jupyter notebook kernels dead after running "import adaptive"

[mingweii]

I just installed adaptive and tried to run "import adaptive" on the jupyter notebook. However, the kernel died immediately and the terminal shows the following message:

A requested component was not found, or was unable to be opened. This
means that this component is either not installed or is unable to be
used on your system (e.g., sometimes this means that shared libraries
that the component requires are unable to be found/loaded). Note that
Open MPI stopped checking at the first component that it did not find.
Host: XXXXX.fios-router.home
Framework: btl
Component: tcpecho

---

It looks like MPI_INIT failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during MPI_INIT; some of which are due to configuration or environment
problems. This failure appears to be an internal failure; here's some
additional information (which may only be relevant to an Open MPI
developer):
mca_bml_base_open() failed
--> Returned "Not found" (-13) instead of "Success" (0)

[XXXXX:82047] *** An error occurred in MPI_Init_thread
[XXXXX:82047] *** reported by process [246677505,0]
[XXXXX:82047] *** on a NULL communicator
[XXXXX:82047] *** Unknown error
[XXXXX:82047] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
[XXXXX:82047] *** and potentially your MPI job)
[I 11:28:13.520 NotebookApp] KernelRestarter: restarting kernel (1/5), keep random ports
WARNING:root:kernel fdac667e-04be-4c91-9452-bdbd31cbeeff restarted

These are the packages installed in the conda environment I am using:

