celerite
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Published
20 hours ago •
dfm
dfm
Import error on Python 3.9
Hi Dan,
I understand celerite is superseded by celerite2, but it would still be nice to keep the functionality alive for allesfitter users on Python 3.9.
To replicate the error: I set up a brand new conda environment with Python 3.9 and full anaconda. Then I pip-installed celerite and tried to import it as shown below:
(env_python39) Maximilians-iMac-Pro:~ mx$ pip install celerite
Collecting celerite
Using cached celerite-0.4.0-cp39-cp39-macosx_10_9_x86_64.whl
Requirement already satisfied: pybind11 in ./opt/anaconda3/envs/env_python39/lib/python3.9/site-packages (from celerite) (2.7.1)
Requirement already satisfied: numpy in ./opt/anaconda3/envs/env_python39/lib/python3.9/site-packages (from celerite) (1.20.1)
Installing collected packages: celerite
Successfully installed celerite-0.4.0
(env_python39) Maximilians-iMac-Pro:~ mx$ python
Python 3.9.4 (default, Apr 9 2021, 09:32:38)
[Clang 10.0.0 ] :: Anaconda, Inc. on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import celerite
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Users/mx/opt/anaconda3/envs/env_python39/lib/python3.9/site-packages/celerite/__init__.py", line 34, in <module>
from . import terms, solver, modeling
File "/Users/mx/opt/anaconda3/envs/env_python39/lib/python3.9/site-packages/celerite/terms.py", line 18, in <module>
from .solver import get_kernel_value, get_psd_value, check_coefficients
ImportError: dlopen(/Users/mx/opt/anaconda3/envs/env_python39/lib/python3.9/site-packages/celerite/solver.cpython-39-darwin.so, 2): Symbol not found: __ZTIN10__cxxabiv115__forced_unwindE
Referenced from: /Users/mx/opt/anaconda3/envs/env_python39/lib/python3.9/site-packages/celerite/solver.cpython-39-darwin.so
Expected in: flat namespace
in /Users/mx/opt/anaconda3/envs/env_python39/lib/python3.9/site-packages/celerite/solver.cpython-39-darwin.so
celerite is tested and regularly used on Python 3.9 so I'm not sure that this is a generic issue. Can you say more about your system, setup, and exactly what commands you ran?
System:
macOS Catalina Version 10.15.7 iMac Pro (2017) Processor 3 GHz 10-Core Intel Xeon W
Terminal commands from scratch, leading to error:
(base) Maximilians-iMac-Pro:~ mx$ conda create -n env_test python=3.9 anaconda
Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /Users/mx/opt/anaconda3/envs/env_test
added / updated specs:
- anaconda
- python=3.9
The following NEW packages will be INSTALLED:
alabaster pkgs/main/noarch::alabaster-0.7.12-pyhd3eb1b0_0
anaconda pkgs/main/osx-64::anaconda-2021.05-py39_0
