
libssh2 conda-forge/osx-64::libssh2-1.9.0-h8a08a2b_5
libtiff conda-forge/osx-64::libtiff-4.2.0-h355d032_0
libwebp-base conda-forge/osx-64::libwebp-base-1.1.0-hbcb3906_3
llvm-openmp conda-forge/osx-64::llvm-openmp-11.0.1-h7c73e74_0
llvm-tools conda-forge/osx-64::llvm-tools-10.0.1-h1341992_3
lz4-c conda-forge/osx-64::lz4-c-1.9.3-h046ec9c_0
mako conda-forge/noarch::mako-1.1.4-pyh44b312d_0
markupsafe conda-forge/osx-64::markupsafe-1.1.1-py38h5406a74_3
matplotlib-base conda-forge/osx-64::matplotlib-base-3.3.3-py38hdcc317e_0
mkl conda-forge/osx-64::mkl-2020.4-h08c4f10_301
ncurses conda-forge/osx-64::ncurses-6.2-h2e338ed_4
netcdf4 conda-forge/osx-64::netcdf4-1.5.5.1-nompi_py38h0bc7383_100
numpy conda-forge/osx-64::numpy-1.19.5-py38h6ced74f_1
olefile conda-forge/noarch::olefile-0.46-pyh9f0ad1d_1
openssl conda-forge/osx-64::openssl-1.1.1i-h35c211d_0
opt_einsum conda-forge/noarch::opt_einsum-3.3.0-py_0
packaging conda-forge/noarch::packaging-20.8-pyhd3deb0d_0
pandas conda-forge/osx-64::pandas-1.2.0-py38he9f00de_1
patsy conda-forge/noarch::patsy-0.5.1-py_0
pillow conda-forge/osx-64::pillow-8.1.0-py38hc1d52f7_1
pip conda-forge/noarch::pip-20.3.3-pyhd8ed1ab_0
pygpu conda-forge/osx-64::pygpu-0.7.6-py38hc7193ba_1002
pymc3 conda-forge/noarch::pymc3-3.10.0-pyhd8ed1ab_0
pyparsing conda-forge/noarch::pyparsing-2.4.7-pyh9f0ad1d_0
python conda-forge/osx-64::python-3.8.6-h624753d_4_cpython
python-dateutil conda-forge/noarch::python-dateutil-2.8.1-py_0
python-flatbuffers conda-forge/noarch::python-flatbuffers-1.11-py_0
python_abi conda-forge/osx-64::python_abi-3.8-1_cp38
pytz conda-forge/noarch::pytz-2020.5-pyhd8ed1ab_0
readline conda-forge/osx-64::readline-8.0-h0678c8f_2
scipy conda-forge/osx-64::scipy-1.6.0-py38h95ea19e_0
setuptools conda-forge/osx-64::setuptools-49.6.0-py38h50d1736_3
six conda-forge/noarch::six-1.15.0-pyh9f0ad1d_0
sqlite conda-forge/osx-64::sqlite-3.34.0-h17101e1_0
tapi conda-forge/osx-64::tapi-1100.0.11-h9ce4665_0
theano-pymc conda-forge/osx-64::theano-pymc-1.0.11-py38hf416894_0
tk conda-forge/osx-64::tk-8.6.10-h0419947_1
tornado conda-forge/osx-64::tornado-6.1-py38h5406a74_1
typing-extensions conda-forge/noarch::typing-extensions-3.7.4.3-0
typing_extensions conda-forge/noarch::typing_extensions-3.7.4.3-py_0
wheel conda-forge/noarch::wheel-0.36.2-pyhd3deb0d_0
xarray conda-forge/noarch::xarray-0.16.2-pyhd8ed1ab_0
xz conda-forge/osx-64::xz-5.2.5-haf1e3a3_1
zlib conda-forge/osx-64::zlib-1.2.11-h7795811_1010
zstd conda-forge/osx-64::zstd-1.4.8-hf387650_1
1 Like
@drbenvincent What I did was checkout the pymc3 repo and build a conda environment using its conda-envs/environment-dev-py38.yml (note that you don’t have to check out the repo to do this – you could just download that one file from the github repo).
With that conda environment set up, I then did
pip install theano-pymc – to make sure I didn’t get the stock version of Theano.
then
pip install pymc3
That worked for me. Installing with pip alone – without setting up the conda environment – just gave me all kinds of cryptic errors when Theano tried to compile my PyMC3 models. There’s deep magic in there with clang and mkl, and I really don’t want to think about it!
Hope that helps.
1 Like
This is on an intel iMac.
