Tutorial not working

[EliseAld]

Hello, I'm trying to run the tutorial but I can't seem to be able to have the integration step (MultiMAP.Integration) working with my Mac:

• I get a "illegal hardware instruction" with Python3.8
• I can't install it with Python3.9
• I get the following error with Python3.7 and the kernel dies: OMP: Info #271: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.

Additionnally I don't find the info about the Python version you're using. Do you think you could help me out ? Thanks !

[ktpolanski]

I have not heard of anything similar to this from any other users. I've just successfully ran MultiMAP on python 3.7.6 on a mac, and python 3.8.8 on ubuntu. Here's the pip3 freeze of the mac in case it helps anything.

airr==1.3.0
alabaster==0.7.12
aniso8601==9.0.1
anndata==0.7.5
annoy==1.16.3
appdirs==1.4.3
appnope==0.1.0
attrs==19.3.0
Babel==2.9.0
backcall==0.1.0
bbknn==1.5.1
beautifulsoup4==4.8.0
black==20.8b1
bleach==3.1.1
bokeh==2.2.3
boto3==1.17.24
botocore==1.20.24
braceexpand==0.1.7
Brotli==1.0.9
build==0.4.0
cellxgene==0.16.7
certifi==2019.11.28
cfgv==3.2.0
chardet==3.0.4
click==7.1.2
cloudpickle==1.6.0
colorama==0.4.4
cycler==0.10.0
Cython==0.29.21
dask==2.30.0
dbus-python==1.2.16
decorator==4.4.2
defusedxml==0.6.0
distlib==0.3.1
distributed==2.30.0
docopt==0.6.2
docutils==0.16
entrypoints==0.3
fastobo==0.10.0
fbpca==1.0
filelock==3.0.12
Flask==1.1.2
Flask-Compress==1.9.0
Flask-Cors==3.0.10
Flask-RESTful==0.3.8
flask-server-timing==0.1.2
flask-talisman==0.7.0
flatbuffers==1.12
flatten-dict==0.3.0
fsspec==0.7.4
geosketch==1.1
get-version==2.1
goatools==1.1.6
gower==0.0.5
gunicorn==20.0.4
h5py==2.10.0
HeapDict==1.0.1
humanize==0.5.1
identify==1.5.10
idna==2.8
imageio==2.3.0
imagesize==1.2.0
importlib-metadata==3.7.3
ipykernel==5.1.4
ipython==7.13.0
ipython-genutils==0.2.0
ipywidgets==7.5.1
itsdangerous==1.1.0
jedi==0.16.0
Jinja2==2.11.1
jmespath==0.10.0
joblib==0.14.1
jsonschema==3.2.0
jupyter==1.0.0
jupyter-client==6.0.0
jupyter-console==6.1.0
jupyter-core==4.6.3
keyring==21.8.0
kiwisolver==1.1.0
legacy-api-wrap==1.2
leidenalg==0.8.3
llvmlite==0.35.0
locket==0.2.0
logzero==1.5.0
loompy==3.0.6
lxml==4.3.3
lyricsgenius==1.4.0
lyricwikia==0.1.11
MarkupSafe==1.1.1
matplotlib==3.2.0
mistune==0.8.4
mofapy2==0.5.3
moviepy==0.2.3.5
msgpack==1.0.2
MultiMAP==0.0.1
mutagen==1.44.0
mypy-extensions==0.4.3
natsort==7.0.1
nbconvert==5.6.1
nbformat==5.0.4
networkx==2.4
nodeenv==1.5.0
notebook==6.0.3
notify2==0.3.1
numba==0.52.0
numexpr==2.7.1
numpy==1.19.5
numpy-groupies==0.9.13
packaging==20.3
pafy==0.5.5
pandas==1.0.1
pandocfilters==1.4.2
parasail==1.2
parso==0.6.2
partd==1.1.0
pathlib==1.0.1
pathlib2==2.3.5
pathspec==0.8.1
patsy==0.5.1
pep517==0.9.1
pexpect==4.8.0
pickleshare==0.7.5
Pillow==8.1.0