anaconda-client pkgs/main/osx-64::anaconda-client-1.7.2-py39hecd8cb5_0
anaconda-project pkgs/main/noarch::anaconda-project-0.9.1-pyhd3eb1b0_1
anyio pkgs/main/osx-64::anyio-2.2.0-py39hecd8cb5_1
appdirs pkgs/main/noarch::appdirs-1.4.4-py_0
applaunchservices pkgs/main/noarch::applaunchservices-0.2.1-py_0
appnope pkgs/main/osx-64::appnope-0.1.2-py39hecd8cb5_1001
appscript pkgs/main/osx-64::appscript-1.1.2-py39h9ed2024_0
argh pkgs/main/osx-64::argh-0.26.2-py39hecd8cb5_0
argon2-cffi pkgs/main/osx-64::argon2-cffi-20.1.0-py39h9ed2024_1
asn1crypto pkgs/main/noarch::asn1crypto-1.4.0-py_0
astroid pkgs/main/osx-64::astroid-2.5-py39hecd8cb5_1
astropy pkgs/main/osx-64::astropy-4.2.1-py39h9ed2024_1
async_generator pkgs/main/noarch::async_generator-1.10-pyhd3eb1b0_0
atomicwrites pkgs/main/noarch::atomicwrites-1.4.0-py_0
attrs pkgs/main/noarch::attrs-20.3.0-pyhd3eb1b0_0
autopep8 pkgs/main/noarch::autopep8-1.5.6-pyhd3eb1b0_0
babel pkgs/main/noarch::babel-2.9.0-pyhd3eb1b0_0
backcall pkgs/main/noarch::backcall-0.2.0-pyhd3eb1b0_0
backports pkgs/main/noarch::backports-1.0-pyhd3eb1b0_2
backports.shutil_~ pkgs/main/noarch::backports.shutil_get_terminal_size-1.0.0-pyhd3eb1b0_3
beautifulsoup4 pkgs/main/noarch::beautifulsoup4-4.9.3-pyha847dfd_0
bitarray pkgs/main/osx-64::bitarray-1.9.2-py39h9ed2024_1
bkcharts pkgs/main/osx-64::bkcharts-0.2-py39hecd8cb5_0
black pkgs/main/noarch::black-19.10b0-py_0
blas pkgs/main/osx-64::blas-1.0-mkl
bleach pkgs/main/noarch::bleach-3.3.0-pyhd3eb1b0_0
blosc pkgs/main/osx-64::blosc-1.21.0-h2842e9f_0
bokeh pkgs/main/osx-64::bokeh-2.3.2-py39hecd8cb5_0
boto pkgs/main/osx-64::boto-2.49.0-py39hecd8cb5_0
bottleneck pkgs/main/osx-64::bottleneck-1.3.2-py39he3068b8_1
brotli pkgs/main/osx-64::brotli-1.0.9-hb1e8313_2
brotlipy pkgs/main/osx-64::brotlipy-0.7.0-py39h9ed2024_1003
brunsli pkgs/main/osx-64::brunsli-0.1-h23ab428_0
bzip2 pkgs/main/osx-64::bzip2-1.0.8-h1de35cc_0
c-ares pkgs/main/osx-64::c-ares-1.17.1-h9ed2024_0
ca-certificates pkgs/main/osx-64::ca-certificates-2021.4.13-hecd8cb5_1
certifi pkgs/main/osx-64::certifi-2020.12.5-py39hecd8cb5_0
cffi pkgs/main/osx-64::cffi-1.14.5-py39h2125817_0
chardet pkgs/main/osx-64::chardet-4.0.0-py39hecd8cb5_1003
charls pkgs/main/osx-64::charls-2.2.0-h23ab428_0
click pkgs/main/noarch::click-7.1.2-pyhd3eb1b0_0
cloudpickle pkgs/main/noarch::cloudpickle-1.6.0-py_0
clyent pkgs/main/osx-64::clyent-1.2.2-py39hecd8cb5_1
colorama pkgs/main/noarch::colorama-0.4.4-pyhd3eb1b0_0
contextlib2 pkgs/main/noarch::contextlib2-0.6.0.post1-py_0
cryptography pkgs/main/osx-64::cryptography-3.4.7-py39h2fd3fbb_0
curl pkgs/main/osx-64::curl-7.71.1-hb0a8c7a_1
cycler pkgs/main/osx-64::cycler-0.10.0-py39hecd8cb5_0