That is very odd… following the exact steps of @twiecki I’m getting the wrong version of pymc3.
(base) benjamv@x86_64-apple-darwin13 ~ % conda create -n pymc3conda
Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /Users/benjamv/opt/anaconda3/envs/pymc3conda
Proceed ([y]/n)? y
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate pymc3conda
#
# To deactivate an active environment, use
#
# $ conda deactivate
(base) benjamv@x86_64-apple-darwin13 ~ % conda activate pymc3conda
(pymc3conda) benjamv@x86_64-apple-darwin13 ~ %
(pymc3conda) benjamv@x86_64-apple-darwin13 ~ % conda install -c conda-forge mkl pymc3
Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /Users/benjamv/opt/anaconda3/envs/pymc3conda
added / updated specs:
- mkl
- pymc3
The following packages will be downloaded:
package | build
---------------------------|-----------------
bzip2-1.0.8 | hc929b4f_4 155 KB conda-forge
c-ares-1.17.1 | hc929b4f_0 95 KB conda-forge
ca-certificates-2020.12.5 | h033912b_0 138 KB conda-forge
certifi-2020.12.5 | py38h50d1736_1 143 KB conda-forge
curl-7.71.1 | hcb81553_8 131 KB conda-forge
cycler-0.10.0 | py_2 9 KB conda-forge
freetype-2.10.4 | h4cff582_1 890 KB conda-forge
h5py-2.10.0 |nompi_py38h106b333_102 1022 KB conda-forge
hdf4-4.2.13 | h71d84a9_1004 850 KB conda-forge
hdf5-1.10.5 |nompi_h0cbb7df_1103 2.7 MB conda-forge
jpeg-9d | hbcb3906_0 250 KB conda-forge
kiwisolver-1.3.1 | py38hd9c93a9_1 57 KB conda-forge
krb5-1.17.2 | h60d9502_0 1.2 MB conda-forge
lcms2-2.11 | h11f7e16_1 387 KB conda-forge
libcurl-7.71.1 | h9bf37e3_8 297 KB conda-forge
libcxx-11.0.0 | h4c3b8ed_1 1.0 MB conda-forge
libedit-3.1.20191231 | h0678c8f_2 103 KB conda-forge
libev-4.33 | haf1e3a3_1 99 KB conda-forge
libffi-3.3 | h046ec9c_2 45 KB conda-forge
libgfortran-3.0.1 | 0 495 KB conda-forge
libllvm10-10.0.1 | h009f743_3 20.8 MB conda-forge
libnetcdf-4.7.4 |nompi_he461dc0_101 1.2 MB conda-forge
libnghttp2-1.41.0 | h7580e61_2 831 KB conda-forge
libpng-1.6.37 | h7cec526_2 313 KB conda-forge
libssh2-1.9.0 | h8a08a2b_5 214 KB conda-forge
libtiff-4.2.0 | h355d032_0 639 KB conda-forge
libwebp-base-1.1.0 | hbcb3906_3 757 KB conda-forge
lz4-c-1.9.3 | h046ec9c_0 155 KB conda-forge
markupsafe-1.1.1 | py38h5406a74_3 25 KB conda-forge
matplotlib-base-3.3.3 | py38hdcc317e_0 6.7 MB conda-forge
mkl-2019.5 | 281 158.1 MB conda-forge
mkl-service-2.3.0 | py38h0b31af3_0 46 KB conda-forge
ncurses-6.2 | h2e338ed_4 881 KB conda-forge
netcdf4-1.5.3 |nompi_py38h645dd01_103 495 KB conda-forge
olefile-0.46 | pyh9f0ad1d_1 32 KB conda-forge
openssl-1.1.1i | h35c211d_0 1.9 MB conda-forge
packaging-20.8 | pyhd3deb0d_0 34 KB conda-forge
pandas-1.2.0 | py38he9f00de_1 10.6 MB conda-forge
patsy-0.5.1 | py_0 187 KB conda-forge
pillow-8.1.0 | py38hc1d52f7_1 646 KB conda-forge
pip-20.3.3 | pyhd8ed1ab_0 1.1 MB conda-forge
pyparsing-2.4.7 | pyh9f0ad1d_0 60 KB conda-forge
python-3.8.6 |h624753d_4_cpython 12.4 MB conda-forge
python-dateutil-2.8.1 | py_0 220 KB conda-forge
pytz-2020.5 | pyhd8ed1ab_0 244 KB conda-forge
readline-8.0 | h0678c8f_2 255 KB conda-forge
setuptools-49.6.0 | py38h50d1736_3 931 KB conda-forge
six-1.15.0 | pyh9f0ad1d_0 14 KB conda-forge