Name Version Build Channel

adaptive 0.11.1 py37hf985489_3 conda-forge
appnope 0.1.2 py37hecd8cb5_1001
argon2-cffi 20.1.0 py37haf1e3a3_1
async_generator 1.10 py37h28b3542_0
atomicwrites 1.4.0 py_0
attrs 20.3.0 pyhd3eb1b0_0
backcall 0.2.0 py_0
bleach 3.2.1 py_0
bokeh 2.2.3 py37_0
brotlipy 0.7.0 py37h9ed2024_1003
ca-certificates 2020.12.5 h033912b_0 conda-forge
certifi 2020.12.5 py37hf985489_1 conda-forge
cffi 1.14.4 py37h2125817_0
chardet 4.0.0 py37hecd8cb5_1003
cloudpickle 1.6.0 py_0
colorcet 2.0.2 py_0 pyviz
cryptography 3.3.1 py37hbcfaee0_0
cycler 0.10.0 py37_0
cython 0.29.21 pypi_0 pypi
dbus 1.13.18 h18a8e69_0
decorator 4.4.2 py_0
defusedxml 0.6.0 py_0
entrypoints 0.3 py37_0
expat 2.2.10 hb1e8313_2
freetype 2.10.4 ha233b18_0
gettext 0.19.8.1 hb0f4f8b_2
glib 2.66.1 h9bbe63b_0
gmp 6.1.2 hb37e062_1
gmpy2 2.0.8 py37h6ef4df4_2
holoviews 1.14.1 py_0 pyviz
icu 58.2 h0a44026_3
idna 2.10 py_0
importlib-metadata 2.0.0 py_1
importlib_metadata 2.0.0 1
iniconfig 1.1.1 py_0
ipykernel 5.3.4 py37h5ca1d4c_0
ipyparallel 6.3.0 py37_0
ipython 7.19.0 py37h01d92e1_0
ipython_genutils 0.2.0 pyhd3eb1b0_1
ipywidgets 7.6.1 pyhd3eb1b0_0
jedi 0.18.0 py37hf985489_1 conda-forge
jinja2 2.11.2 py_0
jpeg 9b he5867d9_2
jsonschema 3.2.0 py_2
jupyter 1.0.0 py37_7
jupyter_client 6.1.7 py_0
jupyter_console 6.2.0 py_0
jupyter_core 4.7.0 py37hecd8cb5_0
jupyterlab_pygments 0.1.2 py_0
jupyterlab_widgets 1.0.0 pyhd3eb1b0_1
kiwisolver 1.3.0 py37h23ab428_0
kwant 1.4.2 py37hc44a957_3 conda-forge
kwantspectrum 0.1.0 py_0 conda-forge
lcms2 2.11 h92f6f08_0
libblas 3.9.0 7_openblas conda-forge
libcblas 3.9.0 7_openblas conda-forge
libcxx 11.0.0 h4c3b8ed_1 conda-forge
libedit 3.1.20191231 h1de35cc_1
libffi 3.3 hb1e8313_2
libgfortran 4.0.0 h1a10cd1_15 conda-forge
libgfortran4 7.5.0 h1a10cd1_15 conda-forge
libiconv 1.16 h1de35cc_0
liblapack 3.9.0 7_openblas conda-forge
libopenblas 0.3.12 openmp_h63d9170_1 conda-forge
libpng 1.6.37 ha441bb4_0
libsodium 1.0.18 h1de35cc_0
libtiff 4.1.0 hcb84e12_1
llvm-openmp 11.0.0 h73239a0_1 conda-forge
loky 2.9.0 pyh9f0ad1d_0 conda-forge
lz4-c 1.9.2 h79c402e_3
markdown 3.3.3 py37hecd8cb5_0
markupsafe 1.1.1 py37h1de35cc_0
matplotlib 3.3.2 hecd8cb5_0
matplotlib-base 3.3.2 py37h181983e_0
metis 5.1.0 0 menpo
mistune 0.8.4 py37h1de35cc_0
more-itertools 8.6.0 pyhd3eb1b0_0
mpc 1.1.0 h6ef4df4_1
mpfr 4.0.2 h9066e36_1
mpi 1.0 openmpi
mpi4py 3.0.3 py37h27a7d74_0
mpmath 1.1.0 py37_0
mumps-include 5.2.1 h694c41f_10 conda-forge
mumps-seq 5.2.1 h0fefb41_10 conda-forge
nbclient 0.5.1 py_0
nbconvert 6.0.7 py37_0
nbformat 5.0.8 py_0
ncurses 6.2 h0a44026_1
nest-asyncio 1.4.3 pyhd3eb1b0_0
notebook 6.1.6 py37hecd8cb5_0
numpy 1.19.5 py37hec87de9_0 conda-forge
olefile 0.46 py37_0
openmpi 4.0.5 h809c96e_4 conda-forge
openssl 1.1.1i h35c211d_0 conda-forge
packaging 20.8 pyhd3eb1b0_0
pandas 1.2.0 py37hb2f4e1b_0
pandoc 2.11 h0dc7051_0
pandocfilters 1.4.3 py37hecd8cb5_1
panel 0.10.2 py_0 pyviz
param 1.10.1 py_0 pyviz
parso 0.8.1 pyhd3eb1b0_0
pcre 8.44 hb1e8313_0
pexpect 4.8.0 pyhd3eb1b0_3
pickleshare 0.7.5 pyhd3eb1b0_1003
pillow 8.1.0 py37h5270095_0
pip 20.3.3 py37hecd8cb5_0
plotly 4.14.3 pypi_0 pypi
pluggy 0.13.1 py37_0
prometheus_client 0.9.0 pyhd3eb1b0_0
prompt-toolkit 3.0.8 py_0
prompt_toolkit 3.0.8 0
psutil 5.7.2 py37haf1e3a3_0
ptyprocess 0.7.0 pyhd3eb1b0_2
py 1.10.0 pyhd3eb1b0_0
pycparser 2.20 py_2
pyct 0.4.8 py_0 pyviz
pyct-core 0.4.8 py_0 pyviz
pygments 2.7.3 pyhd3eb1b0_0
pyopenssl 20.0.1 pyhd3eb1b0_1
pyparsing 2.4.7 py_0
pyqt 5.9.2 py37h655552a_2
pyrsistent 0.17.3 py37haf1e3a3_0
pysocks 1.7.1 py37hecd8cb5_0
pytest 6.2.1 py37hecd8cb5_0
python 3.7.9 h26836e1_0
python-dateutil 2.8.1 py_0
python_abi 3.7 1_cp37m conda-forge
pytz 2020.5 pyhd3eb1b0_0
pyviz_comms 2.0.1 py_0 pyviz
pyyaml 5.3.1 py37haf1e3a3_1
pyzmq 20.0.0 py37h23ab428_1
qsymm 1.3.0 pyhd8ed1ab_0 conda-forge
qt 5.9.7 h468cd18_1
qtconsole 4.7.7 py_0
qtpy 1.9.0 py_0
readline 8.0 h1de35cc_0
requests 2.25.1 pyhd3eb1b0_0
retrying 1.3.3 pypi_0 pypi
scipy 1.5.3 py37h04d6967_0 conda-forge
scotch 6.0.9 h57311db_1 conda-forge
send2trash 1.5.0 pyhd3eb1b0_1
setuptools 51.0.0 py37hecd8cb5_2
sip 4.19.8 py37h0a44026_0
six 1.15.0 py37hecd8cb5_0
sortedcollections 1.2.3 pyhd3eb1b0_0
sortedcontainers 2.3.0 pyhd3eb1b0_0
sqlite 3.33.0 hffcf06c_0
sympy 1.7.1 py37hecd8cb5_0
terminado 0.9.2 py37hecd8cb5_0
testpath 0.4.4 py_0
tinyarray 1.2.3 py37h6d0141a_0 conda-forge
tk 8.6.10 hb0a8c7a_0
tkwant 1.0.1 py37ha805f5d_0 conda-forge
toml 0.10.1 py_0
tornado 6.1 py37h9ed2024_0
tqdm 4.55.1 pyhd3eb1b0_0
traitlets 5.0.5 py_0
typing_extensions 3.7.4.3 py_0
urllib3 1.26.2 pyhd3eb1b0_0
wcwidth 0.2.5 py_0
webencodings 0.5.1 py37_1
wheel 0.36.2 pyhd3eb1b0_0
widgetsnbextension 3.5.1 py37_0
xz 5.2.5 h1de35cc_0
yaml 0.2.5 haf1e3a3_0
zeromq 4.3.3 hb1e8313_3
zipp 3.4.0 pyhd3eb1b0_0
zlib 1.2.11 h1de35cc_3
zstd 1.4.5 h41d2c2f_0

My system is Python 3.7.9, macOS Catalina 10.15.7, MacBook Pro mid 2012, 16GB memory and 2.9GHz Dual-Core Intel Core i7. I tried to run it on python in the Terminal and it shows the same message. It seems to be the Open MPI problem.

Sorry I am not very good at formating for the post.

Does anyone know how to fix it?

Thank you very much!

[akhmerov]

@basnijholt I think you're running adaptive on a mac without problems. Any ideas?

[basnijholt]

This doesn't seem to be related to Adaptive but rather a dependency of Adaptive that has issues.

My guess is that mpi4py is the cause. Probably removing that package (if you don't use it) will solve the issue.

[basnijholt]

I am going ahead and close this because I am relatively sure this is unrelated to Adaptive.

Let me know if I should reopen it.