cython pkgs/main/osx-64::cython-0.29.23-py39h23ab428_0
cytoolz pkgs/main/osx-64::cytoolz-0.11.0-py39h9ed2024_0
dask pkgs/main/noarch::dask-2021.4.0-pyhd3eb1b0_0
dask-core pkgs/main/noarch::dask-core-2021.4.0-pyhd3eb1b0_0
decorator pkgs/main/noarch::decorator-5.0.6-pyhd3eb1b0_0
defusedxml pkgs/main/noarch::defusedxml-0.7.1-pyhd3eb1b0_0
diff-match-patch pkgs/main/noarch::diff-match-patch-20200713-py_0
distributed pkgs/main/osx-64::distributed-2021.4.0-py39hecd8cb5_0
docutils pkgs/main/osx-64::docutils-0.17-py39hecd8cb5_1
entrypoints pkgs/main/osx-64::entrypoints-0.3-py39hecd8cb5_0
et_xmlfile pkgs/main/noarch::et_xmlfile-1.0.1-py_1001
fastcache pkgs/main/osx-64::fastcache-1.1.0-py39h9ed2024_0
filelock pkgs/main/noarch::filelock-3.0.12-pyhd3eb1b0_1
flake8 pkgs/main/noarch::flake8-3.9.0-pyhd3eb1b0_0
flask pkgs/main/noarch::flask-1.1.2-pyhd3eb1b0_0
freetype pkgs/main/osx-64::freetype-2.10.4-ha233b18_0
fsspec pkgs/main/noarch::fsspec-0.9.0-pyhd3eb1b0_0
future pkgs/main/osx-64::future-0.18.2-py39hecd8cb5_1
get_terminal_size pkgs/main/osx-64::get_terminal_size-1.0.0-h7520d66_0
gevent pkgs/main/osx-64::gevent-21.1.2-py39h9ed2024_1
giflib pkgs/main/osx-64::giflib-5.1.4-h1de35cc_1
glob2 pkgs/main/noarch::glob2-0.7-pyhd3eb1b0_0
gmp pkgs/main/osx-64::gmp-6.2.1-h23ab428_2
gmpy2 pkgs/main/osx-64::gmpy2-2.0.8-py39h4b98818_3
greenlet pkgs/main/osx-64::greenlet-1.0.0-py39h23ab428_2
h5py pkgs/main/osx-64::h5py-2.10.0-py39h90fc2a2_0
hdf5 pkgs/main/osx-64::hdf5-1.10.6-hdbbcd12_0
heapdict pkgs/main/noarch::heapdict-1.0.1-py_0
html5lib pkgs/main/noarch::html5lib-1.1-py_0
icu pkgs/main/osx-64::icu-58.2-h0a44026_3
idna pkgs/main/noarch::idna-2.10-pyhd3eb1b0_0
imagecodecs pkgs/main/osx-64::imagecodecs-2021.3.31-py39h2ea9c00_0
imageio pkgs/main/noarch::imageio-2.9.0-pyhd3eb1b0_0
imagesize pkgs/main/noarch::imagesize-1.2.0-pyhd3eb1b0_0
importlib-metadata pkgs/main/osx-64::importlib-metadata-3.10.0-py39hecd8cb5_0
importlib_metadata pkgs/main/noarch::importlib_metadata-3.10.0-hd3eb1b0_0
iniconfig pkgs/main/noarch::iniconfig-1.1.1-pyhd3eb1b0_0
intel-openmp pkgs/main/osx-64::intel-openmp-2021.2.0-hecd8cb5_564
intervaltree pkgs/main/noarch::intervaltree-3.1.0-py_0
ipykernel pkgs/main/osx-64::ipykernel-5.3.4-py39h01d92e1_0
ipython pkgs/main/osx-64::ipython-7.22.0-py39h01d92e1_0
ipython_genutils pkgs/main/noarch::ipython_genutils-0.2.0-pyhd3eb1b0_1
ipywidgets pkgs/main/noarch::ipywidgets-7.6.3-pyhd3eb1b0_1
isort pkgs/main/noarch::isort-5.8.0-pyhd3eb1b0_0
itsdangerous pkgs/main/noarch::itsdangerous-1.1.0-pyhd3eb1b0_0
jbig pkgs/main/osx-64::jbig-2.1-h4d881f8_0
jdcal pkgs/main/noarch::jdcal-1.4.1-py_0
jedi pkgs/main/osx-64::jedi-0.17.2-py39hecd8cb5_1