sqlite-3.34.0 | h17101e1_0 1.7 MB conda-forge
tk-8.6.10 | h0419947_1 3.3 MB conda-forge
tornado-6.1 | py38h5406a74_1 643 KB conda-forge
tqdm-4.56.0 | pyhd8ed1ab_0 76 KB conda-forge
typing_extensions-3.7.4.3 | py_0 25 KB conda-forge
wheel-0.36.2 | pyhd3deb0d_0 31 KB conda-forge
xz-5.2.5 | haf1e3a3_1 228 KB conda-forge
zlib-1.2.11 | h7795811_1010 102 KB conda-forge
zstd-1.4.8 | hf387650_1 870 KB conda-forge
------------------------------------------------------------
Total: 236.5 MB
The following NEW packages will be INSTALLED:
arviz conda-forge/noarch::arviz-0.11.0-pyhd8ed1ab_0
blas pkgs/main/osx-64::blas-1.0-mkl
bzip2 conda-forge/osx-64::bzip2-1.0.8-hc929b4f_4
c-ares conda-forge/osx-64::c-ares-1.17.1-hc929b4f_0
ca-certificates conda-forge/osx-64::ca-certificates-2020.12.5-h033912b_0
cctools conda-forge/osx-64::cctools-949.0.1-h22b1bf0_1
cctools_osx-64 conda-forge/osx-64::cctools_osx-64-949.0.1-h5ba7a2e_1
certifi conda-forge/osx-64::certifi-2020.12.5-py38h50d1736_1
cftime conda-forge/osx-64::cftime-1.3.1-py38hc7193ba_0
clang pkgs/main/osx-64::clang-10.0.0-default_hf57f61e_0
clang_osx-64 pkgs/main/osx-64::clang_osx-64-10.0.0-h05bbb7f_0
clangxx pkgs/main/osx-64::clangxx-10.0.0-default_hf57f61e_0
clangxx_osx-64 pkgs/main/osx-64::clangxx_osx-64-10.0.0-h05bbb7f_1
compiler-rt pkgs/main/osx-64::compiler-rt-10.0.0-h47ead80_0
compiler-rt_osx-64 pkgs/main/noarch::compiler-rt_osx-64-10.0.0-hbcc88fd_0
curl conda-forge/osx-64::curl-7.71.1-hcb81553_8
cycler conda-forge/noarch::cycler-0.10.0-py_2
fastprogress conda-forge/noarch::fastprogress-1.0.0-py_0
freetype conda-forge/osx-64::freetype-2.10.4-h4cff582_1
h5py conda-forge/osx-64::h5py-2.10.0-nompi_py38h106b333_102
hdf4 conda-forge/osx-64::hdf4-4.2.13-h71d84a9_1004
hdf5 conda-forge/osx-64::hdf5-1.10.5-nompi_h0cbb7df_1103
jpeg conda-forge/osx-64::jpeg-9d-hbcb3906_0
kiwisolver conda-forge/osx-64::kiwisolver-1.3.1-py38hd9c93a9_1
krb5 conda-forge/osx-64::krb5-1.17.2-h60d9502_0
lcms2 conda-forge/osx-64::lcms2-2.11-h11f7e16_1
ld64 conda-forge/osx-64::ld64-530-1
ld64_osx-64 conda-forge/osx-64::ld64_osx-64-530-h3c32e8a_1
libcurl conda-forge/osx-64::libcurl-7.71.1-h9bf37e3_8
libcxx conda-forge/osx-64::libcxx-11.0.0-h4c3b8ed_1
libedit conda-forge/osx-64::libedit-3.1.20191231-h0678c8f_2
libev conda-forge/osx-64::libev-4.33-haf1e3a3_1
libffi conda-forge/osx-64::libffi-3.3-h046ec9c_2
libgfortran conda-forge/osx-64::libgfortran-3.0.1-0
libgpuarray conda-forge/osx-64::libgpuarray-0.7.6-h1de35cc_1003
libllvm10 conda-forge/osx-64::libllvm10-10.0.1-h009f743_3
libnetcdf conda-forge/osx-64::libnetcdf-4.7.4-nompi_he461dc0_101
libnghttp2 conda-forge/osx-64::libnghttp2-1.41.0-h7580e61_2
libpng conda-forge/osx-64::libpng-1.6.37-h7cec526_2
libssh2 conda-forge/osx-64::libssh2-1.9.0-h8a08a2b_5
libtiff conda-forge/osx-64::libtiff-4.2.0-h355d032_0
libwebp-base conda-forge/osx-64::libwebp-base-1.1.0-hbcb3906_3
llvm-openmp pkgs/main/osx-64::llvm-openmp-10.0.0-h28b9765_0
lz4-c conda-forge/osx-64::lz4-c-1.9.3-h046ec9c_0
mako conda-forge/noarch::mako-1.1.4-pyh44b312d_0
markupsafe conda-forge/osx-64::markupsafe-1.1.1-py38h5406a74_3