pkginfo==1.7.0
pre-commit==2.9.2
prettytable==0.7.2
prometheus-client==0.7.1
prompt-toolkit==3.0.4
psutil==5.8.0
ptyprocess==0.6.0
pydot==1.4.2
pygame==1.9.6
Pygments==2.6.1
pynndescent==0.5.2
pyparsing==2.4.6
PyQt5==5.14.1
PyQt5-sip==12.7.1
PyQtWebEngine==5.14.0
pyrsistent==0.15.7
pysam==0.16.0.1
pySankey==0.0.1
python-dateutil==2.8.1
python-igraph==0.8.2
python-Levenshtein==0.12.0
pytoml==0.1.21
pytube==9.5.1
pytz==2019.3
PyWavelets==1.1.1
PyYAML==5.3.1
pyzmq==19.0.0
qtconsole==4.7.1
QtPy==1.9.0
rbcde==1.0.0
readme-renderer==28.0
regex==2020.11.13
requests==2.25.1
requests-toolbelt==0.9.1
rfc3986==1.4.0
s3fs==0.4.2
s3transfer==0.3.4
scanpy==1.6.0
scanpydoc==0.7.1
scikit-image==0.18.1
scikit-learn==0.24.1
scikit-misc==0.1.3
scipy==1.4.1
scirpy==0.5.0
scrublet==0.2.3
scvelo==0.2.2
seaborn==0.11.0
Send2Trash==1.5.0
setuptools-scm==3.5.0
sinfo==0.3.1
six==1.14.0
sklearn==0.0
snowballstemmer==2.0.0
sortedcontainers==2.3.0
soupsieve==2.0
Sphinx==3.3.1
sphinx-autodoc-typehints==1.12.0
sphinx-rtd-theme==0.5.0
sphinxcontrib-applehelp==1.0.2
sphinxcontrib-devhelp==1.0.2
sphinxcontrib-htmlhelp==1.0.3
sphinxcontrib-jsmath==1.0.1
sphinxcontrib-qthelp==1.0.3
sphinxcontrib-serializinghtml==1.1.4
spotipy==2.4.4
SQLAlchemy==1.3.23
squarify==0.4.3
statsmodels==0.11.1
stdlib-list==0.7.0
tables==3.6.1
tbb==2019.0
tblib==1.7.0
terminado==0.8.3
testpath==0.4.4
texttable==1.6.3
threadpoolctl==2.1.0
tifffile==2020.12.8
tiledb==0.8.4
titlecase==0.12.0
toml==0.10.2
toolz==0.11.1
tornado==6.0.4
tqdm==4.43.0
traitlets==4.3.3
twine==3.4.1
typed-ast==1.4.1
typing-extensions==3.7.4.3
umap-learn==0.4.6
unicode-slugify==0.1.3
Unidecode==1.1.1
UpSetPlot==0.4.1
urllib3==1.24.3
virtualenv==20.2.1
wcwidth==0.1.8
webencodings==0.5.1
Werkzeug==1.0.0
wget==3.2
widgetsnbextension==3.5.1
xlrd==1.2.0
XlsxWriter==3.0.2
yamlordereddictloader==0.4.0
zict==2.0.0
zipp==3.1.0

[EliseAld]

Thanks for the quick reply! Unfortunately it didn't help. I'm afraid it has something to do with the M1 chip... The kernel keeps dying

[ktpolanski]

Sorry, my mac is pre-M1.

Do you have some sort of linux server you could SSH to and try to run from there?

[EliseAld]

Yes I'll try with one of the servers. Thanks for the help!

[szalata]

I can confirm the issues with python >=3.8. the installation is possible with Python 3.7 but that won't help on M1

[ktpolanski]

I did some tweaks to Mika's code base. The installation limitations were due to a little quirk in a UMAP-sourced numba function, and the segfaults/crashes in 3.7 were likely due to annoy - a package that keeps on giving in BBKNN. I removed annoy entirely and updated the UMAP-sourced function to be in line with current numba. MultiMAP should now install on more modern pythons and hopefully run with fewer issues.