jinja2 pkgs/main/noarch::jinja2-2.11.3-pyhd3eb1b0_0
joblib pkgs/main/noarch::joblib-1.0.1-pyhd3eb1b0_0
jpeg pkgs/main/osx-64::jpeg-9b-he5867d9_2
json5 pkgs/main/noarch::json5-0.9.5-py_0
jsonschema pkgs/main/noarch::jsonschema-3.2.0-py_2
jupyter pkgs/main/osx-64::jupyter-1.0.0-py39hecd8cb5_7
jupyter-packaging pkgs/main/noarch::jupyter-packaging-0.7.12-pyhd3eb1b0_0
jupyter_client pkgs/main/noarch::jupyter_client-6.1.12-pyhd3eb1b0_0
jupyter_console pkgs/main/noarch::jupyter_console-6.4.0-pyhd3eb1b0_0
jupyter_core pkgs/main/osx-64::jupyter_core-4.7.1-py39hecd8cb5_0
jupyter_server pkgs/main/osx-64::jupyter_server-1.4.1-py39hecd8cb5_0
jupyterlab pkgs/main/noarch::jupyterlab-3.0.14-pyhd3eb1b0_1
jupyterlab_pygmen~ pkgs/main/noarch::jupyterlab_pygments-0.1.2-py_0
jupyterlab_server pkgs/main/noarch::jupyterlab_server-2.4.0-pyhd3eb1b0_0
jupyterlab_widgets pkgs/main/noarch::jupyterlab_widgets-1.0.0-pyhd3eb1b0_1
jxrlib pkgs/main/osx-64::jxrlib-1.1-haf1e3a3_2
keyring pkgs/main/osx-64::keyring-22.3.0-py39hecd8cb5_0
kiwisolver pkgs/main/osx-64::kiwisolver-1.3.1-py39h23ab428_0
krb5 pkgs/main/osx-64::krb5-1.18.2-h75d18d8_0
lazy-object-proxy pkgs/main/osx-64::lazy-object-proxy-1.6.0-py39h9ed2024_0
lcms2 pkgs/main/osx-64::lcms2-2.12-hf1fd2bf_0
lerc pkgs/main/osx-64::lerc-2.2.1-h23ab428_0
libaec pkgs/main/osx-64::libaec-1.0.4-hb1e8313_1
libarchive pkgs/main/osx-64::libarchive-3.4.2-haa3ed63_0
libcurl pkgs/main/osx-64::libcurl-7.71.1-h8a08a2b_1
libcxx pkgs/main/osx-64::libcxx-10.0.0-1
libdeflate pkgs/main/osx-64::libdeflate-1.7-h9ed2024_5
libedit pkgs/main/osx-64::libedit-3.1.20210216-h9ed2024_1
libev pkgs/main/osx-64::libev-4.33-haf1e3a3_0
libffi pkgs/main/osx-64::libffi-3.3-hb1e8313_2
libgfortran pkgs/main/osx-64::libgfortran-3.0.1-h93005f0_2
libiconv pkgs/main/osx-64::libiconv-1.16-h1de35cc_0
liblief pkgs/main/osx-64::liblief-0.10.1-h23ab428_1
libllvm10 pkgs/main/osx-64::libllvm10-10.0.1-h76017ad_5
libpng pkgs/main/osx-64::libpng-1.6.37-ha441bb4_0
libsodium pkgs/main/osx-64::libsodium-1.0.18-h1de35cc_0
libspatialindex pkgs/main/osx-64::libspatialindex-1.9.3-h23ab428_0
libssh2 pkgs/main/osx-64::libssh2-1.9.0-ha12b0ac_1
libtiff pkgs/main/osx-64::libtiff-4.1.0-hcb84e12_1
libuv pkgs/main/osx-64::libuv-1.40.0-haf1e3a3_0
libwebp pkgs/main/osx-64::libwebp-1.0.1-hd73b212_0
libxml2 pkgs/main/osx-64::libxml2-2.9.10-h7cdb67c_3
libxslt pkgs/main/osx-64::libxslt-1.1.34-h83b36ba_0
libzopfli pkgs/main/osx-64::libzopfli-1.0.3-hb1e8313_0
llvm-openmp pkgs/main/osx-64::llvm-openmp-10.0.0-h28b9765_0
llvmlite pkgs/main/osx-64::llvmlite-0.36.0-py39he4411ff_4
locket pkgs/main/osx-64::locket-0.2.1-py39hecd8cb5_1
lxml pkgs/main/osx-64::lxml-4.6.3-py39h26b266a_0
lz4-c pkgs/main/osx-64::lz4-c-1.9.3-h23ab428_0