matplotlib-base conda-forge/osx-64::matplotlib-base-3.3.3-py38hdcc317e_0
mkl conda-forge/osx-64::mkl-2019.5-281
mkl-service conda-forge/osx-64::mkl-service-2.3.0-py38h0b31af3_0
mkl_fft pkgs/main/osx-64::mkl_fft-1.2.0-py38hc64f4ea_0
mkl_random pkgs/main/osx-64::mkl_random-1.1.1-py38h959d312_0
ncurses conda-forge/osx-64::ncurses-6.2-h2e338ed_4
netcdf4 conda-forge/osx-64::netcdf4-1.5.3-nompi_py38h645dd01_103
numpy pkgs/main/osx-64::numpy-1.19.2-py38h456fd55_0
numpy-base pkgs/main/osx-64::numpy-base-1.19.2-py38hcfb5961_0
olefile conda-forge/noarch::olefile-0.46-pyh9f0ad1d_1
openssl conda-forge/osx-64::openssl-1.1.1i-h35c211d_0
packaging conda-forge/noarch::packaging-20.8-pyhd3deb0d_0
pandas conda-forge/osx-64::pandas-1.2.0-py38he9f00de_1
patsy conda-forge/noarch::patsy-0.5.1-py_0
pillow conda-forge/osx-64::pillow-8.1.0-py38hc1d52f7_1
pip conda-forge/noarch::pip-20.3.3-pyhd8ed1ab_0
pygpu conda-forge/osx-64::pygpu-0.7.6-py38hc7193ba_1002
pymc3 conda-forge/noarch::pymc3-3.9.3-py_1
pyparsing conda-forge/noarch::pyparsing-2.4.7-pyh9f0ad1d_0
python conda-forge/osx-64::python-3.8.6-h624753d_4_cpython
python-dateutil conda-forge/noarch::python-dateutil-2.8.1-py_0
python_abi conda-forge/osx-64::python_abi-3.8-1_cp38
pytz conda-forge/noarch::pytz-2020.5-pyhd8ed1ab_0
readline conda-forge/osx-64::readline-8.0-h0678c8f_2
scipy pkgs/main/osx-64::scipy-1.5.2-py38h2515648_0
setuptools conda-forge/osx-64::setuptools-49.6.0-py38h50d1736_3
six conda-forge/noarch::six-1.15.0-pyh9f0ad1d_0
sqlite conda-forge/osx-64::sqlite-3.34.0-h17101e1_0
tapi conda-forge/osx-64::tapi-1000.10.8-h879752b_4
theano conda-forge/osx-64::theano-1.0.5-py38hf416894_1
tk conda-forge/osx-64::tk-8.6.10-h0419947_1
tornado conda-forge/osx-64::tornado-6.1-py38h5406a74_1
tqdm conda-forge/noarch::tqdm-4.56.0-pyhd8ed1ab_0
typing-extensions conda-forge/noarch::typing-extensions-3.7.4.3-0
typing_extensions conda-forge/noarch::typing_extensions-3.7.4.3-py_0
wheel conda-forge/noarch::wheel-0.36.2-pyhd3deb0d_0
xarray conda-forge/noarch::xarray-0.16.2-pyhd8ed1ab_0
xz conda-forge/osx-64::xz-5.2.5-haf1e3a3_1
zlib conda-forge/osx-64::zlib-1.2.11-h7795811_1010
zstd conda-forge/osx-64::zstd-1.4.8-hf387650_1
So I bailed on installing that and tried what @rpgoldman suggests…pip install theano-pymc and then pip install pymc3 and I get pymc3 3.10.0. Have successfully fitted an example model… no Theano headaches.
Interesting. We have not had other users report this, but I will add this information to our install instructions incase others find it helpful.
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To clarify, I only did those two pip install instructions in a fresh environment in a fresh anaconda install.
That looks very much like what I was seeing, and I note that in your transcript conda is going to install theano instead of theano-pymc.
That aligns with my experience, where I added theano-pymc manually, removed theano and conda removed pymc3.
My only guess is that something is going wrong with the replacement of theano by theano-pymc.
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. I see that we’re now on 3.10.0 - well done to all involved.