lzo pkgs/main/osx-64::lzo-2.10-haf1e3a3_2
markupsafe pkgs/main/osx-64::markupsafe-1.1.1-py39h9ed2024_0
matplotlib pkgs/main/osx-64::matplotlib-3.3.4-py39hecd8cb5_0
matplotlib-base pkgs/main/osx-64::matplotlib-base-3.3.4-py39h8b3ea08_0
mccabe pkgs/main/osx-64::mccabe-0.6.1-py39hecd8cb5_1
mistune pkgs/main/osx-64::mistune-0.8.4-py39h9ed2024_1000
mkl pkgs/main/osx-64::mkl-2021.2.0-hecd8cb5_269
mkl-service pkgs/main/osx-64::mkl-service-2.3.0-py39h9ed2024_1
mkl_fft pkgs/main/osx-64::mkl_fft-1.3.0-py39h4a7008c_2
mkl_random pkgs/main/osx-64::mkl_random-1.2.1-py39hb2f4e1b_2
mock pkgs/main/noarch::mock-4.0.3-pyhd3eb1b0_0
more-itertools pkgs/main/noarch::more-itertools-8.7.0-pyhd3eb1b0_0
mpc pkgs/main/osx-64::mpc-1.1.0-h6ef4df4_1
mpfr pkgs/main/osx-64::mpfr-4.0.2-h9066e36_1
mpmath pkgs/main/osx-64::mpmath-1.2.1-py39hecd8cb5_0
msgpack-python pkgs/main/osx-64::msgpack-python-1.0.2-py39hf7b0b51_1
multipledispatch pkgs/main/osx-64::multipledispatch-0.6.0-py39hecd8cb5_0
mypy_extensions pkgs/main/osx-64::mypy_extensions-0.4.1-py39hecd8cb5_0
nbclassic pkgs/main/noarch::nbclassic-0.2.6-pyhd3eb1b0_0
nbclient pkgs/main/noarch::nbclient-0.5.3-pyhd3eb1b0_0
nbconvert pkgs/main/osx-64::nbconvert-6.0.7-py39hecd8cb5_0
nbformat pkgs/main/noarch::nbformat-5.1.3-pyhd3eb1b0_0
ncurses pkgs/main/osx-64::ncurses-6.2-h0a44026_1
nest-asyncio pkgs/main/noarch::nest-asyncio-1.5.1-pyhd3eb1b0_0
networkx pkgs/main/noarch::networkx-2.5-py_0
nltk pkgs/main/noarch::nltk-3.6.1-pyhd3eb1b0_0
nose pkgs/main/noarch::nose-1.3.7-pyhd3eb1b0_1006
notebook pkgs/main/osx-64::notebook-6.3.0-py39hecd8cb5_0
numba pkgs/main/osx-64::numba-0.53.1-py39hb2f4e1b_0
numexpr pkgs/main/osx-64::numexpr-2.7.3-py39h5873af2_1
numpy pkgs/main/osx-64::numpy-1.20.1-py39hd6e1bb9_0
numpy-base pkgs/main/osx-64::numpy-base-1.20.1-py39h585ceec_0
numpydoc pkgs/main/noarch::numpydoc-1.1.0-pyhd3eb1b0_1
olefile pkgs/main/noarch::olefile-0.46-py_0
openjpeg pkgs/main/osx-64::openjpeg-2.3.0-hb95cd4c_1
openpyxl pkgs/main/noarch::openpyxl-3.0.7-pyhd3eb1b0_0
openssl pkgs/main/osx-64::openssl-1.1.1k-h9ed2024_0
packaging pkgs/main/noarch::packaging-20.9-pyhd3eb1b0_0
pandas pkgs/main/osx-64::pandas-1.2.4-py39h23ab428_0
pandoc pkgs/main/osx-64::pandoc-2.12-hecd8cb5_0
pandocfilters pkgs/main/osx-64::pandocfilters-1.4.3-py39hecd8cb5_1
parso pkgs/main/noarch::parso-0.7.0-py_0
partd pkgs/main/noarch::partd-1.2.0-pyhd3eb1b0_0
path pkgs/main/osx-64::path-15.1.2-py39hecd8cb5_0
path.py pkgs/main/noarch::path.py-12.5.0-0
pathlib2 pkgs/main/osx-64::pathlib2-2.3.5-py39hecd8cb5_2
pathspec pkgs/main/noarch::pathspec-0.7.0-py_0
patsy pkgs/main/osx-64::patsy-0.5.1-py39hecd8cb5_0
pep8 pkgs/main/osx-64::pep8-1.7.1-py39hecd8cb5_0
pexpect pkgs/main/noarch::pexpect-4.8.0-pyhd3eb1b0_3
pickleshare pkgs/main/noarch::pickleshare-0.7.5-pyhd3eb1b0_1003
pillow pkgs/main/osx-64::pillow-8.2.0-py39h5270095_0
pip pkgs/main/osx-64::pip-21.0.1-py39hecd8cb5_0
pkginfo pkgs/main/osx-64::pkginfo-1.7.0-py39hecd8cb5_0
pluggy pkgs/main/osx-64::pluggy-0.13.1-py39hecd8cb5_0
ply pkgs/main/osx-64::ply-3.11-py39hecd8cb5_0
prometheus_client pkgs/main/noarch::prometheus_client-0.10.1-pyhd3eb1b0_0
prompt-toolkit pkgs/main/noarch::prompt-toolkit-3.0.17-pyh06a4308_0
prompt_toolkit pkgs/main/noarch::prompt_toolkit-3.0.17-hd3eb1b0_0
psutil pkgs/main/osx-64::psutil-5.8.0-py39h9ed2024_1
ptyprocess pkgs/main/noarch::ptyprocess-0.7.0-pyhd3eb1b0_2
py pkgs/main/noarch::py-1.10.0-pyhd3eb1b0_0
py-lief pkgs/main/osx-64::py-lief-0.10.1-py39h23ab428_1
pycodestyle pkgs/main/noarch::pycodestyle-2.6.0-pyhd3eb1b0_0
pycosat pkgs/main/osx-64::pycosat-0.6.3-py39h9ed2024_0
pycparser pkgs/main/noarch::pycparser-2.20-py_2
pycurl pkgs/main/osx-64::pycurl-7.43.0.6-py39hbcfaee0_0
pydocstyle pkgs/main/noarch::pydocstyle-6.0.0-pyhd3eb1b0_0
pyerfa pkgs/main/osx-64::pyerfa-1.7.3-py39h9ed2024_0
pyflakes pkgs/main/noarch::pyflakes-2.2.0-pyhd3eb1b0_0
pygments pkgs/main/noarch::pygments-2.8.1-pyhd3eb1b0_0
pylint pkgs/main/osx-64::pylint-2.7.4-py39hecd8cb5_1
pyls-black pkgs/main/noarch::pyls-black-0.4.6-hd3eb1b0_0
pyls-spyder pkgs/main/noarch::pyls-spyder-0.3.2-pyhd3eb1b0_0
pyodbc pkgs/main/osx-64::pyodbc-4.0.30-py39h23ab428_0
pyopenssl pkgs/main/noarch::pyopenssl-20.0.1-pyhd3eb1b0_1
pyparsing pkgs/main/noarch::pyparsing-2.4.7-pyhd3eb1b0_0
pyqt pkgs/main/osx-64::pyqt-5.9.2-py39h23ab428_6
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Proceed ([y]/n)? y
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate env_test
#
# To deactivate an active environment, use
#
# $ conda deactivate
(base) Maximilians-iMac-Pro:~ mx$ conda activate env_test
(env_test) Maximilians-iMac-Pro:~ mx$ pip install celerite
Collecting celerite
Using cached celerite-0.4.0-cp39-cp39-macosx_10_9_x86_64.whl
Collecting pybind11
Downloading pybind11-2.8.0-py2.py3-none-any.whl (207 kB)
|████████████████████████████████| 207 kB 1.1 MB/s
Requirement already satisfied: numpy in ./opt/anaconda3/envs/env_test/lib/python3.9/site-packages (from celerite) (1.20.1)
Installing collected packages: pybind11, celerite
Successfully installed celerite-0.4.0 pybind11-2.8.0
(env_test) Maximilians-iMac-Pro:~ mx$ python
Python 3.9.4 (default, Apr 9 2021, 09:32:38)
[Clang 10.0.0 ] :: Anaconda, Inc. on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import celerite
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Users/mx/opt/anaconda3/envs/env_test/lib/python3.9/site-packages/celerite/__init__.py", line 34, in <module>
from . import terms, solver, modeling
File "/Users/mx/opt/anaconda3/envs/env_test/lib/python3.9/site-packages/celerite/terms.py", line 18, in <module>
from .solver import get_kernel_value, get_psd_value, check_coefficients
ImportError: dlopen(/Users/mx/opt/anaconda3/envs/env_test/lib/python3.9/site-packages/celerite/solver.cpython-39-darwin.so, 2): Symbol not found: __ZTIN10__cxxabiv115__forced_unwindE
Referenced from: /Users/mx/opt/anaconda3/envs/env_test/lib/python3.9/site-packages/celerite/solver.cpython-39-darwin.so
Expected in: flat namespace
in /Users/mx/opt/anaconda3/envs/env_test/lib/python3.9/site-packages/celerite/solver.cpython-39-darwin.so
>>>
I can't reproduce this issue, but I'm currently on an ARM mac with osx v11.6 so I can't directly test on your environment. I'd recommend trying to uninstall celerite and then re-install it from conda-forge:
conda install -c conda-forge celerite
or from source
python -m pip install --no-binary celerite
Thanks for your quick responses, Dan!
Unfortunately the two suggested ways also did not work. The conda-forge install got stuck in an endless "solving environment" loop, while the source install resulted in a C compiler error.
I also updated to Mac OS Big Sur 11.6, but still face the same issue.
I think the reason is that I am using a custom gcc-8 compiler instead of the Mac compiler, because other Python packages (like ellc) do not work with the default Mac compiler.
In any case, I think this issue can just be closed, seen that it is unique to me and works for other Python 3.9 users, as you said above. I will just use celerite1 on Python 3.8 and switch over to celerite2 in the future.
I'm happy to try to help you debug this. Do you want to share the error message you get when compiling from source? There shouldn't be any gcc compatibility issues.
Thanks Dan!
I didn't want to steal more of your time, but since you offer it... ;)
First, I set up a fresh environment, just as described above. Next, I clone celerite into a local folder. Finally, I go into said folder and execute python setup.py install, which leads to the error. All shown below:
(env_python39) Maximilians-iMac-Pro:Code mx$ git clone https://github.com/dfm/celerite.git
Cloning into 'celerite'...
remote: Enumerating objects: 21534, done.
remote: Counting objects: 100% (136/136), done.
remote: Compressing objects: 100% (100/100), done.
remote: Total 21534 (delta 63), reused 69 (delta 21), pack-reused 21398
Receiving objects: 100% (21534/21534), 244.24 MiB | 3.09 MiB/s, done.
Resolving deltas: 100% (8288/8288), done.
(env_python39) Maximilians-iMac-Pro:Code mx$ cd celerite/
(env_python39) Maximilians-iMac-Pro:celerite mx$ ls
AUTHORS.rst MANIFEST.in cpp pyproject.toml
CITATION README.rst docs readthedocs.yml
HISTORY.rst celerite examples setup.py
LICENSE cholesky.ipynb paper tests
(env_python39) Maximilians-iMac-Pro:celerite mx$ python setup.py install
/Users/mx/opt/anaconda3/envs/env_python39/lib/python3.9/distutils/dist.py:274: UserWarning: Unknown distribution option: 'use_scm_version'
warnings.warn(msg)
running install
running bdist_egg
running egg_info
creating celerite.egg-info
writing celerite.egg-info/PKG-INFO
writing dependency_links to celerite.egg-info/dependency_links.txt
writing requirements to celerite.egg-info/requires.txt
writing top-level names to celerite.egg-info/top_level.txt
writing manifest file 'celerite.egg-info/SOURCES.txt'
reading manifest file 'celerite.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no directories found matching 'cpp/lib'
writing manifest file 'celerite.egg-info/SOURCES.txt'
installing library code to build/bdist.macosx-10.9-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib.macosx-10.9-x86_64-3.9
creating build/lib.macosx-10.9-x86_64-3.9/celerite
copying celerite/terms.py -> build/lib.macosx-10.9-x86_64-3.9/celerite
copying celerite/build.py -> build/lib.macosx-10.9-x86_64-3.9/celerite
copying celerite/timer.py -> build/lib.macosx-10.9-x86_64-3.9/celerite
copying celerite/__init__.py -> build/lib.macosx-10.9-x86_64-3.9/celerite
copying celerite/celerite.py -> build/lib.macosx-10.9-x86_64-3.9/celerite
copying celerite/plot_setup.py -> build/lib.macosx-10.9-x86_64-3.9/celerite
copying celerite/modeling.py -> build/lib.macosx-10.9-x86_64-3.9/celerite
copying celerite/solver.cpp -> build/lib.macosx-10.9-x86_64-3.9/celerite
running build_ext
/usr/local/bin/gcc-8 -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/mx/opt/anaconda3/envs/env_python39/include -arch x86_64 -fPIC -O2 -isystem /Users/mx/opt/anaconda3/envs/env_python39/include -arch x86_64 -I/Users/mx/opt/anaconda3/envs/env_python39/include/python3.9 -c flagcheck.cpp -o flagcheck.o -std=c++17
building 'celerite.solver' extension
creating build/temp.macosx-10.9-x86_64-3.9
creating build/temp.macosx-10.9-x86_64-3.9/celerite
/usr/local/bin/gcc-8 -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/mx/opt/anaconda3/envs/env_python39/include -arch x86_64 -fPIC -O2 -isystem /Users/mx/opt/anaconda3/envs/env_python39/include -arch x86_64 -Icpp/include -Icpp/lib/eigen -I/Users/mx/opt/anaconda3/envs/env_python39/lib/python3.9/site-packages/pybind11/include -I/Users/mx/opt/anaconda3/envs/env_python39/include/python3.9 -c celerite/solver.cpp -o build/temp.macosx-10.9-x86_64-3.9/celerite/solver.o -std=c++17 -mmacosx-version-min=10.14 -fvisibility=hidden -g0 -stdlib=libc++
gcc-8: error: unrecognized command line option '-stdlib=libc++'
Note: I used the above approach because
python -m pip install --no-binary celerite
resulted in the following error:
(env_python39) Maximilians-iMac-Pro:Code mx$ python -m pip install --no-binary celerite
ERROR: You must give at least one requirement to install (see "pip help install")
(Side note: the correct --no-binary command is python -m pip install celerite --no-binary celerite, sorry!)
I pulled out my old laptop to try this out and I can reproduce your issues on it when using gcc. I got confused because the log in your first message said that you were installing using a wheel, but there is no wheel released for py3.9, so you must have already tried to install it from source with gcc as your compiler.
The actual issues are two different pybind11 incompatibilities with gcc, so if you have to install celerite from source, I'd recommend using clang. I'll push a new set of wheels later today so that a wheel installation will work.
v0.4.2 is now available with a macos py39 (and py310!) wheel. python -m pip install -U celerite should do the trick now.
Awesome, thanks Dan! Works like a charm, now I can pip-install, import, and run celerite on Python 3.9 while using gcc-8!